Alexander Diehl Ceri van Slyke Chris Mungall David Osumi-Sutherland Jim Balhoff Melissa Haendel Nicole Vasilevsky Terry Meehan Yvonne Bradford An ontology of cell types. Cell Ontology See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo. 2021-06-21 definition IAO:0000116 uberon editor_note true editor_note editor note editor note expand expression to expand expression to preferred_root term replaced by tooth SubClassOf 'never in taxon' value 'Aves' S never_in_taxon T iff: S SubClassOf in_taxon only not T x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. Chris Mungall ?X DisjointWith RO_0002162 some ?Y Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y) RO:0002161 uberon never_in_taxon true true never_in_taxon never in taxon never_in_taxon S never_in_taxon T iff: S SubClassOf in_taxon only not T S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S https://orcid.org/0000-0002-6601-2165 RO:0002175 applicable for taxon uberon present_in_taxon true true present_in_taxon present in taxon present_in_taxon S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S 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 preferred term when talking about an instance of this class in Homo sapiens latin term plural term abstract upper-level terms not directly useful for analysis uberon dc-contributor true dc-contributor contributor uberon dc-creator true dc-creator creator uberon dc-description true dc-description description uberon dc-title true dc-title title uberon dcterms-license true dcterms-license license subset_property synonym_type_property consider has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym has_synonym_type in_subset shorthand http://www.w3.org/2000/01/rdf-schema#seeAlso uberon seeAlso true seeAlso see also uberon depicted_by true depicted_by depicted by 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 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 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 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 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 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 superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion. BSPO:0001101 uberon in_deep_part_of in_deep_part_of in_deep_part_of X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion. 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:0015014 uberon immediately_superficial_to immediately_superficial_to immediately_superficial_to BSPO:0015101 uberon in_dorsal_side_of in_dorsal_side_of in_dorsal_side_of 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 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 RO:0000086 protein has_quality false has_quality has_quality RO:0000087 chebi_ontology has_role false false has_role has role this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) 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 This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. RO:0001000 protein derives_from derives_from derives from derives_from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new 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 This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into 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. RO:0002002 uberon has_boundary has_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 David Osumi-Sutherland has synaptic terminal of 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. 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 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 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 Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) has soma location relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. David Osumi-Sutherland fasciculates with (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) (and ("neuron ; CL_0000540" ?x) ("neuron projection bundle ; CARO_0001001" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500' " ?npbs) (part_of ?npbs ?y) (part_of ?nps ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) )))))) fasciculates with Relation between a neuron and some structure its axon forms (chemical) synapses in. Chris Mungall David Osumi-Sutherland David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) axon synapses in Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. Chris Mungall David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) synapsed by Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. Alexander Diehl Chris Mungall Lindsay Cowell <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) has plasma membrane part Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. Chris Mungall David Osumi-Sutherland synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) has postsynaptic terminal in Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. synapses in <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) has presynaptic terminal in Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. Chris Mungall David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) N1 synapsed_to some N2 Expands to: N1 SubclassOf ( has_part some ( ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( ‘synapse ; GO:0045202’ that has_part some ( ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) synapsed to A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. David Osumi-Sutherland has synapse in <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?) has synaptic terminal in x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps true The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. David Osumi-Sutherland has fasciculating component (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) (and ("neuron projection bundle ; CARO_0001001" ?x) ("neuron projection ; GO0043005" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500" ?npbs) (part_of ?nps ?y) (part_of ?npbs ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) )))))) has fasciculating neuron projection 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 RO:0002150 uberon continuous_with continuous_with continuous_with RO:0002158 uberon homologous_to homologous_to homologous_to 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. 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. 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 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. RO:0002177 uberon attaches_to_part_of attaches_to_part_of attaches_to_part_of true relation between an artery and the structure is supplies with blood. RO:0002178 arterial supply of uberon supplies supplies source: FMA supplies arterial supply of FMA:86003 RO:0002179 drains blood from drains from uberon drains drains source: Wikipedia 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 inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 uberon develops_into develops_into develops into develops_into 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process Chris Mungall expressed in RO:0002207 uberon directly_develops_from directly_develops_from directly_develops_from 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: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:0002216 uberon capable_of_part_of capable_of_part_of capable of part of capable of part of true x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y RO:0002219 uberon 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 RO:0002221 uberon 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. RO:0002223 uberon starts starts starts Relation between occurrents, shares a start boundary with. Allen:starts RO:0002224 uberon starts_with starts_with starts with RO:0002225 uberon develops_from_part_of develops_from_part_of develops_from_part_of RO:0002226 uberon develops_in develops_in This relation take from EHDAA2 - precise semantics yet to be defined develops_in Relation between occurrents, shares an end boundary with. RO:0002229 finishes uberon ends ends ends Relation between occurrents, shares an end boundary with. Allen:starts ZFS:finishes RO:0002230 uberon ends_with ends_with ends with 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 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. 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 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 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 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 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 RO:0002285 uberon developmentally_replaces developmentally_replaces developmentally_replaces Inverse of developmentally preceded by Chris Mungall developmentally succeeded by Inverse of 'expressed in' Chris Mungall expresses 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 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 holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to 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 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 RO:0002350 uberon member_of member_of member of RO:0002351 uberon has_member has_member has member inverse of has input Chris Mungall input of RO:0002353 protein output_of false output_of output_of RO:0002371 uberon attaches_to attaches_to 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. 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 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. 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 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. RO:0002376 uberon drains into tributary_of tributary_of tributary_of 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 we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve RO:0002380 uberon branching_part_of branching_part_of branching_part_of 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 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 Chris Mungall 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 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 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 directly regulates activity of 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 molecularly decreases activity of directly negatively regulates activity of 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 directly activates molecularly increases 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) x composed_primarily_of y iff: more than half of the mass of x is made from parts of y 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 See notes for inverse relation Chris Mungall receives input from This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. Chris Mungall sends output to Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. 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. 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. RO:0002491 uberon existence_starts_and_ends_during existence_starts_and_ends_during 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. RO:0002492 ceases_to_exist_during uberon RO:0002492 existence_ends_during existence_ends_during 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. RO:0002493 uberon existence_ends_with existence_ends_with existence ends with Relation between continuant and occurrent, such that c ceases to exist at the end of p. RO:0002494 transforms from uberon transformation_of transformation_of transformation of transforms from SIO:000657 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 RO:0002496 uberon existence_starts_during_or_after existence_starts_during_or_after existence starts during or after RO:0002497 uberon existence_ends_during_or_before existence_ends_during_or_before 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 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 A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. RO:0002551 uberon has sekeletal support has supporting framework has_skeleton has_skeleton has skeleton 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 Chris Mungall interaction relation helper property https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall molecular interaction relation helper property 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 m1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. RO:0002568 uberon 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. RO:0002569 uberon has_branching_part has_branching_part has branching part RO:0002571 uberon lumen_of lumen_of lumen of 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. has modifier 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 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 A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. 2020-07-17T09:26:52Z has synaptic input or output in has synaptic IO in has_completed A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). has_high_plasma_membrane_amount A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). PMID:19243617 A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). has_low_plasma_membrane_amount A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). PMID:19243617 has_not_completed http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y lacks_part http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y) lacks_plasma_membrane_part 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 s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. quality has_cross_section Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. has_cross_section s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. PATOC:CJM quality has_relative_magnitude has_relative_magnitude 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 protein has_gene_template false has_gene_template protein lacks_part false lacks_part 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 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 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 http://semanticscience.org/resource/SIO_000658 direct_transformation_of immediately transforms from immediate_transformation_of immediate_transformation_of direct_transformation_of https://orcid.org/0000-0002-6601-2165 immediately transforms from SIO:000658 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. continuant An entity that has temporal parts and that happens, unfolds or develops through time. occurrent A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant spatial region An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process bfo BFO:0000019 quality quality 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. specifically dependent continuant bfo BFO:0000024 fiat object part bfo BFO:0000030 object 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. generically dependent continuant An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. bfo BFO:0000040 material entity material entity immaterial entity anatomical entity connected anatomical structure material anatomical entity multi-cell-part structure neuron projection bundle organism or virus or viroid 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 Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. 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 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 Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). chebi_ontology CHEBI:24651 hydroxides 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:6727 chebi_ontology CHEBI:25179 melanins 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 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 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 An endogenous molecular entity that results in a colour of an organism as the consequence of the selective absorption of light. chebi_ontology pigments CHEBI:26130 biological pigment pigments ChEBI Members of the class of phenols that contain 2 or more benzene rings each of which is substituted by at least one hydroxy group. Wikipedia:Polyphenol chebi_ontology polyphenols CHEBI:26195 polyphenol polyphenols ChEBI 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 particle not known to have substructure. elementary particle chebi_ontology elementary particles CHEBI:33233 fundamental particle elementary particle IUPAC elementary particles 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 CHEBI:33247 organic group 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 nutrient is a food component that an organism uses to survive and grow. chebi_ontology nutrients CHEBI:33284 nutrient nutrients 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 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 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 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 chebi_ontology hydrogen compounds hydrogen molecular entities CHEBI:33608 hydrogen molecular entity hydrogen compounds ChEBI hydrogen molecular entities ChEBI 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 chebi_ontology organic aromatic compounds CHEBI:33659 organic aromatic compound organic aromatic compounds 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 When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue. amino acid residue protein residue chebi_ontology CHEBI:33708 amino-acid residue When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue. Dummy:dummy protein residue PRO:DAN 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 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 Organic aromatic compounds having one or more hydroxy groups attached to a benzene or other arene ring. 0 C6HOR5 89.072 89.00274 C1(=C(C(=C(C(=C1*)*)*)*)*)O CHEBI:13664 CHEBI:13825 CHEBI:25969 CHEBI:2857 KEGG:C15584 MetaCyc:Phenols Wikipedia:Phenols phenols chebi_ontology Aryl alcohol a phenol arenols CHEBI:33853 phenols phenols IUPAC Aryl alcohol KEGG_COMPOUND a phenol UniProt arenols IUPAC Any nutrient required in large quantities by organisms throughout their life in order to orchestrate a range of physiological functions. Macronutrients are usually chemical elements (carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur) that humans consume in the largest quantities. Calcium, sodium, magnesium and potassium are sometimes included as macronutrients because they are required in relatively large quantities compared with other vitamins and minerals. chebi_ontology macronutrients CHEBI:33937 macronutrient macronutrients 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 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 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 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 CHEBI:50047 organic amino compound 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 is particular behaviour which a material entity may exhibit. chebi_ontology CHEBI:50906 role chebi_ontology CHEBI:52208 biophysical role chebi_ontology CHEBI:52211 physiological role 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 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. chebi_ontology dietary component dietary components food components CHEBI:78295 food component dietary component ChEBI dietary components ChEBI food components 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 cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. BTO:0002290 primary cell culture cell unpassaged cultured cell cell primary cell line cell Covers cells actively being cultured or stored in a quiescent state for future use. primary cultured cell A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. ReO:mhb OBSOLETE: A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite growth/propagation in vitro as part of a immortal cell line. continuous cell line cell permanent cell line cell cell Obsoleted in July 2013 and replaced by the CLO 'immortal cell line cell' class, as a result of CLO-OBI-CL alignment efforts. Covers cells actively being cultured or stored in a quiescent state for future use. obsolete immortal cell line cell true OBSOLETE: A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite growth/propagation in vitro as part of a immortal cell line. ReO:mhb 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 OBSOLETE: A classification of cells by the organisms within which they are contained. CL:0000000 CL:0000003 CL:0001034 cell This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified by its species. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate. obsolete cell by organism true OBSOLETE: A classification of cells by the organisms within which they are contained. FB:ma Any fibroblast that is deriived from the neural crest. cell fibroblast neural crest derived Any fibroblast that is deriived from the neural crest. https://orcid.org/0000-0001-5208-3432 neuronal receptor cell (sensu Animalia) cell neuronal receptor cell A cell found in the embryo before the formation of all the gem layers is complete. cell early embryonic cell (metazoa) A cell found in the embryo before the formation of all the gem layers is complete. GOC:tfm Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination. cell migratory cranial neural crest cell Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination. ZFA:0007091 https://orcid.org/0000-0001-5208-3432 Obsolete. Use PO:0000079 from Plant Ontology instead. An elongated cell with approximately wedge-shaped ends, found in the vascular cambium, which gives rise to the elements of the axial system in the secondary vascular tissues. CL:0000274 cell xylem initial xylem mother cell replaced_by: PO:0000079 obsolete fusiform initial true Obsolete. Use PO:0000079 from Plant Ontology instead. An elongated cell with approximately wedge-shaped ends, found in the vascular cambium, which gives rise to the elements of the axial system in the secondary vascular tissues. ISBN:0471245208 A cell in vitro that is or has been maintained or propagated as part of a cell culture. cell Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture. cultured cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. ReO:mhb Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination. cell migratory trunk neural crest cell Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination. ZFA:0007095 https://orcid.org/0000-0001-5208-3432 CL:0000000 CL:0000003 CL:0001034 cell This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate. obsolete cell by class true CL:0000140 cell obsolete dentine secreting cell true germline stem cell cell germ line stem cell true true Male germ cell is a germ cell that supports male gamete production. FMA:72290 MA:0002765 VHOG:0001531 ncithesaurus:Spermatogenic_Cell cell male germ cell true Male germ cell is a germ cell that supports male gamete production. https://orcid.org/0000-0001-5208-3432 cell male germ line stem cell A male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids. BTO:0001275 CALOHA:TS-0951 EMAPA:31484 FBbt:00004936 FMA:84049 WBbt:0006799 cell spermatocyte true A male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids. GOC:tfm MESH:A05.360.490.890.880 A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa. BTO:0001274 CALOHA:TS-0950 EMAPA:31486 FBbt:00004942 FMA:72294 WBbt:0006800 nematoblast cell spermatid true A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa. MESH:A05.360.490.890.860 A mature male germ cell that develops from a spermatid. BTO:0001277 BTO:0002046 CALOHA:TS-0949 FBbt:00004954 FMA:67338 WBbt:0006798 sperm cell spermatozoid spermatozoon cell sperm true A mature male germ cell that develops from a spermatid. GOC:tfm MESH:A05.360.490.890 An euploid male germ cell of an early stage of spermatogenesis. BTO:0000958 CALOHA:TS-2193 EMAPA:31482 FBbt:00004935 FMA:72291 cell spermatogonium An euploid male germ cell of an early stage of spermatogenesis. MESH:A05.360.490.890.900 Female germ cell is a germ cell that supports female gamete production. MA:0000388 VHOG:0001530 ncithesaurus:Egg cell female germ cell true Female germ cell is a germ cell that supports female gamete production. GOC:tfm PMID:11023867 PMID:20454446 cell female germ line stem cell true true A female germ cell that has entered meiosis. BTO:0000964 CALOHA:TS-0711 FBbt:00004886 FMA:18644 WBbt:0006797 cell oogonium oocyte true A female germ cell that has entered meiosis. GOC:tfm ISBN:0721662544 An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes. FMA:83673 cell oogonial cell true An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes. GOC:tfm ISBN:0721662544 A female gamete where meiosis has progressed to metaphase II and is able to participate in fertilization. BTO:0000369 BTO:0003801 CALOHA:TS-2191 FBbt:00057012 FMA:67343 MA:0000388 mature oocyte ovum cell egg cell true A female gamete where meiosis has progressed to metaphase II and is able to participate in fertilization. GOC:tfm ISBN:0721662544 A germline cell that contributes to the development of the oocyte by transferring cytoplasm directly to oocyte. BTO:0000953 FBbt:00004878 cell nurse cell invertebrate nurse cell A germline cell that contributes to the development of the oocyte by transferring cytoplasm directly to oocyte. GOC:tfm PMID:15848391 A smooth muscle cell derived from the neural crest. cell smooth muscle cell neural crest derived true A smooth muscle cell derived from the neural crest. https://orcid.org/0000-0001-5208-3432 cell CNS neuron (sensu Nematoda and Protostomia) cell neuron neural crest derived true FBbt:00005145 cell glioblast A cell that will develop into a neuron often after a migration phase. CL:0000337 BTO:0000930 FMA:70563 neuroblast cell neuroblast (sensu Vertebrata) A cell that will develop into a neuron often after a migration phase. GOC:NV http://en.wikipedia.org/wiki/Neuroblast A cell of a platelike structure, especially a thickened plate of ectoderm in the early embryo, from which a sense organ develops. neural placode cell cell neuroplacodal cell A cell of a platelike structure, especially a thickened plate of ectoderm in the early embryo, from which a sense organ develops. GOC:tfm ISBN:0618947256 An apocrine cell is a secretory cell characterized loss of part of the cytoplasm during the process of secretion - secretions are budded off through the plasma membrane producing membrane bound vesicles containing the secreted substance. cell apocrine cell An apocrine cell is a secretory cell characterized loss of part of the cytoplasm during the process of secretion - secretions are budded off through the plasma membrane producing membrane bound vesicles containing the secreted substance. GOC:tfm ISBN:0721662544 A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. CALOHA:TS-2086 FMA:63368 cell stem cell A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. GOC:tfm MESH:A11.872 A stem cell that self-renews as well as give rise to a single mature cell type. FMA:70569 unipotent stem cell unipotential stem cell cell single fate stem cell A stem cell that self-renews as well as give rise to a single mature cell type. GOC:tfm cell epithelial fate stem cell A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119. BTO:0000725 CALOHA:TS-0448 FMA:70337 FMA:86475 VHOG:0001485 HSC blood forming stem cell hemopoietic stem cell cell colony forming unit hematopoietic Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative. hematopoietic stem cell A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119. GOC:add GOC:dsd GOC:tfm PMID:19022770 http://en.wikipedia.org/wiki/Hematopoietic_stem_cell A progenitor cell committed to the erythroid lineage. BTO:0004911 cell BFU-E CFU-E blast forming unit erythroid burst forming unit erythroid colony forming unit erythroid erythroid stem cell erythroid progenitor cell true A progenitor cell committed to the erythroid lineage. GOC:add ISBN:0721601464 A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. cell Originally this term had some plant germ line cell children. germ line cell A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. GOC:tfm ISBN:0721662544 A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus. CALOHA:TS-1195 FMA:83553 cell CFU-M colony forming unit macrophage colony forming unit monocyte monocyte stem cell Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. monoblast true A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus. GOC:add PMID:1104740 http://en.wikipedia.org/wiki/Monoblast http://www.copewithcytokines.de A fully differentiated eosinophil, a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Cells are also differentiated from other granulocytes by a small nuclear-to-cytoplasm ratio (1:3). This cell type is CD49d-positive. The status of eosinophils as true professional antigen presenting cells is unclear, despite their ability to present exogenous peptides and peptides processed from exogenous proteins (in certain studies) via MHC Class II and activate T cells. Per the equivalence axioms, 'eosinophil' is reasoned to be a subclass of 'professional antigen presenting cell', though the role of eosinophils as such in the body may be limited. polymorphonuclear leucocyte polymorphonuclear leukocyte mature eosinocyte mature eosinophil leucocyte mature eosinophil leukocyte cell Eosinophils are CD125-positive (IL-5R), GM-CSFR-positive, IL-3R-positive, VLA4-positive. They can also express MHC Class I & II, CD4, CD9, CD11a, CD11b, CD11c, CD13, CD15, CD16, CD17, CD18, CD24, CD25,CD28, CD29, CD32, CD33, CD35, CD37, CD39, CD43, CD44, CD45, CD45RB, CD45RO, CD46, CD47, CD48, CD49d, CD49f, CD50, CD52, CD53, CD54, CD55, CD58, CD59, CD62L, CD63, CD65, CD66, CD69, CD71, CD76, CD80, CD81, CD82, CD86, CD87, CD88, CD89, CD92, CD95, CD97, CD98, CD99, CD100, CD101, CD116, CD117, CD119, CD120, CD123, CD124, CD125, CD131, CD137, CD139, CD148, CD149, CD151, CD153, CD156, CD162, CD161, CD162, CD165, CD174, CD182, CD183, CD191, CD192, CD193, CD196, CD213, IL9R, ad integrin, beta-7 integrin, FceRI, IL13Ra1, TGFbR, PAFR, LTB4R, C3aR, CystLT1R, CystLT2R, fMLPR, CRTH2 (PGD2 receptor), histamine 4R, IDO, KYN, PAR-2, Siglec-8, Siglec-10, LIR1, LIR2, LIR3, LIR7, TLR7, TLR8, and VLA-4. Eosinophils can also secrete CXCL1, eotaxin-1, GM-CSF, IL-2, IL-3, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12, IL-13, IL-16, IL-18, IFN-gamma, LTC4, MIP-1alpha, NGF, PAF, RANTES, substance P, TGF-alpha, TGF-beta, TNF-alpha, and VIP. mature eosinophil true A fully differentiated eosinophil, a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Cells are also differentiated from other granulocytes by a small nuclear-to-cytoplasm ratio (1:3). This cell type is CD49d-positive. GOC:add GOC:dsd GOC:tfm ISBN:0721601464 http://www.cap.org A myeloblast committed to the neutrophil lineage. This cell type is GATA-1 positive, C/EBPa-positive, AML-1-positive, c-myb-positive and has low expression of PU.1 transcription factor. cell neutrophilic granuloblast These cells are CD11b-negative, CD15-negative, CD16-negative, CD35-negative, CD49d-positive, CD68-positive, lactotransferrin-negative, and fMLP receptor-negative. They are found in the Band 3 fraction. neutrophilic myeloblast true A myeloblast committed to the neutrophil lineage. This cell type is GATA-1 positive, C/EBPa-positive, AML-1-positive, c-myb-positive and has low expression of PU.1 transcription factor. GOC:add ISBN:0721601464 PMID:12560239 PMID:15514007 A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. CL:0000739 polymorphonuclear leucocyte polymorphonuclear leukocyte BTO:0001026 CALOHA:TS-0688 mature basophil leucocyte mature basophil leukocyte cell Mature basophils are also capable of producing IL-3, IL-5, IL-6, IL-8, IL-13, IL-25, CCL22, tslp, vegf, and LTC4. mature basophil true A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. GOC:add GOC:dsd GOC:tfm ISBN:0721601464 PMID:18466030 PMID:19231594 PMID:20837449 http://www.cap.org OBSOLETE (was not defined before being made obsolete). cell Consider using term 'pro-T cell ; CL:0000827' or the term 'thymocyte ; CL:0000893' or one of its children instead. obsolete thymus processed stem cell true OBSOLETE (was not defined before being made obsolete). cell Consider using term 'pro-B cell ; CL:0000826' or the term 'immature B cell ; CL:0000816 or one of its children instead. obsolete bursa processed stem cell true Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors. BTO:0002881 CALOHA:TS-2360 FMA:86684 NSC neural stem cell cell neuronal stem cell true Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors. GOC:tfm MESH:D058953 PMID:15247488 http://en.wikipedia.org/wiki/Neural_stem_cell A stem cell that can give rise to multiple lineages of cells. FMA:84789 multi-fate stem cell multifate stem cell multipotent cell multipotent stem cell cell multi fate stem cell A stem cell that can give rise to multiple lineages of cells. GOC:add A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. BTO:0004730 CMP common myeloid precursor cell CFU-GEMM CFU-S colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte multipotential myeloid stem cell myeloid stem cell pluripotent stem cell (bone marrow) This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). common myeloid progenitor true A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. GOC:add ISBN:0878932437 MESH:D023461 CMP ISBN:0878932437 CFU-GEMM ISBN:0878932437 CFU-S ISBN:0878932437 colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte ISBN:0878932437 multipotential myeloid stem cell ISBN:0878932437 myeloid stem cell ISBN:0878932437 pluripotent stem cell (bone marrow) ISBN:0878932437 A progenitor cell committed to the megakaryocyte and erythroid lineages. CFU-EM CFU-MegE MEP Meg/E progenitor colony forming unit erythroid megakaryocyte megakaryocyte/erythrocyte progenitor megakaryocyte/erythroid progenitor cell cell MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. megakaryocyte-erythroid progenitor cell true A progenitor cell committed to the megakaryocyte and erythroid lineages. GOC:add GOC:dsd GOC:tfm MESH:D055015 PMID:16647566 http://en.wikipedia.org/wiki/Megakaryocyte-erythroid_progenitor_cell A oligopotent progenitor cell committed to the lymphoid lineage. CL:0000044 CLP common lymphocyte precursor common lymphocyte progenitor common lymphoid precursor cell ELP committed lymphopoietic stem cell early lymphocyte progenitor lymphoid stem cell lymphopoietic stem cell CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative. common lymphoid progenitor true A oligopotent progenitor cell committed to the lymphoid lineage. GOC:add GOC:dsd GOC:tfm PMID:10407577 PMID:16551251 A stem cell from which all cells of the body can form. FMA:84790 totipotential stem cell cell totipotent stem cell A stem cell from which all cells of the body can form. GOC:add GOC:tfm cell bone matrix secreting cell A precursor cell with a limited number of potential fates. BTO:0000125 FMA:84782 blast cell cell define using PATO mulit-potent or oligopotent? non-terminally differentiated cell A precursor cell with a limited number of potential fates. SANBI:mhl A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair. BTO:0000222 CALOHA:TS-0650 FBbt:00005083 FMA:70335 VHOG:0001529 cell myoblast A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair. GOC:tfm MESH:A11.635 PMID:21849021 A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. BTO:0000452 CALOHA:TS-0362 FMA:63877 VHOG:0001482 cell These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. fibroblast A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. ISBN:0517223651 MESH:A11.329.228 MESH:D005347 http://en.wikipedia.org/wiki/Fibroblast Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell. BTO:0003607 FMA:66783 chrondoplast cell chondroblast Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell. GOC:tfm GO_REF:0000034 ISBN:0618947256 Skeletogenic cell that produces enamel, overlies the odontogenic papilla, and arises from the differentiation of a preameloblast cell. CL:0000053 CL:0000139 BTO:0001663 FMA:70576 amelocyte enamel secreting cell cell non-encoded relationship from VSAO produces VSAO:0000066 ameloblast Skeletogenic cell that produces enamel, overlies the odontogenic papilla, and arises from the differentiation of a preameloblast cell. GOC:tfm GO_REF:0000034 MESH:A11.436.107 Skeletogenic cell that secretes dentine matrix, is derived from the odontogenic papilla, and develops from a preodontoblast cell. BTO:0001769 CALOHA:TS-0696 FMA:62999 cell legacy def: One of the cells forming the outer surface of dental pulp that produces tooth dentin. odontoblast Skeletogenic cell that secretes dentine matrix, is derived from the odontogenic papilla, and develops from a preodontoblast cell. GO_REF:0000034 ISBN:0618947256 Skeletogenic cell that produces cementum (a bony substance that covers the root of a tooth), is part of the odontogenic papilla, and develops from a precementoblast cell. CL:0000859 CALOHA:TS-1164 FMA:63002 cementum secreting cell cell Legacy def: A cell of ectomesenchymal origin that aids in the formation the cementum layer on the roots of teeth. cementoblast Skeletogenic cell that produces cementum (a bony substance that covers the root of a tooth), is part of the odontogenic papilla, and develops from a precementoblast cell. GO_REF:0000034 ISBN:0781733901 Skeletogenic cell that secretes osteoid, is capable of producing mineralized (hydroxyapatite) matrix, is located adjacent to or within osteoid tissue, and arises from the transformation of a preosteoblast cell. BTO:0001593 CALOHA:TS-0720 FMA:66780 cell non-encoded relationships from VSAO - capable_of_producing VSAO:0000020 osteoblast Skeletogenic cell that secretes osteoid, is capable of producing mineralized (hydroxyapatite) matrix, is located adjacent to or within osteoid tissue, and arises from the transformation of a preosteoblast cell. GO_REF:0000034 MESH:A11.329.629 OBSOLETE: A classification of cells by their microscopic appearance. CL:0000000 CL:0000003 CL:0001034 cell This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified by its microscopic appearance. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate. obsolete cell by histology true OBSOLETE: A classification of cells by their microscopic appearance. FB:ma GOC:tfm A cell that has a filiform extrusion of the cell surface. VHOG:0001532 XAO:0000031 cell ciliated cell A cell that has a filiform extrusion of the cell surface. GOC:tfm A neurectoderm derived cell that lines the neural lumen. BTO:0001724 FMA:70550 ependymocyte cell ependymal cell A neurectoderm derived cell that lines the neural lumen. GOC:tfm JB:jb PMID:9550134 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 has a cilia. FMA:70605 cell ciliated epithelial cell An epithelial cell that has a cilia. GOC:tfm 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 cell obsolete epithelial cell of gland true 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 cell non-branched duct epithelial cell cell barrier epithelial cell Obsolete. Use PO:0000066 from Plant Ontology instead. A cell that constitutes the mesophyll of a hydathode and is located between the xylem endings and the epidermis. Proposed to be involved in the retrieval of solutes from the xylem sap. cell replaced_by: PO:0000066 obsolete epithem cell true Obsolete. Use PO:0000066 from Plant Ontology instead. A cell that constitutes the mesophyll of a hydathode and is located between the xylem endings and the epidermis. Proposed to be involved in the retrieval of solutes from the xylem sap. ISBN:0471245208 PMID:12662305 A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. cell columnar/cuboidal epithelial cell A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. GO:0002065 https://orcid.org/0000-0001-5208-3432 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 cell peridermal cell cell stratified epithelial cell 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 A cell found predominately in the blood. FMA:62844 cell blood cell true A cell found predominately in the blood. GOC:add GOC:tfm 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 A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. CL:0000804 CL:0000812 BTO:0000782 CALOHA:TS-1001 FMA:62870 VHOG:0001479 T lymphocyte T-cell T-lymphocyte cell immature T cell mature T cell T cell true A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. GOC:add GOC:tfm ISBN:0781735149 cell germ line stem cell (sensu Vertebrata) FBbt:00004861 cell germ line stem cell (sensu Nematoda and Protostomia) FBbt:00004929 cell male germ line stem cell (sensu Nematoda and Protostomia) FBbt:00004873 cell female germ line stem cell (sensu Nematoda and Protostomia) spermatogonial stem cell cell male germ line stem cell (sensu Vertebrata) spermatogonial stem cell PMID:19948499 cell female germ line stem cell (sensu Vertebrata) A tissue-resident macrophage of the reticuloendothelial system found on the luminal surface of the hepatic sinusoids involved in erythrocyte clearance. Markers include F4/80+, CD11b-low, CD68-positive, sialoadhesin-positive, CD163/SRCR-positive. Irregular, with long processes including lamellipodia extending into the sinusoid lumen, have flattened nucleus with cytoplasm containing characteristic invaginations of the plasma membrane (vermiform bodies); lie within the sinusoid lumen attached to the endothelial surface; derived from the bone marrow, form a major part of the body's mononuclear phagocyte system. BTO:0000685 FMA:14656 hepatic macrophage littoral cell of hepatic sinusoid liver macrophage macrophagocytus stellatus stellate cell of von Kupffer von Kupffer cell cell Markers: Mouse: F4/80+, CD11b-low, CD68+, sialoadhesin+, CD163/SRCR+; role or process: immune, antigen-presentation, clearance of senescent erythrocytes, iron metabolism. Kupffer cells are also reportedly C3aR-positive, CD14-low, CD54-positive, CD88-positive, and CD284-positive. They are also capable of producing IL-1, IL-6, TNF-alpha, nitric oxide, PGD2, PGE2, PGF2alpha, and TXA2. Kupffer cell true A tissue-resident macrophage of the reticuloendothelial system found on the luminal surface of the hepatic sinusoids involved in erythrocyte clearance. Markers include F4/80+, CD11b-low, CD68-positive, sialoadhesin-positive, CD163/SRCR-positive. Irregular, with long processes including lamellipodia extending into the sinusoid lumen, have flattened nucleus with cytoplasm containing characteristic invaginations of the plasma membrane (vermiform bodies); lie within the sinusoid lumen attached to the endothelial surface; derived from the bone marrow, form a major part of the body's mononuclear phagocyte system. GOC:add GOC:tfm GO_REF:0000031 ISBN:0517223651 MESH:A11.329.372.588 PMID:15771589 PMID:17105582 A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive. BTO:0000968 CALOHA:TS-0721 FMA:66781 cell chondroclast Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid. osteoclast true true A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive. GOC:add GOC:tfm GO_REF:0000031 ISBN:0781735149 PMID:10428500 PMID:15055519 PMID:17380158 OBSOLETE (was not defined before being made obsolete). cell Consider using 'osteoclast ; CL:0000092' instead. obsolete osteochondroclast true A leukocyte with abundant granules in the cytoplasm. BTO:0000539 BTO:0001026 CALOHA:TS-0422 FMA:62854 granular leucocyte granular leukocyte polymorphonuclear leukocyte cell granulocyte true A leukocyte with abundant granules in the cytoplasm. GOC:amm GOC:tfm MESH:A11.118.637.415 MESH:D006098 http://en.wikipedia.org/wiki/Granulocyte cell neuron associated cell A fully differentiated neutrophil, a granular leukocyte having a nucleus with three to five lobes connected by slender threads, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. They are produced in bone marrow at a rate of 5e10-10e10/day and have a half-life of 6-8 hours. Neutrophils are CD15-positive, CD16-positive, CD32-positive, CD43-positive, CD181-positive, and CD182-positive. poly polymorphonuclear leucocyte polymorphonuclear leukocyte BTO:0003473 PMN mature neutrocyte mature neutrophil leucocyte mature neutrophil leukocyte mature neutrophilic leucocyte mature neutrophilic leukocyte polymorphonuclear neutrophil polynuclear neutrophilic leucocyte polynuclear neutrophilic leukocyte cell Neutrophils are also capable of secreting GRO-alpha, IL-1beta, IL-1ra, IL-3, IL-12, IP-10, MIG, MIP-1alpha, MIP-1beta, TGF-beta, TNF-alpha, VEGF, and anti-microbial peptides. They can positively influence the chemotaxis of basophils, T-cells, monocytes, macrophages, dendritic cells, and other neutrophils. Neutrophils are also CD35-positive, CD64-positive, CD89-positive, CD184-positive, and fMLP receptor-positive Ly-6G-positive (mouse), TLR2-low, TLR4-low, and lineage-negative (CD2, CD3, CD5, CD9, CD19, CD36, CD49d, CD56, CD61, CD235a (glycophorin-A)). mature neutrophil true A fully differentiated neutrophil, a granular leukocyte having a nucleus with three to five lobes connected by slender threads, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. They are produced in bone marrow at a rate of 5e10-10e10/day and have a half-life of 6-8 hours. Neutrophils are CD15-positive, CD16-positive, CD32-positive, CD43-positive, CD181-positive, and CD182-positive. GOC:add GOC:tfm MESH:A11.118.637.415.583 MESH:D009504 PMID:11138776 PMID:12560239 PMID:15514007 PMID:7880385 http://www.cap.org A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development. BTO:0000830 CALOHA:TS-0603 FMA:66784 histaminocyte labrocyte mastocyte cell tissue basophil Mast cells are generally integrin beta-7-negative and positive for TLR2, TLR3, TLR4, TLR5, TLR7, TLR9, C3aR, C5aR, CR3, CR4, VEGF, FGF2, and renin. They can express MHC Class I and II on their surface. Activated murine mast cells (IgE+Antigen) were capable of expressing the following co-stimulatory molecules: CD95 (Fas), CD120b, CD137 (4-1BB), CD153 (CD30L), CD154 (CD40L), GITR, ICOSL, OX40L, PD-L1, and PD-L2. Note that there was some mouse strain variation. Mast cells have also been demonstrated to produce bFGF, CCL2, CCL4, CCL5, CCL11, CCL20, CXCL2, CXCL8, CXCL10, GM-CSF, IFN-gamma, IL-1, IL-2, IL-3, IL-8, IL-10, IL-11, IL-12, IL-13, IL-16, IL-25, IL-18, MIP-1, prostaglandin D2, SCF, TGF-beta, TNF-alpha, TSLP, VEGF, and XCL1. They express the transcription factors Transcription factors AP-1, GATA1, MITF, Notch2, PIAS3, PU.1, and STAT5. mast cell true A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development. GOC:add GOC:dsd GOC:tfm ISBN:068340007X MESH:A11.329.427 MESH:D008407 PMCID:PMC1312421 PMCID:PMC2855166 PMID:15153310 PMID:16455980 PMID:19671378 PMID:212366338 PMID:9354811 labrocyte ISBN:0721601464 mastocyte ISBN:0721601464 tissue basophil ISBN:068340007X A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells. neuroepithelial cell BTO:0004301 cell The term "neuroepithelial cell" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710). sensory epithelial cell A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells. GOC:tfm ISBN:0517223651 ISBN:0721662544 Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. BTO:0003811 FBbt:00005125 FMA:67313 WBbt:0005113 cell interneuron Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. GOC:tfm MESH:A08.663.358 An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement. BTO:0000312 FMA:83617 WBbt:0005409 motoneuron cell motor neuron An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement. MESH:A08.663.655.500 PMID:16875686 Any neuron having a sensory function; an afferent neuron conveying sensory impulses. BTO:0001037 FBbt:00005124 FMA:84649 WBbt:0005759 cell sensory neuron Any neuron having a sensory function; an afferent neuron conveying sensory impulses. ISBN:0721662544 cell polymodal neuron A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body. FMA:67282 cell bipolar neuron A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body. GOC:tfm ISBN:0444009442 Neuron with an axon and two or more dendrites. FMA:67287 cell multipolar neuron Neuron with an axon and two or more dendrites. FMA:67287 GOC:tfm Neuron with two neurites that are fused grossly when they protrude from the soma and bifurcate a short distance from the soma. FMA:67305 cell pseudounipolar neuron Neuron with two neurites that are fused grossly when they protrude from the soma and bifurcate a short distance from the soma. FMA:67305 GOC:tfm Neuron with one neurite that extends from the cell body. FMA:67278 cell unipolar neuron Neuron with one neurite that extends from the cell body. FMA:67278 GOC:nv A neruon whose cell body is within an autonomic ganglion. FMA:80121 cell autonomic neuron A neruon whose cell body is within an autonomic ganglion. GOC:tfm A neuron that uses acetylcholine as a vesicular neurotransmitter. BTO:0004902 FMA:84796 WBbt:0006840 cell cholinergic neuron A neuron that uses acetylcholine as a vesicular neurotransmitter. GOC:tfm cell adrenergic neuron cell peptidergic neuron A neuron that is part of nerve found outside the central nervous system. FMA:84664 cell peripheral neuron A neuron that is part of nerve found outside the central nervous system. ISBN:0721662544 cell columnar neuron columnar neuron A vertebrate phagocyte with a single nucleus. BTO:0001433 cell mononuclear phagocyte true A vertebrate phagocyte with a single nucleus. GOC:add GOC:tfm ISBN:0781735149 FMA:72552 cell of surface ectoderm surface ectoderm cell cell surface ectodermal 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. 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 Pioneer neurons establish a pathway in the developing central nervous system and then undergo programmed cell death once the adult axons, which follow them, have made connections with the target site. Thus, they are a transient cell type involved in axon guidance. FBbt:00005128 cell pioneer neuron Pioneer neurons establish a pathway in the developing central nervous system and then undergo programmed cell death once the adult axons, which follow them, have made connections with the target site. Thus, they are a transient cell type involved in axon guidance. GOC:cvs GOC:tfm cell CNS neuron (sensu Vertebrata) https://orcid.org/0000-0002-2825-0621 Basket cells are inhibitory GABAergic interneurons of the brain. In general, dendrites of basket cells are free branching and contain smooth spines. Axons are highly branched. The branched axonal arborizations give rise to basket-like structures that surround the soma of the target cell. Basket cells form axo-somatic synapses, meaning their synapses target somas of other cells. cell basket cell Basket cells are inhibitory GABAergic interneurons of the brain. In general, dendrites of basket cells are free branching and contain smooth spines. Axons are highly branched. The branched axonal arborizations give rise to basket-like structures that surround the soma of the target cell. Basket cells form axo-somatic synapses, meaning their synapses target somas of other cells. WikipediaVersioned:Basket_cell&oldid=951703880 Large intrinsic neuron located in the granule layer of the cerebellar cortex that extends its dendrites into the molecular layer where they receive contact from parallel fibers. The axon of the Golgi cell enters ramifies densely in the granule layer and enters into a complex arrangement with mossy fiber terminals and granule cell dendrites to form the cerebellar glomerulus. Llinas, Walton and Lang. In The Synaptic Organization of the Brain. 5th ed. 2004. Golgi cell Golgi neuron cerebellar Golgi neuron cerebellum Golgi cell cell cerebellar Golgi cell Large intrinsic neuron located in the granule layer of the cerebellar cortex that extends its dendrites into the molecular layer where they receive contact from parallel fibers. The axon of the Golgi cell enters ramifies densely in the granule layer and enters into a complex arrangement with mossy fiber terminals and granule cell dendrites to form the cerebellar glomerulus. Llinas, Walton and Lang. In The Synaptic Organization of the Brain. 5th ed. 2004. NIFSTD:sao1415726815 BTO:0003393 cell granule cell The output neuron of the cerebellar cortex. BTO:0001011 CALOHA:TS-0845 FMA:67969 Purkinje neuron Purkinje's cell cerebellar Purkinje cell cerebellum Purkinje cell cell Purkinje cell The output neuron of the cerebellar cortex. MESH:A08.186.211.132.810.428.200.212.600 A neuron that has dendritic processes radiating from the cell body forming a star-like shape. BTO:0002316 cell stellate neuron A neuron that has dendritic processes radiating from the cell body forming a star-like shape. ISBN:9780123973481 cell neuron associated cell (sensu Vertebrata) FBbt:00005144 cell This is a grouping class that is no longer needed or wanted. obsolete glial cell (sensu Nematoda and Protostomia) https://github.com/obophenotype/cell-ontology/issues/715 true A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. BTO:0002606 CALOHA:TS-0415 FMA:54536 neuroglial cell cell neuroglia glial cell It is unclear that all glial cells develop from a cell type called a glioblast. Radial glial cells develop from neuroepithelial cells and other types of glial cells develop from other precursors. Unless glioblast is meant to describe any cell that can give rise to a glial cell, this relationship needs further investigation. A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. MESH:A08.637 A neuroglial cell of ectodermal origin, i.e., the astrocytes and oligodendrocytes considered together. BTO:0000771 CALOHA:TS-2027 FMA:54538 macrogliocyte cell macroglial cell A neuroglial cell of ectodermal origin, i.e., the astrocytes and oligodendrocytes considered together. GOC:tfm ISBN:0721662544 A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with 'end feet' which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and 'reactive astrocytes' (along with microglia) respond to injury. BTO:0000099 CALOHA:TS-0060 FMA:54537 astrocytic glia cell Astrocytes are reportedly CD68-negative, CD121a-positive, CD184-positive, CD192-positive, CRF-positive, EGFR-positive, GFAP-positive, GLUT1-positive, MBP-negative, and NGFR-positive. astrocyte A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with 'end feet' which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and 'reactive astrocytes' (along with microglia) respond to injury. GOC:dsd GOC:tfm MESH:A08.637.200 MESH:D001253 PMID:11746784 PMID:12162730 PMID:12898703 PMID:20942978 http://en.wikipedia.org/wiki/Astrocyte A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system. BTO:0000962 CALOHA:TS-0709 FMA:54540 OLs cell oligodendroglia Oligodendrocytes are reportedly MDP-positive and CD4-negative. oligodendrocyte true A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system. MESH:A08.637.600 MESH:D009836 http://en.wikipedia.org/wiki/Oligodendrocyte OLs PMID:8734446 A central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive. brain macrophage BTO:0000078 BTO:0000962 FMA:54539 FMA:54540 brain-resident macrophage hortega cells microglia microgliocyte cell MF.microglia.CNS Markers: Mouse: CD11b+, F4/80+, CD68+. They represent ~12% of the cells in the CNS, but they are not uniformly distributed within the CNS. A normal adult mouse brain has approximately 3.5x10e6 microglia. Microglia are also reportedly CD3-negative, CD4-positive, CD8-negative, CD11b-positive, CD11c-high, CD14-negative, CD19-negative, CD45-low, CD56-negative, CD163-negative, CD200R-positive, CD281-positive, CD282-positive, CD283-positive, CD284-positive, CD285-positive, CD286-positive, CD287-positive, CD288-positive, CD289-positive, Gr1-negative, nestin-positive, and PU.1-positive. microglial cell A central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive. GOC:add GOC:dsd GOC:tfm ISBN:0721601464 MESH:D017628 PMID:11517395 PMID:12430718 PMID:14561199 PMID:14612429 PMID:16177057 PMID:19461673 PMID:2089275 http://en.wikipedia.org/wiki/Microglia hortega cells http://www.copewithcytokines.de/ microgliocyte http://www.copewithcytokines.de/ cell neuron associated cell (sensu Nematoda and Protostomia) cell gut endothelial cell Cell of the single layer of large flattened cells covering the surface of the cornea. CALOHA:TS-0172 FMA:70614 cell corneal endothelial cell Cell of the single layer of large flattened cells covering the surface of the cornea. GOC:tfm MESH:A09.371.060.067.31 Ectoderm destined to be nervous tissue. neurectoderm cell cell neurectodermal cell Ectoderm destined to be nervous tissue. GOC:tfm ISBN:068340007X A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs. CL:0002452 BTO:0002625 BTO:0003298 FMA:70546 BMSC bone marrow stromal cells colony-forming unit-fibroblast marrow stromal cells cell CFU-F MSC mesenchymal precursor cell mesenchymal progenitor cells mesenchymal stem cell mesenchymal stromal cell mesenchymal stromal cells stem cells, mesenchymal Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. mesenchymal stem cell https://github.com/obophenotype/cell-ontology/issues/474 true A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs. FB:ma GOC:dsd PMCID:PMC2613570 PMID:10102814j PMID:16923606 PMID:17986482 PMID:19960544 http://en.wikipedia.org/wiki/Mesenchymal_stem_cell http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells marrow stromal cells PMID:11378515 MSC PMID:11378515 mesenchymal progenitor cells MESH:D044982 mesenchymal stromal cells stem cells, mesenchymal MESH:D044982 An inactive fibroblast; cytoplasm is sparse, endoplasmic reticulum is scanty with flattened nucleus. Term used by some histologists; when fibroblasts become relatively inactive in fiber formation. However, this cell has the potential for fibrogenesis in quiescent connective tissue of the adult, as well as during development, other histologists prefer to use the term fibroblast in all circumstances. These cells represent ~0.5% of peripheral blood leukocytes. FMA:63879 cell Cultured human fibrocytes are MHCI-positive, MHCII-positive, CD1a-negative, CD3-negative, CD4-negative, CD8-negative, CD10-negative, CD11b-positive, CD13-positive, CD14-negative, CD16-negative, CD18-positive, CD19-negative, CD25-negative, CD29-positive, CD32-positive, CD33-negative, CD34-positive, CD38-negative, CD40-positive, CD44-negative, CD45RO-positive, CD49a-positive, CD49b-positive, CD49c-negative, CD49d-negative, CD49e-positive, CD49f-negative, CD56-negative, CD58-positive, CD61-positive, CD64-positive, CD70-negative, CD71-positive, CD80-positive, CD83-negative, CD86-positive, CD103-negative, CD105-positive, CD181-positive, CD182-negative, CD183-positive, CD184-positive, CD185-negative, CD186-negative, CD191-positive, CD192-negative, CD193-positive, CD194-positive, CD195-positive, CD196-negative, CD197-positive, CD199-positive, desmin-negative, F4/80-positive, Gr1-positive, LSP-1-positive, MHCI-positive, MHCII-positive, alpha-SMA-negative, TCRab-negative, TCRgd-negative, and vimentin-positive. Fibrocytes are also capable of secreting angiogenin, bFGF, CCL2, CCL3, CCL4, CCL8, CXCL1, type I collagen, type III collagen, CTGF, fibronectin, GM-CSF, IL-1a, IL-6, IL-8, IL-10, M-CSF, MMP-9, PDGF-A, TGF-alpha, TGF-beta1, TNF-alpha, and VEGF-A. fibrocyte true An inactive fibroblast; cytoplasm is sparse, endoplasmic reticulum is scanty with flattened nucleus. Term used by some histologists; when fibroblasts become relatively inactive in fiber formation. However, this cell has the potential for fibrogenesis in quiescent connective tissue of the adult, as well as during development, other histologists prefer to use the term fibroblast in all circumstances. These cells represent ~0.5% of peripheral blood leukocytes. GOC:dsd GOC:tfm ISBN:0412046911 ISBN:0517223651 PMID:11641248 PMID:15010326 PMID:17607298 PMID:18222966 PMID:8790603 PMID:9551999 http://en.wikipedia.org/wiki/Fibrocyte A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides. CL:0000450 BTO:0000443 CALOHA:TS-0012 FMA:63880 adipocyte adipose cell cell fat cell A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides. MESH:A11.329.114 A mature osteoblast that has become embedded in the bone matrix. They occupy a small cavity, called lacuna, in the matrix and are connected to adjacent osteocytes via protoplasmic projections called canaliculi. bone cell BTO:0002038 CALOHA:TS-1167 FMA:66779 VSAO:0000124 cell VSAO relationship simplified OBO_REL:integral_part_of VSAO:0000118 osteocyte A mature osteoblast that has become embedded in the bone matrix. They occupy a small cavity, called lacuna, in the matrix and are connected to adjacent osteocytes via protoplasmic projections called canaliculi. GOC:tfm MESH:A11.329.629.500 Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell. BTO:0000249 CALOHA:TS-0138 FMA:66782 cartilage cell cell chondrocyte Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell. GO_REF:0000034 MESH:A11.329.171 Skeletogenic cell that secretes dentine matrix, is derived from odontogenic papilla. Embedded in dentine tissue, and is the transformation of a non-terminally differentiated odontoblast cell. cell odontocyte Skeletogenic cell that secretes dentine matrix, is derived from odontogenic papilla. Embedded in dentine tissue, and is the transformation of a non-terminally differentiated odontoblast cell. GO_REF:0000034 An osteocytelike cell with numerous processes, trapped in a lacuna in the cement of the tooth. FMA:63003 cell CHECK: wikipedia says that cementocytes no longer produce cementum, but the phenoscape def is: Skeletogenic cell that produces cementum, is part of the odontogenic papilla, and is a transformation of a cementoblast cell (no change to existing def). cementocyte An osteocytelike cell with numerous processes, trapped in a lacuna in the cement of the tooth. ISBN:0781733901 A cell occurring in the peripheral part of the vitreous body of the eye that may be responsible for production of hyaluronic acid and collagen. BTO:0004271 FMA:70620 cell vitreous cell hyalocyte A cell occurring in the peripheral part of the vitreous body of the eye that may be responsible for production of hyaluronic acid and collagen. GOC:tfm PMID:19073178 cell guidepost cell OBSOLETE: A classification of cells by their primary end goal or behavior. CL:0000000 CL:0000003 CL:0001034 cell This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified by its function or behavior. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate. obsolete cell by function true OBSOLETE: A classification of cells by their primary end goal or behavior. FB:ma A cell capable of processing and presenting lipid and protein antigens to T cells in order to initiate an immune response. APC cell Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells. professional antigen presenting cell A cell capable of processing and presenting lipid and protein antigens to T cells in order to initiate an immune response. GOC:add ISBN:0781735149 cell simple columnar epithelial cell A pigment cell is a cell that contains pigment granules. VHOG:0001678 chromatocyte chromatophore cell pigment cell A pigment cell is a cell that contains pigment granules. GOC:tfm A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. CL:0000572 BTO:0000847 CALOHA:TS-0613 FMA:70545 VHOG:0001679 melanophore cell melanocyte true A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. SANBI:mhl pigment cell cell visual pigment cell 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 A cell that secretes glycosaminoglycans. GAG secreting cell hyaluronic acid secreting cell cell glycosaminoglycan secreting cell A cell that secretes glycosaminoglycans. GOC:tfm cell protein secreting cell A cell that is usually basal in position, cuboidal with round nucleus, short microvilli, secretes pepsinogen. FMA:62902 chief cell of stomach gastric chief cell pepsinogen secreting cell zymogenic cell cell peptic cell A cell that is usually basal in position, cuboidal with round nucleus, short microvilli, secretes pepsinogen. GOC:tfm OBSOLETE: A cell of the lymphoid series that can react with antigen to produce specific cell products called antibodies. Various cell subpopulations, often B cells, can be defined, based on the different classes of immunoglobulins that they synthesize. cell Consider using 'B cell ; CL:0000236' or one of its children instead. obsolete antibody secreting cell true A cell that specializes in secretion of surfactant in the alveoli of the lung. cell surfactant secreting cell true A cell that specializes in secretion of surfactant in the alveoli of the lung. GOC:tfm ISBN:0721662544 Epithelial progenitor cell of the lung. Club cells are dome-shaped with short microvilli but no cilia. They function to protect the bronchiolar epithelium. Club cells also multiply and differentiate into ciliated cells to regenerate the bronchiolar epithelium. BTO:0004811 FMA:14119 Clara cell bronchiolar non-ciliated cell club cell of bronchiole cell club cell true Epithelial progenitor cell of the lung. Club cells are dome-shaped with short microvilli but no cilia. They function to protect the bronchiolar epithelium. Club cells also multiply and differentiate into ciliated cells to regenerate the bronchiolar epithelium. DOI:10.1183/09031936.00146609 DOI:https://doi.org/10.1378/chest.12-2762 GOC:tfm PMID:28128362 PMID:7905712 cell seromucus secreting cell A cell of the epithelial lining that produce and secrete mucins. BTO:0001540 FMA:13148 http://en.wikipedia.org/wiki/Goblet_cell chalice cell cell goblet cell A cell of the epithelial lining that produce and secrete mucins. MESH:A03.492.411.369.320 cell acid secreting cell true A large, oval stomach epithelial cell with a central nucleus; source of gastric acid. Secretes HCl. BTO:0001780 FMA:62901 oxyntic cell cell parietal cell A large, oval stomach epithelial cell with a central nucleus; source of gastric acid. Secretes HCl. GOC:tfm ISBN:0517223651 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 An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas. BTO:0003865 FMA:62930 cell enteroendocrine cell An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas. GOC:tfm SANBI:mhl An endocrine cell that has the specialized function to produce and secrete hormones in response to neuronal signals. BTO:0002691 FMA:83810 neurosecretory cell cell neuroendocrine cell An endocrine cell that has the specialized function to produce and secrete hormones in response to neuronal signals. MESH:A06.688 A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system. BTO:0000259 FMA:69263 phaeochromocyte cell chromaffin cell A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system. MESH:A06.224.161 cell peptide hormone secreting cell BTO:0000783 cell insulin secreting cell A cell that secretes insulin and is located towards the center of the islets of Langerhans. beta cell BTO:0000783 EV:0200009 FMA:70586 MA:0002419 ncithesaurus:Beta_Cell B-cell of pancreatic islet beta cell of pancreatic islet insulin-secreting cell pancreatic B cell pancreatic B-cell pancreatic beta cell pancreatic islet core type B enteroendocrine cell cell beta cell islet Pancreatic beta cells are also reportedly CD284-positive. Upon activation, they upregulate their CD14 expression. type B pancreatic cell true true A cell that secretes insulin and is located towards the center of the islets of Langerhans. GOC:tfm ISBN:0517223651 http://en.wikipedia.org/wiki/Pancreatic_b_cell beta cell ZFA:0009102 B-cell of pancreatic islet FMA:70586 beta cell of pancreatic islet FMA:70586 insulin-secreting cell FMA:70586 pancreatic B-cell FMA:70586 pancreatic beta cell FMA:70586 pancreatic islet core MA:0002419 type B enteroendocrine cell FMA:70586 beta cell islet MA:0002419 A cell that secretes glucagon. FMA:84045 glucagon-secreting cell cell glucagon secreting cell A cell that secretes glucagon. GOC:tfm A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon. BTO:0000990 FMA:70585 alpha cell of islet of Langerhans pancreatic alpha cell cell pancreatic A cell A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon. GOC:tfm ISBN:0721662544 cell somatostatin secreting cell A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin. BTO:0000803 FMA:70587 D-cell of pancreatic islet delta cell of islet delta cell of pancreatic islet pancreatic D-cell pancreatic delta cell somatostatin-secreting pancreatic cell cell pancreatic D cell A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin. FMA:0517223651 GOC:tfm cell steroid hormone secreting cell A progesterone secreting cell in the corpus luteum. The large luteal cells develop from the granulosa cells. The small luteal cells develop from the theca cells. BTO:0003939 FMA:18688 lutein cell cell luteal cell A progesterone secreting cell in the corpus luteum. The large luteal cells develop from the granulosa cells. The small luteal cells develop from the theca cells. MESH:A05.360.319.114.630.278.400 cell ecdysteroid secreting cell cell testosterone secreting cell A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis. interstitial cell BTO:0000755 CALOHA:TS-1150 EMAPA:29655 FMA:72297 interstitial cell of Leydig cell Note that the Amphibian Anatomy Ontology (AA) has a class 'leydig cells' but this is unrelated Leydig cell A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis. GOC:tfm PMID:12050120 cell progesterone secreting cell A steroid hormone secreting cell that secretes estradiol. cell estradiol secreting cell A steroid hormone secreting cell that secretes estradiol. https://orcid.org/0000-0001-5208-3432 A cell whose primary function is intermediary metabolism. cell Removing this grouping class, because the groupings are incomplete and too hard to maintain. obsolete metabolising cell https://github.com/obophenotype/cell-ontology/issues/720 true A cell whose primary function is intermediary metabolism. FB:ma The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. BTO:0000575 CALOHA:TS-0454 FMA:14515 cell Hepatocytes are reportedly MHC Class I-positive and MHC Class II-positive. hepatocyte The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. GOC:tfm ISBN:0412046911 MESH:A11.436.348 PMID:19717280 http://en.wikipedia.org/wiki/Hepatocyte A cell whose primary function is to shorten. cell contractile cell A cell whose primary function is to shorten. FB:ma Contractile cells resembling smooth muscle cells that are present in glands, notably the mammary gland, and aid in secretion. This cell has long weaving dendritic processes containing myofilament. BTO:0002309 CALOHA:TS-2379 FMA:67799 basket epithelial cell myoepitheliocyte cell myoepithelial cell Contractile cells resembling smooth muscle cells that are present in glands, notably the mammary gland, and aid in secretion. This cell has long weaving dendritic processes containing myofilament. GOC:tfm ISBN:0721662544 An animal cell that has characteristics of both a fibroblast cell and a smooth muscle cell. MFB cell Myofibroblasts are alpha-SMA-positive, CD34-negative, CD45-negative. They are reportedly capable of secreting IL-1beta, IL-6, and TNF-alpha. myofibroblast cell An animal cell that has characteristics of both a fibroblast cell and a smooth muscle cell. GOC:dsd GOC:tfm MESH:D058628 PMID:19800625 PMID:20630469 MFB PMID:8731193 A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. BTO:0000888 BTO:0000902 CALOHA:TS-2032 FBbt:00005074 FMA:67328 WBbt:0003675 muscle fiber myocyte cell muscle cell A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. MESH:A11.620 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 muscle cell that develops tension more slowly than a fast-twitch fiber. FMA:84448 cell slow muscle fiber slow muscle cell A muscle cell that develops tension more slowly than a fast-twitch fiber. GOC:tfm ISBN:0323052908 slow muscle fiber ISBN:0815316208 A muscle cell that can develop high tension rapidly. It is usually innervated by a single alpha neuron . glycolytic muscle fiber cell fast muscle cell A muscle cell that can develop high tension rapidly. It is usually innervated by a single alpha neuron . GOC:tfm ISBN:0323052908 A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast). CL:0000191 BTO:0004576 CALOHA:TS-2159 FMA:14072 SMCs myocytes, smooth muscle smooth muscle fiber non-striated muscle cell cell smooth muscle cell A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast). MESH:A11.620.520 MESH:D032389 PMID:9315361 http://en.wikipedia.org/wiki/Smooth_muscle_cell SMCs PMID:9315361 myocytes, smooth muscle MESH:D032389 A striated muscle cell of an arthropod heart that participates in heart contraction. CL:0000466 cell cardiac muscle cell (sensu Arthopoda) A striated muscle cell of an arthropod heart that participates in heart contraction. MESH:A11.620.500 cell Consider CL:0002072. obsolete nodal cardiac cell true cell obsolete Purkinje fiber true cell flight muscle cell A cell that is capable of detection of a stimulus involved in sensory perception. receptor cell cell sensory receptor cell The peripheral receptor for pain. Includes receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. All mammalian nociceptors are free nerve endings. nociceptor nocireceptor cell Editor note: request detection of stimulus involved in sensory perception of pain; add develops_from relationship pain receptor cell The peripheral receptor for pain. Includes receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. All mammalian nociceptors are free nerve endings. MESH:A08.800.550.700.650 A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system. cell mechanoreceptor mechanoreceptor cell A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system. MESH:A08.800.550.700.500 mechanoreceptor MP:0000972 cell touch receptor cell A mechanoreceptor cell located in the inner ear that is sensitive to auditory stimuli. The accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system. CL:0000201 FMA:62364 auditory receptor cell cochlear hair cell cell inner ear hair cell inner ear receptor cell In mammals these cells are located in the organ of Corti. auditory hair cell A mechanoreceptor cell located in the inner ear that is sensitive to auditory stimuli. The accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system. MESH:A08.663.650.250 inner ear hair cell GO:0060119 inner ear receptor cell GO:0060119 cell gravity sensitive cell cell acceleration receptive cell A cellular receptor which mediates the sense of temperature. Thermoreceptor cells in vertebrates are mostly located under the skin. In mammals there are separate types of thermoreceptors for cold and for warmth and pain receptor cells which detect cold or heat extreme enough to cause pain. cell thermoreceptor cell A cellular receptor which mediates the sense of temperature. Thermoreceptor cells in vertebrates are mostly located under the skin. In mammals there are separate types of thermoreceptors for cold and for warmth and pain receptor cells which detect cold or heat extreme enough to cause pain. GOC:tfm MESH:A08.800.550.700.840 MP:0000971 A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood. cell chemoreceptor cell A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood. MESH:A08.800.550.700.120 BTO:0004185 FMA:67860 Wikipedia:Olfactory_receptor_neuron Schultze's cell odorant receptor cell olfactory receptor neuron olfactory sensory neuron cell olfactory receptor cell cell pH receptor cell A cell type found in the spherical or ovoid clusters of receptor cells found mainly in the epithelium of the tongue and constituting the end organs of the sense of taste. FMA:67910 taste bud cell cell taste receptor cell A cell type found in the spherical or ovoid clusters of receptor cells found mainly in the epithelium of the tongue and constituting the end organs of the sense of taste. GOC:tfm ISBN:0618947256 A cell specialized to detect and transduce light. BTO:0001060 CALOHA:TS-0868 FBbt:00004211 FMA:86740 cell photoreceptor cell true A cell specialized to detect and transduce light. MESH:A08.663.650.650 A cell whose function is determined by the generation or the reception of an electric signal. cell electrically active cell A cell whose function is determined by the generation or the reception of an electric signal. FB:ma A cell that takes up and metabolizes substances. cell absorptive cell A cell that takes up and metabolizes substances. CL:CVS 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 meso-epithelial cell that lies between the cartilaginous fibers in the synovial membrane of a joint and produces hyaluronic acid. BTO:0003652 CALOHA:TS-0995 FMA:66786 synoviocyte hyaluronic acid secreting cell cell synovial cell true A meso-epithelial cell that lies between the cartilaginous fibers in the synovial membrane of a joint and produces hyaluronic acid. GOC:tfm ISBN:0721662544 PMID:17942474 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 cell insulating cell A neuroglial cell of the peripheral nervous system which forms the insulating myelin sheaths of peripheral axons. Schwann cell peripheral neuroglial cell CALOHA:TS-0898 FMA:62121 neurilemmal cell cell myelinating Schwann cell A neuroglial cell of the peripheral nervous system which forms the insulating myelin sheaths of peripheral axons. GOC:cvs GOC:tfm MESH:A08.637.800 A cell that moves by its own activities. cell motile cell A cell that moves by its own activities. FB:ma CL:0000000 CL:0000003 CL:0001034 cell This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell in a multicellular organiam, apart from a zygote, can potentially be classified by its lineage. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate. obsolete cell by lineage true 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 OBSOLETE: A classification of cells by the number of their nuclei. CL:0000000 CL:0000003 CL:0001034 cell This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified by its nuclear number (note that this term was previously used as a parent class of enucleate cell). If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate. obsolete cell by nuclear number true OBSOLETE: A classification of cells by the number of their nuclei. FB:ma GOC:tfm 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 OBSOLETE (was not defined before being made obsolete). cell Refers to an activated mature lymphocyte phenotype rather than a distinct cell type; consider using 'lymphocyte ; CL:0000542' or one of its children instead. obsolete lymphoblast true OBSOLETE (was not defined before being made obsolete). cell Refers to an activated mature T lymphocyte phenotype rather than a distinct cell type; consider using 'T cell ; CL:0000084' or one of its children instead. obsolete T lymphoblast true OBSOLETE (was not defined before being made obsolete). cell Refers to an activated mature B lymphocyte phenotype rather than a distinct cell type; consider using 'B cell ; CL:0000236' or one of its children instead. obsolete B lymphoblast true A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. BTO:0000424 CALOHA:TS-0290 FMA:81100 RBC red blood cell cell erythrocyte true A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. GOC:tfm MESH:A11.118.290 A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation. BTO:0000132 CALOHA:TS-0803 FMA:62851 anucleate thrombocyte blood platelet enucleate thrombocyte cell Platelets are reportedly CCR1-positive, CCR2-negative, CCR3-positive, CCR4-positive, CCR5-negative, CCR6-negative, CCR7-negative, CCR8-negative, CCR9-negative, CCR10-negative, CD16-positive, CD23-positive, CD32-positive, CD40-positive, CD41-positive CD42-positive, CD61-positive, CD62P-positive, CD64-positive, CD89-positive, CD102-positive, CD147-positive (activated platelets), CD154-positive (activated platelets), CD162-positive, CD209, CD282-positive, CD284-positive, CD289-positive, CD181-negative, CD182-negative, CD183-negative, CD184-positive, CLEC2-positive, GPVI-positive, JAMC-positive, PAR1-positive, PAR2-negative, PAR3-positive, PAR4-positive, TSP1-positive, and TXA2R-positive. Platelets can reportedly produce CCL2, CCL3, CCL5, CCL7, CCL17, CD40L, CXCL1, CXCL4, CXCL4L1, CXCL5, CXCL7, CXCL8, CXCL12, EGF, factor V, factor VII, factor XI, factor XIII, bFGF, histamine, IGF-1, IL-1beta, PAI-1, PDGF, plasminogen, protein S, serotonin, TGF-beta, TFPI, VEGF, and vWF. platelet true A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation. GOC:add GOC:dsd GOC:tfm MESH:A11.118.188 MESH:D001792 PMID:11110672 PMID:16987572 PMID:17204662 PMID:17479180 PMID:20414831 http://en.wikipedia.org/wiki/Platelet Any cell capable of ingesting particulate matter via phagocytosis. BTO:0001044 FMA:83806 cell phagocyte Any cell capable of ingesting particulate matter via phagocytosis. GOC:add ISBN:0721601464 A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. BTO:0000801 CALOHA:TS-0587 FMA:63261 FMA:83585 histiocyte cell Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid. macrophage true A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. GOC:add GOC:tfm GO_REF:0000031 PMID:16213494 PMID:1919437 A lymphocyte of B lineage that is capable of B cell mediated immunity. A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity. BTO:0000776 CALOHA:TS-0068 FMA:62869 VHOG:0001480 B lymphocyte B-cell B-lymphocyte cell CL:0000236 B cell true A lymphocyte of B lineage that is capable of B cell mediated immunity. GOC:add GOC:tfm GO_REF:0000031 ISBN:0781735149 A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity. GOC:add GOC:tfm GO_REF:0000031 ISBN:0781735149 cell keratinizing barrier epithelial cell cell non keratinizing barrier epithelial cell cell brush border epithelial cell cell stratified squamous epithelial cell cell stratified cuboidal epithelial cell A modified epidermal cell located in the stratum basale. They are found mostly in areas where sensory perception is acute. Merkel cells are closely associated with an expanded terminal bulb of an afferent myelinated nerve fiber. FMA:70548 Merkel's cell cell Merkel cell PMID:19782676 A modified epidermal cell located in the stratum basale. They are found mostly in areas where sensory perception is acute. Merkel cells are closely associated with an expanded terminal bulb of an afferent myelinated nerve fiber. MESH:A08.800.550.700.500.425 A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Form the myelin insulation of nervous pathways, guide neuronal migration during development, and exchange metabolites with neurons. Neuroglia have high-affinity transmitter uptake systems, voltage-dependent and transmitter-gated ion channels, and can release transmitters, but their role in signaling (as in many other functions) is unclear. cell This is a grouping class that is no longer needed or wanted. obsolete glial cell (sensu Vertebrata) https://github.com/obophenotype/cell-ontology/issues/715 true A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Form the myelin insulation of nervous pathways, guide neuronal migration during development, and exchange metabolites with neurons. Neuroglia have high-affinity transmitter uptake systems, voltage-dependent and transmitter-gated ion channels, and can release transmitters, but their role in signaling (as in many other functions) is unclear. MESH:A08.637 A cell characteristically found lining hollow organs that are subject to great mechanical change due to contraction and distention; originally thought to represent a transition between stratified squamous and columnar epithelium. FMA:66778 cell transitional epithelial cell A cell characteristically found lining hollow organs that are subject to great mechanical change due to contraction and distention; originally thought to represent a transition between stratified squamous and columnar epithelium. GOC:tfm ISBN:0721662544 Obsolete. Use PO:0000353 from Plant Ontology instead. Cell in exodermis or endodermis that remains thin walled when the associated cells develop thick secondary walls. Has casparian strip in endodermis. cell replaced_by: PO:0000353 obsolete passage cell true Obsolete. Use PO:0000353 from Plant Ontology instead. Cell in exodermis or endodermis that remains thin walled when the associated cells develop thick secondary walls. Has casparian strip in endodermis. ISBN:0471245208 cell Mauthner neuron Type of neuron that is a primary mechanosensory cell, with peripheral neurites innervating the skin with free nerve endings. AAO:0010316 EFO:0003711 VHOG:0001484 Rohon Beard cell Rohon-Beard cell cell RB neuron Rohon-Beard neuron Type of neuron that is a primary mechanosensory cell, with peripheral neurites innervating the skin with free nerve endings. VHOG:0001484 Rohon Beard cell VHOG:0001484 RB neuron VHOG:0001484 Obsolete. Use PO:0020047 from Plant Ontology instead. A diploid (2n) cell that undergoes meiosis and forms four haploid (1n) microspores; also called microspore mother cell and, in seed plants, pollen mother cell. pollen mother cell primary sporogenous cell cell replaced_by: PO:0020047 obsolete microsporocyte true Obsolete. Use PO:0020047 from Plant Ontology instead. A diploid (2n) cell that undergoes meiosis and forms four haploid (1n) microspores; also called microspore mother cell and, in seed plants, pollen mother cell. ISBN:0471245208 cell hatching gland cell Obsolete. Use PO:0020019 from Plant Ontology instead. A haploid (1n) spore developing into a female gametophyte in heterosporous plants. cell replaced_by: PO:0020019 obsolete megaspore true Obsolete. Use PO:0020019 from Plant Ontology instead. A haploid (1n) spore developing into a female gametophyte in heterosporous plants. ISBN:0471245208 cell extramedullary cell Obsolete. Use PO:0020048 from Plant Ontology instead. A haploid (1n) spore developing into a male gametophyte in heterosporous plants; the uninucleate pollen grain in seed plants. cell replaced_by: PO:0020048 obsolete microspore true Obsolete. Use PO:0020048 from Plant Ontology instead. A haploid (1n) spore developing into a male gametophyte in heterosporous plants; the uninucleate pollen grain in seed plants. ISBN:0471245208 cell eurydendroid cell Obsolete. Use PO:0020094 from Plant Ontology instead. The female gamete of plants. female gametophyte egg cell cell replaced_by: PO:0020094 obsolete egg cell true Obsolete. Use PO:0020094 from Plant Ontology instead. The female gamete of plants. TAIR:lr cell eukaryotic cell cell uric acid accumulating cell cell Eumycetozoan cell Obsolete. Use PO:0000355 from Plant Ontology instead. A fiber like tracheid in the secondary xylem; commonly thick walled, with pointed ends and bordered pits that have lenticular to slit like apertures. cell replaced_by: PO:0000355 obsolete fiber tracheid true Obsolete. Use PO:0000355 from Plant Ontology instead. A fiber like tracheid in the secondary xylem; commonly thick walled, with pointed ends and bordered pits that have lenticular to slit like apertures. ISBN:0471245208 DDANAT:0000403 obsolete aggregate cell true Obsolete. Use PO:0000373 from Plant Ontology instead. Cell containing mucilages or gums or similar carbohydrate material characterized by the property of swelling in water. cell replaced_by: PO:0000373 obsolete mucilage cell true Obsolete. Use PO:0000373 from Plant Ontology instead. Cell containing mucilages or gums or similar carbohydrate material characterized by the property of swelling in water. ISBN:0471245208 false http://purl.obolibrary.org/obo/DDANAT_0000002 cell Obsoleted becuase this term has an overly general name, no definition, and by it's classification appears to refer to a very specific cell type in dictystelium. If needed, the term should be in DDANAT - probably as a subclass of http://purl.obolibrary.org/obo/DDANAT_0000002 obsolete anterior cell true Obsolete. Use PO:0000351 from Plant Ontology instead. An epidermal cell that divides to produce the guard cells. cell replaced_by: PO:0000351 obsolete guard mother cell true Obsolete. Use PO:0000351 from Plant Ontology instead. An epidermal cell that divides to produce the guard cells. ISBN:0471245208 DDANAT:0000002 obsolete vegetative cell (sensu Mycetozoa) true Obsolete. Use PO:0000400 from Plant Ontology instead. A cambial cell on the phloem side of the cambial zone that is the source of one or more cells arising by periclinal divisions and differentiating into phloem elements with or without additional divisions in various planes. phloem mother cell cell replaced_by: PO:0000400 obsolete phloem initial true Obsolete. Use PO:0000400 from Plant Ontology instead. A cambial cell on the phloem side of the cambial zone that is the source of one or more cells arising by periclinal divisions and differentiating into phloem elements with or without additional divisions in various planes. ISBN:0471245208 DDANAT:0000404 obsolete anterior like cell true Obsolete. Use PO:0004011 from Plant Ontology instead. A cell constituting an active locus of meristematic activity in a tissue composed of somewhat older, differentiating cells. cell replaced_by: PO:0004011 obsolete meristemoid true Obsolete. Use PO:0004011 from Plant Ontology instead. A cell constituting an active locus of meristematic activity in a tissue composed of somewhat older, differentiating cells. ISBN:0471245208 DDANAT:0000405 obsolete prespore cell true Obsolete. Consult Plant Ontology instead. The cell in the phloem tissue concerned with mainly longitudinal conduction of food materials. Classified into sieve cell and sieve tube member. cell obsolete sieve element true Obsolete. Consult Plant Ontology instead. The cell in the phloem tissue concerned with mainly longitudinal conduction of food materials. Classified into sieve cell and sieve tube member. ISBN:0471245208 DDANAT:0000406 obsolete prestalk cell true Obsolete. Use PO:0000284 from Plant Ontology instead. An epidermal cell associated with a stoma and at least morphologically distinguishable from the epidermal cells composing the groundmass of the tissue. cell replaced_by: PO:0000284 obsolete subsidiary cell true Obsolete. Use PO:0000284 from Plant Ontology instead. An epidermal cell associated with a stoma and at least morphologically distinguishable from the epidermal cells composing the groundmass of the tissue. ISBN:047124520 DDANAT:0000408 obsolete prestalk A cell true OBSOLETE, use term from Plant Ontology. A cell localized in the vascular cambium or phellogen. Its periclinal division can contribute cells either to the outside or to the inside of the axis; in vascular cambium, classified into fusiform initials (source of axial cells of xylem and phloem) and ray initials (source of the ray cells). cell replaced_by PO:0000295 obsolete cambial initial true OBSOLETE, use term from Plant Ontology. A cell localized in the vascular cambium or phellogen. Its periclinal division can contribute cells either to the outside or to the inside of the axis; in vascular cambium, classified into fusiform initials (source of axial cells of xylem and phloem) and ray initials (source of the ray cells). ISBN:0471245208 DDANAT:0000410 obsolete prestalk AB cell true DDANAT:0000409 obsolete prestalk B cell true Obsolete. Use PO:0000077 from Plant Ontology instead. Cell variable in form and size, being more or less thick, often lignified, secondary walls. Belongs to the category of subcells and may or may not be devoid of protoplast at maturity. cell replaced_by: PO:0000077 obsolete sclerenchyma cell true Obsolete. Use PO:0000077 from Plant Ontology instead. Cell variable in form and size, being more or less thick, often lignified, secondary walls. Belongs to the category of subcells and may or may not be devoid of protoplast at maturity. ISBN:0471245208 OBSOLETE: Initial population of prestalk cells that activate the ecmA promoter at the mound stage and that presumably further differentiate into pstA and pstO cells. DDANAT:0000406 cell This cell type does not exist in Dictyostelium. it has been long deleted in their anatomy ontology. obsolete prestalk I cell true OBSOLETE: Initial population of prestalk cells that activate the ecmA promoter at the mound stage and that presumably further differentiate into pstA and pstO cells. DictyBase:DDB Obsolete. Use PO:0020090 from Plant Ontology instead. OBSOLETED, use term from Plant Ontology. A cell containing the two polar nuclei which, after double fertilization, will develop into the endosperm. cell replaced_by: PO:0020090 obsolete central cell true Obsolete. Use PO:0020090 from Plant Ontology instead. OBSOLETED, use term from Plant Ontology. A cell containing the two polar nuclei which, after double fertilization, will develop into the endosperm. TAIR:lr DDANAT:0000407 obsolete prestalk 0 cell true Obsolete. Use PO:0020097 from Plant Ontology instead. The cell that will give rise to the generative nuclei which will participate in fertilization. cell replaced_by: PO:0020097 obsolete generative cell true Obsolete. Use PO:0020097 from Plant Ontology instead. The cell that will give rise to the generative nuclei which will participate in fertilization. TAIR:lr DDANAT:0000411 obsolete pstAB/ALC true Obsolete. Use PO:0000282 from Plant Ontology instead. An outgrowth from the epidermis. Trichomes vary in size and complexity and include hairs, scales, and other structures and may be glandular. In Arabidopsis, patterning of trichome development is not random but does not appear to be lineage-based like stomata. cell replaced_by: PO:0000282 obsolete trichome true Obsolete. Use PO:0000282 from Plant Ontology instead. An outgrowth from the epidermis. Trichomes vary in size and complexity and include hairs, scales, and other structures and may be glandular. In Arabidopsis, patterning of trichome development is not random but does not appear to be lineage-based like stomata. ISBN:0471245208 PMID:10938806 DDANAT:0000412 obsolete pstO/ALC true Obsolete. Use PO:0000071 from Plant Ontology instead. A specialized parenchyma cell associated with a sieve-tube member in angiosperm phloem and arising from the same mother cell as the sieve-tube member. cell replaced_by: PO:0000071 obsolete companion cell true Obsolete. Use PO:0000071 from Plant Ontology instead. A specialized parenchyma cell associated with a sieve-tube member in angiosperm phloem and arising from the same mother cell as the sieve-tube member. ISBN:0879015322 DDANAT:0000413 obsolete stalk cell true A cell of a filament of a fungal mycelium. cell hyphal cell A cell of a filament of a fungal mycelium. ISBN:08199377X cell eye photoreceptor cell Obsolete. Use PO:0000191 from Plant Ontology instead. A cell in the micropylar end of the embryo sac associated with the egg in the egg apparatus of angiosperms. Plays a vital role in fertilization. cell replaced_by: PO:0000191 obsolete synergid true Obsolete. Use PO:0000191 from Plant Ontology instead. A cell in the micropylar end of the embryo sac associated with the egg in the egg apparatus of angiosperms. Plays a vital role in fertilization. ISBN:047125208 DDANAT:0000402 obsolete chemotactic amoeboid cell (sensu Mycetozoa) true Obsolete. Use PO:0000274 from Plant Ontology instead. A fiber of the xylem tissue, Two types are recognized in the secondary xylem: fiber tracheids and libriform fibers. cell replaced_by: PO:0000274 obsolete xylem fiber cell true Obsolete. Use PO:0000274 from Plant Ontology instead. A fiber of the xylem tissue, Two types are recognized in the secondary xylem: fiber tracheids and libriform fibers. ISBN:0471245208 DDANAT:0000414 obsolete spore (sensu Mycetozoa) true Obsolete. Use PO:0000293 from Plant Ontology instead. One of a pair of cells flanking the stomatal pore and causing the opening and closing of the pore by changes in turgor. stomatal guard cell cell replaced_by: PO:0000293 obsolete guard cell true Obsolete. Use PO:0000293 from Plant Ontology instead. One of a pair of cells flanking the stomatal pore and causing the opening and closing of the pore by changes in turgor. ISBN:0471245208 A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism. cell structural cell A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism. TAIR:sr Obsolete. Consult Plant Ontology instead. A type of sieve element that has relatively undifferentiated sieve areas (with narrow pores), rather uniform in structure on all walls; that is, there are no sieve plates. Typical of gymnosperms and lower vascular plants. cell obsolete sieve cell true Obsolete. Consult Plant Ontology instead. A type of sieve element that has relatively undifferentiated sieve areas (with narrow pores), rather uniform in structure on all walls; that is, there are no sieve plates. Typical of gymnosperms and lower vascular plants. ISBN:0471245208 A peptide hormone secreting cell that produces growth hormone, somatotropin. CL:0000471 growth hormone secreting cell somatotrophin secreting cell cell somatotropin secreting cell A peptide hormone secreting cell that produces growth hormone, somatotropin. GOC:tfm SANBI:mhl Obsolete. Use PO:0020099 from Plant Ontology instead. Cell type formed after the first mitotic division of the microgametophye, The nucleus of this cell migrates to the tip of the pollen tube after germination and disintegrates when the pollen tube penetrates the nucellus. cell replaced_by: PO:0020099 obsolete vegetative cell true Obsolete. Use PO:0020099 from Plant Ontology instead. Cell type formed after the first mitotic division of the microgametophye, The nucleus of this cell migrates to the tip of the pollen tube after germination and disintegrates when the pollen tube penetrates the nucellus. ISBN:0140514031 TAIR:lr Obsolete. Use PO:0000115 from Plant Ontology instead. A cell that surrounds a trichome and provides support for the trichome. cell replaced_by: PO:0000115 obsolete socket cell true Obsolete. Use PO:0000115 from Plant Ontology instead. A cell that surrounds a trichome and provides support for the trichome. PMID:10938806 Obsolete. Use PO:0000273 from Plant Ontology instead. A cell composing the xylem. cell replaced_by: PO:0000273 obsolete xylem element true Obsolete. Use PO:0000273 from Plant Ontology instead. A cell composing the xylem. ISBN:0471245208 OBSOLETED. Commonly used for a cell in root epidermis that gives rise to a root hair. The daughter cell produced by the asymmetric division of a root epidermal cell that gives rise to a root hair. cell Obsoleted. Use trichoblast from the plant ontology (PO:0000262). obsolete trichoblast true OBSOLETED. Commonly used for a cell in root epidermis that gives rise to a root hair. The daughter cell produced by the asymmetric division of a root epidermal cell that gives rise to a root hair. ISBN:0471245208 A mature sexual reproductive cell having a single set of unpaired chromosomes. CALOHA:TS-0395 FBbt:00005412 FMA:18649 haploid nucleated cell cell haploid germ cell gamete true A mature sexual reproductive cell having a single set of unpaired chromosomes. GOC:tfm ISBN:0721662544 FBbt:00000092 cell pole cell OBSOLETE (was not defined before being made obsolete). cell Not a differentiation state per se; consider using 'B cell ; CL:0000236' or one of its children instead. obsolete IgM B cell true OBSOLETE (was not defined before being made obsolete). cell Not a differentiation state per se, and IgG isotypes vary by species; consider using 'B cell ; CL:0000236' or one of its children instead. obsolete IgG B cell true OBSOLETE (was not defined before being made obsolete). cell Not a differentiation state per se, and IgA isotypes vary by species. Consider using 'B cell ; CL:0000236' or one of its children instead. obsolete IgA B cell true OBSOLETE (was not defined before being made obsolete). cell Not a differentiation state per se; consider using 'B cell ; CL:0000236' or one of its children instead. obsolete IgE B cell true FBbt:00004193 lens cell cell crystallin accumulating 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 cell metal ion accumulating cell cuprophilic cell cell copper accumulating cell cell iron accumulating cell cell keratin accumulating cell An epidermal cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the basal layers of the epidermis to the cornified (horny) layer of the skin. Successive stages of differentiation of the keratinocytes forming the epidermal layers are basal cell, spinous or prickle cell, and the granular cell. CL:0002185 BTO:0000667 CALOHA:TS-0500 FMA:62879 keratinized cell of epidermis malpighian cell cell Keratinocytes are reportedly CDw210a-negative, CDw210b-positive, CD281-positive, CD282-positive, CD285-positive, IL22Ra1-positive, Human keratinocytes are reportedly capable of secreting BD-2, BD-3, hCAP-18, CXCL1, CXCL5, CXCL8, elafin, MMP-3, NGAL, PDGF-A, S100A7, S100A8, and S100A9. Transcription factors: STAT3-positive. keratinocyte true true An epidermal cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the basal layers of the epidermis to the cornified (horny) layer of the skin. Successive stages of differentiation of the keratinocytes forming the epidermal layers are basal cell, spinous or prickle cell, and the granular cell. GOC:dsd MESH:A11.436.397 MESH:D015603 PMID:15582983 PMID:15749908 PMID:19727116 http://en.wikipedia.org/wiki/Keratinocyte Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid. BTO:0003687 FMA:62511 serous cell cell serous secreting cell Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid. GOC:tfm ISBN:0517223651 ISBN:0721662544 cell milk secreting cell A cell secreting tears, the fluid secreted by the lacrimal glands. This fluid moistens the conjunctiva and cornea. cell tears secreting cell A cell secreting tears, the fluid secreted by the lacrimal glands. This fluid moistens the conjunctiva and cornea. MESH:A12.200.882 Obsolete. Use PO:0000082 from Plant Ontology instead. A meristemic ray cell in the vascular cambium that gives rise to ray cells of the secondary xylem and secondary phloem. cell replaced_by: PO:0000082 obsolete ray initial true Obsolete. Use PO:0000082 from Plant Ontology instead. A meristemic ray cell in the vascular cambium that gives rise to ray cells of the secondary xylem and secondary phloem. ISBN:0471245208 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 A cell secreting sweat, the fluid excreted by the sweat glands of mammals. It consists of water containing sodium chloride, phosphate, urea, ammonia, and other waste products. cell sweat secreting cell A cell secreting sweat, the fluid excreted by the sweat glands of mammals. It consists of water containing sodium chloride, phosphate, urea, ammonia, and other waste products. MESH:A12.200.849 BTO:0003689 mucous cell cell mucus secreting cell Obsolete. Use PO:0000431 from Plant Ontology instead. A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) megaspores; also called megaspore mother cell. archesporial cell megaspore mother cell cell replaced_by: PO:0000431 obsolete megasporocyte true Obsolete. Use PO:0000431 from Plant Ontology instead. A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) megaspores; also called megaspore mother cell. ISBN:0471245208 cell seminal fluid secreting cell An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates. BTO:0000395 CALOHA:TS-2168 FMA:62499 alveolar epithelial cell pneumonocyte cell pneumocyte An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates. GOC:tfm PMID:20054144 cell lysozyme secreting cell cell metanephric mesenchyme stem cell A cell that is specialised to accumulate a particular substance(s). cell stuff accumulating cell A cell that is specialised to accumulate a particular substance(s). FB:ma cell glycogen accumulating cell cell extracellular matrix secreting cell cell myelin accumulating cell cell oxygen accumulating cell Obsolete. Use PO:0000075 from Plant Ontology instead. An elongated living cell with unevenly thickened nonlignified primary walls. cell replaced_by: PO:0000075 obsolete collenchymal cell true Obsolete. Use PO:0000075 from Plant Ontology instead. An elongated living cell with unevenly thickened nonlignified primary walls. ISBN:0471245208 Obsolete. Use PO:0000301 from Plant Ontology instead. A tracheary element of the xylem that has no perforations, as contrasted with a vessel member. May occur in primary and in secondary xylem. May have any kind of secondary wall thickening found in tracheary elements. cell replaced_by: PO:0000301 obsolete tracheid true Obsolete. Use PO:0000301 from Plant Ontology instead. A tracheary element of the xylem that has no perforations, as contrasted with a vessel member. May occur in primary and in secondary xylem. May have any kind of secondary wall thickening found in tracheary elements. ISBN:0471245208 OBSOLETE, use term from Plant Ontology. A cell formed after asymmetric division of root epidermal cell that does not give rise to a root hair. cell non-hair cell replaced_by: PO:0020090 obsolete atrichoblast true OBSOLETE, use term from Plant Ontology. A cell formed after asymmetric division of root epidermal cell that does not give rise to a root hair. ISBN:0387987819 A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body. FMA:86667 cell migratory neural crest cell A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body. MESH:A16.254.600 BTO:0002307 FAO:0000032 cell yeast-form vegetative cell (sensu Fungi) A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors. cell mesenchyme condensation cell A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors. GOC:tfm PMID:5025404 A cell found within the adrenal medulla that secrete biogenic amine hormones upon stimulation. CL:1000422 FMA:69262 medullary chromaffin cell of adrenal gland cell adrenal medulla chromaffin cell A cell found within the adrenal medulla that secrete biogenic amine hormones upon stimulation. GOC:tfm http://www.britannica.com/EBchecked/topic/6405/adrenal-gland medullary chromaffin cell of adrenal gland FMA:69262 neuroblast cell neuroblast (sensu Nematoda and Protostomia) An early neural cell developing from the early ependymal cell of the neural tube. FMA:70564 spongioblast cell glioblast (sensu Vertebrata) An early neural cell developing from the early ependymal cell of the neural tube. GOC:tfm ISBN:0618947256 cell glioblast (sensu Nematoda and Protostomia) cell pigment cell (sensu Nematoda and Protostomia) Any animal cell containing pigment granules. cell pigment cell (sensu Vertebrata) Any animal cell containing pigment granules. GOC:tfm ISBN:0721662544 A pigment cell that is capable of detecting light stimulus that is involved in visual perception. FMA:63846 cell visual pigment cell (sensu Vertebrata) true A pigment cell that is capable of detecting light stimulus that is involved in visual perception. GOC:tfm cell obsolete non-visual cell (sensu Vertebrata) true A mesenchymal cell that is part of a small mass of condensed mesenchyme in the enamel organ; it differentiates into the dentin and dental pulp. cell Merge with odontoblast? dental papilla cell A mesenchymal cell that is part of a small mass of condensed mesenchyme in the enamel organ; it differentiates into the dentin and dental pulp. GOC:tfm ISBN:0721662544 A specialized mesenchymal cell that resides in the dermal papilla located at the bottom of hair follicles. This cell plays a pivotal roles in hair formation, growth, and cycling. cell Are these really all stem cells? hair follicle dermal papilla cell true A specialized mesenchymal cell that resides in the dermal papilla located at the bottom of hair follicles. This cell plays a pivotal roles in hair formation, growth, and cycling. GOC:tfm PMID:9893172 A cell of the sclera of the eye. cell scleral cell A cell of the sclera of the eye. GOC:add A cell of the choroid of the eye. cell choroidal cell of the eye A cell of the choroid of the eye. GOC:add cell extraembryonic cell cell amnioserosal cell A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface. FMA:83028 trophoblastic cell cell trophoblast cell true A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface. GOC:tfm MESH:A11.936 A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. cell epiblast cell A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. GOC:tfm ISBN:0618947256 An undifferentiated cell produced by early cleavages of the fertilized egg (zygote). BTO:0001473 FMA:72551 blastomere cell blastoderm cell An undifferentiated cell produced by early cleavages of the fertilized egg (zygote). MESH:A11.104 ncithesaurus:Blastemal_Cell blastema cell cell blastemal cell A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell. FMA:86767 cell Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo. multi-potent skeletal muscle stem cell true A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell. PMID:18282570 cell hair matrix stem cell cell stratified epithelial stem cell A smooth muscle cell that is part of a sphincter. A sphincter is a typically circular muscle that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning. cell sphincter associated smooth muscle cell true A smooth muscle cell that is part of a sphincter. A sphincter is a typically circular muscle that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning. GOC:cjm A smooth muscle cell assocatiated with the vasculature. VSMC vascular smooth muscle cell cell vascular associated smooth muscle cell true A smooth muscle cell assocatiated with the vasculature. GOC:dsd GOC:tfm A cell of the early embryo at the developmental stage in which the blastomeres, resulting from repeated mitotic divisions of the fertilized ovum (zygote), form a compact cell mass. cell morula cell A cell of the early embryo at the developmental stage in which the blastomeres, resulting from repeated mitotic divisions of the fertilized ovum (zygote), form a compact cell mass. MESH:A16.254.270.550 A cell of the embryo in the early stage following the blastula, characterized by morphogenetic cell movements, cell differentiation, and the formation of the three germ layers. cell gastrula cell A cell of the embryo in the early stage following the blastula, characterized by morphogenetic cell movements, cell differentiation, and the formation of the three germ layers. MESH:A16.254.412 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 Obsolete. Use PO:0000081 from Plant Ontology instead. OBSOLETE, use term from the Plant Ontology. A secondary vascular cell that develops from the fusiform cambial initials and oriented with their longest diameter parallel with the main axis of stem or root. These cells make up the axial system, also known as vertical or longitudinal system. cell replaced_by: PO:0000081 obsolete axial cell true Obsolete. Use PO:0000081 from Plant Ontology instead. OBSOLETE, use term from the Plant Ontology. A secondary vascular cell that develops from the fusiform cambial initials and oriented with their longest diameter parallel with the main axis of stem or root. These cells make up the axial system, also known as vertical or longitudinal system. ISBN:0471245208 Obsolete. Consult Plant Ontology. A cell that develops from the ray initial and composes all rays (panels of tissue variable in height and width, formed by the ray initials in the vascular cambium and extending radially in the secondary xylem and secondary phloem) in the secondary vascular tissues. cell obsolete ray cell true Obsolete. Consult Plant Ontology. A cell that develops from the ray initial and composes all rays (panels of tissue variable in height and width, formed by the ray initials in the vascular cambium and extending radially in the secondary xylem and secondary phloem) in the secondary vascular tissues. ISBN:0471245208 Diploid cell produced by the fusion of sperm cell nucleus and egg cell. zygote BTO:0000854 EHDAA2:0004546 FMA:72395 cell animal zygote Diploid cell produced by the fusion of sperm cell nucleus and egg cell. ISBN:0471245208 Obsolete. Use PO:0000084 from Plant Ontology instead. Male gamete, part of male germ unit. cell gametophyte sperm cell male gametophyte sperm cell pollen germ cell replaced_by: PO:0000084 obsolete sperm cell (sensu Viridiplantae) true Obsolete. Use PO:0000084 from Plant Ontology instead. Male gamete, part of male germ unit. ISBN:0471245208 cell glial cell (sensu Nematoda) sheath cell (sensu Nematoda) Obsolete. Use PO:0000352 from Plant Ontology instead. Cell containing glucosinolates ('mustard oil glucosides') and myrosinases, enzymes hydrolyzing the glucosinolates. Occurs in eleven dicotyledon families, the two largest of which are the Brassicaceae and Euphorbiaceae. cell replaced_by: PO:0000352 obsolete myrosin cell true Obsolete. Use PO:0000352 from Plant Ontology instead. Cell containing glucosinolates ('mustard oil glucosides') and myrosinases, enzymes hydrolyzing the glucosinolates. Occurs in eleven dicotyledon families, the two largest of which are the Brassicaceae and Euphorbiaceae. ISBN:0471245208 Obsolete. Use PO:0000078 from Plant Ontology instead. Parenchyma cell with the wall ingrowth (or invaginations) that increase the surface of the plasmalemma. Appears to be specialized for short-distance transfer of solutes. cell intermediary cell replaced_by: PO:0000078 obsolete transfer cell true Obsolete. Use PO:0000078 from Plant Ontology instead. Parenchyma cell with the wall ingrowth (or invaginations) that increase the surface of the plasmalemma. Appears to be specialized for short-distance transfer of solutes. ISBN:0471245208 The cell protoplasm after removal of the cell wall. cell protoplast The cell protoplasm after removal of the cell wall. ISBN:08199377X An epidermal cell that is part of a cell cluster organ of the insect integument (such as a sensillum) and that secretes a cuticular specialization that forms a socket around the base of a cuticular specialization produced by a trichogen cell. socket cell FBbt:00005171 cell tormogen cell An epidermal cell that is part of a cell cluster organ of the insect integument (such as a sensillum) and that secretes a cuticular specialization that forms a socket around the base of a cuticular specialization produced by a trichogen cell. ISBN:978-0801481253 socket cell ISBN:978-0801481253 FBbt:00001789 cell histoblast An epidermal cell that is part of a cell cluster organ of the insect integument (such as a sensillum) and that secretes a cuticular specialization, often in the form of a hair, bristle, peg or scale. The base of this specialization is often surrounded by a socket produced by a closely associated tormogen cell. hair cell BTO:0004744 FBbt:00005169 cell trichogen cell An epidermal cell that is part of a cell cluster organ of the insect integument (such as a sensillum) and that secretes a cuticular specialization, often in the form of a hair, bristle, peg or scale. The base of this specialization is often surrounded by a socket produced by a closely associated tormogen cell. ISBN:978-0801481253 CL:0007010 BTO:0002051 cell obsolete osteoprogenitor cell true cell humidity receptor cell cell tracheoblast cell support cell (sensu Nematoda and Protostomia) cell sensory processing neuron The support cell that makes the thecogen dendritic cap - a cuticle-like matrix around the tip of the eo-dendrite and which encloses the soma of the eo-neuron. fly sheath cell cell thecogen cell The support cell that makes the thecogen dendritic cap - a cuticle-like matrix around the tip of the eo-dendrite and which encloses the soma of the eo-neuron. Fbbt:00005173 FBbt:00005130 cell neurosecretory neuron FBbt:00005219 cell scolopale cell cell nephrogenic mesenchyme stem cell cell ligament cell FBbt:00005062 cell prohemocyte (sensu Nematoda and Protostomia) cell attachment cell FBbt:00005063 cell hemocyte (sensu Arthropoda) PMID:18025161 An elongated fibrocyte that is part of a tendon. The cytoplasm is stretched between the collagen fibres of the tendon. They have a central cell nucleus with a prominent nucleolus. Tendon cells have a well-developed rough endoplasmic reticulum and they are responsible for synthesis and turnover of tendon fibres and ground substance. muscle attachment cell cell tenocyte tendon cell true An elongated fibrocyte that is part of a tendon. The cytoplasm is stretched between the collagen fibres of the tendon. They have a central cell nucleus with a prominent nucleolus. Tendon cells have a well-developed rough endoplasmic reticulum and they are responsible for synthesis and turnover of tendon fibres and ground substance. GOC:NV GOC:tfm PMID:957445 cell socket cell (sensu Nematoda) cell blood cell (sensu Nematoda and Protostomia) An insect immune cell that develops from plasmatocyte. FBbt:00001688 cell podocyte (sensu Diptera) An insect immune cell that develops from plasmatocyte. PMID:12930778 FMA:63847 cell crystal cell A cell whose function is determined by its response to an electric signal. cell electrically responsive cell A cell whose function is determined by its response to an electric signal. FB:ma FBbt:00001685 cell plasmatocyte FBbt:00001689 cell procrystal cell FBbt:00001687 cell lamellocyte cell ganglion interneuron true FBbt:00001691 cell polygonal cell Obsolete. Consult Plant Ontology instead. OBSOLETED, not defined prior to obsoletion. cell obsolete phloem element true Obsolete. Consult Plant Ontology instead. OBSOLETED, not defined prior to obsoletion. GOC:tfm Obsolete. Use PO:0000332 from Plant Ontology instead. An epidermal cell with a characteristic convoluted anticlinal cell wall that gives a jigsaw like appearance to the lamina. cell replaced_by: PO:0000332 obsolete pavement cell true Obsolete. Use PO:0000332 from Plant Ontology instead. An epidermal cell with a characteristic convoluted anticlinal cell wall that gives a jigsaw like appearance to the lamina. ISBN:087694289 FBbt:00001686 cell macrophage (sensu Diptera) cell CNS interneuron true A cell that initiates an electrical signal and passes that signal to another cell. cell electrically signaling cell A cell that initiates an electrical signal and passes that signal to another cell. FB:ma FBbt:00005148 cell neuroepidermoblast cell CNS short range interneuron FBbt:00005221 cell scolopidial ligament cell BTO:0001277 CALOHA:TS-0949 cell male gamete true true FBbt:00005219 cell scolopidial sheath cell cell CNS long range interneuron An epithelial cell of the hypodermis of flatworms. WBbt:0007846 cell flatworm hypodermal cell An epithelial cell of the hypodermis of flatworms. GOC:tfm http://www.wormatlas.org/hermaphrodite/hypodermis/mainframe.htm A cell whose nucleus, or nuclei, each contain more than two haploid genomes. cell polyploid cell A cell whose nucleus, or nuclei, each contain more than two haploid genomes. FB:ma A cell whose nucleus contains a single haploid genome. cell haploid cell A cell whose nucleus contains a single haploid genome. FB:ma GOC:tfm OBSOLETE: A classification of cells by the number of haploid genome equivalents of their nucleus or nuclei. CL:0000000 CL:0000003 CL:0000255 CL:0001034 cell This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell with chromosomes can be classified by its ploidy. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), eukaryotic cell (CL:0000255) or cell in vitro (CL:0001034) as appropriate. obsolete cell by ploidy true OBSOLETE: A classification of cells by the number of haploid genome equivalents of their nucleus or nuclei. FB:ma GOC:tfm A cell whose nucleus has two haploid genomes. FMA:72300 cell diploid cell A cell whose nucleus has two haploid genomes. FB:ma cell polytene cell cell endopolyploid cell An epithelial cell found in C. elegans that firmly hold the outer body wall and the lips to the inner cylinder of the pharynx in a manner that keeps these organs from breaking apart, while still giving each organ freedom of movement during feeding. WBbt:0005793 cell arcade cell An epithelial cell found in C. elegans that firmly hold the outer body wall and the lips to the inner cylinder of the pharynx in a manner that keeps these organs from breaking apart, while still giving each organ freedom of movement during feeding. GOC:tfm http://www.wormatlas.org/ver1/handbook/hypodermis/hypsupportother.htm#arcadecells An epithelial fate stem cell found in flatworms. BTO:0003039 cell seam cell An epithelial fate stem cell found in flatworms. GOC:tfm http://www.wormatlas.org/hermaphrodite/seam%20cells/mainframe.htm cell syncytial epithelial cell A free floating cell, including amebocytes and eleocytes, in the coelom of certain animals, especially annelids. BTO:0002856 WBbt:0005751 coelomocyte A free floating cell, including amebocytes and eleocytes, in the coelom of certain animals, especially annelids. GOC:tfm ISBN:0721662544 A cell whose primary function is to cause growth by stimulating cell division in its immediate cellular environment. cell mitogenic signaling cell A cell whose primary function is to cause growth by stimulating cell division in its immediate cellular environment. FB:ma cell tip cell A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids. WBbt:0005812 cell excretory cell A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids. GOC:tfm PMID:19783135 Forms the terminal part of the cuticle-lined excretory duct of C. elegans. cell pore cell Forms the terminal part of the cuticle-lined excretory duct of C. elegans. JB:jb cell This is a cell used in tissue engineering and is out of scope for CL. obsolete scaffold cell https://github.com/obophenotype/cell-ontology/issues/708 true A scaffolding cell type found in C. elegans, this cell plays a supportive role to the muscle arms. May also have an endocrine role. cell GLR cell A scaffolding cell type found in C. elegans, this cell plays a supportive role to the muscle arms. May also have an endocrine role. GOC:tfm http://wormatlas.psc.edu/hermaphrodite/muscleGLR/mainframe.htm cell yolk cell cell imaginal disc cell A pigment cell derived from the neural crest. Contains cartenoid pigments in structures called pterinosomes or xanthosomes. This gives an appearance ranging from a golden yellow to orange and red. cell xanthophore xanthophore cell A pigment cell derived from the neural crest. Contains cartenoid pigments in structures called pterinosomes or xanthosomes. This gives an appearance ranging from a golden yellow to orange and red. SANBI:mhl A pigment cell derived from the neural crest. The cell contains flat light-reflecting platelets, probably of guanine, in stacks called reflecting platets or iridisomes. The color-generating components produce a silver, gold, or iridescent color. cell guanophore iridophore A pigment cell derived from the neural crest. The cell contains flat light-reflecting platelets, probably of guanine, in stacks called reflecting platets or iridisomes. The color-generating components produce a silver, gold, or iridescent color. SANBI:mhl Large, stellate fibroblast found along the network of collagen fibers of the reticulum of the spleen; synthesize the matrix components of the reticulum. FMA:62877 reticulum cell cell reticular cell Large, stellate fibroblast found along the network of collagen fibers of the reticulum of the spleen; synthesize the matrix components of the reticulum. GOC:tfm ISBN:0517223651 http://en.wikipedia.org/wiki/Reticular_cell Obsolete. Use PO:0000244 from Plant Ontology instead. In monosporic and bisporic megasporogenesis: the megaspore(s) that will undergo megagametogenesis. cell replaced_by: PO:0000244 obsolete functional megaspore true Obsolete. Use PO:0000244 from Plant Ontology instead. In monosporic and bisporic megasporogenesis: the megaspore(s) that will undergo megagametogenesis. TAIR:lr A secretory cell that discharges its product without loss of cytoplasm. cell eccrine cell A secretory cell that discharges its product without loss of cytoplasm. ISBN:0198547684 cell alkali secreting cell cell vaginal lubricant secreting cell A rounded cell that is usually situated next to sinusoids; secretes follicular stimulating hormone (FSH) and luteinizing hormone (LH). BTO:0002482 FMA:83100 delta basophil follicle stimulating hormone secreting cell gonadotrope gonadotrope cell gonadotroph gonadotropic cell pituitary delta cell cell gonadtroph A rounded cell that is usually situated next to sinusoids; secretes follicular stimulating hormone (FSH) and luteinizing hormone (LH). GOC:tfm ISBN:0517223651 http://en.wikipedia.org/wiki/Gonadotroph A peptide hormone secreting cell pituitary that produces luteinizing hormone. cell luteinizing hormone secreting cell A peptide hormone secreting cell pituitary that produces luteinizing hormone. GOC:tfm A peptide hormone cell that secretes prolactin. cell prolactin secreting cell A peptide hormone cell that secretes prolactin. GOC:tfm SANBI:mhl A cell of the intermediate pituitary that produces melanocyte stimulating hormone. BTO:0002277 melanotrope melanotroph cell melanocyte stimulating hormone secreting cell A cell of the intermediate pituitary that produces melanocyte stimulating hormone. SANBI:mhl FBbt:00004903 cell follicle stem cell A cell with extensive dendritic processes found in the B cell areas (primary follicles and germinal centers) of lymphoid tissue. They are unrelated to the dendritic cell associated with T cells. Follicular dendritic cells have Fc receptors and C3b receptors, but unlike other dendritic cells, they do not process or present antigen in a way that allows recognition by T cells. Instead, they hold antigen in the form of immune complexes on their surfaces for long periods and can present antigen to B cells during an immune response. BTO:0004267 FMA:83037 cell Due to its unique lineage and distinct function, this is not a type of dendritic cell; CL:0000451. follicular dendritic cell A cell with extensive dendritic processes found in the B cell areas (primary follicles and germinal centers) of lymphoid tissue. They are unrelated to the dendritic cell associated with T cells. Follicular dendritic cells have Fc receptors and C3b receptors, but unlike other dendritic cells, they do not process or present antigen in a way that allows recognition by T cells. Instead, they hold antigen in the form of immune complexes on their surfaces for long periods and can present antigen to B cells during an immune response. ISBN:127520252 cell calcitonin secreting cell A muscle cell in which the fibers are organised into sarcomeres but in which adjacent myofibrils are offset from each other, producing an oblique banding pattern. cell Examples include the somatic muscles of nemotodes and cephalopods. obliquely striated muscle cell A muscle cell in which the fibers are organised into sarcomeres but in which adjacent myofibrils are offset from each other, producing an oblique banding pattern. GOC:DOS PMID:8720463 cell apoptosis fated cell An epithelial cell of the parathyroid gland that is arranged in wide, irregular interconnecting columns; responsible for the synthesis and secretion of parathyroid hormone. BTO:0004712 CALOHA:TS-2140 FMA:69078 parathyroid chief cell parathyroid gland chief cell parathyroid hormone secreting cell principal cell of parathyroid gland cell chief cell of parathyroid gland An epithelial cell of the parathyroid gland that is arranged in wide, irregular interconnecting columns; responsible for the synthesis and secretion of parathyroid hormone. FMA:69078 GOC:tfm ISBN:0517223651 cell carbohydrate secreting cell Fat cells with light coloration and few mitochondria. They contain a scant ring of cytoplasm surrounding a single large lipid droplet or vacuole. CALOHA:TS-1119 FMA:83434 white adipose cell white fat cell cell white adipocyte white fat cell Fat cells with light coloration and few mitochondria. They contain a scant ring of cytoplasm surrounding a single large lipid droplet or vacuole. GOC:tfm MESH:A11.329.114.500 A cell from the thermogenic form of adipose tissue found in many species, particularly in newborns and hibernating mammals, but also in lesser amounts in adults of other mammals including humans. Brown fat is capable of rapid liberation of energy and seems to be important in the maintenance of body temperature immediately after birth and upon waking from hibernation. CALOHA:TS-0099 FMA:83435 brown adipocyte brown adipose cell cell brown fat cell A cell from the thermogenic form of adipose tissue found in many species, particularly in newborns and hibernating mammals, but also in lesser amounts in adults of other mammals including humans. Brown fat is capable of rapid liberation of energy and seems to be important in the maintenance of body temperature immediately after birth and upon waking from hibernation. MESH:A10.165.114.322 A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative). BTO:0002042 CALOHA:TS-0194 FMA:83036 cell interdigitating cell veiled cell dendritic cell A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative). GOC:add ISBN:0781735149 cell thyroid hormone secreting cell Langerhans cell is a conventional dendritic cell that has plasma membrane part CD207. A Langerhans cell is a stellate dendritic cell of myeloid origin, that appears clear on light microscopy and has a dark-staining, indented nucleus and characteristic inclusions (Birbeck granules) in the cytoplasm; Langerhans cells are found principally in the stratum spinosum of the epidermis, but they also occur in other stratified epithelia and have been identified in the lung, lymph nodes, spleen, and thymus. BTO:0000705 CALOHA:TS-2375 FMA:63072 LC Langerhans' cell cell Originally described in the dendritic cell ontology (DC_CL:0000021 )(PMID:19243617). These cells are also CD1a-high, CD14-negative, CD207-positive (langerin), CD324-positive (E-cadherin), and DCIR-positive. They reside in the epidermis. Langerhans cell true Langerhans cell is a conventional dendritic cell that has plasma membrane part CD207. A Langerhans cell is a stellate dendritic cell of myeloid origin, that appears clear on light microscopy and has a dark-staining, indented nucleus and characteristic inclusions (Birbeck granules) in the cytoplasm; Langerhans cells are found principally in the stratum spinosum of the epidermis, but they also occur in other stratified epithelia and have been identified in the lung, lymph nodes, spleen, and thymus. GOC:add GOC:amm GO_REF:0000031 ISBN:0721601464 ISBN:0781735149 PMCID:PMC2346585 PMID:17850486 A cell capable of producing epinephrine. Epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme, which is expressed in the adrenal glands, androgenic neurons, and in other cell types. adrenaline secreting cell epinephrin secreting cell cell epinephrine secreting cell A cell capable of producing epinephrine. Epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme, which is expressed in the adrenal glands, androgenic neurons, and in other cell types. GOC:tfm PMID:12438093 adrenaline secreting cell GO:0048242 Obsolete. Use PO:0004531 from Plant Ontology instead. A cell characterized by conspicuous and rather stable accumulation of starch. cell replaced_by: PO:0004531 obsolete starch sheath cell true Obsolete. Use PO:0004531 from Plant Ontology instead. A cell characterized by conspicuous and rather stable accumulation of starch. ISBN:044174520 cell mineralocorticoid secreting cell cell biogenic amine secreting cell A cell type that secretes 5-Hydroxytryptamine (serotonin). 5-HT secreting cell 5-Hydroxytryptamine secreting cell cell serotonin secreting cell A cell type that secretes 5-Hydroxytryptamine (serotonin). GOC:tfm PMID:19630576 A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme. noradrenaline secreting cell norepinephrin secreting cell norepinephrine secreting cell cell noradrenergic cell A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme. GOC:tfm ISBN:068340007X cell glucocorticoid secreting cell FBbt:00003219 cell adepithelial cell An epidermal cell that secretes chitinous cuticle from its apical side. cell While insect epidermis is generally columnar/cuboidal, there are certainly well studied cases where it is not (e.g.- Rhodnius prolixus when starved). So it would be safer to add this as a differentium for particular species where this is known. -DSJ. epidermal cell (sensu arthropoda) An epidermal cell that secretes chitinous cuticle from its apical side. FlyBase:ds ISBN:ISBN:978-0801481253 An epidermal progenitor cell that arises from neuroectoderm and in turn gives rise to the epidermal sheath of ventral and cephalic regions. FBbt:00004994 cell epidermoblast An epidermal progenitor cell that arises from neuroectoderm and in turn gives rise to the epidermal sheath of ventral and cephalic regions. GOC:tfm PMID:7576311 FBbt:00001666 cell cardioblast (sensu Arthropoda) A peptide hormone secreting cell that produces adrenocorticotropin, or corticotropin. CL:0000640 ACTH secreting cell adrenocorticotrophic hormone secreting cell corticotrophin hormone secreting cell corticotropin hormone secreting cell corticotropin secreting cell cell adrenocorticotropic hormone secreting cell A peptide hormone secreting cell that produces adrenocorticotropin, or corticotropin. GOC:tfm SANBI:mhl ACTH secreting cell GO:0051458 corticotropin secreting cell GO:0051458 FBbt:00005147 neuroglioblast cell neuroglioblast (sensu Nematoda and Protostomia) A neural progenitor cell that is the daughter of a neuroblast (sensu arthopoda). The progeny of ganglion mother cells develop into neurons, glia and (occasionally) epithelial cells. FBbt:00005149 cell ganglion mother cell cell digestive enzyme secreting cell Obsolete. Use PO:0000076 from Plant Ontology instead. OBSOLETE, use term from Plant Ontology. Parenchyma cells containing chloroplasts; a component of leaf mesophyll and other green parenchyma tissue. cell replaced_by: PO:0000076 obsolete chlorenchyma cell true Obsolete. Use PO:0000076 from Plant Ontology instead. OBSOLETE, use term from Plant Ontology. Parenchyma cells containing chloroplasts; a component of leaf mesophyll and other green parenchyma tissue. ISBN:0471245208 A cell whose primary function is to protect the organism. cell defensive cell A cell whose primary function is to protect the organism. JB:jb An insect renal cell that filters hemolymph and is found with other pericardial nephrocytes in two rows flanking the dorsal vessel. FBbt:00005058 pericardial cell cell pericardial nephrocyte An insect renal cell that filters hemolymph and is found with other pericardial nephrocytes in two rows flanking the dorsal vessel. FBbt:00003184 GO:0061320 GOC:tfm PMID:19783135 pericardial cell FBbt:00005058 GO:0061320 Obsolete. Use PO:0000245 from Plant Ontology instead. In monosporic and bisporic megasporogenesis: the megaspore(s) that do not participate in megagametogenesis. cell replaced_by: PO:0000245 obsolete degenerate megaspore true Obsolete. Use PO:0000245 from Plant Ontology instead. In monosporic and bisporic megasporogenesis: the megaspore(s) that do not participate in megagametogenesis. TAIR:lr A basophil cell of the anterior pituitary that produces thyroid stimulating hormone, thyrotrophin. This cell type is elongated, polygonal and lie in clusters towards the adenohypophyseal center. FMA:83099 beta-basophil thyroid stimulating hormone secreting cell thyrotrope cell thyrotroph A basophil cell of the anterior pituitary that produces thyroid stimulating hormone, thyrotrophin. This cell type is elongated, polygonal and lie in clusters towards the adenohypophyseal center. ISBN:0517223651 SANBI:mhl A somatic epithelial cell of the ovarian follicle/egg chamber. follicle cell FBbt:00004904 cell Editors note: check this. Currently used in goxp ovarian follicle cell A peptide hormone secreting cell that secretes oxytocin stimulating hormone cell oxytocin stimulating hormone secreting cell A peptide hormone secreting cell that secretes oxytocin stimulating hormone GO:tfm A peptide hormone secreting cell that secretes vasopressin stimulating hormone cell vasopressin stimulating hormone secreting cell A peptide hormone secreting cell that secretes vasopressin stimulating hormone GO:tfm A peptide hormone secreting cell that secretes secretin stimulating hormone cell secretin stimulating hormone secreting cell A peptide hormone secreting cell that secretes secretin stimulating hormone GO:tfm A peptide hormone secreting cell that secretes cholecystokin stimulating hormone. cell cholecystokin stimulating hormone secreting cell A peptide hormone secreting cell that secretes cholecystokin stimulating hormone. GO:tfm An endocrine cell that secretes juvenile hormone. cell juvenile hormone secreting cell An endocrine cell that secretes juvenile hormone. GO:tfm A peptide hormone secreting cell that secretes bombesin stimulating hormone. cell bombesin stimulating hormone secreting cell A peptide hormone secreting cell that secretes bombesin stimulating hormone. GO:tfm https://orcid.org/0000-0001-5208-3432 Mast cell subtype whose granules contain both the serine proteases tryptase and chymase. These cells are primarily found in connective tissue, such as the peritoneal cavity, skin, and intestinal submucosa. Their development is T-cell independent. MC(TC) MCTC TC mast cells cell They are CD88-positive. The cytoplasmic granules contain high levels of histamine and heparin (mouse) or major neutral proteases, tryptase, chymase, carboxypeptidase A, and cathepsin G (humans). Reportedly, they cannot produce leukotrienes (LTC4) and IL-4. They are reportedly very heterogeneous depending upon location and can convert to the MC(T) phenotype. connective tissue type mast cell true Mast cell subtype whose granules contain both the serine proteases tryptase and chymase. These cells are primarily found in connective tissue, such as the peritoneal cavity, skin, and intestinal submucosa. Their development is T-cell independent. GOC:add GOC:dsd GOC:tfm PMID:19923473 PMID:9354811 Mast cell subtype that contains only the serine protease trypase in its granules. These cells are primarily found in mucosal tissue, such as intestinal mucosa and alveoli. They depend upon T-cells for development of phenotype. MC(T) MCT T mast cells cell They are CD88-negative. The cytoplasmic granules contain low levels of histamine and high levels of chondroitin sulfate (mouse) or major neutral proteases and tryptase (humans). Additionally, they can produce leukotrienes (LTC4), IL-5, IL-6, and low levels of IL-4. They are reportedly very heterogeneous depending upon location and can convert to the MC(T) phenotype. mucosal type mast cell true Mast cell subtype that contains only the serine protease trypase in its granules. These cells are primarily found in mucosal tissue, such as intestinal mucosa and alveoli. They depend upon T-cells for development of phenotype. GOC:add GOC:dsd PMID:19923473 PMID:9354811 A large binucleate cell that forms a 'garland' around the anterior end of the proventriculus (cardia) at its junction with the esophagus in both adults and larvae flies. Each cell is surrounded by a basement membrane and there are numerous micro-invaginations (lacunae) extending from the surface into the cytoplasm. At the mouth of each lacuna is a doubled filament forming a specialised filtration system (diaphragm). The filtrate is endocytosed from the lacunae. garland nephrocyte BTO:0004596 FBbt:00005059 cell garland cell A large binucleate cell that forms a 'garland' around the anterior end of the proventriculus (cardia) at its junction with the esophagus in both adults and larvae flies. Each cell is surrounded by a basement membrane and there are numerous micro-invaginations (lacunae) extending from the surface into the cytoplasm. At the mouth of each lacuna is a doubled filament forming a specialised filtration system (diaphragm). The filtrate is endocytosed from the lacunae. GOC:tfm PMID:19783135 fbbt:00005059 garland nephrocyte GO:0061321 A large secretory cell found in clusters underlying the epidermis of the abdominal segments of larval abdominal segments. FBbt:00004995 cell oenocyte A large secretory cell found in clusters underlying the epidermis of the abdominal segments of larval abdominal segments. GOC:bf PMID:11171397 A photoreceptor cell that detects visible light. cell visible light photoreceptor cell A photoreceptor cell that detects visible light. GOC:tfm cell scotopic photoreceptor cell cell photopic photoreceptor cell OBSOLETE: A cell responsible for spontaneous cytotoxicity of a variety of tumor cells without prior immunization. These natural killer cells are found in non-immune humans and experimental animals and are thought by some to be the same as killer cells (killing by antibody-dependent cell cytotoxicity), but they can also kill in the absence of antibody. cell This term had an incorrect definition and was overly broad. Consider using 'cytotoxic T cell ; CL:0000910' (in most cases) or another lymphocyte cell type if cytotoxicity is shown to be part of the cell's phenotype in a particular experimental situation. obsolete cytotoxic T cell true A CD4-positive, alpha-beta T cell that cooperates with other lymphocytes via direct contact or cytokine release to initiate a variety of immune functions. CALOHA:TS-1146 FMA:70572 CD4-positive T-helper cell CD4-positive helper T lymphocyte CD4-positive helper T-cell CD4-positive helper T-lymphocyte cell CD4-positive helper T cell true A CD4-positive, alpha-beta T cell that cooperates with other lymphocytes via direct contact or cytokine release to initiate a variety of immune functions. GOC:add GOC:pam GOC:tfm GO_REF:0000031 ISBN:0781735149 MESH:A11.118.637.555.567.569.200.400 OBSOLETE: Subpopulation of CD4+ cells which induce CD8+ suppressor T cells to suppress antibody production by B cells. They also stimulate other cellular immune responses. cell This term was defined too narrowly; consider using the term 'regulatory T cell ; CL:0000815' instead. obsolete regulatory T cell true A photoreceptor cell that detects ultraviolet light. cell UV sensitive photoreceptor cell A photoreceptor cell that detects ultraviolet light. GOC:tfm A photoreceptor cell that is sensitive to blue light. cell blue sensitive photoreceptor cell A photoreceptor cell that is sensitive to blue light. GO:tfm A photoreceptor cell that is sensitive to green light. cell green sensitive photoreceptor cell A photoreceptor cell that is sensitive to green light. GO:tfm A photoreceptor cell that is sensitive to red light. cell red sensitive photoreceptor cell A photoreceptor cell that is sensitive to red light. GO:tfm An interneuron (also called relay neuron, association neuron or local circuit neuron) is a multipolar neuron which connects afferent neurons and efferent neurons in neural pathways. Like motor neurons, interneuron cell bodies are always located in the central nervous system (CNS). FMA:84776 cell inhibitory interneuron An interneuron (also called relay neuron, association neuron or local circuit neuron) is a multipolar neuron which connects afferent neurons and efferent neurons in neural pathways. Like motor neurons, interneuron cell bodies are always located in the central nervous system (CNS). GOC:tfm http://en.wikipedia.org/wiki/Interneuron A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere. BTO:0002064 FMA:83624 cell stromal cell A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere. GOC:tfm MESH:A11.329.830 cell follicular epithelial cell A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors. BTO:0000542 CALOHA:TS-0729 FMA:18718 granulosa cell of ovary cell granulosa cell A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors. MESH:A05.360.319.114.630.535.200 A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin. FMA:62935 D cell cell type D enteroendocrine cell A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin. MESH:A03.492.766.440.175 A flattened stroma cell forming a sheath or theca outside the basal lamina lining the mature ovarian follicle. Thecal interstitial or stromal cells are steroidogenic, and produce primarily androgens which serve as precusors of estrogens in the granulosa cells. BTO:0002850 FMA:18690 cell theca cell A flattened stroma cell forming a sheath or theca outside the basal lamina lining the mature ovarian follicle. Thecal interstitial or stromal cells are steroidogenic, and produce primarily androgens which serve as precusors of estrogens in the granulosa cells. MESH:A05.360.319.114.630.535.400 A enteroendocrine cell part of the glands of the gastric mucosa. They produce histamine and peptides such as chromogranins. This cell type respond to gastrin by releasing histamine which acts as a paracrine stimulator of the release of hydrochloric acid from the gastric parietal cells. BTO:0002692 ECL cell Consider enterochromaffin cell (CL:0002065). For several years this cell type was "enterochromaffin cell" despite a MESH dbxref and a free text definition that clearly meant enterochromaffin-like cell. enterochromaffin-like cell A enteroendocrine cell part of the glands of the gastric mucosa. They produce histamine and peptides such as chromogranins. This cell type respond to gastrin by releasing histamine which acts as a paracrine stimulator of the release of hydrochloric acid from the gastric parietal cells. GOC:tfm MESH:A06.224.365 A peptide hormone secreting cell that secretes substance P. cell substance P secreting cell A peptide hormone secreting cell that secretes substance P. GO:tfm An endorphine cell that secretes enkephalin. cell enkephalin secreting cell An endorphine cell that secretes enkephalin. GO:tfm A peptide hormone secreting cell that secretes endorphin. cell endorphin secreting cell A peptide hormone secreting cell that secretes endorphin. GO:tfm An endocrine cell found in the pyloric gland mucosa (antral mucosa) of the stomach of mammals and responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli. BTO:0004108 FMA:67609 G cell cell type G enteroendocrine cell An endocrine cell found in the pyloric gland mucosa (antral mucosa) of the stomach of mammals and responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli. GOC:tfm ISBN:0517223651 MESH:A03.492.766.440.300 A peptide hormone secreting cell that secretes gastrin. cell gastrin secreting cell A peptide hormone secreting cell that secretes gastrin. GO:tfm An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix. BTO:0000993 FMA:62897 cell paneth cell true An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix. GOC:tfm ISBN:0517223651 MESH:A03.492.411.369.700 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 A paracrine cell is a secretory cell that secretes an agonist into intercellular spaces in which it diffuses to a target cell other than that which produced it. cell paracrine cell A paracrine cell is a secretory cell that secretes an agonist into intercellular spaces in which it diffuses to a target cell other than that which produced it. GOC:tfm ISBN:0198529171 A precursor cell destined to differentiate into cardiac muscle cell. CL:0000714 FMA:84797 cardiac muscle progenitor cell cardiomyocyte progenitor cell cell cardiac muscle myoblast A precursor cell destined to differentiate into cardiac muscle cell. GOC:tfm MESH:A11.635.470 A precursor cell destined to differentiate into smooth muscle myocytes. FMA:84798 myoblast, smooth muscle cell satellite cell smooth muscle myoblast true A precursor cell destined to differentiate into smooth muscle myocytes. GOC:tfm MESH:A11.635.510 MESH:D032390 myoblast, smooth muscle MESH:D032390 A myoblast that differentiates into skeletal muscle fibers. FMA:84799 skeletal myoblast cell skeletal muscle myoblast true A myoblast that differentiates into skeletal muscle fibers. SANBI:mhl A non-neuronal cell that surrounds the neuronal cell bodies of the ganglia. FMA:54550 perineural satellite cell perineuronal satellite oligodendroglial cell satellite oligodendrocyte cell perineuronal satellite cell A non-neuronal cell that surrounds the neuronal cell bodies of the ganglia. GOC:tfm MESH:A08.340.685 A type of foam cell derived from a macrophage containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions. cell macrophage derived foam cell A type of foam cell derived from a macrophage containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions. GOC:add PMID:20213546 A phagocyte in vertebrates that is able to phagocytosis. cell phagocyte (sensu Vertebrata) A phagocyte in vertebrates that is able to phagocytosis. GOC:tfm A phagocyte from organisms in the Nematoda or Protostomia clades. cell phagocyte (sensu Nematoda and Protostomia) A phagocyte from organisms in the Nematoda or Protostomia clades. GOC:tfm cell prokaryotic cell cell fungal cell OBSOLETE: The reproductive structure of bacteria, fungi and cryptograms. cell obsolete spore true OBSOLETE: The reproductive structure of bacteria, fungi and cryptograms. ISBN:08199377X A cell from the inner layer of the trophoblast of the early mammalian embryo that gives rise to the outer surface and villi of the chorion. Mononuclear crytoblasts fuse to give rise to a multinuclear cytotrophoblast. FMA:83042 Langhans' cell cell mononuclear cytotrophoblast cell A cell from the inner layer of the trophoblast of the early mammalian embryo that gives rise to the outer surface and villi of the chorion. Mononuclear crytoblasts fuse to give rise to a multinuclear cytotrophoblast. GOC:tfm ISBN:0323052908 A cell, usually of bacteria or yeast, which has partially lost its cell wall. sphaeroplast cell spheroplast A cell, usually of bacteria or yeast, which has partially lost its cell wall. MESH:A11.868 A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo, directly associated with the maternal blood supply. It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy. FMA:83043 plasmidotrophoblast syncytial trophoblast syntrophoblast cell syncytiotrophoblast cell A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo, directly associated with the maternal blood supply. It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy. GOC:tfm ISBN:0323052908 A neuron which conveys sensory information centrally from the periphery. FMA:87653 input neuron cell afferent neuron A neuron which conveys sensory information centrally from the periphery. GOC:tfm MESH:A08.663.650 A neuron which sends impulses peripherally to activate muscles or secretory cells. output neuron cell efferent neuron A neuron which sends impulses peripherally to activate muscles or secretory cells. MESH:A08.663.655 A nerve cell where transmission is mediated by nitric oxide. FMA:84792 cell nitrergic neuron A nerve cell where transmission is mediated by nitric oxide. MESH:A08.663.748 cell pigmented epithelial cell cell primary neuron cell primary sensory neuron cell CAP motoneuron FMA:83619 cell primary motor neuron cell primary interneuron cell secondary neuron FMA:83620 cell secondary motor neuron Obsolete. Use PO:0020093 from Plant Ontology instead. OBSOLETE, use term from plant ontology. A cell located at the chalazal end of the mature embryo sac in angiosperms. cell replaced_by: PO:0020093 obsolete antipodal cell true Obsolete. Use PO:0020093 from Plant Ontology instead. OBSOLETE, use term from plant ontology. A cell located at the chalazal end of the mature embryo sac in angiosperms. ISBN:047125208 Obsolete. Use PO:0000349 from Plant Ontology instead. A relatively unspecialized cell that will give rise to specialized cell types of the epidermis. cell replaced_by: PO:0000349 obsolete epidermal initial true Obsolete. Use PO:0000349 from Plant Ontology instead. A relatively unspecialized cell that will give rise to specialized cell types of the epidermis. TAIR:lr OBSOLETE: A cell in a tissue that markedly differs in form, size, or contents from other cells in the same tissue. cell obsolete idioblast true OBSOLETE: A cell in a tissue that markedly differs in form, size, or contents from other cells in the same tissue. ISBN:0471245208 The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. BTO:0000938 CALOHA:TS-0683 FBbt:00005106 FMA:54527 VHOG:0001483 WBbt:0003679 nerve cell cell These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. neuron neuron The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. MESH:A08.663 MESH:D009474 http://en.wikipedia.org/wiki/Neuron A cell that originates from the neural crest and differentiates into a pigment cell. BTO:0003217 FMA:83377 cell Derived from UBERON:0002342 neural crest. melanoblast A cell that originates from the neural crest and differentiates into a pigment cell. GOC:tfm SANBI:mhl A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. BTO:0000775 CALOHA:TS-0583 FMA:62863 VHOG:0001535 cell Editors note: consider adding taxon constraint to vertebrata (PMID:18025161) lymphocyte A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. GOC:add ISBN:0683073696 ISBN:0781735149 Obsolete. Use PO:0000289 from Plant Ontology instead. One of the series of cellular components of a sieve tube. It shows a more or less pronounced differentiation between sieve plates (wide pores) and lateral sieve areas (narrow pores). Also sieve tube element and the obsolete sieve tube segment. sieve tube element cell replaced_by: PO:0000289 obsolete sieve tube member true Obsolete. Use PO:0000289 from Plant Ontology instead. One of the series of cellular components of a sieve tube. It shows a more or less pronounced differentiation between sieve plates (wide pores) and lateral sieve areas (narrow pores). Also sieve tube element and the obsolete sieve tube segment. ISBN:0471245208 cell slowly adapting mechanoreceptor cell A CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive, CXCR3-positive, CCR6-negative, and is capable of producing interferon-gamma. BTO:0001678 FMA:84382 T helper cells type 1 T(H)-1 cell Th1 CD4+ T cell Th1 T cell Th1 T lymphocyte Th1 T-cell Th1 T-lymphocyte Th1 cell helper T cell type 1 cell This cell type is compatible with the HIPC Lyoplate markers for 'Th1 CD4+ T cell', but its logical definition includes additional known characteristics of T-helper 1 T cells. T-helper 1 cell true A CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive, CXCR3-positive, CCR6-negative, and is capable of producing interferon-gamma. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:19375293 PMID:20303875 PMID:22343568 T helper cells type 1 PMID:9419219 Th1 CD4+ T cell PMID:22343568 A CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive, CXCR3-negative, CCR6-negative, and is capable of producing interleukin-4. BTO:0001679 FMA:84385 T helper cells type 2 T(H)-2 cell Th2 T cell Th2 T lymphocyte Th2 T-cell Th2 T-lymphocyte Th2 cell helper T cell type 2 cell This cell type is compatible with the HIPC Lyoplate markers for 'non-Th1/Th17 CD4+ T cell' (see CL:0001051), but includes the additional necessary and sufficient conditions to allow classification as a T-helper 2 T cell. T-helper 2 cell true A CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive, CXCR3-negative, CCR6-negative, and is capable of producing interleukin-4. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:19375293 PMID:20103781 PMID:22343568 T helper cells type 2 PMID:9419219 An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers. FMA:83518 rubriblast cell pronormoblast proerythroblast true An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers. ISBN:0721601464 MESH:A11.118.290.350.200 PMID:1638021 rubriblast ISBN:0721601464 cell animal cell A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers. FMA:83505 basophilic normoblast early erythroblast early normoblast prorubricyte cell basophilic erythroblast true A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers. GOC:tfm ISBN:0721601464 basophilic normoblast ISBN:0721601464 early erythroblast ISBN:0721601464 early normoblast ISBN:0721601464 prorubricyte ISBN:0721601464 A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers. FMA:83506 intermediate erythroblast intermediate normoblast polychromatic erythroblast polychromatic normoblast polychromatophilic normoblast rubricyte cell polychromatophilic erythroblast true A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers. ISBN:0721601464 intermediate erythroblast ISBN:0721601464 intermediate normoblast ISBN:0721601464 polychromatic erythroblast ISBN:0721601464 polychromatic normoblast ISBN:0721601464 polychromatophilic normoblast ISBN:0721601464 rubricyte ISBN:0721601464 cell unimodal nocireceptor The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated. FMA:84646 acidophilic erythroblast eosinophilic erythroblast late erythoblast orthochromatic normoblast pyknotic eto enrythroblast cell orthochromatic erythroblast true The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated. ISBN:0721601464 acidophilic erythroblast ISBN:0721601464 eosinophilic erythroblast ISBN:0721601464 orthochromatic normoblast ISBN:0721601464 pyknotic eto enrythroblast ISBN:0721601464 The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative). BTO:0001164 CALOHA:TS-0610 FMA:84235 CFU-Meg Meg-CFC MkP colony-forming unit-megakaryocyte megacaryoblast megacaryocyte progenitor cell megakaryoblast megakaryocytic progenitor cell cell promegacaryocyte promegakaryocyte Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. megakaryocyte progenitor cell true The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative). GOC:dsd GOC:tfm ISBN:0721601464 CFU-Meg PMID:11722431 PMID:12482498 Meg-CFC PMCID:PMC1794060 MkP PMID:21116988 megakaryocytic progenitor cell PMID:12482498 A peptide hormone secreting cell that secretes gastrin stimulating hormone. cell gastrin stimulating hormone secreting cell A peptide hormone secreting cell that secretes gastrin stimulating hormone. GOC:tfm cell neuronal brush cell A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm. BTO:0000843 CALOHA:TS-0611 FMA:83555 megacaryocyte megalocaryocyte megalokaryocyte cell Megakaryocytes are reportedly CD181-positive and CD182-positive. megakaryocyte true A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm. ISBN:0721601464 MESH:D008533 http://en.wikipedia.org/wiki/Megakaryocyte A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1. CFU-C , Colony forming unit in culture CFU-GM GMP colony forming unit granulocyte macrophage granulocyte-macrophage progenitor granulocyte/monocyte precursor granulocyte/monocyte progenitor cell Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. granulocyte monocyte progenitor cell A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1. GOC:amm GOC:dsd GOC:tfm GO_REF:0000031 ISBN:0721601464 MESH:D055014 PMCID:PMC2213186 PMCID:PMC548021 PMID:16551251 PMID:16647566 http://en.wikipedia.org/wiki/CFU-GM http://www.copewithcytokines.de CFU-C , Colony forming unit in culture http://www.copewithcytokines.de CFU-GM ISBN:0721601464 PMCID:PMC2213186 PMCID:PMC548021 GMP ISBN:0721601464 PMCID:PMC2213186 PMCID:PMC548021 colony forming unit granulocyte macrophage ISBN:0721601464 PMCID:PMC2213186 PMCID:PMC548021 granulocyte-macrophage progenitor ISBN:0721601464 PMCID:PMC2213186 PMCID:PMC548021 An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. BTO:0001173 CALOHA:TS-0864 cell reticulocyte true An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. GOC:add GOC:tfm PMID:15946868 PMID:2037622 A precursor in the monocytic series, being a cell intermediate in development between the monoblast and monocyte. This cell is CD11b-positive and has fine azurophil granules. BTO:0004657 FMA:83551 cell Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. promonocyte true A precursor in the monocytic series, being a cell intermediate in development between the monoblast and monocyte. This cell is CD11b-positive and has fine azurophil granules. GOC:tfm ISBN:0721601464 A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative. band band cell band form stab cell rod neutrophil cell Found in the Band 1 fraction. band form neutrophil true A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative. GOC:add GOC:dsd GOC:tfm ISBN:0721601464 PMID:10618520 PMID:12560239 PMID:15514007 http://www.cap.org Interneuron of the vertebrate retina. They integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. They lack large axons. BTO:0004044 FBbt:00005127 FMA:67766 amacrine neuron cell Not clear if this term overlaps with retinal bipolar neuron (CL:0000748). amacrine cell Interneuron of the vertebrate retina. They integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. They lack large axons. GOC:tfm MESH:A08.663.358.050 An erythrocyte having a nucleus. RBC red blood cell cell nucleate erythrocyte true An erythrocyte having a nucleus. GOC:add GOc:tfm A rounded, inactive form that certain bacteria assume under conditions of extreme temperature, dryness, or lack of food. The bacterium develops a waterproof cell wall that protects it from being dried out or damaged. BTO:0002779 bacterial spore cell endospore A rounded, inactive form that certain bacteria assume under conditions of extreme temperature, dryness, or lack of food. The bacterium develops a waterproof cell wall that protects it from being dried out or damaged. GOC:tfm ISBN:0618947256 A promyelocyte committed to the neutrophil lineage. This cell type is GATA-1-positive, C/EBPa-positive, AML-1-positive, MPO-positive, has low expression of PU.1 transcription factor and lacks lactotransferrin expression. FMA:84196 neutrophilic premyelocyte neutrophilic progranulocyte cell These cells are CD11b-negative, CD15-positive, CD16-negative, CD49d-positive, CD68-positive, CD35-negative, and fMLP receptor-negative. They are found in the Band 3 fraction. neutrophilic promyelocyte true A promyelocyte committed to the neutrophil lineage. This cell type is GATA-1-positive, C/EBPa-positive, AML-1-positive, MPO-positive, has low expression of PU.1 transcription factor and lacks lactotransferrin expression. GOC:add GOC:dsd GOC:tfm ISBN:0721601464 PMID:12560239 PMID:15514007 A cell found in fat bodies whose primary function is intermediary metabolism. cell fat body cell A cell found in fat bodies whose primary function is intermediary metabolism. FB:ma A mesenchymal stem cell capable of developing into blood vessel endothelium. angioblast chondroplast cell These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. angioblastic mesenchymal cell true A mesenchymal stem cell capable of developing into blood vessel endothelium. GOC:dsd GOC:tfm PMID:12768659 cell polymodal nocireceptor A cell that originates in the neural crest, that has certain cytochemical and ultrastructural characteristics and is found scattered throughout the body; types include melanocytes, the cells of the chromaffin system, and cells in the hypothalamus, hypophysis, thyroid, parathyroids, lungs, gastrointestinal tract, and pancreas. This cell type concentrates the amino acid precursors of certain amines and decarboxylate them, forming amines that function as regulators and neurotransmitters. This cell type produces substances such as epinephrine, norepinephrine, dopamine, serotonin, enkephalin, somatostatin, neurotensin, and substance P, the actions of which may affect contiguous cells, nearby groups of cells, or distant cells, thus functioning as local or systemic hormones. The name is an acronym for amine precursor uptake and decarboxylation cell. BTO:0003866 FMA:83114 APUD cell cell amine precursor uptake and decarboxylation cell A cell that originates in the neural crest, that has certain cytochemical and ultrastructural characteristics and is found scattered throughout the body; types include melanocytes, the cells of the chromaffin system, and cells in the hypothalamus, hypophysis, thyroid, parathyroids, lungs, gastrointestinal tract, and pancreas. This cell type concentrates the amino acid precursors of certain amines and decarboxylate them, forming amines that function as regulators and neurotransmitters. This cell type produces substances such as epinephrine, norepinephrine, dopamine, serotonin, enkephalin, somatostatin, neurotensin, and substance P, the actions of which may affect contiguous cells, nearby groups of cells, or distant cells, thus functioning as local or systemic hormones. The name is an acronym for amine precursor uptake and decarboxylation cell. GOC:tfm ISBN:0721662544 MESH:A11.070 A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field. cell cardiac mesenchymal cell A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field. PMID:18816864 A neuroepithelial cells that occurs singly or in small groups, close to the outer follicular borders but within the follicular basement membrane of the thyroid. Expresses a form of the neural cell adhesion molecule (N-CAM) on their surface. Secretes calcitonin, 5-hydroxytryptamine and dopamine. FMA:68653 SCTID:176770005 C cell C cell of thyroid gland clear cell of thyroid gland parafollicular cell of thyroid gland thyroid parafollicular cell cell parafollicular cell true true A neuroepithelial cells that occurs singly or in small groups, close to the outer follicular borders but within the follicular basement membrane of the thyroid. Expresses a form of the neural cell adhesion molecule (N-CAM) on their surface. Secretes calcitonin, 5-hydroxytryptamine and dopamine. GOC:tfm ISBN:0517223651 C cell of thyroid gland FMA:68653 clear cell of thyroid gland FMA:68653 parafollicular cell of thyroid gland FMA:68653 thyroid parafollicular cell FMA:68653 A pigment cell derived from the neural crest. Contains uric acid or other purine crystals deposited in stacks called leucosomes. The crystals reflect light and this gives a white appearance under white light. cell leucophore A pigment cell derived from the neural crest. Contains uric acid or other purine crystals deposited in stacks called leucosomes. The crystals reflect light and this gives a white appearance under white light. SANBI:mhl One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision. BTO:0001036 CALOHA:TS-0866 FMA:67748 cell retinal cone cell One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision. MESH:A08.663.650.650.670.100 A pigment cell derived from the neural crest. Contains pteridine and/or carotenoid pigments in structures called pterinosomes or erythrosomes. This gives an orange to red appearance. cell erythrophore A pigment cell derived from the neural crest. Contains pteridine and/or carotenoid pigments in structures called pterinosomes or erythrosomes. This gives an orange to red appearance. SANBI:mhl 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 Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. BTO:0000876 CALOHA:TS-0638 FMA:62864 cell Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid. monocyte true Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. GO_REF:0000031 MESH:A11.118.637.555.652 A subtype of enteroendocrine cells found in the gastrointestinal mucosa, particularly in the glands of pyloric antrum; duodenum; and ileum. These cell type secretes serotonin and some neurotransmitters including enkephalins and substance P. Their secretory granules stain readily with silver (argentaffin stain). CL:0002065 FMA:62934 FMA:83132 Kulchitsky cell argentaffin cell enterochromaffin cell cell type EC enteroendocrine cell A subtype of enteroendocrine cells found in the gastrointestinal mucosa, particularly in the glands of pyloric antrum; duodenum; and ileum. These cell type secretes serotonin and some neurotransmitters including enkephalins and substance P. Their secretory granules stain readily with silver (argentaffin stain). MESH:A03.492.766.440.250 PMID:9505449 A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. cell This class has been re-labeled to imply reference only to in vitro experimentally modified cells, similarly, the definition has been slightly updated to reflect this. 'experimentally modified cell' refers only to cells in vitro, and not modified in vivo/in environment cells. There is currently no class representing unmodified in vitro cells (other than the parent 'cell in vitro'), or a class representing modified native cells. More granular subclassing of experimentally modified cell can be found in ReO. MHB 1.12.12 experimentally modified cell in vitro A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. FB:ma ReO:mhb FBbt:00004905 cell border follicle cell A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and neutrophil-specific granules has started. No nucleolus is present. This cell type is CD13-positive, CD16-negative, integrin alpha-M-positive, CD15-positive, CD33-positive, CD24-positive, C/EBP-a-positive, C/EBPe-positive, PU.1-positive, lactotransferrin-positive, myeloperoxidase-positive and NGAL-positive. BTO:0003455 FMA:83540 cell These cells are also CD15-positive, CD35-negative, CD49d-positive, and fMLP receptor-negative. They are found in the Band 2 fraction. neutrophilic myelocyte true A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and neutrophil-specific granules has started. No nucleolus is present. This cell type is CD13-positive, CD16-negative, integrin alpha-M-positive, CD15-positive, CD33-positive, CD24-positive, C/EBP-a-positive, C/EBPe-positive, PU.1-positive, lactotransferrin-positive, myeloperoxidase-positive and NGAL-positive. GOC:add GOC:dsd GOC:tfm ISBN:0721601464 PMID:10618520 PMID:12560239 PMID:15514007 http://www.cap.org A macrophage resident in the peritoneum under non-inflammatory conditions. Markers include F4/80-high, CD11b-high, CD68-positive, SIGNR1-positive, CD115-high, MHC-II-negative, and Dectin-1-positive. BTO:0001034 FMA:83025 cell Markers: Mouse: F4/80-high, CD11b-high, CD68+, SIGNR1+, Dectin-1+. peritoneal macrophage true A macrophage resident in the peritoneum under non-inflammatory conditions. Markers include F4/80-high, CD11b-high, CD68-positive, SIGNR1-positive, CD115-high, MHC-II-negative, and Dectin-1-positive. MESH:A11.329.372.630 PMID:15771589 PMID:19201820 A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and the band form neutrophil. The protein synthesis seen in earlier stages decreases or stops; the nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare; and the cytoplasm becomes amphophilic like that of a mature granulocyte. This cell type is integrin alpha-M-positive, CD13-negative, CD15-positive, CD16-positive, CD33-positive, CD24-positive, fMLP receptor-negative and has expression of C/EBP-a, C/EBP-e, PU.1 transcription factor, lactotransferrin, myeloperoxidase and neutrophil gelatinase associated lipocalin. FMA:84197 juvenile neutrophil cell These cells are also CD35-negative, CD49d-positive, and fMLP receptor-negative. They are found in the Band 2 fraction. neutrophilic metamyelocyte true A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and the band form neutrophil. The protein synthesis seen in earlier stages decreases or stops; the nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare; and the cytoplasm becomes amphophilic like that of a mature granulocyte. This cell type is integrin alpha-M-positive, CD13-negative, CD15-positive, CD16-positive, CD33-positive, CD24-positive, fMLP receptor-negative and has expression of C/EBP-a, C/EBP-e, PU.1 transcription factor, lactotransferrin, myeloperoxidase and neutrophil gelatinase associated lipocalin. GOC:add GOC:dsd GOC:tfm ISBN:0721601464 PMID:10618520 PMID:12560239 PMID:15514007 http://www.cap.org A tissue-resident macrophage found in the alveoli of the lungs. Ingests small inhaled particles resulting in degradation and presentation of the antigen to immunocompetent cells. Markers include F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. BTO:0000802 CALOHA:TS-0030 FMA:83023 dust cell cell MF.Lu Markers: Mouse: F4/80mid, CD11b-/low, CD11c+, CD68+, sialoadhesin+, dectin-1+, MR+, CX3CR1-. alveolar macrophage true A tissue-resident macrophage found in the alveoli of the lungs. Ingests small inhaled particles resulting in degradation and presentation of the antigen to immunocompetent cells. Markers include F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. GOC:ana GOC:dsd GOC:tfm GO_REF:0000031 MESH:A11.329.372.600 An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen. BTO:0000398 FMA:62122 cell enterocyte An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen. SANBI:mhl OBSOLETE: A class of lymphocytes characterized by the lack of surface markers specific for either T or B cells. cell This term is rather archaic; consider using 'natural killer cell ; CL:0000623', 'pro-B cell ; CL:0000826', 'pro-T cell ; CL:0000827', or other appropriate lymphocyte-related term depending on the context. obsolete null cell true The reproductive cell in multicellular organisms. BTO:0000535 VHOG:0001534 WBbt:0006796 cell germ cell true The reproductive cell in multicellular organisms. MESH:A05.360.490 A thermoreceptor cell that detects reduced temperatures. cell cold sensing thermoreceptor cell A thermoreceptor cell that detects reduced temperatures. GOC:tfm A specialized osteoclast associated with the absorption and removal of cementum. BTO:0002516 FMA:83027 cell odontoclast true A specialized osteoclast associated with the absorption and removal of cementum. GOC:add MESH:A11.329.679 A bulbous cell that is medially placed in one row in the organ of Corti. In contrast to the outer hair cells, the inner hair cells are fewer in number, have fewer sensory hairs, and are less differentiated. inner hair cell BTO:0003667 FMA:62365 cell cochlear inner hair cell A bulbous cell that is medially placed in one row in the organ of Corti. In contrast to the outer hair cells, the inner hair cells are fewer in number, have fewer sensory hairs, and are less differentiated. MESH:A08.663.650.250.250 A progesterone secreting cell in the corpus luteum that develops from theca cells. BTO:0002850 FMA:18690 small lutein cell theca lutein cell cell small luteal cell A progesterone secreting cell in the corpus luteum that develops from theca cells. GOC:tfm MESH:A05.360.319.114.630.278.400 A thermoreceptor cell that detects increased temperatures. cell warmth sensing thermoreceptor cell A thermoreceptor cell that detects increased temperatures. GOC:tfm https://orcid.org/0000-0001-5208-3432 A large, progesterone secreting cell in the corpus luteum that develops from the granulosa cells. FMA:18689 granulosa lutein cell cell granulosoluteocytus large luteal cell A large, progesterone secreting cell in the corpus luteum that develops from the granulosa cells. GOC:tfm MESH:A05.360.319.114.630.278.400 A steroid hormone secreting cell that secretes androgen. cell androgen secreting cell A steroid hormone secreting cell that secretes androgen. GOC:tfm An elongated, spindle-shaped, cell that is located between the basal lamina and the plasmalemma of a muscle fiber. These cells are mostly quiescent, but upon activation they divide to produce cells that generate new muscle fibers. cell Skeletal muscle satellite cells are not traditionally referred to as myoblasts. They are a heterogeneous population whose division, following activiation, contributes to the formation of skeletal muscle fibers and to maintenance of the skeletal muscle statelite cell population. skeletal muscle satellite cell An elongated, spindle-shaped, cell that is located between the basal lamina and the plasmalemma of a muscle fiber. These cells are mostly quiescent, but upon activation they divide to produce cells that generate new muscle fibers. GOC:tfm MESH:A11.635.500.700 PMID:21849021 PMID:23303905 An erythrocyte lacking a nucleus. RBC red blood cell cell enucleate erythrocyte true An erythrocyte lacking a nucleus. GOC:add GOC:tfm A spore formed following meiosis. Sometimes following meiosis, prospores may undergo one or more rounds of mitosis before they are fully mature. FAO:0000017 meiotically-derived spore cell sexual spore A spore formed following meiosis. Sometimes following meiosis, prospores may undergo one or more rounds of mitosis before they are fully mature. FAO:0000017 GOC:tfm SGD:clt The smaller of two types of asexual spores formed by some fungi. An ovoid to pear-shaped asexual spore that contains very little cytoplasm and organelles, is uninucleate, and forms in vegetative hypae within a mycelium. Micronidia are extruded from the hyphal cell wall. FAO:0000028 cell microconidium The smaller of two types of asexual spores formed by some fungi. An ovoid to pear-shaped asexual spore that contains very little cytoplasm and organelles, is uninucleate, and forms in vegetative hypae within a mycelium. Micronidia are extruded from the hyphal cell wall. GOC:tfm ISBN:0471940526 PMID:8357339 SGD:clt Pyramidal neurons have a pyramid-shaped soma with a single axon, a large apical dendrite and multiple basal dendrites. The apex and an apical dendrite typically point toward the pial surface and other dendrites and an axon emerging from the base. The axons may have local collaterals but also project outside their region. Pyramidal neurons are found in the cerebral cortex, the hippocampus, and the amygdala. BTO:0003102 FMA:67310 FMA:86775 NIFSTD:sao862606388 projection neuron pyramidal cell pyramidal neuron cell pyramidal neuron Pyramidal neurons have a pyramid-shaped soma with a single axon, a large apical dendrite and multiple basal dendrites. The apex and an apical dendrite typically point toward the pial surface and other dendrites and an axon emerging from the base. The axons may have local collaterals but also project outside their region. Pyramidal neurons are found in the cerebral cortex, the hippocampus, and the amygdala. GOC:tfm MESH:A08.186.211.577.405.700 An asexual, nonmotile spore formed by higher fungi; conidia are usually made from the side or tip of specialized sporogenous cells and do not form by progressive cleavage of the cytoplasm. BTO:0000283 FAO:0000024 cell conidium An asexual, nonmotile spore formed by higher fungi; conidia are usually made from the side or tip of specialized sporogenous cells and do not form by progressive cleavage of the cytoplasm. ISBN:08199377X PMID:2524423 PMID:9529886 SGD:clt A fungal cell with two or more genetically distinct nuclei. cell heterokaryon A fungal cell with two or more genetically distinct nuclei. ISBN:08199377X A mechanoreceptor in the organ of Corti. In mammals the outer hair cells are arranged in three rows which are further from the modiolus than the single row of inner hair cells. The motile properties of the outer hair cells may contribute actively to tuning the sensitivity and frequency selectivity of the cochlea. BTO:0003666 FMA:62366 cochlear outer hair cell cell outer hair cell A mechanoreceptor in the organ of Corti. In mammals the outer hair cells are arranged in three rows which are further from the modiolus than the single row of inner hair cells. The motile properties of the outer hair cells may contribute actively to tuning the sensitivity and frequency selectivity of the cochlea. MESH:A08.663.650.250.315 A receptor in the vascular system, particularly the aorta and carotid sinus, which is sensitive to stretch of the vessel walls. cell pressoreceptor cell A receptor in the vascular system, particularly the aorta and carotid sinus, which is sensitive to stretch of the vessel walls. MESH:A08.800.050.800.900.700 A fungal cell with two genetically distinct haploid nuclei. cell dikaryon A fungal cell with two genetically distinct haploid nuclei. ISBN:08199377X One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision. BTO:0001024 CALOHA:TS-0870 FMA:67747 cell retinal rod cell One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision. MESH:A08.663.650.650.670.650 A spore formed following mitosis or mitoses. FAO:0000023 cell fungal asexual spore A spore formed following mitosis or mitoses. GOC:tfm PMID:2524423 PMID:9529886 SGD:clt The larger of two types of asexual spores formed by some fungi; usually round or oblong. FAO:0000038 cell macroconidium The larger of two types of asexual spores formed by some fungi; usually round or oblong. GOC:tfm ISBN:0471940526 SGD:clt A thick walled spore that stores and protects one or more nuclei following sexual reproduction in an Ascomycete. BTO:0000097 FAO:0000020 cell ascospore A thick walled spore that stores and protects one or more nuclei following sexual reproduction in an Ascomycete. GOC:tfm ISBN:08199377X SGD:clt A thick walled, sexual, resting spore formed by Zygomycetes; sometimes refers to the spore and the multi-layered cell wall that encloses the spore, the zygosporangium. FAO:0000040 cell zygospore A thick walled, sexual, resting spore formed by Zygomycetes; sometimes refers to the spore and the multi-layered cell wall that encloses the spore, the zygosporangium. ISBN:0471940526 ISBN:08199377X SGD:clt A mechanoreceptor located in the acoustic maculae and the semicircular canals that mediates the sense of balance, movement, and head position. The vestibular hair cells are connected to accessory structures in such a way that movements of the head displace their stereocilia. This influences the membrane potential of the cells which relay information about movements via the vestibular part of the vestibulocochlear nerve to the brain stem. FMA:62351 vestibular receptor cell cell vestibular hair cell A mechanoreceptor located in the acoustic maculae and the semicircular canals that mediates the sense of balance, movement, and head position. The vestibular hair cells are connected to accessory structures in such a way that movements of the head displace their stereocilia. This influences the membrane potential of the cells which relay information about movements via the vestibular part of the vestibulocochlear nerve to the brain stem. GOC:tfm MESH:A08.663.650.250.380 PO:0009002 cell This term was obsoleted as it is redundant with PO:0009002 in the cell ontology (PO) obsolete plant cell true EoP cell CFU-Eo colony forming unit eosinophil eosinophil stem cell These cells are CD34-positive, CD45RA-negative, CD71-negative, and lineage-negative (CD2, CD3 epsilon, CD4, CD5, CD8a, CD14, CD19, CD20, integrin alpha-M, NCAM-1, SCA-1, Ly6G, Ly76). eosinophil progenitor cell true EoP PMCID:PMC2212039 PMCID:PMC2626675 A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte;in this stage, production of primary granules is complete and eosinophil-specific granules has started. No nucleolus is present. These cells are integrin alpha-M-positive, CD13-positive, CD15-positive, CD16-negative, CD24-positive, and CD33-positive. BTO:0003454 FMA:83542 cell eosinophilic myelocyte true A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte;in this stage, production of primary granules is complete and eosinophil-specific granules has started. No nucleolus is present. These cells are integrin alpha-M-positive, CD13-positive, CD15-positive, CD16-negative, CD24-positive, and CD33-positive. GOC:add GOC:dsd ISBN:0721601464 PMID:19622087 http://www.cap.org A progenitor cell committed to the basophil lineage. This cell lacks hematopoietic lineage markers (lin-negative) and is CD34-positive, T1/ST2-low, CD117-negative, and FceRIa-high. This cell also expresses Gata-1, Gata-2 and C/EBPa. BaP cell CFU-Bas basophilic stem cell colony forming unit basophil BaP are also CD13-low and integrin beta-7-low. They are lin-negative (CD2, CD3e, CD4, CD5, CD8, CD11b, CD14, CD19, CD20, ly6g, ly76, and NCAM-1). They also lack expression of mast cell protease 1 (MCP-1) and microphthalmia-associated transcription factor (mitf). basophil progenitor cell true A progenitor cell committed to the basophil lineage. This cell lacks hematopoietic lineage markers (lin-negative) and is CD34-positive, T1/ST2-low, CD117-negative, and FceRIa-high. This cell also expresses Gata-1, Gata-2 and C/EBPa. GOC:add GOC:dsd PMCID:PMC1312421 http://www.copewithcytokines.de A basophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and basophil-specific granules has started. No nucleolus is present. Markers are being integrin alpha-M-positive, fucosyltransferase FUT4-positive, CD33-positive, CD24-positive, aminopeptidase N-positive. BTO:0003456 FMA:83543 cell basophilic myelocyte true A basophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and basophil-specific granules has started. No nucleolus is present. Markers are being integrin alpha-M-positive, fucosyltransferase FUT4-positive, CD33-positive, CD24-positive, aminopeptidase N-positive. GOC:add GOC:tfm ISBN:0721601464 PMID:18466030 http://www.cap.org A thick walled spore containing one or more haploid nuclei produced by sexual reproduction in an Basidiomycete; formed externally on extrusions of the basidium. BTO:0002166 FAO:0000021 cell basidiospore A thick walled spore containing one or more haploid nuclei produced by sexual reproduction in an Basidiomycete; formed externally on extrusions of the basidium. GOC:clt ISBN:0471940526 ISBN:08199377X OBSOLETE: A walled spore produced in a sporangium. cell obsolete sporangiospore true OBSOLETE: A walled spore produced in a sporangium. ISBN:08199377X A neuron that uses GABA as a vesicular neurotransmitter FMA:84788 WBbt:0005190 GABA-ergic neuron cell GABAergic neuron A neuron that uses GABA as a vesicular neurotransmitter GOC:tfm cell sheath cell cell support cell (sensu Nematoda) OBSOLETE: A sporangiospore that is motile, having flagella. FAO:0000039 cell obsolete zoospore true OBSOLETE: A sporangiospore that is motile, having flagella. ISBN:08199377X A myoblast that is committed to a myotube-specific program of differentiation but not yet fused. It undergoes very limited additional proliferation. After fusion, it will take on a muscle identity specified by a `muscle founder cell` (CL:0008006). cell fusion competent myoblast A myoblast that is committed to a myotube-specific program of differentiation but not yet fused. It undergoes very limited additional proliferation. After fusion, it will take on a muscle identity specified by a `muscle founder cell` (CL:0008006). PMID:22274696 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 lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells. large granular lymphocyte null cell BTO:0000914 BTO:0004716 CALOHA:TS-0664 FMA:63147 FMA:83601 VHOG:0001697 NK cell cell natural killer cell A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells. GOC:add ISBN:0781735149 PMID:15771571 A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor. CD4-positive, alpha-beta T lymphocyte CD4-positive, alpha-beta T-cell CD4-positive, alpha-beta T-lymphocyte cell CD4-positive, alpha-beta T cell true A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor. GOC:add ISBN:0781735149 A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor. CD8-positive, alpha-beta T lymphocyte CD8-positive, alpha-beta T-cell CD8-positive, alpha-beta T-lymphocyte cell CD8-positive, alpha-beta T cell true A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor. GOC:add GOC:tfm ISBN:0781735149 Granule cell that is part of the olfactory bulb. cell olfactory granule cell Granule cell that is part of the olfactory bulb. GOC:mah A cell involved in transporting nutrients, minerals, water, gases and other chemicals between cells for a variety of purposes including conveying nutrition to other tissues, removing waste products from the tissues, conveying gases for respiration, distributing heat and repelling invasion of foreign substances. cell transporting cell A cell involved in transporting nutrients, minerals, water, gases and other chemicals between cells for a variety of purposes including conveying nutrition to other tissues, removing waste products from the tissues, conveying gases for respiration, distributing heat and repelling invasion of foreign substances. TAIR:sr A cell that can perform photosynthesis, in which carbohydrates are synthesized from carbon dioxide and water, using light as the energy source. cell see PMID:21177950, The making of a photosynthetic animal. photosynthetic cell A cell that can perform photosynthesis, in which carbohydrates are synthesized from carbon dioxide and water, using light as the energy source. TAIR:sr A cell that is specialized to store a particular substance(s), which is(are) later released from the store for a particular purpose. cell storage cell A cell that is specialized to store a particular substance(s), which is(are) later released from the store for a particular purpose. FB:ma 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 Cells forming a framework supporting the organ of Corti. Specific cells are those of Claudius, Deiters and Hensen. cell labyrinth supporting cell Cells forming a framework supporting the organ of Corti. Specific cells are those of Claudius, Deiters and Hensen. MESH:A09.246.631.246.577.543 A cell that is found in the perisinusoidal space of the liver that is capable of multiple roles including storage of retinol, presentation of antigen to T cells (including CD1d-restricted NKT cells), and upon activation, production of extracellular matrix components that can contribute to liver fibrosis. This activated state has a myofibroblast-like phenotype, though it's not clear in the literature if this is terminally differentiated. This cell type comprises approximately 8-15% of total cells in the liver. BTO:0002741 CALOHA:TS-0452 FMA:67763 Ito cell hepatic perisinusoidal cell perisinusoidal cell cell fat-storing cell lipocyte vitamin A-storing cells Hepatic stellate cells are CD271-positive, desmin-positive, DDR-2-positive, GFAP-positive, synamin-positive, synaptophysin-positive, vimentin-positive, They are capable of producing angiotensin II, fibronectin, laminin, MMP-1, MMP-2, MMP-3, MMP-9, MMP-11, TGF-beta1, TIMP-1, TIMP-2, type I collagen, type III collagen, type IV collagen, and type VI collagen. hepatic stellate cell A cell that is found in the perisinusoidal space of the liver that is capable of multiple roles including storage of retinol, presentation of antigen to T cells (including CD1d-restricted NKT cells), and upon activation, production of extracellular matrix components that can contribute to liver fibrosis. This activated state has a myofibroblast-like phenotype, though it's not clear in the literature if this is terminally differentiated. This cell type comprises approximately 8-15% of total cells in the liver. GOC:dsd MESH:D055166 PMID:12808230 PMID:17239632 PMID:18222966 PMID:9302568 http://en.wikipedia.org/wiki/Hepatic_stellate_cell vitamin A-storing cells PMID:12808230 A tall supporting cell that is arranged in rows adjacent to the last row of outer phalangeal cells. This cell type constitutes the outer border of the organ of Corti. FMA:79799 Hensen's cell cell of Hensen external limiting cell of organ of Corti cell Hensen cell A tall supporting cell that is arranged in rows adjacent to the last row of outer phalangeal cells. This cell type constitutes the outer border of the organ of Corti. GOC:tfm ISBN:0721662544 A cuboidal cell which along with Boettcher's cells form the floor of the external spiral sulcus, external to the organ of Corti. FMA:79802 cell of Claudius external supporting cell of vestibular epithelium cell external supporting cell of Claudius Claudius cell A cuboidal cell which along with Boettcher's cells form the floor of the external spiral sulcus, external to the organ of Corti. GOC:tfm ISBN:0721662544 The outer phalangeal cells of the organ of Corti. This cell holds the base of the hair cell in a cup-shaped depression. FMA:75725 Deiters cell outer phalangeal cell cell Deiter's cell The outer phalangeal cells of the organ of Corti. This cell holds the base of the hair cell in a cup-shaped depression. GOC:tfm ISBN:0721662544 http://www.britannica.com/EBchecked/topic/156177/Deiters-cell BTO:0003064 cell Mueller cell A cell that stains readily in the anterior pituitary gland. FMA:83089 cell chromophil cell of anterior pituitary gland A cell that stains readily in the anterior pituitary gland. GOC:tfm ISBN:0618947256 An acidophilic chromophil cell that of the anterior pituitary gland. FMA:83093 acidophil cell of pars anterior of adenohypophysis acidophil of pars anterior of adenohypophysis acidophil of pars distalis of adenohypophysis pituitary alpha cell cell acidophil cell of pars distalis of adenohypophysis An acidophilic chromophil cell that of the anterior pituitary gland. GOC:tfm A basophillic chromophil cell that of the anterior pituitary gland. FMA:83094 basophil cell of anterior lobe of hypophysis cell beta cell pituitary beta cell basophil cell of pars distalis of adenohypophysis A basophillic chromophil cell that of the anterior pituitary gland. GOC:tfm A cell that is resistant to stains. FMA:83626 chromophobic cell cell chromophobe cell A cell that is resistant to stains. GOC:tfm A supportive cell of the vertebrate pituitary that provides macromolecular transport and secretes hormones. cell folliculostellate cell A supportive cell of the vertebrate pituitary that provides macromolecular transport and secretes hormones. JB:jb Type of radial astrocyte in the cerebellar cortex that have their cell bodies in the Purkinje cell layer and processes that extend into the molecular layer, terminating with bulbous endfeet at the pial surface. Bergmann glia express high densities of glutamate transporters that limit diffusion of the neurotransmitter glutamate during its release from synaptic terminals. Besides their role in early development of the cerebellum, Bergmann glia are also required for the pruning or addition of synapses. FMA:54559 Bergmann astrocyte Bergmann glial cell of cerebellum cell Bergmann glial cell Type of radial astrocyte in the cerebellar cortex that have their cell bodies in the Purkinje cell layer and processes that extend into the molecular layer, terminating with bulbous endfeet at the pial surface. Bergmann glia express high densities of glutamate transporters that limit diffusion of the neurotransmitter glutamate during its release from synaptic terminals. Besides their role in early development of the cerebellum, Bergmann glia are also required for the pruning or addition of synapses. GOC:tfm http://www.neurolex.org/wiki/Category:Bergmann_Glial_Cell A cell with long processes running parallel to adjacent axons in the proximal infundibulum of the neurohypophysis. These processes form a three-dimensional network among the axons of the hypothalamic neurosecretory cells and are connected by gap junctions which provide for their metabolic coupling. This cell type constitutes most of the nonexcitable tissue in the neurohypophsis; function may include possibly acting as an intermediate in the modulation of oxytocin and vasopressin release. This cell type is highly variable in size and shape and commonly contain lipid droplets and deposits of lipochrome pigment. BTO:0003793 FMA:83503 cell pituicyte A cell with long processes running parallel to adjacent axons in the proximal infundibulum of the neurohypophysis. These processes form a three-dimensional network among the axons of the hypothalamic neurosecretory cells and are connected by gap junctions which provide for their metabolic coupling. This cell type constitutes most of the nonexcitable tissue in the neurohypophsis; function may include possibly acting as an intermediate in the modulation of oxytocin and vasopressin release. This cell type is highly variable in size and shape and commonly contain lipid droplets and deposits of lipochrome pigment. ISBN:0412046911 ISBN:0517223651 http://en.wikipedia.org/wiki/Pituicyte Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament. BTO:0000939 FMA:62516 cell basal cell Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament. GOC:tfm ISBN:0517223651 A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes. BTO:0003107 FMA:83035 Langerhans giant cell foreign body giant cell macrophage polykaryon multinucleate giant cell syncytial giant cell cell Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this. multinucleated giant cell true A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes. GOC:add GOC:tfm ISBN:0702022918 ISBN:0702024783 Langerhans giant cell ISBN:0702022918 ISBN:0702024783 foreign body giant cell ISBN:0702022918 ISBN:0702024783 macrophage polykaryon ISBN:0702022918 ISBN:0702024783 multinucleate giant cell ISBN:0702022918 ISBN:0702024783 syncytial giant cell ISBN:0702022918 ISBN:0702024783 A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus. While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation. CL:0000461 juxtaglomerular cell FMA:84138 JG cell renin secreting cell cell kidney granular cell A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus. While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation. GOC:cvs GOC:tfm PMID:11457727 A cell with delicate radiating processes known as desmosomes that form intercellular bridges between other cells of this type. This cell type forms the stratum spinosum (prickle cell layer). A function of this cell is to generate keratin. CL:0002186 FMA:69059 prickle cell of epidermis cell prickle cell A cell with delicate radiating processes known as desmosomes that form intercellular bridges between other cells of this type. This cell type forms the stratum spinosum (prickle cell layer). A function of this cell is to generate keratin. GOC:tfm ISBN:0721662544 ISBN:0815332181 A cell type that encapsulates the capillaries and venules in the kidney. This cell secretes mesangial matrix that provides the structural support for the capillaries. BTO:0000853 CALOHA:TS-0617 FMA:70972 kidney mesangial cell cell Do all of these cells really develop from some mesenchymal stem cell? mesangial cell A cell type that encapsulates the capillaries and venules in the kidney. This cell secretes mesangial matrix that provides the structural support for the capillaries. GOC:tfm http://www.copewithcytokines.de/cope.cgi?key=mesangial%20cells A mucus-secreting cell, with numerous apical secretory vesicles containing mucins; nucleus are basally displaced; numerous at the neck of mucus secreting glands neck cell cell mucous neck cell A mucus-secreting cell, with numerous apical secretory vesicles containing mucins; nucleus are basally displaced; numerous at the neck of mucus secreting glands GOC:tfm This cell type produces and secretes melatonin and forms the pineal parenchyma. Extending from each cell body, which has a spherical, oval or lobulated mucleus, are one or more tortuous basophilic processes, containing parallel microtubules known as synaptic ribbons. These processes end in expanded terminal buds near capillaries or less, frequently, ependymal cells of the pineal recess. The terminal buds contain granular endoplasmic reticulum, mitochondria and electron-dense cored vesicles, which store monoamines and polypeptide hormones, release of which appears to require sympathetic innervation. BTO:0001068 FMA:83417 cell pinealocyte This cell type produces and secretes melatonin and forms the pineal parenchyma. Extending from each cell body, which has a spherical, oval or lobulated mucleus, are one or more tortuous basophilic processes, containing parallel microtubules known as synaptic ribbons. These processes end in expanded terminal buds near capillaries or less, frequently, ependymal cells of the pineal recess. The terminal buds contain granular endoplasmic reticulum, mitochondria and electron-dense cored vesicles, which store monoamines and polypeptide hormones, release of which appears to require sympathetic innervation. GOC:tfm ISBN:0517223651 PMID:16687276 http://en.wikipedia.org/wiki/Pinealocyte A glomerular visceral epithelial cell is a specialized kidney epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells. epithelial cell of visceral layer of glomerular capsule BTO:0002295 FMA:70967 glomerular podocyte podocyte cell GO has podocyte as a related synonym due to concern this may refer to more than one cell type. However, this did not turn up in my search. If podocyte does refer to more than one cell type, then we should classify the synonym to 'related'[tfm]. glomerular visceral epithelial cell A glomerular visceral epithelial cell is a specialized kidney epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells. GOC:tfm epithelial cell of visceral layer of glomerular capsule FMA:70967 glomerular podocyte FMA:70967 A primary oocyte is an oocyte that has not completed female meosis I. BTO:0000512 FMA:18645 cell primary oogonium primary oocyte true A primary oocyte is an oocyte that has not completed female meosis I. GOC:tfm ISBN:0721662544 A secondary oocyte is an oocyte that has not completed meiosis II. BTO:0003094 FMA:18646 cell primary oogonium secondary oocyte true A secondary oocyte is an oocyte that has not completed meiosis II. GOC:tfm ISBN:0721662544 A diploid cell that has derived from a spermatogonium and can subsequently begin meiosis and divide into two haploid secondary spermatocytes. BTO:0001115 CALOHA:TS-2194 FMA:72292 cell primary spermatocyte true A diploid cell that has derived from a spermatogonium and can subsequently begin meiosis and divide into two haploid secondary spermatocytes. GOC:tfm ISBN:0721662544 One of the two haploid cells into which a primary spermatocyte divides, and which in turn gives origin to spermatids. BTO:0000709 CALOHA:TS-2195 FBbt:00004941 FMA:72293 cell secondary spermatocyte true One of the two haploid cells into which a primary spermatocyte divides, and which in turn gives origin to spermatids. GOC:tfm ISBN:0721662544 An epithelial cell that secretes cuticle. cell cuticle secreting cell An epithelial cell that secretes cuticle. GOC:tfm An extracellular matrix secreting cell that secretes eggshell. cell eggshell secreting cell An extracellular matrix secreting cell that secretes eggshell. GOC:tfm An extracellular matrix secreting cell that secretes glycocalyx. cell glycocalyx secreting cell An extracellular matrix secreting cell that secretes glycocalyx. GOC:tfm cell distal tip cell (sensu Nematoda) cell neuroglioblast (sensu Nematoda) false cell valve cell cell closable valve cell cell permanently open valve cell window cell cell fenestrated cell An extracellular matrix secreting cell that secretes collagen. cell collagen secreting cell An extracellular matrix secreting cell that secretes collagen. GOC:tfm OBSOLETE: The cell characteristic of an organ, as distinguished from associated connective or supporting tissues. BTO:0002174 FMA:84638 cell OBSOLETE: Term was made obsolete to avoid confusion with plant parenchymal cell. Cell type has a similar but slightly different meaning in botany (plants): see PO:0000074. obsolete parenchymal cell true OBSOLETE: The cell characteristic of an organ, as distinguished from associated connective or supporting tissues. ISBN:0471245208 An elongated, contractile cell found wrapped about precapillary arterioles outside the basement membrane. Pericytes are present in capillaries where proper adventitia and muscle layer are missing (thus distingushing this cell type from adventitial cells). They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells. CL:0000184 BTO:0002441 FMA:63174 ARC adventitial reticular cell cell of Rouget pericyte pericyte of Rouget cell adventitial cell Pericytes are CD10-positive, CD13-positive, CD31-negative, CD45-negative, CD106-positive, CD117-negative, CD140-positive, CD144-negative, CD146-positive, CD271-positive, CD325-positive, NG2-positive, RGS5-positive, SMA-positive, and desmin-positive. A subpopulation is CD248-positive. They are also capable of producing angiopoietin 1, CXCL12, TGF-beta, and VEGF-A. pericyte cell An elongated, contractile cell found wrapped about precapillary arterioles outside the basement membrane. Pericytes are present in capillaries where proper adventitia and muscle layer are missing (thus distingushing this cell type from adventitial cells). They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells. GOC:dsd GOC:tfm ISBN:0721662544 MESH:D020286 PMID:16807374 PMID:17986482 PMID:20024907 ARC PMID:17986482 A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells. FMA:70567 gonocyte primitive germ cell cell primordial germ cell true true A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells. GOC:tfm PMID:1381289 FBbt:00004906 cell centripetally migrating follicle cell Obsolete. Use PO:0000290 from Plant Ontology instead. A water conducting cell, tracheid or vessel member. cell replaced_by: PO:0000290 obsolete tracheary element true Obsolete. Use PO:0000290 from Plant Ontology instead. A water conducting cell, tracheid or vessel member. ISBN:0471245208 cell Kenyon cell FBbt:00004910 fly stalk cell cell interfollicle cell A mature sexual reproductive cell of the female germline. cell female gamete true A mature sexual reproductive cell of the female germline. GOC:tfm BTO:0001033 cell cap cell Cell of the intestinal epithelium with a brush border made up of many parallel packed microvilli; associated with absorption, particularly of macromolecules. cell gut absorptive cell Cell of the intestinal epithelium with a brush border made up of many parallel packed microvilli; associated with absorption, particularly of macromolecules. JB:jb cell commissural neuron WBbt:0006829 cell glutamatergic neuron A non-terminally differentiated cell that is capable of developing into a muscle cell. cell muscle precursor cell A non-terminally differentiated cell that is capable of developing into a muscle cell. GOC:add A cell present in the developing CNS. Functions as both a precursor cell and as a scaffold to support neuronal migration. forebrain radial glial cell cell Unlike that of mammals, the brain of adult teleost fish exhibits an intense and widespread neurogenic activity as a result of the persistence of radial glial cells acting as neural progenitors throughout life. radial glial cell A cell present in the developing CNS. Functions as both a precursor cell and as a scaffold to support neuronal migration. GOC:dph An absorptive cell of the gut epithelium that endocytoses microorganisms and intact macromolecules from the gut lumen and transports them to the subepithelial space where they are presented to antigen-presenting cells and lymphocytes. M cell BTO:0003600 FMA:62929 M-cell microfold cell cell Should double check and see if M cells are particular to a specific region. M cell of gut An absorptive cell of the gut epithelium that endocytoses microorganisms and intact macromolecules from the gut lumen and transports them to the subepithelial space where they are presented to antigen-presenting cells and lymphocytes. GOC:jb GOC:tfm A cell that transports hormones from neurosecretory cells. This nerve cell is characterized by bipolar shape and endfeet that contact a basal lamina around blood vessels, and/or the pia mater or vitreous body of the eye and additionally contact the ventricular surface or sub-retinal space. ependymal astrocyte cell ependymoglial cell A cell that transports hormones from neurosecretory cells. This nerve cell is characterized by bipolar shape and endfeet that contact a basal lamina around blood vessels, and/or the pia mater or vitreous body of the eye and additionally contact the ventricular surface or sub-retinal space. JB:jb http://neurolex.org/wiki/Category:Ependymoglial_Cell cell littoral cell of liver Obsolete. Use PO:0004010 from Plant Ontology instead. A cell synthesizing protoplasm and producing new cells by division and with only a primary cell wall. cell replaced_by: PO:0004010 obsolete meristematic cell true Obsolete. Use PO:0004010 from Plant Ontology instead. A cell synthesizing protoplasm and producing new cells by division and with only a primary cell wall. PO:0004010 A columnar/cuboidal epithelial cell that secretes cerebrospinal fluid. cell cerebrospinal fluid secreting cell true A columnar/cuboidal epithelial cell that secretes cerebrospinal fluid. GOC:tfm R1 cell cell R1 photoreceptor cell A fibroblast-like cell that provides support at neuromuscular junctions in vertebrates and are localized outside the synaptic basal lamina. cell perijunctional fibroblast A fibroblast-like cell that provides support at neuromuscular junctions in vertebrates and are localized outside the synaptic basal lamina. JB:jb A cell with both myofibrils and secretory granules. cell myoendocrine cell A cell with both myofibrils and secretory granules. JB:jb R2 cell cell R2 photoreceptor cell cell stellate interneuron A neuroglial cell of the peripheral nervous system inside the basal lamina of the neuromuscular junction providing chemical and physical support to the synapse. Schwann cell cell terminal Schwann cell A neuroglial cell of the peripheral nervous system inside the basal lamina of the neuromuscular junction providing chemical and physical support to the synapse. JB:jb PMID:16136171 An interneuron that has spider-like appearance with a small round soma, a large number (7-10) of short, smooth, or slightly beaded primary dendrites that give rise to only a few secondary branches, and a branched axon that establishes a dense axonal mesh with thin shafts. NGF cell neuroglioform cell spiderweb cell cell neurogliaform cell An interneuron that has spider-like appearance with a small round soma, a large number (7-10) of short, smooth, or slightly beaded primary dendrites that give rise to only a few secondary branches, and a branched axon that establishes a dense axonal mesh with thin shafts. JB:jb PMID:17122314 NGF cell PMID:18568015 neuroglioform cell PMID:3235828 R3 cell cell R3 photoreceptor cell One of a transient population of pioneering neurons in the cerebral cortex. These cells are slender bipolar cells of the developing marginal zone. One feature of these cells in mammals is that they express the Reelin gene. cell Cajal-Retzius cell One of a transient population of pioneering neurons in the cerebral cortex. These cells are slender bipolar cells of the developing marginal zone. One feature of these cells in mammals is that they express the Reelin gene. PMID:10600995 PMID:9728912 A cell that stores and secretes pancreatic polypeptide hormone. FMA:62938 FMA:83409 type F enteroendocrine cell cell PP cell A cell that stores and secretes pancreatic polypeptide hormone. GOC:tfm JB:jb PMID:15153415 R4 cell cell R4 photoreceptor cell cell obsolete paraganglial cell true A type of glomus or chief cell, is sensitive to hypoxia and produce catecholamines. cell paraganglial type 1 cell A type of glomus or chief cell, is sensitive to hypoxia and produce catecholamines. GOC:tfm A neuron that releases dopamine as a neurotransmitter. BTO:0004032 FMA:84787 WBbt:0006746 dopaminergic cell cell dopaminergic neuron A neuron that releases dopamine as a neurotransmitter. GOC:dhill Supports paraganglial type 1 cell. cell paraganglia type 2 cell Supports paraganglial type 1 cell. JB:jb R5 cell cell R5 photoreceptor cell Cell that provides some or all mechanical, nutritional and phagocytic support to their neighbors. BTO:0002315 cell sustentacular cell Cell that provides some or all mechanical, nutritional and phagocytic support to their neighbors. JB:jb A specialized endothelial cell that senses extracellular signals and guides the directed growth of blood vessels. cell endothelial tip cell A specialized endothelial cell that senses extracellular signals and guides the directed growth of blood vessels. PMID:15376331 R6 cell cell R6 photoreceptor cell Specialized ependymal cell that produces the cerebrospinal fluid from the blood and secretes it into the lumen of the brain and spinal chord. CL:1000430 FMA:70549 epithelial cell of choroid plexus cell choroid plexus epithelial cell Specialized ependymal cell that produces the cerebrospinal fluid from the blood and secretes it into the lumen of the brain and spinal chord. GOC:add GOC:tfm JB:jb PMID:9550134 R7 cell cell R7 photoreceptor cell Stromal cell that forms the internal covering of the vertebrate brain and produces ECM for this and the choroid plexus. cell leptomemingeal cell leptomeningeal cell true Stromal cell that forms the internal covering of the vertebrate brain and produces ECM for this and the choroid plexus. JB:jb R8 cell cell R8 photoreceptor cell Epithelial cells derived from neural plate and neural crest. neuroepithelial cell BTO:0004301 FMA:70557 cell The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098). neurecto-epithelial cell Epithelial cells derived from neural plate and neural crest. GOC:tfm Cumulus cell is a specialized granulosa cell that surrounds and nourishes the oocyte. This cell-type surrounds the fully-grown oocyte to form a cumulus-oocyte complex (abbr. COC). The terms cumulus oophorus cells, cumulus granulosa cells, cumulus oophorous granulosa cells, granulosa-cumulus cells are used to make a distinction between this cell and the other functionally different subpopulation of granulosa cells at the wall of the Graafian follicle. BTO:0002236 cell cumulus cell Cumulus cell is a specialized granulosa cell that surrounds and nourishes the oocyte. This cell-type surrounds the fully-grown oocyte to form a cumulus-oocyte complex (abbr. COC). The terms cumulus oophorus cells, cumulus granulosa cells, cumulus oophorous granulosa cells, granulosa-cumulus cells are used to make a distinction between this cell and the other functionally different subpopulation of granulosa cells at the wall of the Graafian follicle. GOC:tfm http://www.copewithcytokines.org/cope.cgi?key=cumulus%20cells cell stratum granulosum cell cell corona radiata cell cell embryonic crystal cell cell lymph gland crystal cell A subset of motor neurons that innervates intrafusal muscle fibers and has small diameter axons. cell fusimotor neuron A subset of motor neurons that innervates intrafusal muscle fibers and has small diameter axons. PMID:15582775 cell cone cell (sensu Endopterygota) compound eye cone cell cell posterior cone cell (sensu Endopterygota) cell anterior cone cell (sensu Endopterygota) cell equatorial cone cell (sensu Endopterygota) cell cystoblast A stem cell that can give rise to cell types of the body other than those of the germ-line. CALOHA:TS-2086 FMA:63368 cell somatic stem cell true A stem cell that can give rise to cell types of the body other than those of the germ-line. GO:0048103 A differentiated cell that functions as a site of nitrogen fixation under aerobic conditions. BTO:0000600 cell heterocyst A differentiated cell that functions as a site of nitrogen fixation under aerobic conditions. MA:ma cell nitrogen fixing cell An asexual 1-celled spore (primarily for perennation, not dissemination). Originates endogenously and singly within part of a pre-existing cell by the contraction of the protoplast. Possesses an inner secondary and often thickened hyaline or brown wall, usually impregnated with hydrophobic material. cell Considering obsoleting as sometimes used to refer to protozoans too. But reference indicates term was intended for fungus. chlamydospore An asexual 1-celled spore (primarily for perennation, not dissemination). Originates endogenously and singly within part of a pre-existing cell by the contraction of the protoplast. Possesses an inner secondary and often thickened hyaline or brown wall, usually impregnated with hydrophobic material. GOC:tfm ISBN:085199377X cell primary pigment cell cell secondary pigment cell cell tertiary pigment cell A cell at the front of a migrating epithelial sheet. cell leading edge cell A cell at the front of a migrating epithelial sheet. MA:ma A cell of a layer of transitional epithelium in the wall of the bladder, ureter, and renal pelvis, external to the lamina propria. FMA:84127 bladder transitional cell transitional epithelial cell of urinary bladder urinary tract transitional epithelial cell cell urothelial cell true A cell of a layer of transitional epithelium in the wall of the bladder, ureter, and renal pelvis, external to the lamina propria. GOC:tfm MA:ma cell amoeboid cell cell lymph gland plasmatocyte cell embryonic gland plasmatocyte cell lymph gland hemocyte cell embryonic gland hemocyte Muscle cell which has as its direct parts myofilaments organized into sarcomeres. BTO:0002916 CALOHA:TS-2157 FMA:86936 cell striated muscle cell Muscle cell which has as its direct parts myofilaments organized into sarcomeres. GOC:tfm ISBN:0721662544 An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. BTO:0000751 CALOHA:TS-0549 FMA:62852 immune cell leucocyte white blood cell cell leukocyte true An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. GOC:add GOC:tfm ISBN:978-0-323-05290-0 The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve. BTO:0001800 FMA:67765 RGC gangliocyte ganglion cell of retina cell retinal ganglion cell The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve. GOC:dph A motor neuron that is located in the cervical region of the spinal cord and selectively innervates the sternocleidmastoid or trapezius muscle. Unlike other motor neurons, they extend axons dorsally along lateral margins of the spinal cord. SACMN cell spinal accessory motor neuron A motor neuron that is located in the cervical region of the spinal cord and selectively innervates the sternocleidmastoid or trapezius muscle. Unlike other motor neurons, they extend axons dorsally along lateral margins of the spinal cord. PMID:16267219 A round chondrocyte that first differentiates in the late embryonic growth plate of bone. cell periarticular chondrocyte A round chondrocyte that first differentiates in the late embryonic growth plate of bone. PMID:15951842 Chondrocyte that is terminally differentiated, produces type X collagen, is large in size, and often associated with the replacement of cartilage by bone (endochondral ossification). cell is hypertrophic pathological or normal? and can it be described using a pato term? hypertrophic chondrocyte Chondrocyte that is terminally differentiated, produces type X collagen, is large in size, and often associated with the replacement of cartilage by bone (endochondral ossification). GO_REF:0000034 PMID:15951842 A columnar chondrocyte that differentiates in the late embryonic growth plate of bone. Columnar chondrocytes vigorously proliferate and form columns in the growth plate. cell columnar chondrocyte A columnar chondrocyte that differentiates in the late embryonic growth plate of bone. Columnar chondrocytes vigorously proliferate and form columns in the growth plate. PMID:15951842 A neuron that laterally connects other neurons in the inner nuclear layer of the retina. BTO:0004120 horizontal cell cell retina horizontal cell A neuron that laterally connects other neurons in the inner nuclear layer of the retina. ISBN:0195088433 Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei. FMA:83808 cardiocyte BTO:0001539 CALOHA:TS-0115 FMA:14067 cardiac muscle fiber cardiac myocyte cardiomyocyte heart muscle cell cell This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction. cardiac muscle cell Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei. GOC:mtg_cardiacconduct_nov11 GOC:tfm ISBN:0323052908 PMID:22426062 PMID:4711263 cardiac muscle fiber GO:0048739 A pigment cell derived from the neural crest. Contains blue pigment of unknown chemical composition in fibrous organelles termed cyanosomes. This gives a blue appearance. cell blue chromatophore cyanophore A pigment cell derived from the neural crest. Contains blue pigment of unknown chemical composition in fibrous organelles termed cyanosomes. This gives a blue appearance. SANBI:mhl A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner plexiform layer. retinal bipolar neuron A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner plexiform layer. PMID:14689473 A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner half of the inner plexiform layer. These cells depolarize in response to light stimulation of their corresponding photoreceptors. cell ON-bipolar cell A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner half of the inner plexiform layer. These cells depolarize in response to light stimulation of their corresponding photoreceptors. PMID:14689473 A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the outer half of the inner plexiform layer. These cells depolatize in response to light to dark transition. cell OFF-bipolar cell A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the outer half of the inner plexiform layer. These cells depolatize in response to light to dark transition. PMID:14689473 A bipolar neuron found in the retina that is synapsed by rod photoreceptor cells but not by cone photoreceptor cells. These neurons depolarize in response to light. FMA:67750 cell rod bipolar cell A bipolar neuron found in the retina that is synapsed by rod photoreceptor cells but not by cone photoreceptor cells. These neurons depolarize in response to light. GOC:tfm PMID:14689473 A bipolar neuron found in the retina and having connections with cone photoreceptor cells and neurons in the inner plexiform layer. cell cone retinal bipolar cell A bipolar neuron found in the retina and having connections with cone photoreceptor cells and neurons in the inner plexiform layer. PMID:14689473 An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell body of these cells is in the middle of the inner plexiform layer. The dendritic tree is stout and the axon terminates in sublamina 1. The axonal terminal is wide and has only a few varicosities. DB1 cone bipolar cell type 1 cone bipolar cell (sensu Mus) An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell body of these cells is in the middle of the inner plexiform layer. The dendritic tree is stout and the axon terminates in sublamina 1. The axonal terminal is wide and has only a few varicosities. PMID:14689473 An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is not well filled and the dendrites are more delicate than in type 1 cells. The axon terminal is bushier and exhibits a dense plexus of varicosities in the inner part of sublamina 1 (Ghosh et al., 2004). It can be differentiated from other retinal bipolar neurons by its expression of marker genes: Neto1, Lhx3 and Irx-6 (Shekhar, 2016). FMB cone bipolar cell cell type 2 cone bipolar cell (sensu Mus) PMID:27565351 An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is not well filled and the dendrites are more delicate than in type 1 cells. The axon terminal is bushier and exhibits a dense plexus of varicosities in the inner part of sublamina 1 (Ghosh et al., 2004). It can be differentiated from other retinal bipolar neurons by its expression of marker genes: Neto1, Lhx3 and Irx-6 (Shekhar, 2016). PMID:14689473 PMID:27565351 An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is delicate and the dendritic tips appear small when compared with type 1 cells. The axon terminal is stratified and restricted to sublamina 2 of the inner plexiform layer. DB2 cone bipolar cell cell type 3 cone bipolar cell (sensu Mus) An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is delicate and the dendritic tips appear small when compared with type 1 cells. The axon terminal is stratified and restricted to sublamina 2 of the inner plexiform layer. PMID:14689473 An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell has a diffuse axon terminal with varicosities in sublaminae 1 and 2 of the inner plexiform layer. DB3 cone bipolar cell cell type 4 cone bipolar cell (sensu Mus) An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell has a diffuse axon terminal with varicosities in sublaminae 1 and 2 of the inner plexiform layer. PMID:14689473 An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is restricted to sublamina 3 of the inner plexiform layer. It is narrowly stratified and branched. The dendritic tree has many delicate branches. DB4 cone bipolar cell cell type 5 cone bipolar cell (sensu Mus) An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is restricted to sublamina 3 of the inner plexiform layer. It is narrowly stratified and branched. The dendritic tree has many delicate branches. PMID:14689473 An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The cell has a loose, delicate axon terminal that opens in sublamina 3 of the inner plexiform layer and descends into sublamina 4. DB5 cone bipolar cell cell type 6 cone bipolar cell (sensu Mus) An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The cell has a loose, delicate axon terminal that opens in sublamina 3 of the inner plexiform layer and descends into sublamina 4. PMID:14689473 An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is narrowly stratified and are found just below a calretinin-expressing band in sublamina 4 of the inner plexiform layer. IMB cone bipolar cell cell type 7 cone bipolar cell (sensu Mus) An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is narrowly stratified and are found just below a calretinin-expressing band in sublamina 4 of the inner plexiform layer. PMID:14689473 An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. This cell has the widest dendritic field and the widest axon terminal of all retinal bipolar cells. The axon terminal is delicate and stratified through sublaminae 4 and 5 of the inner plexiform layer. DB6 cone bipolar cell cell type 8 cone bipolar cell (sensu Mus) An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. This cell has the widest dendritic field and the widest axon terminal of all retinal bipolar cells. The axon terminal is delicate and stratified through sublaminae 4 and 5 of the inner plexiform layer. PMID:14689473 An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The dendritic tree is wide and the dendritic convergence indicates cone selectivity. The axon terminal is sparsely branched and terminates in sublamina 5 of the inner plexiform layer. BB cone bipolar cell cell type 9 cone bipolar cell (sensu Mus) An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The dendritic tree is wide and the dendritic convergence indicates cone selectivity. The axon terminal is sparsely branched and terminates in sublamina 5 of the inner plexiform layer. PMID:14689473 A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates. cell Note that this is a non-mammalian cell type. Use platelet ; CL:0000233 for thrombocytes (platelets) in mammals. nucleated thrombocyte true A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates. GOC:add GOC:tfm PMID:16360205 A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage. BTO:0001441 CALOHA:TS-0647 cell myeloid cell true A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage. GOC:add A immature or mature cell in the lineage leading to and including erythrocytes. CL:0002156 CALOHA:TS-0290 FMA:62845 FMA:83516 erythropoietic cell cell Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. erythroid lineage cell A immature or mature cell in the lineage leading to and including erythrocytes. GOC:add GOC:tfm A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers. BTO:0001571 CALOHA:TS-0289 FMA:83504 normoblast cell erythroblast true A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers. GOC:add ISBN:0721601464 PMID:18174176 A cell of the monocyte, granulocyte, or mast cell lineage. cell myeloid leukocyte true A cell of the monocyte, granulocyte, or mast cell lineage. GOC:add Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive. polymorphonuclear leucocyte polymorphonuclear leukocyte BTO:0000129 CALOHA:TS-0073 FMA:62862 basophilic leucocyte basophilic leukocyte cell Matures in the bone marrow and account for <1% of leukocytes in the peripheral blood, spleen, and bone marrow. Basophils are described as being CD11a-positive, CD11b-positive, CD13-positive, CD15-positive, CD18-positive, CD21-positive, CD25-positive, CD29-positive, CD35-positive, CD40-positive, CD40L-positive, CD44-positive, CD45R-negative, CD46-positive, CD49a-positive, CD49b-positive, CD49d-positive, CD55-positive, CD59-positive, CD62L-positive, CD63-positive, CD69-positive, CD90-negative, CD116-positive, CD117-negative, CD124-positive, CD125-positive, CD131-positive, CD161-positive, CD184-positive, CD191-positive, CD192-positive, CD197-positive, CD200R3-positive, CD218-positive, CD282-positive, CD284-positive, CD289-positive, CD290-positive, CD294-positive, natural killer cell receptor 2B4-positive, smad1-positive, CD3-negative, CD4-negative, CD7-negative, CD8-negative, CD14-negative, CD15-negative, CD16-negative, CD19-negative, CD20-negative, CD34-negative, CD36-negative, CD45R-negative, CD56-negative, CD57-negative, CD235a-negative, and GR1-negative. Transcription factors- GATA1-positive, PU.1-positive. basophil true Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive. GOC:add GOC:amm GOC:dsd GOC:tfm ISBN:0721601464 MESH:D001491 PMCID:PMC2626675 PMID:11927641 PMID:19741522 PMID:21236338 PMID:9933081 Any of the immature forms of a basophil, in which basophilic specific granules are present but other phenotypic features of the mature form may be lacking. immature basophilic leucocyte immature basophilic leukocyte cell immature basophil true Any of the immature forms of a basophil, in which basophilic specific granules are present but other phenotypic features of the mature form may be lacking. GOC:add ISBN:0721601464 A basophil precursor in the granulocytic series, being a cell intermediate in development between a basophilic myelocyte and a band form basophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are CD11b-positive, CD15-positive, CD16-positive, CD24-positive, CD33-positive, and CD13-positive. FMA:84198 cell basophilic metamyelocyte true A basophil precursor in the granulocytic series, being a cell intermediate in development between a basophilic myelocyte and a band form basophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are CD11b-positive, CD15-positive, CD16-positive, CD24-positive, CD33-positive, and CD13-positive. GOC:tfm ISBN:0721601464 PMID:18466030 A late basophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature basophil. cell band form basophil true A late basophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature basophil. GOC:add ISBN:0721601464 PMID:18466030 http://www.cap.org Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive. polymorphonuclear leucocyte polymorphonuclear leukocyte BTO:0000399 CALOHA:TS-0279 FMA:62861 eosinocyte eosinophilic granulocyte eosinophilic leucocyte eosinophilic leukocyte cell Eosinophils are also CD14-negative, CD32-positive, CD44-positive, CD48-positive, CD69-positive, CD192-negative, MBP1-positive, MBP2-positive, TLR2-negative, TLR4-negative, and lineage-negative (B220, CD2, CD14, CD19, CD56, CD71, CD117, CD123, CD235a (glycophorin A), and TER119). The cytokines IL-3, IL-5, and GM-CSF are involved in their development and differentiation. Usually considered CD16-negative, CD16 is observed on eosinophilic metamyelocyte. eosinophil true Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive. GOC:add GOC:amm GOC:dsd GOC:tfm ISBN:0721601464 PMCID:PMC2626675 PMID:10914487 PMID:1662676 Any of the immature forms of an eosinophil, in which eosinophilic specific granules are present but other phenotypic features of the mature form may be lacking. immature eosinocyte immature eosinophilic leucocyte immature eosinophilic leukocyte cell immature eosinophil true Any of the immature forms of an eosinophil, in which eosinophilic specific granules are present but other phenotypic features of the mature form may be lacking. GOC:add ISBN:0721601464 A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a eosinophilic myelocyte and a band form eosinophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are integrin alpha-M-positive, fucosyltransferase FUT4-positive, low affinity immunoglobulin gamma Fc region receptor III-positive, CD33-positive, CD24-positive and aminopeptidase N-negative. cell eosinophilic metamyelocyte true A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a eosinophilic myelocyte and a band form eosinophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are integrin alpha-M-positive, fucosyltransferase FUT4-positive, low affinity immunoglobulin gamma Fc region receptor III-positive, CD33-positive, CD24-positive and aminopeptidase N-negative. GOC:add GOC:tfm ISBN:0721601464 PMID:19622087 A late eosinophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature eosinophil. cell band form eosinophil true A late eosinophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature eosinophil. GOC:add GOC:tfm ISBN:0721601464 PMID:19622087 http://www.cap.org Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. PMN poly polymorphonuclear leucocyte polymorphonuclear leukocyte polymorphonuclear neutrophil polynuclear neutrophilic leucocyte polynuclear neutrophilic leukocyte BTO:0000130 CALOHA:TS-0688 FMA:62860 neutrocyte neutrophil leucocyte neutrophil leukocyte neutrophilic leucocyte neutrophilic leukocyte cell neutrophil true Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. GOC:add GOC:amm GOC:tfm ISBN:0721601464 Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking. immatuer neutrophilic leukocyte immature neutrocyte immature neutrophil leucocyte immature neutrophil leukocyte immature neutrophilic leucocyte cell immature neutrophil true Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking. GOC:add ISBN:0721601464 A tissue-resident macrophage of the renal glomerular mesangium involved in the disposal and degradation of filtration residues, presentation of antigen to T cells and in tissue remodeling. mesangial cell cell mesangial phagocyte true A tissue-resident macrophage of the renal glomerular mesangium involved in the disposal and degradation of filtration residues, presentation of antigen to T cells and in tissue remodeling. GOC:add GOC:tfm ISBN:0702022918 ISBN:3540536663 PMID:1600140 PMID:16146841 A specialized mononuclear osteoclast associated with the absorption and removal of bone, precursor of multinuclear osteoclasts. cell Morphology: mononuclear, highly vesicular. mononuclear osteoclast true A specialized mononuclear osteoclast associated with the absorption and removal of bone, precursor of multinuclear osteoclasts. GOC:add GOC:tfm PMID:12713016 PMID:15055519 PMID:17380158 PMID:9415452 A specialized multinuclear osteoclast associated with the absorption and removal of bone. multinucleated osteoclast cell Morphology: multinucleated, highly vesicular. multinuclear osteoclast true A specialized multinuclear osteoclast associated with the absorption and removal of bone. GOC:add PMID:12713016 PMID:9415452 A specialized multinuclear osteoclast associated with the absorption and removal of cementum. multinucleated odontoclast cell Morphology: multinucleated, highly vesicular; location: roots of deciduous (milk) teeth. multinuclear odontoclast true A specialized multinuclear osteoclast associated with the absorption and removal of cementum. GOC:add PMID:9415452 A specialized mononuclear osteoclast associated with the absorption and removal of cementum. cell Morphology: Mononuclear, highly vesicular; location: roots of deciduous (milk) teeth. mononuclear odontoclast true true A specialized mononuclear osteoclast associated with the absorption and removal of cementum. GOC:add PMID:9415452 A dendritic cell of the myeloid lineage. interdigitating cell veiled cell BTO:0004721 CD11c+CD123- DC mDC cell These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8). myeloid dendritic cell true A dendritic cell of the myeloid lineage. GOC:add PMID:10449155 PMID:17332250 PMID:9521319 A phagocyte formed by the fusion of mononuclear phagocytes. cell multinucleated phagocyte true A phagocyte formed by the fusion of mononuclear phagocytes. GOC:add GOC:tfm A dendritic cell type of distinct morphology, localization, and surface marker expression (CD123-positive) from other dendritic cell types and associated with early stage immune responses, particularly the release of physiologically abundant amounts of type I interferons in response to infection. BTO:0004625 DC2 IPC T-associated plasma cell interferon-producing cell lymphoid dendritic cell pDC plasmacytoid T cell plasmacytoid monocyte type 2 DC cell plasmacytoid dendritic cell true A dendritic cell type of distinct morphology, localization, and surface marker expression (CD123-positive) from other dendritic cell types and associated with early stage immune responses, particularly the release of physiologically abundant amounts of type I interferons in response to infection. GOC:add GOC:dsd PMCID:PMC2118448 PMCID:PMC538703 PMID:15549123 PMID:17332250 PMID:17850486 PMID:20304825 A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen. mature B lymphocyte mature B-cell mature B-lymphocyte cell Mature B cells are also reportedly CD10-negative, CD19-positive, CD22-positive, CD34-negative, CD48-positive, CD79a-positive, CD84-positive, CD127-negative, CD352-positive, RAG-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Transcription factors expressed: Pax5-positive. mature B cell true A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen. GOC:add GOC:dsd ISBN:0781735149 A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin. BTO:0000392 FMA:70574 plasma B cell plasma B-cell plasmacyte plasmocyte cell effector B cell effector B-cell Plasma cells develop in the spleen and migrate to the bone marrow. Plasma cells are also reportedly CD5-negative, CD10-negative, CD19-positive, CD20-negative, CD21-negative, CD22-negative, CD23-negative, CD24-negative, CD25-negative, CD27-positive, CD34-negative, CD38-positive, CD40-positive, CD43-positive, CD45-positive, CD48-positive, CD53-low, CD80-negative, CD81-positive, CD86-positive, CD95-positive, CD196-negative, CD229-positive, CD270-positive, CD352-positive, CD361-positive, and IgD-negative. Transcription factors: BLIMP1-positive, IRF4-positive, PAX5-negative, SpiB-negative, Ets1-negative, and XBP1-positive. plasma cell true A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin. GOC:add GOC:dsd GO_REF:0000031 ISBN:0721601464 ISBN:0781735149 PMID:19447676 PMID:20081059 PMID:20839338 PMID:20951740 http://en.wikipedia.org/wiki/Plasma_cell A memory B cell is a mature B cell that is long-lived, readily activated upon re-encounter of its antigenic determinant, and has been selected for expression of higher affinity immunoglobulin. This cell type has the phenotype CD19-positive, CD20-positive, MHC Class II-positive, and CD138-negative. memory B lymphocyte memory B-cell memory B-lymphocyte cell Memory B-cells are also reportedly CD5-negative, CD10-negative, CD21-positive, CD22-positive, CD23-negative, CD24-positive, CD25-positive, CD27-positive, CD34-negative, CD38-negative, CD40-positive, CD43-negative, CD44-positive, CD45-positive, CD53-positive, CD80-negative, CD81-negative, CD86-positive, and CD196/CCR6-positive. memory B cell true A memory B cell is a mature B cell that is long-lived, readily activated upon re-encounter of its antigenic determinant, and has been selected for expression of higher affinity immunoglobulin. This cell type has the phenotype CD19-positive, CD20-positive, MHC Class II-positive, and CD138-negative. GOC:add GOC:dsd GOC:rhs GO_REF:0000031 ISBN:0781735149 PMID:20081059 PMID:20839338 http://en.wikipedia.org/wiki/Memory_B_cell A naive B cell is a mature B cell that has the phenotype surface IgD-positive, surface IgM-positive, CD20-positive, CD27-negative and that has not yet been activated by antigen in the periphery. naive B lymphocyte naive B-cell naive B-lymphocyte cell This cell type is compatible with the HIPC Lyoplate markers for 'naive B cell'. Per DSD: Naive B cells are also reportedly CD10-negative, CD19-positive, CD20-positive, CD21-positive, CD22-positive, CD25-negative, CD27-negative, CD34-negative, CD40-positive, CD43-negative, CD45-positive, CD48-positive, CD53-positive, CD80-negative, CD81-positive, CD84-positive, CD86-negative, CD95-negative, CD138-negative, CD150-positive, CD184/CXCR4-positive, CD185/CXCR5-positive, CD196/CCR6-positive, CD200-positive, CD229-positive, CD243-positive, CD289-positive, CD290-positive, CD352-positive, MHCII/HLA-DR-positive, cadherin 9-positive, and sIgH-positive, Transcription factors: Pax5-positive, ETS1-positive, FOXO1A-positive, KLF4-positive, KLF9-positive, MiTF-positive, OBF1-positive, PLZF-positive, and SpiB-positive. naive B cell true A naive B cell is a mature B cell that has the phenotype surface IgD-positive, surface IgM-positive, CD20-positive, CD27-negative and that has not yet been activated by antigen in the periphery. GOC:add GOC:dsd GOC:rhs GO_REF:0000031 ISBN:0781765196 PMID:19447676 PMID:20081059 PMID:20839338 PMID:20933013 PMID:22343568 A T cell that expresses an alpha-beta T cell receptor complex. alpha-beta T lymphocyte alpha-beta T-cell alpha-beta T-lymphocyte cell alpha-beta T cell true A T cell that expresses an alpha-beta T cell receptor complex. GOC:add GOC:tfm ISBN:0781735149 An alpha-beta T cell that has an immature phenotype and has not completed T cell selection. immature alpha-beta T lymphocyte immature alpha-beta T-cell immature alpha-beta T-lymphocyte cell immature alpha-beta T cell true An alpha-beta T cell that has an immature phenotype and has not completed T cell selection. GOC:add GOC:tfm ISBN:0781735149 A alpha-beta T cell that has a mature phenotype. mature alpha-beta T lymphocyte mature alpha-beta T-cell mature alpha-beta T-lymphocyte cell mature alpha-beta T cell true A alpha-beta T cell that has a mature phenotype. GOC:add GOC:tfm ISBN:0781735149 A CD4-positive, CD25-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release. Treg suppressor T cell suppressor T lymphocyte suppressor T-cell suppressor T-lymphocyte CD4-positive, CD25-positive, alpha-beta regulatory T lymphocyte CD4-positive, CD25-positive, alpha-beta regulatory T-cell CD4-positive, CD25-positive, alpha-beta regulatory T-lymphocyte cell This cell type is compatible with the HIPC Lyoplate markers for 'Treg'. The inclusion of CD127lo in the logical definition is compatible with both human and mouse T cells of this subtype. CD4-positive, CD25-positive, alpha-beta regulatory T cell true A CD4-positive, CD25-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release. GOC:add GOC:tfm ISBN:0781735149 PMID:19464985 PMID:22343568 Treg PMID:22343568 A CD4-positive, alpha-beta T cell that is found in the columnar epithelium of the gastrointestinal tract. IEL intraepithelial lymphocyte CD4-positive, alpha-beta intraepithelial T lymphocyte CD4-positive, alpha-beta intraepithelial T-cell CD4-positive, alpha-beta intraepithelial T-lymphocyte cell CD4-positive, alpha-beta intraepithelial T cell true A CD4-positive, alpha-beta T cell that is found in the columnar epithelium of the gastrointestinal tract. GOC:add GOC:tfm ISBN:0781735149 A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive. cytotoxic T cell cytotoxic T lymphocyte cytotoxic T-cell cytotoxic T-lymphocyte killer T cell killer T lymphocyte killer T-cell killer T-lymphocyte CALOHA:TS-0190 FMA:70573 CD8-positive, alpha-beta cytotoxic T lymphocyte CD8-positive, alpha-beta cytotoxic T-cell CD8-positive, alpha-beta cytotoxic T-lymphocyte cell Note that while T cells of this subset are loosely referred to 'cytotoxic T cells,' as many other T cell types, including CD4-positive, alpha-beta T cells and gamma-delta T cells exhibit cytotoxicity in vitro and in vivo. CD8-positive, alpha-beta cytotoxic T cell true A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive. GOC:add GOC:pam GOC:tfm GO_REF:0000031 ISBN:0781735149 A CD8-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release. suppressor T cell suppressor T lymphocyte suppressor T-cell suppressor T-lymphocyte CD8+ T(reg) CD8+ Treg CD8+ regulatory T cell CD8-positive T(reg) CD8-positive Treg CD8-positive, alpha-beta Treg CD8-positive, alpha-beta regulatory T lymphocyte CD8-positive, alpha-beta regulatory T-cell CD8-positive, alpha-beta regulatory T-lymphocyte cell CD8-positive, alpha-beta regulatory T cell true A CD8-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release. GOC:add GOC:tfm ISBN:0781735149 A alpha-beta intraepithelial T cell found in the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements. IEL intraepithelial lymphocyte CD8-positive, alpha-beta intraepithelial T lymphocyte CD8-positive, alpha-beta intraepithelial T-cell CD8-positive, alpha-beta intraepithelial T-lymphocyte cell CD8-alpha-beta-positive, alpha-beta intraepithelial T cell true A alpha-beta intraepithelial T cell found in the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements. GOC:add ISBN:0781735149 A mature alpha-beta T cell of the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements. IEL intraepithelial lymphocyte alpha-beta intraepithelial T lymphocyte alpha-beta intraepithelial T-cell alpha-beta intraepithelial T-lymphocyte cell alpha-beta intraepithelial T cell true A mature alpha-beta T cell of the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements. GOC:add GOC:tfm ISBN:0781735149 A T cell that expresses a gamma-delta T cell receptor complex. gamma-delta T lymphocyte gamma-delta T-cell gamma-delta T-lymphocyte gammadelta T cell cell gd T cell Note that gamma-delta T cells have both thymic and extrathymic differentiation pathways. gamma-delta T cell true A T cell that expresses a gamma-delta T cell receptor complex. GOC:add GOC:tfm ISBN:0781735149 A gamma-delta T cell that has an immature phenotype. immature gamma-delta T lymphocyte immature gamma-delta T-cell immature gamma-delta T-lymphocyte cell Note that gamma-delta T cells have both thymic and extrathymic differentiation pathways. immature gamma-delta T cell true A gamma-delta T cell that has an immature phenotype. GOC:add ISBN:0781735149 A gamma-delta T cell that has a mature phenotype. These cells can be found in tissues and circulation where they express unique TCR repertoire depending on their location. mature gamma-delta T lymphocyte mature gamma-delta T-cell mature gamma-delta T-lymphocyte cell mature gamma-delta T cell true A gamma-delta T cell that has a mature phenotype. These cells can be found in tissues and circulation where they express unique TCR repertoire depending on their location. GOC:add GOC:tfm ISBN:0781735149 A mature gamma-delta T cell that is found in the columnar epithelium of the gastrointestinal tract. These cells participate in mucosal immune responses. IEL intraepithelial lymphocyte gamma-delta intraepithelial T lymphocyte gamma-delta intraepithelial T-cell gamma-delta intraepithelial T-lymphocyte cell gamma-delta intraepithelial T cell true A mature gamma-delta T cell that is found in the columnar epithelium of the gastrointestinal tract. These cells participate in mucosal immune responses. GOC:add GOC:tfm ISBN:0781735149 A gamma-delta intraepithelial T cell that has the phenotype CD8-alpha alpha-positive. IEL intraepithelial lymphocyte CD8-positive, gamma-delta intraepithelial T lymphocyte CD8-positive, gamma-delta intraepithelial T-cell CD8-positive, gamma-delta intraepithelial T-lymphocyte cell CD8-alpha alpha positive, gamma-delta intraepithelial T cell true A gamma-delta intraepithelial T cell that has the phenotype CD8-alpha alpha-positive. GOC:add GOC:tfm ISBN:0781735149 A gamma-delta intraepithelial T cell that has the phenotype CD4-negative and CD8-negative. IEL intraepithelial lymphocyte CD4-positive, gamma-delta intraepithelial T lymphocyte CD4-positive, gamma-delta intraepithelial T-cell CD4-positive, gamma-delta intraepithelial T-lymphocyte cell CD4-negative CD8-negative gamma-delta intraepithelial T cell true A gamma-delta intraepithelial T cell that has the phenotype CD4-negative and CD8-negative. GOC:add GOC:tfm ISBN:0781735149 A thymocyte that has the phenotype CD4-negative, CD8-positive, CD44-negative, CD25-negative, and pre-TCR-positive. ISP T.ISP.th immature single positive T cell immature single positive T lymphocyte immature single positive T-lymphocyte cell Note that this type of thymocyte has passed the beta-selection checkpoint and is rapidly proliferating and rearranging the T cell receptor alpha chain and expressing the CD8 coreceptor. This stage comes between the DN4 and DP stages. immature single positive thymocyte true A thymocyte that has the phenotype CD4-negative, CD8-positive, CD44-negative, CD25-negative, and pre-TCR-positive. GOC:add GOC:tfm GO_REF:0000031 ISBN:0781735149 http://www.immgen.org/index_content.html A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-positive. DN2 alpha-beta immature T lymphocyte DN2 alpha-beta immature T-cell DN2 alpha-beta immature T-lymphocyte DN2 cell DN2 immature T cell TN2 cell TN2 thymocyte double negative 2 preT.DN2.Th cell Note that this type of thymocyte is at the earliest stage of T cell receptor rearrangement of the beta, gamma, and delta T cell receptor chains. DN2 thymocyte A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-positive. GOC:add GOC:tfm GO_REF:0000031 ISBN:0781735149 A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, and CD25-positive and expressing the T cell receptor beta-chain in complex with the pre-T cell receptor alpha chain. early cortical thymocyte DN3 alpha-beta immature T lymphocyte DN3 alpha-beta immature T-cell DN3 alpha-beta immature T-lymphocyte DN3 cell DN3 immature T cell TN3 cell TN3 thymocyte double negative 3 preT.DN3.Th cell DN3 thymocyte A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, and CD25-positive and expressing the T cell receptor beta-chain in complex with the pre-T cell receptor alpha chain. GOC:add GOC:tfm GO_REF:0000031 ISBN:0781735149 A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, CD25-negative, and pre-TCR-positive. early cortical thymocyte DN4 alpha-beta immature T lymphocyte DN4 alpha-beta immature T-lymphocyte DN4 cell DN4 immature T cell DN4 immature T-cell T.DN4.th double negative 4 cell Note that this type of thymocyte has passed the beta-selection checkpoint and is rapidly proliferating and beginning to rearrange the T cell receptor alpha chain. DN4 thymocyte A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, CD25-negative, and pre-TCR-positive. GOC:add GOC:tfm GO_REF:0000031 ISBN:0781735149 A thymocyte expressing the alpha-beta T cell receptor complex as well as both the CD4 and CD8 coreceptors. late cortical thymocyte DP cell DP thymocyte double-positive, alpha-beta immature T lymphocyte cell Thymocytes of this stage are undergoing positive and negative selection. double-positive, alpha-beta thymocyte true A thymocyte expressing the alpha-beta T cell receptor complex as well as both the CD4 and CD8 coreceptors. GOC:add GOC:tfm GO_REF:0000031 ISBN:0781735149 An immature alpha-beta T cell that is located in the thymus and is CD4-positive and CD8-negative. CD4-positive, alpha-beta immature T lymphocyte CD4-positive, alpha-beta immature T-cell CD4-positive, alpha-beta immature T-lymphocyte SP CD4 cell cell CD4-positive, alpha-beta thymocyte true An immature alpha-beta T cell that is located in the thymus and is CD4-positive and CD8-negative. GOC:add GOC:tfm GO_REF:0000031 ISBN:0781735149 An immature alpha-beta T cell that is located in the thymus and is CD8-positive and CD4-negative. CD8-positive, alpha-beta immature T lymphocyte CD8-positive, alpha-beta immature T-cell CD8-positive, alpha-beta immature T-lymphocyte SP CD8 cell cell CD8-positive, alpha-beta immature T cell CD8-positive, alpha-beta thymocyte true An immature alpha-beta T cell that is located in the thymus and is CD8-positive and CD4-negative. GOC:add GOC:tfm GO_REF:0000031 ISBN:0781735149 A long-lived, antigen-experienced T cell that has acquired a memory phenotype including distinct surface markers and the ability to differentiate into an effector T cell upon antigen reexposure. BTO:0003435 memory T lymphocyte memory T-cell memory T-lymphocyte cell memory T cell true A long-lived, antigen-experienced T cell that has acquired a memory phenotype including distinct surface markers and the ability to differentiate into an effector T cell upon antigen reexposure. GOC:add GOC:pam GOC:tfm GO_REF:0000031 ISBN:0781735149 A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response. mature NK T lymphocyte mature NK T-cell mature NK T-lymphocyte mature NKT cell mature natural killer T cell mature natural killer T lymphocyte mature natural killer T-cell mature natural killer T-lymphocyte cell mature NK T cell true A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response. GOC:add ISBN:0781735149 A T cell which regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release. suppressor T cell suppressor T lymphocyte suppressor T-cell suppressor T-lymphocyte BTO:0004520 FMA:84070 Treg regulatory T lymphocyte regulatory T-cell regulatory T-lymphocyte cell This cell type may express FoxP3 and CD25 and secretes IL-10 and TGF-beta. regulatory T cell true A T cell which regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release. GOC:add GO_REF:0000031 An immature B cell is a B cell that has the phenotype surface IgM-positive and surface IgD-negative, and have not undergone class immunoglobulin class switching or peripheral encounter with antigen and activation. immature B lymphocyte immature B-cell immature B-lymphocyte newly formed B cell cell Immature B cells are also reportedly CD5-positive, CD10-positive, CD19-positive, CD20-positive, CD21-positive, CD22-positive, CD24-positive, CD25-negative, CD27-negative, CD34-negative, CD38-positive, CD40-positive, CD43-negative, CD45-positive, CD48-positive, CD53-positive, CD79a-positive, CD80-negative, CD81-positive, CD86-negative, CD95-negative, CD127-negative, CD138-negative, CD185-positive, CD196-positive, MHCII/HLA-DR-positive, RAG-positive, TdT-negative, Vpre-B-negative, and preBCR-negative. Transcription factors expressed: Pax5-positive. immature B cell An immature B cell is a B cell that has the phenotype surface IgM-positive and surface IgD-negative, and have not undergone class immunoglobulin class switching or peripheral encounter with antigen and activation. GOC:add GOC:dsd GOC:rhs GOC:tfm GO_REF:0000031 ISBN:0781735149 PMID:20081059 PMID:20839338 newly formed B cell ISBN:781735149 A precursor B cell is a B cell with the phenotype CD10-positive. BTO:0001133 CALOHA:TS-0819 cell pre-B cell precursor B cell true A precursor B cell is a B cell with the phenotype CD10-positive. GOC:rhs GOC:tfm GO_REF:0000031 An immature B cell of an intermediate stage between the pre-B cell stage and the mature naive stage with the phenotype surface IgM-positive and CD19-positive, and are subject to the process of B cell selection. A transitional B cell migrates from the bone marrow into the peripheral circulation, and then to the spleen. transitional B cell transitional stage B lymphocyte transitional stage B-cell transitional stage B-lymphocyte T1 B cell T2 B cell T3 B cell cell This cell type is compatible with the HIPC Lyoplate markers for 'transitional B cell'. transitional stage B cell true An immature B cell of an intermediate stage between the pre-B cell stage and the mature naive stage with the phenotype surface IgM-positive and CD19-positive, and are subject to the process of B cell selection. A transitional B cell migrates from the bone marrow into the peripheral circulation, and then to the spleen. GOC:add GO_REF:0000031 ISBN:0781735149 PMID:12810111 PMID:22343568 transitional B cell PMID:22343568 A B cell of distinct lineage and surface marker expression. B-1 B cells are thought to be the primary source of natural IgM immunoglobulin, that is, IgM produced in large quantities without prior antigenic stimulation and generally reactive against various microorganisms, as well as the source of T-independent IgA immunoglobulin in the mucosal areas. These cells are CD43-positive. B-1 B lymphocyte B-1 B-cell B-1 B-lymphocyte B-1 cell B1 B cell B1 B lymphocyte B1 B-cell B1 B-lymphocyte B1 cell cell There are small numbers of B-1 cells found in the lymph nodes and spleen, while larger numbers can be found in the peritoneal and pleural cavities. B-1 B cells are reportedly CD11b-positive, CD20-positive, CD21-positive, CD27-positive, CD44-positive, CD45RB-positive, CD48-positive, CD70-negative, CD150-positive, CD244-negative, CD352-positive, sIgM-positive, and sIgD-low. B-1 B cell true A B cell of distinct lineage and surface marker expression. B-1 B cells are thought to be the primary source of natural IgM immunoglobulin, that is, IgM produced in large quantities without prior antigenic stimulation and generally reactive against various microorganisms, as well as the source of T-independent IgA immunoglobulin in the mucosal areas. These cells are CD43-positive. GOC:add GOC:dsd GO_REF:0000031 PMID:11861604 PMID:20933013 PMID:21220451 http://en.wikipedia.org/wiki/B-1_cell A B-1 B cell that has the phenotype CD5-positive. B-1a B lymphocyte B-1a B-cell B-1a B-lymphocyte B1a B cell B1a B lymphocyte B1a B-cell B1a B-lymphocyte B1a cell CD5(+) B1 cell CD5+ B1 cell CD5-positive B1 cell cell B-1a B cell true A B-1 B cell that has the phenotype CD5-positive. GOC:add PMID:11861604 A B-1 B cell that has the phenotype CD5-negative, but having other phenotypic attributes of a B-1 B cell. B-1b B lymphocyte B-1b B-cell B-1b B-lymphocyte B1b B cell B1b B lymphocyte B1b B-cell B1b B-lymphocyte B1b cell cell B-1b B cell true A B-1 B cell that has the phenotype CD5-negative, but having other phenotypic attributes of a B-1 B cell. GOC:add PMID:11861604 A conventional B cell subject to antigenic stimulation and dependent on T cell help and with a distinct surface marker expression pattern from B-1 B cells. These cells are CD43-negative. B-2 B lymphocyte B-2 B-cell B-2 B-lymphocyte B2 B cell B2 B lymphocyte B2 B-cell B2 B-lymphocyte B2 cell cell B-0 B cell B-2 B cells are reportedly CD48-positive, CD244-negative, and CD352-positive. B-2 B cell true A conventional B cell subject to antigenic stimulation and dependent on T cell help and with a distinct surface marker expression pattern from B-1 B cells. These cells are CD43-negative. GOC:add GOC:dsd GOC:tfm ISBN:0781735149 PMID:11861604 PMID:20933013 A natural killer cell that is developmentally immature and expresses natural killer cell receptors (NKR). immature NK cell cell p-NK In mouse the NKR are Ly49 molecules and in human these cells express KIR molecules. immature natural killer cell A natural killer cell that is developmentally immature and expresses natural killer cell receptors (NKR). GOC:add GO_REF:0000031 ISBN:0781735149 PMID:12457618 p-NK PMID:12457618 A natural killer cell that is developmentally mature and expresses a variety of inhibitory and activating receptors that recognize MHC class I and other stress related molecules. LAK cell lymphokine activated killer cell mature NK cell cell mature natural killer cell A natural killer cell that is developmentally mature and expresses a variety of inhibitory and activating receptors that recognize MHC class I and other stress related molecules. GOC:add GO_REF:0000031 ISBN:0781735149 PMID:14685782 LAK cell PMID:14685782 lymphokine activated killer cell PMID:14685782 A lymphoid progenitor cell that is committed to the natural killer cell lineage, expressing CD122 (IL-15) receptor, but lacking many of the phenotypic characteristics of later stages of natural killer cell development such as expression of NK activating and inhibitory molecules. In human this cell has the phenotype CD34-positive, CD45RA-positive, CD10-positive, CD117-negative, and CD161 negative. NKP natural killer cell progenitor pro-natural killer cell cell null cell preNK cell Most markers only described for human pro NK cells. pro-NK cell true A lymphoid progenitor cell that is committed to the natural killer cell lineage, expressing CD122 (IL-15) receptor, but lacking many of the phenotypic characteristics of later stages of natural killer cell development such as expression of NK activating and inhibitory molecules. In human this cell has the phenotype CD34-positive, CD45RA-positive, CD10-positive, CD117-negative, and CD161 negative. GOC:add GOC:pam GO_REF:0000031 PMID:11532393 PMID:12457618 PMID:15032583 PMID:15766674 NKP PMID:12457618 PMID:15032583 PMID:15766674 null cell PMID:11532393 preNK cell PMID:11532393 A progenitor cell of the B cell lineage, with some lineage specific activity such as early stages of recombination of B cell receptor genes, but not yet fully committed to the B cell lineage until the expression of PAX5 occurs. pre-pro B cell BTO:0003104 pro-B lymphocyte pro-B-cell pro-B-lymphocyte progenitor B cell progenitor B lymphocyte progenitor B-cell progenitor B-lymphocyte cell pre-B cell (Philadelphia nomenclature) Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative. pro-B cell true A progenitor cell of the B cell lineage, with some lineage specific activity such as early stages of recombination of B cell receptor genes, but not yet fully committed to the B cell lineage until the expression of PAX5 occurs. GOC:add GOC:dsd ISBN:0781735149 PMID:12633665 PMID:16551251 PMID:18432934 pre-pro B cell PMID:17582343 pre-B cell (Philadelphia nomenclature) PMID:11244048 A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage. pro-T lymphocyte progenitor T cell DN1 cell DN1 thymocyte TN1 cell cell pro-T cell true A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage. GOC:add ISBN:0781735149 A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates. cell Note that this is a non-mammalian cell type. thromboblast true A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates. GOC:add GOC:tfm PMID:7758949 A myeloblast committed to the basophil lineage. cell basophilic myeloblast true A myeloblast committed to the basophil lineage. GOC:add ISBN:0721601464 A promyelocyte committed to the basophil lineage. FMA:84208 cell basophilic promyelocyte true A promyelocyte committed to the basophil lineage. GOC:add ISBN:0721601464 A progenitor cell of the mast cell lineage. Markers for this cell are FceRIa-low, CD117-positive, CD9-positive, T1/ST2-positive, SCA1-negative, and lineage-negative. MCP cell CFU-MC CFU-Mast colony forming unit mast cell MCP are CD16-positive, CD32-positive, CD34-positive, CD45-positive, integrin beta-7-positive, and lin-negative (CD2, CD3e, CD4, CD5, CD8a, CD14, CD19, CD20, CD27, integrin alpha-M, ly6c, ly6g, NCAM-1, and ter119). These cells also express the transcription factors GATA-1, GATA-2, and MITF, but not C/EBPa. mast cell progenitor true A progenitor cell of the mast cell lineage. Markers for this cell are FceRIa-low, CD117-positive, CD9-positive, T1/ST2-positive, SCA1-negative, and lineage-negative. GOC:add GOC:dsd PMCID:PMC1183570 PMCID:PMC1312421 PMID:8629001 PMID:9354811 http://www.copewithcytokines.de A myeloblast committed to the eosinophil lineage. cell eosinophilic myeloblast true A myeloblast committed to the eosinophil lineage. GOC:add ISBN:0721601464 A promyelocyte committed to the eosinophil lineage. FMA:84199 cell eosinophilic promyelocyte true A promyelocyte committed to the eosinophil lineage. GOC:add ISBN:0721601464 A progenitor cell of the neutrophil lineage. cell neutrophil stem cell neutrophil progenitor cell true A progenitor cell of the neutrophil lineage. GOC:add GOC:tfm ISBN:0721601464 The most primitive precursor in the granulocytic series, having fine, evenly distributed chromatin, several nucleoli, a high nuclear-to-cytoplasmic ration (5:1-7:1), and a nongranular basophilic cytoplasm. They reside in the bone marrow. BTO:0000187 FMA:83524 cell myeloblast true The most primitive precursor in the granulocytic series, having fine, evenly distributed chromatin, several nucleoli, a high nuclear-to-cytoplasmic ration (5:1-7:1), and a nongranular basophilic cytoplasm. They reside in the bone marrow. GOC:add ISBN:0721601464 http://en.wikipedia.org/wiki/Myeloblast http://www.cap.org A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative. CALOHA:TS-0825 FMA:83530 cell promyelocyte A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative. GOC:add GOC:amm GOC:tfm ISBN:0721601464 http://www.cap.org A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans. BTO:0000725 CALOHA:TS-0448 MPP hemopoietic progenitor cell cell Markers differ between mouse and human. hematopoietic multipotent progenitor cell A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans. GOC:add GOC:tfm PMID:19022770 A progenitor cell restricted to the lymphoid lineage. lymphoid progenitor cell BTO:0004731 CALOHA:TS-2025 FMA:70338 cell Note that this is a class of cell types, not an identified single cell type. lymphoid lineage restricted progenitor cell true A progenitor cell restricted to the lymphoid lineage. GOC:add GOC:tfm A progenitor cell restricted to the myeloid lineage. myeloid progenitor cell BTO:0004730 CALOHA:TS-2099 FMA:70339 cell Note that this is a class of cell types, not an identified single cell type. myeloid lineage restricted progenitor cell true A progenitor cell restricted to the myeloid lineage. GOC:add GOC:tfm PMID:19022770 An immature cell of the conventional dendritic cell lineage, characterized by high levels of antigen uptake via endocytosis, macropinocytosis, and phagocytosis, and typically found resident in the tissues. Markers for this cell are CD80-low, CD86-low, and MHC-II-low. immature myeloid dendritic cell cell immature conventional dendritic cell true An immature cell of the conventional dendritic cell lineage, characterized by high levels of antigen uptake via endocytosis, macropinocytosis, and phagocytosis, and typically found resident in the tissues. Markers for this cell are CD80-low, CD86-low, and MHC-II-low. GOC:add GOC:tfm PMID:9521319 A mature cell of the conventional dendritic cell lineage, characterized by a high capacity for antigen presentation and typically found in a lymph node. mature dendritic cell FMA:83038 mature myeloid dendritic cell cell mature conventional dendritic cell true A mature cell of the conventional dendritic cell lineage, characterized by a high capacity for antigen presentation and typically found in a lymph node. GOC:add GOC:tfm PMID:9521319 mature dendritic cell GOC:add A leukocyte with a single non-segmented nucleus in the mature form. BTO:0000878 CALOHA:TS-0768 FMA:86713 mononuclear leukocyte peripheral blood mononuclear cell cell mononuclear cell true A leukocyte with a single non-segmented nucleus in the mature form. GOC:add A resting mature B cell that has the phenotype IgM-positive, IgD-positive, CD23-positive and CD21-positive, and found in the B cell follicles of the white pulp of the spleen or the corticol areas of the peripheral lymph nodes. This cell type is also described as being CD19-positive, B220-positive, AA4-negative, CD43-negative, and CD5-negative. Fo B cell Fo B-cell follicular B lymphocyte follicular B-cell follicular B-lymphocyte cell Follicular B cells are also reportedly CD48-positive, CD84-positive, CD229-positive, and CD352-positive. follicular B cell A resting mature B cell that has the phenotype IgM-positive, IgD-positive, CD23-positive and CD21-positive, and found in the B cell follicles of the white pulp of the spleen or the corticol areas of the peripheral lymph nodes. This cell type is also described as being CD19-positive, B220-positive, AA4-negative, CD43-negative, and CD5-negative. GOC:add GOC:dsd ISBN:0781735149 PMCID:PMC2193793 PMID:20933013 http://en.wikipedia.org/wiki/Follicular_B_Cells A rapidly cycling mature B cell that has distinct phenotypic characteristics and is involved in T-dependent immune responses and located typically in the germinal centers of lymph nodes. This cell type expresses Ly77 after activation. GC B cell GC B lymphocyte GC B-cell GC B-lymphocyte germinal center B lymphocyte germinal center B-cell germinal center B-lymphocyte cell Germinal center B cells are also reportedly CD10-positive, CD19-positive, CD20-positive, CD38-positive, CD44-low, CD45-positive, CD48-positive, CD95-positive, CD352-positive, and HLA-DR-positive. Transcription factors: BCL6-positive, Ets1-positive, IRF8-positive, MTA3-positive, OBF1-positive, PAX5-positive, SpiB-positive, and STAT3-positive. germinal center B cell true A rapidly cycling mature B cell that has distinct phenotypic characteristics and is involved in T-dependent immune responses and located typically in the germinal centers of lymph nodes. This cell type expresses Ly77 after activation. GOC:add GOC:dsd GOC:tfm ISBN:0781735149 PMID:19447676 PMID:20933013 A mature B cell that is located in the marginal zone of the spleen with the phenotype CD23-negative and CD21-positive and expressing a B cell receptor usually reactive to bacterial cell wall components or senescent self components such as oxidized-LDL. This cell type is also described as being CD19-positive, B220-positive, IgM-high, AA4-negative, CD35-high. MZ B cell MZ B lymphocyte MZ B-cell MZ B-lymphocyte marginal zone B lymphocyte marginal zone B-cell marginal zone B-lymphocyte cell MZ B cells are reportedly CD1-positive (mice), CD20-positive, CD48-positive, CD84-positive, CD150-positive, CD229-positive, and CD352-positive. marginal zone B cell true A mature B cell that is located in the marginal zone of the spleen with the phenotype CD23-negative and CD21-positive and expressing a B cell receptor usually reactive to bacterial cell wall components or senescent self components such as oxidized-LDL. This cell type is also described as being CD19-positive, B220-positive, IgM-high, AA4-negative, CD35-high. GOC:add GOC:dsd ISBN:0781735149 PMID:10933592 PMID:20933013 http://en.wikipedia.org/wiki/Marginal-zone_B_cell An epithelial cell of the vestibular sensory organ that is characterized by intense enzymatic activities and numerous basal membrane infoldings. cell vestibular dark cell An epithelial cell of the vestibular sensory organ that is characterized by intense enzymatic activities and numerous basal membrane infoldings. PMID:11223304 An olfactory receptor cell in which the apical ending of the dendrite is a pronounced ciliated olfactory knob. ciliated olfactory sensory neuron ciliated sensory neuron cell ciliated olfactory receptor neuron An olfactory receptor cell in which the apical ending of the dendrite is a pronounced ciliated olfactory knob. PMID:16841163 An olfactory receptor cell in which the apical ending of the dendrite is a knob that bears numerous microvilli. microvillous olfactory sensory neuron cell microvillous sensory neuron microvillous olfactory receptor neuron An olfactory receptor cell in which the apical ending of the dendrite is a knob that bears numerous microvilli. PMID:16841163 An olfactory receptor cell with short cilia growing in an invagination bordered by microvilli. crypt cell crypt olfactory sensory neuron crypt sensory neuron cell crypt olfactory receptor neuron An olfactory receptor cell with short cilia growing in an invagination bordered by microvilli. PMID:16841163 A neuron that releases serotonin as a neurotransmitter. CL:0000403 FBbt:00005133 WBbt:0006837 5-HT neuron 5-hydroxytryptamine neuron cell serotinergic neuron serotonergic neuron A neuron that releases serotonin as a neurotransmitter. SANBI:mhl Neuromast mantle cell is a non-sensory cell. Neuromast mantle cells surround the neuromast support cells and neuromast hair cells, separating the neuromast from the epidermis, and secrete cupula in which the ciliary bundles of all the hair cells are embedded. cell neuromast mantle cell Neuromast mantle cell is a non-sensory cell. Neuromast mantle cells surround the neuromast support cells and neuromast hair cells, separating the neuromast from the epidermis, and secrete cupula in which the ciliary bundles of all the hair cells are embedded. ISBN:0125296509 Neuromast support cell is a non-sensory cell of the neuromast that extend between the sensory hair cells from the basement membrane to the apical surface; neuromast support cells are surrounded by neuromast mantle cells. cell neuromast support cell Neuromast support cell is a non-sensory cell of the neuromast that extend between the sensory hair cells from the basement membrane to the apical surface; neuromast support cells are surrounded by neuromast mantle cells. ISBN:0125296509 Olfactory epithelial support cell is a columnar cell that extends from the epithelial free margin to the basement membrane of the olfactory epithelium. This cell type has a large, vertically, elongate, euchromatic nucleus, along with other nuclei, forms a layer superficial to the cell body of the receptor cell; sends long somewhat irregular microvilli into the mucus layer; at the base, with expanded end-feet containing numerous lamellated dense bodies resembling lipofuscin of neurons. FMA:62302 olfactory sustentacular cell supporting cell of olfactory epithelium sustentaculocyte of olfactory epithelium cell olfactory epithelial support cell Olfactory epithelial support cell is a columnar cell that extends from the epithelial free margin to the basement membrane of the olfactory epithelium. This cell type has a large, vertically, elongate, euchromatic nucleus, along with other nuclei, forms a layer superficial to the cell body of the receptor cell; sends long somewhat irregular microvilli into the mucus layer; at the base, with expanded end-feet containing numerous lamellated dense bodies resembling lipofuscin of neurons. GOC:tfm ISBN:0517223651 SANBI:mhl Interneuromast cell is a neuroectodermal cell deposited by the migrating lateral line primordium between the neuromasts. Interneuromast cells proliferate and migrate to form additional neuromasts. cell interneuromast cell Interneuromast cell is a neuroectodermal cell deposited by the migrating lateral line primordium between the neuromasts. Interneuromast cells proliferate and migrate to form additional neuromasts. SANBI:mhl Hair cell is a mechanoreceptor cell that is sensitive to movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system. hair cell BTO:0004744 cell sensory hair cell Hair cell is a mechanoreceptor cell that is sensitive to movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system. SANBI:mhl Neuromast hair cell is a hair cell that acts as a sensory receptor of the neuromast; it is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface. cell neuromast hair cell Neuromast hair cell is a hair cell that acts as a sensory receptor of the neuromast; it is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface. SANBI:mhl A skeletal muscle myoblast that differentiates into slow muscle fibers. cell slow muscle myoblast A skeletal muscle myoblast that differentiates into slow muscle fibers. SANBI:mhl A skeletal muscle myoblast that differentiates into fast muscle fibers. cell fast muscle myoblast A skeletal muscle myoblast that differentiates into fast muscle fibers. SANBI:mhl A monocyte that responds rapidly to microbial stimuli by secreting cytokines and antimicrobial factors and which is characterized by high expression of CCR2 in both rodents and humans, negative for the lineage markers CD3, CD19, and CD20, and of larger size than non-classical monocytes. inflammatory monocyte cell Markers: CCR2+CXCCR1<low> (human, mouse, rat). classical monocyte true A monocyte that responds rapidly to microbial stimuli by secreting cytokines and antimicrobial factors and which is characterized by high expression of CCR2 in both rodents and humans, negative for the lineage markers CD3, CD19, and CD20, and of larger size than non-classical monocytes. GOC:add GO_REF:0000031 PMID:16322748 PMID:18303997 PMID:20628149 PMID:20870168 A macrophage which develops from an inflammatory monocyte and is recruited into the tissues in response to injury and infection as part of an inflammatory response. Markers include CD11b-positive, CD68-positive, and F4/80-positive. FMA:84643 FMA:84645 free macrophage wandering histiocyte cell Markers: CD11b+, CD68+; Mouse: F4/80+; role or process: immune, inflammation (inflammatory response). elicited macrophage true A macrophage which develops from an inflammatory monocyte and is recruited into the tissues in response to injury and infection as part of an inflammatory response. Markers include CD11b-positive, CD68-positive, and F4/80-positive. GOC:add GOC:ana GOC:tfm GO_REF:0000031 PMID:15771589 A macrophage that suppresses immune responses. cell Markers: May express: IL10, TGFbeta. suppressor macrophage true A macrophage that suppresses immune responses. GOC:add GOC:tfm PMID:20402419 An elicited macrophage that is recruited into the tissues in response to injury and infection as part of an inflammatory response, expresses high levels of pro-inflammatory cytokines, ROS and NO, and shows potent microbicidal activity. classically activated macrophage cell M1 macrophage Markers: Express: TNFa, IL1b, IL6, iNOS, NADPH-oxidase; produce: reactive oxygen species, nitric oxide; role or process: immune, inflammation (inflammatory response). inflammatory macrophage true An elicited macrophage that is recruited into the tissues in response to injury and infection as part of an inflammatory response, expresses high levels of pro-inflammatory cytokines, ROS and NO, and shows potent microbicidal activity. GOC:ana GO_REF:0000031 PMID:19132917 A macrophage constitutively resident in a particular tissue under non-inflammatory conditions, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. FMA:84642 FMA:84644 fixed macrophage resting histiocyte cell tissue-resident macrophage true A macrophage constitutively resident in a particular tissue under non-inflammatory conditions, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. GOC:ana GO_REF:0000031 PMID:19770654 A gut-associated lymphoid tissue macrophage found in lamina propria of the gut. gastrointestinal system (lamina propria) macrophage macrophage of gastrointestinal system (lamina propria) macrophage of gastrointestinal tract (lamina propria) cell gastrointestinal tract (lamina propria) macrophage A gut-associated lymphoid tissue macrophage found in lamina propria of the gut. GOC:ana GOC:tfm GO_REF:0000031 https://orcid.org/0000-0002-2825-0621 A tissue-resident macrophage resident found in the thymus, involved in the clearance of apoptotic thymocytes. cell Role or process: immune, clearance of apoptotic thymocytes, antigen-presentation. thymic macrophage true A tissue-resident macrophage resident found in the thymus, involved in the clearance of apoptotic thymocytes. GOC:ana GOC:tfm GO_REF:0000031 PMID:9048205 A tissue-resident macrophage found in a secondary lymphoid organ. cell secondary lymphoid organ macrophage A tissue-resident macrophage found in a secondary lymphoid organ. GOC:ana GOC:tfm GO_REF:0000031 A secondary lymphoid organ macrophage found in a lymph node. This cell is CD169-high. MF.LN cell Marker was observed on rat cells. lymph node macrophage true A secondary lymphoid organ macrophage found in a lymph node. This cell is CD169-high. GOC:ana GOC:tfm GO_REF:0000031 PMID:11971865 A gut-associated lymphoid tissue macrophage found in tonsils. cell tonsillar macrophage A gut-associated lymphoid tissue macrophage found in tonsils. GOC:ana GO_REF:0000031 PMID:16048540 A gut-associated lymphoid tissue macrophage found in the Peyer's patches. cell Peyer's patch macrophage true A gut-associated lymphoid tissue macrophage found in the Peyer's patches. GOC:ana GOC:tfm GO_REF:0000031 A secondary lymphoid organ macrophage found in the spleen. FMA:83026 cell Role or process: immune, clearance of apoptotic and senescent cells. splenic macrophage true A secondary lymphoid organ macrophage found in the spleen. GO_REF:0000031 PMID:15771589 PMID:16322748 A splenic macrophage found in the marginal zone of the spleen, involved in recognition and clearance of particulate material from the splenic circulation. Markers include F4/80-negative, MARCO-positive, SR-A-positive, SIGN-R1-positive, and Dectin2-positive. cell Markers: Mouse: F4/80-, MARCO+, SR-A+, SIGN-R1+, Dectin2+. splenic marginal zone macrophage true A splenic macrophage found in the marginal zone of the spleen, involved in recognition and clearance of particulate material from the splenic circulation. Markers include F4/80-negative, MARCO-positive, SR-A-positive, SIGN-R1-positive, and Dectin2-positive. GOC:ana GO_REF:0000031 PMID:16861066 A splenic macrophage found in the areas surrounding the white pulp of the spleen, adjacent to the marginal sinus. Markers include F4/80-negative, Dectin2-low, sialoadhesin-positive. cell Markers: Mouse: F4/80-, Dectin2-low, sialoadhesin+. splenic metallophillic macrophage true A splenic macrophage found in the areas surrounding the white pulp of the spleen, adjacent to the marginal sinus. Markers include F4/80-negative, Dectin2-low, sialoadhesin-positive. GOC:ana GO_REF:0000031 PMID:20018690 A splenic macrophage found in the red-pulp of the spleen, and involved in immune responses to blood-borne pathogens and in the clearance of senescent erythrocytes. Markers include F4/80-positive, CD68-positive, MR-positive, Dectin2-positive, macrosialin-positive, and sialoadhesin-low. cell Markers: Mouse: F4/80+, CD68+, MR+, Dectin2+, macrosialin+, sialoadhesin-low; role or process: immune, clearance of senescent erythrocytes. splenic red pulp macrophage true A splenic macrophage found in the red-pulp of the spleen, and involved in immune responses to blood-borne pathogens and in the clearance of senescent erythrocytes. Markers include F4/80-positive, CD68-positive, MR-positive, Dectin2-positive, macrosialin-positive, and sialoadhesin-low. GOC:ana GO_REF:0000031 PMID:19644016 A type of monocyte characterized by low expression of CCR2, low responsiveness to monocyte chemoattractant CCL2/MCP1, low phagocytic activity, and decrease size relative to classical monocytes, but increased co-stimulatory activity. May also play a role in tissue repair. patrolling monocyte resident monocyte cell Markers: CCR2-CX3CCR1+ (human, mouse, rat); human: CD16+, CCR5+, CD32/FcgRII-high, MHCII+, CD86+; mouse: CD62L-Ly6C-. non-classical monocyte true A type of monocyte characterized by low expression of CCR2, low responsiveness to monocyte chemoattractant CCL2/MCP1, low phagocytic activity, and decrease size relative to classical monocytes, but increased co-stimulatory activity. May also play a role in tissue repair. GOC:add GO_REF:0000031 PMID:16322748 PMID:18303997 PMID:20628149 PMID:20870168 A splenic macrophage found in the white pulp of the spleen. Markers include F4/80-negative, CD68-positive, and macrosialin-positive. cell Markers: Mouse: F4/80-, CD68+, macrosialin+. splenic white pulp macrophage true A splenic macrophage found in the white pulp of the spleen. Markers include F4/80-negative, CD68-positive, and macrosialin-positive. GOC:ana GO_REF:0000031 PMID:11207597 A splenic white pulp macrophage found in and around the germinal centers of the white pulp of the spleen that participates in phagocytosis of apoptotic B cells from the germinal centers. A marker for a cell of this type is Mertk-positive. cell splenic tingible body macrophage true A splenic white pulp macrophage found in and around the germinal centers of the white pulp of the spleen that participates in phagocytosis of apoptotic B cells from the germinal centers. A marker for a cell of this type is Mertk-positive. GOC:ana GOC:tfm GO_REF:0000031 PMID:19631584 A tissue-resident macrophage found in the central nervous system. CNS macrophage cell central nervous system macrophage true A tissue-resident macrophage found in the central nervous system. GO_REF:0000031 PMID:16322748 A central nervous system macrophage found in the meninges (the three membranes that surround the brain). This macrophage types is highly phagocytic and expresses scavenger receptors. cell meningeal macrophage true A central nervous system macrophage found in the meninges (the three membranes that surround the brain). This macrophage types is highly phagocytic and expresses scavenger receptors. GOC:ana GO_REF:0000031 PMID:11591794 A central nervous system macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This cell expresses scavenger receptors. cell choroid-plexus macrophage true A central nervous system macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This cell expresses scavenger receptors. GOC:ana GO_REF:0000031 PMID:9550136 A central nervous system macrophage found in small blood vessels in the brain. Markers include CD14+CD16+CD163+. cell Markers: Human/monkey, mice: CD163. Human: CD14+CD16+CD163+. perivascular macrophage true A central nervous system macrophage found in small blood vessels in the brain. Markers include CD14+CD16+CD163+. GOC:tfm GO_REF:0000031 PMID:16507898 A thymic macrophage found in the thymic medulla. cell thymic medullary macrophage true A thymic macrophage found in the thymic medulla. GOC:ana GO_REF:0000031 PMID:9048205 A thymic macrophage found in the thymic cortex. cell thymic cortical macrophage true A thymic macrophage found in the thymic cortex. GOC:ana GOC:tfm GO_REF:0000031 PMID:9048205 A tissue-resident macrophage found in the mucosa associated lymphoid tissue. cell mucosa-associated lymphoid tissue macrophage true A tissue-resident macrophage found in the mucosa associated lymphoid tissue. GOC:ana GOC:tfm GO_REF:0000031 PMID:19906191 A mucosa-associated lymphoid tissue macrophage found in the mucosa-associated lymphoid tissues of the gut. cell gut-associated lymphoid tissue macrophage true A mucosa-associated lymphoid tissue macrophage found in the mucosa-associated lymphoid tissues of the gut. GOC:ana GO_REF:0000031 PMID:19906191 A mucosa-associated lymphoid tissue macrophage found in the nasal and bronchial mucosa-associated lymphoid tissues. cell nasal and broncial associated lymphoid tissue macrophage true A mucosa-associated lymphoid tissue macrophage found in the nasal and bronchial mucosa-associated lymphoid tissues. GOC:ana GO_REF:0000031 PMID:16048540 A lymph node macrophage found in the subcapsular sinus of lymph nodes that participates in sensing, clearance, and antigen presentation of lymph-borne particulate antigens. This macrophage is capable of activating invaraint NKT cells and is CD169-positive. cell lymph node subcapsular sinus macrophage true A lymph node macrophage found in the subcapsular sinus of lymph nodes that participates in sensing, clearance, and antigen presentation of lymph-borne particulate antigens. This macrophage is capable of activating invaraint NKT cells and is CD169-positive. GOC:tfm GO_REF:0000031 PMID:14668803 PMID:17934446 PMID:20228797 A lymph node macrophage found in the cortex of lymph nodes, in particular in and around the germinal centers, and that participates in phagocytosis of apoptotic B cells from the germinal centers. cell lymph node tingible body macrophage true A lymph node macrophage found in the cortex of lymph nodes, in particular in and around the germinal centers, and that participates in phagocytosis of apoptotic B cells from the germinal centers. GOC:ana GOC:tfm GO_REF:0000031 PMID:19631584 An immature myeloid leukocyte of heterogeneous phenotype found particularly in cancer and sepsis patients that is capable of suppressing activity of T cells in ex vivo assays. This cell type is CD45-positive, CD11b-positive. cell Markers: Mouse: CD11b+GR1+CD31+; Human: CD34+ CD33+CD15-CD13+. (According to some reports in humans these cells are iNOS+ARG1+IL13+IFNg+); location: In cancerous tissue; in the blood and lymphoid organs in sepsis. myeloid suppressor cell true An immature myeloid leukocyte of heterogeneous phenotype found particularly in cancer and sepsis patients that is capable of suppressing activity of T cells in ex vivo assays. This cell type is CD45-positive, CD11b-positive. GOC:add GOC:ana GO_REF:0000031 PMID:16168663 PMID:17016554 PMID:17016559 An elicited macrophage characterized by low production of pro-inflammatory and Th1 polarizing cytokines and high expression of arginase-1, and associated with tissue remodelling. cell M2 macrophage Role or process: tissue remodeling. alternatively activated macrophage true An elicited macrophage characterized by low production of pro-inflammatory and Th1 polarizing cytokines and high expression of arginase-1, and associated with tissue remodelling. GOC:ana GOC:tfm GO_REF:0000031 PMID:20510870 A type of cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions. BTO:0003872 FMA:83586 cell foam cell A type of cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions. GOC:add A type of foam cell derived from a smooth muscle cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions. cell smooth muscle cell derived foam cell A type of foam cell derived from a smooth muscle cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions. GOC:add An immature T cell located in the thymus. immature T cell immature T lymphocyte immature T-cell immature T-lymphocyte BTO:0001372 CALOHA:TS-1042 FMA:72202 XAO:0003159 thymic lymphocyte cell thymocyte true An immature T cell located in the thymus. GOC:add GOC:tfm GO_REF:0000031 PMID:12415312 A pro-T cell that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-negative. DN1 thymic pro-T lymphocyte DN1 thymic pro-T-cell DN1 thymic pro-T-lymphocyte DN1 thymic progenitor T cell DN1 thymocyte double negative 1 preT.DN1.Th cell DN1 thymic pro-T cell true A pro-T cell that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-negative. GOC:add GOC:tfm GO_REF:0000031 An antigen inexperienced CD4-positive, alpha-beta T cell with the phenotype CCR7-positive, CD127-positive and CD62L-positive. This cell type develops in the thymus. This cell type is also described as being CD25-negative, CD62L-high, and CD44-low. naive CD4+ T cell T.4Nve.Sp Th0 naive thymus-derived CD4-positive, alpha-beta T lymphocyte naive thymus-derived CD4-positive, alpha-beta T-cell naive thymus-derived CD4-positive, alpha-beta T-lymphocyte cell These cells have not been exposed to antigen following thymic T-cell selection; found in blood and secondary lymphoid organs. This cell type is compatible with the HIPC Lyoplate markers for 'naive CD4+ T cell', but includes additional markers known to be expressed on naive CD4+ T cells. naive thymus-derived CD4-positive, alpha-beta T cell true An antigen inexperienced CD4-positive, alpha-beta T cell with the phenotype CCR7-positive, CD127-positive and CD62L-positive. This cell type develops in the thymus. This cell type is also described as being CD25-negative, CD62L-high, and CD44-low. GOC:add GOC:tfm GO_REF:0000031 PMID:19100699 PMID:22343568 http://www.immgen.org/index_content.html naive CD4+ T cell PMID:22343568 Th0 GOC:tfm A recently activated CD4-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive. activated CD4-positive, alpha-beta T lymphocyte activated CD4-positive, alpha-beta T-cell activated CD4-positive, alpha-beta T-lymphocyte cell activated CD4-positive, alpha-beta T cell true A recently activated CD4-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive. GOC:add GOC:pam GO_REF:0000031 A CD4-positive, alpha-beta T cell that has differentiated into a memory T cell. https://orcid.org/0000-0001-9990-8331 CD4-positive, alpha-beta memory T lymphocyte CD4-positive, alpha-beta memory T-cell CD4-positive, alpha-beta memory T-lymphocyte cell T4.Mem.Sp CD4-positive, alpha-beta memory T cell A CD4-positive, alpha-beta T cell that has differentiated into a memory T cell. GOC:add ISBN:0781735149 http://www.immgen.org/index_content.html Mature T cell not yet exposed to antigen with the phenotype CCR7-positive, CD45RA-positive, and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low. naive T lymphocyte naive T-cell naive T-lymphocyte cell naive T cell true Mature T cell not yet exposed to antigen with the phenotype CCR7-positive, CD45RA-positive, and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:19100699 CD4-positive, alpha-beta T cell with the phenotype RORgamma-t-positive, CXCR3-negative, CCR6-positive, and capable of producing IL-17. IL-17-producing CD4+ T helper T helper cells type 17 T(H)-17 cell Th17 CD4+ T cell Th17 T cell Th17 T lymphocyte Th17 T-cell Th17 T-lymphocyte Th17 cell helper T cell type 17 cell This cell type is compatible with the HIPC Lyoplate markers for 'Th17 CD4+ T cell', but its logical definition includes additional known characteristics of T-helper 17 T cells. T-helper 17 cell true CD4-positive, alpha-beta T cell with the phenotype RORgamma-t-positive, CXCR3-negative, CCR6-positive, and capable of producing IL-17. GOC:add GOC:pam GO_REF:0000031 PMID:20303875 PMID:20969597 PMID:22343568 Th17 CD4+ T cell PMID:22343568 A CD8-positive, alpha-beta T cell that has not experienced activation via antigen contact and has the phenotype CD45RA-positive, CCR7-positive and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low. naive CD8+ T cell naive thymus-dervied CD8-positive, alpha-beta T lymphocyte naive thymus-dervied CD8-positive, alpha-beta T-cell naive thymus-dervied CD8-positive, alpha-beta T-lymphocyte T.8Nve.Sp cell This cell traffics in secondary lymphoid organs and blood. This cell type is compatible with the HIPC Lyoplate markers for 'naive CD8+ T cell', but includes additional markers known to be expressed on naive CD8+ T cells. naive thymus-derived CD8-positive, alpha-beta T cell true A CD8-positive, alpha-beta T cell that has not experienced activation via antigen contact and has the phenotype CD45RA-positive, CCR7-positive and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low. GOC:add GOC:tfm GO_REF:0000031 ISBN:0781735149 PMID:22343568 http://www.immgen.org/index_content.html naive CD8+ T cell PMID:22343568 CD4-positive alpha-beta T cell with regulatory function that produces IL-10. T-regulatory T cell type 1 Tr1 T cell Tr1 T lymphocyte Tr1 T-cell Tr1 T-lymphocyte cell These cells are reportedly induced by IL-10 and are capable of producing IFN-gamma, IL-5, IL-10, and TGF-beta.) Tr1 cell CD4-positive alpha-beta T cell with regulatory function that produces IL-10. GOC:add GOC:pam GO_REF:0000031 PMID:16903904 CD4-positive alpha-beta T cell with the phenotype CD25-positive, CTLA-4-positive, and FoxP3-positive with regulatory function. iTreg induced Treg induced regulatory T cell induced regulatory T lymphocyte induced regulatory T-cell induced regulatory T-lymphocyte cell aTreg adaptive Treg induced T-regulatory cell true CD4-positive alpha-beta T cell with the phenotype CD25-positive, CTLA-4-positive, and FoxP3-positive with regulatory function. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:19464985 CD4-positive alpha-beta T cell with the phenotype FoxP3-positive, CD25-positive, CD62L-positive, and CTLA-4 positive with regulatory function. nTreg natural Treg natural regulatory T cell natural regulatory T lymphocyte natural regulatory T-cell natural regulatory T-lymphocyte cell natural T-regulatory cell true CD4-positive alpha-beta T cell with the phenotype FoxP3-positive, CD25-positive, CD62L-positive, and CTLA-4 positive with regulatory function. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:19464985 CD4-positive, alpha-beta memory T cell with the phenotype CCR7-positive, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative. central memory CD4+ T cell central CD4-positive, alpha-beta memory T cell central CD4-positive, alpha-beta memory T lymphocyte central CD4-positive, alpha-beta memory T-cell central CD4-positive, alpha-beta memory T-lymphocyte central memory CD4-positive, alpha-beta T lymphocyte central memory CD4-positive, alpha-beta T-cell central memory CD4-positive, alpha-beta T-lymphocyte cell This cell type is compatible with the HIPC Lyoplate markers for 'central memory CD4+ T cell', but includes additional markers known to be expressed on central memory CD4+ T cells. central memory CD4-positive, alpha-beta T cell true CD4-positive, alpha-beta memory T cell with the phenotype CCR7-positive, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative. GOC:add GOC:pam GO_REF:0000031 PMID:22343568 central memory CD4+ T cell PMID:22343568 CD4-positive, alpha-beta memory T cell with the phenotype CCR7-negative, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative. effector memory CD4+ T cell effector CD4-positive, alpha-beta memory T cell effector CD4-positive, alpha-beta memory T lymphocyte effector CD4-positive, alpha-beta memory T-cell effector CD4-positive, alpha-beta memory T-lymphocyte effector memory CD4-positive, alpha-beta T lymphocyte effector memory CD4-positive, alpha-beta T-cell effector memory CD4-positive, alpha-beta T-lymphocyte cell This cell type is compatible with the HIPC Lyoplate markers for 'effector memory CD4+ T cell', but includes additional markers known to be expressed on effector memory CD4+ T cells. effector memory CD4-positive, alpha-beta T cell true CD4-positive, alpha-beta memory T cell with the phenotype CCR7-negative, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:22343568 effector memory CD4+ T cell PMID:22343568 A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, CD25-positive, and CCR7-negative. activated CD8-positive, alpha-beta T lymphocyte activated CD8-positive, alpha-beta T-cell activated CD8-positive, alpha-beta T-lymphocyte cell activated CD8-positive, alpha-beta T cell true A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, CD25-positive, and CCR7-negative. GOC:add GOC:pam GOC:tfm GO_REF:0000031 CD8-positive, alpha-beta memory T cell with the phenotype CCR7-positive, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative. central memory CD8+ T cell central CD8-positive, alpha-beta memory T cell central CD8-positive, alpha-beta memory T lymphocyte central CD8-positive, alpha-beta memory T-cell central CD8-positive, alpha-beta memory T-lymphocyte central memory CD8-positive, alpha-beta T lymphocyte central memory CD8-positive, alpha-beta T-cell central memory CD8-positive, alpha-beta T-lymphocyte cell This cell type is compatible with the HIPC Lyoplate markers for 'central memory CD8+ T cell', but includes additional markers known to be expressed on central memory CD8+ T cells. central memory CD8-positive, alpha-beta T cell true CD8-positive, alpha-beta memory T cell with the phenotype CCR7-positive, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:20146720 PMID:22343568 central memory CD8+ T cell PMID:22343568 A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive, that secretes cytokines. CD8-positive, alpha-beta cytokine secreting effector T lymphocyte CD8-positive, alpha-beta cytokine secreting effector T-cell CD8-positive, alpha-beta cytokine secreting effector T-lymphocyte cell CD8-positive, alpha-beta cytokine secreting effector T cell true A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive, that secretes cytokines. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:20146720 A CD8-positive, alpha-beta T cell that has differentiated into a memory T cell. https://orcid.org/0000-0001-9990-8331 CD8-positive, alpha-beta memory T lymphocyte CD8-positive, alpha-beta memory T-cell CD8-positive, alpha-beta memory T-lymphocyte cell T.8Mem.Sp CD8-positive, alpha-beta memory T cell A CD8-positive, alpha-beta T cell that has differentiated into a memory T cell. GOC:add PMID:20146720 A mature T cell that differentiated and acquired cytotoxic function with the phenotype perforin-positive and granzyme-B positive. BTO:0000289 CALOHA:TS-0190 FMA:70573 cytotoxic T lymphocyte cytotoxic T-cell cytotoxic T-lymphocyte cell cytotoxic T cell true A mature T cell that differentiated and acquired cytotoxic function with the phenotype perforin-positive and granzyme-B positive. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:18395547 A differentiated T cell with ability to traffic to peripheral tissues and is capable of mounting a specific immune response. effector T lymphocyte effector T-cell effector T-lymphocyte cell effector T cell true A differentiated T cell with ability to traffic to peripheral tissues and is capable of mounting a specific immune response. GOC:PAM-ADD GOC:tfm ISBN:0877799148 PMID:18395547 A effector T cell that provides help in the form of secreted cytokines to other immune cells. BTO:0002417 T-helper cell helper T lymphocyte helper T-cell helper T-lymphocyte cell helper T cell true A effector T cell that provides help in the form of secreted cytokines to other immune cells. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:18395547 CD8-positive, alpha-beta memory T cell with the phenotype CCR7-negative, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative. effector memory CD8+ T cell effector CD8-positive, alpha-beta memory T cell effector CD8-positive, alpha-beta memory T lymphocyte effector CD8-positive, alpha-beta memory T-cell effector CD8-positive, alpha-beta memory T-lymphocyte effector memory CD8-positive, alpha-beta T lymphocyte effector memory CD8-positive, alpha-beta T-cell effector memory CD8-positive, alpha-beta T-lymphocyte cell This cell type is compatible with the HIPC Lyoplate markers for 'effector memory CD8+ T cell', but includes additional markers known to be expressed on effector memory CD8+ T cells. effector memory CD8-positive, alpha-beta T cell true CD8-positive, alpha-beta memory T cell with the phenotype CCR7-negative, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative. GOC:add GOC:pam GO_REF:0000031 PMID:20146720 PMID:22343568 effector memory CD8+ T cell PMID:22343568 An immature alpha-beta T-cell that express Egr2. These cells give rise to T cells expressing NK markers. immature NK T lymphocyte immature NK T-cell immature NK T-lymphocyte immature NKT cell cell immature NK T cell true An immature alpha-beta T-cell that express Egr2. These cells give rise to T cells expressing NK markers. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:17589542 PMID:19169262 An alpha-beta intraepithelial T cell with the phenotype CD8-alpha-alpha-positive located in the columnar epithelium of the gastrointestinal tract. These cells have a memory phenotype of CD2-negative and CD5-negative. CD8-alpha-alpha-positive, alpha-beta intraepithelial T lymphocyte CD8-alpha-alpha-positive, alpha-beta intraepithelial T-cell CD8-alpha-alpha-positive, alpha-beta intraepithelial T-lymphocyte cell CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell true An alpha-beta intraepithelial T cell with the phenotype CD8-alpha-alpha-positive located in the columnar epithelium of the gastrointestinal tract. These cells have a memory phenotype of CD2-negative and CD5-negative. GOC:add GOC:pam GO_REF:0000031 PMID:11685222 A mature gamma-delta T cell located in the epidermis that regulates wound healing. DETC dendritic epidermal T lymphocyte dendritic epidermal T-cell dendritic epidermal T-lymphocyte cell In mice, DETC have an invariant T cell receptor. dendritic epidermal T cell true A mature gamma-delta T cell located in the epidermis that regulates wound healing. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:11976459 A CD8-positive, alpha-beta positive T cell that has the phenotype T-bet-positive, eomesodermin-positive, CXCR3-positive, CCR6-negative, and is capable of producing interferon-gamma. BTO:0004793 BTO:0004888 FMA:84793 CD8-positive Th1 cell T-cytotoxic T cell type 1 Tc1 CD8+ T cell Tc1 T cell Tc1 T lymphocyte Tc1 T-cell Tc1 T-lymphocyte Th1 CD8-positive T cell Th1 non-TFH CD8-positive T cell cell This cell type is compatible with the HIPC Lyoplate markers for 'Tc1 CD8+ T cell', but its logical definition includes additional known characteristics of Tc1 T cells. Tc1 cell true A CD8-positive, alpha-beta positive T cell that has the phenotype T-bet-positive, eomesodermin-positive, CXCR3-positive, CCR6-negative, and is capable of producing interferon-gamma. GOC:add GOC:pam GO_REF:0000031 PMID:22343568 PMID:9914231 Tc1 CD8+ T cell PMID:22343568 A CD8-positive, alpha-beta positive T cell expressing GATA-3 and secreting IL-4. BTO:0004794 FMA:84794 CD8-positive Th2 cell T-cytotoxic T cell type 2 Tc2 T cell Tc2 T lymphocyte Tc2 T-cell Tc2 T-lymphocyte Th2 CD8-positive T cell Th2 non-TFH CD8-positive T cell cell This cell type is compatible with the HIPC Lyoplate markers for 'non-Tc1/Tc17 CD8+ T cell' (see CL:0001052), but includes the additional necessary and sufficient conditions to allow classification as a Tc2 T cell. Tc2 cell true A CD8-positive, alpha-beta positive T cell expressing GATA-3 and secreting IL-4. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:9914231 A CD8-positive alpha beta-positive T cell with the phenotype FoxP3-positive and having suppressor function. CD8+CD25+ T cell CD8+CD25+ T lymphocyte CD8+CD25+ T(reg) CD8+CD25+ T-cell CD8+CD25+ T-lymphocyte CD8+CD25+ Treg CD8-positive, CD25-positive Treg CD8-positive, CD25-positive, alpha-beta regulatory T lymphocyte CD8-positive, CD25-positive, alpha-beta regulatory T-cell CD8-positive, CD25-positive, alpha-beta regulatory T-lymphocyte cell CD8-positive, CD25-positive, alpha-beta regulatory T cell true A CD8-positive alpha beta-positive T cell with the phenotype FoxP3-positive and having suppressor function. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:19118505 CD8-positive, alpha-beta positive regulatory T cell with the phenotype CD28-negative and FoxP3-positive. CD8+CD28- T cell CD8+CD28- T lymphocyte CD8+CD28- T(reg) CD8+CD28- T-cell CD8+CD28- T-lymphocyte CD8+CD28- Treg CD8-positive, CD28-negative T(reg) CD8-positive, CD28-negative Treg CD8-positive, CD28-negative, alpha-beta regulatory T lymphocyte CD8-positive, CD28-negative, alpha-beta regulatory T-cell CD8-positive, CD28-negative, alpha-beta regulatory T-lymphocyte cell CD8-positive, CD28-negative, alpha-beta regulatory T cell true CD8-positive, alpha-beta positive regulatory T cell with the phenotype CD28-negative and FoxP3-positive. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:19118505 An alpha-beta T cell expressing NK cell markers that is CD1d restricted and expresses specific V-alpha chains. NK T cells of this type recognize the glycolipid alpha-galactosylceramide in the context of CD1d. classical NK T cell type I NK T lymphocyte type I NK T-cell type I NK T-lymphocyte type I NKT cell cell invariant NK T cell In mouse the canonical TCR is V-alpha-14, and in humans it is V-alpha 24. type I NK T cell true An alpha-beta T cell expressing NK cell markers that is CD1d restricted and expresses specific V-alpha chains. NK T cells of this type recognize the glycolipid alpha-galactosylceramide in the context of CD1d. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:15039760 An alpha-beta T cell expressing NK call markers that is CD1d restricted and expresses a diverse TCR repertoire. Type II NKT cells do not become activated by alpha-galactosylceramide when presented by CD1d. type II NK T lymphocyte type II NK T-cell type II NK T-lymphocyte type II NKT cell cell type II NK T cell true An alpha-beta T cell expressing NK call markers that is CD1d restricted and expresses a diverse TCR repertoire. Type II NKT cells do not become activated by alpha-galactosylceramide when presented by CD1d. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:15039760 A type I NK T cell that has the phenotype CD4-positive. CD4-positive type I NK T lymphocyte CD4-positive type I NK T-cell CD4-positive type I NK T-lymphocyte CD4-positive type I NKT cell NKT.4+.SP cell CD4-positive type I NK T cell true A type I NK T cell that has the phenotype CD4-positive. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:17303398 A type I NK T cell that has the phenotype CD4-negative and CD8-negative. CD4-negative, CD8-negative type I NK T lymphocyte CD4-negative, CD8-negative type I NK T-cell CD4-negative, CD8-negative type I NK T-lymphocyte CD4-negative, CD8-negative type I NKT cell NKT.4-.Sp cell CD4-negative, CD8-negative type I NK T cell true A type I NK T cell that has the phenotype CD4-negative and CD8-negative. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:18997862 A type I NK T cell that has been recently activated, secretes interferon-gamma and IL-4, and has the phenotype CD4-positive, CD69-positive, and downregulated NK markers. activated CD4-positive type I NK T lymphocyte activated CD4-positive type I NK T-cell activated CD4-positive type I NK T-lymphocyte activated CD4-positive type I NKT cell cell activated CD4-positive type I NK T cell A type I NK T cell that has been recently activated, secretes interferon-gamma and IL-4, and has the phenotype CD4-positive, CD69-positive, and downregulated NK markers. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:17303398 A mature NK T cell that secretes interferon-gamma and enhances type 1 immune responses. CD4-positive type I NK T cell secreting IFN-gamma CD4-positive type I NK T lymphocyte secreting interferon-gamma CD4-positive type I NK T-cell secreting interferon-gamma CD4-positive type I NK T-lymphocyte secreting interferon-gamma CD4-positive type I NKT cell secreting interferon-gamma cell CD4-positive type I NK T cell secreting interferon-gamma A mature NK T cell that secretes interferon-gamma and enhances type 1 immune responses. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:17303398 A mature NK T cell that predominantly secretes type 2 cytokines such as interleukin-4 and interleukin-13 and enhances type 2 immune responses. CD4-positive type I NK T cell secreting IL-4 CD4-positive type I NK T lymphocyte secreting interleukin-4 CD4-positive type I NK T-cell secreting interleukin-4 CD4-positive type I NK T-lymphocyte secreting interleukin-4 CD4-positive type I NKT cell secreting interleukin-4 cell CD4-positive type I NK T cell secreting interleukin-4 A mature NK T cell that predominantly secretes type 2 cytokines such as interleukin-4 and interleukin-13 and enhances type 2 immune responses. GOC:add GOC:pam GOC:tfm GO_REF:0000031 A type I NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has phenotype CD4-negative, CD8-negative, CD69-positive, and downregulated NK markers. activated CD4-negative, CD8-negative type I NK T lymphocyte activated CD4-negative, CD8-negative type I NK T-cell activated CD4-negative, CD8-negative type I NK T-lymphocyte activated CD4-negative, CD8-negative type I NKT cell cell activated CD4-negative, CD8-negative type I NK T cell A type I NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has phenotype CD4-negative, CD8-negative, CD69-positive, and downregulated NK markers. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:17303398 A mature NK T cell that secretes interferon-gamma and enhances Th1 immune responses. CD4-negative, CD8-negative type I NK T cell secreting IFN-gamma CD4-negative, CD8-negative type I NK T lymphocyte secreting interferon-gamma CD4-negative, CD8-negative type I NK T-cell secreting interferon-gamma CD4-negative, CD8-negative type I NK T-lymphocyte secreting interferon-gamma CD4-negative, CD8-negative type I NKT cell secreting interferon-gamma cell CD4-negative, CD8-negative type I NK T cell secreting interferon-gamma A mature NK T cell that secretes interferon-gamma and enhances Th1 immune responses. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:17303398 A mature NK T cell that secretes interleukin-4 and enhances Th2 immune responses. CD4-negative, CD8-negative type I NK T cell secreting IL-4 CD4-negative, CD8-negative type I NK T lymphocyte secreting interleukin-4 CD4-negative, CD8-negative type I NK T-cell secreting interleukin-4 CD4-negative, CD8-negative type I NK T-lymphocyte secreting interleukin-4 CD4-negative, CD8-negative type I NKT cell secreting interleukin-4 cell CD4-negative, CD8-negative type I NK T cell secreting interleukin-4 A mature NK T cell that secretes interleukin-4 and enhances Th2 immune responses. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:17303398 A type II NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has the phenotype CD69-positive and downregulated NK markers. activated type II NK T lymphocyte activated type II NK T-cell activated type II NK T-lymphocyte activated type II NKT cell cell activated type II NK T cell true A type II NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has the phenotype CD69-positive and downregulated NK markers. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:17964217 A type II NK T cell that has been recently activated, secretes interferon-gamma, and has the phenotype CD69-positive and downregulated NK markers. type II NK T cell secreting IFN-gamma type II NK T lymphocyte secreting interferon-gamma type II NK T-cell secreting interferon-gamma type II NK T-lymphocyte secreting interferon-gamma type II NKT cell secreting interferon-gamma cell type II NK T cell secreting interferon-gamma true A type II NK T cell that has been recently activated, secretes interferon-gamma, and has the phenotype CD69-positive and downregulated NK markers. GOC:add GOC:pam GO_REF:0000031 PMID:17964217 A type II NK T cell that has been recently activated, secretes interleukin-4, and has the phenotype CD69-positive and downregulated NK markers. type II NK T cell secreting IL-4 type II NK T lymphocyte secreting interleukin-4 type II NK T-cell secreting interleukin-4 type II NK T-lymphocyte secreting interleukin-4 type II NKT cell secreting interleukin-4 cell type II NK T cell secreting interleukin-4 true A type II NK T cell that has been recently activated, secretes interleukin-4, and has the phenotype CD69-positive and downregulated NK markers. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:17964217 A CD4-positive, alpha-beta T cell that has cytotoxic function. CD4-positive, alpha-beta cytotoxic T lymphocyte CD4-positive, alpha-beta cytotoxic T-cell CD4-positive, alpha-beta cytotoxic T-lymphocyte cell CD4-positive, alpha-beta cytotoxic T cell true A CD4-positive, alpha-beta T cell that has cytotoxic function. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:18440213 A CD4-negative, CD8-negative, alpha-beta intraepithelial T cell that is found in the columnar epithelium of the gastrointestinal tract. CD4-negative, CD8-negative, alpha-beta intraepithelial T lymphocyte CD4-negative, CD8-negative, alpha-beta intraepithelial T-cell CD4-negative, CD8-negative, alpha-beta intraepithelial T-lymphocyte cell CD4-negative, CD8-negative, alpha-beta intraepithelial T cell true A CD4-negative, CD8-negative, alpha-beta intraepithelial T cell that is found in the columnar epithelium of the gastrointestinal tract. GOC:add GOC:pam GO_REF:0000031 PMID:11685222 A lymphoid progenitor cell that is found in bone marrow, gives rise to B cells, T cells, natural killer cells and dendritic cells, and has the phenotype Lin-negative, Kit-positive, Sca-1-positive, FLT3-positive, CD34-positive, CD150 negative, and GlyA-negative. ELP LMPP lymphoid-primed multipotent progenitor cell GMLP Markers are associated with mouse cells. ELP transcription factors include E2A-positive, Ikaros-positive, EBF-negative, Pax5-negative, PU.1-negative. early lymphoid progenitor true A lymphoid progenitor cell that is found in bone marrow, gives rise to B cells, T cells, natural killer cells and dendritic cells, and has the phenotype Lin-negative, Kit-positive, Sca-1-positive, FLT3-positive, CD34-positive, CD150 negative, and GlyA-negative. GOC:add GOC:dsd GOC:pam GOC:tfm GO_REF:0000031 PMID:19022770 GMLP PMID:18371378 Cell committed to natural killer cell lineage that has the phenotype CD122-positive, CD34-positive, and CD117-positive. This cell type lacks expression of natural killer receptor proteins. pre-NK cell cell These cells are also reportedly CD7-low, CD10-negative, CD45RA-positive, alpha-4-beta-7 integrin-high. pre-natural killer cell Cell committed to natural killer cell lineage that has the phenotype CD122-positive, CD34-positive, and CD117-positive. This cell type lacks expression of natural killer receptor proteins. GOC:add GOC:dsd GOC:pam GOC:tfm GO_REF:0000031 PMID:16551251 PMID:17100874 NK cell that has the phenotype CD56-bright, CD16-negative, and CD84-positive with the function to secrete interferon-gamma but is not cytotoxic. CD16-CD56bright NK cell CD16-negative, CD56-bright NK cell CD56-bright cytokine secreting NK cell CD56-bright cytokine secreting natural killer cell cell This cell type is compatible with the HIPC Lyoplate markers for 'CD16-CD56bright NK cell'. Markers are associated with human cell types. CD16-negative, CD56-bright natural killer cell, human NK cell that has the phenotype CD56-bright, CD16-negative, and CD84-positive with the function to secrete interferon-gamma but is not cytotoxic. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:19796267 PMID:22343568 CD16-CD56bright NK cell PMID:22343568 A mature natural killer cell that has the phenotype CD56-low, CD16-positive and which is capable of cytotoxicity and cytokine production. CD16+CD56+ NK cell CD16-positive, CD56-dim NK cell CD16-positive, CD56-low NK cell CD16-positive, CD56-low natural killer cell CD16-positive, CD56-positive NK cell CD16-positive, CD56-positive natural killer cell cytotoxic CD56-dim NK cell cytotoxic CD56-dim natural killer cell cell This cell type is compatible with the HIPC Lyoplate markers for 'CD16+CD56+ NK cell'. Markers are associated with human cell types. CD16-positive, CD56-dim natural killer cell, human A mature natural killer cell that has the phenotype CD56-low, CD16-positive and which is capable of cytotoxicity and cytokine production. GOC:add GOC:pam GO_REF:0000031 PMID:19796267 PMID:22343568 CD16+CD56+ NK cell PMID:22343568 An alpha-beta T cell that is found in the lamina propria of mucosal tissues and is restricted by the MR-1 molecule. mucosal invariant T lymphocyte mucosal invariant T-cell mucosal invariant T-lymphocyte cell mucosal invariant T cell true An alpha-beta T cell that is found in the lamina propria of mucosal tissues and is restricted by the MR-1 molecule. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:19416870 A dendritic cell arising in thymus that has the phenotype CD11c-positive, CD11b-negative, and CD45RA-negative. cell In the mouse this cell expresses CD8-alpha-alpha. thymic conventional dendritic cell true A dendritic cell arising in thymus that has the phenotype CD11c-positive, CD11b-negative, and CD45RA-negative. GOC:add GOC:pam GO_REF:0000031 PMID:19273629 A plasmacytoid dendritic cell developing in the thymus with phenotype CD11c-negative or low, CD45RA-positive, CD11b-negative, and CD123-positive. cell thymic plasmacytoid dendritic cell true A plasmacytoid dendritic cell developing in the thymus with phenotype CD11c-negative or low, CD45RA-positive, CD11b-negative, and CD123-positive. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:19941119 A Be cell that facilitates development of T-helper 1 (Th1) phenotype in CD4-positive T cells, and secretes high levels of interleukin-2, tumor necrosis factor-alpha and interferon-gamma. B effector 1 cell cell B effector cell type 1 Be1 cells are also reportedly capable of secreting IL-6, IL-10, and IL-12. They are also reportedly CD11b-negative and B220-positive. Be1 Cell true A Be cell that facilitates development of T-helper 1 (Th1) phenotype in CD4-positive T cells, and secretes high levels of interleukin-2, tumor necrosis factor-alpha and interferon-gamma. GOC:dsd GOC:msz GOC:tfm GO_REF:0000031 PMID:11101868 PMID:20224569 B effector 1 cell PMID:11101868 PMID:20224569 A Be cell that facilitates development of T-helper 2 (Th2) phenotype T cells, and secretes high levels of interleukin-2, interleukin-10, interleukin-4, and interleukin-6. B effector 2 cell cell B effector cell type 2 Be2 cells are also reportedly capable of secreting IL-13 and TNF. They are also reportedly CD11b-negative and B220-positive. Be2 cell true A Be cell that facilitates development of T-helper 2 (Th2) phenotype T cells, and secretes high levels of interleukin-2, interleukin-10, interleukin-4, and interleukin-6. GOC:dsd GOC:msz GOC:tfm GO_REF:0000031 PMID:11101868 PMID:20224569 B effector 2 cell PMID:11101868 PMID:20224569 A lymphocyte of B lineage with the commitment to express an immunoglobulin complex. cell Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). lymphocyte of B lineage true A lymphocyte of B lineage with the commitment to express an immunoglobulin complex. GOC:add GOC:rhs GOC:tfm GO_REF:0000031 ISBN:0781735149 A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin. cell antibody secreting cell true A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin. GOC:add GOC:tfm GO_REF:0000031 ISBN:0721601464 ISBN:0781735149 A long lived plasma cell that secretes IgE. cell IgE plasma cell true A long lived plasma cell that secretes IgE. GOC:msz GO_REF:0000031 ISBN:781735149 A class switched memory B cell that expresses IgE on the cell surface. IgE memory B lymphocyte IgE memory B-cell IgE memory B-lymphocyte memory IgE B cell memory IgE B lymphocyte memory IgE B-cell memory IgE B-lymphocyte cell IgE memory B cell true A class switched memory B cell that expresses IgE on the cell surface. GOC:rhs GO_REF:0000031 ISBN:0781765196 A plasmablast that secretes IgD, and which occur in a small proportion of B cells in the adult. cell IgD plasmablast true A plasmablast that secretes IgD, and which occur in a small proportion of B cells in the adult. GOC:msz GO_REF:0000031 A plasmablast that secretes IgE. cell IgE plasmablast true A plasmablast that secretes IgE. GOC:msz GO_REF:0000031 A short lived plasma cell that secretes IgE. cell IgE short lived plasma cell true A short lived plasma cell that secretes IgE. GOC:msz GO_REF:0000031 ISBN:781735149 An preBRC-positive large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-positive, composed of surrogate light chain protein (SL), which is composed of VpreB , Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu) on the cell surface. cell preBCR-positive large pre-B-II cell true An preBRC-positive large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-positive, composed of surrogate light chain protein (SL), which is composed of VpreB , Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu) on the cell surface. GOC:rhs GOC:tfm GO_REF:0000031 PMID:9785673 A pre-BCR-negative large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-negative, composed of surrogate light chain protein (SL), which is composed of VpreB and Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu), on the cell surface, and lack a DNA rearrangement of immunoglobulin light chain genes. cell preBCR-negative large pre-B-II cell true A pre-BCR-negative large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-negative, composed of surrogate light chain protein (SL), which is composed of VpreB and Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu), on the cell surface, and lack a DNA rearrangement of immunoglobulin light chain genes. GOC:rhs GOC:tfm GO_REF:0000031 PMID:9785673 A small pre-B-II cell is a pre-B-II cell that is Rag1-positive, Rag2-positive, pre-BCR-negative, and BCR-negative, is not proliferating, and carries a DNA rearrangement of one or more immunoglobulin light chain genes. small pre-BII cell cell Small pre-B-II cells are also reportedly CD10-positive, CD19-positive, CD34-negative, CD79a-positive, CD127-negative, TdT-negative, Vpre-B-negative, sIgM-negative, and sIgD-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. small pre-B-II cell true A small pre-B-II cell is a pre-B-II cell that is Rag1-positive, Rag2-positive, pre-BCR-negative, and BCR-negative, is not proliferating, and carries a DNA rearrangement of one or more immunoglobulin light chain genes. GOC:dsd GOC:rhs GOC:tfm GO_REF:0000031 PMID:16551251 PMID:18432934 PMID:9785673 A pre-B-II cell is a precursor B cell that expresses immunoglobulin mu heavy chain (IgHmu+), and lack expression of CD34, TdT, immunoglobulin kappa light chain and immunoglobulin lambda light chain. BTO:0001133 CALOHA:TS-0819 pre-B-lymphocyte pre-BII cell cell pre-B-II cell are also reportedly CD19-positive, CD22-positive, CD38-positive, CD45-positive, and CD48-positive. pre-B-II cell true A pre-B-II cell is a precursor B cell that expresses immunoglobulin mu heavy chain (IgHmu+), and lack expression of CD34, TdT, immunoglobulin kappa light chain and immunoglobulin lambda light chain. GOC:dsd GOC:rhs GOC:tfm GO_REF:0000031 PMID:9785673 A pre-B-I cell is a precursor B cell that expresses CD34 and surrogate immunoglobulin light chain (VpreB , Lambda 5 (mouse)/14.1 (human)) on the cell surface, and TdT, Rag1,and Rag2 intracellularly. Cell type carries a D-JH DNA rearrangement, and lacks expression of immunglobulin heavy chain protein. pre-BI cell cell pro-B cell (Philadelphia nomenclature) Human pre-B-I cells are reportedly CD10-positive, CD19-positive, CD22-positive, CD38-positive, CD45-low, CD79a-positive, CD127-negative, pre-BCR-negative, IgM-negative, IgD-negative, and Tdt-positive. Transcription factors expressed: Pax5-positive. pre-B-I cell true A pre-B-I cell is a precursor B cell that expresses CD34 and surrogate immunoglobulin light chain (VpreB , Lambda 5 (mouse)/14.1 (human)) on the cell surface, and TdT, Rag1,and Rag2 intracellularly. Cell type carries a D-JH DNA rearrangement, and lacks expression of immunglobulin heavy chain protein. GOC:dsd GOC:rhs GOC:tfm GO_REF:0000031 PMID:16551251 PMID:18432934 PMID:20839338 PMID:9785673 pro-B cell (Philadelphia nomenclature) PMID:11244048 A large pre-B-II cell is a pre-B-II cell that is proliferating and is Rag1-negative and Rag2-negative. large pre-B cell large pre-BII cell cell Large pre-B-II cells are also reportedly CD10-positive, CD19-positive, CD34-negative, CD79a-positive, CD127-negative, TdT-negative, Vpre-B-positive, pre-BCR-positive, sIgM-negative, and sIgD-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. large pre-B-II cell true A large pre-B-II cell is a pre-B-II cell that is proliferating and is Rag1-negative and Rag2-negative. GOC:dsd GOC:rhs GO_REF:0000031 PMID:16551251 PMID:18432934 PMID:9785673 large pre-B cell PMID:11244048 A transitional stage B cell that migrates from the bone marrow into the peripheral circulation, and finally to the spleen. This cell type has the phenotype surface IgM-positive, surface IgD-negative, CD21-negative, CD23-negative, and CD62L-negative, and CD93-positive. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-negative. T1 B lymphocyte T1 B-cell T1 B-lymphocyte transitional stage 1 B cell cell T1 B cells are also reportedly CD10-negative/positive??, CD20-positive, CD24-positive, CD38-positive, CD48-positive, CD84-positive, CD150-positive, CD244-negative, and CD352-positive. T1 B cell true A transitional stage B cell that migrates from the bone marrow into the peripheral circulation, and finally to the spleen. This cell type has the phenotype surface IgM-positive, surface IgD-negative, CD21-negative, CD23-negative, and CD62L-negative, and CD93-positive. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-negative. GOC:dsd GOC:msz GOC:tfm GO_REF:0000031 PMCID:PMC2193793 PMID:12810111 A transitional stage B cell that has the phenotype surface IgM-positive, surface IgD-postive, CD21-positive, CD23-positive, CD62L-negative, CD93-positive and is located in the splenic B follicles. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-positive. T2 B lymphocyte T2 B-cell T2 B-lymphocyte transitional stage 2 B cell cell T2 B cells are also reportedly CD20-positive, CD24-positive, CD38-positive, CD48-positive, CD84-positive, CD150-positive, CD244-negative, and CD352-positive. T2 B cell true A transitional stage B cell that has the phenotype surface IgM-positive, surface IgD-postive, CD21-positive, CD23-positive, CD62L-negative, CD93-positive and is located in the splenic B follicles. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-positive. GOC:dsd GOC:msz GOC:tfm GO_REF:0000031 PMCID:PMC2193793 PMID:12810111 A transitional stage B cell that expresses surface IgM and IgD, and CD62L. This cell type appears to be an anergic B cell that does not proliferate upon BCR signaling, is found in the spleen and lymph nodes, and has the phenotype surface IgM-positive, surface IgD-positive, CD21-positive, CD23-positive, CD62L-positive, and CD93-positive. This cell type has also been described as IgM-low, CD19-positive, B220-positive, AA4-positive, and CD23-positive (i.e. this cell-type is distinguished from T2 cells by surface expression of IgM). An1 B cell T3 B lymphocyte T3 B-cell T3 B-lymphocyte transitional stage 3 B cell cell T3 B cell true A transitional stage B cell that expresses surface IgM and IgD, and CD62L. This cell type appears to be an anergic B cell that does not proliferate upon BCR signaling, is found in the spleen and lymph nodes, and has the phenotype surface IgM-positive, surface IgD-positive, CD21-positive, CD23-positive, CD62L-positive, and CD93-positive. This cell type has also been described as IgM-low, CD19-positive, B220-positive, AA4-positive, and CD23-positive (i.e. this cell-type is distinguished from T2 cells by surface expression of IgM). GOC:msz GOC:tfm GO_REF:0000031 PMID:12810111 PMID:17174121 http://www.immgen.org/index_content.html An1 B cell PMID:17174121 A follicular B cell that is IgD-positive, CD23-negative, and CD38-negative. This naive cell type is activated in the extrafollicular areas through interaction with interdigitating dendritic cells and antigen-specific CD4-positive T cells. Bm1 B lymphocyte Bm1 B-cell Bm1 B-lymphocyte cell These cells are also reportedly CD10-negative, CD39-positive, CD44-positive, CD71-negative, CD77-negative, IgM-positive, IgG-negative, IgA-negative, and IgE-negative. Bm1 B cell true A follicular B cell that is IgD-positive, CD23-negative, and CD38-negative. This naive cell type is activated in the extrafollicular areas through interaction with interdigitating dendritic cells and antigen-specific CD4-positive T cells. GOC:dsd GOC:msz GO_REF:0000031 PMID:17992590 PMID:18432934 PMID:8006591 A follicular B cell that is IgD-positive and CD23-positive and CD38-positive. This naive cell type is activated in the extrafollicular areas via interaction with dendritic cells and antigen specific T cells. Bm2 B lymphocyte Bm2 B-cell Bm2 B-lymphocyte cell These cells are also CD10-negative, CD39-positive, CD44-positive, CD71-negative, CD77-negative, IgM-positive, IgG-negative, IgA-negative, and IgE-negative. Bm2 B cell true A follicular B cell that is IgD-positive and CD23-positive and CD38-positive. This naive cell type is activated in the extrafollicular areas via interaction with dendritic cells and antigen specific T cells. GOC:dsd GOC:msz GO_REF:0000031 PMID:17992590 PMID:18432934 PMID:8006591 A germinal center B cell that develops from a Bm3 B cell. This cell has the phenotype IgM-negative, IgD-positive, and CD38-positive. Bm3-delta B lymphocyte Bm3-delta B-cell Bm3-delta B-lymphocyte cell Bm3-delta B cell true A germinal center B cell that develops from a Bm3 B cell. This cell has the phenotype IgM-negative, IgD-positive, and CD38-positive. GOC:add GOC:msz GOC:tfm GO_REF:0000031 PMID:9280752 A germinal center B cell that founds a germinal center, and has the phenotype IgD-positive, CD38-positive, and CD23-negative. Bm2' B lymphocyte Bm2' B-cell Bm2-prime B cell Bm2-prime B-lymphocyte cell germinal center founder cell Bm2' B cells are also reportedly CD10-positive, CD39-negative, CD44-negative, CD71-positive, CD77-negative, IgM-positive, IgG-negative, IgA-negative, and IgE-negative. Bm2' B cell true A germinal center B cell that founds a germinal center, and has the phenotype IgD-positive, CD38-positive, and CD23-negative. GOC:dsd GOC:msz GOC:tfm GO_REF:0000031 PMID:17992590 PMID:18432934 PMID:8006591 A germinal center B cell that is rapidly dividing and has the phenotype IgD-negative, CD38-positive, and CD77-positive. Somatic hypermutation of the immunoglobulin V gene region can occur during proliferation of this cell type. Bm3 B lymphocyte Bm3 B-cell Bm3 B-lymphocyte cell centroblast Bm3 B cells are also reportedly CD10-positive, CD23-negative, CD39-negative, CD44-negative, CD71-positive, and CD77-positive. Bm3 B cell true A germinal center B cell that is rapidly dividing and has the phenotype IgD-negative, CD38-positive, and CD77-positive. Somatic hypermutation of the immunoglobulin V gene region can occur during proliferation of this cell type. GOC:dsd GOC:msz GO_REF:0000031 PMID:18432934 PMID:8006591 centroblast PMID:8006591 A germinal center B cell that has the phenotype CD77-negative, IgD-negative, and CD38-positive. These cells have undergone somatic mutation of the B cell receptor. Bm4 B lymphocyte Bm4 B-cell Bm4 B-lymphocyte cell centrocyte Bm4 B cells are also reportedly CD10-positive, CD23-negative, CD39-negative, CD44-positive, and CD71-positive. Bm4 B cell true A germinal center B cell that has the phenotype CD77-negative, IgD-negative, and CD38-positive. These cells have undergone somatic mutation of the B cell receptor. GOC:dsd GOC:msz GO_REF:0000031 PMID:18432934 PMID:8006591 centrocyte PMID:17992590 A memory B cell arising in the germinal center that is IgD-negative and has undergone somatic mutation of the variable region of the immunoglobulin heavy and light chain genes. Bm5 B lymphocyte Bm5 B-cell Bm5 B-lymphocyte cell Bm5 B cells are also reportedly CD10-positive, CD23-negative, CD38-negative, CD39-positive, CD44-positive, CD71-positive, and CD77-negative. Bm5 B cell A memory B cell arising in the germinal center that is IgD-negative and has undergone somatic mutation of the variable region of the immunoglobulin heavy and light chain genes. GOC:dsd GOC:msz GOC:tfm GO_REF:0000031 PMID:18432934 PMID:8006591 A mature B cell that produces cytokines that can influence CD4 T cell differentiation. B effector cell effector B cell effector B lymphocyte effector B-cell effector B-lymphocyte cell Be cell true A mature B cell that produces cytokines that can influence CD4 T cell differentiation. GOC:msz GOC:tfm GO_REF:0000031 PMID:11101868 PMID:20224569 A mature B cell that has the phenotype CD1d-positive and expresses interleukin-10. This cell type has been associated with suppression of chronic inflammatory responses and T cell responses. B(reg) B10 cell Breg regulatory B lymphocyte regulatory B-cell regulatory B-lymphocyte cell Regulatory B cells reportedly represent 1-2% of the spleen and 7-8% of the peritoneal B220-positive cells in mice. They are also found in the bone marrow, lymph node, and blood of mice. These cells are also reportedly capable of secreting IL-10 and are reportedly CD5-positive, CD21-positive, CD24-positive, CD93-negative, B220-positive, IgM-positive, and IgD-positive. regulatory B cell true A mature B cell that has the phenotype CD1d-positive and expresses interleukin-10. This cell type has been associated with suppression of chronic inflammatory responses and T cell responses. GOC:dsd GOC:msz GOC:tfm GO_REF:0000031 MESH:D060151 PMID:11869683 PMID:18482568 PMID:20224569 PMID:20809522 An unswitched memory B cell is a memory B cell that has the phenotype IgM-positive, IgD-positive, CD27-positive, CD138-negative, IgG-negative, IgE-negative, and IgA-negative. IgD+ memory B cell non-class-switched memory B cell unswitched memory B lymphocyte unswitched memory B-cell unswitched memory B-lymphocyte cell This cell type is compatible with the HIPC Lyoplate markers for 'IgD+ memory B cell'. Per DSD: Unswitched memory B cells are also reportedly CD48-positive, CD84-positive, CD229-positive, and CD352-positive. unswitched memory B cell true An unswitched memory B cell is a memory B cell that has the phenotype IgM-positive, IgD-positive, CD27-positive, CD138-negative, IgG-negative, IgE-negative, and IgA-negative. GOC:add GOC:dsd GOC:rhs GO_REF:0000031 ISBN:0781765196 PMID:20933013 PMID:22343568 IgD+ memory B cell PMID:22343568 non-class-switched memory B cell HP:0032126 An IgM memory B cell is an unswitched memory B cell with the phenotype IgM-positive and IgD-negative. IgM memory B lymphocyte IgM memory B-cell IgM memory B-lymphocyte memory IgM B cell memory IgM B lymphocyte memory IgM B-cell memory IgM B-lymphocyte cell IgM memory B cells are also reportedly CD1c-positive, CD95-positive, CD80-positive, CD84-positive, CD86-positive, CD150-negative, CD229-positive, CD289-positive, and CD290-positive. Transcription factors: Notch2-positive, PAX5-positive, SpiB-positive, Ets1-positive, and OBF1-positive. IgM memory B cell An IgM memory B cell is an unswitched memory B cell with the phenotype IgM-positive and IgD-negative. GOC:dsd GOC:rhs GO_REF:0000031 ISBN:0781765196 PMID:19447676 A class switched memory B cell is a memory B cell that has undergone Ig class switching and therefore is IgM-negative on the cell surface. These cells are CD27-positive and have either IgG, IgE, or IgA on the cell surface. class switched memory B lymphocyte class switched memory B-cell class switched memory B-lymphocyte cell Per DSD: Class switched memory B cells are also reportedly CD48-positive, CD229-positive, and CD352-positive. class switched memory B cell true A class switched memory B cell is a memory B cell that has undergone Ig class switching and therefore is IgM-negative on the cell surface. These cells are CD27-positive and have either IgG, IgE, or IgA on the cell surface. GOC:add GOC:dsd GOC:rhs GO_REF:0000031 ISBN:0781765196 PMID:20933013 PMID:9295047 A class switched memory B cell that expresses IgA. IgA memory B lymphocyte IgA memory B-cell IgA memory B-lymphocyte memory IgA B cell memory IgA B lymphocyte memory IgA B-cell memory IgA B-lymphocyte cell IgA memory B cell are also reportedly RORalpha-positive. IgA memory B cell true A class switched memory B cell that expresses IgA. GOC:dsd GOC:msz GO_REF:0000031 ISBN:0781765196 A fully differentiated plasma cell that lives for years, as opposed to months, secretes immunoglobulin, and has the phenotype weakly CD19-positive, CD20-negative, CD38-negative, strongly CD138-positive, MHC Class II-negative, surface immunoglobulin-negative, IgD-negative, and strongly CXCR4-positive. The majority of these cells of this type reside in the bone marrow. cell long lived plasma cell true A fully differentiated plasma cell that lives for years, as opposed to months, secretes immunoglobulin, and has the phenotype weakly CD19-positive, CD20-negative, CD38-negative, strongly CD138-positive, MHC Class II-negative, surface immunoglobulin-negative, IgD-negative, and strongly CXCR4-positive. The majority of these cells of this type reside in the bone marrow. GOC:msz GOC:tfm GO_REF:0000031 ISBN:9780781765190 PMID:16014527 A fully differentiated plasma cell that lives for months. cell short lived plasma cell true A fully differentiated plasma cell that lives for months. GOC:msz GO_REF:0000031 PMID:16014527 A short lived plasma cell that secretes IgA. These cells may be found in the bone marrow as well as in the mucosal immune system. cell IgA short lived plasma cell true A short lived plasma cell that secretes IgA. These cells may be found in the bone marrow as well as in the mucosal immune system. GOC:msz GO_REF:0000031 ISBN:781735149 A short lived plasma cell that secretes IgG. cell IgG short lived plasma cell true A short lived plasma cell that secretes IgG. GOC:msz GO_REF:0000031 ISBN:781735149 A short lived plasma cell that secretes IgM. cell IgM short lived plasma cell true A short lived plasma cell that secretes IgM. GOC:msz GO_REF:0000031 ISBN:781735149 An IgG memory B cell is a class switched memory B cell that is class switched and expresses IgG on the cell surface. IgG memory B lymphocyte IgG memory B-cell IgG memory B-lymphocyte memory IgG B cell memory IgG B lymphocyte memory IgG B-cell memory IgG B-lymphocyte cell IgG memory B cell true An IgG memory B cell is a class switched memory B cell that is class switched and expresses IgG on the cell surface. GOC:rhs GO_REF:0000031 ISBN:0781765196 An activated mature (naive or memory) B cell that is secreting immunoglobulin, typified by being CD27-positive, CD38-positive, CD138-negative. CD20-negative B cell FMA:84371 CD27-positive, CD38-positive, CD20-negative B cell cell This cell type is compatible with the HIPC Lyoplate markers for 'plasmablast'. Plasmablasts are also reportedly CD48-positive, CD63-positive, CD229-positive, CD270-positive, CD319-positive, CD352-positive, CD361-positive, and IgD-negative. plasmablast true An activated mature (naive or memory) B cell that is secreting immunoglobulin, typified by being CD27-positive, CD38-positive, CD138-negative. GOC:dsd GOC:msz GOC:tfm GO_REF:0000031 PMCID:PMC2673126 A memory B cell with the phenotype IgD-negative and CD27-negative. dn memory B cell dn memory B lymphocyte dn memory B-cell dn memory B-lymphocyte double negative memory B lymphocyte double negative memory B-cell double negative memory B-lymphocyte cell double negative memory B cell A memory B cell with the phenotype IgD-negative and CD27-negative. GOC:msz GOC:tfm GO_REF:0000031 A plasmablast that secretes IgG. cell IgG plasmablast true A plasmablast that secretes IgG. GOC:msz GO_REF:0000031 A plasmablast that secretes IgM. cell IgM plasmablast true A plasmablast that secretes IgM. GOC:msz GO_REF:0000031 A plasmablast that secretes IgA. cell IgA plasmablast true A plasmablast that secretes IgA. GOC:msz GO_REF:0000031 A fully differentiated plasma cell that secretes IgG. cell IgG plasma cell true A fully differentiated plasma cell that secretes IgG. GOC:msz GO_REF:0000031 ISBN:781735149 A fully differentiated plasma cell that secretes IgM. cell IgM plasma cell true A fully differentiated plasma cell that secretes IgM. GOC:msz GO_REF:0000031 ISBN:781735149 A fully differentiated plasma cell that secretes IgA. cell IgA plasma cell true A fully differentiated plasma cell that secretes IgA. GOC:msz GO_REF:0000031 ISBN:781735149 A cell of a hematopoietic lineage. BTO:0000574 CALOHA:TS-2017 FMA:70366 FMA:83598 haematopoietic cell haemopoietic cell hemopoietic cell cell hematopoietic cell A cell of a hematopoietic lineage. GOC:add GO_REF:0000031 CD11c-low plasmacytoid dendritic cell is a leukocyte that is CD11c-low, CD45R-positive, GR1-positive and CD11b-negative. cell Originally described in the dendritic cell ontology (DC_CL:0000001)(PMID:19243617). These cells are CD281-positive (TLR1), CD282-positive (TLR2), CD285-positive (TLR5), CD286-positive (TLR6), and CD288-positive (TLR8). CD11c-low plasmacytoid dendritic cell true CD11c-low plasmacytoid dendritic cell is a leukocyte that is CD11c-low, CD45R-positive, GR1-positive and CD11b-negative. GOC:amm GOC:dsd GO_REF:0000031 PMID:15771572 PMID:17850486 Conventional dendritic cell is a dendritic cell that is CD11c-high. interdigitating cell veiled cell FMA:84191 DC1 cDC dendritic reticular cell type 1 DC cell Originally described in the dendritic cell ontology (DC_CL:0000003)(PMID:19243617) These cells are also CD20-negative, MHCII-positive. conventional dendritic cell true Conventional dendritic cell is a dendritic cell that is CD11c-high. GOC:amm GO_REF:0000031 PMID:17850486 CD11c-negative plasmacytoid dendritic cell is a leukocyte is CD11c-negative, CD45RA-positive, CD85g-positive(ILT7), CD123-positive, CD303-positive. CD303-positive dendritic cell cell Originally described in the dendritic cell ontology (DC_CL:0000004)(PMID:19243617). These cells are CD281-positive (TLR1), CD286-positive (TLR6), and CD290-positive (TLR10). CD11c-negative plasmacytoid dendritic cell true CD11c-negative plasmacytoid dendritic cell is a leukocyte is CD11c-negative, CD45RA-positive, CD85g-positive(ILT7), CD123-positive, CD303-positive. GOC:amm GO_REF:0000031 PMID:15771572 PMID:17850486 Immature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD80-low and CD86-low. cell Originally described in the dendritic cell ontology (DC_CL:0000006)(PMID:19243617). immature CD11c-low plasmacytoid dendritic cell true Immature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD80-low and CD86-low. GOC:amm GO_REF:0000031 PMID:15771572 PMID:17850486 Mature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD83-high and is CD80-positive, CD86-positive, and MHCII-positive. cell Originally described in the dendritic cell ontology (DC_CL:0000007)(PMID:19243617). mature CD11c-low plasmacytoid dendritic cell true Mature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD83-high and is CD80-positive, CD86-positive, and MHCII-positive. GOC:amm GO_REF:0000031 PMID:15771572 PMID:17850486 Immature CD11c-negative plasmacytoid dendritic cell is a CD11c-negative plasmacytoid dendritic cell is CD80-negative, CD86-low and MHCII-low. cell Originally described in the dendritic cell ontology (DC_CL:0000008)(PMID:19243617). immature CD11c-negative plasmacytoid dendritic cell true Immature CD11c-negative plasmacytoid dendritic cell is a CD11c-negative plasmacytoid dendritic cell is CD80-negative, CD86-low and MHCII-low. GOC:amm GO_REF:0000031 PMID:15771572 PMID:17850486 CD71-positive common myeloid precursor OR CD7-negative lymphoid precursor OR CD7-positive lymphoid cell Originally described in the dendritic cell ontology (DC_CL:1100000)(PMID:19243617). CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor Mature CD11c-negative plasmacytoid dendritic cell is a CD11c-negative plasmacytoid dendritic cell is CD80-high, CD86-high, MHCII-high and is CD83-positive. cell Originally described in the dendritic cell ontology (DC_CL:0000009)(PMID:19243617). mature CD11c-negative plasmacytoid dendritic cell true Mature CD11c-negative plasmacytoid dendritic cell is a CD11c-negative plasmacytoid dendritic cell is CD80-high, CD86-high, MHCII-high and is CD83-positive. GOC:amm GO_REF:0000031 PMID:15771572 PMID:17850486 Immature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-low, CD86-low, and MHCII-low. cell Originally described in the dendritic cell ontology (DC_CL:0000010)(PMID:19243617). immature CD8_alpha-negative CD11b-positive dendritic cell true Immature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-low, CD86-low, and MHCII-low. GOC:amm GOC:tfm GO_REF:0000031 PMCID:PMC2346585 CD8_alpha-negative CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative CD8_alpha-negative and is CD205-positive. This cell is able to cross- present antigen to CD8-alpha-positive T cells. DC.8-4-11b- triple negative dendritic cell cell These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000011)(PMID:19243617). CD8_alpha-negative CD11b-negative dendritic cell true CD8_alpha-negative CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative CD8_alpha-negative and is CD205-positive. This cell is able to cross- present antigen to CD8-alpha-positive T cells. GOC:amm GO_REF:0000031 PMCID:PMC2346585 http:www.immgen.org/index_content.html CD8_alpha-negative CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-positive and is CD205-negative and CD8_alpha-negative. DC.4+ cell Defined as having a disposition to secreting anti-inflammatory cytokines. These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000012)(PMID:19243617). CD4-positive CD11b-positive dendritic cell CD8_alpha-negative CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-positive and is CD205-negative and CD8_alpha-negative. GOC:amm GOC:tfm GO_REF:0000031 PMCID:PMC2346585 CD8_alpha-positive CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative and is CD205-positive and CD8_alpha-positive. DC.8+ cell Cells are defined as having a disposition to secreting inflammatory cytokines. Originally described in the dendritic cell ontology (DC_CL:0000013)(PMID:19243617). CD8_alpha-positive CD11b-negative dendritic cell true CD8_alpha-positive CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative and is CD205-positive and CD8_alpha-positive. GOC:amm GOC:tfm GO_REF:0000031 PMCID:PMC2346585 Immature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low. cell These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000014)(PMID:19243617). immature CD8_alpha-negative CD11b-negative dendritic cell true Immature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low. GOC:amm GO_REF:0000031 PMCID:PMC2346585 Mature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. cell These markers are associated with mouse cells. Defined as having a disposition to secretion of anti-inflammatory cytokines. Originally described in the dendritic cell ontology (DC_CL:0000015)(PMID:19243617). mature CD8_alpha-negative CD11b-negative dendritic cell true Mature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. GOC:amm GOC:tfm GO_REF:0000031 PMCID:PMC2346585 Mature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. cell Originally described in the dendritic cell ontology (DC_CL:0000016)(PMID:19243617). mature CD8_alpha-negative CD11b-positive dendritic cell true Mature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. GOC:amm GOC:tfm GO_REF:0000031 PMCID:PMC2346585 Immature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low. cell Originally described in the dendritic cell ontology (DC_CL:0000017)(PMID:19243617). immature CD8_alpha-positive CD11b-negative dendritic cell true Immature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low. GOC:amm GOC:tfm GO_REF:0000031 PMCID:PMC2346585 Mature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. cell Originally described in the dendritic cell ontology (DC_CL:0000018)(PMID:19243617). mature CD8_alpha-positive CD11b-negative dendritic cell true Mature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. GOC:amm GO_REF:0000031 PMCID:PMC2346585 Dermal dendritic cell is a conventional dendritic cell that is CD11b-positive, CD205-positive and CD8 alpha-negative. BTO:0004812 cell Originally described in the dendritic cell ontology (DC_CL:0000019)(PMID:19243617). These cells are also CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD284-positive (TLR4), CD285-positive (TLR5), CD288-positive (TLR8), and CD289-positive (TLR9). dermal dendritic cell Dermal dendritic cell is a conventional dendritic cell that is CD11b-positive, CD205-positive and CD8 alpha-negative. GOC:amm GO_REF:0000031 PMCID:PMC2346585 Interstitial dendritic cell is a conventional dendritic cell that is CD11b-positive, CD1a-positive, CD206-positive, CD209-positive, and CD36-positive. cell Originally described in the dendritic cell ontology (DC_CL:0000020)(PMID:19243617). These cells are also CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD284-positive (TLR4), CD286-positive (TLR6), CD288-positive (TLR8), and CD290-positive (TLR10). interstitial dendritic cell Interstitial dendritic cell is a conventional dendritic cell that is CD11b-positive, CD1a-positive, CD206-positive, CD209-positive, and CD36-positive. GOC:amm GO_REF:0000031 PMID:17850486 A hematopoietic stem cell that has plasma membrane part Kit-positive, SCA-1-positive, CD150-positive and CD34-negative. LSK stem cell Sca1-positive hematopoietic stem cell cell Cell markers are associated with mouse hematopoietic stem cell. Originally described in the dendritic cell ontology (DC_CL:0000043)(PMID:19243617). Kit and Sca1-positive hematopoietic stem cell true A hematopoietic stem cell that has plasma membrane part Kit-positive, SCA-1-positive, CD150-positive and CD34-negative. GOC:add GOC:amm GOC:tfm GO_REF:0000031 PMID:17952047 PMID:19022770 Immature dermal dendritic cell is a dermal dendritic cell that is CD80-low, CD86-low, and MHCII-low. cell Originally described in the dendritic cell ontology (DC_CL:0000022)(PMID:19243617). immature dermal dendritic cell true Immature dermal dendritic cell is a dermal dendritic cell that is CD80-low, CD86-low, and MHCII-low. GOC:amm GO_REF:0000031 PMCID:PMC2346585 Mature dermal dendritic cell is a dermal dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. cell Originally described in the dendritic cell ontology (DC_CL:0000023)(PMID:19243617). mature dermal dendritic cell true Mature dermal dendritic cell is a dermal dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. GOC:amm GO_REF:0000031 PMCID:PMC2346585 Immature interstitial dendritic cell is a interstitial dendritic cell that is CD80-low, CD86-low, and MHCII-low. cell Originally described in the dendritic cell ontology (DC_CL:0000024)(PMID:19243617). immature interstitial dendritic cell true Immature interstitial dendritic cell is a interstitial dendritic cell that is CD80-low, CD86-low, and MHCII-low. GOC:amm GOC:tfm GO_REF:0000031 PMID:17850486 cell Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617). CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor Mature interstitial dendritic cell is a interstitial dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. cell Originally described in the dendritic cell ontology (DC_CL:0000025)(PMID:19243617). mature interstitial dendritic cell true Mature interstitial dendritic cell is a interstitial dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. GOC:amm GOC:tfm GO_REF:0000031 PMID:17850486 CD1a-positive Langerhans cell is a Langerhans_cell that is CD1a-positive and CD324-positive. CD1a-LC cell These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000026)(PMID:19243617). These cells are also CD281-positive (TLR1), CD282-positive (TLR2), CD284-positive (TLR4), CD286-positive (TLR6), CD287-positive (TLR7), and CD290-positive (TLR10). When activated, these cells are capable of producing IL-6, IL-8, and IL-15. CD1a-positive Langerhans cell true CD1a-positive Langerhans cell is a Langerhans_cell that is CD1a-positive and CD324-positive. GOC:amm GO_REF:0000031 PMID:17850486 CD8_alpha-low Langerhans cell is a Langerhans cell that is CD205-high and is CD8_alpha-low. cell These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000027)(PMID:19243617). They are also CD205-high, CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD285-positive (TLR5), CD286-positive (TLR6), and CD289-positive (TLR9). CD8_alpha-low Langerhans cell true CD8_alpha-low Langerhans cell is a Langerhans cell that is CD205-high and is CD8_alpha-low. GOC:amm GO_REF:0000031 PMCID:PMC2346585 Immature CD1a-positive Langerhans cell is a CD1a-positive Langerhans cell that is CD80-low, CD86-low, and MHCII-low. cell Originally described in the dendritic cell ontology (DC_CL:0000028)(PMID:19243617). immature CD1a-positive Langerhans cell true Immature CD1a-positive Langerhans cell is a CD1a-positive Langerhans cell that is CD80-low, CD86-low, and MHCII-low. GOC:amm GOC:tfm GO_REF:0000031 PMID:17850486 Mature CD1a-positive Langerhans cell is a CD1a-positive Langerhans cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. cell Originally described in the dendritic cell ontology (DC_CL:0000029)(PMID:19243617). When activated, these cells produce IL-6, IL-8, and IL-15. mature CD1a-positive Langerhans cell true Mature CD1a-positive Langerhans cell is a CD1a-positive Langerhans cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. GOC:amm GOC:tfm GO_REF:0000031 PMID:17850486 Immature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that is CD80-low, CD86-low, and MHCII-low. cell These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000030)(PMID:19243617). immature CD8_alpha-low Langerhans cell true Immature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that is CD80-low, CD86-low, and MHCII-low. GOC:amm GOC:tfm GO_REF:0000031 PMCID:PMC2346585 cell Originally described in the dendritic cell ontology (DC_CL:1111000)(PMID:19243617). CD115-positive monocyte OR common dendritic progenitor Mature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that that is CD80-high, CD86-high, MHCII-high and is CD83-positive. cell These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000031)(PMID:19243617). mature CD8_alpha-low Langerhans cell true Mature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that that is CD80-high, CD86-high, MHCII-high and is CD83-positive. GOC:amm GO_REF:0000031 PMCID:PMC2346585 A common lymphoid progenitor that is CD10-positive, CD45RA-positive, CD34-positive and CD38-positive. CD10-positive common lymphocyte precursor CD10-positive common lymphocyte progenitor CD10-positive common lymphoid precursor cell These markers are associated with human common lymphoid progenitors. Originally described in the dendritic cell ontology (DC_CL:0000032)(PMID:19243617). CD34-positive, CD38-positive common lymphoid progenitor true A common lymphoid progenitor that is CD10-positive, CD45RA-positive, CD34-positive and CD38-positive. GOC:add GOC:amm GOC:tfm GO_REF:0000031 PMCID:PMC2346585 PMID:19022770 CD115-positive monocyte is a monocyte that is CD115-positive and CD11b-positive. cell These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000033)(PMID:19243617). CD115-positive monocyte true CD115-positive monocyte is a monocyte that is CD115-positive and CD11b-positive. GOC:add GOC:amm GO_REF:0000031 PMID:17952047 A common myeloid progenitor that is Kit-positive and CD34-positive, Il7ra-negative, and is SCA1-low and Fcgr2-low and Fcgr3-low. CD117-positive common myeloid precursor cell Markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000034)(PMID:19243617). Kit-positive, CD34-positive common myeloid progenitor true A common myeloid progenitor that is Kit-positive and CD34-positive, Il7ra-negative, and is SCA1-low and Fcgr2-low and Fcgr3-low. GOC:add GOC:amm GOC:tfm GO_REF:0000031 PMID:1261582 PMID:17952047 http://www.immgen.org/index_content.html CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive. CALOHA:TS-0448 FMA:86475 CD133-positive hematopoietic stem cell cell Cell markers are associated with human hematopoietic stem cells. Originally described in the dendritic cell ontology (DC_CL:0000035)(PMID:19243617). CD34-positive, CD38-negative hematopoietic stem cell true CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive. GOC:add GOC:amm GOC:tfm GO_REF:0000031 PMID:10430905 PMID:11750107 PMID:16551251 PMID:20024907 PMID:9389721 CD133-positive hematopoietic stem cell PMID:16140871 A common lymphoid progenitor that is Kit-low, FLT3-positive, IL7ralpha-positive, and SCA1-low. CD217-positive common lymphocyte precursor CD217-positive common lymphocyte progenitor CD217-positive common lymphoid precursor cell Markers are associated with mouse cells. Kit-positive, Sca1-positive common lymphoid progenitor true A common lymphoid progenitor that is Kit-low, FLT3-positive, IL7ralpha-positive, and SCA1-low. GOC:add GOC:amm GOC:tfm GO_REF:0000031 PMID:17952047 http://www.immgen.org/index_content.html A common myeloid progenitor that is CD34-positive, CD38-positive, IL3ra-low, CD10-negative, CD7-negative, CD45RA-negative, and IL-5Ralpha-negative. CD71-positive common myeloid precursor cell Markers are associated with human cell type. Originally described in the dendritic cell ontology (DC_CL:0000038)(PMID:19243617). CD34-positive, CD38-positive common myeloid progenitor A common myeloid progenitor that is CD34-positive, CD38-positive, IL3ra-low, CD10-negative, CD7-negative, CD45RA-negative, and IL-5Ralpha-negative. GOC:add GOC:amm GO_REF:0000031 PMCID:PMC2626675 PMID:16551251 CD7-negative lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-negative and CD45RA-negative. CD7-negative lymphoid precursor cell These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000039)(PMID:19243617). CD7-negative lymphoid progenitor cell true CD7-negative lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-negative and CD45RA-negative. GOC:amm GO_REF:0000031 PMID:16551251 CD7-positive lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-positive and is CD45RA-negative. CD7-positive lymphoid precursor cell These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000040)(PMID:19243617). CD7-positive lymphoid progenitor cell true CD7-positive lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-positive and is CD45RA-negative. GOC:amm GOC:tfm GO_REF:0000031 PMID:16551251 PMID:19491395 Common dendritic precursor is a hematopoietic progenitor cell that is CD117-low, CD135-positive, CD115-positive and lacks plasma membrane parts for hematopoietic lineage markers. CDP common dendritic precursor pro-DCs cell Surface markers are for mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000041) CDP are reportedly CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD11c-positive, CD14-negative, CD19-negative, CD20-negative, CD56-negative, B220-negative, Ly6g-negative, MHCII-positive, and Ter119-negative. (PMID:19243617). common dendritic progenitor Common dendritic precursor is a hematopoietic progenitor cell that is CD117-low, CD135-positive, CD115-positive and lacks plasma membrane parts for hematopoietic lineage markers. GOC:amm GOC:tfm GO_REF:0000031 PMID:16551251 PMID:17922016 PMID:19286519 CDP PMID:21219184 pro-DCs PMID:21219184 cell Originally described in the dendritic cell ontology (DC_CL:1111100)(PMID:19243617). CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor Granule cell that is part of the cerebellum. BTO:0004278 cell cerebellar granule cell true Granule cell that is part of the cerebellum. GOC:mah Granule cell that is part of the cerebral cortex. cell cortical granule cell Granule cell that is part of the cerebral cortex. GOC:mah Granule cell that is part of the hippocampus. cell hippocampal granule cell Granule cell that is part of the hippocampus. GOC:mah A cell that is maintained or propagated in a controlled artificial environment for use in an investigation. haendel 2012-01-12T09:58:38Z cell 'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. 'In vitro' is intended to contrast with 'native',which refers to cells or other biological entities that are found in a natural setting. It describes unicellular organisms removed from a natural environement and multicellular organism cells removed from an organism, or cells derived in culture from such displaced cells. cell in vitro A cell that is maintained or propagated in a controlled artificial environment for use in an investigation. ReO:mhb 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 Osteoblast that is terminally differentiated, located adjacent to acellular or cellular bone tissue within periosteum, and is capable of mineralizing the matrix. VSAO:0000116 cl terminally differentiated osteoblast Osteoblast that is terminally differentiated, located adjacent to acellular or cellular bone tissue within periosteum, and is capable of mineralizing the matrix. VSAO:curator Osteoblast that is non-terminally differentiated and located in cellular bone tissue or under the periosteum in acellular bone. VSAO:0000117 cl VSAO relationship simplified OBO_REL:integral_part_of VSAO:0000118 non-terminally differentiated osteoblast Osteoblast that is non-terminally differentiated and located in cellular bone tissue or under the periosteum in acellular bone. VSAO:curator A CD8-positive alpha-beta-positive T cell with the phenotype CXCR3-positive and having suppressor function. They are capable of producing IL-10, suppressing proliferation, and suppressing IFN-gamma production. CD8+CXCR3+ T cell CD8+CXCR3+ T lymphocyte CD8+CXCR3+ T(reg) CD8+CXCR3+ T-cell CD8+CXCR3+ Treg CD8-positive, CXCR3-positive, T(reg) CD8-positive, CXCR3-positive, Treg CD8-positive, CXCR3-positive, alpha-beta regulatory T lymphocyte CD8-positive, CXCR3-positive, alpha-beta regulatory T-cell CD8-positive, CXCR3-positive, alpha-beta regulatory T-lymphocyte cell These cells may be the human equivalent of murine CD8-positive, CD122-positive alpha-beta regulatory T cell. They are also found in the CD45RA-negative and CD62L-positive fraction. CD8-positive, CXCR3-positive, alpha-beta regulatory T cell true A CD8-positive alpha-beta-positive T cell with the phenotype CXCR3-positive and having suppressor function. They are capable of producing IL-10, suppressing proliferation, and suppressing IFN-gamma production. GOC:dsd PMID:19609979 CD4-positive, alpha-beta T cell that produces IL-22. T(H)-22 cell Th22 T cell Th22 T lymphocyte Th22 T-cell Th22 T-lymphocyte Th22 cell helper T cell type 22 cell TH22 cells are also reportedly CCR4-positive, CCR6-positive, CCR10-positive, CXCR3-negative. TH22 cells are reportedly capable of secreting IL-13. T-helper 22 cell true CD4-positive, alpha-beta T cell that produces IL-22. GOC:dsd PMID:19578368 PMID:19578369 A recently activated CD4-positive, alpha-beta T cell with the phenotype HLA-DRA-positive, CD38-positive, CD69-positive, CD62L-negative, CD127-negative, and CD25-positive. activated CD4+ T cell activated CD4-positive, alpha-beta T lymphocyte, human activated CD4-positive, alpha-beta T-cell, human activated CD4-positive, alpha-beta T-lymphocyte, human cell This cell type is compatible with the HIPC Lyoplate markers for 'activated CD4+ T cell', but includes via logical inference from its parent additional markers known to be expressed on activated CD4+ T cells. The inclusion of HLA-DRA in the definition restricts this definition to human activated CD4+ T cells, as activated mouse T cells do not express MHC class II. activated CD4-positive, alpha-beta T cell, human A recently activated CD4-positive, alpha-beta T cell with the phenotype HLA-DRA-positive, CD38-positive, CD69-positive, CD62L-negative, CD127-negative, and CD25-positive. GOC:add PMID:22343568 activated CD4+ T cell PMID:22343568 A CD4-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive. effector CD4+ T cell effector CD4-positive, alpha-beta T lymphocyte effector CD4-positive, alpha-beta T-cell effector CD4-positive, alpha-beta T-lymphocyte cell This cell type is compatible with the HIPC Lyoplate markers for 'effector CD4+ T cell'. The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy. effector CD4-positive, alpha-beta T cell A CD4-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive. GOC:add PMID:22343568 effector CD4+ T cell PMID:22343568 A naive regulatory T cell with the phenotype CD4-positive, CD25-positive, CD127lo, CCR4-positive, and CD45RO-negative. naive CCR4+ Treg naive CCR4-positive regulatory T lymphocyte naive CCR4-positive regulatory T-cell naive CCR4-positive regulatory T-lymphocyte cell This cell type is compatible with the HIPC Lyoplate markers for 'naive CCR4+ Treg'. The definition is valid for human; its applicability for mouse and other species is unknown. naive CCR4-positive regulatory T cell A naive regulatory T cell with the phenotype CD4-positive, CD25-positive, CD127lo, CCR4-positive, and CD45RO-negative. GOC:add PMID:22343568 naive CCR4+ Treg PMID:22343568 A memory regulatory T cell with phenotype CD4-positive, CD25-positive, CD127lo, CCR4-positive, and CD45RO-positive. memory CCR4+ Treg memory CCR4-positive regulatory T lymphocyte memory CCR4-positive regulatory T-cell memory CCR4-positive regulatory T-lymphocyte cell This cell type is compatible with the HIPC Lyoplate markers for 'memory CCR4+ Treg'. The definition is valid for human; its applicability for mouse and other species is unknown. memory CCR4-positive regulatory T cell A memory regulatory T cell with phenotype CD4-positive, CD25-positive, CD127lo, CCR4-positive, and CD45RO-positive. GOC:add PMID:22343568 memory CCR4+ Treg PMID:22343568 A CD4-positive, CD25-positive, alpha-beta regulatory T cell with the additional phenotype CCR4-positive. CCR+ Treg CD4-positive, CD25-positive, CCR4-positive, alpha-beta regulatory T lymphocyte CD4-positive, CD25-positive, CCR4-positive, alpha-beta regulatory T-cell CD4-positive, CD25-positive, CCR4-positive, alpha-beta regulatory T-lymphocyte cell This cell type is compatible with the HIPC Lyoplate markers for 'CCR4+ Treg'. The definition is valid for human; its applicability for mouse and other species is unknown. CD4-positive, CD25-positive, CCR4-positive, alpha-beta regulatory T cell A CD4-positive, CD25-positive, alpha-beta regulatory T cell with the additional phenotype CCR4-positive. GOC:add PMID:22343568 CCR+ Treg PMID:22343568 A CD4-positive, CD25-positive, CCR4-positive, alpha-beta T regulatory cell with the phenotype HLA-DRA-positive, indicating recent activation. activated CCR4+ Treg activated CD4-positive, CD25-positive, CCR4-positive, alpha-beta regulatory T lymphocyte activated CD4-positive, CD25-positive, CCR4-positive, alpha-beta regulatory T-cell activated CD4-positive, CD25-positive, CCR4-positive, alpha-beta regulatory T-lymphocyte cell This cell type is compatible with the HIPC Lyoplate markers for 'activated CCR4+ Treg'. The inclusion of HLA-DRA in the definition restricts this definition to human activated CD4+ T cells, as activated mouse T cells do not express MHC class II. activated CD4-positive, CD25-positive, CCR4-positive, alpha-beta regulatory T cell, human A CD4-positive, CD25-positive, CCR4-positive, alpha-beta T regulatory cell with the phenotype HLA-DRA-positive, indicating recent activation. GOC:add PMID:22343568 activated CCR4+ Treg PMID:22343568 A recently activated CD8-positive, alpha-beta T cell with the phenotype HLA-DRA-positive, CD38-positive, CD69-positive, CD62L-negative, CD127-negative, CCR7-negative, and CD25-positive. activated CD8+ T cell activated CD8-positive, alpha-beta T lymphocyte, human activated CD8-positive, alpha-beta T-cell, human activated CD8-positive, alpha-beta T-lymphocyte, human cell This cell type is compatible with the HIPC Lyoplate markers for 'activated CD8+ T cell', but includes via logical inference from its parent additional markers known to be expressed on activated CD8+ T cells. The inclusion of HLA-DRA in the definition restricts this definition to human activated CD8+ T cells, as activated mouse T cells do not express MHC class II. activated CD8-positive, alpha-beta T cell, human A recently activated CD8-positive, alpha-beta T cell with the phenotype HLA-DRA-positive, CD38-positive, CD69-positive, CD62L-negative, CD127-negative, CCR7-negative, and CD25-positive. GOC:add PMID:22343568 activated CD8+ T cell PMID:22343568 A CD8-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive. effector CD8+ T cell effector CD8-positive, alpha-beta T lymphocyte effector CD8-positive, alpha-beta T-cell effector CD8-positive, alpha-beta T-lymphocyte cell This cell type is compatible with the HIPC Lyoplate markers for 'effector CD8+ T cell'. The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy. effector CD8-positive, alpha-beta T cell A CD8-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive. GOC:add PMID:22343568 effector CD8+ T cell PMID:22343568 A CD4-positive, alpha-beta T cell that has the phenotype CXCR3-negative, CCR6-negative. non-Th1/Th17 CD4+ T cell CD4-positive, CXCR3-negative, CCR6-negative, alpha-beta T lymphocyte CD4-positive, CXCR3-negative, CCR6-negative, alpha-beta T-cell CD4-positive, CXCR3-negative, CCR6-negative, alpha-beta T-lymphocyte cell This cell type is compatible with the HIPC Lyoplate markers for 'non-Th1/Th17 CD4+ T cell'. Cells of this phenotype may include T-helper 2 T cells and some naive CD4+ T cells. CD4-positive, CXCR3-negative, CCR6-negative, alpha-beta T cell A CD4-positive, alpha-beta T cell that has the phenotype CXCR3-negative, CCR6-negative. GOC:add PMID:22343568 non-Th1/Th17 CD4+ T cell PMID:22343568 A CD8-positive, alpha-beta T cell that has the phenotype CXCR3-negative, CCR6-negative. non-Tc1/Tc17 CD8+ T cell CD8-positive, CXCR3-negative, CCR6-negative, alpha-beta T lymphocyte CD8-positive, CXCR3-negative, CCR6-negative, alpha-beta T-cell CD8-positive, CXCR3-negative, CCR6-negative, alpha-beta T-lymphocyte cell This cell type is compatible with the HIPC Lyoplate markers for 'non-Tc1/Tc17 CD8+ T cell'. Cells of this phenotype may include Tc2 T cells and some naive CD8+ T cells. CD8-positive, CXCR3-negative, CCR6-negative, alpha-beta T cell A CD8-positive, alpha-beta T cell that has the phenotype CXCR3-negative, CCR6-negative. GOC:add PMID:22343568 non-Tc1/Tc17 CD8+ T cell PMID:22343568 A memory B cell that lacks expression of surface IgD. IgD- memory B cell cell This cell type is compatible with the HIPC Lyoplate markers for 'IgD- memory B cell'. The majority of these cells are class-switched, though some are IgM-positive. IgD-negative memory B cell A memory B cell that lacks expression of surface IgD. GOC:add PMID:22343568 IgD- memory B cell PMID:22343568 A monocyte that expresses CD14 and is negative for the lineage markers CD3, CD19, and CD20. monocyte cell This cell type is compatible with the HIPC Lyoplate markers for 'monocyte'. Note that while CD14 is considered a reliable marker for human monocytes, it is only expressed on approximately 85% of mouse monocytes. CD14-positive monocyte A monocyte that expresses CD14 and is negative for the lineage markers CD3, CD19, and CD20. GOC:add PMID:22343568 monocyte PMID:22343568 An intermediate monocyte that is CD14-positive and with low amounts of CD16. intermediate monocyte, human cell Definition is valid for human intermediate monocytes. CD14-positive, CD16-low monocyte An intermediate monocyte that is CD14-positive and with low amounts of CD16. GOC:add PMID:20628149 A dendritic cell with the phenotype HLA-DRA-positive. dendritic cell cell This cell type is compatible with the HIPC Lyoplate markers for 'dendritic cell'. The inclusion of HLA-DRA in the definition restricts this definition to human dendritic cells. dendritic cell, human A dendritic cell with the phenotype HLA-DRA-positive. GOC:add PMID:22343568 dendritic cell PMID:22343568 A myeloid dendritic cell with the phenotype HLA-DRA-positive. myeloid dendritic cell cell This cell type is compatible with the HIPC Lyoplate markers for 'myeloid dendritic cell'. The inclusion of HLA-DRA in the definition restricts this definition to human myeloid dendritic cells. myeloid dendritic cell, human A myeloid dendritic cell with the phenotype HLA-DRA-positive. GOC:add PMID:22343568 myeloid dendritic cell PMID:22343568 A plasmacytoid dendritic cell with the phenotype HLA-DRA-positive, CD123-positive, and CD11c-negative. plasmacytoid dendritic cell cell This cell type is compatible with the HIPC Lyoplate markers for 'plasmacytoid dendritic cell'. The inclusion of HLA-DRA in the definition restricts this definition to human plasmacytoid dendritic cells. plasmacytoid dendritic cell, human A plasmacytoid dendritic cell with the phenotype HLA-DRA-positive, CD123-positive, and CD11c-negative. GOC:add PMID:22343568 plasmacytoid dendritic cell PMID:22343568 A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. These cells are CD34-positive, and express Gata1, Gata2, C/EBPa, and Pu.1. CMP common myeloid precursor, CD34-positive cell CFU-GEMM CFU-S colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte multipotential myeloid stem cell myeloid stem cell pluripotent stem cell (bone marrow) CMP are reportedly CD16-positive, CD32-positive, CD38-positive, CD45RA-negative, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. common myeloid progenitor, CD34-positive A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. These cells are CD34-positive, and express Gata1, Gata2, C/EBPa, and Pu.1. GOC:add GOC:dsd GOC:tfm ISBN:0878932437 PMCID:PMC2212039 PMID:10724173 PMID:16551251 PMID:16647566 CMP ISBN:0878932437 CFU-GEMM ISBN:0878932437 CFU-S ISBN:0878932437 colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte ISBN:0878932437 multipotential myeloid stem cell ISBN:0878932437 myeloid stem cell ISBN:0878932437 pluripotent stem cell (bone marrow) ISBN:0878932437 A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. tmeehan 2010-01-06T03:43:27Z cell hematopoietic oligopotent progenitor cell, lineage-negative A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. GOC:tfm PMID:19022770 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 CD8-positive, alpha beta memory T cell with the phenotype CD45RA-positive, CD45RO-negative, and CCR7-negative. TEMRA CD8+ TEMRA CD8-positive TEMRA cell This cell type is seen in human but not found in the mouse. effector memory CD8-positive, alpha-beta T cell, terminally differentiated A CD8-positive, alpha beta memory T cell with the phenotype CD45RA-positive, CD45RO-negative, and CCR7-negative. GOC:add GOC:dos PMID:15032595 PMID:16237082 PMID:26883338 TEMRA PMID:15032595 CD8+ TEMRA PMID:15032595 CD8-positive TEMRA PMID:15032595 An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism. 2017-01-30T19:16:26Z https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12922 cell tumor cell tumour cell https://github.com/obophenotype/cell-ontology/issues/448 neoplastic cell An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism. GOC:add GOC:cg GOC:wdd A neoplastic cell that is capable of entering a surrounding tissue 2017-01-30T19:39:12Z https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12917 cell cancer cell https://github.com/obophenotype/cell-ontology/issues/448 malignant cell A neoplastic cell that is capable of entering a surrounding tissue GOC:add GOC:cg GOC:wdd A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and dendritic cell markers, that functions as part of the innate immune response to produce cytokines and other effector responses. 2017-01-30T20:20:48Z cell innate lymphoid cell A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and dendritic cell markers, that functions as part of the innate immune response to produce cytokines and other effector responses. GOC:add GOC:dsd PMID:23292121 PMID:23348417 A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative). BTO:0004911 cell BFU-E CFU-E blast forming unit erythroid burst forming unit erythroid colony forming unit erythroid erythroid stem cell erythroid progenitor cell, mammalian A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative). GOC:add ISBN:0721601464 An innate lymphoid cell that is capable of producing the type 1 cytokine IFN-gamma, but not Th2 or Th17 cell-associated cytokines. 2017-01-30T20:42:44Z cell group 1 innate lymphoid cell An innate lymphoid cell that is capable of producing the type 1 cytokine IFN-gamma, but not Th2 or Th17 cell-associated cytokines. GOC:add GOC:dsd PMID:23348417 A group 1 innate lymphoid cell that is non-cytotoxic. 2017-01-30T20:54:12Z cell ILC1 A group 1 innate lymphoid cell that is non-cytotoxic. GOC:add GOC:dsd PMID:23292121 PMID:23348417 An innate lymphoid cell that is capable of producing T-helper 2-cell associated cytokines upon stimulation. 2017-01-30T21:20:08Z ILC2 natural helper cell nuocyte cell group 2 innate lymphoid cell An innate lymphoid cell that is capable of producing T-helper 2-cell associated cytokines upon stimulation. GOC:add GOC:dsd PMID:23292121 PMID:23562755 A fat cell that is beige in color, thermogenic, and which differentiates in white fat tissue from a Myf5-negative progenitor. beige brown adipocyte beige fat cell beige/brite adipocyte brite adipocyte brite cell brite fat cell cell beige adipocyte A fat cell that is beige in color, thermogenic, and which differentiates in white fat tissue from a Myf5-negative progenitor. GOC:add GOC:cvs GOC:ymb PMID:22796012 PMID:25851693 An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22. 2017-01-31T20:21:26Z ILC3 cell group 3 innate lymphoid cell An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22. GOC:add GOC:dsd PMID:23292121 PMID:23348417 An innate lymphoid cell in the human with the phenotype CD34-negative, CD117-positive, and a precusor to NK cells, ILC2 cells, and ILC3 cells. CD34-negative, CD117-positive ILC CD34-negative, CD117-positive ILCP CD34-negative, CD117-positive innate lymphoid cell precusor CD34-negative, CD117-positive innate lymphoid cell, human An innate lymphoid cell in the human with the phenotype CD34-negative, CD117-positive, and a precusor to NK cells, ILC2 cells, and ILC3 cells. GOC:add PMID:30193847 PMID:31201208 An innate lymphoid cell in the human with the phenotype CD34-negative, CD56-positive, CD117-positive.Thie cell type may include precusors to NK cells and ILC3 cells. CD34-negative, CD56-positive, CD117-positive ILC CD34-negative, CD56-positive, CD117-positive ILCP CD34-negative, CD56-positive, CD117-positive innate lymphoid cell precursor CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human An innate lymphoid cell in the human with the phenotype CD34-negative, CD56-positive, CD117-positive.Thie cell type may include precusors to NK cells and ILC3 cells. GOC:add PMID:30193847 PMID:31201208 An innate lymphoid cell precursor in the human with the phenotype CD34-positive, CD56-positive, CD117-positive.Thie cell type may include precusors to NK cells and ILC3 cells. CD34-positive, CD56-positive, CD117-positive CILP CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human An innate lymphoid cell precursor in the human with the phenotype CD34-positive, CD56-positive, CD117-positive.Thie cell type may include precusors to NK cells and ILC3 cells. GOC:add PMID:30193847 An innate lymphoid cell in the human with the phenotype KLRG1-positive that is a precusor for ILC2 cells. KLRG1-positive ILC KLRG1-positive innate lymphoid cell, human An innate lymphoid cell in the human with the phenotype KLRG1-positive that is a precusor for ILC2 cells. GOC:add PMID:31201208 An innate lymphoid cell in the human with the phenotype NKp46-positive that is a precusor for NK cells and ILC3 cells. NKp46-positive ILC NKp46-positive innate lymphoid cell, human An innate lymphoid cell in the human with the phenotype NKp46-positive that is a precusor for NK cells and ILC3 cells. GOC:add PMID:31201208 PMID:31337734 An ILC1 cell in the human with the phenotype CD56-negative, IL-7Ralpha-positive, T-bet-positive. innate lymphoid cell 1, human ILC1, human An ILC1 cell in the human with the phenotype CD56-negative, IL-7Ralpha-positive, T-bet-positive. GOC:add PMID:31500958 A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha-positive. ILC3, human group 3 innate lymphoid cell, human A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha-positive. GOC:add PMID:31500958 A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha-positive, and NKp44-positive. NKp44-positive group 3 innate lymphoid cell, human A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha-positive, and NKp44-positive. GOC:add PMID:24778151 PMID:31500958 A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha-positive, and NKp44-negative. NKp44-negative group 3 innate lymphoid cell, human A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha-positive, and NKp44-negative. GOC:add PMID:24778151 PMID:31500958 A group 2 innate lymphoid cell in the human with the phenotype CD25-positive, CD127-positive, CD161-positive, and GATA-3-positive. ILC2, human group 2 innate lymphoid cell, human A group 2 innate lymphoid cell in the human with the phenotype CD25-positive, CD127-positive, CD161-positive, and GATA-3-positive. GOC:add PMID:24778151 PMID:26844414 An innate lyphoid cell with an immature phenotype. immature ILC immature innate lymphoid cell An innate lyphoid cell with an immature phenotype. GOC:add A CD4-positive, alpha beta memory T cell with the phenotype CD45RA-positive, CD45RO-negative, and CCR7-negative. 2021-01-18T16:32:44Z TEMRA CD4+ TEMRA CD4-positive TEMRA cell This cell type is seen in human but not found in the mouse. effector memory CD4-positive, alpha-beta T cell, terminally differentiated A CD4-positive, alpha beta memory T cell with the phenotype CD45RA-positive, CD45RO-negative, and CCR7-negative. GOC:add PMID:17465678 PMID:26883338 PMID:27997758 PMID:29133794 TEMRA PMID:17465678 CD4+ TEMRA PMID:17465678 CD4-positive TEMRA PMID:17465678 A lymphocyte of B lineage that is CD19-positive. https://orcid.org/0000-0001-9990-8331 cell Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). lymphocyte of B lineage, CD19-positive A lymphocyte of B lineage that is CD19-positive. GOC:add A B cell that is CD19-positive. https://orcid.org/0000-0001-9990-8331 B lymphocyte, CD19-positive B-cell, CD19-positive B-lymphocyte, CD19-positive CD19+ B cell CD19-positive B cell cell B cell, CD19-positive A B cell that is CD19-positive. GOC:add A plasmablast that is CD86-positive. https://orcid.org/0000-0001-9990-8331 CD86-positive, CD20-negative plasmablast CD86+ plasmablast cell CD86-positive plasmablast A plasmablast that is CD86-positive. GOC:add PMID:20398308 A CD8-positive, alpha-beta T cell with memory phenotype indicated by being CD45RO and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122-high. CD8-positive, alpha-beta memory T lymphocyte, CD45RO-positive CD8-positive, alpha-beta memory T-cell, CD45RO-positive CD8-positive, alpha-beta memory T-lymphocyte, CD45RO-positive cell CD8-positive, alpha-beta memory T cell, CD45RO-positive true A CD8-positive, alpha-beta T cell with memory phenotype indicated by being CD45RO and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122-high. GOC:tfm GO_REF:0000031 PMID:20146720 CD4-positive, alpha-beta long-lived T cell with the phenotype CD45RO-positive and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122-high. CD4-positive, alpha-beta memory T lymphocyte, CD45RO-positive CD4-positive, alpha-beta memory T-cell, CD45RO-positive CD4-positive, alpha-beta memory T-lymphocyte, CD45RO-positive cell CD4-positive, alpha-beta memory T cell, CD45RO-positive true CD4-positive, alpha-beta long-lived T cell with the phenotype CD45RO-positive and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122-high. GOC:add GOC:tfm GO_REF:0000031 ISBN:0781735149 http://www.immgen.org/index_content.html FBbt:00004230 cell visual pigment cell (sensu Nematoda and Protostomia) An erythroid progenitor cell is Kit-positive, Ly6A-negative, CD41-negative, CD127-negative, and CD123-negative. This cell type is also described as being lin-negative, Kit-positive, CD150-negative, CD41-negative, CD105-positive, and FcgR-negative. tmeehan 2010-04-26T10:14:16Z c- Kit-positive erythroid progenitor cell cell Markers found on mouse cells. Kit-positive erythroid progenitor cell true An erythroid progenitor cell is Kit-positive, Ly6A-negative, CD41-negative, CD127-negative, and CD123-negative. This cell type is also described as being lin-negative, Kit-positive, CD150-negative, CD41-negative, CD105-positive, and FcgR-negative. GOC:ak GOC:tfm PMID:19805084 http://www.immgen.org/index_content.html A granulocyte monocyte progenitor is CD34-positive, CD38-positive, IL-3receptor-alpha-positive and is CD45RA-negative. tmeehan 2010-01-13T03:19:22Z cell Markers are for human cells. According to different research groups, CD45RA is present or absent on this cell population. CD34-positive, CD38-positive granulocyte monocyte progenitor true A granulocyte monocyte progenitor is CD34-positive, CD38-positive, IL-3receptor-alpha-positive and is CD45RA-negative. GOC:tfm PMID:12615892 PMID:19022770 A granulocyte monocyte progenitor that is Kit-positive, CD34-positive, Fc-gamma receptor II/II-positive, and is Sca-1-negative, Il7ra-negative, Cxc3r1-negative, and CD90-negative. tmeehan 2010-01-13T03:19:28Z cell Markers are found on mouse cells. Kit-positive granulocyte monocyte progenitor true A granulocyte monocyte progenitor that is Kit-positive, CD34-positive, Fc-gamma receptor II/II-positive, and is Sca-1-negative, Il7ra-negative, Cxc3r1-negative, and CD90-negative. GOC:tfm PMID:12615892 PMID:16322423 PMID:19022770 PMID:19273628 http://www.immgen.org/index_content.html An erythroid progenitor cell that is CD34-positive and is GlyA-negative. tmeehan 2010-04-26T10:14:30Z FMA:83517 cell Cell markers associated with human cells. CD34-positive, GlyA-negative erythroid progenitor cell true An erythroid progenitor cell that is CD34-positive and is GlyA-negative. GOC:ak GOC:tfm PMID:19621348 A proerythoblast that is CD34-negative and GlyA-negative. tmeehan 2010-04-26T10:31:50Z cell Cell surface markers are associated with human cells. CD34-negative, GlyA-negative proerythroblast true A proerythoblast that is CD34-negative and GlyA-negative. GOC:ak GOC:tfm PMID:19621348 A megakaryocyte erythroid progenitor cell is CD34-positive, CD38-positive and is IL3-receptor alpha-negative and CD45RA-negative. tmeehan 2010-01-13T03:43:10Z cell Markers are associated with human cell type. CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell true A megakaryocyte erythroid progenitor cell is CD34-positive, CD38-positive and is IL3-receptor alpha-negative and CD45RA-negative. GOC:tfm PMID:12615892 PMID:190227700 A megakaryocyte erythroid progenitor cell that is Kit-positive and is Sca1-negative, CD34-negative, CD90-negative, IL7r-alpha-negative and Fcgr II/III-low. tmeehan 2010-01-13T03:43:12Z cell Markers are associated with mouse cells. Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell true A megakaryocyte erythroid progenitor cell that is Kit-positive and is Sca1-negative, CD34-negative, CD90-negative, IL7r-alpha-negative and Fcgr II/III-low. GOC:tfm PMID:12615892 PMID:19022770 http://www.immgen.org/index_content.html A lineage marker-negative, CD34-positive, IL5r-alpha-positive, and Sca1-negative eosinophil progenitor cell. tmeehan 2010-01-14T03:25:15Z cell Markers are found on mouse cells. Kit-low, CD34-positive eosinophil progenitor cell true A lineage marker-negative, CD34-positive, IL5r-alpha-positive, and Sca1-negative eosinophil progenitor cell. GOC:tfm PMID:17582345 A lineage marker-negative, CD34-positive, CD38-positive, IL3r-alpha-positive, IL5r-alpha-positive, and CD45RA-negative eosinophil progenitor cell. tmeehan 2010-01-14T03:25:17Z cell Markers are associated with human cells. CD34-positive, CD38-positive eosinophil progenitor cell true A lineage marker-negative, CD34-positive, CD38-positive, IL3r-alpha-positive, IL5r-alpha-positive, and CD45RA-negative eosinophil progenitor cell. GOC:tfm PMCID:PMC2626675 A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. tmeehan 2010-01-19T02:51:58Z MDP cell macrophage dendritic cell progenitor true A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. GOC:tfm PMID:19273628 A lin-negative, MHC-II-negative, CD11c-positive, FLT3-positive cell with intermediate expression of SIRP-alpha. tmeehan 2010-01-19T03:39:30Z cell pre-conventional dendritic cell true A lin-negative, MHC-II-negative, CD11c-positive, FLT3-positive cell with intermediate expression of SIRP-alpha. GOC:tfm A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. Marker for this cell is Kit-high, CD115-positive, CD135-positive, Cx3cr1-positive, and is Il7ra-negative. tmeehan 2010-01-26T02:43:40Z murine MDP cell Markers are associated with mouse cells. Kit-positive macrophage dendritic cell progenitor true A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. Marker for this cell is Kit-high, CD115-positive, CD135-positive, Cx3cr1-positive, and is Il7ra-negative. GOC:tfm PMID:19273628 A proerythoblast that is Kit-low, Lyg76-positive, and CD71-positive. tmeehan 2010-04-26T10:31:56Z cell Markers are associated with mouse cells. Kit-low proerythroblast true A proerythoblast that is Kit-low, Lyg76-positive, and CD71-positive. GOC:ak GOC:tfm PMID:19805084 A basophilic erythroblast that is GlyA-positive. tmeehan 2010-04-26T10:41:15Z cell Markers are associated with human cells. GlyA-positive basophillic erythroblast true A basophilic erythroblast that is GlyA-positive. GOC:ak GOC:tfm PMID:1638021 A basophilic erythroblast that is Lyg 76-high and is Kit-negative. tmeehan 2010-04-26T10:41:22Z cell Cell surface markers are associated with mouse cells. Kit-negative, Ly-76 high basophilic erythroblast true A basophilic erythroblast that is Lyg 76-high and is Kit-negative. GOC:ak GOC:tfm PMID:19805084 A polychromatophilic erythroblast that is Lyg 76-high and is Kit-negative. tmeehan 2010-04-26T10:53:11Z late basophilic and polychromatophilic erythroblast cell Kit-negative, Ly-76 high polychromatophilic erythroblast true A polychromatophilic erythroblast that is Lyg 76-high and is Kit-negative. GOC:ak GOC:tfm PMID:19805084 A polychromatiic erythroblast that is Gly-A-positive and CD71-low. tmeehan 2010-04-26T10:53:16Z cell Cell surface markers are associated with human cells. CD71-low, GlyA-positive polychromatic erythroblast true A polychromatiic erythroblast that is Gly-A-positive and CD71-low. GOC:ak GOC:tfm PMID:1638021 An orthochromatophilic erythroblast that is ter119-high, CD71-low, and Kit-negative. tmeehan 2010-04-26T11:04:15Z cell Cell surface markers associated with mouse cells. Kit-negative, Ly-76 high orthochromatophilic erythroblasts true An orthochromatophilic erythroblast that is ter119-high, CD71-low, and Kit-negative. GOC:ak GOC:tfm PMID:19805084 An erythroblast that is GlyA-positive and CD71-negative. tmeehan 2010-04-26T11:04:21Z cell Markers associated with human cells. CD71-negative, GlyA-positive orthochromatic erythroblast true An erythroblast that is GlyA-positive and CD71-negative. GOC:ak GOC:tfm PMID:1638021 A reticulocyte that is Ly76-high and is Kit-negative. tmeehan 2010-04-26T11:37:00Z cell Marker associated with mouse cells. Ly-76 high reticulocyte true A reticulocyte that is Ly76-high and is Kit-negative. GOC:ak GOC:tfm PMID:18539294 A reticulocyte that is GlyA-positive. tmeehan 2010-04-26T11:48:25Z cell Markers is associated with human cells. GlyA-positive reticulocytes true A reticulocyte that is GlyA-positive. GOC:ak GOC:tfm PMID:1638021 An enucleate erythrocyte that is GlyA-positive. tmeehan 2010-04-26T11:51:22Z cell Marker is associated with human cell types. GlyA-positive erythrocyte true An enucleate erythrocyte that is GlyA-positive. GOC:ak GOC:tfm PMID:20134094 An enucleate erythrocyte that is Lyg-76-high. tmeehan 2010-04-26T11:51:27Z cell Marker is associated with mouse cell types. Ly-76 high positive erythrocyte true An enucleate erythrocyte that is Lyg-76-high. GOC:ak GOC:tfm PMID:19805084 A megakaroycotye progenitor cell that is CD34-positive, CD41-positive and CD42-positive on the cell surface. tmeehan 2010-04-26T02:39:09Z cell Markers are associated with human cell type. CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell true A megakaroycotye progenitor cell that is CD34-positive, CD41-positive and CD42-positive on the cell surface. GOC:ak GOC:tfm PMID:15232614 A megakaryocyte progenitor cell that is Kit-positive, CD41-positive, CD9-positive, Sca-1-negative, IL7ralpha-negative, CD150-negative, and Fcgamma receptor II/III-low. tmeehan 2010-04-26T02:39:15Z cell Markers are associated with mouse cells. Kit-positive megakaryocyte progenitor cell true A megakaryocyte progenitor cell that is Kit-positive, CD41-positive, CD9-positive, Sca-1-negative, IL7ralpha-negative, CD150-negative, and Fcgamma receptor II/III-low. GOC:ak GOC:tfm PMID:16951553 A megakaryocyte progenitor cell that is CD34-positive, CD41-positive, and CD42-negative. tmeehan 2010-04-26T03:52:47Z cell Markers are commonly associated with human cells. CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell true A megakaryocyte progenitor cell that is CD34-positive, CD41-positive, and CD42-negative. GOC:ak GOC:tfm PMID:15232614 A megakaryocyte progenitor cell that is CD34-negative, CD41-positive and CD42-positive. tmeehan 2010-04-26T03:59:22Z cell Markers are commonly associated with human cells. CD34-negative, CD41-positive, CD42-positive megakaryocyte cell true A megakaryocyte progenitor cell that is CD34-negative, CD41-positive and CD42-positive. GOC:ak GOC:tfm PMID:15232614 A megakaryocyte cell with is CD9-positive and CD41-positive. tmeehan 2010-04-27T10:39:07Z cell Markers are commonly associated with mouse cells. CD9-positive, CD41-positive megakaryocyte cell true A megakaryocyte cell with is CD9-positive and CD41-positive. GOC:tfm A cell type that can give rise to basophil and mast cells. This cell is CD34-positive, CD117-positive, CD125-positive, FceRIa-negative, and T1/ST2-negative, and expresses Gata-1, Gata-2, C/EBPa tmeehan 2010-04-27T12:46:33Z BMCP cell There may be an intermediate cell type. These cells also CD13-positive, CD16-positive, CD32-positive, and integrin beta 7-positive. Transcription factors: GATA1-positive, MCP-1-positive, mitf-positive, PU.1-positive, and CEBP/a-low. basophil mast progenitor cell A cell type that can give rise to basophil and mast cells. This cell is CD34-positive, CD117-positive, CD125-positive, FceRIa-negative, and T1/ST2-negative, and expresses Gata-1, Gata-2, C/EBPa GOC:ak GOC:dsd GOC:tfm PMCID:PMC1312421 A lineage-negative, Kit-positive, CD45-positive mast cell progenitor that is Fc-epsilon RIalpha-low. tmeehan 2010-04-27T01:22:19Z cell Fc-epsilon RIalpha-low mast cell progenitor true A lineage-negative, Kit-positive, CD45-positive mast cell progenitor that is Fc-epsilon RIalpha-low. GOC:tfm PMCID:PMC1312421 A lineage negative, Sca1-negative basophil progenitor cell that is Fc epsilon RIalpha-high. tmeehan 2010-04-27T01:22:32Z cell Markers are associated with mouse cells. Fc-epsilon RIalpha-high basophil progenitor cell true A lineage negative, Sca1-negative basophil progenitor cell that is Fc epsilon RIalpha-high. GOC:tfm PMCID:PMC1312421 A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. tmeehan 2010-01-06T03:43:20Z cell hematopoietic lineage restricted progenitor cell A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. GOC:tfm PMID:19022770 A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. tmeehan 2010-01-06T03:43:27Z cell This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. GOC:tfm PMID:19022770 https://orcid.org/0000-0001-5208-3432 A hematopoietic stem cell capable of rapid replenishment of myeloerythroid progenitors and limited self renewal capability. This cell is Kit-positive, Sca1-positive, CD34-positive, CD150-positive, and is Flt3-negative. tmeehan 2010-01-08T09:19:25Z ST stem cell ST-HSC cell Markers are associated with mouse cells. These cells are also reportedly CD11b-low and CD90-low. short term hematopoietic stem cell true A hematopoietic stem cell capable of rapid replenishment of myeloerythroid progenitors and limited self renewal capability. This cell is Kit-positive, Sca1-positive, CD34-positive, CD150-positive, and is Flt3-negative. GOC:tfm PMID:15572596 PMID:19022770 A hematopoietic stem cell with long term self renewal capability. This cell is Kit-positive, Sca1-positive, CD150-positive, CD90-low, CD34-negative and Flt3-negative. tmeehan 2010-01-08T09:19:28Z LT stem cell LT-HSC cell Markers are associated with mouse cells. long term hematopoietic stem cell true A hematopoietic stem cell with long term self renewal capability. This cell is Kit-positive, Sca1-positive, CD150-positive, CD90-low, CD34-negative and Flt3-negative. GOC:tfm PMID:15572596 PMID:17582345 A hematopoietic progenitor that has restricted self-renewal capability. Cell is Kit-positive, Ly6-positive, CD150-negative and Flt3-negative. tmeehan 2010-01-08T11:16:33Z cell Markers are associated with mouse cells. Slamf1-negative multipotent progenitor cell true A hematopoietic progenitor that has restricted self-renewal capability. Cell is Kit-positive, Ly6-positive, CD150-negative and Flt3-negative. GOC:tfm PMID:19022770 A hematopoietic progenitor that has some limited self-renewal capability. Cells are lin-negative, Kit-positive, CD34-positive, and Slamf1-positive. tmeehan 2010-01-08T11:16:35Z KSL cell cell Markers are associated with mouse cells. Slamf1-positive multipotent progenitor cell true A hematopoietic progenitor that has some limited self-renewal capability. Cells are lin-negative, Kit-positive, CD34-positive, and Slamf1-positive. GOC:tfm PMID:19022770 Intraepithelial T cells with a memory phenotype of CD2-positive, CD5-positive, and CD44-positive. tmeehan 2009-10-20T02:20:43Z memory alpha beta IEL cell CD2-positive, CD5-positive, CD44-positive alpha-beta intraepithelial T cell true Intraepithelial T cells with a memory phenotype of CD2-positive, CD5-positive, and CD44-positive. GOC:tfm PMID:16048545 memory alpha beta IEL PMID:16048545 A CD4-positive, CXCR5-positive, CCR7-negative alpha-beta T cell located in follicles of secondary lymph nodes that expresses is BCL6-high, ICOS-high and PD1-high, and stimulates follicular B cells to undergo class-switching and antibody production. tmeehan 2009-10-29T04:01:27Z T(FH) Tfh cell follicular B helper T cell follicular T cell follicular T-cell follicular T-helper cell follicular helper T cell follicular helper T-cell T follicular helper cell true A CD4-positive, CXCR5-positive, CCR7-negative alpha-beta T cell located in follicles of secondary lymph nodes that expresses is BCL6-high, ICOS-high and PD1-high, and stimulates follicular B cells to undergo class-switching and antibody production. GOC:tfm PMID:19855402 PMID:20107805 PMID:22043829 T(FH) PMID:20207847 Tfh PMID:20107805 PMID:20383172 follicular B helper T cell PMID:22043829 follicular T cell PMID:20107805 PMID:21914188 follicular T-helper cell PMID:22552227 follicular helper T cell PMID:22649468 follicular helper T-cell PMID:22508770 A CD24-high, CD4-low, CD8-low, CD44-negative, NK1.1-negative NK T cell. tmeehan 2009-10-29T04:09:16Z cell immature NK T cell stage I true A CD24-high, CD4-low, CD8-low, CD44-negative, NK1.1-negative NK T cell. GOC:tfm PMID:17589542 A CD24-low, CD44-negative, NK1.1-negative NK T cell. tmeehan 2009-10-29T04:13:43Z NKT.44-NK1.1-.Th cell NKT.44-NK1.1-.Th was assigned as an exact synonym based on sorting strategy displayed at immgene.org. immature NK T cell stage II true A CD24-low, CD44-negative, NK1.1-negative NK T cell. GOC:tfm PMID:17589542 http://www.immgen.org/index_content.html A CD24-low, CD44-positive, DX5-low, NK1.1-negative NK T cell. tmeehan 2009-10-29T04:14:48Z NKT.44+.NK1.1-.Th cell immature NK T cell stage III true A CD24-low, CD44-positive, DX5-low, NK1.1-negative NK T cell. PMID:17589542 A CD24-low, CD44-positive, DX5-high, NK1.1-negative NK T cell. tmeehan 2009-10-29T04:17:38Z NKT.44+.NK1.1-.Th cell immature NK T cell stage IV true A CD24-low, CD44-positive, DX5-high, NK1.1-negative NK T cell. GOC:tfm PMID:17589542 http://www.immgen.org/index_content.html A hematopoietic multipotent progenitor cell that is CD34-positive, CD38-negative, CD45RA-negative, and CD90-negative. tmeehan 2010-01-12T11:14:15Z cell Cell markers are associated with human hematopoietic multipotent progenitor cells. CD34-positive, CD38-negative multipotent progenitor cell true A hematopoietic multipotent progenitor cell that is CD34-positive, CD38-negative, CD45RA-negative, and CD90-negative. GOC:tfm PMID:18371405 PMID:19022770 A basophil mast progenitor cell that is Beta-7 integrin-high, Kit-positive FcRgammaII/III-positive and Sca1-negative. tmeehan 2010-04-27T01:22:38Z cell Markers are associated with mouse cells. Kit-positive, integrin beta7-high basophil mast progenitor cell true A basophil mast progenitor cell that is Beta-7 integrin-high, Kit-positive FcRgammaII/III-positive and Sca1-negative. GOC:ak GOC:tfm A pro-B cell that CD45R/B220-positive, CD43-positive, HSA-low, BP-1-negative and Ly6c-negative. This cell type is also described as being lin-negative, AA4-positive, Kit-positive, IL7Ra-positive and CD45R-positive. tmeehan 2010-04-28T10:50:07Z fraction A cell pre pro B cell Markers associated with mouse cells. Fraction A pre-pro B cell true A pro-B cell that CD45R/B220-positive, CD43-positive, HSA-low, BP-1-negative and Ly6c-negative. This cell type is also described as being lin-negative, AA4-positive, Kit-positive, IL7Ra-positive and CD45R-positive. GOC:ak GOC:tfm PMID:12633665 PMID:17582343 http://www.immgen.org/index_content.html A pro-B cell that is CD22-positive, CD34-positive, CD38-positive and TdT-positive (has TdT activity). Pre-BCR is expressed on the cell surface. Cell is CD19-negative, CD20-negative, complement receptor type 2-negative and CD10-low. D-to-J recombination of the heavy chain occurs at this stage. tmeehan 2010-04-28T11:19:11Z cell Markers are commonly associated with human cells. These cells are also reportedly CD21-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. early pro-B cell true A pro-B cell that is CD22-positive, CD34-positive, CD38-positive and TdT-positive (has TdT activity). Pre-BCR is expressed on the cell surface. Cell is CD19-negative, CD20-negative, complement receptor type 2-negative and CD10-low. D-to-J recombination of the heavy chain occurs at this stage. GOC:dsd GOC:tfm PMID:18432934 A precursor B cell that is CD45RA-positive, CD43-positive, CD24-positive and BP-1-negative. tmeehan 2010-04-28T11:56:21Z Fr. B Fraction B cell Markers are commonly associated with mouse cells. These cells are also reportedly RAG1-positive and RAG2-positive. Fraction B precursor B cell true A precursor B cell that is CD45RA-positive, CD43-positive, CD24-positive and BP-1-negative. GOC:ak GOC:tfm PMID:18432934 A pre-B cell precursor is CD19-low, CD22-positive , CD34-positive, CD38-positive. tmeehan 2010-04-28T12:06:06Z cell Late pro-B cells are also reportedly CD10-positive, CD20-negative, CD21-negative, and TdT-positive. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. late pro-B cell true A pre-B cell precursor is CD19-low, CD22-positive , CD34-positive, CD38-positive. GOC:dsd GOC:tfm PMID:18432934 A precursor B cell is CD45R-positive, CD43-positive, CD24-positive, and BP-positive. Intracellularly expression of surrogate light chain, Rag1 and Rag2, TdT, occurs while there is no expression of mu heavy chain. tmeehan 2010-04-28T02:04:01Z cell Fraction C Fraction C precursor B cell true A precursor B cell is CD45R-positive, CD43-positive, CD24-positive, and BP-positive. Intracellularly expression of surrogate light chain, Rag1 and Rag2, TdT, occurs while there is no expression of mu heavy chain. GOC:tfm PMID:17582343 A pre-BCR-positive precursor B cell that is CD24-high, CD25-positive, CD43-positive, CD45R-positive and BP-positive. tmeehan 2010-04-28T02:13:46Z Fr. C' Fraction C-prime cell Fraction C' precursor B cell true A pre-BCR-positive precursor B cell that is CD24-high, CD25-positive, CD43-positive, CD45R-positive and BP-positive. GOC:tfm PMID:17582343 A pre-BCR positive B cell that is CD38-high. tmeehan 2010-04-28T02:27:47Z cell large pre-B cell type I Markers are associated with human cells. CD38-high pre-BCR positive cell true A pre-BCR positive B cell that is CD38-high. GOC:tfm PMID:18432934 A pre-B cell that is pre-BCR-negative, and the kappa- and lambda- light immunoglobulin light chain-negative, CD43-low, and is BP-1-positive, CD45R-positive and CD25-positive. This cell type is also described as being AA4-positive, IgM-negative, CD19-positive, CD43-low/negative, and HSA-positive. tmeehan 2010-04-28T02:55:16Z Fr. D Fraction D pre-B cell cell Fraction D precursor B cells are also reportedly CD24-positive and sIgD-negative. Fraction D precursor B cell A pre-B cell that is pre-BCR-negative, and the kappa- and lambda- light immunoglobulin light chain-negative, CD43-low, and is BP-1-positive, CD45R-positive and CD25-positive. This cell type is also described as being AA4-positive, IgM-negative, CD19-positive, CD43-low/negative, and HSA-positive. GOC:ak GOC:dsd GOC:tfm PMID:17582343 PMID:18432934 http://www.immgen.org/index_content.html Fraction D pre-B cell GOC:tfm A small pre-B cell that is CD22-positive and CD38-low. tmeehan 2010-04-28T03:04:48Z small pre-B cell cell Markers are associated with human cell. RAG expression maybe diminishing. CD22-positive, CD38-low small pre-B cell true A small pre-B cell that is CD22-positive and CD38-low. GOC:tfm PMID:18432934 An immature B cell that is IgM-positive, CD45R-positive, CD43-low, CD25-negative, and CD127-negative. This cell type has also been described as being AA4-positive, IgM-positive, CD19-positive, CD43-low/negative, and HSA-positive. tmeehan 2010-04-28T03:13:47Z cell Markers associated with mouse cells. These cells are also reportedly sIgD-negative. Fraction E immature B cell true An immature B cell that is IgM-positive, CD45R-positive, CD43-low, CD25-negative, and CD127-negative. This cell type has also been described as being AA4-positive, IgM-positive, CD19-positive, CD43-low/negative, and HSA-positive. GOC:ak GOC:dsd GOC:tfm PMID:17582343 PMID:18432934 An immature B cell that is CD38-negative, CD10-low, CD21-low, and CD22-high. tmeehan 2010-04-28T03:19:14Z cell Markers are associated with human cell type. CD38-negative immature B cell true An immature B cell that is CD38-negative, CD10-low, CD21-low, and CD22-high. GOC:tfm PMID:18432934 A mature B cell subset originally defined as having being CD45R-positive, IgM-positive, IgD-positive and CD43-negative. Subsequent research demonstrated being CD21-positive and CD23-negative and CD93 negative. tmeehan 2010-04-30T03:01:48Z cell Fraction F mature B cell A mature B cell subset originally defined as having being CD45R-positive, IgM-positive, IgD-positive and CD43-negative. Subsequent research demonstrated being CD21-positive and CD23-negative and CD93 negative. GOC:tfm PMID:17582343 A classical monocyte that is CD14-positive, CD16-negative, CD64-positive, CD163-positive. tmeehan 2010-06-05T08:25:41Z CD16- monocyte CD16-negative monocyte cell This cell type is compatible with the HIPC Lyoplate markers for 'CD16- monocyte'. The markers used in the definition are associated with human monocytes. CD14-positive, CD16-negative classical monocyte true A classical monocyte that is CD14-positive, CD16-negative, CD64-positive, CD163-positive. GOC:add GOC:tfm PMID:15615263 PMID:1706877 PMID:19689341 PMID:22343568 CD16- monocyte PMID:22343568 A resident monocyte that is Gr-1 low, CD43-positive, and CX3CR1-positive. tmeehan 2010-06-05T08:25:44Z cell Markers are associated with mice. The Gr epitope is used to describe this cell type is found on both Ly6c and Ly6g. However, its the Ly6c that is considered the specific marker, and thus used in the cross-product. Also, this cell-type is sometimes described as being Gr1-negative. Gr1-low non-classical monocyte true A resident monocyte that is Gr-1 low, CD43-positive, and CX3CR1-positive. GOC:tfm PMID:8890901 A conventional thymic dendritic cell that is CD8alpha-positive. tmeehan 2010-06-07T02:48:36Z CD8alpha-alpha-positive thymic conventional dendritic cell DC.8+.Th cell CD8alpha-positive thymic conventional dendritic cell true A conventional thymic dendritic cell that is CD8alpha-positive. GOC:tfm PMID:19273629 http://www.immgen.org/index_content.html A melanin-containing macrophage that obtains the pigment by phagocytosis of melanosomes. tmeehan 2010-06-22T10:46:12Z cell melanophage true A melanin-containing macrophage that obtains the pigment by phagocytosis of melanosomes. GOC:tfm PMID:20479296 PMID:2943821 A T-helper cell that is characterized by secreting interleukin 9 and responding to helminth infections. This cell-type can derives from Th2 cells in the presence of TGF-beta and IL-4. Th2 cytokine production is surpressed. tmeehan 2010-06-22T11:18:44Z T helper cells type 9 T(H)-9 cell Th9 cell T-helper 9 cell true A T-helper cell that is characterized by secreting interleukin 9 and responding to helminth infections. This cell-type can derives from Th2 cells in the presence of TGF-beta and IL-4. Th2 cytokine production is surpressed. GOC:tfm PMID:18931678 PMID:19604299 PMID:20154671 Th9 PMID:18931678 A type I pneumocyte is a flattened, branched pneumocyte that covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange. tmeehan 2010-06-23T04:37:54Z BTO:0000780 FMA:62500 AT1 ATI lung type 1 cells membranous pneumocytes pulmonary alveolar type I cell small alveolar cells squamous alveolar cell squamous alveolar lining cell type 1 alveolar epithelial cells type 1 pneumocyte type I alveolar cells type I alveolar epithelial cells cell type I pneumocyte A type I pneumocyte is a flattened, branched pneumocyte that covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange. GOC:tfm PMID:20054144 http://www.copewithcytokines.de A type II pneumocyte is a pneumocyte that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a type I pneumocyte. Thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli. tmeehan 2010-06-24T12:04:13Z BTO:0000538 FMA:62501 AT2 ATII TII cuboidal type II cell granular pneumocyte great alveolar cell lung type 2 cell type 2 alveolar epithelial cell type 2 alveolocyte type 2 pneumocyte type II alveolar cell type II alveolar epithelial cell type II alveolocyte cell lung type II cell type II pneumocyte A type II pneumocyte is a pneumocyte that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a type I pneumocyte. Thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli. GOC:tfm ISBN:0412046911 PMID:8540632 http://www.copewithcytokines.de 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 A neuroendocrine cell found in the epithelium of the lungs and respiratory tract. This cell type is rounded or elliptical in shape, situated mainly in the basal part of the epithelium; regulates bronchial secretion, smooth muscle contraction, lobular growth, ciliary activity and chemoreception. Cell has an electron-lucent cytoplasm, contains numerous dense-cored vesicles with a clear halo between the core and the limiting membrane. tmeehan 2010-06-28T08:24:30Z P cell FMA:14118 Kultschitzky cell of bronchiole bronchiolar Kulchitsky cell respiratory enterochromaffin cell cell Feyrter cell A neuroendocrine cell found in the epithelium of the lungs and respiratory tract. This cell type is rounded or elliptical in shape, situated mainly in the basal part of the epithelium; regulates bronchial secretion, smooth muscle contraction, lobular growth, ciliary activity and chemoreception. Cell has an electron-lucent cytoplasm, contains numerous dense-cored vesicles with a clear halo between the core and the limiting membrane. GOC:tfm ISBN:0412046911 ISBN:0517223651 An enteroendocrine cell that produces glucagon. tmeehan 2010-09-10T10:48:54Z FMA:62939 cell type A enteroendocrine cell An enteroendocrine cell that produces glucagon. GOC:tfm ISBN:0412046911 Specialized cardiac myocyte that is subendocardially interspersed with the regular cardiac muscle cell. They are uninucleate cylindrical cells, associated end-to-end in long rows, continue from the node to the atrioventricular bundle; relatively short compared to ordinary myocytes but are nearly twice their diameter. tmeehan 2010-06-28T08:36:15Z BTO:0001032 FMA:14146 Purkinje cell fiber Purkinje muscle cell myocytus conducens cardiacus cell Purkinje myocyte Specialized cardiac myocyte that is subendocardially interspersed with the regular cardiac muscle cell. They are uninucleate cylindrical cells, associated end-to-end in long rows, continue from the node to the atrioventricular bundle; relatively short compared to ordinary myocytes but are nearly twice their diameter. FMA:0412046911 GOC:tfm PMID:19939742 Mostly cylindrical, resemble Type 1 in their contents and the presence of a kinocilium and stereocilium apically; much greater variation in size, some almost span the entire thickness of the sensory epithelium, while others are smaller than Type 1; receive multiple efferent nerve boutons around their bases as well as afferent endings, which are small expansions rather than chalices. tmeehan 2010-06-29T09:58:13Z FMA:67909 type 2 vestibular hair cell type 2 vestibular sensory cell type II hair cell cell type II vestibular sensory cell Mostly cylindrical, resemble Type 1 in their contents and the presence of a kinocilium and stereocilium apically; much greater variation in size, some almost span the entire thickness of the sensory epithelium, while others are smaller than Type 1; receive multiple efferent nerve boutons around their bases as well as afferent endings, which are small expansions rather than chalices. GOC:tfm ISBN:0517223651 Bottle-shaped with narrow neck; broad, rounded basal portion where nucleus is located; stereocilia and a single kinocilium is present apically; receive nerve bouton at their base from an afferent cup-shaped (chalice or calyx) nerve ending. tmeehan 2010-06-29T09:58:19Z FMA:62352 type 1 vestibular hair cell type 1 vestibular sensory cell type I hair cell cell type I vestibular sensory cell Bottle-shaped with narrow neck; broad, rounded basal portion where nucleus is located; stereocilia and a single kinocilium is present apically; receive nerve bouton at their base from an afferent cup-shaped (chalice or calyx) nerve ending. GOC:tfm ISBN:0517223651 Columnar cell which populate the epithelium of large intestine and absorb water. This cell is the most numerous of the epithelial cell types in the large intestine; bear apical microvilli, contain secretory granules in their apical cytoplasm; secretion appears to be largely mucins, but is also rich in antibodies of the IgA type. tmeehan 2010-06-29T11:07:25Z columnar cell BTO:0002484 FMA:63638 FMA:66771 columnar cell of the colon vacuolar absorptive cell cell enterocyte of epithelium of large intestine true Columnar cell which populate the epithelium of large intestine and absorb water. This cell is the most numerous of the epithelial cell types in the large intestine; bear apical microvilli, contain secretory granules in their apical cytoplasm; secretion appears to be largely mucins, but is also rich in antibodies of the IgA type. GOC:tfm ISBN:0517223651 A specialized cardiac myocyte in the sinoatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery. tmeehan 2010-06-29T11:41:37Z pacemaker cell BTO:0004190 FMA:67101 P cell cardiac pacemaker cell myocytus nodalis cell nodal myocyte A specialized cardiac myocyte in the sinoatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery. FMA:67101 GOC:tfm cardiac pacemaker cell GOC:pr Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes. tmeehan 2010-06-29T02:39:32Z FMA:67142 cell transitional myocyte Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes. FMA:67142 GOC:tfm The myoendocrine cellis a specialized myocyte localized mainly in the right and left atrial appendages, and also scattered within other areas of the atria and along the conductive system in the ventricular septum. The most conspicuous feature distinguishing myoendocrine cells from other atrial myoctyes is the presence of membane-bounded secretory granules (these granules contain precursor of cardiodilatins or atrial natriuretic polypeptides). tmeehan 2010-06-29T11:50:47Z FMA:67111 cell myocardial endocrine cell The myoendocrine cellis a specialized myocyte localized mainly in the right and left atrial appendages, and also scattered within other areas of the atria and along the conductive system in the ventricular septum. The most conspicuous feature distinguishing myoendocrine cells from other atrial myoctyes is the presence of membane-bounded secretory granules (these granules contain precursor of cardiodilatins or atrial natriuretic polypeptides). FMA:67111 GOC:tfm Infrequent type of columnar epithelial cell. This cell is characterized by the presence of a tuft of blunt, squat microvilli (approximately 120-140/cell) on the cell surface. The microvilli contain filaments that stretch into the underlying cytoplasm. They have a distinctive pear shape with a wide base and a narrow microvillous apex. Function not known. tmeehan 2010-06-29T03:22:46Z cell pulmonary brush cell brush cell of trachebronchial tree Infrequent type of columnar epithelial cell. This cell is characterized by the presence of a tuft of blunt, squat microvilli (approximately 120-140/cell) on the cell surface. The microvilli contain filaments that stretch into the underlying cytoplasm. They have a distinctive pear shape with a wide base and a narrow microvillous apex. Function not known. GOC:tfm ISBN:0517223651 PMID:15817800 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 Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH. tmeehan 2010-06-30T08:49:43Z FMA:63099 cell pancreatic ductal cell Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH. FMA:63099 GOC:tfm PMID:14740223 A cubodial epithelial cell that is continuous with the lining of intercalated ducts that drain the acinus. This cell type secretes a high pH solution to aid in activation of zymogens, and can differentiate into endocrine and exocrine pancreatic cell types. tmeehan 2010-06-30T08:49:52Z FMA:62455 centroacinar cell of Langerhans pancreatic centroacinar cell cell pancreatic centro-acinar cell A cubodial epithelial cell that is continuous with the lining of intercalated ducts that drain the acinus. This cell type secretes a high pH solution to aid in activation of zymogens, and can differentiate into endocrine and exocrine pancreatic cell types. GOC:tfm PMID:12142741 PMID:20018761 PMID:8185160 This cell resembles a glia cell, express the glial marker S100 and act as a supporting cell to type I cell. This cell is located in a small cluster of type I and type II cells near the fork of the carotid artery. tmeehan 2010-06-30T04:23:42Z FMA:84187 sheath cell of carotid body cell type II cell of carotid body This cell resembles a glia cell, express the glial marker S100 and act as a supporting cell to type I cell. This cell is located in a small cluster of type I and type II cells near the fork of the carotid artery. GOC:tfm PMID:7938227 http://en.wikipedia.org/wiki/Carotid_body A chromaffin cell of the adrenal medulla that produces epinephrine. tmeehan 2010-07-14T09:41:42Z FMA:69322 adremergic chromaffin cell adrenal secreting cell of the adrenal medulla epiniphrine secreting cell of the adrenal medulla cell type II cell of adrenal medulla true A chromaffin cell of the adrenal medulla that produces epinephrine. GOC:tfm A chromaffin cell of the adrenal medulla that produces norepinephrine. tmeehan 2010-07-14T10:12:24Z FMA:69321 noradrenergic chromaffin cell cell type I cell of adrenal medulla true A chromaffin cell of the adrenal medulla that produces norepinephrine. GOC:tfm ISBN:068340007X A Boettcher cell is a polyhedral cells on the basilar membrane of the cochlea, and is located beneath Claudius cells. A Boettcher cell is considered a supporting cell for the organ of Corti, and is present only in the lower turn of the cochlea. These cells interweave with each other, and project microvilli into the intercellular space. Because of their structural specialization, a Boettcher cell is believed to play a significant role in the function of the cochlea. They demonstrate high levels of calmodulin, and may be involved in mediating Ca(2+) regulation and ion transport. tmeehan 2010-07-14T03:22:02Z Boettcher's cell Bottcher cell Bottcher's cell cell Boettcher cell A Boettcher cell is a polyhedral cells on the basilar membrane of the cochlea, and is located beneath Claudius cells. A Boettcher cell is considered a supporting cell for the organ of Corti, and is present only in the lower turn of the cochlea. These cells interweave with each other, and project microvilli into the intercellular space. Because of their structural specialization, a Boettcher cell is believed to play a significant role in the function of the cochlea. They demonstrate high levels of calmodulin, and may be involved in mediating Ca(2+) regulation and ion transport. GOC:tfm http://en.wikipedia.org/wiki/Boettcher_cell Specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. Resemble spongioblasts seen in developing brain. Found in the adult brain in the third ventricle, cerebral aqueduct, spinal canal and floor of the fourth ventricle. tmeehan 2010-07-15T11:21:11Z CL:0000643 BTO:0001953 FMA:54560 stretch cell cell tanycyte Specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. Resemble spongioblasts seen in developing brain. Found in the adult brain in the third ventricle, cerebral aqueduct, spinal canal and floor of the fourth ventricle. GOC:tfm http://neurolex.org/wiki/Category:Tanycyte A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart. tmeehan 2010-07-21T01:33:38Z FMA:67968 cell specialized cardiac myocyte A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart. FMA:67968 GOC:tfm A leukocyte that lacks granules. tmeehan 2010-07-22T11:30:33Z FMA:62855 agranular leukocyte cell nongranular leukocyte true A leukocyte that lacks granules. GOC:tfm This is a cell found in the gastrointestinal tract of mammals and serves as a pacemaker that triggers gut contraction. ICCs mediate inputs from the enteric nervous system to smooth muscle cells and are thought to be the cells from which gastrointestinal stromal tumors (GISTs) arise. tmeehan 2010-07-22T03:26:00Z BTO:0003914 FMA:86573 ICC intestinal pacemaker cell cell Some argue this cell type is of mesenchymal origin. interstitial cell of Cajal true This is a cell found in the gastrointestinal tract of mammals and serves as a pacemaker that triggers gut contraction. ICCs mediate inputs from the enteric nervous system to smooth muscle cells and are thought to be the cells from which gastrointestinal stromal tumors (GISTs) arise. GOC:tfm PMID:16460275 PMID:19520112 intestinal pacemaker cell GOC:pr A group 2 innate lymphoid cell in the mouse capable of secreting IL-13 in response to a helminth infection. This cell is lineage-negative, ICOS-positive, IL1RL1-positive, IL7Ralpha-positive, and IL17Br-positive. tmeehan 2010-08-12T02:22:19Z nuocyte cell group 2 innate lymphoid cell, mouse A group 2 innate lymphoid cell in the mouse capable of secreting IL-13 in response to a helminth infection. This cell is lineage-negative, ICOS-positive, IL1RL1-positive, IL7Ralpha-positive, and IL17Br-positive. GOC:add GOC:tfm PMID:20200518 One of two small cells formed by the first and second meiotic division of oocytes. tmeehan 2010-08-23T09:49:53Z EHDAA2:0004716 FMA:85543 WBbt:0008429 XAO:0000262 cell polar body One of two small cells formed by the first and second meiotic division of oocytes. GOC:tfm ISBN:068340007X http://en.wikipedia.org/wiki/Polar_body A small cell formed by the first meiotic division of oocytes. tmeehan 2010-08-23T09:49:58Z EHDAA2:0000541 EMAPA:16032 FMA:18650 VHOG:0000464 first polar body polocytus primarius cell primary polar body A small cell formed by the first meiotic division of oocytes. GOC:tfm ISBN:068340007X first polar body EHDAA2:0000541 polocytus primarius FMA:18650 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 small cell formed by the second meiotic division of oocytes. In mammals, the second polar body may fail to form unless the ovum has been penetrated by a sperm cell. tmeehan 2010-08-23T09:50:01Z EHDAA2:0001820 EMAPA:16034 EMAPA:16045 FMA:18651 polocytus secundarius second polar body cell secondary polar body A small cell formed by the second meiotic division of oocytes. In mammals, the second polar body may fail to form unless the ovum has been penetrated by a sperm cell. GOC:tfm ISBN:068340007X polocytus secundarius FMA:18651 second polar body EHDAA2:0001820 A cell that makes up the loose connective tissue of the ovary. tmeehan 2010-08-23T11:11:34Z FMA:18709 cell interstitial cell of ovary A cell that makes up the loose connective tissue of the ovary. GOC:tfm A cell in the hilum of the ovary that produces androgens. tmeehan 2010-08-23T11:18:18Z FMA:18710 hilar cell of ovary cell hilus cell of ovary A cell in the hilum of the ovary that produces androgens. GOC:tfm ISBN:068340007X A specialised myocyte that lies between the sinoatrial node and the atrioventricular node and is involved in the conduction of electrical signals. tmeehan 2010-08-23T11:24:11Z FMA:223275 cell internodal tract myocyte A specialised myocyte that lies between the sinoatrial node and the atrioventricular node and is involved in the conduction of electrical signals. GOC:tfm ISBN:0781729300 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 A cardiac myocyte that is connected to other cardiac myocytes by transverse intercalated discs (GO:0014704) at a regular interval. tmeehan 2010-08-23T11:33:10Z FMA:67967 regular cardiac muscle cell regular cardiac muscle fiber cell regular cardiac myocyte A cardiac myocyte that is connected to other cardiac myocytes by transverse intercalated discs (GO:0014704) at a regular interval. GOC:tfm A small, polyhedral, cell found in rounded groups or curved columns with deeply staining nuclei, scanty basophilic cytoplasm and a few lipid droplets. This cell in the zona glomerulosa produces mineralocorticoids. tmeehan 2010-08-24T01:42:02Z CL:1000423 FMA:69273 epithelial cell of zona glomerulosa of adrenal gland cell type I cell of adrenal cortex true A small, polyhedral, cell found in rounded groups or curved columns with deeply staining nuclei, scanty basophilic cytoplasm and a few lipid droplets. This cell in the zona glomerulosa produces mineralocorticoids. GOC:tfm ISBN:0517223651 A regular cardiac myocyte of the interventricular region of the heart. tmeehan 2010-08-23T11:40:52Z FMA:228792 cell regular interventricular cardiac myocyte A regular cardiac myocyte of the interventricular region of the heart. GOC:tfm A CD38-positive naive B cell is a mature B cell that has the phenotype CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, and that has not yet been activated by antigen in the periphery. CD38+ naive B cell CD38+ naive B lymphocyte CD38+ naive B-cell CD38+ naive B-lymphocyte CD38-positive naive B lymphocyte CD38-positive naive B-cell CD38-positive naive B-lymphocyte cell CD38-positive naive B cell true A CD38-positive naive B cell is a mature B cell that has the phenotype CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, and that has not yet been activated by antigen in the periphery. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 A CD38-negative naive B cell is a mature B cell that has the phenotype CD38-negative, surface IgD-positive, surface IgM-positive, and CD27-negative, that has not yet been activated by antigen in the periphery. CD38- naive B cell CD38- naive B lymphocyte CD38- naive B-cell CD38- naive B-lymphocyte CD38-negative naive B lymphocyte CD38-negative naive B-cell CD38-negative naive B-lymphocyte cell CD38-negative naive B cell true A CD38-negative naive B cell is a mature B cell that has the phenotype CD38-negative, surface IgD-positive, surface IgM-positive, and CD27-negative, that has not yet been activated by antigen in the periphery. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 An IgG-positive double negative memory B cell is a double negative memory B cell with the phenotype IgG-positive, IgD-negative, and CD27-negative. IgG+ dn memory B cell IgG+ dn memory B lymphocyte IgG+ dn memory B-cell IgG+ dn memory B-lymphocyte IgG+ double negative memory B cell IgG+ double negative memory B lymphocyte IgG+ double negative memory B-cell IgG+ double negative memory B-lymphocyte IgG-positive dn memory B cell IgG-positive dn memory B lymphocyte IgG-positive dn memory B-cell IgG-positive dn memory B-lymphocyte IgG-positive double negative memory B lymphocyte IgG-positive double negative memory B-cell IgG-positive double negative memory B-lymphocyte cell IgG-positive double negative memory B cell true An IgG-positive double negative memory B cell is a double negative memory B cell with the phenotype IgG-positive, IgD-negative, and CD27-negative. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 An IgG-negative double negative memory B cell is a double negative memory B cell with the phenotype IgG-negative, IgD-negative, and CD27-negative. IgG- dn memory B cell IgG- dn memory B lymphocyte IgG- dn memory B-cell IgG- dn memory B-lymphocyte IgG- double negative memory B cell IgG- double negative memory B lymphocyte IgG- double negative memory B-cell IgG- double negative memory B-lymphocyte IgG-negative dn memory B cell IgG-negative dn memory B lymphocyte IgG-negative dn memory B-cell IgG-negative dn memory B-lymphocyte IgG-negative double negative memory B lymphocyte IgG-negative double negative memory B-cell IgG-negative double negative memory B-lymphocyte cell IgG-negative double negative memory B cell true An IgG-negative double negative memory B cell is a double negative memory B cell with the phenotype IgG-negative, IgD-negative, and CD27-negative. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 A CD38-positive IgG memory B cell is a class switched memory B cell that expresses IgG on the cell surface with the phenotype CD38-positive and IgG-positive. CD38+ IgG memory B cell CD38+ IgG memory B lymphocyte CD38+ IgG memory B-cell CD38+ IgG memory B-lymphocyte CD38-positive IgG memory B lymphocyte CD38-positive IgG memory B-cell CD38-positive IgG memory B-lymphocyte cell CD38-positive IgG memory B cell true A CD38-positive IgG memory B cell is a class switched memory B cell that expresses IgG on the cell surface with the phenotype CD38-positive and IgG-positive. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 An IgD-positive CD38-positive IgG memory B cell is a CD38-positive IgG-positive class switched memory B cell that has class switched and expresses IgD on the cell surface with the phenotype IgD-positive, CD38-positive, and IgG-positive. cell IgD-positive CD38-positive IgG memory B cell true An IgD-positive CD38-positive IgG memory B cell is a CD38-positive IgG-positive class switched memory B cell that has class switched and expresses IgD on the cell surface with the phenotype IgD-positive, CD38-positive, and IgG-positive. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 An IgD-negative CD38-positive IgG memory B cell is a CD38-positive IgG-positive that has class switched and lacks expression of IgD on the cell surface with the phenotype IgD-negative, CD38-positive, and IgG-positive. cell IgD-negative CD38-positive IgG memory B cell true An IgD-negative CD38-positive IgG memory B cell is a CD38-positive IgG-positive that has class switched and lacks expression of IgD on the cell surface with the phenotype IgD-negative, CD38-positive, and IgG-positive. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 A CD38-negative IgG memory B cell is a IgG-positive class switched memory B cell that has class switched and expresses IgG on the cell surface with the phenotype CD38-negative, IgD-negative, and IgG-positive. cell CD38-negative IgG memory B cell true A CD38-negative IgG memory B cell is a IgG-positive class switched memory B cell that has class switched and expresses IgG on the cell surface with the phenotype CD38-negative, IgD-negative, and IgG-positive. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 A B220-positive CD38-positive naive B cell is a CD38-positive naive B cell that has the phenotype B220-positive, CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, and that has not yet been activated by antigen in the periphery. B220+CD38+ naive B cell B220+CD38+ naive B lymphocyte B220+CD38+ naive B-cell B220+CD38+ naive B-lymphocyte B220-positive CD38-positive naive B lymphocyte B220-positive CD38-positive naive B-cell B220-positive CD38-positive naive B-lymphocyte CD38+B220+ naive B cell CD38+B220+ naive B lymphocyte CD38+B220+ naive B-cell CD38+B220+ naive B-lymphocyte cell B220-positive CD38-positive naive B cell true A B220-positive CD38-positive naive B cell is a CD38-positive naive B cell that has the phenotype B220-positive, CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, and that has not yet been activated by antigen in the periphery. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 A B220-low CD38-positive naive B cell is a CD38-positive naive B cell that has the phenotype B220-low, CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, that has not yet been activated by antigen in the periphery. cell B220-low CD38-positive naive B cell A B220-low CD38-positive naive B cell is a CD38-positive naive B cell that has the phenotype B220-low, CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, that has not yet been activated by antigen in the periphery. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 An CD38-negative unswitched memory B cell is an unswitched memory B cell that has the phenotype CD38-negative, IgD-positive, CD138-negative, and IgG-negative. CD38- unswitched memory B cell CD38- unswitched memory B lymphocyte CD38- unswitched memory B-cell CD38- unswitched memory B-lymphocyte CD38-negative unswitched memory B lymphocyte CD38-negative unswitched memory B-cell CD38-negative unswitched memory B-lymphocyte cell CD38-negative unswitched memory B cell true An CD38-negative unswitched memory B cell is an unswitched memory B cell that has the phenotype CD38-negative, IgD-positive, CD138-negative, and IgG-negative. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 A B220-positive CD38-negative unswitched memory B cell is a CD38-negative unswitched memory B cell that has the phenotype B220-positive, CD38-negative, IgD-positive, CD138-negative, and IgG-negative. cell B220-positive CD38-negative unswitched memory B cell true A B220-positive CD38-negative unswitched memory B cell is a CD38-negative unswitched memory B cell that has the phenotype B220-positive, CD38-negative, IgD-positive, CD138-negative, and IgG-negative. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 A B220-low CD38-negative unswitched memory B cell is a CD38-negative unswitched memory B cell that has the phenotype B220-low, CD38-negative, IgD-positive, CD138-negative, and IgG-negative. cell B220-low CD38-negative unswitched memory B cell A B220-low CD38-negative unswitched memory B cell is a CD38-negative unswitched memory B cell that has the phenotype B220-low, CD38-negative, IgD-positive, CD138-negative, and IgG-negative. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 A CD38-positive unswitched memory B cell is an unswitched memory B cell that has the phenotype CD38-positive, IgD-positive, CD138-negative, and IgG-negative. CD38+ unswitched memory B cell CD38+ unswitched memory B lymphocyte CD38+ unswitched memory B-cell CD38+ unswitched memory B-lymphocyte CD38-positive unswitched memory B lymphocyte CD38-positive unswitched memory B-cell CD38-positive unswitched memory B-lymphocyte cell CD38-positive unswitched memory B cell true A CD38-positive unswitched memory B cell is an unswitched memory B cell that has the phenotype CD38-positive, IgD-positive, CD138-negative, and IgG-negative. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 A B220-positive CD38-positive unswitched memory B cell is a CD38-positive unswitched memory B cell that has the phenotype B220-positive, CD38-positive, IgD-positive, CD138-negative, and IgG-negative. cell B220-positive CD38-positive unswitched memory B cell true A B220-positive CD38-positive unswitched memory B cell is a CD38-positive unswitched memory B cell that has the phenotype B220-positive, CD38-positive, IgD-positive, CD138-negative, and IgG-negative. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 A B220-low CD38-positive unswitched memory B cell is a CD38-positive unswitched memory B cell that has the phenotype B220-low, CD38-positive, IgD-positive, CD138-negative, and IgG-negative. cell B220-low CD38-positive unswitched memory B cell A B220-low CD38-positive unswitched memory B cell is a CD38-positive unswitched memory B cell that has the phenotype B220-low, CD38-positive, IgD-positive, CD138-negative, and IgG-negative. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 A class switched memory B cell that lacks IgG on the cell surface. IgG- class switched memory B cell IgG- class switched memory B lymphocyte IgG- class switched memory B-cell IgG- class switched memory B-lymphocyte IgG-negative class switched memory B lymphocyte IgG-negative class switched memory B-cell IgG-negative class switched memory B-lymphocyte cell IgG-negative class switched memory B cell true A class switched memory B cell that lacks IgG on the cell surface. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 A CD38-negative IgG-negative memory B cell is a IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD38-negative and IgG-negative. cell CD38-negative IgG-negative class switched memory B cell true A CD38-negative IgG-negative memory B cell is a IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD38-negative and IgG-negative. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 A CD38-positive IgG-negative memory B cell is an IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD38-positive and IgG-negative. cell CD38-positive IgG-negative class switched memory B cell true A CD38-positive IgG-negative memory B cell is an IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD38-positive and IgG-negative. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 An CD24-positive CD38-negative IgG-negative memory B cell is a CD38-negative IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD24-positive, CD38-negative, and IgG-negative. cell CD24-positive CD38-negative IgG-negative class switched memory B cell true An CD24-positive CD38-negative IgG-negative memory B cell is a CD38-negative IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD24-positive, CD38-negative, and IgG-negative. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 A CD24-negative CD38-negative IgG-negative memory B cell is a CD38-negative IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD24-negative, CD38-negative, and IgG-negative. cell CD24-negative CD38-negative IgG-negative class switched memory B cell true A CD24-negative CD38-negative IgG-negative memory B cell is a CD38-negative IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD24-negative, CD38-negative, and IgG-negative. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 A B220-positive CD38-positive IgG-negative memory B cell is a CD38-positive IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype B220-positive, CD38-positive, and IgG-negative. cell B220-positive CD38-positive IgG-negative class switched memory B cell true A B220-positive CD38-positive IgG-negative memory B cell is a CD38-positive IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype B220-positive, CD38-positive, and IgG-negative. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 A B220-low CD38-positive IgG-negative memory B cell is a CD38-positive IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype B220-low, CD38-positive, and IgG-positive. cell B220-low CD38-positive IgG-negative class switched memory B cell A B220-low CD38-positive IgG-negative memory B cell is a CD38-positive IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype B220-low, CD38-positive, and IgG-positive. GOC:dsd GOC:rhs GOC:tfm PMID:20123131 A circulating gamma-delta T cell that is CD27-positive and capable of producing IFN-gamma. tmeehan 2010-08-18T09:57:19Z gammadelta27-positive gd27-positive cell CD27-positive gamma-delta T cell true A circulating gamma-delta T cell that is CD27-positive and capable of producing IFN-gamma. GOC:dsd GOC:tfm PMID:19270712 A circulating gamma-delta T cell that expresses RORgamma(t), is CD27-negative and is capable of IL-17 secretion. tmeehan 2010-08-18T09:57:29Z gammadelta-17 cells cell CD27-negative gamma-delta T cell true A circulating gamma-delta T cell that expresses RORgamma(t), is CD27-negative and is capable of IL-17 secretion. GOC:dsd GOC:tfm PMID:19270712 gammadelta-17 cells PMID:21976777 A CD25-positive, CD27-positive immature gamma-delta T cell found in the thymus that has an immature phenotype (i.e. CD24-high, CD25-high, CD62L-high, CD44-high, CD2-low, CD5-low). tmeehan 2010-08-18T10:35:37Z cell CD25-positive, CD27-positive immature gamma-delta T cell true A CD25-positive, CD27-positive immature gamma-delta T cell found in the thymus that has an immature phenotype (i.e. CD24-high, CD25-high, CD62L-high, CD44-high, CD2-low, CD5-low). GOC:tfm PMID:19270712 A T cell with a receptor of limited diversity that is capable of immediate effector functions upon stimulation. tmeehan 2010-08-20T02:14:25Z cell innate effector T cell true A T cell with a receptor of limited diversity that is capable of immediate effector functions upon stimulation. GOC:tfm PMID:20581831 A CD8-positive, alpha-beta T cell that has the phenotype CXCR3-negative, CCR6-positive, CCR5-high, CD45RA-negative, and capable of producing IL-17 and some IFNg. CD8-positive Th17 cell Tc17 CD8+ T cell Tc17 T cell Tc17 T lymphocyte Tc17 T-cell Tc17 T-lymphocyte Th17 CD8-positive T cell Th17 non-TFH CD8-positive T cell cell This cell type is compatible with the HIPC Lyoplate markers for 'Tc17 CD8+ T cell', but its logical definition includes additional known characteristics of Tc17 T cells. Found in the CD27-positive, CD28-positive or CD27-negative, CD28-positive fractions with the phenotype CCR4-negative and CCR7-negative (this sentence not part of definition). Tc17 cell true A CD8-positive, alpha-beta T cell that has the phenotype CXCR3-negative, CCR6-positive, CCR5-high, CD45RA-negative, and capable of producing IL-17 and some IFNg. GOC:add GOC:dsd GOC:tfm PMID:19201830 PMID:22343568 Tc17 CD8+ T cell PMID:22343568 Regular cardiac myocyte of a cardiac atrium. tmeehan 2010-08-23T11:41:03Z FMA:83108 atrial cardiac muscle cell atrial myocyte regular atrial cardiac muscle fiber regular cardiac muscle cell of atrium cell regular atrial cardiac myocyte Regular cardiac myocyte of a cardiac atrium. GOC:tfm atrial cardiac muscle cell GOC:pr A cardiac myocyte of the interatrial region of the heart. tmeehan 2010-08-23T11:41:09Z FMA:228790 cell regular interatrial cardiac myocyte A cardiac myocyte of the interatrial region of the heart. GOC:tfm Regular cardiac myocyte of a cardiac ventricle. tmeehan 2010-08-23T11:41:13Z ventricular cardiac muscle cell FMA:83109 regular cardiac muscle cell of ventricle regular ventricular cardiac muscle fiber ventricular myocyte cell regular ventricular cardiac myocyte Regular cardiac myocyte of a cardiac ventricle. GOC:tfm ventricular cardiac muscle cell GOC:pr A stomal cell of the ovary tmeehan 2010-08-23T12:10:31Z FMA:72299 ovarian stromal cell cell stromal cell of ovary A stomal cell of the ovary GOC:tfm ovarian stromal cell GOC:cjm A stromal cell of the ovarian cortex. tmeehan 2010-08-23T12:12:15Z FMA:256169 cell stromal cell of ovarian cortex A stromal cell of the ovarian cortex. GOC:tfm A stromal cell of the ovarian medulla. tmeehan 2010-08-23T12:12:17Z FMA:256171 cell stromal cell of ovarian medulla true A stromal cell of the ovarian medulla. GOC:tfm Epidermal cells that do not contain keratin. Cell type is usually associated with moist epidermal tissues. tmeehan 2010-08-24T08:43:27Z FMA:62880 cell nonkeratinized cell of epidermis Epidermal cells that do not contain keratin. Cell type is usually associated with moist epidermal tissues. GO:tfm PMID:1987287 A cell in the zona fasciculata that produce glucocorticoids, e.g cortisol. tmeehan 2010-08-24T01:50:42Z FMA:69547 type II cortical cell of adrenal gland cell type II cell of adrenal cortex A cell in the zona fasciculata that produce glucocorticoids, e.g cortisol. GOC:tfm ISBN:0517223651 A cell in the zona reticularis that produce sex hormones. tmeehan 2010-08-24T01:50:44Z FMA:69564 cell type III cell of adrenal cortex A cell in the zona reticularis that produce sex hormones. GOC:tfm ISBN:0517223651 A endothelial cell of a lymphatic vessel. The border of the oak leaf-shaped endothelial cell of initial lymphatics are joined by specialized buttons. The discontinuous feature of buttons distinguishes them from zippers in collecting lymphatics, but both types of junctions are composed of proteins typical of adherens junctions and tight junctions found in the endothelium of blood vessels. Buttons seal the sides of flaps of the oak leaf-shaped endothelial cell, leaving open the tips of flaps as routes for fluid entry without disassembly and reformation of intercellular junctions. tmeehan 2010-08-24T02:05:28Z CL:1000421 BTO:0004167 FMA:68458 LEC lymphatic endothelial cell cell endothelial cell of lymphatic vessel true A endothelial cell of a lymphatic vessel. The border of the oak leaf-shaped endothelial cell of initial lymphatics are joined by specialized buttons. The discontinuous feature of buttons distinguishes them from zippers in collecting lymphatics, but both types of junctions are composed of proteins typical of adherens junctions and tight junctions found in the endothelium of blood vessels. Buttons seal the sides of flaps of the oak leaf-shaped endothelial cell, leaving open the tips of flaps as routes for fluid entry without disassembly and reformation of intercellular junctions. GOC:tfm PMID:17846148 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 A parathyroid chief cell that is actively secreting hormone. Have large Golgi complexes with numerous vesicles and small membrane-bound granules; secretory granules are rare, cytoplasmic glycogen sparse, much of the cytoplasm being occupied by flat sacs of granular endoplasmic reticulum in parallel arrays; in normal humans, inactive chief cells outnumber active chief cells in a ratio of 3-5:1 tmeehan 2010-08-24T09:30:15Z FMA:69082 cell active chief cell of parathyroid gland A parathyroid chief cell that is actively secreting hormone. Have large Golgi complexes with numerous vesicles and small membrane-bound granules; secretory granules are rare, cytoplasmic glycogen sparse, much of the cytoplasm being occupied by flat sacs of granular endoplasmic reticulum in parallel arrays; in normal humans, inactive chief cells outnumber active chief cells in a ratio of 3-5:1 FMA:0517223651 GOC:tfm A cell pyramidal in shape, with their broad ends facing and forming the greater extent of the lining of the main lumen. Secretes glycoproteins associated with mucus. tmeehan 2010-08-24T02:15:16Z FMA:70659 cell dark cell of eccrine sweat gland A cell pyramidal in shape, with their broad ends facing and forming the greater extent of the lining of the main lumen. Secretes glycoproteins associated with mucus. ISBN:0517223651 A chief cell that is smaller than light chief cells and has a smaller and darker nucleus and a finely granular cytoplasm with many granules. tmeehan 2010-08-24T02:18:36Z FMA:69080 cell dark chief cell of parathyroid gland A chief cell that is smaller than light chief cells and has a smaller and darker nucleus and a finely granular cytoplasm with many granules. GOC:tfm ISBN:0721662544 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 A ciliated columnar cell found in the trachea and bronchus. Vary from low to tall columnar; possesses up to 300 cilia at its surface, interspersed with long irregular microvilli with the cilia varying in length from about 6um in the trachea to about 4um in the terminal bronchioles; driving force of the ciliary current in the bronchial tree. tmeehan 2010-08-24T03:38:29Z FMA:70542 cell ciliated columnar cell of tracheobronchial tree A ciliated columnar cell found in the trachea and bronchus. Vary from low to tall columnar; possesses up to 300 cilia at its surface, interspersed with long irregular microvilli with the cilia varying in length from about 6um in the trachea to about 4um in the terminal bronchioles; driving force of the ciliary current in the bronchial tree. GOC:tfm ISBN:0517223651 A sweat producing cell of eccrine sweat glands. Pyramidal in shape, with its base resting on the basal lamina or myoepitheliocytes, and its microvillus-covered apical plasma membrane line up the intercellular canaliculi. Cell is not stained by hematoxylin or eosin. tmeehan 2010-08-24T10:33:02Z FMA:70658 cell clear cell of eccrine sweat gland A sweat producing cell of eccrine sweat glands. Pyramidal in shape, with its base resting on the basal lamina or myoepitheliocytes, and its microvillus-covered apical plasma membrane line up the intercellular canaliculi. Cell is not stained by hematoxylin or eosin. GOC:tfm ISBN:0517223651 A chief cell of parathyroid glands that does not stain with hematoxylin or eosin. This cell is larger, has a larger nucleus and fewer secretory granules than dark chief cells. tmeehan 2010-08-24T10:39:42Z FMA:69081 clear chief cell of parathyroid cell cell clear chief cell of parathyroid gland A chief cell of parathyroid glands that does not stain with hematoxylin or eosin. This cell is larger, has a larger nucleus and fewer secretory granules than dark chief cells. GOC:tfm ISBN:0618947256 A cell found within the dental pulp. tmeehan 2010-08-24T02:52:09Z BTO:0000339 CALOHA:TS-0195 FMA:87170 cell dental pulp cell A cell found within the dental pulp. GOC:tfm PMID:11087820 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 Epithelioid macrophage is an activated macrophage that resembles an epithelial cell with finely granular, pale eosinophilic cytoplasm and central, ovoid nucleus (oval or elongate). This cell type is able to merge into one another to form aggregates. The presence of such aggregates may characterize some pathologic conditions, mainly granulomatous inflammation. tmeehan 2010-08-24T03:48:30Z epithelioid cell FMA:83514 epithelioid histocyte epitheloid macrophage cell epithelioid macrophage Epithelioid macrophage is an activated macrophage that resembles an epithelial cell with finely granular, pale eosinophilic cytoplasm and central, ovoid nucleus (oval or elongate). This cell type is able to merge into one another to form aggregates. The presence of such aggregates may characterize some pathologic conditions, mainly granulomatous inflammation. MESH:A11.329.372.300 PMID:12673090 epithelioid histocyte MESH:A11.329.372.300 PMID:12673090 A promyelocyte that is considerably smaller, with more condensed chromatin, and nucleoli are no longer conspicuous. tmeehan 2010-08-24T03:07:50Z FMA:83534 cell late promyelocyte A promyelocyte that is considerably smaller, with more condensed chromatin, and nucleoli are no longer conspicuous. ISBN:0412046911 A columnar cell of the cervix uteri. tmeehan 2010-08-24T10:47:47Z FMA:86486 cell columnar cell of endocervix A columnar cell of the cervix uteri. GOC:tfm ISBN:0721662544 The dead keratin-filled squamous cell of the stratum corneum. This cell type lacks a nucleus. tmeehan 2010-08-24T10:53:03Z BTO:0001943 FMA:68650 cell corneocyte The dead keratin-filled squamous cell of the stratum corneum. This cell type lacks a nucleus. GOC:tfm ISBN:068340007X A promyelocyte with a nucleus that is indented and contains more marginated heterochromatin compared to its precursor cell (myeloblast); cytoplasm is deeply basophilic and contains numerous mitochondria and meandering cysternae of endoplasmic reticulum; largest of the granulocyte lineages. tmeehan 2010-08-24T03:07:53Z FMA:83533 cell early promyelocyte A promyelocyte with a nucleus that is indented and contains more marginated heterochromatin compared to its precursor cell (myeloblast); cytoplasm is deeply basophilic and contains numerous mitochondria and meandering cysternae of endoplasmic reticulum; largest of the granulocyte lineages. FMA:0412046911 GOC:tfm A crenated erythrocyte with 30+ crenations, bumps or spurs that are the result of damage due to age or disease. tmeehan 2010-08-24T03:15:21Z FMA:81099 burr cell cell echinocyte A crenated erythrocyte with 30+ crenations, bumps or spurs that are the result of damage due to age or disease. GOC:tfm A cell type that makes up the highly vascular membrane lining the marrow cavity of long bones. tmeehan 2010-08-24T03:33:58Z FMA:86495 cell endosteal cell A cell type that makes up the highly vascular membrane lining the marrow cavity of long bones. FMA:0618947256 GOC:tfm Epithelial cell found on the external side of the tympanic membrane tmeehan 2010-08-25T10:25:31Z FMA:70558 cell external epithelial cell of tympanic membrane Epithelial cell found on the external side of the tympanic membrane GOC:tfm PMID:5686391 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 A cell type found in the basal epithelial layer on the external side of the tympanic membrane. Cell type is flattened with intracellular spaces of variable dimensions. tmeehan 2010-08-25T10:28:44Z cell basal external epithelial cell of tympanic membrane A cell type found in the basal epithelial layer on the external side of the tympanic membrane. Cell type is flattened with intracellular spaces of variable dimensions. PMID:5686391 A cell type found on the superficial layer of the external side of the tympanic membrane. This cell-type lacks a nucleus. tmeehan 2010-08-25T10:28:48Z cell superficial external epithelial cell of tympanic membrane A cell type found on the superficial layer of the external side of the tympanic membrane. This cell-type lacks a nucleus. PMID:5686391 An extremely flattened cell type found on the inner side of the tympanic membrane. The surface of this cell type carries sparse pleomorphic microvilli that are more common near the junctional zones. tmeehan 2010-08-25T10:49:46Z FMA:70626 cell internal epithelial cell of tympanic membrane An extremely flattened cell type found on the inner side of the tympanic membrane. The surface of this cell type carries sparse pleomorphic microvilli that are more common near the junctional zones. FMA:5686391 GOC:tfm A rod-shpaed cell that forms a single row adjacent to and supporting the inner hair cells. tmeehan 2010-08-25T11:05:21Z FMA:75722 FMA:75726 cell internal pillar cell of cochlea A rod-shpaed cell that forms a single row adjacent to and supporting the inner hair cells. GOC:tfm http://www.theodora.com/anatomy/the_internal_ear_or_labyrinth.html A rod-shaped cell found in 3 or 4 rows that lie adjacent to and support the outer hair cells. tmeehan 2010-08-25T11:05:23Z FMA:75727 cell external pillar cell of cochlea A rod-shaped cell found in 3 or 4 rows that lie adjacent to and support the outer hair cells. GOC:tfm http://www.theodora.com/anatomy/the_internal_ear_or_labyrinth.html A supporting cell that is attached to the basement membrane and forms rows that support the hair cells. tmeehan 2010-08-25T01:29:07Z FMA:79800 cell phalangeal cell A supporting cell that is attached to the basement membrane and forms rows that support the hair cells. GOC:tfm ISBN:0618947256 An epithelial cell that remains from the disintegration of the epithelial root sheath involved in the development of teeth. tmeehan 2010-08-26T08:51:27Z FMA:62987 epithelial cell rests of Malassez epithelial debris of Malassez cell epithelial cell of Malassez true An epithelial cell that remains from the disintegration of the epithelial root sheath involved in the development of teeth. GOC:tfm ISBN:0517223651 ISBN:0815129521 A specialized cell involved in sensory perception of smell. tmeehan 2010-08-26T01:47:13Z FMA:67870 cell olfactory epithelial cell A specialized cell involved in sensory perception of smell. GOC:tfm PMID:7143026 A border cell is a slender columnar cell on the medial portion of the basilar membrane. tmeehan 2010-08-25T01:47:12Z FMA:79798 cell border cell of cochlea A border cell is a slender columnar cell on the medial portion of the basilar membrane. FMA:0412046911 GOC:tfm An epithelial cell located on the basal lamina of the olfactory epithelium. tmeehan 2010-08-26T01:58:54Z CL:1000395 horizontal basal call FMA:62303 cell basal cell of olfactory epithelium true An epithelial cell located on the basal lamina of the olfactory epithelium. GOC:tfm PMID:7143026 A keratinized cell located in the hard palate or gingiva. tmeehan 2010-08-26T02:51:30Z cell keratinized cell of the oral mucosa A keratinized cell located in the hard palate or gingiva. GOC:tfm PMID:12014572 A rounded or elliptical epithelial cell, with pale-staining open face nucleus and pale cytoplasm rich in free ribosomes and clusters of centrioles; form a distinct basal zone spaced slightly from the basal surface of the epithelium. tmeehan 2010-08-26T01:59:18Z FMA:67874 blastema cell of olfactory epithelium cell globose cell of olfactory epithelium A rounded or elliptical epithelial cell, with pale-staining open face nucleus and pale cytoplasm rich in free ribosomes and clusters of centrioles; form a distinct basal zone spaced slightly from the basal surface of the epithelium. GOC:tfm PMID:17468753 A long, spindle-shaped supporting cells arranged in parallel rows that secretes components of the tectorial membrane and potassium ions into the endolymph. tmeehan 2010-08-25T02:02:48Z FMA:79797 interdental cell cell interdental cell of cochlea A long, spindle-shaped supporting cells arranged in parallel rows that secretes components of the tectorial membrane and potassium ions into the endolymph. GOC:tfm MP:0004482 PMID:2111803 A cell that is a specialized type of pericyte providing structural support for the capillary loops of kidney. A flat, elongated cell with extensive fine cytoplasmic processes found outside the kidney glomerulus near the macula densa and bound laterally by afferent and efferent arterioles. Being phagocytic, this cell participates in the continuous turnover of the basal lamina by removing its outer portion containing residues of filtration, while the lamina is renewed on its inner surface by the endothelial cells. tmeehan 2010-08-25T02:20:55Z FMA:84143 KUPO:0001033 Goormaghtigh cell polar cushion cells cell lacis cell extraglomerular mesangial cell true A cell that is a specialized type of pericyte providing structural support for the capillary loops of kidney. A flat, elongated cell with extensive fine cytoplasmic processes found outside the kidney glomerulus near the macula densa and bound laterally by afferent and efferent arterioles. Being phagocytic, this cell participates in the continuous turnover of the basal lamina by removing its outer portion containing residues of filtration, while the lamina is renewed on its inner surface by the endothelial cells. GOC:tfm ISBN:0412046911 http:/www.copewithcytokines.de/cope.cgi?key=Lacis%20cells A cell within the follicle of an ovary. tmeehan 2010-08-25T03:01:27Z EMAPA:31247 FMA:70589 cell follicular cell of ovary A cell within the follicle of an ovary. GOC:tfm A cell within the primary follicle of the ovary. tmeehan 2010-08-25T03:03:42Z FMA:70590 cell primary follicular cell of ovary A cell within the primary follicle of the ovary. GOC:tfm A cell of a secondary follicile within the ovary. tmeehan 2010-08-25T03:03:48Z FMA:70591 cell secondary follicular cell of ovary A cell of a secondary follicile within the ovary. GOC:tfm A supporting cell of the anterior pituitary gland involved in trophic and catabolic processes; expresses a broad spectrum of cytokeratins indicative of their epithelial nature. tmeehan 2010-08-25T03:10:10Z FMA:83102 folliculostellate cell of pars anterior of adenohypophysis cell folliculostellate cell of pars distalis of adenohypophysis true A supporting cell of the anterior pituitary gland involved in trophic and catabolic processes; expresses a broad spectrum of cytokeratins indicative of their epithelial nature. 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 An epithelial cell within one of the pits in the embryonic gastric mucosa from which the gastric glands develop . tmeehan 2010-08-25T03:23:22Z FMA:86552 cell foveolar cell of stomach An epithelial cell within one of the pits in the embryonic gastric mucosa from which the gastric glands develop . GOC:tfm http://www.merriam-webster.com/medical/foveolar 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 A neck cell that secretes mucus within the stomach. Its products are distinct histochemically from those of the surface mucous cells of stomach. tmeehan 2010-08-25T03:41:30Z CL:1000401 FMA:62954 cell mucus neck cell of gastric gland true true A neck cell that secretes mucus within the stomach. Its products are distinct histochemically from those of the surface mucous cells of stomach. GOC:tfm ISBN:0517223651 A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall. tmeehan 2010-08-25T03:45:10Z FMA:62949 cell surface mucosal cell of stomach A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall. GOC:tfm ISBN:0517223651 A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit. tmeehan 2010-08-25T03:57:08Z CL:1000400 FMA:62953 cell stem cell of gastric gland true A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit. GOC:tfm ISBN:0517223651 A flat or angular epithelial cell with condensed nuclei and darkly staining cytoplasm containing numerous intermediate filaments inserted into desmosomes contacting surrounding supporting cells; lie in contact with the basal lamina of olfactory epithelium. tmeehan 2010-08-26T01:59:22Z FMA:62304 horizontal basal cells cell basal proper cell of olfactory epithelium A flat or angular epithelial cell with condensed nuclei and darkly staining cytoplasm containing numerous intermediate filaments inserted into desmosomes contacting surrounding supporting cells; lie in contact with the basal lamina of olfactory epithelium. GOC:tfm PMID:0517223651 PMID:11891623 A basally situated, mitotically active, columnar-shaped keratinocyte attached to the basement membrane. tmeehan 2010-08-26T03:12:49Z CL:1000439 FMA:70571 cell basal cell of epidermis true A basally situated, mitotically active, columnar-shaped keratinocyte attached to the basement membrane. GOC:tfm ISBN:0517223651 An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. tmeehan 2010-08-26T10:59:44Z BTO:0004632 FMA:70970 cell glomerular endothelial cell true An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. GOC:tfm PMID:15840009 A keratinocyte of the epidermis that is characterized by containing granules of keratohyalin and lamellar granules. tmeehan 2010-08-26T03:19:00Z FMA:70543 cell granular cell of epidermis A keratinocyte of the epidermis that is characterized by containing granules of keratohyalin and lamellar granules. ISBN:1416031855 A flat keratinocyte immediately below the cornified layer. tmeehan 2010-08-26T03:37:02Z FMA:86925 cell squamous cell of epidermis A flat keratinocyte immediately below the cornified layer. GOC:tfm ISBN:0517223651 A cell involved in the formation of a granulocyte. tmeehan 2010-08-30T12:54:27Z FMA:83519 cell granulocytopoietic cell true A cell involved in the formation of a granulocyte. GOC:tfm A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. tmeehan 2010-08-30T01:08:15Z FMA:83541 cell metamyelocyte A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. GOC:tfm ISBN:0721601464 http://en.wikipedia.org/wiki/Metamyelocyte A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses. tmeehan 2010-08-30T01:08:19Z BTO:0000734 FMA:83525 cell myelocyte A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses. GOC:tfm ISBN:0323052908 http://en.wikipedia.org/wiki/Myelocyte A cell involved in the formation of a monocyte (monopoiesis). tmeehan 2010-08-30T01:27:48Z FMA:83552 cell monopoietic cell true A cell involved in the formation of a monocyte (monopoiesis). GOC:tfm A stem cell that can give rise to the cells of the liver. tmeehan 2010-08-30T02:00:42Z FMA:86577 cell hepatic stem cell true A stem cell that can give rise to the cells of the liver. GOC:tfm A transient hepatic stem cell observed after liver injury with a high nuclear to cytoplasm ratio that can differentiate into mature hepatocytes and bile duct cells. Arises from more than one tissue. tmeehan 2010-08-30T02:01:49Z CL:1000036 BTO:0004270 FMA:86576 hepatic oval cell cell hepatic oval stem cell A transient hepatic stem cell observed after liver injury with a high nuclear to cytoplasm ratio that can differentiate into mature hepatocytes and bile duct cells. Arises from more than one tissue. PMID:17901986 A parathyroid chief cell that is not actively secreting hormone. Contains small Golgi complexes with only a few grouped vesicles and membrane-bound secretory granules; glycogen and many lipofuscin granules abound but sacs of granular endoplasmic reticulum are rare and dispersed. In normal humans, inactive chief cells out number active chief cells in a ratio of 3-5:1. tmeehan 2010-09-02T11:14:01Z cell inactive chief cell of parathyoid gland A parathyroid chief cell that is not actively secreting hormone. Contains small Golgi complexes with only a few grouped vesicles and membrane-bound secretory granules; glycogen and many lipofuscin granules abound but sacs of granular endoplasmic reticulum are rare and dispersed. In normal humans, inactive chief cells out number active chief cells in a ratio of 3-5:1. GOC:tfm ISBN:0517223651 A large epithelial cell with an extremely acidophilic and granular cytoplasm, containing vast numbers of mitochondria; such cells may undergo neoplastic transformation. From the Greek word onkos meaning swelling, this cell type is found in parathyroid, salivary and thyroid glands. tmeehan 2010-09-02T11:26:49Z FMA:67606 oxyphil cell oncocyte A large epithelial cell with an extremely acidophilic and granular cytoplasm, containing vast numbers of mitochondria; such cells may undergo neoplastic transformation. From the Greek word onkos meaning swelling, this cell type is found in parathyroid, salivary and thyroid glands. GOC:tfm ISBN:0721662544 PMID:20013317 An oncocyte located in the parathyroid gland. tmeehan 2010-09-02T11:33:23Z FMA:69084 cell oxyphil cell of parathyroid gland An oncocyte located in the parathyroid gland. PMID:20013317 An oncocyte located in the thyroid. tmeehan 2010-09-02T11:33:26Z FMA:87169 Askanazy cells Hurthle cells cell oxyphil cell of thyroid An oncocyte located in the thyroid. GOC:tfm PMID:20013317 A renal intercalated cell that secretes base and reabsorbs acid in the coritcal collecting duct to mantain acid/base balance. tmeehan 2010-09-02T01:43:55Z cell renal beta-intercalated cell A renal intercalated cell that secretes base and reabsorbs acid in the coritcal collecting duct to mantain acid/base balance. GOC:tfm PMID:11781354 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 Brush cell found in the epithelial layer of the colon. tmeehan 2010-09-02T02:20:50Z CL:1000387 FMA:263222 brush cell of large intestine tuft cell of epithelium of large intestine tuft cell of large intestine cell Brush cells are a distinct cell type from brush border cell-types. brush cell of epithelium proper of large intestine Brush cell found in the epithelial layer of the colon. GOC:tfm brush cell of large intestine http://orcid.org/0000-0003-4183-8865 tuft cell of epithelium of large intestine http://orcid.org/0000-0003-4183-8865 tuft cell of large intestine http://orcid.org/0000-0003-4183-8865 A cell type found in the gastrointestinal and respiratory tracts that is characterized by the presence of a tuft of blunt, squat microvilli (120-140 per cell). Function of this cell type is not known. tmeehan 2010-09-02T02:28:53Z FMA:67978 caveolated cell fibrillovesicular cell multivesicular cell tuft cell cell brush cell A cell type found in the gastrointestinal and respiratory tracts that is characterized by the presence of a tuft of blunt, squat microvilli (120-140 per cell). Function of this cell type is not known. GOC:tfm ISBN:0517223651 PMID:15817800 A brush cell found in the epithelium of lobular bronchiole. tmeehan 2010-09-02T02:38:34Z CL:1000386 FMA:263220 cell brush cell of lobular bronchiole A brush cell found in the epithelium of lobular bronchiole. GOC:tfm A brush cell of the epithelium in the terminal bronchiole. tmeehan 2010-09-02T02:38:36Z CL:1000390 FMA:263228 cell brush cell of terminal bronchiole A brush cell of the epithelium in the terminal bronchiole. GOC:tfm Brush cell of the epithelium in the trachea. tmeehan 2010-09-02T02:38:37Z CL:1000388 FMA:263224 cell brush cell of trachea true true Brush cell of the epithelium in the trachea. GOC:tfm A brush cell found in the epithelium of bronchus. tmeehan 2010-09-02T02:38:42Z CL:1000389 FMA:263226 cell brush cell of bronchus true true A brush cell found in the epithelium of bronchus. GOC:tfm An epithelial cell present in the trachea and bronchi; columnar in shape; generally lack cilia; immature forms of ciliated or secretory cells which have been formed from stem cells. tmeehan 2010-09-02T02:53:59Z FMA:69060 undifferentiated columnar cell of tracheobronchial tree cell intermediate epitheliocyte An epithelial cell present in the trachea and bronchi; columnar in shape; generally lack cilia; immature forms of ciliated or secretory cells which have been formed from stem cells. GOC:tfm ISBN:0517223651 A slow muscle cell that contains high levels of myoglobin and oxygen storing proteins giving the cell a red appearance. tmeehan 2010-09-02T03:20:03Z FMA:84448 oxidative muscle fiber red muscle fiber cell red muscle cell A slow muscle cell that contains high levels of myoglobin and oxygen storing proteins giving the cell a red appearance. GOC:tfm ISBN:0517223651 A slow muscle cell that has large amounts of myoglobin, stores energy as triglycerides, generates ATP by the oxidative method and is resistant to fatigue. tmeehan 2010-09-02T03:24:05Z BTO:0001812 CALOHA:TS-0940 FMA:84413 MESH:A02.633.565.700 slow twitch fiber slow twitch muscle cell type 1 muscle cell type 1 muscle fiber type I muscle fiber cell intermediate muscle fiber slow twitch muscle fiber slow-twitch muscle fiber type I muscle cell A slow muscle cell that has large amounts of myoglobin, stores energy as triglycerides, generates ATP by the oxidative method and is resistant to fatigue. GOC:tfm ISBN:0517223651 intermediate muscle fiber MESH:A02.633.565.700 slow twitch muscle fiber MESH:A02.633.565.700 slow-twitch muscle fiber MESH:A02.633.565.700 A fast muscle fiber cell that stores energy in the form of glycogen and creatine phosphate. tmeehan 2010-09-02T03:28:45Z BTO:0001813 FMA:84414 type 2 muscle cell type 2 muscle fiber type II muscle fiber cell type II muscle cell A fast muscle fiber cell that stores energy in the form of glycogen and creatine phosphate. GOC:tfm A muscle cell with low content of myoglobin and other oxygen storing proteins. This muscle cell has a white appearance. tmeehan 2010-09-02T03:28:48Z FMA:84449 cell white muscle cell A muscle cell with low content of myoglobin and other oxygen storing proteins. This muscle cell has a white appearance. GOC:tfm ISBN:0517223651 A type II muscle cell that contains large amounts of myoglobin, has many mitochondria and very many blood capillaries. Type II A cells are red, have a very high capacity for generating ATP by oxidative metabolic processes, split ATP at a very rapid rate, have a fast contraction velocity and are resistant to fatigue. tmeehan 2010-09-02T03:31:38Z BTO:0001813 FMA:84415 fast twitch A fatigue resistant fast twitch muscle cell type 2a muscle cell type 2a muscle fiber type IIa muscle fiber cell type IIa muscle cell A type II muscle cell that contains large amounts of myoglobin, has many mitochondria and very many blood capillaries. Type II A cells are red, have a very high capacity for generating ATP by oxidative metabolic processes, split ATP at a very rapid rate, have a fast contraction velocity and are resistant to fatigue. GOC:tfm A type II muscle cell that contains a low content of myoglobin, relatively few mitochondria, relatively few blood capillaries and large amounts of glycogen. Type II B fibres are white, geared to generate ATP by anaerobic metabolic processes, not able to supply skeletal muscle fibres continuously with sufficient ATP, fatigue easily, split ATP at a fast rate and have a fast contraction velocity. tmeehan 2010-09-02T03:31:42Z FMA:84416 type 2b muscle cell type 2b muscle fiber type IIb muscle fiber cell type IIb muscle cell A type II muscle cell that contains a low content of myoglobin, relatively few mitochondria, relatively few blood capillaries and large amounts of glycogen. Type II B fibres are white, geared to generate ATP by anaerobic metabolic processes, not able to supply skeletal muscle fibres continuously with sufficient ATP, fatigue easily, split ATP at a fast rate and have a fast contraction velocity. GOC:tfm ISBN:0517223651 http://en.wikipedia.org/wiki/Skeletal_muscle An intermediate muscle cell that has characteristics of both fast and slow muscle cells. tmeehan 2010-09-02T03:51:17Z FMA:84450 cell intermediate muscle cell An intermediate muscle cell that has characteristics of both fast and slow muscle cells. GOC:tfm A trophoblast that leaves the placenta and invades the endometrium and myometrium. This cell type is crucial in increasing blood flow to the fetus. tmeehan 2010-09-02T04:04:36Z BTO:0002366 FMA:86564 cell intermediate trophoblast cell A trophoblast that leaves the placenta and invades the endometrium and myometrium. This cell type is crucial in increasing blood flow to the fetus. GOC:tfm http://www.med.yale.edu/obgyn/kliman/placenta/articles/EOR_Placenta/Trophtoplacenta.html A double negative thymocyte that has a T cell receptor consisting of a gamma chain that has as part a Vgamma3 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive. This cell-type is found in the fetal thymus with highest numbers occurring at E17-E18. tmeehan 2010-10-07T01:58:00Z immature DEC precursor immature DETC precursor cell NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. immature dendritic epithelial T cell precursor A double negative thymocyte that has a T cell receptor consisting of a gamma chain that has as part a Vgamma3 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive. This cell-type is found in the fetal thymus with highest numbers occurring at E17-E18. GOC:tfm http://www.immgen.org A trophoblast found at the junction of the placenta. This cell type makes a unique fibronectin-trophouteronectin junction that helps mediate attachment of the placenta to the uterus. This cell type is also found junction of the chorion layer of the external membranes and the decidua. tmeehan 2010-09-02T04:14:28Z cell anchoring trophoblast A trophoblast found at the junction of the placenta. This cell type makes a unique fibronectin-trophouteronectin junction that helps mediate attachment of the placenta to the uterus. This cell type is also found junction of the chorion layer of the external membranes and the decidua. GOC:tfm http://www.med.yale.edu/obgyn/kliman/placenta/articles/EOR_Placenta/Trophtoplacenta.html A cell located between the pinealocytes. tmeehan 2010-09-02T04:28:41Z FMA:86575 cell interstitial cell of pineal gland A cell located between the pinealocytes. GOC:tfm ISBN:0517223651 A squamous cell that has keratin in the esophagus. tmeehan 2010-09-07T10:11:06Z FMA:86549 cell keratinized squamous cell of esophagus A squamous cell that has keratin in the esophagus. GOC:tfm PMID:11694559 A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye. tmeehan 2010-09-07T10:38:03Z FMA:70950 cell vertebrate lens cell A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye. GOC:tfm ISBN:0721662544 A cell of the transparent layer of simple cuboidal epithelium over the anterior surface of the lens; transform into lens fiber(s). tmeehan 2010-09-07T10:45:45Z FMA:63181 cell anterior lens cell A cell of the transparent layer of simple cuboidal epithelium over the anterior surface of the lens; transform into lens fiber(s). GOC:tfm ISBN:0517223651 A cell of the cuboidal epithelium that covers the lens. The cells of the lens epithelium regulate most of the homeostatic functions of the lens. As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions. The cells of the lens epithelium also serve as the progenitors for new lens fibers. It constantly lays down fibers in the embryo, fetus, infant, and adult, and continues to lay down fibers for lifelong growth. tmeehan 2010-09-07T10:45:47Z FMA:67559 cell lens epithelial cell true A cell of the cuboidal epithelium that covers the lens. The cells of the lens epithelium regulate most of the homeostatic functions of the lens. As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions. The cells of the lens epithelium also serve as the progenitors for new lens fibers. It constantly lays down fibers in the embryo, fetus, infant, and adult, and continues to lay down fibers for lifelong growth. GOC:tfm ISBN:0721662544 http://en.wikipedia.org/wiki/Lens_%28anatomy%29#Lens_epithelium A lens fiber cell that develops from primary lens fiber; located towards the center of lens; cell organelles are normally degraded or in the process of being degraded. tmeehan 2010-09-07T10:53:39Z secondary lens fibre cell secondary lens fiber A lens fiber cell that develops from primary lens fiber; located towards the center of lens; cell organelles are normally degraded or in the process of being degraded. GOC:tfm ISBN:0517223651 A secondary lens fiber cell that lacks a nucleus. tmeehan 2010-09-07T11:15:23Z FMA:67561 non-nucleated secondary lens fibre cell non-nucleated secondary lens fiber A secondary lens fiber cell that lacks a nucleus. GOC:tfm A secondary fiber cell that contains a nucleus. tmeehan 2010-09-07T11:15:26Z FMA:70949 nucleated secondary lens fibre cell nucleated secondary lens fiber A secondary fiber cell that contains a nucleus. GOC:tfm An elongating cell that rapidly obliterates the lumen of the lens vesicle. Subsequently, differentiation of this cell type at the lens equator leads to the formation of secondary fiber cells that come to overlie the primary fibers. tmeehan 2010-09-07T11:19:01Z FMA:70613 primary lens fibre cell primary lens fiber An elongating cell that rapidly obliterates the lumen of the lens vesicle. Subsequently, differentiation of this cell type at the lens equator leads to the formation of secondary fiber cells that come to overlie the primary fibers. GOC:tfm PMID:10711704 A chief cell that is bigger than dark chief cells and has a larger and lighter nucleus and a cytoplasm with few granules. tmeehan 2010-09-07T11:46:54Z FMA:69079 cell light chief cell of parathyroid gland A chief cell that is bigger than dark chief cells and has a larger and lighter nucleus and a cytoplasm with few granules. GOC:tfm ISBN:0721662544 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 An epithelial cell of prostatic duct. tmeehan 2010-09-07T01:55:51Z CL:1000462 FMA:74224 ductal epithelial cell of prostate cell epithelial cell of prostatic duct true An epithelial cell of prostatic duct. GOC:tfm ductal epithelial cell of prostate FMA:74224 An epithelial cell of the prostatic acinus. tmeehan 2010-09-07T01:55:53Z CL:1000461 FMA:74223 acinar epithelial cell of prostate cell epithelial cell of prostatic acinus true An epithelial cell of the prostatic acinus. GOC:tfm PMCID:PMC2673349 acinar epithelial cell of prostate FMA:74223 A cell of the basal layer of the epithelium in the prostatic acinus. tmeehan 2010-09-07T01:59:08Z CL:1000464 FMA:74265 basal epithelial cell of prostatic acinus cell basal cell of prostatic acinus A cell of the basal layer of the epithelium in the prostatic acinus. GOC:tfm basal epithelial cell of prostatic acinus FMA:74265 A cell of the luminal layer of the epithelium in the prostatic acinus. tmeehan 2010-09-07T01:59:10Z FMA:74266 cell luminal cell of prostatic acinus A cell of the luminal layer of the epithelium in the prostatic acinus. GOC:tfm A cell that constitutes the basal layer of epithelium in the prostatic duct. tmeehan 2010-09-07T01:59:12Z CL:1000463 FMA:74226 cell basal epithelial cell of prostatic duct A cell that constitutes the basal layer of epithelium in the prostatic duct. GOC:tfm PMID:15226377 A cell that constitutes the luminal layer of epithelium of prostatic duct. tmeehan 2010-09-07T01:59:16Z FMA:74225 cell luminal epithelial cell of prostatic duct A cell that constitutes the luminal layer of epithelium of prostatic duct. GOC:tfm A primordial germ cell that is destined to become a male germ cell. tmeehan 2010-09-07T02:11:13Z EHDAA2:0001053 EMAPA:18686 FMA:84771 VHOG:0000662 male primordial germ cell testis primordial germ cell cell male gonocyte A primordial germ cell that is destined to become a male germ cell. GOC:tfm testis primordial germ cell VHOG:0000662 A primordial cell from which an oocyte (ovum) ultimately is developed. tmeehan 2010-09-07T02:11:16Z EHDAA2:0000505 EMAPA:17965 FMA:84772 ISBN:0721662544 VHOG:0000661 ovary primordial germ cell ovigerm cell ooblast A primordial cell from which an oocyte (ovum) ultimately is developed. GOC:tfm ovary primordial germ cell VHOG:0000661 ovigerm FMA:84772 A fibroblast in the bone marrow. tmeehan 2010-09-07T02:25:18Z FMA:84377 cell marrow fibroblast A fibroblast in the bone marrow. GOC:tfm A fibroblasts found in interstitial spaces in the pulmonary tract. Greater numbers of these cells are found in idiopathic pulmonary fibrosis. tmeehan 2010-09-07T02:29:38Z FMA:84467 pulmonary myofibroblast pulmonary septal cell cell pulmonary interstitial fibroblast true A fibroblasts found in interstitial spaces in the pulmonary tract. Greater numbers of these cells are found in idiopathic pulmonary fibrosis. 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 A circular smooth muscle cell of the iris, innervated by the ciliary nerves (parasympathetic), and acting to contract the pupil. This muscle cell derives from neuroectoderm. This smooth muscle cell results from transformation of epithelial cells to smooth muscle cells. tmeehan 2010-09-08T08:53:42Z FMA:70611 smooth muscle fiber of sphincter of pupil cell smooth muscle fibre of sphincter of pupil smooth muscle cell of sphincter of pupil true A circular smooth muscle cell of the iris, innervated by the ciliary nerves (parasympathetic), and acting to contract the pupil. This muscle cell derives from neuroectoderm. This smooth muscle cell results from transformation of epithelial cells to smooth muscle cells. GOC:tfm ISBN:0721662544 ISBN:0721694128 A nonstratified squamous cell located in the ectocervix. tmeehan 2010-09-08T09:12:23Z FMA:86483 ectocervical squamous cell cell squamous cell of ectocervix A nonstratified squamous cell located in the ectocervix. GOC:tfm http://www.bu.edu/histology/p/19404loa.htm OBSOLETE: A lymphocyte that lacks T or B cell surface markers. tmeehan 2010-09-07T03:43:42Z FMA:83601 cell obsolete null lymphocyte true OBSOLETE: A lymphocyte that lacks T or B cell surface markers. GOC:tfm ISBN:068340007X A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells). tmeehan 2010-09-07T03:57:09Z BTO:0002669 FMA:86711 PBSC cell peripheral blood stem cell true A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells). GOC:tfm A tissue macrophage that is in the pleural space. tmeehan 2010-09-07T04:16:43Z FMA:83024 cell pleural macrophage A tissue macrophage that is in the pleural space. GOC:tfm A pluripotent stem cell has the ability to form cells from all three germ layers (ectoderm, mesoderm, and endoderm). However, unlike totipotent stem cells, they cell can not generate all the cells of the whole organism such as placenta. tmeehan 2010-09-07T04:26:06Z FMA:70570 cell pluripotent stem cell A pluripotent stem cell has the ability to form cells from all three germ layers (ectoderm, mesoderm, and endoderm). However, unlike totipotent stem cells, they cell can not generate all the cells of the whole organism such as placenta. GOC:tfm PMID:19343304 A stem cell that can differentiate into a cardiac myocyte. tmeehan 2010-09-07T04:40:32Z FMA:75620 cell primitive cardiac myocyte A stem cell that can differentiate into a cardiac myocyte. GOC:tfm PMID:16938308 A cell that is found in a zone occupying the bottom region of the crypt; provide the source of most of the cell types of the intestinal epithelium; proliferate by mitotic division; differentiates into columnar or goblet cells. tmeehan 2010-09-08T09:21:22Z FMA:63379 stem cell of intestinal crypt of Lieberkuhn cell intestinal crypt stem cell A cell that is found in a zone occupying the bottom region of the crypt; provide the source of most of the cell types of the intestinal epithelium; proliferate by mitotic division; differentiates into columnar or goblet cells. GOC:tfm ISBN:0517223651 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 Connective tissue cells of the endometrium, these cells are fibroblastic in appearance. During decidualization they tranform into decidual (stromal) cells, swellling up and adopt an epithelial cell-like appearance due to the accumulation of glycogen and lipid droplets. tmeehan 2010-09-08T09:50:04Z CALOHA:TS-1266 FMA:86490 endometrial stromal cell cell stromal cell of endometrium true Connective tissue cells of the endometrium, these cells are fibroblastic in appearance. During decidualization they tranform into decidual (stromal) cells, swellling up and adopt an epithelial cell-like appearance due to the accumulation of glycogen and lipid droplets. PMID:11331626 PMID:30013421 Wiki:Decidualization&oldid=908981933#Endometrial_stromal_cells_(ESCs) A supportive cell that has characteristics of glial cell. Processes of this cell envelope the junctions between glomus cells and nerve endings. tmeehan 2010-09-08T10:34:45Z FMA:84188 carotid body sustentacular cell cell supporting cell of carotid body A supportive cell that has characteristics of glial cell. Processes of this cell envelope the junctions between glomus cells and nerve endings. GOC:tfm PMID:8985136 http://www.copewithcytokines.de/cope.cgi?key=glomus%20cells 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 A cell type that varies from squamous to columnar, depending on their activity with microvillus directed luminally. This cell produces and secretes thyroid hormones. tmeehan 2010-09-08T01:50:08Z BTO:0003736 CALOHA:TS-1285 FMA:68782 follicular cell of thyroid gland principal cell of thyroid gland thyroid gland follicular cell cell thyroid follicular cell A cell type that varies from squamous to columnar, depending on their activity with microvillus directed luminally. This cell produces and secretes thyroid hormones. GOC:tfm ISBN:0517223651 The stem cell from which glial precursor cell arises from. tmeehan 2010-09-08T02:14:14Z FMA:87171 totipotent neuroepithelial stem cell cell neuroepithelial stem cell The stem cell from which glial precursor cell arises from. GOC:tfm PMID:11687496 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 found in the mucosa associated with the facial skeleton. tmeehan 2010-09-14T10:40:12Z CL:1000446 FMA:70627 cell endothelial cell of viscerocranial mucosa An endothelial cell found in the mucosa associated with the facial skeleton. GOC:tfm ISBN:0618947256 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 One of three types of epithelial cells that populate the parathyroid gland; cytological characteristics intermediate between those of the chief cell and of the oxyphil cell. Because only one hormone is produced, the three cell forms are widely believed to be different phases in the life cycle of a single cell type, with the chief cell being its physiologically active stage. tmeehan 2010-09-08T02:33:50Z FMA:69324 cell transitional cell of parathyroid gland One of three types of epithelial cells that populate the parathyroid gland; cytological characteristics intermediate between those of the chief cell and of the oxyphil cell. Because only one hormone is produced, the three cell forms are widely believed to be different phases in the life cycle of a single cell type, with the chief cell being its physiologically active stage. GOC:tfm ISBN:0412046911 A type of enteroendocrine cell found in the stomach that secretes glucagon. tmeehan 2010-09-10T10:54:42Z FMA:83411 cell type A cell of stomach A type of enteroendocrine cell found in the stomach that secretes glucagon. GOC:tfm A D cell located in the colon. tmeehan 2010-09-10T11:37:35Z FMA:268744 colon D-cell colonic delta cell delta cell of colon cell type D cell of colon A D cell located in the colon. GOC:tfm A type D cell of the small intestine. tmeehan 2010-09-10T01:34:22Z FMA:268736 delta cell of small intestine small intestine D-cell small intestine delta cell cell type D cell of small intestine A type D cell of the small intestine. GOC:tfm A type D cell found in the stomach. tmeehan 2010-09-10T01:36:03Z FMA:83410 delta cell of stomach stomach D-cell stomach delta cell cell type D cell of stomach A type D cell found in the stomach. GOC:tfm An enteroendocrine cell that stores and secretes Ghrelin. tmeehan 2010-09-10T01:47:45Z FMA:63207 FMA:63418 cell P/D1 enteroendocrine cell An enteroendocrine cell that stores and secretes Ghrelin. GOC:tfm ISBN:0517223651 PMID:15153415 An endocrine cell that secretes vasoactive intestinal peptide. tmeehan 2010-09-10T01:52:20Z cell vasoactive intestinal peptide secreting cell An endocrine cell that secretes vasoactive intestinal peptide. GOC:tfm A type EC enteroendocrine cell in the duodenum and jejunum that stores and secretes motilin and 5-hydroxytryptamine. tmeehan 2010-09-10T02:13:47Z Mo enteroendocrine cell FMA:62941 cell type EC2 enteroendocrine cell A type EC enteroendocrine cell in the duodenum and jejunum that stores and secretes motilin and 5-hydroxytryptamine. GOC:tfm ISBN:0517223651 PMID:15153415 A type EC enteredocrine cell in the intestines that stores and secretes substance P and 5-hydroxytryptamine. tmeehan 2010-09-10T02:13:49Z FMA:62940 cell type EC1 enteroendocrine cell A type EC enteredocrine cell in the intestines that stores and secretes substance P and 5-hydroxytryptamine. GOC:tfm ISBN:0517223651 A cell that secretes motilin, a gastric hormone that at low pH inhibits gastric motor activity, whereas at high pH has a stimulating effect. tmeehan 2010-09-10T02:31:13Z cell motilin secreting cell A cell that secretes motilin, a gastric hormone that at low pH inhibits gastric motor activity, whereas at high pH has a stimulating effect. GOC:tfm MESH:D06.472.317.525 A type EC enteroendocrine cell type that is numerous in the fundus of the stomach; stores 5-hydroxytryptamine and histamine. tmeehan 2010-09-10T02:35:17Z FMA:63208 cell type ECL enteroendocrine cell A type EC enteroendocrine cell type that is numerous in the fundus of the stomach; stores 5-hydroxytryptamine and histamine. GOC:tfm ISBN:0517223651 PMID:15153415 A cell type that secretes histamine. tmeehan 2010-09-10T03:04:42Z cell histamine secreting cell A cell type that secretes histamine. GOC:tfm A PP cell located in the islets of the pancreas. tmeehan 2010-09-10T03:30:31Z BTO:0000805 FMA:70588 PP cell of pancreatic islet PP-cell of pancreatic islet pancreatic polypeptide-secreting cell cell The term PP cell of pancreatic acinus was obsoleted due to a lack of evidence, making PP cell of pancreatic islets synonymous with pancreatic PP cell. pancreatic PP cell A PP cell located in the islets of the pancreas. GOC:tfm OBSOLETE: A PP cell located in the pancreatic acinus. Obsoleted due to a lack of published evidence that this cell type is actually found in the pancreatic acinus. tmeehan 2010-09-10T03:30:33Z FMA:85400 type F cell of pancreatic acinus cell obsolete PP cell of pancreatic acinus true OBSOLETE: A PP cell located in the pancreatic acinus. Obsoleted due to a lack of published evidence that this cell type is actually found in the pancreatic acinus. GOC:tfm An enteroendocrine cell commonest in the duodenum and jejunum, rare in ileum, that secretes cholecystokinin. This cell type is involved in the regulation of digestive enzymes and bile. tmeehan 2010-09-10T03:44:36Z FMA:62937 CCK cell cell type I enteroendocrine cell An enteroendocrine cell commonest in the duodenum and jejunum, rare in ileum, that secretes cholecystokinin. This cell type is involved in the regulation of digestive enzymes and bile. GOC:tfm An enteroendocrine cell of duodenum and jejunum that produces gastric inhibitory peptide. tmeehan 2010-09-10T03:51:47Z FMA:62942 type K enteroendocrine cell cell GIP cell An enteroendocrine cell of duodenum and jejunum that produces gastric inhibitory peptide. GOC:tfm A enteroendocrine cell type that is numerous in ileum, present in jejunum and large intestine, few in duodenum. This cell type produces glucagon-like immunoreactants (glicentin, glucagon-37, glucagon-29, GLP-1 and -2) and PYY. tmeehan 2010-09-10T03:59:09Z FMA:62944 cell type L enteroendocrine cell A enteroendocrine cell type that is numerous in ileum, present in jejunum and large intestine, few in duodenum. This cell type produces glucagon-like immunoreactants (glicentin, glucagon-37, glucagon-29, GLP-1 and -2) and PYY. ISBN:0517223651 PMID:15153415 An enteroendorcine cell found in the ileum and jejunum that produces neurotensin. tmeehan 2010-09-10T04:08:29Z FMA:62943 N cell cell type N enteroendocrine cell An enteroendorcine cell found in the ileum and jejunum that produces neurotensin. GOC:tfm Scattered in duodenojejunal mucosa, this enteroendocrine cell secretes secretin and serotonin. tmeehan 2010-09-10T04:44:46Z FMA:62936 cell type S enteroendocrine cell Scattered in duodenojejunal mucosa, this enteroendocrine cell secretes secretin and serotonin. GOC:tfm PMID:15153415 An enteroendocrine cell which produces a gastrin- and cholecystokinin-like peptide. The apical microvilli-rich plasma membrane is in open contact with the small intestine mucosa. This cell type is devoid of gastrin-17 but contains other fragments of the gastrin polypeptide. tmeehan 2010-09-13T09:48:34Z FMA:63421 cell type TG enteroendocrine cell An enteroendocrine cell which produces a gastrin- and cholecystokinin-like peptide. The apical microvilli-rich plasma membrane is in open contact with the small intestine mucosa. This cell type is devoid of gastrin-17 but contains other fragments of the gastrin polypeptide. DOI:10.1007/978-3-211-99390-3 GOC:tfm PMID:7013499 An epithelial cell of the mucosa associated with facial skeleton. tmeehan 2010-09-14T11:04:02Z CL:1000440 FMA:70581 cell ecto-epithelial cell of viscerocranial mucosa An epithelial cell of the mucosa associated with facial skeleton. GOC:tfm ISBN:0323052908 An enteroendorcine cell found in the fundus and pylorus, this cell type has dense round secretory granules that contain ghrelin. tmeehan 2010-09-13T10:12:12Z FMA:63209 A-like X/A-like cell type X enteroendocrine cell An enteroendorcine cell found in the fundus and pylorus, this cell type has dense round secretory granules that contain ghrelin. GOC:tfm PMID:20616512 A taste receptor cell that is characterized by morphologically identifiable synaptic contacts with the gustatory nerve fibers and expression of the synaptic membrane protein-25 (SNAP-25) and NCAM. tmeehan 2010-09-13T10:57:21Z taste bud basal cell FMA:67940 type 3 taste cell cell type III taste bud cell A taste receptor cell that is characterized by morphologically identifiable synaptic contacts with the gustatory nerve fibers and expression of the synaptic membrane protein-25 (SNAP-25) and NCAM. GOC:tfm ISBN:0517223651 PMID:15738192 A taste receptor cell that has a short microvilli, a projecting apical region, a large rounded nucleus, and expresses taste chemoreceptors thus making them the transducing cell for taste qualities. tmeehan 2010-09-13T10:57:26Z FMA:62381 type 2 taste cell cell type II taste cell A taste receptor cell that has a short microvilli, a projecting apical region, a large rounded nucleus, and expresses taste chemoreceptors thus making them the transducing cell for taste qualities. GOC:tfm PMID:15738192 A rounded, mitotically active stem cell which is the source of new cells of the taste bud; located basally. tmeehan 2010-09-13T10:57:29Z taste bud basal cell FMA:62380 type 4 taste cell cell There is debate about the exact lineage of these cell types from this progenitor. See PMID:15738192. type IV taste receptor cell A rounded, mitotically active stem cell which is the source of new cells of the taste bud; located basally. GOC:tfm ISBN:0517223651 PMID:15738192 A cell type that forms the boundary with the surrounding epithelium. tmeehan 2010-09-13T10:57:31Z FMA:67941 cell type V taste receptor cell A cell type that forms the boundary with the surrounding epithelium. GOC:tfm ISBN:0517223651 A densely staining taste receptor cell that contains many dense vacuoles in their apical regions which project into the apical space and bear microvilli. This cell type serves as a supporting cell by surrounding and isolating the other cell types from each other; secrete a dense amorphous material that surrounds the microvilli in the taste pore. This cell type expresses a glial glutumate transporter, GLAST. tmeehan 2010-09-13T10:57:35Z FMA:62356 dark tongue cell type I taste cell type taste 1 cell cell type I taste bud cell A densely staining taste receptor cell that contains many dense vacuoles in their apical regions which project into the apical space and bear microvilli. This cell type serves as a supporting cell by surrounding and isolating the other cell types from each other; secrete a dense amorphous material that surrounds the microvilli in the taste pore. This cell type expresses a glial glutumate transporter, GLAST. GOC:tfm ISBN:0412046911 ISBN:0517223651 PMID:15738192 A sperm bearing a Y chromosome. Chromosomal and genetic sex is established at fertilization in mammals and depends upon whether an X-bearing sperm or a Y-bearing sperm fertilizes the X-bearing ovum. tmeehan 2010-09-13T11:35:24Z FMA:84058 Y bearing sperm Y-bearing sperm cell Y chromosome-bearing sperm cell A sperm bearing a Y chromosome. Chromosomal and genetic sex is established at fertilization in mammals and depends upon whether an X-bearing sperm or a Y-bearing sperm fertilizes the X-bearing ovum. GOC:tfm ISBN:0721669743 A sperm bearing an X chromosome. Chromosomal and genetic sex is established at fertilization in mammals and depends upon whether an X-bearing sperm or a Y-bearing sperm fertilizes the X-bearing ovum. tmeehan 2010-09-13T11:35:26Z FMA:84057 X bearing sperm X-bearing sperm cell X chromosome-bearing sperm cell A sperm bearing an X chromosome. Chromosomal and genetic sex is established at fertilization in mammals and depends upon whether an X-bearing sperm or a Y-bearing sperm fertilizes the X-bearing ovum. GOC:tfm ISBN:0721669743 A round or oval neuroepithelial cell that contacts other type I cells or capillaries. They occur in clusters that are surrounded by sheath cells (type-II cells) in the carotid body. This cell type is capable of secreting a number of neurotransmitters. tmeehan 2010-09-13T01:40:21Z FMA:84186 glomus cell cell type I cell of carotid body A round or oval neuroepithelial cell that contacts other type I cells or capillaries. They occur in clusters that are surrounded by sheath cells (type-II cells) in the carotid body. This cell type is capable of secreting a number of neurotransmitters. GOC:tfm ISBN:0517223651 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 with a well defined Golgi apparatus that makes up the continuous layer of cells bordering the thymic tissue beneath the capsule. tmeehan 2010-09-13T02:37:23Z FMA:72209 subcapsular thymic epithelial cell cell type-1 epithelial cell of thymus An epithelial cell with a well defined Golgi apparatus that makes up the continuous layer of cells bordering the thymic tissue beneath the capsule. GOC:tfm PMID:9264335 A thymic epithelial cell that has an eccentric, round, or irregularly shaped hetero or euchromatic nucleus. The hallmark of this cell type is the presence of vacuoles, which are clustered in one area of the cytoplasm in the vicinity of the nucleus. The vacuoles are small and acquire a grape-like form, occasionally showing delicate internal microvillous projections. tmeehan 2010-09-13T02:37:26Z FMA:72214 cystic thymic epithelial cells large mTEC large medullary thymic epithelial cells cell type-6 epithelial cell of thymus A thymic epithelial cell that has an eccentric, round, or irregularly shaped hetero or euchromatic nucleus. The hallmark of this cell type is the presence of vacuoles, which are clustered in one area of the cytoplasm in the vicinity of the nucleus. The vacuoles are small and acquire a grape-like form, occasionally showing delicate internal microvillous projections. GOC:tfm PMID:19721455 PMID:9264335 An epithelial cell with high nuclear and cytoplasmic electron-density. This cell type is found in the deeper portions of the cortex but is more abundant in the medulla of the thymus. tmeehan 2010-09-13T02:37:45Z FMA:72212 dark thymic epithelial cell cell type-4 epithelial cell of thymus An epithelial cell with high nuclear and cytoplasmic electron-density. This cell type is found in the deeper portions of the cortex but is more abundant in the medulla of the thymus. FMA:0412046911 GOC:tfm PMID:9264335 A thymic epithelial cell with moderate nuclear and cytoplasmic electron-density. Scattered in the cortex, this cell type is predominant in the mid and deep cortex. tmeehan 2010-09-13T02:37:51Z FMA:72211 intermediate thymic epithelial cell cell type-3 epithelial cell of thymus A thymic epithelial cell with moderate nuclear and cytoplasmic electron-density. Scattered in the cortex, this cell type is predominant in the mid and deep cortex. PMID:9264335 A thymic epithelial cell type with low nuclear and cytoplasmic electrondensity; has a round, euchromatic nucleus and occurs in small groups at the corticomedullary junction or scattered singly in the medulla. tmeehan 2010-09-13T02:37:54Z FMA:72213 undifferentiated mTEC undifferentiated medullary thymic epithelial cell undifferentiated thymic epithelial cell cell type-5 epithelial cell of thymus A thymic epithelial cell type with low nuclear and cytoplasmic electrondensity; has a round, euchromatic nucleus and occurs in small groups at the corticomedullary junction or scattered singly in the medulla. GOC:tfm ISBN:0412046911 PMID:19721455 PMID:9264335 An epithelial cell scattered in the cortex, predominant in the outer cortex with a large pale nucleus and a prominent nucleolus. tmeehan 2010-09-13T02:37:58Z FMA:72210 pale thymic epithelial cell cell type-2 epithelial cell of thymus An epithelial cell scattered in the cortex, predominant in the outer cortex with a large pale nucleus and a prominent nucleolus. GOC:tfm ISBN:0412046911 PMID:9264335 A small medullary thymic epithelial cell with a spindle shape, often arranged in groups and connected to each other by large desmosomes and interdigitations. The cytoplasm is sparse, with scanty organelles and thick bundles of cytokeratin. tmeehan 2010-09-13T03:23:25Z spindle shaped mTEC spindle shaped medullary thymic epithelial cell cell type-7 epithelial cell of thymus A small medullary thymic epithelial cell with a spindle shape, often arranged in groups and connected to each other by large desmosomes and interdigitations. The cytoplasm is sparse, with scanty organelles and thick bundles of cytokeratin. GOC:tfm PMID:19721455 A synovial cell type that resembles fibroblasts, has abundant granular endoplasmic reticulum but contains fewer vacuoles and vesicles. This cell type secretes glycoproteins and hyaluronic acid. tmeehan 2010-09-13T03:39:14Z FMA:66788 cell type B synovial cell A synovial cell type that resembles fibroblasts, has abundant granular endoplasmic reticulum but contains fewer vacuoles and vesicles. This cell type secretes glycoproteins and hyaluronic acid. GOC:tfm ISBN:0517223651 A synovial cell that is macrophage-like, characterized by surface ruffles or lamellipodia, plasma membrane invaginations and associated micropinocytotic vesicles, Golgi apparatus and little granular endoplasmic reticulum. tmeehan 2010-09-13T03:39:17Z FMA:66787 type A synoviocyte cell type A synovial cell A synovial cell that is macrophage-like, characterized by surface ruffles or lamellipodia, plasma membrane invaginations and associated micropinocytotic vesicles, Golgi apparatus and little granular endoplasmic reticulum. GOC:tfm ISBN:0517223651 A ciliated epithelial cell of the retina, this cell type uptakes sodium chloride and passes it to non-pigmented ciliary epithelial cells. tmeehan 2010-09-13T04:09:27Z FMA:70606 PE cell pigmented ciliary epithelial cell A ciliated epithelial cell of the retina, this cell type uptakes sodium chloride and passes it to non-pigmented ciliary epithelial cells. PMID:15106942 A multi-ciliated cell of the retina that lacks visual pigment and contributes to aqueous humor by secreting chloride ions. This cell type maintains gap junctions with pigmented epithelial cells. tmeehan 2010-09-13T04:09:31Z FMA:70607 NPE cell non-pigmented ciliary epithelial cell A multi-ciliated cell of the retina that lacks visual pigment and contributes to aqueous humor by secreting chloride ions. This cell type maintains gap junctions with pigmented epithelial cells. GOC:tfm PMID:15106942 An epithelial cell of the distal convoluted tubule of the kidney that helps regulate systemic levels of potassium, sodium, calcium, and pH. FMA:62125 FMA:70981 KUPO:0001055 kidney distal tubule epithelial cell cell epithelial cell of distal tubule true An epithelial cell of the distal convoluted tubule of the kidney that helps regulate systemic levels of potassium, sodium, calcium, and pH. GOC:tfm ISBN:0517223651 An epithelial cell of the proximal tubule of the kidney. FMA:62125 FMA:70973 KUPO:0001044 kidney proximal tubule epithelial cell cell epithelial cell of proximal tubule true An epithelial cell of the proximal tubule of the kidney. GOC:tfm ISBN:1-4160-2328-3 A brush border epithelial cell located in the proximal tubule of the kidney that detects fluid flow. tmeehan 2010-09-14T11:29:20Z cell brush border cell of the proximal tubule A brush border epithelial cell located in the proximal tubule of the kidney that detects fluid flow. GOC:tfm ISBN:1-4160-2328-3 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 A basophil chromphil cell of the anterior pitiutary gland that produce adrenocorticotropic hormone, melanocyte-stimulating hormone and lipotropin. This cell type is irregular in shape and has short dendritic processes which are inserted among other neighboring cells; tmeehan 2010-09-14T02:08:23Z BTO:0002509 FMA:83098 cell corticotroph A basophil chromphil cell of the anterior pitiutary gland that produce adrenocorticotropic hormone, melanocyte-stimulating hormone and lipotropin. This cell type is irregular in shape and has short dendritic processes which are inserted among other neighboring cells; GOC:tfm ISBN:0517223651 An acidophil cell of the anterior pitiuatry gland that produces both prolactin and growth hormone. tmeehan 2010-09-14T02:25:34Z FMA:83097 cell mammosomatotroph An acidophil cell of the anterior pitiuatry gland that produces both prolactin and growth hormone. GOC:tfm An acidophilic cell of the anterior pituitary that produces prolactin. tmeehan 2010-09-14T02:30:57Z FMA:83096 epsilon-acidophil lactotrope lactotroph lactotropic cell mammotrope mammotrophic cell mammotropic cell cell mammotroph An acidophilic cell of the anterior pituitary that produces prolactin. SANBI:mhl An acidophilic cell of the anterior pituitary that produces growth hormone, somatotropin. tmeehan 2010-09-14T02:33:09Z FMA:83095 somatotrope somatotropic cell somatrophic cell cell somatotroph An acidophilic cell of the anterior pituitary that produces growth hormone, somatotropin. SANBI:mhl 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 An auditory epithelial support cell located in the vestibular epithelium that has many hallmarks of glial cells. This cell type express glial markers such as vimentin, S100, glutamate-aspartate transporter, low affinity neurotrophin receptor p75, glial fibrillary acidic protein, and proteolipid protein. tmeehan 2010-09-14T03:20:01Z FMA:75809 cell external supporting cell of vestibular epithelium An auditory epithelial support cell located in the vestibular epithelium that has many hallmarks of glial cells. This cell type express glial markers such as vimentin, S100, glutamate-aspartate transporter, low affinity neurotrophin receptor p75, glial fibrillary acidic protein, and proteolipid protein. GOC:tfm PMID:20837532 An epithelial supporting cell located in the cochlea. tmeehan 2010-09-14T03:31:38Z FMA:79796 cell supporting cell of cochlea An epithelial supporting cell located in the cochlea. GOC:tfm A supporting cell of the vestibular epithelium. tmeehan 2010-09-14T03:31:44Z FMA:75607 cell supporting cell of vestibular epithelium A supporting cell of the vestibular epithelium. GOC:tfm PMID:20837532 An external limiting cell found in the vestibular epithelium. tmeehan 2010-09-14T03:33:50Z FMA:75808 cell external limiting cell of vestibular epithelium An external limiting cell found in the vestibular epithelium. GOC:tfm A mesothelial cell capable of circulating in the blood by first losing its squamous character. This cell can incorporate into the regenerating mesothelium. tmeehan 2010-09-15T10:47:11Z FMA:86712 cell periperhal blood mesothelial cell A mesothelial cell capable of circulating in the blood by first losing its squamous character. This cell can incorporate into the regenerating mesothelium. GOC:tfm PMID:14592528 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 (metazoa) A cell of the embryo. FMA:0618947256 A stem cell of embryonic origin. tmeehan 2010-09-15T03:44:35Z BTO:0001086 CALOHA:TS-0263 FMA:82841 ESC cell This is an in vitro cell type and may be removed in future releases. These cells are reportedly SSEA-4-positive, CD73-negative, and CD324-positive. embryonic stem cell A stem cell of embryonic origin. GOC:dsd GOC:tfm ISBN:068340007X PMID:18179856 A cell of a fetus which is suspended in the amniotic fluid. Amniocytes are considered to arise from several tissues including fetal skin, the fetal urinary tract, umbilical cord, and the inner amniotic surface. tmeehan 2010-09-20T10:13:37Z BTO:0000066 cell amniocyte true A cell of a fetus which is suspended in the amniotic fluid. Amniocytes are considered to arise from several tissues including fetal skin, the fetal urinary tract, umbilical cord, and the inner amniotic surface. BFO:0000066 GOC:tfm PMID:3211847 A myoepithelial cell that surrounds milk-secreting luminal epithelial cells. This cell type contracts under the stimulation of oxytocin and is attached to the basement membrane by hemidesmosomes and to the adjacent luminal cells by desmosomes. This cell type expresses high level of keratin-14 and is estrogen receptor alpha negative. tmeehan 2010-09-20T11:42:14Z cell myoepithelial cell of mammary gland A myoepithelial cell that surrounds milk-secreting luminal epithelial cells. This cell type contracts under the stimulation of oxytocin and is attached to the basement membrane by hemidesmosomes and to the adjacent luminal cells by desmosomes. This cell type expresses high level of keratin-14 and is estrogen receptor alpha negative. GOC:tfm PMID:11250738 PMID:19022771 The milk-producing cell of the alveolar unit that emerges during pregnancy. tmeehan 2010-09-20T01:30:57Z CL:0002230 CL:1000476 FMA:74506 FMA:79866 epithelial cell of lactiferous gland luminal cell of alveolus of lactiferous gland cell mammary alveolar cell true The milk-producing cell of the alveolar unit that emerges during pregnancy. GOC:tfm PMID:19022771 A mammary epithelial cell that occurs in the lumen of the ductal and alveoli structure in the breast. tmeehan 2010-09-20T01:37:53Z FMA:73280 cell luminal epithelial cell of mammary gland A mammary epithelial cell that occurs in the lumen of the ductal and alveoli structure in the breast. GOC:tfm PMID:19022771 An epithelial cell of the mammary gland. tmeehan 2010-09-20T01:49:37Z BTO:0004300 breast epithelial cell mammary epithelial cell cell mammary gland epithelial cell An epithelial cell of the mammary gland. GOC:tfm PMID:19022771 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 epithelial cell type that lacks the columnar shape typical for other respiratory epithelial cells. This cell type is able to differentiate into other respiratory epithelial cells in response to injury. tmeehan 2010-09-20T02:10:36Z cell basal epithelial cell of tracheobronchial tree An epithelial cell type that lacks the columnar shape typical for other respiratory epithelial cells. This cell type is able to differentiate into other respiratory epithelial cells in response to injury. GOC:tfm An undifferentiated columnar cell of the bronchus epithelium tmeehan 2010-09-20T02:17:58Z cell undifferentiated cell of bronchus epithelium An undifferentiated columnar cell of the bronchus epithelium GOC:tfm PMID:18757316 A ciliated cell of the bronchus. tmeehan 2010-09-20T02:21:12Z cell ciliated cell of the bronchus A ciliated cell of the bronchus. GOC:tfm PMID:18757316 A fat cell derived from a neural crest cell. tmeehan 2010-09-20T02:25:25Z cell neural crest derived fat cell A fat cell derived from a neural crest cell. GOC:tfm PMID:17507398 An undifferentiated fibroblast that can be stimulated to form a fat cell. tmeehan 2010-09-20T02:31:53Z BTO:0001107 cell preadipocyte An undifferentiated fibroblast that can be stimulated to form a fat cell. GOC:tfm PMID:18793119 A preadipocyte that is capable of differentiating into a brown adipocyte. This cell type expresses uncoupling protein-1, PPAR-gamma, PR-domain-containing 16; and PGC-1alpha (peroxisome proliferator-activated receptor-gamma (PPARgamma) coactivator-1alpha). tmeehan 2010-09-20T02:38:38Z cell brown preadipocyte A preadipocyte that is capable of differentiating into a brown adipocyte. This cell type expresses uncoupling protein-1, PPAR-gamma, PR-domain-containing 16; and PGC-1alpha (peroxisome proliferator-activated receptor-gamma (PPARgamma) coactivator-1alpha). GOC:tfm PMID:18719589 An endothelial cell that lines the oral cavitiy including the mucosa of the gums, the palate, the lip, and the cheek. tmeehan 2010-09-20T02:52:54Z cell buccal mucosa cell An endothelial cell that lines the oral cavitiy including the mucosa of the gums, the palate, the lip, and the cheek. GOC:tfm MESH:A10.615.550.599 A stem cell located in the bulge of the hair follicle that can give rise to regenerate the new follicle with each hair cycle and to reepithelialize the epidermis during wound repair. tmeehan 2010-09-20T03:07:03Z bulge keratinocyte cell keratinocyte stem cell A stem cell located in the bulge of the hair follicle that can give rise to regenerate the new follicle with each hair cycle and to reepithelialize the epidermis during wound repair. PMID:15339667 A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-positive, CD117-positive, CD122-positive,and CD161-positive. tmeehan 2010-09-21T10:06:53Z cell p-NK Human markers; killer cell immunoglobulin-like receptor 2DL1 is used as a representative example (PRO at this time lacks a KIR superfamily). CD56-positive, CD161-positive immature natural killer cell, human A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-positive, CD117-positive, CD122-positive,and CD161-positive. GOC:add GO_REF:0000031 ISBN:0781735149 PMID:12457618 p-NK PMID:12457618 A prostate epithelial cell that is CD133-positive, CD44-positive, integrin A2beta3-high. This cell is a stem cell for the prostate epithelium. tmeehan 2010-09-20T03:21:06Z CD133-positive prostate epithelial cell cell prostate stem cell A prostate epithelial cell that is CD133-positive, CD44-positive, integrin A2beta3-high. This cell is a stem cell for the prostate epithelium. GOC:tfm PMID:15226377 The exocrine cell of the prostate, this epithelial cell secretes prostatic acid phosphotase and PSA, and is dependent on androgen hormones for survival. tmeehan 2010-09-20T03:34:05Z cell luminal cell of prostate epithelium The exocrine cell of the prostate, this epithelial cell secretes prostatic acid phosphotase and PSA, and is dependent on androgen hormones for survival. GOC:tfm An undifferentiated cell of the prostate epithelium that lacks secretory activity. tmeehan 2010-09-20T03:34:10Z cell basal cell of prostate epithelium An undifferentiated cell of the prostate epithelium that lacks secretory activity. GOC:tfm PMCID:PMC2673349 A circulating endothelial cell of the phenotype CD146-positive, CD105-positive, CD45-negative. This cell type is indicative of recent vascular damage. tmeehan 2010-09-20T03:49:58Z cell circulating endothelial cell A circulating endothelial cell of the phenotype CD146-positive, CD105-positive, CD45-negative. This cell type is indicative of recent vascular damage. GOC:tfm PMID:19652886 A natural killer cell subset that is found in the decidual of the uterus and is CD56-high, Galectin-1-positive and CD16-negative. This cell type represents the most abundant immune cell type in the decidual during the first trimester of pregnancy. tmeehan 2010-09-20T04:00:02Z dNK cell decidual NK cell cell decidual natural killer cell, human A natural killer cell subset that is found in the decidual of the uterus and is CD56-high, Galectin-1-positive and CD16-negative. This cell type represents the most abundant immune cell type in the decidual during the first trimester of pregnancy. PMID:14568979 PMID:19800965 A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-negative, CD117-positive, CD122-positive,and CD161-positive. tmeehan 2010-09-20T04:33:11Z cell p-NK Human markers; killer cell immunoglobulin-like receptor 2DL1 is used as a representative example (PRO at this time lacks a KIR superfamily). CD56-negative, CD161-positive immature natural killer cell, human A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-negative, CD117-positive, CD122-positive,and CD161-positive. GOC:add GO_REF:0000031 ISBN:0781735149 PMID:12457618 p-NK PMID:12457618 An immature natural killer cell that is NK1.1-positive, DX5-positive, Ly49-positive, CD27-low and CD11b-low. This cell type is found in high numbers in the liver. tmeehan 2010-09-20T04:41:01Z preNK.BM cell Markers are associated with mouse cells. CD27-low, CD11b-low immature natural killer cell, mouse An immature natural killer cell that is NK1.1-positive, DX5-positive, Ly49-positive, CD27-low and CD11b-low. This cell type is found in high numbers in the liver. GOC:tfm PMID:19949422 http:www.immgen.org/index_content.html An immature natural killer cell that is NK1.1-positive and DX-5 negative. tmeehan 2010-09-21T10:11:44Z cell Dx5-negative, NK1.1-positive immature natural killer cell, mouse An immature natural killer cell that is NK1.1-positive and DX-5 negative. GOC:tfm PMID:12766763 A mature natural killer cell that is CD27-high and CD11b-high. This cell type is capable of interferon-gamma secretion. tmeehan 2010-09-21T10:19:49Z cell CD27-high, CD11b-high natural killer cell, mouse A mature natural killer cell that is CD27-high and CD11b-high. This cell type is capable of interferon-gamma secretion. GOC:tfm PMID:19949422 A CD27-low, CD11b-high natural killer cell that has a higher threshold of activation due to higher expression of inhibitory receptors. tmeehan 2010-09-21T10:19:54Z cell CD27-low, CD11b-high natural killer cell, mouse A CD27-low, CD11b-high natural killer cell that has a higher threshold of activation due to higher expression of inhibitory receptors. GOC:tfm PMID:1994922 A natural killer cell that is CD27-high and CD11b-low. tmeehan 2010-09-21T10:20:00Z cell CD27-high, CD11b-low natural killer cell, mouse A natural killer cell that is CD27-high and CD11b-low. GOC:tfm PMID:1994922 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 A multi-fate stem cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1. tmeehan 2010-09-21T04:41:06Z pancreatic endocrine progenitor pancreatic islet progenitor cell cell progenitor cell of endocrine pancreas A multi-fate stem cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1. GOC:tfm PMID:20025937 PMID:20217494 A hematopoietic stem cell that exists during embryogenesis. tmeehan 2010-09-22T09:05:13Z cell gestational hematopoietic stem cell A hematopoietic stem cell that exists during embryogenesis. GOC:tfm ISBN:978-60327-246-6 A hematopoietic stem cell that resides in the fetal liver. In mice, this cell type is first observed at E10.5. This cell type is MHC-positive, HSA-positive, AA4.1-positive, CD45-positive, Sca-1 positive, CD150-positive, CD48-negative and CD244-negative. tmeehan 2010-09-22T09:08:32Z cell fetal liver hematopoietic progenitor cell true A hematopoietic stem cell that resides in the fetal liver. In mice, this cell type is first observed at E10.5. This cell type is MHC-positive, HSA-positive, AA4.1-positive, CD45-positive, Sca-1 positive, CD150-positive, CD48-negative and CD244-negative. GOC:tfm ISBN:978-1-60327-346-6 PMID:16569764 A hematopoietic stem found in the yolk sac. In mice, this cell type is Sca-1-negative, CD45-negative, MHC-negative, HSA-positive, AA4.1-positive, CD44-positive. tmeehan 2010-09-22T09:08:34Z hemangioblast precursor cell yolk sac hematopoietic stem cell true A hematopoietic stem found in the yolk sac. In mice, this cell type is Sca-1-negative, CD45-negative, MHC-negative, HSA-positive, AA4.1-positive, CD44-positive. GOC:tfm doi:10.1097/MOH.0b013e3282f97ae1 A large nucleated basophilic erythrocyte found in mammalian embryos. This cell type arises from the blood islands of yolk sacs and expresses different types of hemoglobins (beta-H1, gamma-1 and zeta) than adult erythrocytes. Considered a type of erythroblast as this cell type can enucleate in circulation. tmeehan 2010-09-22T09:27:05Z primitive erythroblast primitive erythrocyte primitive erythroid cell cell primitive red blood cell true A large nucleated basophilic erythrocyte found in mammalian embryos. This cell type arises from the blood islands of yolk sacs and expresses different types of hemoglobins (beta-H1, gamma-1 and zeta) than adult erythrocytes. Considered a type of erythroblast as this cell type can enucleate in circulation. DOI:10.1097/MOH.0b013e3282f97ae1 GOC:tfm PMID:11495698 A primitive erythrocyte that has undergone enucleation. This cell type is 3-6 fold bigger than the fetal derived erythrocytes that they co-circulate with during fetal development. Expresses epsilon-gamma hemoglobin chains. tmeehan 2010-09-22T09:35:16Z megalocyte cell primitive reticulocyte true A primitive erythrocyte that has undergone enucleation. This cell type is 3-6 fold bigger than the fetal derived erythrocytes that they co-circulate with during fetal development. Expresses epsilon-gamma hemoglobin chains. GOC:tfm PMID:11495698 doi:10.1097/MOH.0b013e3282f97ae1 A fetal liver derived enucleated erythrocyte. This erythrocyte resembles adult erythrocytes in that they are small (3- to 6- times smaller than primitive erythrocytes) and produce adult hemaglobins. tmeehan 2010-09-22T09:38:32Z macrocyte cell fetal derived definitive erythrocyte true A fetal liver derived enucleated erythrocyte. This erythrocyte resembles adult erythrocytes in that they are small (3- to 6- times smaller than primitive erythrocytes) and produce adult hemaglobins. GOC:tfm PMID:11495698 Derived from the Greek word pyren (the pit of a stone fruit), this is a transient nucleated cell type that results from exclusion of the nucleus from the primitive erythrocyte. tmeehan 2010-09-22T10:02:37Z cell pyrenocyte true Derived from the Greek word pyren (the pit of a stone fruit), this is a transient nucleated cell type that results from exclusion of the nucleus from the primitive erythrocyte. GOC:tfm A hematopoietic stem cell of the placenta. This cell type is first observed E10.5 This cell type may give rise to fetal liver hematopoietic stem cells. tmeehan 2010-09-22T10:30:02Z cell placental hematopoietic stem cell A hematopoietic stem cell of the placenta. This cell type is first observed E10.5 This cell type may give rise to fetal liver hematopoietic stem cells. GOC:tfm ISBN:978-1-60327-346-6 A hematopoietic stem cell from the aorta-gonad-mesonephros region of the developing embryo. First seen at E10.5 in mouse embryos. May give rise to fetal liver HSC. tmeehan 2010-09-22T10:31:49Z cell AGM hematopoietic stem cell A hematopoietic stem cell from the aorta-gonad-mesonephros region of the developing embryo. First seen at E10.5 in mouse embryos. May give rise to fetal liver HSC. GOC:tfm ISBN:978-1-60327-346-6 A progenitor cell that is capable of forming colonies of primitive erythrocytes in the blood island of the yolk sac. First arrive at E7.5 in mouse and expresses CD41. tmeehan 2010-09-22T10:47:28Z EryP-CFC inner blood island hemangioblast cell primitive erythroid progenitor true A progenitor cell that is capable of forming colonies of primitive erythrocytes in the blood island of the yolk sac. First arrive at E7.5 in mouse and expresses CD41. GOC:tfm ISBN:0813817986 PMID:20711979 A cell located in the outermost proliferative zone of the external germinal layer that can differentiate into astroglial cells and granule cells. This cell type is glial fibrillary acidic protein-positive and NK1-positive. tmeehan 2010-09-22T01:40:44Z cell granule cell precursor A cell located in the outermost proliferative zone of the external germinal layer that can differentiate into astroglial cells and granule cells. This cell type is glial fibrillary acidic protein-positive and NK1-positive. GOC:tfm PMID:14745007 A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic cell located between the lamellae with a large flattened nucleus and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratin sulfate. tmeehan 2010-09-22T01:57:40Z corneal fibroblast corneal keratocyte cell keratocyte A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic cell located between the lamellae with a large flattened nucleus and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratin sulfate. GOC:tfm ISBN:978-0-7020-2958-5 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 smooth muscle cell of the myometrium that enlarges and stretches during pregnancy, and contracts in response to oxytocin. tmeehan 2010-09-23T03:46:34Z BTO:0004519 myometrium smooth muscle cell cell myometrial cell A smooth muscle cell of the myometrium that enlarges and stretches during pregnancy, and contracts in response to oxytocin. GOC:tfm PMID:11429640 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 differentiated form of a fungus produced during or as a result of an asexual or sexual reproductive process; usually a cell with a thick cell wall that stores and protects one or more nuclei. Spores may be produced in response to, and are characteristically resistant to, adverse environmental conditions. tmeehan 2010-10-01T09:02:42Z cell fungal spore A differentiated form of a fungus produced during or as a result of an asexual or sexual reproductive process; usually a cell with a thick cell wall that stores and protects one or more nuclei. Spores may be produced in response to, and are characteristically resistant to, adverse environmental conditions. FAO:0000019 GOC:tfm A simple columnar epithelial cell that secretes mucin. Rough endoplasmic reticulum, mitochondria, the nucleus, and other organelles are concentrated in the basal portion. The apical plasma membrane projects microvilli to increase surface area for secretion. tmeehan 2010-09-23T04:42:27Z respiratory mucosa goblet cells cell respiratory goblet cell A simple columnar epithelial cell that secretes mucin. Rough endoplasmic reticulum, mitochondria, the nucleus, and other organelles are concentrated in the basal portion. The apical plasma membrane projects microvilli to increase surface area for secretion. GOC:tfm ISBN:0721662544 respiratory mucosa goblet cells MP:0010863 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 transversely striated, synctial muscle cell, formed by the fusion of myoblasts. tmeehan 2010-09-24T01:13:01Z CL:0000369 myotubule single cell sarcomere cell myotube A transversely striated, synctial muscle cell, formed by the fusion of myoblasts. GOC:dos GOC:tfm ISBN:0323052908 PMID:22274696 A peptide hormone secreting cell that secretes growth hormone releasing hormone. tmeehan 2010-09-24T01:36:44Z GHRH secreting cell somatocrinin secreting cell cell growth hormone releasing hormone secreting cell A peptide hormone secreting cell that secretes growth hormone releasing hormone. GOC:dph GOC:tfm A hair cell of the ear that contains the organs of balance and hearing. tmeehan 2010-09-24T01:49:31Z ear receptor cell cell ear hair cell A hair cell of the ear that contains the organs of balance and hearing. GOC:dph GOC:tfm ISBN:0192801023 A giioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19. tmeehan 2010-09-24T02:06:10Z Schwann cell precursor cell cell Schwann cell precursor A giioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19. GOC:tfm A glial cell that ensheaths multiple small diameter axons in the peripheral nervous system. The non-myelinating Schwann cell is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has a basal lamina. Cells can survive without an axon present. These cells can de-differentiate into immature Schwann cells. tmeehan 2010-09-24T02:10:26Z Schwann cell cell non-myelinating Schwann cell A glial cell that ensheaths multiple small diameter axons in the peripheral nervous system. The non-myelinating Schwann cell is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has a basal lamina. Cells can survive without an axon present. These cells can de-differentiate into immature Schwann cells. GOC:cvs GOC:tfm ISBN:0721662544 A glial cell that develops from a Schwann cell precursor. The immature Schwann cell is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has a basal lamina. Cells can survive without an axon present. Immature Schwann cell can be found communally ensheathing large groups of axons. tmeehan 2010-09-24T02:10:31Z Schwann cell ZFA:0001725 cell immature Schwann cell A glial cell that develops from a Schwann cell precursor. The immature Schwann cell is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has a basal lamina. Cells can survive without an axon present. Immature Schwann cell can be found communally ensheathing large groups of axons. GOC:cvs GOC:tfm ISBN:0721662544 A double negative thymocyte that has a T cell receptor consisting of a gamma chain containing a Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive and is found in the fetal thymus. tmeehan 2010-10-07T02:21:07Z fetal Vgamma2+ thymocyte cell NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. immature Vgamma2-positive fetal thymocyte A double negative thymocyte that has a T cell receptor consisting of a gamma chain containing a Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive and is found in the fetal thymus. GOC:tfm http://www.immgen.org A neurecto-epithelial cell found in the arachnoid villi of dura mater. This cell type facilitates flow of cerebrospinal fluid into the blood. tmeehan 2010-09-28T02:23:46Z FMA:86588 arachnoid cap cell cell meningothelial cell A neurecto-epithelial cell found in the arachnoid villi of dura mater. This cell type facilitates flow of cerebrospinal fluid into the blood. GOC:tfm http://www.aippg.net/forum/viewtopic.php?t=62590 An asexual spore formed by Oomycetes; formed upon fertilization of an oosphere. tmeehan 2010-10-01T09:22:45Z FAO:0000039 cell oospore An asexual spore formed by Oomycetes; formed upon fertilization of an oosphere. GOC:tfm ISBN:0851988857 SGD:clt A conidium that has only one nucleus. tmeehan 2010-10-01T09:26:39Z FAO:0000025 cell uninucleate conidium A conidium that has only one nucleus. GOC:tfm SGD:clt A conidium that has more than one nucleus. tmeehan 2010-10-01T09:31:28Z FAO:0000033 cell multinucleate conidium A conidium that has more than one nucleus. GOC:tfm SGD:clt A uninucleate spore formed on specialized cells or projections, sterigma, of a conidiophore head. FAO:0000033 cell conidium of conidiophore head A uninucleate spore formed on specialized cells or projections, sterigma, of a conidiophore head. GOC:tfm PMID:9529886 SGD:clt A macroconidium that has only one nucleus. FAO:0000029 cell uninucleate macroconidium A macroconidium that has only one nucleus. GOC:tfm SGD:clt An oblong or round asexual spore formed from conidial chains. BTO:0000127 FAO:0000042 cell blastospore blastoconidium An oblong or round asexual spore formed from conidial chains. GOC:tfm PMID:2524423 SGD:clt A macroconidium that has more than one nucleus. FAO:0000035 cell multinucleate macroconidium A macroconidium that has more than one nucleus. GOC:tfm SGD:clt Cylindrical spore formed by development and compartmentation of hyphae; the hyphae are often supporting blastoconidiophores. FAO:0000041 cell arthrospore arthroconidium Cylindrical spore formed by development and compartmentation of hyphae; the hyphae are often supporting blastoconidiophores. GOC:tfm PMID:2524423 SGD:clt An arthroconidium that has more than one nucleus. FAO:0000037 cell multinucleate arthroconidium An arthroconidium that has more than one nucleus. GOC:tfm SGD:clt An arthroconidium that has only one nucleus. FAO:0000031 cell uninucleate arthroconidium An arthroconidium that has only one nucleus. GOC:tfm SGD:clt A blastoconidium that has only one nucleus. FAO:0000030 cell uninucleate blastconidium A blastoconidium that has only one nucleus. GOC:tfm SGD:clt A blastoconidium that has more than one nucleus. FAO:0000036 cell multinucleate blastoconidium A blastoconidium that has more than one nucleus. GOC:tfm SGD:clt Obsolete. Use PO:0025017 from Plant Ontology instead. A plant cell that arises through meiosis and develops into a gametophyte. cell replaced_by: PO:0025017 obsolete plant spore true Obsolete. Use PO:0025017 from Plant Ontology instead. A plant cell that arises through meiosis and develops into a gametophyte. GOC:tfm PO:0025017 A monocyte that has characteristics of both patrolling and inflammatory monocytes. tmeehan 2010-10-04T10:52:03Z cell intermediate monocyte A monocyte that has characteristics of both patrolling and inflammatory monocytes. GOC:tfm PMID:20628149 PMID:20870168 A myeloid dendritic cell found in the blood, lymph nodes, tonsil, bone marrow, and spleen that is CD141-positive (BDCA-3), XCR1-positive, and Clec9A-positive. This cell-type can cross-present antigen to CD8-positive T cells and can produce inteferon-beta. tmeehan 2010-10-04T02:38:58Z cell Markers are found in human cells. Normally they represent 3-5% of peripheral blood mDCs (human). These cells express high levels of CD283 (TLR3), are capable of producing IL-12p70 and IFN-beta upon stimulation, and inducing a TH1 response [PMCID:PMC2882828]. They are also Necl2-positive. May be human equivalent of murine CD8alpha-positive DCs. CD141-positive myeloid dendritic cell true A myeloid dendritic cell found in the blood, lymph nodes, tonsil, bone marrow, and spleen that is CD141-positive (BDCA-3), XCR1-positive, and Clec9A-positive. This cell-type can cross-present antigen to CD8-positive T cells and can produce inteferon-beta. GOC:dsd GOC:tfm PMCID:PMC2882828 PMCID:PMC2882837 PMID:17332250 PMID:20628149 A resident monocyte that is Gr-1 high, CD43-negative, CX3CR1-negative, CD115-positive, and B220-negative. tmeehan 2010-10-04T11:26:18Z cell Markers are associated with mice. The Gr epitope is used to describe this cell type is found on both Ly6c and Ly6g. However, its the Ly6c that is considered the specific marker, and thus used in the cross-product. Gr1-high classical monocyte true A resident monocyte that is Gr-1 high, CD43-negative, CX3CR1-negative, CD115-positive, and B220-negative. GOC:tfm PMID:20628149 PMID:8890901 http://www.immgen.org/index_content.html A patrolling monocyte that is CD14-low and CD16-positive. tmeehan 2010-10-04T12:25:42Z non-classical monocyte, human cell Markers are associated with human monocytes. CD14-low, CD16-positive monocyte true A patrolling monocyte that is CD14-low and CD16-positive. GOC:tfm PMID:20870168 A CD14-positive monocyte that is also CD16-positive and CCR2-negative. tmeehan 2010-10-04T12:49:47Z CD16+ monocyte cell This cell type is compatible with the HIPC Lyoplate markers for 'CD16+ monocyte'. Markers are associated with human cells. Note that this cell type encompasses both human intermediate monocytes (CD14+, CD16-low), and human non-classical monocytes (CD14-low, CD16+). CD14-positive, CD16-positive monocyte A CD14-positive monocyte that is also CD16-positive and CCR2-negative. GOC:tfm PMID:20628149 PMID:21937707 PMID:22343568 CD16+ monocyte PMID:22343568 An intermediate monocyte that is Gr1-positive, CD43-positive. tmeehan 2010-10-04T12:49:49Z cell Gr1-positive, CD43-positive monocyte An intermediate monocyte that is Gr1-positive, CD43-positive. GOC:tfm PMID:20628149 A myeloid dendritic cell found in the blood that is CD1c-positive. tmeehan 2010-10-04T02:39:01Z cell Normally represent 10-20% of peripheral blood mDCs (human). They are also CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD284-positive (TLR4), CD285-positive (TLR5), CD286-positive (TLR6), CD288-positive (TLR8), and CD290-positive (TLR10) [PMID:20204387]. Upon TLR stimulation, these cells were potent producers of CXCL8 (IL-8), while producing little TNF-alpha. CD1c-positive myeloid dendritic cell true A myeloid dendritic cell found in the blood that is CD1c-positive. GOC:dsd GOC:tfm PMID:20204387 PMID:20628149 A precursor B cell that is AA4-positive, IgM-negative, CD19-positive, CD43-positive and HSA-positive. tmeehan 2010-10-05T10:11:38Z cell Fraction B/C precursor B cell true A precursor B cell that is AA4-positive, IgM-negative, CD19-positive, CD43-positive and HSA-positive. GOC:tfm http://www.immgen.org/index_content.html A thymocyte that has a T cell receptor consisting of a gamma chain that has as part a Vgamma3 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus with highest numbers occurring at E17-E18. tmeehan 2010-10-07T02:05:46Z mature DEC precursor mature DETC precursor cell NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. mature dendritic epithelial T cell precursor A thymocyte that has a T cell receptor consisting of a gamma chain that has as part a Vgamma3 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus with highest numbers occurring at E17-E18. GOC:tfm http://www.immgen.org/index_content.html A resting mature B cell within the Peyer's patch that is CD19-positive, B220-positive, IgM-positive, AA4-negative, CD23-positive, CD43-negative, and CD5-negative. tmeehan 2010-10-05T11:18:03Z Peyers patch B cell cell Peyer's patch B cell A resting mature B cell within the Peyer's patch that is CD19-positive, B220-positive, IgM-positive, AA4-negative, CD23-positive, CD43-negative, and CD5-negative. GOC:tfm http://www.immgen.org/index_content.html A thymocyte that has a T cell receptor consisting of a gamma chain containing Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus. tmeehan 2010-10-07T02:24:36Z fetal Vgamma2-positive cell NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. mature Vgamma2-positive fetal thymocyte A thymocyte that has a T cell receptor consisting of a gamma chain containing Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus. GOC:tfm http://www.immgen.org/index_content.html A thymocyte found in the fetal thymus. tmeehan 2010-10-07T02:28:25Z cell fetal thymocyte A thymocyte found in the fetal thymus. GOC:tfm A post-natal thymocyte expressing components of the gamma-delta T cell receptor. This cell type is always double-negative (i.e. CD4-negative, CD8-negative). tmeehan 2010-10-07T02:33:39Z gammadelta thymocyte gd thymocyte cell gamma-delta thymocyte A post-natal thymocyte expressing components of the gamma-delta T cell receptor. This cell type is always double-negative (i.e. CD4-negative, CD8-negative). GOC:tfm PMID:20725107 A double negative post-natal thymocyte that has a T cell receptor consisting of a gamma chain containing a Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive. tmeehan 2010-10-07T02:53:44Z Vgamma2-positive thymocyte cell NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. immature Vgamma2-positive thymocyte A double negative post-natal thymocyte that has a T cell receptor consisting of a gamma chain containing a Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive. GOC:tfm http://www.immgen.org A thymocyte that has a T cell receptor consisting of a gamma chain containing Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative. tmeehan 2010-10-07T02:53:48Z Vgamma2-positive cell NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. mature Vgamma2-positive thymocyte A thymocyte that has a T cell receptor consisting of a gamma chain containing Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative. GOC:tfm http://www.immgen.org/index_content.html A double negative post-natal thymocyte that has a T cell receptor consisting of a gamma chain that does not contain a Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive. tmeehan 2010-10-07T02:59:05Z Vgamma2-negative thymocyte cell NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. immature Vgamma2-negative thymocyte A double negative post-natal thymocyte that has a T cell receptor consisting of a gamma chain that does not contain a Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive. GOC:tfm http://www.immgen.org A thymocyte that has a T cell receptor consisting of a gamma chain that does not contain the Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative. tmeehan 2010-10-07T02:59:08Z Vgamma2-negative cell NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. mature Vgamma2-negative thymocyte A thymocyte that has a T cell receptor consisting of a gamma chain that does not contain the Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative. GOC:tfm http://www.immgen.org/index_content.html A cell that is found in the periacinar space of the exocrine pancreas and in perivascular and periductal regions of the pancreas, and has long cytoplasmic processes that encircle the base of the acinus. Expresses several intermediate filament proteins including vimentin and nestin. Shares many of the characteristics of hepatatic stellate cells, but not stellate cells of the central nervous system. Upon activation, this cell type undergoes morphological and gene expression changes that make the cell suggestive of being a type of myofibroblast. tmeehan 2010-11-10T09:40:33Z PaSC pancreas stellate cell cell pancreatic stellate cell A cell that is found in the periacinar space of the exocrine pancreas and in perivascular and periductal regions of the pancreas, and has long cytoplasmic processes that encircle the base of the acinus. Expresses several intermediate filament proteins including vimentin and nestin. Shares many of the characteristics of hepatatic stellate cells, but not stellate cells of the central nervous system. Upon activation, this cell type undergoes morphological and gene expression changes that make the cell suggestive of being a type of myofibroblast. GOC:mah GOC:tfm PMID:17200706 A gamma-delta receptor that expresses Vgamma1.1 but does not express Vdelta6.3 chains in the T-cell receptor. tmeehan 2010-10-07T03:07:44Z Vg1.1-positive, Vd6.3-negative T cell cell Vgamma1.1-positive, Vdelta6.3-negative thymocyte A gamma-delta receptor that expresses Vgamma1.1 but does not express Vdelta6.3 chains in the T-cell receptor. GOC:tfm http://www.immgen.org/index_content.html A gamma-delta receptor that expresses Vgamma1.1-Vdelta6.3 chains in the T-cell receptor. tmeehan 2010-10-07T03:03:00Z Vg1.1+Vd6.3+ T cell cell Vgamma1.1-positive, Vdelta6.3-positive thymocyte A gamma-delta receptor that expresses Vgamma1.1-Vdelta6.3 chains in the T-cell receptor. GOC:tfm http://www.immgen.org/index_content.html A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-negative. tmeehan 2010-10-07T03:10:32Z cell mature Vg1.1-positive, Vd6.3-negative T cell mature Vgamma1.1-positive, Vdelta6.3-negative thymocyte A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-negative. GOC:tfm http://www.immgen.org A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-positive. tmeehan 2010-10-07T03:10:35Z cell immature Vg1.1-positive, Vd6.3-negative T cell immature Vgamma1.1-positive, Vdelta6.3-negative thymocyte A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-positive. GOC:tfm http://www.immgen.org/index_content.html A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-positive. tmeehan 2010-10-07T03:10:39Z immature Vg1.1+Vd6.3+ T cell cell immature Vgamma1.1-positive, Vdelta6.3-positive thymocyte A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-positive. GOC:tfm http://www.immgen.org/index_content.html A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-negative. tmeehan 2010-10-07T03:10:41Z mature Vg1.1+Vd6.3+ T cell cell mature Vgamma1.1-positive, Vdelta6.3-positive thymocyte A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-negative. GOC:tfm http://www.immgen.org/index_content.html An immature or mature cell of the first erythroid lineage to arise during embryonic development. tmeehan 2010-10-12T11:22:41Z cell primitive erythroid lineage cell An immature or mature cell of the first erythroid lineage to arise during embryonic development. GOC:tfm A pluripotent cell in the yolk sac that can give rise to mesenchymal cells including erythrocytes and endothelial cells. tmeehan 2010-10-12T12:21:16Z cell hemangioblast A pluripotent cell in the yolk sac that can give rise to mesenchymal cells including erythrocytes and endothelial cells. GOC:tfm ISBN:0813817986 PMID:11495698 A T cell that expresses a T cell receptor complex and has completed T cell selection. tmeehan 2010-10-12T01:56:15Z CD3e-positive T cell mature T-cell cell CD3epsilon T cell mature T cell true A T cell that expresses a T cell receptor complex and has completed T cell selection. GOC:tfm A T cell that has not completed T cell selection. tmeehan 2010-10-12T01:56:17Z BTO:0001372 CALOHA:TS-1042 immature T-cell cell immature T cell true A T cell that has not completed T cell selection. GOC:tfm A reticulocyte that retains the nucleus and other organelles. Found in birds, fish, amphibians and reptiles. tmeehan 2010-10-15T09:24:05Z cell nucleated reticulocyte true A reticulocyte that retains the nucleus and other organelles. Found in birds, fish, amphibians and reptiles. GOC:tfm PMID:18182572 PMID:9011180 PMID:9046052 A reticulocyte lacking a nucleus and showing a basophilic reticulum under vital staining due to the presence of ribosomes. tmeehan 2010-10-15T09:24:08Z CALOHA:TS-0864 FMA:66785 cell enucleated reticulocyte true A reticulocyte lacking a nucleus and showing a basophilic reticulum under vital staining due to the presence of ribosomes. GOC:tfm ISBN:0-12203-052-4 ISBN:0721601464 A DN2 thymocyte that is Kit-hi. tmeehan 2010-10-21T10:12:05Z cell Observed in mice. DN2a thymocyte true A DN2 thymocyte that is Kit-hi. GOC:tfm PMID:20595614 A DN2 thymocyte that is Kit-low. tmeehan 2010-10-21T10:12:08Z cell Observed in mice. DN2b thymocyte true A DN2 thymocyte that is Kit-low. GOC:tfm PMID:20595614 A pro-T cell that is lin-negative, CD25-negative, CD127-negative, CD44-positive and kit-positive. tmeehan 2010-10-21T01:16:24Z ETP preT.ETP.Th cell ETPs are reportedly CD1a-negative, CD4-negative, CD7-positive, CD8a-negative, CD8b-negative, CD33-low, CD34-high, CD38-low, CD45RA-positive, and CD45RO-negative. early T lineage precursor true A pro-T cell that is lin-negative, CD25-negative, CD127-negative, CD44-positive and kit-positive. GOC:dsd GOC:tfm PMID:16551251 http://www.immgen.org/index_content.html A mature natural killer cell that is CD11b-positive and CD27-positive. tmeehan 2010-10-25T03:07:59Z cell A natural killer cell that is NK1.1-positive, CD11b-positive, and CD27-positive. CD11b-positive, CD27-positive natural killer cell, mouse A mature natural killer cell that is CD11b-positive and CD27-positive. GOC:tfm http://www.immgen.org/index_content.html A double-positive, alpha-beta thymocyte that is small and not proliferating. tmeehan 2010-10-21T01:59:06Z T.DP.sm.Th cell resting double-positive thymocyte true A double-positive, alpha-beta thymocyte that is small and not proliferating. GOC:tfm http://www.immgen.org/index_content.html A double-positive thymocyte that is large (i.e. has a high forward scatter signal in flow cytometry) and is actively proliferating. tmeehan 2010-10-21T01:59:11Z T.DPb.Th activated double-positive thymocyte cell double-positive blast true A double-positive thymocyte that is large (i.e. has a high forward scatter signal in flow cytometry) and is actively proliferating. GOC:tfm http://www.immgen.org/index_content.html A double-positive thymocyte that is CD69-positive and has begun positive selection. tmeehan 2010-10-21T02:11:52Z T.DP69+.Th cell CD69-positive double-positive thymocyte true A double-positive thymocyte that is CD69-positive and has begun positive selection. GOC:tfm http://www.immgen.org/index_content.html A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD4 co-receptor. tmeehan 2010-10-21T02:29:19Z T.4int8+.Th cell CD4-intermediate, CD8-positive double-positive thymocyte true A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD4 co-receptor. GOC:tfm http://www.immgen.org/index_content.html A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD8 co-receptor. tmeehan 2010-10-21T02:29:23Z T.4int8+.th cell CD4-positive, CD8-intermediate double-positive thymocyte true A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD8 co-receptor. GOC:tfm http://www.immgen.org/index_content.html A CD4-positive, CD8-negative thymocyte that is CD24-positive and expresses high levels of the alpha-beta T cell receptor. tmeehan 2010-10-21T02:43:52Z CD24-positive, CD4 single-positive semimature thymocyte T.4SP24int.Th cell Described in the immgene database as being CD24-intermediate. CD24-positive, CD4 single-positive thymocyte true A CD4-positive, CD8-negative thymocyte that is CD24-positive and expresses high levels of the alpha-beta T cell receptor. GOC:tfm http://www.immgen.org/index_content.html A CD4-positive, CD8-negative thymocyte that expresses high levels of the alpha-beta T cell receptor and is CD69-positive. tmeehan 2010-10-21T02:46:02Z T.4SP69+.Th intermediate CD4-single-positive cell CD69-positive, CD4-positive single-positive thymocyte true A CD4-positive, CD8-negative thymocyte that expresses high levels of the alpha-beta T cell receptor and is CD69-positive. GOC:tfm http://www.immgen.org/index_content.html A CD8-positive, CD4-negative thymocyte that is CD24-positive and expresses high levels of the alpha-beta T cell receptor. tmeehan 2010-10-21T02:59:10Z CD24-positive, CD8 single-positive semimature thymocyte T.8SP24int.Th cell Described in the immgene database as being CD24-intermediate. CD24-positive, CD8 single-positive thymocyte true A CD8-positive, CD4-negative thymocyte that is CD24-positive and expresses high levels of the alpha-beta T cell receptor. GOC:tfm http://www.immgen.org/index_content.html A CD8-positive, CD4-negative thymocyte that expresses high levels of the alpha-beta T cell receptor and is CD69-positive. tmeehan 2010-10-21T02:59:14Z T.8SP69+.Th intermediate CD8-single-positive cell CD69-positive, CD8-positive single-positive thymocyte true A CD8-positive, CD4-negative thymocyte that expresses high levels of the alpha-beta T cell receptor and is CD69-positive. GOC:tfm http://www.immgen.org/index_content.html https://orcid.org/0000-0001-5208-3432 A mature CD4-positive, CD8-negative alpha-beta T cell found in the thymus that is CD24-low and has high expression of the T cell receptor. tmeehan 2010-10-21T03:31:19Z cell T.4SP24-.Th mature CD4 single-positive thymocyte true A mature CD4-positive, CD8-negative alpha-beta T cell found in the thymus that is CD24-low and has high expression of the T cell receptor. GOC:tfm http://www.immgen.org/index_content.html A mature CD8-positive, CD4-negative alpha-beta T cell found in the thymus that is CD24-low and has high expression of the T cell receptor. tmeehan 2010-10-21T03:51:50Z T.8SP24-.Th cell mature CD8 single-positive thymocyte true A mature CD8-positive, CD4-negative alpha-beta T cell found in the thymus that is CD24-low and has high expression of the T cell receptor. GOC:tfm http:www.immgen.org/index_content.html A mature NK cell that is NK1.1-positive. tmeehan 2010-10-25T03:18:04Z NK.sp NK1.1-positive NK cell cell Note: Nk1.1 expression is restricted to C57BL strains of laboratory mice. NK1.1-positive natural killer cell, mouse A mature NK cell that is NK1.1-positive. GOC:tfm A NK1.1-positive T cell that is NKGA2-positive. tmeehan 2010-10-25T03:31:09Z NK.G2A+.SP cell NKGA2-positive natural killer cell, mouse A NK1.1-positive T cell that is NKGA2-positive. GOC:tfm http://www.immgen.org/index_content.html A NK1.1-positive T cell that is Ly49D-positive. tmeehan 2010-10-25T03:36:19Z NK.49D+.Sp cell Ly49D-positive natural killer cell, mouse A NK1.1-positive T cell that is Ly49D-positive. GOC:tfm http://www.immgen.org/index_content.html A NK1.1-positive T cell that is CD94-positive. tmeehan 2010-10-25T03:36:28Z NK.94+.Sp cell CD94-positive natural killer cell, mouse A NK1.1-positive T cell that is CD94-positive. GOC:tfm http://www.immgen.org/index_content.html A NK1.1-positive T cell that is CD94-negative and Ly49Cl-negative. tmeehan 2010-10-25T03:56:21Z CD94- Ly49I-negative NK cell NK.49Cl-94-.Sp cell CD94-negative, Ly49CI-negative natural killer cell, mouse A NK1.1-positive T cell that is CD94-negative and Ly49Cl-negative. GOC:tfm http://www.immgen.org/index_content.html A NK1.1-positive T cell that is Ly49Cl-positive. tmeehan 2010-10-25T03:36:38Z Ly49I-positive NK cell NK.49Cl+.Sp cell Ly49CI-positive natural killer cell, mouse A NK1.1-positive T cell that is Ly49Cl-positive. GOC:tfm http://www.immgen.org/index_content.html A NK1.1-positive T cell that is Ly49H-positive. tmeehan 2010-10-25T03:36:43Z LyH49H-positive cell Ly49H-positive natural killer cell, mouse A NK1.1-positive T cell that is Ly49H-positive. GOC:tfm http://www.immgen.org/index_content.html A NK1.1-positive T cell that is Ly49D-negative. tmeehan 2010-10-25T03:39:02Z NK.49D-.Sp cell Ly49D-negative natural killer cell, mouse A NK1.1-positive T cell that is Ly49D-negative. GOC:tfm http://www.immgen.org/index_content.html A NK1.1-positive T cell that is Ly49Cl-negative. tmeehan 2010-10-25T03:52:04Z Ly49I-negative NK cell NK.49Cl-.Sp cell Ly49CI-negative natural killer cell, mouse A NK1.1-positive T cell that is Ly49Cl-negative. GOC:tfm http://www.immgen.org/index_content.html A NK1.1-positive T cell that is CD94-negative. tmeehan 2010-10-25T03:54:18Z NK.94-.Sp cell CD94-negative natural killer cell, mouse A NK1.1-positive T cell that is CD94-negative. GOC:tfm http://www.immgen.org/index_content.html A NK1.1-positive T cell that is Ly49H-negative. tmeehan 2010-10-25T03:42:42Z LyH49H-negative cell Ly49H-negative natural killer cell, mouse A NK1.1-positive T cell that is Ly49H-negative. GOC:tfm http://www.immgen.org/index_content.html A NK1.1-positive T cell that is CD94-positive and Ly49Cl-positive. tmeehan 2010-10-25T03:56:27Z NK.49Cl+94+.Sp cell CD94-positive Ly49CI-positive natural killer cell, mouse A NK1.1-positive T cell that is CD94-positive and Ly49Cl-positive. GOC:tfm http://www.immgen.org/index_content.html A specialized hair cell that has an elongated kinocilium upon which an otolith accretes. The tether cell then anchors the otolith in place. tmeehan 2010-11-10T01:41:00Z cell tether cell A specialized hair cell that has an elongated kinocilium upon which an otolith accretes. The tether cell then anchors the otolith in place. GOC:cvs GOC:tfm PMID:9398434 A multi-fate stem cell that is the source of cells for growth of the mammary gland during puberty and gestation. This cell type gives rise to both the luminal and myoepithelial cell types of the gland, and have been shown to have the ability to regenerate the entire organ in mice. This cell type also plays an important role in carcinogenesis of the breast. This cell type is Lin-, CD24-positive, CD29-hi. tmeehan 2010-11-10T01:46:51Z cell mammary stem cell A multi-fate stem cell that is the source of cells for growth of the mammary gland during puberty and gestation. This cell type gives rise to both the luminal and myoepithelial cell types of the gland, and have been shown to have the ability to regenerate the entire organ in mice. This cell type also plays an important role in carcinogenesis of the breast. This cell type is Lin-, CD24-positive, CD29-hi. GOC:hjd GOC:tfm PMID:15987436 PMID:16397499 PMID:17851544 The cell type from which oligodendrocytes develop. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons. tmeehan 2010-11-10T02:51:34Z cell oligodendrocyte precursor cell true The cell type from which oligodendrocytes develop. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons. GOC:tfm PMID:20142420 Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-negative, CD8_alpha-negative and is CD205-positive. tmeehan 2010-11-22T01:10:28Z DC.8-4-11b+ spleen double-negative dendritic cell cell Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell true Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-negative, CD8_alpha-negative and is CD205-positive. GOC:tfm http://www.immgen.org/index_content.html A CD11c-low plasmacytoid dendritic cell that is CD8alpha-negative and CD4-positive. tmeehan 2010-11-22T01:27:37Z DC.pDC.8- cell CD8_alpha-negative plasmactyoid dendritic cell true A CD11c-low plasmacytoid dendritic cell that is CD8alpha-negative and CD4-positive. GOC:tfm http://www.immgen.org/index_content.html A CD11c-low plasmacytoid dendritic cell that is CD8alpha-positive and CD4-positive. tmeehan 2010-11-22T01:23:07Z DC.pDC.8+ cell CD8_alpha-positive plasmactyoid dendritic cell true A CD11c-low plasmacytoid dendritic cell that is CD8alpha-positive and CD4-positive. GOC:tfm http://www.immgen.org/index_content.html A Langerhans cell that is in the epidermis and is CD45-positive, MHCII-positive, and CD11b-positive. tmeehan 2010-11-22T03:57:57Z cell epidermal Langerhans cell true A Langerhans cell that is in the epidermis and is CD45-positive, MHCII-positive, and CD11b-positive. GOC:tfm http://www.immgen.org/index_content.html A dermal dendritic cell that is langerin-positive and CD103-positive. tmeehan 2010-11-22T04:06:22Z cell langerin-positive dermal dendritic cell true A dermal dendritic cell that is langerin-positive and CD103-positive. GOC:tfm http://www.immgen.org/index_content.html A dermal dendritic cell that is langerin-negative, CD103-negative, and CD11b-positive. tmeehan 2010-11-22T04:09:44Z cell langerin-negative dermal dendritic cell true A dermal dendritic cell that is langerin-negative, CD103-negative, and CD11b-positive. GOC:tfm http://www.immgen.org/index_content.html A conventional thymic dendritic cell that is CD8alpha-negative. tmeehan 2010-11-23T10:58:53Z DC.8-.Th cell CD8alpha-negative thymic conventional dendritic cell true A conventional thymic dendritic cell that is CD8alpha-negative. GOC:tfm PMID:19273629 http://www.immgen.org/index_content.html A conventional dendritic cell that is CD103-positive. This cell type is usually found in non-lymphoid tissue. tmeehan 2010-11-23T01:32:43Z cell CD103-positive dendritic cell true A conventional dendritic cell that is CD103-positive. This cell type is usually found in non-lymphoid tissue. GOC:tfm http://www.immgen.org/index_content.html A F4/80-negative dendritic cell located in adipose tissue. tmeehan 2010-11-23T01:38:21Z cell adipose dendritic cell true A F4/80-negative dendritic cell located in adipose tissue. GOC:tfm http://www.immgen.org/index_content.html An adipose dendritic cell that is SIRPa-positive. tmeehan 2010-11-23T01:40:44Z DC.SIRPa+.Ad cell SIRPa-positive adipose dendritic cell An adipose dendritic cell that is SIRPa-positive. GOC:tfm http://www.immgen.org/index_content.html An adipose dendritic cell that is SIRPa-negative. tmeehan 2010-11-23T01:40:46Z DC.SIRPa-.Ad cell SIRPa-negative adipose dendritic cell An adipose dendritic cell that is SIRPa-negative. GOC:tfm http://www.immgen.org/index_content.html A conventional dendritic cell that expresses CD11b (ITGAM). tmeehan 2010-11-23T01:50:05Z cell CD11b-positive dendritic cell true A conventional dendritic cell that expresses CD11b (ITGAM). GOC:tfm http://www.immgen.org/index_content.html A CD11b-positive dendritic cell located in the serosal portion of the small intestine epithelium. This cell type is CD45-positive, MHC-II-positive, CD11c-low, CD103-negative. tmeehan 2010-11-23T02:00:21Z DC.11cloSer.SI cell small intestine serosal dendritic cell true A CD11b-positive dendritic cell located in the serosal portion of the small intestine epithelium. This cell type is CD45-positive, MHC-II-positive, CD11c-low, CD103-negative. GOC:tfm http://www.immgen.org/index_content.html A myeloid suppressor cell that is Gr1-high and CD11c-negative. tmeehan 2010-11-23T02:15:12Z MDS.Gr1hi cell Gr1-high myeloid suppressor cell true A myeloid suppressor cell that is Gr1-high and CD11c-negative. GOC:tfm http://www.immgen.org/index_content.html A myeloid suppressor cell that is Gr1-low and CD11c-positive. tmeehan 2010-11-23T02:19:43Z MDS.Gr1lo cell Gr1-low myeloid suppressor cell true A myeloid suppressor cell that is Gr1-low and CD11c-positive. GOC:tfm http://www.immgen.org/index_content.html Gr1-high monocyte that lacks MHC-II receptor complex. tmeehan 2010-11-23T03:27:12Z Mo.6C+II- cell MHC-II-negative classical monocyte true Gr1-high monocyte that lacks MHC-II receptor complex. GOC:tfm http://www.immgen.org/index_content.html Gr1-high monocyte that has a MHC-II receptor complex. tmeehan 2010-11-23T03:30:21Z Mo.6c+II cell MHC-II-positive classical monocyte true Gr1-high monocyte that has a MHC-II receptor complex. GOC:tfm http://www.immgen.org/index_content.html Gr1-low non-classical monocyte that lacks expression of a MHC-II complex. tmeehan 2010-11-23T03:38:15Z Mo.6C-II- cell MHC-II-negative non-classical monocyte true Gr1-low non-classical monocyte that lacks expression of a MHC-II complex. GOC:tfm http://www.immgen.org/index_content.html Gr1-low non-classical monocyte that has low to intermediate expression of the MHC-II complex. tmeehan 2010-11-23T03:47:53Z Mo.6C-IIint cell MHC-II-low non-classical monocyte true Gr1-low non-classical monocyte that has low to intermediate expression of the MHC-II complex. GOC:tfm http://www.immgen.org/index_content.html Gr1-low non-classical monocyte that has high surface expression of a MHC-II complex. tmeehan 2010-11-23T03:47:55Z Mo.6C-II+ cell MHC-II-high non-classical monocyte true Gr1-low non-classical monocyte that has high surface expression of a MHC-II complex. GOC:tfm http://www.immgen.org/index_content.html A MHC-II-negative classical monocyte located in lymphoid tissue that is F4/80-positive, CD11c-negative, and CD11b-high. tmeehan 2010-11-23T04:00:52Z cell lymphoid MHC-II-negative classical monocyte true A MHC-II-negative classical monocyte located in lymphoid tissue that is F4/80-positive, CD11c-negative, and CD11b-high. GOC:tfm http://www.immgen.org/index_content.html A MHC-II-negative classical monocyte located in lymphoid tissue that is F4/80-positive, CD11c-intermediate, and CD11b-high. tmeehan 2010-11-23T04:09:09Z cell lymphoid MHC-II-negative non-classical monocyte A MHC-II-negative classical monocyte located in lymphoid tissue that is F4/80-positive, CD11c-intermediate, and CD11b-high. GOC:tfm http://www.immgen.org/index_content.html A tissue-resident macrophage located in the bone marrow. This cell type is B220-negative, CD3e-negative, Ly-6C-negative, CD115-positive, F4/80-positive. tmeehan 2010-11-23T04:19:25Z BTO:0004732 cell MF.BM bone marrow macrophage true A tissue-resident macrophage located in the bone marrow. This cell type is B220-negative, CD3e-negative, Ly-6C-negative, CD115-positive, F4/80-positive. GOC:tfm http://www.immgen.org/index_content.html A macrophage located in adipose tissue that is CD45-positive, CD11c-positive, and SIRPa-positive. tmeehan 2010-11-23T04:31:28Z cell adipose macrophage true A macrophage located in adipose tissue that is CD45-positive, CD11c-positive, and SIRPa-positive. GOC:tfm An adipose macrophage that does not express F4/80but is MHC-II-positive. This cell type exhibits autofluorescence under typical flow cyometry conditions. tmeehan 2010-11-23T04:40:50Z MF.Autofl.Ad cell F4/80-negative adipose macrophage true An adipose macrophage that does not express F4/80but is MHC-II-positive. This cell type exhibits autofluorescence under typical flow cyometry conditions. GOC:tfm http://www.immgen.org/index_content.html An adipose macrophage that does not express MHC-II but is F4/80-positive. tmeehan 2010-11-23T04:35:53Z MF.F480+.Ad cell F4/80-positive adipose macrophage true An adipose macrophage that does not express MHC-II but is F4/80-positive. GOC:tfm http://www.immgen.org/index_content.html A goblet cell located in the nasal epithelium. tmeehan 2010-12-03T03:03:02Z MP:0002262 cell nasal mucosa goblet cell A goblet cell located in the nasal epithelium. GOC:cjm GOC:tfm The flattened smooth myoepithelial cells of mesodermal origin that lie just outside the basal lamina of the seminiferous tubule. tmeehan 2010-12-03T03:11:48Z cell peritubular myoid cell true The flattened smooth myoepithelial cells of mesodermal origin that lie just outside the basal lamina of the seminiferous tubule. GOC:cjm GOC:tfm MP:0006420 A melanocyte that produces pigment in the dermis. tmeehan 2010-12-03T03:17:05Z cell dermal melanocyte A melanocyte that produces pigment in the dermis. GOC:cjm GOC:tfm MP:0009386 A melanocyte that produces pigment within the hair follicle. tmeehan 2010-12-03T03:17:09Z cell hair follicle melanocyte A melanocyte that produces pigment within the hair follicle. GOC:tfm MP:0004381 A melanocyte that produces pigment in the epithelium. tmeehan 2010-12-03T03:17:14Z cell The text defintion reference to the MP term appears to reference an epidermal melanocyte term. This term represents any melanocyte in any epithelium. epithelial melanocyte true A melanocyte that produces pigment in the epithelium. GOC:tfm MP:0009388 A melanocyte of the retina. This cell type is distinct from pigmented retinal epithelium. tmeehan 2010-12-03T03:25:32Z cell retinal melanocyte true A melanocyte of the retina. This cell type is distinct from pigmented retinal epithelium. GOC:tfm MP:0010190 A melanocyte located between the epithelial marginal cell layer and the mesodermal basal cell layer within the intrastrial space; the predominant cellular component of the electrogenic machinery that generates an endocochlear potential (80-100 mV) . tmeehan 2010-12-03T03:29:15Z cell strial intermediate cell A melanocyte located between the epithelial marginal cell layer and the mesodermal basal cell layer within the intrastrial space; the predominant cellular component of the electrogenic machinery that generates an endocochlear potential (80-100 mV) . GOC:tfm MP:0000048 A neuronal receptor that respond to mechanical pressure or distortion in the skin. tmeehan 2010-12-06T02:53:30Z cell cutaneous/subcutaneous mechanoreceptor cell A neuronal receptor that respond to mechanical pressure or distortion in the skin. GOC:tfm MP:0000973 A trophoblast cell that has a large volume of cytoplasm, is polyploid and is usually mononuclear but is also occasionally multi-nucleate. This cell type is important in establishing maternal physiology and remodeling of the vasculature of the placenta. tmeehan 2010-12-06T02:55:24Z giant trophoblast cell cell trophoblast giant cell true A trophoblast cell that has a large volume of cytoplasm, is polyploid and is usually mononuclear but is also occasionally multi-nucleate. This cell type is important in establishing maternal physiology and remodeling of the vasculature of the placenta. GOC:tfm MP:0001714 MP:19876834 A thymocyte that lacks expression of CD4 and CD8. tmeehan 2010-12-06T03:03:38Z CD4-CD8- T cell double negative T cell cell These are precursors to mature T cells; normally, they do not circulate, but are found in the thymus and they have not undergone rearrangement of the alpha and beta T cell receptor genes. double negative thymocyte true A thymocyte that lacks expression of CD4 and CD8. GOC:tfm MP:0002407 CD4-CD8- T cell MP:0002407 A supporting cell of the organ of Corti. tmeehan 2010-12-06T03:09:01Z cell organ of Corti supporting cell A supporting cell of the organ of Corti. GOC:tfm MP:0004300 A specialized cell involved in auditory sensory perception. tmeehan 2010-12-06T03:18:43Z cell auditory epithelial cell A specialized cell involved in auditory sensory perception. GOC:tfm A polarized columnar cell that covesr the lateral surface of the cochlear duct, secretes potassium ions and forms a continuous sheet in contact with the endolymph; marginal cells form extensive interdigitations with the basal and intermediate cells in the normal adult stria. tmeehan 2010-12-06T03:20:41Z cell strial marginal cell A polarized columnar cell that covesr the lateral surface of the cochlear duct, secretes potassium ions and forms a continuous sheet in contact with the endolymph; marginal cells form extensive interdigitations with the basal and intermediate cells in the normal adult stria. GOC:tfm MP:0004366 A polarized cell that is juxtaposed to fibrocytes in the underlying spiral ligament. This cell type secretes potassium ions derived from fibrocytes through gap junctions. tmeehan 2010-12-06T03:26:53Z cell Basal cells form a multi-layered epithelial barrier that separates the extracellular spaces of the stria vascularis and the spiral ligament[PMID:18353863] strial basal cell A polarized cell that is juxtaposed to fibrocytes in the underlying spiral ligament. This cell type secretes potassium ions derived from fibrocytes through gap junctions. GOC:tfm MP:0004365 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 fetal and neonatal heart cell that undergoes proliferation and is not yet terminally differentiated into a binucleate or a multinucleate cardiac myocyte. tmeehan 2010-12-07T09:50:41Z embryonic cardiomyocyte neonatal cardiomyocyte cell fetal cardiomyocyte A fetal and neonatal heart cell that undergoes proliferation and is not yet terminally differentiated into a binucleate or a multinucleate cardiac myocyte. GOC:tfm MP:0008788 A T cell that is located in the intestinal epithelium and is capable of a mucosal immune response. tmeehan 2010-12-07T09:54:50Z IEL intraepithelial T cell intraepithelial T-cell cell intraepithelial lymphocyte true A T cell that is located in the intestinal epithelium and is capable of a mucosal immune response. GOC:tfm MP:0008894 A trophoblast giant cell derived from the mural trophectoderm. tmeehan 2010-12-07T10:07:47Z EMAPA:16066 cell primary trophoblast giant cell A trophoblast giant cell derived from the mural trophectoderm. GOC:tfm PMCID:PMC85124 A trophoblast giant cell that is derived from ectoplacental cone and, later in gestation, the spongiotrophoblast. tmeehan 2010-12-07T10:07:52Z cell secondary trophoblast giant cell A trophoblast giant cell that is derived from ectoplacental cone and, later in gestation, the spongiotrophoblast. GOC:tfm PMCID:PMC85124 A trophoblast cell that arises in the junctional zone (basal plate) of the placenta. tmeehan 2010-12-07T12:56:56Z cell spongiotrophoblast cell A trophoblast cell that arises in the junctional zone (basal plate) of the placenta. GOC:tfm MP:0008959 A P/D1 enteroendocrine cell that is Grimelius positive and stores bombesin-like polypeptide. tmeehan 2010-12-07T03:42:06Z cell P enteroendocrine cell A P/D1 enteroendocrine cell that is Grimelius positive and stores bombesin-like polypeptide. FMA:63418 GOC:tfm A P/D1 enteroendocrine cell that is argyrophilic and stores vasoactive intestinal polypeptide. tmeehan 2010-12-07T03:42:09Z FMA:63207 cell type D1 enteroendocrine cell A P/D1 enteroendocrine cell that is argyrophilic and stores vasoactive intestinal polypeptide. FMA:63207 GOC:tfm An enteroendocrine cell of the small intestine that secretes motilin. tmeehan 2010-12-07T03:55:49Z Mo enteroendocrine cell FMA:63420 cell type M enteroendocrine cell An enteroendocrine cell of the small intestine that secretes motilin. GOC:tfm PMID:15153415 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 A smooth muscle cell of the intestine. tmeehan 2011-01-17T03:39:38Z intestinal smooth muscle cell cell enteric smooth muscle cell true A smooth muscle cell of the intestine. GOC:tfm A CD11b-positive dendritic cell that is CD11b-high, CD45-positive, MHC-II-positive and CD103-negative. tmeehan 2011-01-21T01:27:41Z DC.103-11b+.Lv cell liver CD103-negative dendritic cell true A CD11b-positive dendritic cell that is CD11b-high, CD45-positive, MHC-II-positive and CD103-negative. GOC:tfm http:http://www.immgen.org/index_content.html A CD11b-positive dendritic cell that is CD11b-low, CD45-positive, MHC-II-high and CD103-positive that is located in the liver. tmeehan 2011-01-21T01:27:45Z DC.103+11b-.Lv cell liver CD103-positive dendritic cell true A CD11b-positive dendritic cell that is CD11b-low, CD45-positive, MHC-II-high and CD103-positive that is located in the liver. GOC:tfm http:http://www.immgen.org/index_content.html A dermal dendritic cell isolated from skin draining lymph nodes that is langerin-positive, MHC-II-positive, and CD4-negative and CD8a-negative. tmeehan 2011-01-21T01:57:00Z cell langerin-positive lymph node dendritic cell true A dermal dendritic cell isolated from skin draining lymph nodes that is langerin-positive, MHC-II-positive, and CD4-negative and CD8a-negative. GOC:tfm http://www.immgen.org/index_content.html A dermal dendritic cell isolated from skin draining lymph nodes that is langerin-negative, MHC-II-positive, and CD4-negative and CD8a-negative. tmeehan 2011-01-21T02:13:58Z cell langerin-negative, CD103-negative lymph node dendritic cell true A dermal dendritic cell isolated from skin draining lymph nodes that is langerin-negative, MHC-II-positive, and CD4-negative and CD8a-negative. GOC:tfm http://www.immgen.org/index_content.html A langerin-positive lymph node dendritic cell that is CD103-positive and CD11b-low. tmeehan 2011-01-21T02:07:54Z cell CD103-positive, langerin-positive lymph node dendritic cell true A langerin-positive lymph node dendritic cell that is CD103-positive and CD11b-low. GOC:tfm http://www.immgen.org/index_content.html A langerin-positive lymph node dendritic cell that is CD103-negative and CD11b-high. tmeehan 2011-01-21T02:11:14Z cell CD103-negative, langerin-positive lymph node dendritic cell true A langerin-positive lymph node dendritic cell that is CD103-negative and CD11b-high. GOC:tfm http://www.immgen.org/index_content.html A langerin-negative lymph node dendritic cell that is CD103-negative and CD11b-low. tmeehan 2011-01-21T02:22:15Z cell CD11b-low, CD103-negative, langerin-negative lymph node dendritic cell true A langerin-negative lymph node dendritic cell that is CD103-negative and CD11b-low. GOC:tfm http://www.immgen.org/index_content.html A langerin-negative lymph node dendritic cell that is CD103-negative and CD11b-high. tmeehan 2011-01-21T02:16:21Z cell CD11b-high, CD103-negative, langerin-negative lymph node dendritic cell true A langerin-negative lymph node dendritic cell that is CD103-negative and CD11b-high. GOC:tfm http://www.immgen.org/index_content.html A CD8alpha alpha positive gamma-delta intraepithelial T cell that expresses a TCR encoded in part by the Vgamma5 gene segment. tmeehan 2011-01-24T10:22:18Z tgd.vg5+.IEL cell Vgamma5-positive CD8alpha alpha positive gamma-delta intraepithelial T cell A CD8alpha alpha positive gamma-delta intraepithelial T cell that expresses a TCR encoded in part by the Vgamma5 gene segment. GOC:tfm http://www.immgen.org/index_content.html A CD8alpha alpha positive gamma-delta intraepithelial T cell that does not express a TCR partially encoded by the Vgamma5 gene segment. tmeehan 2011-01-24T10:25:44Z tgd.vg5-.IEL cell Vgamma5-negative CD8alpha alpha positive gamma-delta intraepithelial T cell A CD8alpha alpha positive gamma-delta intraepithelial T cell that does not express a TCR partially encoded by the Vgamma5 gene segment. GOC:tfm http://www.immgen.org/index_content.html An interrenal chromaffin cell found in teleosts that contain heterogeneous vesicles with electron-dense granules located asymmetrically within the vesicular membrane. tmeehan 2011-02-08T10:11:55Z interrenal noradrenaline type cell type n interrenal cell cell interrenal norepinephrine type cell An interrenal chromaffin cell found in teleosts that contain heterogeneous vesicles with electron-dense granules located asymmetrically within the vesicular membrane. GOC:MH GOC:tfm PMID:12668625 A chromaffin cell interspersed among the interrenal epithelial layer of the anterior kidney of teloest fish. tmeehan 2011-02-08T10:21:35Z cell interrenal chromaffin cell A chromaffin cell interspersed among the interrenal epithelial layer of the anterior kidney of teloest fish. GOC:MH GOC:tfm PMID:12668625 An interrenal chromaffin cell found in teleosts that contain small, homogeneous electron-lucent granules that are separated from the vesicular membrane by a visible halo. tmeehan 2011-02-08T10:27:05Z type a interrenal cell cell interrenal adrenaline secreting cell interrenal epinephrin secreting cell An interrenal chromaffin cell found in teleosts that contain small, homogeneous electron-lucent granules that are separated from the vesicular membrane by a visible halo. GOC:MH GOC:tfm PMID:12668625 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 interrenal epithelial kidney cell is an epithelial cell found in the anterior kidney of teleosts fish. This cell type is arranged in layers around the posterior cardinal vein and contains many mitochondria with tubulovesicular cristae. Interrenal chromaffin cells are interspersed among the tissue layer created by this cell type. tmeehan 2011-02-08T11:03:32Z cell interrenal epithelial cell An interrenal epithelial kidney cell is an epithelial cell found in the anterior kidney of teleosts fish. This cell type is arranged in layers around the posterior cardinal vein and contains many mitochondria with tubulovesicular cristae. Interrenal chromaffin cells are interspersed among the tissue layer created by this cell type. GOC:mh GOC:tfm PMID:12668625 An insect excretory cell that regulates haemolymph composition by filtration and filtrate endocytosis. tmeehan 2011-02-08T01:34:56Z BTO:0004597 FMA:83807 cell nephrocyte An insect excretory cell that regulates haemolymph composition by filtration and filtrate endocytosis. GOC:tfm PMID:19783135 A fat cell that is part of subcutaneous adipose tissue. tmeehan 2011-02-21T02:51:22Z subcutaneous adipocyte cell subcutaneous fat cell true A fat cell that is part of subcutaneous adipose tissue. GOC:tfm A renal filtration cell is a specialized cell of the renal system that filter fluids by charge, size or both. tmeehan 2011-02-08T01:37:59Z cell renal filtration cell A renal filtration cell is a specialized cell of the renal system that filter fluids by charge, size or both. GOC:tfm A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the mesonephros tmeehan 2011-02-08T01:58:30Z cell mesonephric glomerular visceral epithelial cell A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the mesonephros GOC:tfm A disseminated nephrocyte is a nephrocyte that filters hemolymph and is found at scattered locations in the fat body or other tissues. tmeehan 2011-02-08T02:07:33Z cell disseminated nephrocyte A disseminated nephrocyte is a nephrocyte that filters hemolymph and is found at scattered locations in the fat body or other tissues. GOC:tfm PMID:19783135 A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the metanephros. tmeehan 2011-02-08T02:02:13Z cell metanephric glomerular visceral epithelial cell A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the metanephros. GOC:tfm A dermal dendritic cell that is CD1a-negative and CD14-positive. CD14+ dermal DC cell They are also CD11c-positive, CD40-positive, CD85j-positive (ILT-2), CD163-positive, CD205-positive (DEC205), CD207-negative (langerin), CD209-positive (DC-SIGN), CD274-positive (PD-L1), CD324-negative (E-cadherin), Factor XIIIa-positive, LOX-I-positive, CLEC6-positive, Dectin-1-positive, and DCIR-positive. Upon stimulation, these cells are capable of producing IL1-beta, IL6, IL8, IL10, IL12p40, IL19, IL20, IL24, TGF-beta, TNF-alpha, GM-CSF, and MCP1. They reside in the dermis. CD14-positive dermal dendritic cell true A dermal dendritic cell that is CD1a-negative and CD14-positive. GOC:dsd PMID:19236899 PMID:20309010 An immature CD14-positive dermal dendritic cell is CD80-low, CD86-low, and MHCII-low. cell immature CD14-positive dermal dendritic cell true An immature CD14-positive dermal dendritic cell is CD80-low, CD86-low, and MHCII-low. GOC:dsd A mature CD14-positive dermal dendritic cell is CD80-high, CD86-high, MHCII-high and is CD83-positive. cell mature CD14-positive dermal dendritic cell true A mature CD14-positive dermal dendritic cell is CD80-high, CD86-high, MHCII-high and is CD83-positive. GOC:dsd A dermal dendritic cell that is CD1a-positive and CD14-negative. CD1a+ dermal DC cell Reside in the dermis. They are also CD11c-positive, CD40-positive, CD207-negative (langerin), CD209-negative (DC-SIGN), and CD324-negative (E-cadherin). When activated, they are capable of producing CXCL8 (IL-8) and IL-15. Possibly a precursor of Langerhans cells or equivalent of langerin-positive dermal DCs in the mouse. CD1a-positive dermal dendritic cell true A dermal dendritic cell that is CD1a-positive and CD14-negative. GOC:dsd PMID:20309010 An immature CD1a-positive dermal dendritic cell is CD80-low, CD86-low, and MHCII-low. cell immature CD1a-positive dermal dendritic cell true An immature CD1a-positive dermal dendritic cell is CD80-low, CD86-low, and MHCII-low. GOC:dsd A mature CD1a-positive dermal dendritic cell is CD80-high, CD83-positive, CD86-high, and MHCII-high. cell mature CD1a-positive dermal dendritic cell true A mature CD1a-positive dermal dendritic cell is CD80-high, CD83-positive, CD86-high, and MHCII-high. GOC:dsd A myeloid dendritic cell found in the blood that is CD16-positive. CD16+ mDC CD16-mDC cell Normally represent 65-75% of peripheral blood mDCs (human). They are also CD281-positive (TLR1), CD282-positive (TLR2), CD284-positive (TLR4), CD285-positive (TLR5), CD286-positive (TLR6), CD288-positive (TLR8), CD289-positive (TLR9), and CD290-positive (TLR10) by RT-PCR [PMID:17332250]. Upon TLR stimulation, these cells are potent producers of TNF-alpha, while producing little CXCL8 (IL8). CD16-positive myeloid dendritic cell true A myeloid dendritic cell found in the blood that is CD16-positive. GOC:dsd PMID:17332250 An immature CD16-positive myeloid dendritic cell is CD80-low, CD86-low, and MHCII-low. cell immature CD16-positive myeloid dendritic cell true An immature CD16-positive myeloid dendritic cell is CD80-low, CD86-low, and MHCII-low. GOC:dsd A mature CD16-positive myeloid dendritic cell is CD80-high, CD83-positive, CD86-high, and MHCII-high. cell mature CD16-positive myeloid dendritic cell true A mature CD16-positive myeloid dendritic cell is CD80-high, CD83-positive, CD86-high, and MHCII-high. GOC:dsd 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 that is part of the amnion. tmeehan 2011-02-28T12:38:01Z amniotic epithelial cell cell epithelial cell of amnion true true An epithelial cell that is part of the amnion. GOC:tfm A mesenchymal stem cell of the amnion membrane. tmeehan 2011-02-28T12:44:24Z amniotic membrane stem cell cell amnion mesenchymal stem cell A mesenchymal stem cell of the amnion membrane. GOC:tfm PMID:20446274 PMID:21339039 An epithelial cell of the intrahepatic portion of the bile duct. These cells are flattened or cuboidal in shape, and have a small nuclear-to-cytoplasmic ratio relative to large/extrahepatic cholangiocytes. tmeehan 2011-02-28T01:20:20Z small bile duct cholangiocyte cell intrahepatic cholangiocyte true An epithelial cell of the intrahepatic portion of the bile duct. These cells are flattened or cuboidal in shape, and have a small nuclear-to-cytoplasmic ratio relative to large/extrahepatic cholangiocytes. GOC:tfm PMID:23720296 small bile duct cholangiocyte PMID:23720296 A smooth muscle cell of the aorta. tmeehan 2011-02-28T01:42:12Z BTO:0004577 cell aortic smooth muscle cell A smooth muscle cell of the aorta. GOC:tfm A mesenchymal stem cell that is part of the bone marrow. tmeehan 2011-02-28T01:47:47Z cell mesenchymal stem cell of the bone marrow A mesenchymal stem cell that is part of the bone marrow. GOC:tfm A mesenchymal stem cell of the chorionic membrane. tmeehan 2011-02-28T03:04:35Z cell chorionic membrane mesenchymal stem cell A mesenchymal stem cell of the chorionic membrane. 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 arterial endothelial cell that is part of the aorta endothelium. tmeehan 2011-02-28T03:54:42Z BTO:0003245 CALOHA:TS-0047 cell aortic endothelial cell An arterial endothelial cell that is part of the aorta endothelium. GOC:tfm An endothelial cell that is part of the thoracic endothelium. tmeehan 2011-02-28T03:59:09Z cell thoracic aorta endothelial cell true An endothelial cell that is part of the thoracic endothelium. 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 A fibroblast of the aortic adventitia. tmeehan 2011-02-28T04:43:41Z cell fibroblast of the aortic adventitia true A fibroblast of the aortic adventitia. GOC:tfm A fibroblast that is part of the heart. tmeehan 2011-02-28T04:57:44Z cardiac fibroblast cell fibroblast of cardiac tissue true true A fibroblast that is part of the heart. GOC:tfm A fibroblast that is part of the choroid plexus. tmeehan 2011-02-28T05:01:39Z cell fibroblast of choroid plexus true A fibroblast that is part of the choroid plexus. GOC:tfm A fibroblast that is part of the conjuctiva of the eye. tmeehan 2011-02-28T05:03:44Z cell fibroblast of the conjunctiva A fibroblast that is part of the conjuctiva of the eye. GOC:tfm tmeehan 2011-02-28T05:05:33Z cell fibroblast of dermis true tmeehan 2011-02-28T05:09:12Z cell fibroblast of gingiva true A fibroblast that is part of lung. tmeehan 2011-02-28T05:11:03Z BTO:0000764 CALOHA:TS-0575 cell fibroblast of lung true A fibroblast that is part of lung. GOC:tfm A fibroblast of the lymphatic system. tmeehan 2011-02-28T05:16:18Z cell fibroblast of lymphatic vessel true A fibroblast of the lymphatic system. GOC:tfm A fibroblast that is part of the mammary gland. tmeehan 2011-02-28T05:18:38Z cell fibroblast of mammary gland true A fibroblast that is part of the mammary gland. GOC:tfm A fibroblast of the periodontium. tmeehan 2011-02-28T05:19:48Z cell fibroblast of periodontium true A fibroblast of the periodontium. GOC:tfm A fibroblast of pulmonary artery. tmeehan 2011-02-28T05:22:27Z cell fibroblast of pulmonary artery true A fibroblast of pulmonary artery. GOC:tfm A fibroblast that is part of villous mesenchyme. tmeehan 2011-02-28T05:24:28Z cell fibroblast of villous mesenchyme A fibroblast that is part of villous mesenchyme. 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 that resides in the inner root sheath of the hair follicle. tmeehan 2011-03-01T04:27:51Z cell inner root sheath cell true An epithelial cell that resides in the inner root sheath of the hair follicle. GOC:tfm An epithelial cell that is part of the outer root sheath. tmeehan 2011-03-01T04:29:47Z cell outer root sheath cell true An epithelial cell that is part of the outer root sheath. GOC:tfm An epidermal cell that is part of the germinal matrix. tmeehan 2011-03-01T04:31:06Z trichocyte cell hair germinal matrix cell true An epidermal cell that is part of the germinal matrix. 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 A pigment cell located in the epithelium of the iris. tmeehan 2011-03-01T05:28:52Z cell iris pigment epithelial cell true A pigment cell located in the epithelium of the iris. GOC:tfm A melanocyte that appears darker due to content or amount of melanin granules. tmeehan 2011-03-01T05:57:11Z cell dark melanocyte A melanocyte that appears darker due to content or amount of melanin granules. GOC:tfm A melanocyte that appears lighter in color. tmeehan 2011-03-01T05:58:23Z cell light melanocyte A melanocyte that appears lighter in color. GOC:tfm A mesenchymal stem cell that is part of Wharton's jelly. tmeehan 2011-03-01T09:51:18Z cell mesenchymal stem cell of Wharton's jelly A mesenchymal stem cell that is part of Wharton's jelly. GOC:tfm A mesenchymal stem cell of the umbilical cord. tmeehan 2011-03-01T09:55:12Z cell mesenchymal stem cell of umbilical cord A mesenchymal stem cell of the umbilical cord. GOC:tfm A mesenchymal stem cell of adipose tissue. tmeehan 2011-03-01T09:57:17Z cell mesenchymal stem cell of adipose A mesenchymal stem cell of adipose tissue. GOC:tfm A mesenchymal stem cell of liver. tmeehan 2011-03-01T09:58:51Z cell hepatic mesenchymal stem cell true A mesenchymal stem cell of liver. GOC:tfm A mesenchymal stem cell of the vertebrae. tmeehan 2011-03-01T10:40:27Z cell vertebral mesenchymal stem cell true A mesenchymal stem cell of the vertebrae. GOC:tfm A glial cell that ensheathes axons of neuron in the peripheral nervous system and are necessary for their maintainance and function. tmeehan 2011-03-02T01:19:27Z BTO:0001220 CALOHA:TS-0898 cell Schwann cell A glial cell that ensheathes axons of neuron in the peripheral nervous system and are necessary for their maintainance and function. GOC:tfm A stromal cell of the pancreas. tmeehan 2011-03-02T02:40:41Z cell stromal cell of pancreas true A stromal cell of the pancreas. GOC:tfm A pericyte of the central nervous system. tmeehan 2011-03-02T02:54:18Z cell central nervous system pericyte true A pericyte of the central nervous system. GOC:tfm A myofibroblast that lies in the connective tissue of the spinal cord that has a distinctly lamellar arrangement. tmeehan 2011-03-02T03:03:58Z cell perineural cell true A myofibroblast that lies in the connective tissue of the spinal cord that has a distinctly lamellar arrangement. GO:tfm http://en.wikipedia.org/wiki/Perineurium 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 A preadipocyte found in mesenteric tissue. tmeehan 2011-03-03T04:19:40Z cell mesenteric preadipocyte true A preadipocyte found in mesenteric tissue. GOC:tfm tmeehan 2011-03-03T04:19:42Z cell omentum preadipocyte true A preadipocyte that is part of the breast. tmeehan 2011-03-03T04:19:46Z cell preadipocyte of the breast true A preadipocyte that is part of the breast. GOC:tfm tmeehan 2011-03-03T04:20:04Z cell perirenal preadipocyte true A preadipocyte that is part of visceral tissue. tmeehan 2011-03-03T04:32:56Z cell visceral preadipocyte A preadipocyte that is part of visceral tissue. GOC:tfm A preadipocyte that is part of subcutaneous tissue. tmeehan 2011-03-03T04:33:01Z cell subcutaneous preadipocyte true A preadipocyte that is part of subcutaneous tissue. 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 epithelial cell of the retinal pigmented epithelium. tmeehan 2011-03-06T03:37:09Z BTO:0004910 FMA:75802 cell retinal pigment epithelial cell true An epithelial cell of the retinal pigmented epithelium. GOC:tfm A smooth muscle cell of the umbilical vein. tmeehan 2011-03-06T05:00:51Z cell smooth muscle cell of the umbilical vein A smooth muscle cell of the umbilical vein. GOC:tfm A smooth muscle cell of the bachiocephalic vasculature. tmeehan 2011-03-06T05:00:58Z cell smooth muscle cell of the brachiocephalic vasculature A smooth muscle cell of the bachiocephalic vasculature. GOC:tfm A vascular associated smooth muscle cell of the brain vasculature. tmeehan 2011-03-06T05:01:20Z cell smooth muscle cell of the brain vasculature true A vascular associated smooth muscle cell of the brain vasculature. GOC:tfm A smooth muscle of the pulmonary artery. tmeehan 2011-03-06T05:01:28Z BTO:0003336 cell smooth muscle cell of the pulmonary artery A smooth muscle of the pulmonary artery. GOC:tfm A smooth muscle cell of the coronary artery. tmeehan 2011-03-06T05:01:34Z cell smooth muscle cell of the coronary artery A smooth muscle cell of the coronary artery. GOC:tfm A smooth muscle of the internal thoracic artery. tmeehan 2011-03-06T05:01:41Z cell smooth muscle cell of the internal thoracic artery A smooth muscle of the internal thoracic artery. GOC:tfm A smooth muscle cell of the umbilical artery. tmeehan 2011-03-06T05:01:48Z cell smooth muscle cell of the umbilical artery A smooth muscle cell of the umbilical artery. GOC:tfm A smooth muscle cell of the subclavian artery. tmeehan 2011-03-06T05:01:52Z cell smooth muscle cell of the subclavian artery A smooth muscle cell of the subclavian artery. GOC:tfm Smooth muscle cell of the carotid artery. tmeehan 2011-03-06T05:01:56Z cell smooth muscle cell of the carotid artery Smooth muscle cell of the carotid artery. GOC:tfm A smooth muscle cell of the bladder. tmeehan 2011-03-06T05:43:24Z KUPO:0001122 cell smooth muscle cell of bladder true A smooth muscle cell of the bladder. GC:tfm tmeehan 2011-03-06T05:46:39Z BTO:0004402 cell bronchial smooth muscle cell A smooth muscle cell of the esophagus. tmeehan 2011-03-06T05:48:17Z cell smooth muscle cell of the esophagus true A smooth muscle cell of the esophagus. GOC:tfm A smooth muscle cell of the trachea. tmeehan 2011-03-06T05:50:28Z cell smooth muscle cell of trachea A smooth muscle cell of the trachea. GOC:tfm A smooth muscle cell of the uterus. tmeehan 2011-03-06T05:53:28Z cell uterine smooth muscle cell true A smooth muscle cell of the uterus. GOC:tfm tmeehan 2011-03-06T06:50:53Z anulus pulposus cell cell annulus pulposus cell true An astrocyte of the cerebellum. tmeehan 2011-03-06T06:57:27Z cell astrocyte of the cerebellum true An astrocyte of the cerebellum. GOC:tfm tmeehan 2011-03-06T06:57:33Z cell astrocyte of the hippocampus An astrocyte of the cerebral cortex. tmeehan 2011-03-06T06:57:36Z cell astrocyte of the cerebral cortex An astrocyte of the cerebral cortex. GOC:tfm An astrocyte of the spinal cord. tmeehan 2011-03-06T07:11:26Z cell astrocyte of the spinal cord true An astrocyte of the spinal cord. GOC:tfm A neural crest cell that gives rise to cells of the enteric nervous system. tmeehan 2011-03-06T07:24:35Z cell migratory enteric neural crest cell A neural crest cell that gives rise to cells of the enteric nervous system. GOC:tfm A neuron of the hippocampus. tmeehan 2011-03-06T07:31:49Z cell hippocampal neuron true A neuron of the hippocampus. GOC:tfm A CNS neuron of the cerebral cortex. tmeehan 2011-03-06T07:37:08Z BTO:0004102 FMA:84104 cortical neuron cell neuron of cerebral cortex A CNS neuron of the cerebral cortex. GOC:tfm A neuron of the raphe nuclei. tmeehan 2011-03-06T07:42:06Z cell raphe nuclei neuron true A neuron of the raphe nuclei. GOC:tfm A CNS neuron of the dorsal spinal cord. tmeehan 2011-03-06T07:43:34Z cell neuron of the dorsal spinal cord true A CNS neuron of the dorsal spinal cord. GOC:tfm A neuron of the ventral spinal cord. tmeehan 2011-03-06T07:46:03Z cell neuron of the ventral spinal cord true A neuron of the ventral spinal cord. GOC:tfm A neuron of the striatum. tmeehan 2011-03-06T07:47:12Z cell striatum neuron A neuron of the striatum. GOC:tfm A neuron of the substantia nigra. tmeehan 2011-03-06T07:48:42Z cell neuron of the substantia nigra true A neuron of the substantia nigra. GOC:tfm A fat cell that is part of omentum tissue. tmeehan 2011-03-14T10:17:00Z omental adipocyte omental fat cell cell adipocyte of omentum tissue true A fat cell that is part of omentum tissue. GOC:tfm A fat cell of perirenal fat tissue. tmeehan 2011-03-14T10:17:05Z perirenal fat cell cell perirenal adipocyte cell true A fat cell of perirenal fat tissue. GOC:tfm A fat cell that is part of the breast. tmeehan 2011-03-14T10:17:07Z CALOHA:TS-2377 breast adipocyte fat cell of breast cell Adipocytes found in the subcutaneous adipose tissue of breast. The breast consists of three main components, the skin, the subcutaneous adipose tissue and the functional glandular tissue that comprises both parenchyma and stroma.[CALOHA] adipocyte of breast true A fat cell that is part of the breast. GOC:tfm An endothelial cell of the umbilical vein. tmeehan 2011-03-14T11:36:51Z BTO:0004296 cell endothelial cell of umbilical vein An endothelial cell of the umbilical vein. GOC:tfm An adult angioblastic cell released from the bone marrow, capable of blood circulation and participation in angiogenesis by differentiating into blood vessel endothelial cells. Their existence is controversial. tmeehan 2011-03-14T12:11:18Z EPC cell adult endothelial progenitor cell An adult angioblastic cell released from the bone marrow, capable of blood circulation and participation in angiogenesis by differentiating into blood vessel endothelial cells. Their existence is controversial. GOC:tfm PMID:20807818 PMID:9020076 A fibroblast of skin. tmeehan 2011-03-14T12:31:49Z BTO:0001255 CALOHA:TS-0935 cell skin fibroblast true A fibroblast of skin. GOC:tfm tmeehan 2011-03-14T12:46:28Z cell gingival epithelial cell A stromal cell of the prostate. tmeehan 2011-03-14T02:11:10Z BTO:0003972 cell prostate stromal cell true A stromal cell of the prostate. 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 paneth cell of the appendix. tmeehan 2011-03-15T09:38:18Z cell paneth cell of the appendix A paneth cell of the appendix. 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 An immature astrocyte. immature astrocytic glia cell immature astrocyte An immature astrocyte. GOC:dsd A mature astrocyte that is capable of producing cytokines. activated astrocyte mature astrocytic glia cell Mature astrocytes are reportedly able to produce aspartate, ATP, BDNF, BMP-2a, BMP-3, CCL2, CCL3, CCL4, CCL5, CCL19, CCL20,CD40L, CNTF, CTGF, CXCL1, CXCL2, CXCL8, edn-1, aFGF, bFGF, G-CSF, glutamate, GM-CSF, IFN-alpha, IFN-beta, IFN-gamma, IGF-1, IL-1alpha, IL-1beta, IL-2, Il-4, IL-6, IL-10, IL-12, LIF, MIP-2, NGF, nitric oxide, NT3, taurine, TGF-beta, TNF-alpha, TNF-beta. mature astrocyte A mature astrocyte that is capable of producing cytokines. GOC:dsd PMID:12898703 PMID:8734446 An immature microglial cell with a ramified morphology. immature microglia quiescent microglia resting microglia cell Immature microglia are reportedly CD34-positive, CD163-negative, MHCI-negative, MHCII-negative. immature microglial cell An immature microglial cell with a ramified morphology. GOC:dsd PMID:18396103 PMID:19461673 quiescent microglia PMID:18396103 resting microglia PMID:18396103 A mature microglial cell that has changed shape to an amoeboid morphology and is capable of cytokine production and antigen presentation. activated microglia mature microglia reactive microglia cell Mature microglia are reportedly CCR2-positive, CD4-positive, CD9-positive, CD11a-positive, CD11b-positive, CD11c-positive, CD13-positive, CD16-positive, CDw17-positive, CD18-positive, CD21-positive, CD26-negative, CD32-positive, CD35-positive, CD36-positive, CD40-positive, CD44-positive, CD45-positive, CD53-positive, CD54-positive, CD56-negative, CD58-positive, CD63-positive, CD64-positive, CD66-positive, CD80-positive, CD86-positive, CD87-positive, CD92-positive, CD106-positive, CD107a-positive, CD147-positive, CD155-positive, CD162-positive, CD163-positive, CD171-negative, CD200R-positive, CXCR3-positive, CX3CR1-positive, fibronectin-positive, GD3-positive, GLUT1-positive, GLUT3-negative, GLUT5-positive, MHCI-positive, MHCII-positive, P2X4-positive, RFD7-negative, RGS5-negative, alpha-SMA-negative, vimentin-positive, and vwf-negative. Mature microglia are capable of producing BDNF, CCL3, CCL5, CCL7, CCL8, CCL9, CCL19, CCL20,CD40L, CSF, CXCL1, CXCL2, CXCL4, CXCL5, CXCL8, CXCL9, CXCL10, glutamate, IL-1beta, IL-1ra, IL-3, IL-6, IL-10, IL-12, LT, MMP-2, MMP-9, NGF, nitric oxide, ROS, TGF-beta, TNF-alpha. mature microglial cell true A mature microglial cell that has changed shape to an amoeboid morphology and is capable of cytokine production and antigen presentation. GOC:dsd PMID:11517395 PMID:14612429 PMID:15246020 PMID:16177057 PMID:18396103 PMID:20021364 activated microglia PMID:18396103 reactive microglia PMID:18396103 A spore formed from bacteria in the order Actinomycetales. tmeehan 2011-06-16T01:01:41Z cell actinomycete-type spore A spore formed from bacteria in the order Actinomycetales. GO:0034304 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 basal cell in the respiratory tract. tmeehan 2011-06-21T03:11:10Z airway basal cell airway basal stem cell cell respiratory basal cell A basal cell in the respiratory tract. GOC:tfm PMID:20699479 An epithelial cell of the anal column. tmeehan 2011-07-08T12:11:38Z cell epithelial cell of anal column An epithelial cell of the anal column. GOC:tfm A nonkeratinized epithelial cell of the anal canal. tmeehan 2011-07-08T02:05:33Z FMA:263146 cell nonkeratinized epithelial cell of anal column A nonkeratinized epithelial cell of the anal canal. GOC:tfm A nonkeratinized cell epithleial cell of the inferior part of the anal canal. tmeehan 2011-07-08T02:06:53Z FMA:263144 cell nonkeratinized epithelial cell of inferior part of anal canal A nonkeratinized cell epithleial cell of the inferior part of the anal canal. GOC:tfm An epithelial cell of the anal canal that is keratinized. This cell type is found towards the lower, rectal end of the anal canal. tmeehan 2011-07-08T02:08:40Z cell keratinized epithelial cell of the anal canal An epithelial cell of the anal canal that is keratinized. This cell type is found towards the lower, rectal end of the anal canal. GOC:tfm A respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole. This cell types gives rise to alveolar cell types and club cells in response to lung injury. This cell type expresses markers Scgb1a1 and Sftpc. tmeehan 2011-06-21T03:26:08Z BASC basal epithelial cell of bronchioalveolar duct junction cell bronchioalveolar stem cell A respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole. This cell types gives rise to alveolar cell types and club cells in response to lung injury. This cell type expresses markers Scgb1a1 and Sftpc. GOC:tfm PMID:15960971 An amniotic stem cell is a mesenchymalstem cell extracted from amniotic fluid. Amniotic stem cells are able to differentiate into various tissue type such as skin, cartilage, cardiac tissue, nerves, muscle, and bone tmeehan 2011-06-21T03:55:39Z cell Not clear to me if amniotic stem cell is a different cell type from amnion mesenchymal stem cells. They are treated as distinct in the literature as isolations methods are different, so I will keep them as separate terms for now. amniotic stem cell An amniotic stem cell is a mesenchymalstem cell extracted from amniotic fluid. Amniotic stem cells are able to differentiate into various tissue type such as skin, cartilage, cardiac tissue, nerves, muscle, and bone GOC:tfm PMID:20942606 An epithelial fate stem cell derived form the amnion membrane. tmeehan 2011-06-21T04:06:17Z cell amniotic epithelial stem cell An epithelial fate stem cell derived form the amnion membrane. GOC:tfm PMID:20446274 An epithelial cell of the esophageal gland proper. tmeehan 2011-07-08T02:16:51Z FMA:256141 cell epithelial cell of esophageal gland proper An epithelial cell of the esophageal gland proper. GOC:tfm An epithelial cell of the esophageal cardiac gland that occurs both in the proximal and distal esophagus, within the lamina propia. tmeehan 2011-07-08T02:16:54Z FMA:256143 cell epithelial cell of esophageal cardiac gland An epithelial cell of the esophageal cardiac gland that occurs both in the proximal and distal esophagus, within the lamina propia. GOC:tfm http://web.mac.com/wjkrause/iWeb/Histology/Blog/E3FA5916-1AA9-4885-B579-5051838D98CB.html An epithelial cell of stratum corneum of esophageal epithelium that lacks keratin. tmeehan 2011-07-08T02:22:09Z FMA:263148 cell nonkeratinized cell of stratum corneum of esophageal epithelium An epithelial cell of stratum corneum of esophageal epithelium that lacks keratin. GOC:tfm An endothelial cell of viscerocranial mucosa that is part of the tympanic region of the viscerocranial mucosa. tmeehan 2011-07-08T02:25:44Z FMA:70628 cell endo-epithelial cell of tympanic part of viscerocranial mucosa An endothelial cell of viscerocranial mucosa that is part of the tympanic region of the viscerocranial mucosa. GOC:tfm An endocranial viscerocranial mucosa cell that is part of viscerocranial mucosa. tmeehan 2011-07-08T02:25:46Z FMA:70629 cell endo-epithelial cell of pharyngotympanic part of viscerocranial mucosa An endocranial viscerocranial mucosa cell that is part of viscerocranial mucosa. GOC:tfm An ecto-epithelial cell of the buccal region of the viscerocranial mucosa. tmeehan 2011-07-08T02:34:12Z FMA:70577 cell obsolete epithelial cell of buccal part of viscerocranial mucosa true An ecto-epithelial cell of the buccal region of the viscerocranial mucosa. GOC:tfm An ecto-epithelial cell of the palatal region of the viscerocranial mucosa. tmeehan 2011-07-08T02:34:14Z FMA:70580 cell obsolete epithelial cell of anterior palatal part of viscerocranial mucosa true An ecto-epithelial cell of the palatal region of the viscerocranial mucosa. GOC:tfm An ecto-epithelial cell of the nasal region of the viscerocranial mucosa. tmeehan 2011-07-08T02:36:06Z FMA:70554 cell obsolete epithelial cell of nasal part of viscerocranial mucosa true An ecto-epithelial cell of the nasal region of the viscerocranial mucosa. GOC:tfm An ecto-epithelial cell of the gingival region of the viscerocranial mucosa. tmeehan 2011-07-08T02:36:11Z FMA:70579 cell obsolete epithelial cell of gingival part of viscerocranial mucosa true An ecto-epithelial cell of the gingival region of the viscerocranial mucosa. GOC:tfm An ecto-epithelial cell of the paranasal region of the viscerocranial mucosa. tmeehan 2011-07-08T02:38:18Z FMA:70578 cell obsolete epithelial cell of paranasal sinus part of viscerocranial mucosa true An ecto-epithelial cell of the paranasal region of the viscerocranial mucosa. GOC:tfm An endothelial cell that is part of the venous sinus of spleen. This endothelial cell has an elongated, spindle-shaped, flattened morphology that is parallel to long axis of sinus. This cell type rests on a basement membrane interrupted by numerous narrow slits. tmeehan 2011-07-08T03:06:49Z FMA:72140 stave cell cell endothelial cell of venous sinus of spleen An endothelial cell that is part of the venous sinus of spleen. This endothelial cell has an elongated, spindle-shaped, flattened morphology that is parallel to long axis of sinus. This cell type rests on a basement membrane interrupted by numerous narrow slits. GOC:tfm stave cell FMA:62817 A venule endothelial cell that is cubodial, expresses leukocyte-specific receptors, and allows for passage of lymphocytes into bloodstream. tmeehan 2011-07-08T03:14:10Z FMA:67759 HEV cell endothelial cell of postcapillary venule of lymph node cell Markers expressed on HEV include: MAdCAM-1,PNAd (sulfated and glycosylated molecules, i.e. GlyCAM-1, CD34, endomucin, nepmucin), ICAM-1, ICAM-2,Fuc-TVII, beta 3GlcNAcT-3, GlcNAc6ST2,CCL21, CCL19, CXCL13, CXCL12, Autotaxin, DARC, angiomodulin, LRHG. endothelial cell of high endothelial venule A venule endothelial cell that is cubodial, expresses leukocyte-specific receptors, and allows for passage of lymphocytes into bloodstream. GOC:tfm PMID:20726857 A endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells. tmeehan 2011-07-08T03:31:25Z cell squamous endothelial cell A endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells. GOC:tfm An epithelial cell of stratum corneum of esophageal epithelium. tmeehan 2011-07-08T03:46:35Z FMA:70733 cell epithelial cell of stratum corneum of esophageal epithelium An epithelial cell of stratum corneum of esophageal epithelium. GOC:tfm An epithelial cell of stratum spinosum of esophageal epithelium. tmeehan 2011-07-08T03:48:26Z FMA:70732 cell epithelial cell of stratum spinosum of esophageal epithelium An epithelial cell of stratum spinosum of esophageal epithelium. GOC:tfm 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 A luminal epithelial cell of mammary gland located in acinus of structure. tmeehan 2011-07-11T01:44:31Z FMA:74505 cell Consider if synonymous with mammary alveolar cell CL:0002325. Some use this term to refer to the non-lactating cell type that gives rise to the lactating cell type. luminal cell of acinus of lactiferous gland A luminal epithelial cell of mammary gland located in acinus of structure. GOC:tfm A luminal cell of terminal ducts, i.e.e the terminal branch of a lactiferous duct which alveolar cells drain into. tmeehan 2011-07-11T01:44:33Z FMA:87168 cell luminal cell of lactiferous terminal ductal lobular unit A luminal cell of terminal ducts, i.e.e the terminal branch of a lactiferous duct which alveolar cells drain into. GOC:tfm A luminal epithelial cell of the lactiferous duct. This cuboidal epithelial cell expresses keratin-18 and is estrogen-receptor alpha positive. tmeehan 2011-07-11T01:44:48Z FMA:74504 FMA:74505 cell luminal cell of lactiferous duct A luminal epithelial cell of the lactiferous duct. This cuboidal epithelial cell expresses keratin-18 and is estrogen-receptor alpha positive. GOC:tfm PMID:19022771 A myocardial endocrine cell that is part of the atrium. tmeehan 2011-07-11T02:45:39Z FMA:83389 cell myocardial endocrine cell of atrium true A myocardial endocrine cell that is part of the atrium. GOC:tfm A stem cell that can give rise to multiple cell types (i.e. smooth muscle, endothelial) in the developing heart. tmeehan 2011-07-11T03:15:38Z CPC cardiovascular progenitor cell cell Discrepancy in develops from origins prevents me from making the assertion that cardioblasts give rise to all instances of cardiocytes as we state cardiac muscle cells develop from cardiac myoblast, which in turn develop from muscle stem cell. cardioblast A stem cell that can give rise to multiple cell types (i.e. smooth muscle, endothelial) in the developing heart. GOC:tfm PMID:19745164 CPC PMID:19745164 cardiovascular progenitor cell PMID:17519333 PMID:19745164 A fibrocyte of the cochlea that has specialized structural and molecular adaptions. tmeehan 2011-07-11T03:35:01Z cell otic fibrocyte A fibrocyte of the cochlea that has specialized structural and molecular adaptions. GOC:tfm PMID:18353863 An otic fibrocyte that underlies the spiral prominence and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph. tmeehan 2011-07-11T03:40:40Z type II otic fibrocyte type II spiral ligament fibrocyte cell type 2 otic fibrocyte An otic fibrocyte that underlies the spiral prominence and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph. GOC:tfm PMID:18353863 type II spiral ligament fibrocyte MP:0004488 An otic fibrocyte that resides above the stria vasularis and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph. tmeehan 2011-07-11T03:40:42Z type V otic fibrocyte type V spiral ligament fibrocyte cell type 5 otic fibrocyte An otic fibrocyte that resides above the stria vasularis and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph. GOC:tfm PMID:18353863 An otic fibrocyte that is lateral to the basilar membrane and anchoris it to the lateral wall. tmeehan 2011-07-11T03:40:46Z type IV otic fibrocyte type IV spiral ligament fibrocyte cell type 4 otic fibrocyte An otic fibrocyte that is lateral to the basilar membrane and anchoris it to the lateral wall. GOC:tfm PMID:18353863 type IV spiral ligament fibrocyte MP:0004490 An otic fibrocyte that lines the otic capsule. tmeehan 2011-07-11T03:40:50Z type III otic fibrocyte type III spiral ligament fibrocyte cell type 3 otic fibrocyte An otic fibrocyte that lines the otic capsule. GOC:tfm PMID:18353863 type III spiral ligament fibrocyte MP:0004489 An otic fibrocyte that underlies the stria vascularis and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph. tmeehan 2011-07-11T03:39:27Z type I otic fibrocyte type I spiral ligament fibrocyte cell type 1 otic fibrocyte An otic fibrocyte that underlies the stria vascularis and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph. GOC:tfm PMID:18353863 type I spiral ligament fibrocyte MP:0004487 An endothelial stalk cell is a specialized endothelial cell that follows behind the tip cell of an angiogenic sprout. tmeehan 2011-08-16T01:49:32Z cell endothelial stalk cell An endothelial stalk cell is a specialized endothelial cell that follows behind the tip cell of an angiogenic sprout. GOC:tfm PMID:21521739 A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells. tmeehan 2011-08-16T02:38:01Z cell retinal progenitor cell A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells. GOC:tfm PMID:20959166 PMID:21148186 A skeletal muscle cell that is part of the tongue. tmeehan 2011-08-16T03:10:02Z cell tongue muscle cell A skeletal muscle cell that is part of the tongue. GOC:tfm PMID:18816858 A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus. tmeehan 2011-08-16T03:20:53Z H- cell cell H minus A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus. GOC:tfm A S. pombe cell type determined by mat1-Pc and mat1-Pi on the mat1 locus. tmeehan 2011-08-16T03:20:58Z cell H plus A S. pombe cell type determined by mat1-Pc and mat1-Pi on the mat1 locus. GOC:tfm A neuroblast derived from a neural crest cell. tmeehan 2011-08-22T09:24:15Z cell neural crest derived neuroblast A neuroblast derived from a neural crest cell. GOC:tfm PMID:17407019 A regulatory T cell that has not encountered antigen. tmeehan 2011-08-25T03:17:21Z naive regulatory T lymphocyte naive regulatory T-cell naive regulatory T-lymphocyte cell This cell type has been described as CD45RA-negative, but this doesn't fit with our current definition of naive T cell. naive regulatory T cell A regulatory T cell that has not encountered antigen. GOC:tfm A CD4-positive, CD25-positive alpha-beta regulatory T cell that has encountered antigen. tmeehan 2011-08-25T03:17:34Z cell Cell has been described as being CD45RA-positive in human, but this doesn't fit with our current definition memory T cell. memory regulatory T cell A CD4-positive, CD25-positive alpha-beta regulatory T cell that has encountered antigen. GOC:tfm PMID:21739668 A lymphocyte found in adipose tissue that lacks lineage markers of other lymphocytes but is capable of mediating TH2 cytokine responses. This cell type is found in fat associated lymphoid clusters, proliferates in response to IL2 and produce large amounts of TH2 cytokines such as IL5, IL6 and IL13 tmeehan 2011-08-29T10:08:02Z cell natural helper lymphocyte true A lymphocyte found in adipose tissue that lacks lineage markers of other lymphocytes but is capable of mediating TH2 cytokine responses. This cell type is found in fat associated lymphoid clusters, proliferates in response to IL2 and produce large amounts of TH2 cytokines such as IL5, IL6 and IL13 GOC:tfm PMID:20023630 A PP cell found in intestine. tmeehan 2011-09-27T11:59:01Z cell PP cell of intestine true A PP cell found in intestine. GOC:tfm PMID:2420136 PMID:728970 terryh 2011-10-25T03:49:41Z cell kidney cortical cell true A CNS interneuron located in the spinal cord. cell Is_a interneuron, part_of UBERON:0002240. spinal cord interneuron true A CNS interneuron located in the spinal cord. CL:CVS A non-terminally differentiated cell that originates from the neural crest and differentiates into an iridophore. cell Derived from UBERON:0002342 neural crest. iridoblast A non-terminally differentiated cell that originates from the neural crest and differentiates into an iridophore. CL:CVS A non-terminally differentiated cell that differentiates into a xanthophore. cell xanthoblast A non-terminally differentiated cell that differentiates into a xanthophore. CL:CVS A non-terminally differentiated cell that originates from the neural crest and differentiates into a leucophore. cell leucoblast A non-terminally differentiated cell that originates from the neural crest and differentiates into a leucophore. CL:CVS A non-terminally differentiated cell that originates from the neural crest and differentiates into an erythrophore. cell pigment erythroblast A non-terminally differentiated cell that originates from the neural crest and differentiates into an erythrophore. CL:CVS A non-terminally differentiated cell that originates from the neural crest and differentiates into a cyanophore. cell cyanoblast A non-terminally differentiated cell that originates from the neural crest and differentiates into a cyanophore. CL:CVS Specialized epithelial cells involved in the maintenance of osmotic homeostasis. They are characterized by abundant mitochondria and ion transporters. In amniotes, they are present in the renal system. In freshwater fish, ionocytes in the skin and gills help maintain osmotic homeostasis by absorbing salt from the external environment. cell ionocyte Specialized epithelial cells involved in the maintenance of osmotic homeostasis. They are characterized by abundant mitochondria and ion transporters. In amniotes, they are present in the renal system. In freshwater fish, ionocytes in the skin and gills help maintain osmotic homeostasis by absorbing salt from the external environment. PMID:17555741 PMID:19268451 Kolmer-Agduhr neurons are ciliated GABAergic neurons that contact the central canal of the spinal cord and have ipsilateral ascending axons. KA cell KA interneuron KA neuron Kolmer-Agduhr cell cell Kolmer-Agduhr neuron Kolmer-Agduhr neurons are ciliated GABAergic neurons that contact the central canal of the spinal cord and have ipsilateral ascending axons. PMID:18680739 KA interneuron PMID:15539490 KA neuron PMID:9634146 An auditory hair cell located in the macula that is sensitive to auditory stimuli. cell macular hair cell An auditory hair cell located in the macula that is sensitive to auditory stimuli. GO:cvs A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the cells apical membrane is regulated by aldosterone and vasopressin. In mammals these cells are located in the renal collecting ducts. cell renal principal cell A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the cells apical membrane is regulated by aldosterone and vasopressin. In mammals these cells are located in the renal collecting ducts. CL:CVS A cuboidal epithelial cell of the kidney that regulates acid/base balance. FMA:86560 intercalated cell cell renal intercalated cell A cuboidal epithelial cell of the kidney that regulates acid/base balance. CL:CVS A cuboidal epithelial cell of the kidney which secretes acid and reabsorbs base to regulate acid/base balance. cell renal alpha-intercalated cell A cuboidal epithelial cell of the kidney which secretes acid and reabsorbs base to regulate acid/base balance. CL:CVS A ciliated epithelial cell with many cilium. MCC multi-ciliated cell multiciliated cell multiciliated epithelial cell cell multi-ciliated epithelial cell A ciliated epithelial cell with many cilium. CL:CVS A ciliated epithelial cell with a single cilium. cell single ciliated epithelial cell A ciliated epithelial cell with a single cilium. CL:CVS A non-sensory cell that extends from the basement membrane to the apical surface of the auditory epithelium and provides support for auditory hair cells. cell auditory epithelial support cell A non-sensory cell that extends from the basement membrane to the apical surface of the auditory epithelium and provides support for auditory hair cells. CL:CVS GOC:tfm An auditory epithelial support cell that surrounds the nerve fibers and synapses of the auditory inner hair cells. FMA:79801 cell inner phalangeal cell An auditory epithelial support cell that surrounds the nerve fibers and synapses of the auditory inner hair cells. CL:CVS Obsolete. Use PO:0030007 from Plant Ontology instead. The apical cell is the upper cell formed after the first division of a plant zygote. cell replaced_by: PO:0030007 obsolete apical cell true Obsolete. Use PO:0030007 from Plant Ontology instead. The apical cell is the upper cell formed after the first division of a plant zygote. TAIR:TB Obsolete. Use PO:0002002 from Plant Ontology instead. The lower cell formed after the first division of a plant zygote. cell replaced_by: PO:0002002 obsolete plant basal cell true Obsolete. Use PO:0002002 from Plant Ontology instead. The lower cell formed after the first division of a plant zygote. TAIR:TB A cell that secretes ghrelin, the peptide hormone that stimulates hunger. cell ghrelin secreting cell A cell that secretes ghrelin, the peptide hormone that stimulates hunger. CL:curator Ghrelin secreting cells found in the exocrine pancreas. pancreatic E cell cell In mammals the endocrine pancreas is called the Islets of Langerhans. pancreatic epsilon cell Ghrelin secreting cells found in the exocrine pancreas. PMID:14970313 Lymphatic progenitor cells. Ceri 2012-01-12T04:44:34Z cell Usually express Prox1, or prox1b. lymphangioblast true Lymphatic progenitor cells. CL:CVS Mesenchymal derived lymphatic progenitor cells that give rise to the superficial lymphatics. Ceri 2012-01-12T05:01:22Z cell mesenchymal lymphangioblast Mesenchymal derived lymphatic progenitor cells that give rise to the superficial lymphatics. PMID:15624319 PMID:18430230 Lymphatic progenitor cells, derived from the veins, that give rise to lymphatic endothelial cells. Ceri 2012-01-12T05:21:09Z parachordal lymphangioblast cell vascular lymphangioblast true Lymphatic progenitor cells, derived from the veins, that give rise to lymphatic endothelial cells. CL:CVS Cranial motor neuron which innervates muscles derived from the branchial (pharyngeal) arches. PMID:14699587 branchi motor neuron special visceral motor neuron branchiomotor neuron Cranial motor neuron which innervates muscles derived from the branchial (pharyngeal) arches. ZFIN:CVS A motor neuron that innervates a skeletal muscle. These motor neurons are all excitatory and cholinergic. somatic motor neuron somatomotor neuron A motor neuron that innervates a skeletal muscle. These motor neurons are all excitatory and cholinergic. ZFIN:CVS A motor neuron that synapses to parasympathetic neurons that innervate tear glands, sweat glands, and the smooth muscles and glands of the pulmonary, cardiovascular, and gastrointestinal systems. general visceral motor neuron Note that these neurons do not synapse directly onto muscles visceromotor neuron A motor neuron that synapses to parasympathetic neurons that innervate tear glands, sweat glands, and the smooth muscles and glands of the pulmonary, cardiovascular, and gastrointestinal systems. ZFIN:CVS Multi fate stem cell that gives rise to both hepatocytes and cholangiocytes as descendants. hepatoblast Multi fate stem cell that gives rise to both hepatocytes and cholangiocytes as descendants. GOC:CVS PMID:18356246 PMID:20483998 Skeletogenic cell that has the potential to develop into an ameloblast. Located in the inner enamel epithelium, these cells elongate, their nuclei shift distally (away from the dental papilla), and their cytoplasm becomes filled with organelles needed for synthesis and secretion of enamel proteins. haendel 2012-06-15T01:27:01Z cell unsure of neural crest contribution. In VSAO we have develops_from CL:0000008 preameloblast Skeletogenic cell that has the potential to develop into an ameloblast. Located in the inner enamel epithelium, these cells elongate, their nuclei shift distally (away from the dental papilla), and their cytoplasm becomes filled with organelles needed for synthesis and secretion of enamel proteins. GO_REF:0000034 PMCID:PMC2737325 Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized). haendel 2012-06-15T02:51:27Z scleroblast cell Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) skeletogenic cell Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized). GO_REF:0000034 scleroblast GO_REF:0000034 Skeletogenic cell that has the potential to develop into a cementoblast. haendel 2012-06-15T04:37:13Z cell precementoblast Skeletogenic cell that has the potential to develop into a cementoblast. GO_REF:0000034 Skeletogenic cell that has the potential to form an odontoblast, deposits predentine, and arises from a cranial neural crest cell. haendel 2012-06-15T05:15:11Z cell preodontoblast Skeletogenic cell that has the potential to form an odontoblast, deposits predentine, and arises from a cranial neural crest cell. GO_REF:0000034 Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. haendel 2012-06-27T08:27:35Z cell premigratory neural crest cell Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. UBERONREF:0000002 Cell that is part of the notochord. haendel 2012-06-27T08:47:31Z cell NOTE: TO DO, notochord development still needs work. notochordal cell Cell that is part of the notochord. GO_REF:0000034 Mesodermal cell that is axially located and gives rise to the cells of the notochord. haendel 2012-06-27T08:52:41Z axial mesodermal cell cell chordamesodermal cell Mesodermal cell that is axially located and gives rise to the cells of the notochord. GO_REF:0000034 Notochordal cell that is part of the outer epithelium of the notochord and surrounds the vacuolated notochord cells. haendel 2012-06-27T09:26:37Z cell notochordal sheath cell Notochordal cell that is part of the outer epithelium of the notochord and surrounds the vacuolated notochord cells. CL:MAH Notochordal cell that is inner portion of the notochord and becomes vacuolated as development proceeds. haendel 2012-06-27T09:29:30Z chordablast chordoblast cell notochordal vacuole cell Notochordal cell that is inner portion of the notochord and becomes vacuolated as development proceeds. CL:MAH chordablast GO_REF:0000034 chordoblast PMID:14574572 Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells. haendel 2012-06-27T10:44:01Z cell prechondroblast Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells. GO_REF:0000034 Skeletogenic cell that has the potential to transform into an osteoblast, and develops from neural crest or mesodermal cells. haendel 2012-06-27T10:57:21Z osteoprogenitor cell cell preosteoblast Skeletogenic cell that has the potential to transform into an osteoblast, and develops from neural crest or mesodermal cells. GO_REF:0000034 Neuron that is part of the enteric nervous system. haendel 2012-06-28T08:20:31Z cell enteric neuron Neuron that is part of the enteric nervous system. CL:MAH Odontoblast that non-terminally differentiated, located in the odontogenic papilla and dentine tissue, and transforms from a odontoblast cell. cl non-terminally differentiated odontoblast Odontoblast that non-terminally differentiated, located in the odontogenic papilla and dentine tissue, and transforms from a odontoblast cell. GO_REF:0000034 PSPUB:0000170 Odontoblast that is terminally differentiated and derived from an odontogenic papilla and associated with dentine. cl terminally differentiated odontoblast Odontoblast that is terminally differentiated and derived from an odontogenic papilla and associated with dentine. GO_REF:0000034 OBSOLETE: A cultured cell that has been passaged at least one time in culture. haendel 2012-11-28T11:54:59Z passaged cultured cell cell Obsoleted in July 2013 and replaced by the CLO 'cell line cell' class, as a result of CLO-OBI-CL alignment efforts. Covers cells actively being cultured or stored in a quiescent state for future use. obsolete cell line cell true OBSOLETE: A cultured cell that has been passaged at least one time in culture. ReO:mhb OBSOLETE: A cell line cell that is expected to be capable of replicating a limited number of times in culture before undergoing senescence. Mortal cell line cells cannot be propagated indefinitely (as immortal cell line cells can). haendel 2012-11-28T11:56:20Z finite cell line cell cell primary cell line cell Obsoleted in July 2013 and replaced by the CLO 'mortal cell line cell' class, as a result of CLO-OBI-CL alignment efforts. Covers cells actively being cultured or stored in a quiescent state for future use. obsolete mortal cell line cell true OBSOLETE: A cell line cell that is expected to be capable of replicating a limited number of times in culture before undergoing senescence. Mortal cell line cells cannot be propagated indefinitely (as immortal cell line cells can). ReO:mhb Muscle precursor cell that is adjacent to the notochord and part of the presomitic mesoderm. haendel 2012-12-30T12:43:15Z cell In teleosts, adaxial cells give rise to slow muscle myoblasts. adaxial cell Muscle precursor cell that is adjacent to the notochord and part of the presomitic mesoderm. PMID:8951054 An epidermal cell with apical microvilli or a single apical projection have synaptic associations with nerve fibres in the epidermis. haendel Taxon specificity not yet fully known, but are known in anuran larvae but not in adults. Stiftchenzellen An epidermal cell with apical microvilli or a single apical projection have synaptic associations with nerve fibres in the epidermis. PMID:1087183 Ciliated cell of the embryonic epidermis and functions in embryonic movements. haendel Taxon specificity not clear -present in embryonic anurans. epidermal ciliary cell Ciliated cell of the embryonic epidermis and functions in embryonic movements. PMCID:PMC3046089 haendel taxon specificity not clear. Appears in early larval stages of anurans and persists after metamorphosis. epidermal mucus secreting cell Characteristic early embryonic cell with a bottle or flask shape that is first to migrate inwards at the blastopore during gastrulation in amphibians. haendel bottle cell Characteristic early embryonic cell with a bottle or flask shape that is first to migrate inwards at the blastopore during gastrulation in amphibians. PMID:3197630 Secretory cell that produces a chemical mixture that triggers antipredator behavior. The substance is released only upon disruption of the epidermis. [Behavior of teleost fishes, second edition, edited by Pitcher, 1992] haendel club cell (zebrafish) club cell alarm substance cell Secretory cell that produces a chemical mixture that triggers antipredator behavior. The substance is released only upon disruption of the epidermis. [Behavior of teleost fishes, second edition, edited by Pitcher, 1992] ISBN-10:0412429403 club cell (zebrafish) https://github.com/obophenotype/cell-ontology/issues/583 club cell ISBN-10:0412429403 https://github.com/obophenotype/cell-ontology/issues/583 A specialized pore forming cell of the follicle, located adjacent to the animal pole of the oocyte. The micropylar cell makes the single micropyle (pore) through the chorion through which the sperm fertilizes the egg. haendel plug cell micropylar cell A specialized pore forming cell of the follicle, located adjacent to the animal pole of the oocyte. The micropylar cell makes the single micropyle (pore) through the chorion through which the sperm fertilizes the egg. PMID:18582455 ZFA:0005239 Epidermal cell rich in mitochondria. In amphibians, appears during metamorphosis. haendel flask cell Epidermal cell rich in mitochondria. In amphibians, appears during metamorphosis. DOI:10.1007/BF00717048 Any muscle cell in which the fibers are not organised into sarcomeres. non-striated muscle cell Any muscle cell in which the fibers are not organised into sarcomeres. GOC:DOS Any hematopoietic cell that is a precursor of some other hematopoietic cell type. hematopoietic precursor cell Any hematopoietic cell that is a precursor of some other hematopoietic cell type. GOC:dos A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. skeletal muscle fiber A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. GOC:tfm ISBN:0323052908 A myotube that is part of some somatic muscle. Examples include arthropod somatic muscle cells. somatic muscle myotube A myotube that is part of some somatic muscle. Examples include arthropod somatic muscle cells. PMID:22274696 PMID:8720463 A muscle cell that is part of some somatic muscle. somatic muscle cell A muscle cell that is part of some somatic muscle. GOC:dos A somatic muscle cell that is oblquely striated. Examples include the somatic muscles of nematodes. obliquely striated somatic muscle cell A somatic muscle cell that is oblquely striated. Examples include the somatic muscles of nematodes. PMID:8720463 A myoblast that detemines the properties (size, shape and attachment to the epidermis) of a `somatic muscle myotube` (CL:0008003) . It develops into a somatic muscle myotube via fusion with `fusion component myoblasts` (CL:0000621). cell muscle founder cell A myoblast that detemines the properties (size, shape and attachment to the epidermis) of a `somatic muscle myotube` (CL:0008003) . It develops into a somatic muscle myotube via fusion with `fusion component myoblasts` (CL:0000621). PMID:22274696 A muscle cell that is part of some visceral muscle visceral muscle cell A muscle cell that is part of some visceral muscle GOC:dos A visceral muscle cell that is striated. Examples include the visceral muscle cells of arhtropods. striated visceral muscle cell A visceral muscle cell that is striated. Examples include the visceral muscle cells of arhtropods. GOC:dos A visceral muscle that is transversely striated. Examples include the visceral muscle cells of arthropods. transversely striated visceral muscle cell A visceral muscle that is transversely striated. Examples include the visceral muscle cells of arthropods. GOC:dos A cranial motor neuron whose soma is located in the midbrain andor hindbrain and which innervates the skeletal muscles of the eye or tongue. cranial somatomotor neuron A cranial motor neuron whose soma is located in the midbrain andor hindbrain and which innervates the skeletal muscles of the eye or tongue. PMID:14699587 A skeletal muscle satellite cell that divides by stem cell division. A proportion of this population undergoes symmetric stem cell division, producing two skeletal muscle satellite stem cells. The rest undergo asymmetric stem cell division - retaining their identity while budding off a daughter cell that differentiates into an adult skeletal muscle myoblast. cell skeletal muscle satellite stem cell A skeletal muscle satellite cell that divides by stem cell division. A proportion of this population undergoes symmetric stem cell division, producing two skeletal muscle satellite stem cells. The rest undergo asymmetric stem cell division - retaining their identity while budding off a daughter cell that differentiates into an adult skeletal muscle myoblast. PMID:23303905 A skeletal muscle satellite cell that is mitotically quiescent. These cells are wedge shaped and have a large nuclear to cytoplasmic ratio with few organelles, a small nucleus and condensed interphase chromatin. Satellite cells typically remain in this state until activated following muscle damage. cell quiescent skeletal muscle satellite cell A skeletal muscle satellite cell that is mitotically quiescent. These cells are wedge shaped and have a large nuclear to cytoplasmic ratio with few organelles, a small nucleus and condensed interphase chromatin. Satellite cells typically remain in this state until activated following muscle damage. PMID:21849021 PMID:23303905 A visceromotor motor neuron whose soma is located in the hindbrain, and which synapses to parasympathetic neurons that innervate tear glands, sweat glands, and the smooth muscles of the head. cranial visceromotor neuron A visceromotor motor neuron whose soma is located in the hindbrain, and which synapses to parasympathetic neurons that innervate tear glands, sweat glands, and the smooth muscles of the head. PMID:14699587 A motor neuron that is capable of directly inducing muscle contraction. In vertebrates, all motor neurons are excitatory, but various types of inhibitory motor neurons exist in invertebrates. false obsolete excitatory motor neuron true A motor neuron that is capable of directly inhibiting muscle contraction. In vertebrates, all motor neurons are excitatory, but various types of inhibitory motor neurons exist in invertebrates. inhibitory motor neuron A skeletal muscle cell that has become mitotically active - typically following muscle damage. cell activated skeletal muscle satellite cell More accurately - transformation_of ? A skeletal muscle cell that has become mitotically active - typically following muscle damage. PMID:21849021 PMID:23303905 A skeletal muscle myoblast that is part of a skeletal mucle. These cells are formed following acivation and division of skeletal muscle satellite cells. They form a transient population that is lost when they fuse to form skeletal muscle fibers. myogenic precursor cell cell The vast majority of these cells develop from skeletal muscle satellite cells, although there are some reports of other origins. adult skeletal muscle myoblast A skeletal muscle myoblast that is part of a skeletal mucle. These cells are formed following acivation and division of skeletal muscle satellite cells. They form a transient population that is lost when they fuse to form skeletal muscle fibers. PMID:23303905 myogenic precursor cell PMID:23303905 A myoblast that is commited to developing into a somatic muscle. cell somatic muscle myoblast A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration. mesenchyme cell mesenchymal cell A skeletal muscle satellite cell that undergoes symmetric division to produce two adult skeleltal muscle myoblasts. cell skeletal muscle satellite myogenic cell A skeletal muscle satellite cell that undergoes symmetric division to produce two adult skeleltal muscle myoblasts. GOC:dos PMID:23303905 anterior lateral line ganglion neuron A mesenchymal cell of the endocardial cushion. These cells develop via an epithelial to mesenchymal transition when endocardial cells break cell-to-cell contacts and migrate into the cardiac jelly. Cells from this population form the heart septa and valves. endocardial cushion cell A mesenchymal cell of the endocardial cushion. These cells develop via an epithelial to mesenchymal transition when endocardial cells break cell-to-cell contacts and migrate into the cardiac jelly. Cells from this population form the heart septa and valves. PMID:18816864 Duplicate term. obsolete cardiac fibroblast 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 A neuron that release noradrenaline (noriphinephrine) as a neurotransmitter. noradrenergic neuron A neuron that release noradrenaline (noriphinephrine) as a neurotransmitter. GOC:dos An epithelial cell that is part of the epithelium of a tracheal tube in an open tracheal system, such as that found in insects. cell open tracheal system tracheocyte An epithelial cell that is part of the epithelium of a tracheal tube in an open tracheal system, such as that found in insects. GOC:dos A bipolar neuron found in the retina that is synapsed by rod photoreceptor cells. These neurons have axons that arborize and synapse to targets in inner plexiform layers 4 and 5 and depolarize in response to light. dos 2017-06-29T11:05:22Z rod bipolar cell (sensu Mus) dos 2017-07-09T19:12:36Z visual system neuron dos 2017-07-12T11:10:52Z inhibitory neuron dos 2017-07-12T11:11:06Z excitatory neuron cortical interneuron rosehip neuron A pericyte of the decidual vasculature. dos 2020-02-29T11:45:57Z decidual perivascular cell decidual pericyte A pericyte of the decidual vasculature. PMID:30429548 Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of the microcirculation. dos 2020-02-29T17:33:55Z mural cell Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of the microcirculation. Wiki:Mural_cell&oldid=930603194 dos 2020-02-29T17:37:00Z microcirculation associated smooth muscle cell A trophoblast cell that is not part of a placental villous. dos 2020-03-02T08:45:06Z EVT extravillous cytotrophloblast extravillous trophoblast A trophoblast cell that is not part of a placental villous. PMID:31049600 EVT PMID:31049600 A lower motor neuron that innervates only intrafusal muscle fibers. Unlike the alpha motor neurons, gamma motor neurons do not directly adjust the lengthening or shortening of muscles but function in adjusting the sensitivity of muscle spindles and in keeping muscle spindles taut, thereby allowing the continued firing of alpha neurons. FMA:83660 MESH:D009047 SAO:143800623 gamma motor neuron A lower motor neuron that innervates only intrafusal muscle fibers. Unlike the alpha motor neurons, gamma motor neurons do not directly adjust the lengthening or shortening of muscles but function in adjusting the sensitivity of muscle spindles and in keeping muscle spindles taut, thereby allowing the continued firing of alpha neurons. DOI:10.1093/acprof:oso/9780195159561.001.1 WikipediaVersion:Gamma_motor_neuron&oldid=906640465 A large, multipolar lower motor neuron of the brainstem and spinal cord that innervates the extrafusal muscle fibers of skeletal muscle and are directly responsible for initiating their contraction. While their cell bodies are in the CNS (in the anterior gray horn of the spinal cord), they are part of the somatic nervous system - a branch of the PNS. dos 2020-09-23T20:16:26Z alpha motoneuron alpha motor neuron A large, multipolar lower motor neuron of the brainstem and spinal cord that innervates the extrafusal muscle fibers of skeletal muscle and are directly responsible for initiating their contraction. While their cell bodies are in the CNS (in the anterior gray horn of the spinal cord), they are part of the somatic nervous system - a branch of the PNS. DOI:10.1016/B978-0-12-801238-3.05364-2 Wikipedia:Alpha_motor_neuron&oldid=957148643 The motor neurons of vertebrates that directly innervate skeletal muscles. They receive input from upper motor neurons. dos 2020-09-23T20:22:07Z FMA:84632 lower motor neuron The motor neurons of vertebrates that directly innervate skeletal muscles. They receive input from upper motor neurons. Wikipedia:Lower_motor_neuron&oldid=952547294 A skeletal muscle fiber that is innervated by alpha motor neuron and generates tension by contracting, thereby allowing for skeletal movement. These fibers make up the large mass of skeletal muscle tissue and are attached to bones by tendons. dos 2020-09-26T21:06:15Z TH:H3.03.00.0.00007 myofibra extrafusalis extrafusal muscle fiber A skeletal muscle fiber that is innervated by alpha motor neuron and generates tension by contracting, thereby allowing for skeletal movement. These fibers make up the large mass of skeletal muscle tissue and are attached to bones by tendons. DOI:10.1016/B978-0-443-10321-6.00004-7 Wikipedia:Extrafusal_muscle_fiber&oldid=978415293 A skeletal muscle fiber that is part of a muscle spindle. These are specialized muscle fibers that serve as proprioceptors, detecting the amount and rate of change in length of a muscle. They are innervated by both sensory neurons and motor neurons (gamma and beta motorneurons, collectively referred to as fusimotor neurons). dos 2020-09-26T21:07:01Z H3.03.00.0.00012 myofibra intrafusalis intrafusal muscle fiber A skeletal muscle fiber that is part of a muscle spindle. These are specialized muscle fibers that serve as proprioceptors, detecting the amount and rate of change in length of a muscle. They are innervated by both sensory neurons and motor neurons (gamma and beta motorneurons, collectively referred to as fusimotor neurons). DOI:10.1016/B978-0-443-10321-6.00004-7 Wikipedia:Intrafusal_muscle_fiber&oldid=937508784 A glutamatergic motor neuron with a soma in the brainstem or cerebral cortex. They do not synapse directly to muscles but rather to lower motor neurons, which do. They are the main controllers of voluntary movement. dos 2020-09-28T09:41:48Z upper motor neuron A glutamatergic motor neuron with a soma in the brainstem or cerebral cortex. They do not synapse directly to muscles but rather to lower motor neurons, which do. They are the main controllers of voluntary movement. Wikipedia:Upper_motor_neuron&oldid=943248837 A giant pyramidal neuron with a soma in layer Vb of the primary motor cortex that sends its axons down the spinal cord via the corticospinal tract, either synapsing directly with alpha motor neurons, or targeting interneurons in the spinal cord. In humans, Betz cells are the largest known in the central nervous system. dos 2020-09-28T09:52:58Z pyramidal cell of Betz Betz cell https://en.wikipedia.org/w/index.php?title=Betz_cell&oldid=977472330#/media/File:GolgiStainedPyramidalCell.jpg A giant pyramidal neuron with a soma in layer Vb of the primary motor cortex that sends its axons down the spinal cord via the corticospinal tract, either synapsing directly with alpha motor neurons, or targeting interneurons in the spinal cord. In humans, Betz cells are the largest known in the central nervous system. DOI:10.1101/2020.03.31.016972 Wikipedia:Betz_cell&oldid=977472330 A sensory neuron of the spinal nerve that senses body position and sends information about how much the muscle is stretched to the spinal cord. spinal sensory neuron sensory neuron of spinal nerve true A sensory neuron of the spinal nerve that senses body position and sends information about how much the muscle is stretched to the spinal cord. GOC:nv GOC:pr Any cell in the compound eye, a light sensing organ composed of ommatidia. GOC:pr PMID:12021768 compound eye retinal cell Any cell participating in the inflammatory response to a foreign substance, e.g. neutrophil, macrophage. GOC:pr http://en.wikipedia.org/wiki/Inflammatory_response inflammatory cell Any cell in the midgut (middle subdivision of a digestive tract) of a larva. GOC:pr http://en.wikipedia.org/wiki/Insect#Midgut larval midgut 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. 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 Any cell in a salivary gland. GOC:pr http://en.wikipedia.org/wiki/Salivary_gland salivary gland cell A macrophage which is resident in the lamina propria of the small intestine. macrophage of small intestine small intestine lamina propria resident macrophage gastrointestinal tract (lamina propria) macrophage of small intestine A macrophage which is resident in the lamina propria of the small intestine. https://orcid.org/0000-0003-4183-8865 A macrophage which is resident in the lamina propria of the large intestine. macrophage of large intestine large intestine lamina propria resident macrophage gastrointestinal tract (lamina propria) macrophage of large intestine A macrophage which is resident in the lamina propria of the large intestine. https://orcid.org/0000-0003-4183-8865 A paneth cell that is located in the epithelium of the large intestine. paneth-like cell paneth cell of epithelium of large intestine A paneth cell that is located in the epithelium of the large intestine. PMID:31753849 http://orcid.org/0000-0003-4183-8865 Transit-amplifying cells (TACs) are an undifferentiated population in transition between stem cells and differentiated cells. transient amplifying cell transit-amplifying cell TAC TACs transit amplifying cell Transit-amplifying cells (TACs) are an undifferentiated population in transition between stem cells and differentiated cells. PMID:24813615 PMID:28835754 http://orcid.org/0000-0003-4183-8865 A rapidly proliferating population of cells that differentiate from stem cells of the intestinal crypt of the large intestine. Stem cells located in the crypts of Lieberkühn give rise to proliferating progenitor or transit amplifying cells that differentiate into the four major epithelial cell types. These include columnar absorptive cells or enterocytes, mucous secreting goblet cells, enteroendocrine cells and paneth cells. large intestine transit amplifying cell transient amplifying cell of crypt of Lieberkuhn of large intestine transient amplifying cell of large intestine transit amplifying cell of crypt of Lieberkuhn of large intestine transit-amplifying cell of large intestine transit amplifying cell of large intestine A rapidly proliferating population of cells that differentiate from stem cells of the intestinal crypt of the large intestine. Stem cells located in the crypts of Lieberkühn give rise to proliferating progenitor or transit amplifying cells that differentiate into the four major epithelial cell types. These include columnar absorptive cells or enterocytes, mucous secreting goblet cells, enteroendocrine cells and paneth cells. PMID:20801415 http://orcid.org/0000-0003-4183-8865 A rapidly proliferating population of cells that differentiate from stem cells of the intestinal crypt of the small intestine. Stem cells located in the crypts of Lieberkühn give rise to proliferating progenitor or transit amplifying cells that differentiate into the four major epithelial cell types. These include columnar absorptive cells or enterocytes, mucous secreting goblet cells, enteroendocrine cells and paneth cells. small intestine transit amplifying cell transient amplifying cell of crypt of Lieberkuhn of small intestine transient amplifying cell of small intestine transit amplifying cell of crypt of Lieberkuhn of small intestine transit-amplifying cell of small intestine transit amplifying cell of small intestine A rapidly proliferating population of cells that differentiate from stem cells of the intestinal crypt of the small intestine. Stem cells located in the crypts of Lieberkühn give rise to proliferating progenitor or transit amplifying cells that differentiate into the four major epithelial cell types. These include columnar absorptive cells or enterocytes, mucous secreting goblet cells, enteroendocrine cells and paneth cells. PMID:20801415 http://orcid.org/0000-0003-4183-8865 A progenitor cell with hepatic and biliary lineage potential, identified in mouse and human, and anatomically restricted to the ductal plate of fetal liver. HHyP cell fetal hepatobiliary hybrid progenitor cell fetal hepatobiliary progenitor cell A progenitor cell with hepatic and biliary lineage potential, identified in mouse and human, and anatomically restricted to the ductal plate of fetal liver. PMID:31350390 https://orcid.org/0000-0002-3163-0115 A lymphocyte that is part of a Peyer's patch. These cells have a major role in driving the immune response to antigens sampled from the intestinal lumen, and in regulating the formation of follicle-associated epithelium and M cells in Peyer's patches by converting intestitial enterocytes into M cells. Peyer's patch resident lymphocyte small intestine Peyer's patch lymphocyte Peyer's patch lymphocyte A lymphocyte that is part of a Peyer's patch. These cells have a major role in driving the immune response to antigens sampled from the intestinal lumen, and in regulating the formation of follicle-associated epithelium and M cells in Peyer's patches by converting intestitial enterocytes into M cells. PMID:23525039 PMID:9252325 https://orcid.org/0000-0003-4183-8865 A follicular dendritic cell located in the Peyer's patch. These cells from a meshwork in which Peyer's patch B cells reside. Peyer's patch follicular dendritic cell A follicular dendritic cell located in the Peyer's patch. These cells from a meshwork in which Peyer's patch B cells reside. PMID:24437401 https://orcid.org/0000-0003-4183-8865 An intestinal stem cell that is located in the large intestine crypt of Liberkuhn. These stem cells reside at the bottom of crypts in the large intestine and are highly proliferative. They either differentiate into transit amplifying cells or self-renew to form new stem cells. crypt stem cell of large intestine stem cell of large intestine crypt of Lieberkuhn intestinal crypt stem cell of large intestine An intestinal stem cell that is located in the large intestine crypt of Liberkuhn. These stem cells reside at the bottom of crypts in the large intestine and are highly proliferative. They either differentiate into transit amplifying cells or self-renew to form new stem cells. PMID:20683682 https://orcid.org/0000-0003-4183-8865 An intestinal stem cell that is located in the small intestine crypt of Liberkuhn. These stem cells reside at the bottom of crypts in the small intestine and are highly proliferative. They either differentiate into transit amplifying cells or self-renew to form new stem cells. crypt stem cell of small intestine stem cell of small intestine crypt of Lieberkuhn intestinal crypt stem cell of small intestine An intestinal stem cell that is located in the small intestine crypt of Liberkuhn. These stem cells reside at the bottom of crypts in the small intestine and are highly proliferative. They either differentiate into transit amplifying cells or self-renew to form new stem cells. PMID:20683682 https://orcid.org/0000-0003-4183-8865 A lymphocyte that resides in the lamina propria of the large intestine. lamina propria lymphocyte of large intestine lymphocyte of large intestine lamina propria A lymphocyte that resides in the lamina propria of the large intestine. https://orcid.org/0000-0003-4183-8865 A kidney cortical cell that is part of the nephrogenic zone. cortical nephrogenic niche cell cortical nephrogenic zone cell nephrogenic zone cell A kidney cortical cell that is part of the nephrogenic zone. PMID:29449449 https://orcid.org/0000-0002-3163-0115 An intestinal tuft cell that is a part of a vermiform appendix. appendix tuft cell tuft cell of appendix vermiformis tuft cell of vermiform appendix tuft cell of appendix An intestinal tuft cell that is a part of a vermiform appendix. http://orcid.org/0000-0003-3440-1876 A stromal cell found in the lamina propria of the large intestine. stromal cell of lamina propria of large intestine A stromal cell found in the lamina propria of the large intestine. http://orcid.org/0000-0003-4183-8865 A stromal cell found in the lamina propria of the small intestine. stromal cell of lamina propria of small intestine A stromal cell found in the lamina propria of the small intestine. http://orcid.org/0000-0003-4183-8865 A T cell which resides in the Peyer's patch of the small intestine. T cell of Peyer's patch of small intestine T cell of small intestine Peyer's patch small intestine Peyer's patch T cell A T cell which resides in the Peyer's patch of the small intestine. http://orcid.org/0000-0003-4183-8865 A mesothelial cell that is part of the small intestine. mesothelial cell of small intestine A mesothelial cell that is part of the small intestine. http://orcid.org/0000-0003-4183-8865 A mesothelial cell that is part of the large intestine. mesothelial cell of large intestine A mesothelial cell that is part of the large intestine. http://orcid.org/0000-0003-4183-8865 An enterocyte that is a part of a vermiform appendix. appendix enterocyte enterocyte of appendix vermiformis enterocyte of vermiform appendix enterocyte of appendix An enterocyte that is a part of a vermiform appendix. http://orcid.org/0000-0003-3440-1876 A transit amplifying cell that is part of a crypt of Lieberkuhn of large intestine. appendix transit amplifying cell transit amplifying cell of appendix vermiformis transit amplifying cell of vermiform appendix transit amplifying cell of appendix A transit amplifying cell that is part of a crypt of Lieberkuhn of large intestine. http://orcid.org/0000-0003-3440-1876 An intestinal crypt stem cell that is located in the vermiform appendix. These stem cells reside at the bottom of crypts in the appendix and are highly proliferative. They either differentiate into transit amplifying cells or self-renew to form new stem cells. appendix intestinal crypt stem cell intestinal crypt stem cell of appendix vermiformis intestinal crypt stem cell of vermiform appendix stem cell of intestinal crypt of Lieberkuhn of appendix stem cell of intestinal crypt of Lieberkuhn of appendix vermiformis intestinal crypt stem cell of appendix An intestinal crypt stem cell that is located in the vermiform appendix. These stem cells reside at the bottom of crypts in the appendix and are highly proliferative. They either differentiate into transit amplifying cells or self-renew to form new stem cells. PMID:20683682 http://orcid.org/0000-0003-3440-1876 A mesothelial cell that is located in a vermiform appendix. appendix mesothelial cell mesothelial cell of appendix vermiformis mesothelial cell of vermiform appendix mesothelial cell of appendix A mesothelial cell that is located in a vermiform appendix. http://orcid.org/0000-0003-3440-1876 An intestinal enteroendocrine cell that is located in a vermiform appendix. appendix enteroendocrine cell enteroendocrine cell of appendix vermiformis enteroendocrine cell of vermiform appendix enteroendocrine cell of appendix An intestinal enteroendocrine cell that is located in a vermiform appendix. http://orcid.org/0000-0003-3440-1876 A T cell that is located in a vermiform appendix. T cell of appendix vermiformis T cell of vermiform appendix appendix T cell T cell of appendix A T cell that is located in a vermiform appendix. http://orcid.org/0000-0003-3440-1876 A B cell that is located in a vermiform appendix. B cell of appendix vermiformis B cell of vermiform appendix appendix B cell B cell of appendix A B cell that is located in a vermiform appendix. http://orcid.org/0000-0003-3440-1876 A plasma cell that is located in a vermiform appendix. appendix plasma cell plasma cell of appendix vermiformis plasma cell of vermiform appendix plasma cell of appendix A plasma cell that is located in a vermiform appendix. http://orcid.org/0000-0003-3440-1876 A dendritic cell that is located in a vermiform appendix. appendix dendritic cell dendritic cell of appendix vermiformis dendritic cell of vermiform appendix dendritic cell of appendix A dendritic cell that is located in a vermiform appendix. http://orcid.org/0000-0003-3440-1876 A stromal cell found in the lamina propria of the vermiform appendix. stromal cell of appendix lamina propria stromal cell of lamina propria of appendix vermiformis stromal cell of lamina propria of vermiform appendix A stromal cell found in the lamina propria of the vermiform appendix. http://orcid.org/0000-0003-3440-1876 A macrophage located in the vermiform appendix. macrophage of appendix macrophage of appendix vermiformis macrophage of vermiform appendix appendix macrophage A macrophage located in the vermiform appendix. http://orcid.org/0000-0003-3440-1876 A hair follicle matrix region cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the hair bulb to become the hair medulla cortex and hair root sheath. keratinized cell of hair follicle A hair follicle matrix region cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the hair bulb to become the hair medulla cortex and hair root sheath. A stromal cell that is part_of a bone marrow. GOC:cjm bone marrow stromal cell stromal cell of bone marrow An epithelial cell that is part_of a umbilical artery. GOC:cjm umbilical artery epithelial cell epithelial cell of umbilical artery An epithelial cell that is part_of a alveolus of lung. GOC:cjm alveolus of lung epithelial cell May be merged with pneumocyte in future epithelial cell of alveolus of lung A mononuclear cell that is part_of a bone marrow. GOC:cjm bone marrow mononuclear cell mononuclear cell of bone marrow A specialized cardiomyocyte that transmit signals from the AV node to the cardiac Purkinje fibers. AV bundle cell atrioventricular bundle cell A specialized cardiomyocyte that transmit signals from the AV node to the cardiac Purkinje fibers. GOC:mtg_heart cardiac blood vessel endothelial cell His-Purkinje system cell cardiac endothelial cell camera type eye photoreceptor cell camera-type eye photoreceptor cell cerebellar stellate cell A GABAergic interneuron whose soma is located in the cerebral cortex. cerebral cortex GABAergic interneuron A GABAergic interneuron whose soma is located in the cerebral cortex. GOC:dos A neuron that is part_of a cerebral cortex. cerebral cortex neuron light pinealocyte type I pinealocyte dark pinealocyte type II pinealocyte A highly specialized cell type exclusive to and forming neuroepithelium of the Saccus vasculosus, covering the caudal diverticulum of the infundibular recess. Editor note: remember to link to Saccus vasculosus in next uberon release coronet cell A highly specialized cell type exclusive to and forming neuroepithelium of the Saccus vasculosus, covering the caudal diverticulum of the infundibular recess. GOC:mr PMID:17595538 A cell with a flagellum surrounded by a collar of microvilli. The motion of the flagellum draws water past the microvilli, serving either a feeding or sensory function. Collar cells are found in multiple animals, including sponges, echinoderms, and cnidarians. They are also found outside animals in the choanoflagellates. Although collar cells are superficially similar, their cytoskeletal structure and functional biology are different in different groups of organisms. cell collar cell A cell with a flagellum surrounded by a collar of microvilli. The motion of the flagellum draws water past the microvilli, serving either a feeding or sensory function. Collar cells are found in multiple animals, including sponges, echinoderms, and cnidarians. They are also found outside animals in the choanoflagellates. Although collar cells are superficially similar, their cytoskeletal structure and functional biology are different in different groups of organisms. PMID:25840473 A zygote in a plant or an animal. zygote cardiac glial cell cell cardiac myoblast cardiac neuron A CNS interneuron located in the dorsal horn of the spinal cord. dorsal spinal cord interneuron dorsal horn interneuron true A CNS interneuron located in the dorsal horn of the spinal cord. GOC:nv A motor neuron that passes from the spinal cord toward or to a muscle and conducts an impulse that causes movement. spinal cord motor neuron true A motor neuron that passes from the spinal cord toward or to a muscle and conducts an impulse that causes movement. GOC:nv A motor neuron that is generated only on limb levels and send axons into the limb mesenchyme. Need to MIREOT in 'spinal cord lateral column' from Uberon lateral motor column neuron A motor neuron that is generated only on limb levels and send axons into the limb mesenchyme. GOC:nv A neurosecretory neuron residing mainly in the hypothalamic supraoptic and paraventricular nuclei and in a number of smaller accessory cell groups between these two nuclei, that secretes the hormones oxytocin and vasopressin. magnocellular neuron magnocellular neurosecretory cell (duplicate class) A neurosecretory neuron residing mainly in the hypothalamic supraoptic and paraventricular nuclei and in a number of smaller accessory cell groups between these two nuclei, that secretes the hormones oxytocin and vasopressin. GOC:nv MP:0009467 A vetebrate lens cell that is any of the elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye. lens fibre cell lens fiber cell A vetebrate lens cell that is any of the elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye. GO:0070307 GOC:nv An interneuron that uses GABA as a vesicular neurotransmitter. These interneurons are inhibitory GABAergic inhibitory interneuron The formal and textual definitions of this term will need to be altered if evidence for non-inhibitory GABA-ergic neurons emerges. GABAergic interneuron An interneuron that uses GABA as a vesicular neurotransmitter. These interneurons are inhibitory GOC:CellBLAST GOC:nv PMID:29724907 An inhibitory GABAergic interneuron found in the cerebellar cortex. Lugaro cell An inhibitory GABAergic interneuron found in the cerebellar cortex. GOC:nv 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 hemocyte derived from head mesoderm, which enters the hemolymph as acirculating cell. embryonic hemocyte A hemocyte derived from head mesoderm, which enters the hemolymph as acirculating cell. GOC:NV PMID:17967061 A plasmatocyte derived from head mesoderm. embryonic plasmatocyte A plasmatocyte derived from head mesoderm. GOC:NV PMID:17967061 A cell derived from the mesoderm that is found at the periphery of the embryo. lateral mesodermal cell A cell derived from the mesoderm that is found at the periphery of the embryo. GOC:NV PMID:9169844 A cell derived from the mesoderm that is located between the paraxial mesoderm and the lateral plate. intermediate mesodermal cell A cell derived from the mesoderm that is located between the paraxial mesoderm and the lateral plate. GOC:NV ISBN:978-0-87969-707-5 A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. cell neural crest cell A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9900-7880 A sperm cell that is cabaple of motion (motility). motile sperm cell A sperm cell that is cabaple of motion (motility). PMID:30612620 A sperm cell that is not cabaple of motion (motility). non-motile sperm cell A sperm cell that is not cabaple of motion (motility). PMID:30612620 A motile sperm cell that contain no F-actin, and their motility is powered by a dynamic filament system. amoeboid sperm cell A motile sperm cell that contain no F-actin, and their motility is powered by a dynamic filament system. PMID:17708982 A motile sperm cell that contains a slender threadlike microscopic appendage that enables motion. flagellated sperm cell A motile sperm cell that contains a slender threadlike microscopic appendage that enables motion. PMID:30612620 https://www.lexico.com/en/definition/flagellum Cell that is part of the vagal neural crest population. The vagal neural crest arises from the axial level of somites 1-7 and has been described as a hybrid between the head and the trunk populations. vagal neural crest cell Cell that is part of the vagal neural crest population. The vagal neural crest arises from the axial level of somites 1-7 and has been described as a hybrid between the head and the trunk populations. PMID:22016183 A group 3 innate lymphoid cell that express ROR gamma t and IL-7R alpha in the absence of lineage markers (e.g. CD3, CD19, B220, CD11c, Gr-1), with the functional ability to interact with mesenchymal cells through lymphotoxin and tumor necrosis factor. Lymphoid tissue-inducer cells are key to the development of lymph nodes and Peyer’s patches. LTi lymphoid tissue inducer cell lymphoid tissue–inducer cell A group 3 innate lymphoid cell that express ROR gamma t and IL-7R alpha in the absence of lineage markers (e.g. CD3, CD19, B220, CD11c, Gr-1), with the functional ability to interact with mesenchymal cells through lymphotoxin and tumor necrosis factor. Lymphoid tissue-inducer cells are key to the development of lymph nodes and Peyer’s patches. GOC:add PMID:19029905 PMID:21601793 PMID:27935637 PMID:29454785 PMID:9354470 A mesothelial cell that is part of the epicardium. mesothelial cell of epicardium An undifferentiated cell that originates from a neural stem cell and has the capacity to generate multiple types of lineage-restricted progenitors but not to self-renew. neural progenitor cell An undifferentiated cell that originates from a neural stem cell and has the capacity to generate multiple types of lineage-restricted progenitors but not to self-renew. PMID:30574073 A fibroblast that is part of upper back skin. fibroblast of upper back skin A fibroblast that is part of skin of back. fibroblast of skin of back A mast cell that is CD25+. CD25+ neoplastic mast cell Mast cells do not normally express CD25, but neoplastic mast cells may be CD25-positive. CD25+ mast cell A double negative thymocyte that is CD3-positive, CD4-negative, CD8-negative, that that are present in the periphery in very low numbers and predominantly produce INF-gamma, TNF-alpha, and a low amount of TGF-beta, but not IL-2, IL-4, IL-10 or IL-13 upon activation. CD4-negative, CD8-negative, alpha-beta regulatory T cells DN Treg double-negative alpha-beta regulatory T cell double negative T regulatory cell A double negative thymocyte that is CD3-positive, CD4-negative, CD8-negative, that that are present in the periphery in very low numbers and predominantly produce INF-gamma, TNF-alpha, and a low amount of TGF-beta, but not IL-2, IL-4, IL-10 or IL-13 upon activation. PMID:16285891 An effector T cell that displays impaired effector functions (e.g., rapid production of effector cytokines, cytotoxicity) and has limited proliferative potential. Tex cell exhausted T cell An effector T cell that displays impaired effector functions (e.g., rapid production of effector cytokines, cytotoxicity) and has limited proliferative potential. PMID:26544946 A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses. progenitor cell A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses. ISBN:978-1-62808-994-3 https://doi.org/10.1016/B978-0-12-409503-8.00002-0 Any fibroblast that is part of skeletal muscle tissue. skeleton muscle fibroblast skeletal muscle fibroblast Any fibroblast that is part of skeletal muscle tissue. PMID:28369879 https://orcid.org/0000-0001-6164-0667 BTO:0002771 A neural-crest derived glial cell that supports the growth and survival of primary olfactory neuroons from the neuroepithelium in the nasal cavity to the brain by encasing large bundles of numerous unmyelinated axons. OEC olfactory ensheathing cell A neural-crest derived glial cell that supports the growth and survival of primary olfactory neuroons from the neuroepithelium in the nasal cavity to the brain by encasing large bundles of numerous unmyelinated axons. PMID:22456085 Neuron that secretes the neurotransmitter galanin. galanergic neuron Neuron that secretes the neurotransmitter galanin. GOC:NV PMID:23159249 ZFIN:CVS ZFIN:YB Cells of the uterine chorion that acquire specialized structural and/or functional features that characterize chorionic trophoblasts. These cells will migrate towards the spongiotrophoblast layer and give rise to syncytiotrophoblasts of the labyrinthine layer. chorionic trophoblast cell Cells of the uterine chorion that acquire specialized structural and/or functional features that characterize chorionic trophoblasts. These cells will migrate towards the spongiotrophoblast layer and give rise to syncytiotrophoblasts of the labyrinthine layer. GOC:NV Parasympathetic neurons are part of the parasympathetic nervous sysem and the cell bodies lie in the brain and sacral region of the spinal cord. The neurons are mainly cholinergic. parasympathetic neuron Parasympathetic neurons are part of the parasympathetic nervous sysem and the cell bodies lie in the brain and sacral region of the spinal cord. The neurons are mainly cholinergic. GOC:NV isbn:0080923437 Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides. sympathetic neuron Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides. GOC:NV isbn:0080923437 A type of interneuron in the retinal inner nuclear layer which carries information from the inner plexiform layer and the outer plexiform layer. Need to MIREOT retinal inner nuclear layer (part of) interplexiform cell A type of interneuron in the retinal inner nuclear layer which carries information from the inner plexiform layer and the outer plexiform layer. GOC:NV PMID:12771169 A type of interneuron in the retinal inner nuclear layer which carries information from the inner plexiform layer and the outer plexiform layer, using dopamine. This type of cell is found in Danio rerio. dopamanergic interplexiform cell A type of interneuron in the retinal inner nuclear layer which carries information from the inner plexiform layer and the outer plexiform layer, using dopamine. GOC:NV PMID:12771169 A type of interneuron in the retinal inner nuclear layer which carries information from the inner plexiform layer and the outer plexiform layer using GABA. This type of cell is found in many mammals. GABAnergic interplexiform cell A type of interneuron in the retinal inner nuclear layer which carries information from the inner plexiform layer and the outer plexiform layer using GABA. GOC:NV PMID:12771169 Astrocyte-like radial glial cell that extends vertically throughout the retina, with the nucleus are usually in the middle of the inner nuclear layer. Muller glia Müller cell Muller cell Astrocyte-like radial glial cell that extends vertically throughout the retina, with the nucleus are usually in the middle of the inner nuclear layer. GOC:NV PMID:21911394 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 A neuron that releases hypocretin as a neurotransmitter. orexin hypocretin-secreting neuron A neuron that releases hypocretin as a neurotransmitter. GOC:NV PMID:23848055 Neuron that secretes histamine. histaminergic neuron Neuron that secretes histamine. GOC:NV PMID:22677810 Neuroendocrine cells that are born in the nasal placode during embryonic development and migrate through the nose and forebrain to the hypothalamus, where they regulate reproduction. GnRH neuron GnRH-secreting neuron gonadotropin releasing neuron Neuroendocrine cells that are born in the nasal placode during embryonic development and migrate through the nose and forebrain to the hypothalamus, where they regulate reproduction. GOC:NV PMID:21828096 Neurons part of the hypothalamic supraoptic and paraventricular nuclei that secrete the hormones, oxytocin and vasopressin into the systemic circulation from the posterior pituitary gland. magnocellular neurosecretory cell Neurons part of the hypothalamic supraoptic and paraventricular nuclei that secrete the hormones, oxytocin and vasopressin into the systemic circulation from the posterior pituitary gland. GOC:NV PMID:10711808 Neuron found in the spriral ganglion. spiral ganglion neuron Neuron found in the spriral ganglion. GOC:NV A segmented neutrophilic cell of the bone marrow reserve pool that expresses CD11b (integrin alpha-M) and high levels of CD16 (low affinity immunoglobulin gamma Fc region receptor III) on its cell surface. segmented neutrophil of bone marrow A segmented neutrophilic cell of the bone marrow reserve pool that expresses CD11b (integrin alpha-M) and high levels of CD16 (low affinity immunoglobulin gamma Fc region receptor III) on its cell surface. PMID:11138622 PMID:15514007 A cell that, by division or terminal differentiation, can give rise to other cell types. Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. precursor cell A cell that, by division or terminal differentiation, can give rise to other cell types. GOC:dos An astrocyte of the forebrain. tberardini forebrain astrocyte cell astrocyte of the forebrain true A CNS neuron of the forebrain. tberardini forebrain neuron cell neuron of the forebrain true forebrain radial glial cell Motor neuron that innervate muscles that control eye, jaw, and facial movements of the vertebrate head and parasympathetic neurons that innervate certain glands and organs. PMID:14699587 cranial motoneuron cranial motor neuron Motor neuron that innervate muscles that control eye, jaw, and facial movements of the vertebrate head and parasympathetic neurons that innervate certain glands and organs. ZFIN:CVS An ionocyte that is part of the lung epithelium. The cells from this type are major sources of the CFTR protein in human and mice. cell pulmonary ionocyte An ionocyte that is part of the lung epithelium. The cells from this type are major sources of the CFTR protein in human and mice. PMID:30069044 PMID:30069046 A mesodermal cell that is part of the splanchnic layer of lateral plate mesoderm. splanchnic mesodermal cell Any serous secreting cell that is part of the tracheobronchial epithelium. 2020-05-07T16:03:27Z serous cell of tracheobronchial tree tracheobronchial serous cell Any chondrocyte that is part of the tracheobronchial tree. 2020-05-07T17:29:51Z chondrocyte of tracheobronchial tree tracheobronchial chondrocyte Any goblet cell that is part of the tracheobronchial epithelium. 2020-05-07T18:14:52Z goblet cell of tracheobronchial tree tracheobronchial goblet cell An eosinophil with a ring-shaped nucleus that is resident in the lung parenchyma. In mouse, lung parenchyma resident eosinophils are IL-5-independent Siglec-F(intermediate) CD62L+ CD101(low). In human, they are Siglec-8+ CD62L+ IL-3R(low). 2020-05-26T09:42:19Z lung-resident eosinophil rEos lung parenchyma resident eosinophil An eosinophil with a ring-shaped nucleus that is resident in the lung parenchyma. In mouse, lung parenchyma resident eosinophils are IL-5-independent Siglec-F(intermediate) CD62L+ CD101(low). In human, they are Siglec-8+ CD62L+ IL-3R(low). PMID:27548519 lung-resident eosinophil PMID:27548519 rEos PMID:27548519 A smooth muscle cell that is part of any lymphatic vessel. 2020-07-21T12:29:51Z smooth muscle cell of lymphatic vessel lymphatic vessel smooth muscle cell A smooth muscle cell that is part of any lymphatic vessel. PMID:15109561 A smooth muscle cell that is part of any blood vessel. 2020-07-21T12:42:48Z smooth muscle cell of blood vessel blood vessel smooth muscle cell A smooth muscle cell that is part of any blood vessel. PMID:9108778 A smooth muscle cell that is part of the tracheobronchial tree. 2020-07-21T12:50:22Z smooth muscle cell of tracheobronchial tree tracheobronchial smooth muscle cell A smooth muscle cell that is part of the tracheobronchial tree. PMID:10853867 An epithelial cell of the extrahepatic bile ducts, including the left and right hepatic duct, common hepatic duct, and common bile duct. They are columnar in shape, and have a large nuclear-to-cytoplasmic ratio relative to small/intrahepatic cholangiocytes. 2020-09-03T12:24:24Z large bile duct cholangiocyte extrahepatic cholangiocyte An epithelial cell of the extrahepatic bile ducts, including the left and right hepatic duct, common hepatic duct, and common bile duct. They are columnar in shape, and have a large nuclear-to-cytoplasmic ratio relative to small/intrahepatic cholangiocytes. PMID:23720296 large bile duct cholangiocyte PMID:23720296 An endothelial cell found in the periportal region hepatic sinusoid, near the portal triad. The fenestrae of these cells are larger but fewer in number compared with those of endothelial cells near the centrilobular region of the hepatic sinusoid. 2020-09-09T13:56:47Z periportal LSEC endothelial cell of periportal hepatic sinusoid An endothelial cell found in the periportal region hepatic sinusoid, near the portal triad. The fenestrae of these cells are larger but fewer in number compared with those of endothelial cells near the centrilobular region of the hepatic sinusoid. PMID:27423426 periportal LSEC PMID:28287163 An endothelial cell found in the centrilobular region hepatic sinusoid, near the central vein. The fenestrae of these cells are smaller but more numerous compared with those of endothelial cells near the periportal region of the hepatic sinusoid. 2020-09-10T12:38:29Z pericentral LSEC endothelial cell of pericentral hepatic sinusoid An endothelial cell found in the centrilobular region hepatic sinusoid, near the central vein. The fenestrae of these cells are smaller but more numerous compared with those of endothelial cells near the periportal region of the hepatic sinusoid. PMID:27423426 pericentral LSEC PMID:28287163 Any hepatocyte that is part of the liver lobule periportal region. These cells are primarily involved in oxidative energy metabolism. 2020-10-12T10:29:31Z periportal hepatocyte periportal region hepatocyte Any hepatocyte that is part of the liver lobule periportal region. These cells are primarily involved in oxidative energy metabolism. PMID:29763190 periportal hepatocyte PMID:29763190 Any hepatocyte that is part of the liver lobule midzonal region. These cells have mixed functionality in comparison with those in the other two regions of the liver lobule. 2020-10-12T10:57:40Z midzonal hepatocyte midzonal region hepatocyte Any hepatocyte that is part of the liver lobule midzonal region. These cells have mixed functionality in comparison with those in the other two regions of the liver lobule. PMID:29763190 midzonal hepatocyte PMID:29763190 Any hepatocyte that is part of the liver lobule centrilobular region. These cells are the primary location for the biotransformation of drugs. 2020-10-12T11:03:51Z centrilobular hepatocyte centrilobular region hepatocyte Any hepatocyte that is part of the liver lobule centrilobular region. These cells are the primary location for the biotransformation of drugs. PMID:29763190 centrilobular hepatocyte PMID:29763190 Goblet cells reside throughout the length of the small and large intestine and are responsible for the production and maintenance of the protective mucus blanket by synthesizing and secreting high-molecular-weight glycoproteins known as mucins. Human intestinal goblet cells secrete the MUC2 mucin, as well as a number of typical mucus components: CLCA1, FCGBP, AGR2, ZG16, and TFF3. 2020-10-14T14:59:07Z intestinal goblet cell intestine goblet cell Goblet cells reside throughout the length of the small and large intestine and are responsible for the production and maintenance of the protective mucus blanket by synthesizing and secreting high-molecular-weight glycoproteins known as mucins. Human intestinal goblet cells secrete the MUC2 mucin, as well as a number of typical mucus components: CLCA1, FCGBP, AGR2, ZG16, and TFF3. PMID:1996606 PMID:24942678 intestinal goblet cell PMID:1996606 Any brush cell that is part of the intestinal epithelium. 2020-10-15T12:47:46Z intestinal brush cell intestinal tuft cell Any brush cell that is part of the intestinal epithelium. PMID:22527717 intestinal brush cell PMID:22527717 retrotrapezoid nucleus neuron mesonephric nephron tubule epithelial cell forebrain neuroblast lateral line nerve glial cell spinal cord radial glial cell cell stretch receptor cell cell stratified keratinized epithelial stem cell cell stratified non keratinized epithelial stem cell pronephric nephron tubule epithelial cell metanephric nephron tubule epithelial cell lung goblet cell heart valve cell A specialized epithelial secretory cell that moves chloride ions and water across the tubule epithelium. FBbt:00005797 Malpighian tubule Type II cell Malpighian tubule stellate cell A specialized epithelial secretory cell that moves chloride ions and water across the tubule epithelium. GO:0061330 Malpighian tubule Type II cell FBbt:00005797 malpighian tubule tip cell A rod-like cell in the inner ear, having their heads joined and their bases on the basilar membrane widely separated so as to form a spiral tunnel known as the tunnel of Corti. FMA:75722 pillar cell of cochlea pillar cell of corti rod cell of Corti cell cochlear pillar cell pillar cell A rod-like cell in the inner ear, having their heads joined and their bases on the basilar membrane widely separated so as to form a spiral tunnel known as the tunnel of Corti. GOC:tfm PMID:12417662 growth plate cartilage chondrocyte stomach neuroendocrine cell lung neuroendocrine cell posterior lateral line nerve glial cell anterior lateral line nerve glial cell posterior lateral line ganglion neuron lung ciliated cell lung secretory cell trophectoderm cell cell trophectodermal cell A smooth muscle cell that is part of the small intestine. FMA:15050 non-striated muscle fiber of small intestine cell smooth muscle cell of small intestine true A smooth muscle cell that is part of the small intestine. GOC:tfm non-striated muscle fiber of small intestine FMA:15050 A smooth muscle cell that is part of the duodenum. FMA:15058 non-striated muscle fiber of duodenum cell smooth muscle fiber of duodenum true A smooth muscle cell that is part of the duodenum. GOC:tfm non-striated muscle fiber of duodenum FMA:15058 A smooth muscle cell that is part of the jejunum. FMA:15062 non-striated muscle fiber of jejunum cell smooth muscle fiber of jejunum true A smooth muscle cell that is part of the jejunum. GOC:tfm non-striated muscle fiber of jejunum FMA:15062 A smooth muscle cell that is part of the ileum. FMA:15066 non-striated muscle fiber of ileum cell smooth muscle fiber of ileum true A smooth muscle cell that is part of the ileum. GOC:tfm non-striated muscle fiber of ileum FMA:15066 A smooth muscle cell that is part of the large intestine. FMA:15653 non-striated muscle fiber of large intestine cell smooth muscle cell of large intestine true A smooth muscle cell that is part of the large intestine. GOC:tfm non-striated muscle fiber of large intestine FMA:15653 A smooth muscle cell that is part of the colon. FMA:15663 non-striated muscle fiber of colon cell smooth muscle cell of colon A smooth muscle cell that is part of the colon. GOC:tfm non-striated muscle fiber of colon FMA:15663 A smooth muscle cell that is part of the cecum. FMA:15681 non-striated muscle fiber of cecum smooth muscle fiber of cecum cell smooth muscle cell of cecum A smooth muscle cell that is part of the cecum. GOC:tfm non-striated muscle fiber of cecum FMA:15681 A smooth muscle cell that is part of the ascending colon. FMA:17518 non-striated muscle fiber of ascending colon cell smooth muscle fiber of ascending colon true A smooth muscle cell that is part of the ascending colon. GOC:tfm non-striated muscle fiber of ascending colon FMA:17518 A smooth muscle cell that is part of the transverse colon. FMA:17519 non-striated muscle fiber of transverse colon cell smooth muscle fiber of transverse colon true A smooth muscle cell that is part of the transverse colon. GOC:tfm non-striated muscle fiber of transverse colon FMA:17519 A smooth muscle cell that is part of the descending colon. FMA:17520 non-striated muscle fiber of descending colon cell smooth muscle fiber of descending colon true A smooth muscle cell that is part of the descending colon. GOC:tfm non-striated muscle fiber of descending colon FMA:17520 A smooth muscle cell that is part of the sigmoid colon. FMA:17521 non-striated muscle fiber of sigmoid colon cell smooth muscle cell of sigmoid colon true A smooth muscle cell that is part of the sigmoid colon. GOC:tfm non-striated muscle fiber of sigmoid colon FMA:17521 A smooth muscle cell that is part of the rectum. FMA:17522 non-striated muscle fiber of rectum smooth muscle fiber of rectum cell smooth muscle cell of rectum A smooth muscle cell that is part of the rectum. GOC:tfm non-striated muscle fiber of rectum FMA:17522 A muscle cell that is part of the anterior internodal tract. FMA:223276 cell myocyte of anterior internodal tract A muscle cell that is part of the anterior internodal tract. GOC:tfm A muscle cell that is part of the atrial branch of anterior internodal tract. FMA:223277 cell myocyte of atrial branch of anterior internodal tract A muscle cell that is part of the atrial branch of anterior internodal tract. GOC:tfm A muscle cell that is part of the atrial septal branch of anterior internodal tract. FMA:223278 cell myocyte of atrial septal branch of anterior internodal tract A muscle cell that is part of the atrial septal branch of anterior internodal tract. GOC:tfm A muscle cell that is part of the middle internodal tract. FMA:223279 cell myocyte of middle internodal tract A muscle cell that is part of the middle internodal tract. GOC:tfm A muscle cell that is part of the posterior internodal tract. FMA:223280 cell myocyte of posterior internodal tract A muscle cell that is part of the posterior internodal tract. GOC:tfm 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 A fibroblast that is part of the connective tissue of prostate. FMA:261271 cell fibroblast of connective tissue of prostate A fibroblast that is part of the connective tissue of prostate. GOC:tfm A fibroblast that is part of the outer membrane of prostatic capsule. FMA:261273 cell fibroblast of outer membrane of prostatic capsule A fibroblast that is part of the outer membrane of prostatic capsule. GOC:tfm A fibroblast that is part of the subepithelial connective tissue of prostatic gland. FMA:261275 cell fibroblast of subepithelial connective tissue of prostatic gland A fibroblast that is part of the subepithelial connective tissue of prostatic gland. GOC:tfm A fibroblast that is part of the papillary layer of dermis. FMA:261277 cell fibroblast of papillary layer of dermis true A fibroblast that is part of the papillary layer of dermis. GOC:tfm A fibroblast that is part of the areolar connective tissue. FMA:261279 cell fibroblast of areolar connective tissue true A fibroblast that is part of the areolar connective tissue. GOC:tfm A fibroblast that is part of the connective tissue of nonglandular part of prostate. FMA:261281 cell fibroblast of connective tissue of nonglandular part of prostate A fibroblast that is part of the connective tissue of nonglandular part of prostate. GOC:tfm A fibroblast that is part of the connective tissue of glandular part of prostate. FMA:261283 cell fibroblast of connective tissue of glandular part of prostate A fibroblast that is part of the connective tissue of glandular part of prostate. GOC:tfm A fibroblast that is part of the tunica adventitia of artery. FMA:261285 cell fibroblast of tunica adventitia of artery true A fibroblast that is part of the tunica adventitia of artery. GOC:tfm A fibroblast that is part of the dense regular elastic tissue. FMA:261287 cell fibroblast of dense regular elastic tissue A fibroblast that is part of the dense regular elastic tissue. GOC:tfm A fibrocyte that is part of the adventitia of ureter. FMA:261289 cell fibrocyte of adventitia of ureter true A fibrocyte that is part of the adventitia of ureter. GOC:tfm A fat cell that is part of the epicardial fat. FMA:261293 adipocyte of epicardial fat epicardial fat cell cell epicardial adipocyte A fat cell that is part of the epicardial fat. GOC:tfm adipocyte of epicardial fat FMA:261293 epicardial fat cell FMA:261293 A fat cell that is part of the epicardial fat of right ventricle. FMA:261297 epicardial adipocyte of right ventricle epicardial fat cell of right ventricle cell adipocyte of epicardial fat of right ventricle A fat cell that is part of the epicardial fat of right ventricle. GOC:tfm epicardial adipocyte of right ventricle FMA:261297 epicardial fat cell of right ventricle FMA:261297 A fat cell that is part of the epicardial fat of left ventricle. FMA:261300 epicardial adipocyte of left ventricle epicardial fat cell of left ventricle cell adipocyte of epicardial fat of left ventricle A fat cell that is part of the epicardial fat of left ventricle. GOC:tfm epicardial adipocyte of left ventricle FMA:261300 epicardial fat cell of left ventricle FMA:261300 A goblet cell that is part of the epithelium of bronchus. FMA:263032 goblet cell of epithelium of bronchus cell bronchial goblet cell A goblet cell that is part of the epithelium of bronchus. GOC:tfm goblet cell of epithelium of bronchus FMA:263032 A goblet cell that is part of the epithelium of stomach. FMA:263035 goblet cell of epithelium of stomach cell gastric goblet cell A goblet cell that is part of the epithelium of stomach. GOC:tfm goblet cell of epithelium of stomach FMA:263035 A goblet cell that is part of the epithelium of gastric cardiac gland. FMA:263038 goblet cell of epithelium of gastric cardiac gland cell gastric cardiac gland goblet cell A goblet cell that is part of the epithelium of gastric cardiac gland. GOC:tfm A goblet cell that is part of the epithelium of principal gastric gland. FMA:263040 goblet cell of epithelium of principal gastric gland cell principal gastric gland goblet cell A goblet cell that is part of the epithelium of principal gastric gland. GOC:tfm OBSOLETE: A goblet cell that is part of the epithelium of small intestine. CL:1000495 FMA:263042 cell obsolete goblet cell of epithelium of small intestine true OBSOLETE: A goblet cell that is part of the epithelium of small intestine. GOC:tfm A goblet cell that is part of the epithelium of intestinal villus. FMA:263046 goblet cell of epithelium of intestinal villus cell intestinal villus goblet cell A goblet cell that is part of the epithelium of intestinal villus. GOC:tfm A goblet cell that is part of the epithelium of crypt of lieberkuhn of small intestine. FMA:263050 cell obsolete small intestine crypt goblet cell true A goblet cell that is part of the epithelium of crypt of lieberkuhn of small intestine. GOC:tfm OBSOLETE: A goblet cell that is part of the epithelium proper of small intestine. FMA:263052 cell obsolete goblet cell of epithelium proper of small intestine true OBSOLETE: A goblet cell that is part of the epithelium proper of small intestine. GOC:tfm A goblet cell that is part of the epithelium of large intestine. FMA:263054 goblet cell of epithelium of large intestine cell large intestine goblet cell A goblet cell that is part of the epithelium of large intestine. GOC:tfm A goblet cell that is part of the epithelium of crypt of lieberkuhn of large intestine. FMA:263056 cell large intestine crypt goblet cell A goblet cell that is part of the epithelium of crypt of lieberkuhn of large intestine. GOC:tfm A goblet cell that is part of the epithelium of pancreatic duct. FMA:263058 goblet cell of epithelium of pancreatic duct cell pancreatic goblet cell A goblet cell that is part of the epithelium of pancreatic duct. GOC:tfm goblet cell of epithelium of pancreatic duct FMA:263058 A goblet cell that is part of the epithelium of pyloric gland. FMA:263061 goblet cell of epithelium of pyloric gland cell pyloric gastric gland goblet cell A goblet cell that is part of the epithelium of pyloric gland. GOC:tfm A goblet cell that is part of the epithelium proper of duodenum. FMA:263063 goblet cell of epithelium proper of duodenum cell duodenal goblet cell A goblet cell that is part of the epithelium proper of duodenum. GOC:tfm A goblet cell that is part of the epithelium proper of jejunum. FMA:263065 goblet cell of epithelium proper of jejunum cell jejunal goblet cell A goblet cell that is part of the epithelium proper of jejunum. GOC:tfm A goblet cell that is part of the epithelium proper of ileum. FMA:263067 goblet cell of epithelium proper of ileum cell ileal goblet cell A goblet cell that is part of the epithelium proper of ileum. GOC:tfm A goblet cell that is part of the epithelium proper of appendix. FMA:263069 goblet cell of epithelium proper of appendix cell appendix goblet cell A goblet cell that is part of the epithelium proper of appendix. GOC:tfm OBSOLETE: A goblet cell that is part of the epithelium proper of large intestine. FMA:263071 cell obsolete goblet cell of epithelium proper of large intestine true OBSOLETE: A goblet cell that is part of the epithelium proper of large intestine. GOC:tfm A goblet cell that is part of the epithelium of trachea. FMA:263075 goblet cell of epithelium of trachea cell tracheal goblet cell A goblet cell that is part of the epithelium of trachea. GOC:tfm goblet cell of epithelium of trachea FMA:263075 A serous secreting cell that is part of the epithelium of trachea. FMA:263078 cell serous cell of epithelium of trachea A serous secreting cell that is part of the epithelium of trachea. GOC:tfm A serous secreting cell that is part of the epithelium of bronchus. FMA:263080 cell serous cell of epithelium of bronchus A serous secreting cell that is part of the epithelium of bronchus. GOC:tfm A serous secreting cell that is part of the epithelium of terminal bronchiole. FMA:263082 cell serous cell of epithelium of terminal bronchiole A serous secreting cell that is part of the epithelium of terminal bronchiole. GOC:tfm A serous secreting cell that is part of the epithelium of bronchiole. FMA:263084 cell serous cell of epithelium of lobular bronchiole A serous secreting cell that is part of the epithelium of bronchiole. GOC:tfm An enterocyte that is part of the epithelium of small intestine. FMA:263086 cell enterocyte of epithelium of small intestine true An enterocyte that is part of the epithelium of small intestine. GOC:tfm An enterocyte that is part of the epithelium of intestinal villus. FMA:263088 cell enterocyte of epithelium of intestinal villus An enterocyte that is part of the epithelium of intestinal villus. GOC:tfm An enterocyte that is part of the epithelium of duodenal gland. FMA:263092 cell enterocyte of epithelium of duodenal gland An enterocyte that is part of the epithelium of duodenal gland. GOC:tfm An enterocyte that is part of the epithelium of crypt of lieberkuhn of small intestine. FMA:263094 cell enterocyte of epithelium of crypt of Lieberkuhn of small intestine An enterocyte that is part of the epithelium of crypt of lieberkuhn of small intestine. GOC:tfm An enterocyte that is part of the epithelium proper of small intestine. FMA:263096 cell enterocyte of epithelium proper of small intestine An enterocyte that is part of the epithelium proper of small intestine. GOC:tfm An enterocyte that is part of the epithelium proper of duodenum. FMA:263098 cell enterocyte of epithelium proper of duodenum An enterocyte that is part of the epithelium proper of duodenum. GOC:tfm An enterocyte that is part of the epithelium proper of jejunum. FMA:263100 cell enterocyte of epithelium proper of jejunum An enterocyte that is part of the epithelium proper of jejunum. GOC:tfm An enterocyte that is part of the epithelium proper of ileum. FMA:263102 cell enterocyte of epithelium proper of ileum An enterocyte that is part of the epithelium proper of ileum. GOC:tfm A paneth cell that is part of the epithelium of small intestine. FMA:263104 cell paneth cell of epithelium of small intestine true A paneth cell that is part of the epithelium of small intestine. GOC:tfm A Paneth cell that is part of the epithelium proper of small intestine. FMA:263106 cell paneth cell of epithelium proper of small intestine A Paneth cell that is part of the epithelium proper of small intestine. GOC:tfm A Paneth cell that is part of the epithelium of crypt of lieberkuhn of small intestine. FMA:263108 cell paneth cell of epithelium of crypt of Lieberkuhn of small intestine A Paneth cell that is part of the epithelium of crypt of lieberkuhn of small intestine. GOC:tfm MERGED DEFINITION: TARGET DEFINITION: A columnar cell of the colon that is part of the epithelium proper of large intestine. SOURCE DEFINITION: An enterocyte that is part of the epithelium proper of large intestine. CL:1000336 FMA:263090 FMA:263112 enterocyte of epithelium proper of large intestine cell vacuolar absorptive cell of epithelium proper of large intestine MERGED DEFINITION: TARGET DEFINITION: A columnar cell of the colon that is part of the epithelium proper of large intestine. SOURCE DEFINITION: An enterocyte that is part of the epithelium proper of large intestine. GOC:tfm A columnar cell of the colon that is part of the colonic epithelium. FMA:263114 cell vacuolar absorptive cell of epithelium of colon true A columnar cell of the colon that is part of the colonic epithelium. GOC:tfm A basal cell that is part of the epithelium of trachea. FMA:263118 cell basal cell of epithelium of trachea true A basal cell that is part of the epithelium of trachea. GOC:tfm A basal cell found in the bronchus epithelium. CL:0002331 FMA:263120 basal cell of bronchus cell basal cell of epithelium of bronchus A basal cell found in the bronchus epithelium. GOC:tfm A basal cell that is part of the epithelium of terminal bronchiole. FMA:263122 cell basal cell of epithelium of terminal bronchiole A basal cell that is part of the epithelium of terminal bronchiole. GOC:tfm A basal cell that is part of the epithelium of respiratory bronchiole. FMA:263124 cell basal cell of epithelium of respiratory bronchiole A basal cell that is part of the epithelium of respiratory bronchiole. GOC:tfm A basal cell that is part of the epithelium of bronchiole. FMA:263126 cell basal cell of epithelium of lobular bronchiole A basal cell that is part of the epithelium of bronchiole. GOC:tfm A M cell that is part of the epithelium of small intestine. FMA:263128 cell microfold cell of epithelium of small intestine true A M cell that is part of the epithelium of small intestine. GOC:tfm A M cell that is part of the epithelium of intestinal villus. FMA:263130 cell microfold cell of epithelium of intestinal villus A M cell that is part of the epithelium of intestinal villus. GOC:tfm A M cell that is part of the epithelium proper of small intestine. FMA:263132 cell microfold cell of epithelium proper of small intestine A M cell that is part of the epithelium proper of small intestine. GOC:tfm A M cell that is part of the epithelium proper of duodenum. FMA:263134 cell microfold cell of epithelium proper of duodenum A M cell that is part of the epithelium proper of duodenum. GOC:tfm A M cell that is part of the epithelium proper of jejunum. FMA:263136 cell microfold cell of epithelium proper of jejunum A M cell that is part of the epithelium proper of jejunum. GOC:tfm A M cell that is part of the epithelium proper of ileum. FMA:263138 cell microfold cell of epithelium proper of ileum A M cell that is part of the epithelium proper of ileum. GOC:tfm A M cell that is part of the epithelium proper of appendix. FMA:263140 cell microfold cell of epithelium proper of appendix A M cell that is part of the epithelium proper of appendix. GOC:tfm A M cell that is part of the epithelium proper of large intestine. FMA:263142 cell microfold cell of epithelium proper of large intestine A M cell that is part of the epithelium proper of large intestine. GOC:tfm A transitional myocyte that is part of the interatrial septum. FMA:263152 cell transitional myocyte of interatrial septum true A transitional myocyte that is part of the interatrial septum. GOC:tfm A transitional myocyte that is part of the interventricular septum. FMA:263154 cell transitional myocyte of interventricular septum true A transitional myocyte that is part of the interventricular septum. GOC:tfm A transitional myocyte that is part of the atrial branch of anterior internodal tract. FMA:263156 cell transitional myocyte of atrial branch of anterior internodal tract A transitional myocyte that is part of the atrial branch of anterior internodal tract. GOC:tfm A transitional myocyte that is part of the anterior internodal tract. FMA:263158 cell transitional myocyte of anterior internodal tract A transitional myocyte that is part of the anterior internodal tract. GOC:tfm A transitional myocyte that is part of the atrial septal branch of anterior internodal tract. FMA:263160 cell transitional myocyte of atrial septal branch of anterior internodal tract A transitional myocyte that is part of the atrial septal branch of anterior internodal tract. GOC:tfm A transitional myocyte that is part of the middle internodal tract. FMA:263162 cell transitional myocyte of middle internodal tract A transitional myocyte that is part of the middle internodal tract. GOC:tfm A transitional myocyte that is part of the posterior internodal tract. FMA:263164 cell transitional myocyte of posterior internodal tract A transitional myocyte that is part of the posterior internodal tract. GOC:tfm A transitional myocyte that is part of the anterior division of left branch of atrioventricular bundle. FMA:263166 cell transitional myocyte of anterior division of left branch of atrioventricular bundle A transitional myocyte that is part of the anterior division of left branch of atrioventricular bundle. GOC:tfm A transitional myocyte that is part of the septal division of left branch of atrioventricular bundle. FMA:263168 cell transitional myocyte of septal division of left branch of atrioventricular bundle A transitional myocyte that is part of the septal division of left branch of atrioventricular bundle. GOC:tfm A transitional myocyte that is part of the left branch of atrioventricular bundle. FMA:263170 cell transitional myocyte of left branch of atrioventricular bundle A transitional myocyte that is part of the left branch of atrioventricular bundle. GOC:tfm A transitional myocyte that is part of the right branch of atrioventricular bundle. FMA:263172 cell transitional myocyte of right branch of atrioventricular bundle A transitional myocyte that is part of the right branch of atrioventricular bundle. GOC:tfm A transitional myocyte that is part of the atrial part of atrioventricular bundle. FMA:263174 cell transitional myocyte of atrial part of atrioventricular bundle A transitional myocyte that is part of the atrial part of atrioventricular bundle. GOC:tfm A transitional myocyte that is part of the ventricular part of atrioventricular bundle. FMA:263176 cell transitional myocyte of ventricular part of atrioventricular bundle A transitional myocyte that is part of the ventricular part of atrioventricular bundle. GOC:tfm A transitional myocyte that is part of the posterior division of left branch of atrioventricular bundle. FMA:263178 cell transitional myocyte of posterior division of left branch of atrioventricular bundle A transitional myocyte that is part of the posterior division of left branch of atrioventricular bundle. GOC:tfm A myocardial endocrine cell that is part of the septal division of left branch of atrioventricular bundle. FMA:263180 cell myocardial endocrine cell of septal division of left branch of atrioventricular bundle A myocardial endocrine cell that is part of the septal division of left branch of atrioventricular bundle. GOC:tfm A Purkinje myocyte that is part of the interventricular septum. FMA:263182 cell Purkinje myocyte of interventricular septum true A Purkinje myocyte that is part of the interventricular septum. GOC:tfm A Feyrter cell that is part of the epithelium of trachea. FMA:263184 cell dense-core granulated cell of epithelium of trachea true true A Feyrter cell that is part of the epithelium of trachea. GOC:tfm A type I vestibular sensory cell that is part of the stato-acoustic epithelium. FMA:263186 cell type 1 vestibular sensory cell of stato-acoustic epithelium A type I vestibular sensory cell that is part of the stato-acoustic epithelium. GOC:tfm A type I vestibular sensory cell that is part of the epithelium of macula of utricle of membranous labyrinth. FMA:263188 cell type 1 vestibular sensory cell of epithelium of macula of utricle of membranous labyrinth A type I vestibular sensory cell that is part of the epithelium of macula of utricle of membranous labyrinth. GOC:tfm A type I vestibular sensory cell that is part of the epithelium of macula of saccule of membranous labyrinth. FMA:263190 cell type 1 vestibular sensory cell of epithelium of macula of saccule of membranous labyrinth A type I vestibular sensory cell that is part of the epithelium of macula of saccule of membranous labyrinth. GOC:tfm A type I vestibular sensory cell that is part of the epithelium of crista of ampulla of semicircular duct of membranous labyrinth. FMA:263192 cell type 1 vestibular sensory cell of epithelium of crista of ampulla of semicircular duct of membranous labyrinth A type I vestibular sensory cell that is part of the epithelium of crista of ampulla of semicircular duct of membranous labyrinth. GOC:tfm A type II vestibular sensory cell that is part of the stato-acoustic epithelium. FMA:263194 cell type 2 vestibular sensory cell of stato-acoustic epithelium A type II vestibular sensory cell that is part of the stato-acoustic epithelium. GOC:tfm A type II vestibular sensory cell that is part of the epithelium of macula of utricle of membranous labyrinth. FMA:263196 cell type 2 vestibular sensory cell of epithelium of macula of utricle of membranous labyrinth A type II vestibular sensory cell that is part of the epithelium of macula of utricle of membranous labyrinth. GOC:tfm A type II vestibular sensory cell that is part of the epithelium of macula of saccule of membranous labyrinth. FMA:263198 cell type 2 vestibular sensory cell of epithelium of macula of saccule of membranous labyrinth A type II vestibular sensory cell that is part of the epithelium of macula of saccule of membranous labyrinth. GOC:tfm A type II vestibular sensory cell that is part of the epithelium of crista of ampulla of semicircular duct of membranous labyrinth. FMA:263200 cell type 2 vestibular sensory cell of epithelium of crista of ampulla of semicircular duct of membranous labyrinth A type II vestibular sensory cell that is part of the epithelium of crista of ampulla of semicircular duct of membranous labyrinth. GOC:tfm A melanocyte that is part of the eyelid. FMA:59175 eyelid melanocyte sebaceous gland of wolff cell melanocyte of eyelid true A melanocyte that is part of the eyelid. GOC:tfm eyelid melanocyte FMA:59175 sebaceous gland of wolff FMA:59175 A myoepithelial cell that is part of the intralobular part of terminal lactiferous duct. FMA:62158 cell myoepithelial cell of intralobular lactiferous duct A myoepithelial cell that is part of the intralobular part of terminal lactiferous duct. GOC:tfm An endothelial cell that is part of the venous sinus of red pulp of spleen. FMA:62817 cell todo - add logical definition to UBERON:0009967 endothelial cell of venous sinus of red pulp of spleen An endothelial cell that is part of the venous sinus of red pulp of spleen. GOC:tfm An endothelial cell that is part of the hepatic sinusoid. These cells possess flattened areas containing perforations about 0.1 micrometers in diameter, known as fenestrae. The fenestrae are arranged in groups known as sieve plates. BTO:000125 FMA:62911 LSEC endotheliocyte of hepatic sinusoid liver sinusoidal endothelial cell cell endothelial cell of hepatic sinusoid An endothelial cell that is part of the hepatic sinusoid. These cells possess flattened areas containing perforations about 0.1 micrometers in diameter, known as fenestrae. The fenestrae are arranged in groups known as sieve plates. GOC:tfm PMID:3926620 LSEC PMID:30348985 endotheliocyte of hepatic sinusoid FMA:62911 liver sinusoidal endothelial cell PMID:30348985 An epithelial cell that is part of the appendix. FMA:63602 columnar epitheliocyte of appendix epithelial cell of vermiform appendix cell epithelial cell of appendix An epithelial cell that is part of the appendix. GOC:tfm columnar epitheliocyte of appendix FMA:63602 epithelial cell of vermiform appendix FMA:63602 A muscle cell that is part of the sinoatrial node. FMA:67102 SA nodal myocyte SA node cardiac muscle cell myocyte of sinoatrial node sinoatrial node cell sinoatrial node myocyte sinuatrial node myocyte cell myocyte of sinoatrial node A muscle cell that is part of the sinoatrial node. FMA:67102 GOC:tfm SA nodal myocyte FMA:67102 SA node cardiac muscle cell GOC:pr myocyte of sinoatrial node FMA:67102 sinoatrial node cell GOC:pr sinuatrial node myocyte FMA:67102 A muscle cell that is part of the atrioventricular node. FMA:67106 AV nodal myocyte AV node cardiac muscle cell AV node cell atrioventricular node cell atrioventricular node myocyte cell myocyte of atrioventricular node A muscle cell that is part of the atrioventricular node. FMA:67106 GOC:tfm AV nodal myocyte FMA:67106 AV node cardiac muscle cell GOC:pr AV node cell GOC:pr atrioventricular node cell GOC:pr atrioventricular node myocyte FMA:67106 An endothelial cell that is part of the small intestine Peyer's patch. FMA:67757 cell endothelial cell of Peyer's patch true An endothelial cell that is part of the small intestine Peyer's patch. GOC:tfm 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 A myoepithelial cell that is part of the mammary gland. CALOHA:TS-2378 FMA:67800 basal cell of lactiferous duct cell myoepithelial cell of lactiferous gland true A myoepithelial cell that is part of the mammary gland. GOC:tfm basal cell of lactiferous duct FMA:67800 A myoepithelial cell that is part of the sweat gland. FMA:67801 cell myoepithelial cell of sweat gland true A myoepithelial cell that is part of the sweat gland. GOC:tfm A myoepithelial cell that is part of the mammary gland alveolus. FMA:67802 basal cell of alveolus of lactiferous gland myoepithelial cell of mammary alveolus cell myoepithelial cell of lactiferous alveolus A myoepithelial cell that is part of the mammary gland alveolus. GOC:tfm basal cell of alveolus of lactiferous gland FMA:67802 myoepithelial cell of mammary alveolus FMA:67802 A myoepithelial cell that is part of the lactiferous duct. FMA:67803 cell myoepithelial cell of lactiferous duct A myoepithelial cell that is part of the lactiferous duct. GOC:tfm A myoepithelial cell that is part of the terminal lactiferous duct. FMA:67804 cell myoepithelial cell of terminal lactiferous duct A myoepithelial cell that is part of the terminal lactiferous duct. GOC:tfm A chromaffin cell that is part of the paraaortic body. FMA:69328 chromaffin cell of para-aortic body cell chromaffin cell of paraaortic body A chromaffin cell that is part of the paraaortic body. GOC:tfm chromaffin cell of para-aortic body FMA:69328 A chromaffin cell that is part of the paraganglion. FMA:69335 cell chromaffin cell of paraganglion true A chromaffin cell that is part of the paraganglion. GOC:tfm A chromaffin cell that is part of the adrenal gland. FMA:69794 adrenal chromaffin cell cell chromaffin cell of adrenal gland true A chromaffin cell that is part of the adrenal gland. GOC:tfm adrenal chromaffin cell GO:0061104 A chromaffin cell that is part of the adrenal cortex. FMA:69795 chromaffin cell of adrenal cortex cell Not clear this cell type exists. Can't call it a cortical adrenal cell because of different germ layer origin. adrenal cortex chromaffin cell A chromaffin cell that is part of the adrenal cortex. GOC:tfm A somatic stem cell that is part of the epidermis. FMA:70541 epidermal stem cell cell stem cell of epidermis true A somatic stem cell that is part of the epidermis. GOC:tfm epidermal stem cell FMA:70541 An epithelial cell that is part of the conjunctiva. FMA:70552 epithelial cell of conjunctiva cell conjunctival epithelial cell true An epithelial cell that is part of the conjunctiva. GOC:tfm epithelial cell of conjunctiva FMA:70552 An epithelial cell that is part of the lacrimal canaliculus. FMA:70553 cell epithelial cell of lacrimal canaliculus true An epithelial cell that is part of the lacrimal canaliculus. 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 duct. FMA:70559 cell epithelial cell of lacrimal duct true An epithelial cell that is part of the lacrimal duct. 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 An epithelial cell that is part of the nasolacrimal duct. FMA:70561 cell epithelial cell of nasolacrimal duct An epithelial cell that is part of the nasolacrimal duct. GOC:tfm An epithelial cell that is part of the wall of inferior part of anal canal. FMA:70562 cell epithelial cell of wall of inferior part of anal canal An epithelial cell that is part of the wall of inferior part of anal canal. GOC:tfm An epithelial cell that is part of the viscerocranial mucosa. FMA:70583 cell epithelial cell of viscerocranial mucosa An epithelial cell that is part of the viscerocranial mucosa. GOC:tfm An urothelial cell that is part of the trigone of urinary bladder. FMA:70598 epithelial cell of vesical trigone cell urothelial cell of trigone of urinary bladder true An urothelial cell that is part of the trigone of urinary bladder. GOC:tfm epithelial cell of vesical trigone FMA:70598 A smooth muscle cell that is part of the ciliary body. FMA:70610 smooth muscle cell of ciliary body cell ciliary muscle cell true A smooth muscle cell that is part of the ciliary body. GOC:tfm smooth muscle cell of ciliary body FMA:70610 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 A myoepithelial cell that is part of the dilatator pupillae. FMA:70619 cell myoepithelial cell of dilator pupillae true A myoepithelial cell that is part of the dilatator pupillae. GOC:tfm A basal cell that is part of the epithelium of esophagus. FMA:70731 basal cell of esophageal epithelium cell epithelial cell of stratum germinativum of esophagus true A basal cell that is part of the epithelium of esophagus. GOC:tfm basal cell of esophageal epithelium FMA:70731 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 An epithelial cell that is part of the glomerular capsule. FMA:70966 KUPO:0001034 Bowmans capsule epithelial cell epithelial cell of Bowman's capsule cell epithelial cell of glomerular capsule An epithelial cell that is part of the glomerular capsule. GOC:tfm epithelial cell of Bowman's capsule FMA:70966 CL:0000653 obsolete epithelial cell of visceral layer of glomerular capsule true An epithelial cell that is part of the glomerular parietal epithelium. CL:1000897 FMA:70968 KUPO:0001035 epithelial cell of parietal layer of glomerular capsule cell parietal epithelial cell An epithelial cell that is part of the glomerular parietal epithelium. GOC:tfm epithelial cell of parietal layer of glomerular capsule FMA:70968 An epithelial cell that is part of the intermediate tubule. FMA:70980 cell epithelial cell of intermediate tubule An epithelial cell that is part of the intermediate tubule. GOC:tfm An epithelial cell that is part of the collecting duct of renal tubule. FMA:70982 KUPO:0001059 epithelial cell of renal collecting tubule cell kidney collecting duct epithelial cell true true An epithelial cell that is part of the collecting duct of renal tubule. GOC:tfm epithelial cell of renal collecting tubule FMA:70982 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 melanocyte that is part of the skin of body. CALOHA:TS-2374 FMA:72144 skin melanocyte cell melanocyte of skin true A melanocyte that is part of the skin of body. GOC:tfm skin melanocyte FMA:72144 A chromaffin cell that is part of the ovary. FMA:74319 cell chromaffin cell of ovary true A chromaffin cell that is part of the ovary. GOC:tfm A chromaffin cell that is part of the right ovary. FMA:74320 cell chromaffin cell of right ovary A chromaffin cell that is part of the right ovary. GOC:tfm A chromaffin cell that is part of the left ovary. FMA:74321 cell chromaffin cell of left ovary A chromaffin cell that is part of the left ovary. GOC:tfm A myoepithelial cell that is part of the acinus of lactiferous gland. FMA:74469 basal cell of acinus of lactiferous gland cell myoepithelial cell of acinus of lactiferous gland A myoepithelial cell that is part of the acinus of lactiferous gland. GOC:tfm basal cell of acinus of lactiferous gland FMA:74469 A myoepithelial cell that is part of the main lactiferous duct. FMA:74499 cell myoepithelial cell of main lactiferous duct A myoepithelial cell that is part of the main lactiferous duct. GOC:tfm A myoepithelial cell that is part of the primary lactiferous duct. FMA:74500 cell myoepithelial cell of primary lactiferous duct A myoepithelial cell that is part of the primary lactiferous duct. GOC:tfm A myoepithelial cell that is part of the secondary lactiferous duct. FMA:74501 cell myoepithelial cell of secondary lactiferous duct A myoepithelial cell that is part of the secondary lactiferous duct. GOC:tfm A myoepithelial cell that is part of the tertiary lactiferous duct. FMA:74502 cell myoepithelial cell of tertiary lactiferous duct A myoepithelial cell that is part of the tertiary lactiferous duct. GOC:tfm A myoepithelial cell that is part of the quarternary lactiferous duct. FMA:74503 cell myoepithelial cell of quarternary lactiferous duct A myoepithelial cell that is part of the quarternary lactiferous duct. GOC:tfm A nodal myocyte that is part of the sinoatrial node. FMA:83383 cardiac pacemaker cell of sinuatrial node pacemaker cell of sinoatrial node pacemaker cell of sinuatrial node cell cardiac pacemaker cell of sinoatrial node A nodal myocyte that is part of the sinoatrial node. GOC:tfm A transitional myocyte that is part of the sinoatrial node. FMA:83384 transitinal myocyte of sinuatrial node cell transitional myocyte of sinoatrial node true A transitional myocyte that is part of the sinoatrial node. GOC:tfm A Purkinje myocyte that is part of the atrioventricular node. FMA:83386 cell Purkinje myocyte of atrioventricular node true A Purkinje myocyte that is part of the atrioventricular node. GOC:tfm A transitional myocyte that is part of the internodal tract. FMA:83387 cell transitional myocyte of internodal tract true A transitional myocyte that is part of the internodal tract. GOC:tfm A transitional myocyte that is part of the atrioventricular bundle. FMA:83388 FMA:83885 cell transitional myocyte of atrioventricular bundle true A transitional myocyte that is part of the atrioventricular bundle. GOC:tfm A myocardial endocrine cell that is part of the interventricular septum. FMA:83390 cell myocardial endocrine cell of interventricular septum true A myocardial endocrine cell that is part of the interventricular septum. GOC:tfm A Purkinje myocyte that is part of the internodal tract. FMA:83392 cell Purkinje myocyte of internodal tract true A Purkinje myocyte that is part of the internodal tract. GOC:tfm A Purkinje myocyte that is part of the atrioventricular bundle. FMA:83393 cell Purkinje myocyte of atrioventricular bundle true A Purkinje myocyte that is part of the atrioventricular bundle. GOC:tfm A basal cell that is part of the urothelium. FMA:84150 cell basal cell of urothelium true A basal cell that is part of the urothelium. GOC:tfm A smooth muscle cell that is part of the prostate gland. FMA:84583 smooth muscle fiber of prostate cell smooth muscle cell of prostate true A smooth muscle cell that is part of the prostate gland. GOC:tfm smooth muscle fiber of prostate FMA:84583 An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts. FMA:86481 epithelial cell of bile duct cell cholangiocyte true An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts. GOC:tfm PMID:16550043 PMID:18356246 A reticular cell that is part of the splenic cord. FMA:86497 cell reticular cell of splenic cord true A reticular cell that is part of the splenic cord. 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 A goblet cell that is part of the small intestine. FMA:86929 goblet cell of epithelium of small intestine goblet cell of small intestine small intestinal goblet cell cell small intestine goblet cell A goblet cell that is part of the small intestine. GOC:tfm small intestinal goblet cell FMA:86929 KUPO:0001010 cell kidney cell true KUPO:0001013 cell kidney interstitial cell true KUPO:0001017 cell kidney medulla cell true KUPO:0001018 cell kidney pelvis cell true KUPO:0001020 cell kidney tubule cell KUPO:0001023 cell kidney glomerular epithelial cell KUPO:0001060 cell kidney medulla collecting duct epithelial cell KUPO:0001061 cell kidney inner medulla collecting duct epithelial cell KUPO:0001062 cell kidney outer medulla collecting duct epithelial cell KUPO:0001063 cell kidney cortex collecting duct epithelial cell KUPO:0001064 cell kidney papillary duct principal epithelial cell KUPO:0001111 cell inner renal cortex cell KUPO:0001112 cell papillary tips cell KUPO:0001115 cell lower urinary tract cell true KUPO:0001116 cell ureteral cell true KUPO:0001015 cell kidney nerve cell KUPO:0001021 cell kidney corpuscule cell true KUPO:0001024 cell kidney cortex tubule cell true KUPO:0001025 cell kidney outer medulla cell true KUPO:0001026 cell kidney inner medulla cell true KUPO:0001028 juxtaglomerulus cell cell juxtaglomerular complex cell true juxtaglomerulus cell GO:0072052 KUPO:0001091 cell kidney cortex interstitial cell true KUPO:0001092 cell kidney medulla interstitial cell true true KUPO:0001101 cell kidney interstitial myofibroblast KUPO:0001102 cell kidney interstitial fibroblast KUPO:0001103 cell kidney interstitial fibrocyte KUPO:0001106 cell kidney interstitial alternatively activated macrophage KUPO:0001107 cell kidney interstitial inflammatory macrophage KUPO:0001108 cell kidney interstitial suppressor macrophage KUPO:0001109 cell kidney resident macrophage KUPO:0001110 cell kidney resident dendritic cell KUPO:0001113 cell kidney pelvis smooth muscle cell true true KUPO:0001114 cell kidney pelvis urothelial cell true true KUPO:0001117 cell ureter urothelial cell true true KUPO:0001119 cell ureter adventitial cell true KUPO:0001130 cell kidney cortex collecting duct principal cell true KUPO:0001131 cell kidney cortex collecting duct intercalated cell true KUPO:0001132 cell kidney outer medulla collecting duct principal cell true KUPO:0001133 cell kidney outer medulla collecting duct intercalated cell true KUPO:0001134 cell kidney inner medulla collecting duct principal cell true KUPO:0001135 cell kidney inner medulla collecting duct intercalated cell true KUPO:0001136 cell kidney papillary duct intercalated cell true KUPO:0001137 cell kidney papillary duct principal cell true Intraglomerular mesangial cells are specialized pericytes located among the glomerular capillaries within a renal corpuscle of a kidney. KUPO:0001032 intraglomerular mesangial cell cell glomerular mesangial cell Intraglomerular mesangial cells are specialized pericytes located among the glomerular capillaries within a renal corpuscle of a kidney. Wikipedia:Intraglomerular_mesangial_cell intraglomerular mesangial cell CL:cjm KUPO:0001036 cell glomerular cell true KUPO:0001058 cell kidney connecting tubule epithelial cell true KUPO:0001093 cell kidney inner medulla interstitial cell true true KUPO:0001094 cell kidney outer medulla interstitial cell true true KUPO:0001045 cell kidney proximal convoluted tubule epithelial cell true KUPO:0001046 cell kidney proximal straight tubule epithelial cell true true KUPO:0001056 cell kidney distal convoluted tubule epithelial cell true KUPO:0001057 cell macula densa epithelial cell true 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:0001047 cell kidney loop of Henle epithelial cell true KUPO:0001118 cell ureter smooth muscle cell true true KUPO:0001037 cell glomerular capillary endothelial cell true KUPO:0001038 cell kidney afferent arteriole cell true KUPO:0001041 cell kidney efferent arteriole cell true KUPO:0001048 cell kidney loop of Henle ascending limb epithelial cell true KUPO:0001053 cell kidney loop of Henle descending limb epithelial cell true KUPO:0001065 cell peritubular capillary endothelial cell true KUPO:0001068 cell vasa recta cell true KUPO:0001077 cell kidney cortex artery cell true KUPO:0001084 cell kidney cortex vein cell true KUPO:0001096 cell Note that the source of this term is KUPO:0001096 (artery smooth muscle cell), which we believe actually denotes the kidney specific structure. kidney artery smooth muscle cell KUPO:0001098 cell Note that the source of this term is KUPO:0001098 (arteriole smooth muscle cell), which we believe actually denotes the kidney specific structure. kidney arteriole smooth muscle cell KUPO:0001100 cell Note that the source of this term is KUPO:0001068 (venous system smooth muscle cell), which we believe actually denotes the kidney specific structure. kidney venous system smooth muscle cell KUPO:0001039 cell kidney afferent arteriole endothelial cell true KUPO:0001040 cell kidney afferent arteriole smooth muscle cell KUPO:0001042 cell kidney efferent arteriole endothelial cell true KUPO:0001043 cell kidney efferent arteriole smooth muscle cell KUPO:0001049 cell kidney loop of Henle thick ascending limb epithelial cell true KUPO:0001050 cell kidney loop of Henle thin ascending limb epithelial cell true KUPO:0001051 cell kidney loop of Henle medullary thick ascending limb epithelial cell true KUPO:0001052 cell kidney loop of Henle cortical thick ascending limb epithelial cell KUPO:0001054 cell kidney loop of Henle thin descending limb epithelial cell true KUPO:0001066 cell kidney outer medulla peritubular capillary cell true true KUPO:0001067 cell kidney cortex peritubular capillary cell true KUPO:0001069 cell inner renal medulla vasa recta cell true true KUPO:0001070 cell outer renal medulla vasa recta cell true true KUPO:0001074 cell vasa recta ascending limb cell true KUPO:0001078 cell arcuate artery cell true KUPO:0001081 cell interlobular artery cell true KUPO:0001085 cell arcuate vein cell true KUPO:0001088 cell interlobular vein cell true KUPO:0001075 cell inner medulla vasa recta ascending limb cell true true KUPO:0001076 cell outer medulla vasa recta ascending limb cell true true KUPO:0001079 cell arcuate artery endothelial cell true KUPO:0001080 cell arcuate artery smooth muscle cell KUPO:0001082 cell interlobulary artery endothelial cell KUPO:0001083 cell interlobulary artery smooth muscle cell KUPO:0001086 cell arcuate vein endothelial cell KUPO:0001087 cell arcuate vein smooth muscle cell KUPO:0001089 cell interlobulary vein endothelial cell KUPO:0001090 cell interlobulary vein smooth muscle cell KUPO:0001012 Wikipedia:Kidney_collecting_duct_cell cell kidney collecting duct cell KUPO:0001071 cell vasa recta descending limb cell true KUPO:0001072 cell inner medulla vasa recta descending limb cell true true KUPO:0001073 cell outer medulla vasa recta descending limb cell true true KUPO:0001104 cell renal interstitial pericyte true KUPO:0001120 cell bladder cell KUPO:0001123 cell urethra cell KUPO:0001121 cell bladder urothelial cell true true KUPO:0001124 cell urethra urothelial cell true KUPO:0001128 cell kidney collecting duct principal cell true KUPO:0001129 http://en.wikipedia.org/wiki/Collecting_duct_system#Intercalated_cells cell kidney collecting duct intercalated cell true 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 A neuron residing in the olfactory bulb that serve to process and refine signals arising from olfactory sensory neurons cl olfactory bulb interneuron A neuron residing in the olfactory bulb that serve to process and refine signals arising from olfactory sensory neurons PMID:18603310 The small neuron in the glomerular layer of the olfactory bulb whose dendrites arborize within a glomerulus, where it receives synaptic input from olfactory receptor cell axon terminals, and also engages in dendrodendritic interactions with mitral and tufted cell dendrites; uses both GABA and dopamine as a neurotransmitter. BTO:0003796 NIFSTD:nifext_122 glomerular layer cell olfactory bulb (accessory) glomerular layer cell olfactory bulb glomerular layer cell olfactory bulb glomerularal cell olfactory bulb periglomerular cell periglomerular cell cl periglomerular cell The small neuron in the glomerular layer of the olfactory bulb whose dendrites arborize within a glomerulus, where it receives synaptic input from olfactory receptor cell axon terminals, and also engages in dendrodendritic interactions with mitral and tufted cell dendrites; uses both GABA and dopamine as a neurotransmitter. MP:0009943 glomerular layer cell NIFSTD:nifext_122 olfactory bulb (accessory) glomerular layer cell NIFSTD:nifext_122 olfactory bulb glomerular layer cell NIFSTD:nifext_122 olfactory bulb glomerularal cell MP:0009943 periglomerular cell NIFSTD:nifext_122 The subcutaneous mechanoreceptors that innervate tylotrich hair follicles. cl hair-tylotrich neuron The subcutaneous mechanoreceptors that innervate tylotrich hair follicles. MP:0000977 The subcutaneous mechanoreceptors that innervate vellus hairs. cl hair-down neuron The subcutaneous mechanoreceptors that innervate vellus hairs. MP:0000979 A sensory neuron of the dorsal root ganglia that senses body position and sends information about how much the muscle is stretched to the spinal cord. proprioceptive neuron cl sensory neuron of dorsal root ganglion true A sensory neuron of the dorsal root ganglia that senses body position and sends information about how much the muscle is stretched to the spinal cord. MP:0004297 proprioceptive neuron MP:0004297 The inhibitory projection neurons located in the striatum that integrate glutamatergic signals arising from the cerebral cortex and thalamus. BTO:0004778 striatal medium spiny neuron cl medium-sized densely spiny neuron medium spiny neuron The inhibitory projection neurons located in the striatum that integrate glutamatergic signals arising from the cerebral cortex and thalamus. MP:0008462 striatal medium spiny neuron GO:0021773 medium-sized densely spiny neuron BTO:0004778 The large glutaminergic nerve cells whose dendrites synapse with axons of the olfactory receptor neurons in the glomerular layer of the olfactory bulb, and whose axons pass centrally in the olfactory tract to the olfactory cortex. cl mitral cell The large glutaminergic nerve cells whose dendrites synapse with axons of the olfactory receptor neurons in the glomerular layer of the olfactory bulb, and whose axons pass centrally in the olfactory tract to the olfactory cortex. MP:0009954 The principal glutaminergic neuron located in the outer third of the external plexiform layer of the olfactory bulb; a single short primary dendrite traverses the outer external plexiform layer and terminates within an olfactory glomerulus in a tuft of branches, where it receives the input from olfactory receptor neuron axon terminals; axons of the tufted cells transfer information to a number of areas in the brain, including the piriform cortex, entorhinal cortex, olfactory tubercle, and amygdala. cl olfactory bulb tufted cell The principal glutaminergic neuron located in the outer third of the external plexiform layer of the olfactory bulb; a single short primary dendrite traverses the outer external plexiform layer and terminates within an olfactory glomerulus in a tuft of branches, where it receives the input from olfactory receptor neuron axon terminals; axons of the tufted cells transfer information to a number of areas in the brain, including the piriform cortex, entorhinal cortex, olfactory tubercle, and amygdala. MP:0009955 The secretory neurons of the paraventricular nucleus that synthesize and secrete vasopressin, corticotropin-releasing factor (CRF) and thyrotropin-releasing hormone (TRH) into blood vessels in the hypothalamo-pituitary portal system. parvocellular neuron parvocellular neurosecretory neuron cl parvocellular neurosecretory cell The secretory neurons of the paraventricular nucleus that synthesize and secrete vasopressin, corticotropin-releasing factor (CRF) and thyrotropin-releasing hormone (TRH) into blood vessels in the hypothalamo-pituitary portal system. MP:0010125 The neurons that utilize glycine as a neurotransmitter. cl glycinergic neuron The neurons that utilize glycine as a neurotransmitter. MP:0010385 The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the intestinal tract. cl intestinal enteroendocrine cell The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the intestinal tract. MP:0010802 The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the stomach. cl stomach enteroendocrine cell The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the stomach. MP:0010803 Chemosensitive cells that innervate the vomernasal organ epithelium and are responsible for receiving and transmitting pheromone signals. cl vomeronasal sensory neuron Chemosensitive cells that innervate the vomernasal organ epithelium and are responsible for receiving and transmitting pheromone signals. MP:0011679 A respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole, which gives rise to alveolar cell types and club cells in response to lung injury. cl bronchioalveolar stem cells A respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole, which gives rise to alveolar cell types and club cells in response to lung injury. MP:0011691 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 An interneuron of the hippocampus. FMA:84777 cl hippocampal interneuron An interneuron of the hippocampus. GOC:pr A pyramidal neuron of the hippocampus. NIFSTD:sao131261273 SAO:sao131261273 hippocampus (CA) pyramidal cell hippocampus (CA) pyramidal neuron cl hippocampal pyramidal neuron A pyramidal neuron of the hippocampus. GOC:pr PMID:19342486 hippocampus (CA) pyramidal cell NIFSTD:sao131261273 hippocampus (CA) pyramidal neuron NIFSTD:sao131261273 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 Glial cell of cerebral cortex. CALOHA:TS-1256 brain cortex glial cell cerebral cortex glial cells cerebrum cortex glial cell cerebral cortex glial cell Glial cell of cerebral cortex. NPX:PDR brain cortex glial cell CALOHA:TS-1256 cerebral cortex glial cells CALOHA:TS-1256 cerebrum cortex glial cell CALOHA:TS-1256 Glial cell of hippocampus. CALOHA:TS-1257 hippocampal glial cell hippocampus glial cells hippocampus neuroglial cell hippocampus glial cell Glial cell of hippocampus. NPX:PDR hippocampal glial cell CALOHA:TS-1257 hippocampus glial cells CALOHA:TS-1257 hippocampus neuroglial cell CALOHA:TS-1257 Glial cell of lateral ventricle. CALOHA:TS-1258 lateral ventricle glial cells lateral ventricle glial cell Glial cell of lateral ventricle. NPX:PDR lateral ventricle glial cells CALOHA:TS-1258 Neuron of lateral ventricle. CALOHA:TS-1261 lateral ventricle neural cell lateral ventricle neuronal cell lateral ventricle neuronal cells lateral ventricle neuron Neuron of lateral ventricle. NPX:PDR lateral ventricle neural cell CALOHA:TS-1261 lateral ventricle neuronal cell CALOHA:TS-1261 lateral ventricle neuronal cells CALOHA:TS-1261 OBSOLETE: Adipocytes found in the subcutaneous adipose tissue of breast. The breast consists of three main components, the skin, the subcutaneous adipose tissue and the functional glandular tissue that comprises both parenchyma and stroma. CL:0002617 breast adipocytes obsolete breast adipocyte true OBSOLETE: Adipocytes found in the subcutaneous adipose tissue of breast. The breast consists of three main components, the skin, the subcutaneous adipose tissue and the functional glandular tissue that comprises both parenchyma and stroma. HPA:Breast breast adipocytes CALOHA:TS-2377 Glandular cell of appendix epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells. CALOHA:TS-1271 appendix glandular cells caecal appendix glandular cell cecal appendix glandular cell vermiform appendix glandular cell appendix glandular cell Glandular cell of appendix epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells. NPX:PDR appendix glandular cells CALOHA:TS-1271 caecal appendix glandular cell CALOHA:TS-1271 cecal appendix glandular cell CALOHA:TS-1271 vermiform appendix glandular cell CALOHA:TS-1271 Glandular cell of mammary epithelium. Example: glandular cells of large and intermediate ducts, glandular cells in terminal ducts. CALOHA:TS-1272 breast glandular cell breast glandular cells mammary glandular cell mammary gland glandular cell Glandular cell of mammary epithelium. Example: glandular cells of large and intermediate ducts, glandular cells in terminal ducts. HPA:HPA NPX:PDR breast glandular cell CALOHA:TS-1272 breast glandular cells CALOHA:TS-1272 mammary glandular cell CALOHA:TS-1272 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 Circulating macrophages and tissue macrophages (alveolar macrophages) of lung. CALOHA:TS-0576 lung macrophages lung macrophage Circulating macrophages and tissue macrophages (alveolar macrophages) of lung. HPA:HPA NPX:PDR lung macrophages CALOHA:TS-0576 Keratinocyte from foreskin. CALOHA:TS-0385 foreskin keratinocyte Keratinocyte from foreskin. NPX:PDR Chondrocyte forming the hyaline cartilage found in joints. CALOHA:TS-0056 articular chondrocyte Chondrocyte forming the hyaline cartilage found in joints. NPX:PDR Fibroblast from foreskin. CALOHA:TS-0384 BJ fibroblast foreskin fibroblast Fibroblast from foreskin. NPX:PDR Fibroblast from muscle organ. CALOHA:TS-0643 muscle fibroblast Fibroblast from muscle organ. NPX:PDR Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes. CALOHA:TS-2109 bone marrow hematopoietic cells bone marrow poietic cells bone marrow hematopoietic cell Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes. NPX:PDR bone marrow hematopoietic cells CALOHA:TS-2109 bone marrow poietic cells CALOHA:TS-2109 Neuron of the cerebellum. CALOHA:TS-2359 FMA:84665 cerebellum neuron cerebellar neuron Neuron of the cerebellum. NPX:PDR cerebellum neuron CALOHA:TS-2359 Any melanocyte that is part of a epidermis. TermGenie 2014-02-03T23:03:09Z cell CL:2000000 These cells are found primarily, but not exclusively, in primates including humans epidermal melanocyte Any melanocyte that is part of a epidermis. GOC:TermGenie A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood. TermGenie 2014-02-11T17:29:04Z cell CL:2000001 peripheral blood mononuclear cell A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood. GOC:TermGenie A specialized, enlarged, connective tissue cell of the decidua with enlarged nucleus, dense membrane‐bound secretory granules and cytoplasmic accumulation of glycogen and lipid droplets. These cells develop by the transformation of endometrial stromal cells during decidualization. 2014-02-20T23:06:41Z BTO:0002770 BTO:0005756 NCIT:C32429 decidua cell decidual stromal cell cell CL:2000002 decidual cell A specialized, enlarged, connective tissue cell of the decidua with enlarged nucleus, dense membrane‐bound secretory granules and cytoplasmic accumulation of glycogen and lipid droplets. These cells develop by the transformation of endometrial stromal cells during decidualization. BTO:0002770 NCIT:C32429 PMID:30013421 PMID:30429548 Wiki:Decidual_cells&oldid=937509751 Wiki:Decidualization&oldid=908981933 decidua cell BTO:0002770 NCIT:C32429 decidual stromal cell BTO:0005756 PMID:11719592 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 macroglial cell that is part of a brain. TermGenie 2014-03-28T21:35:27Z cell CL:2000005 brain macroglial cell Any macroglial cell that is part of a brain. GOC:TermGenie Any germinal center B cell that is part of a tonsil. TermGenie 2014-03-28T21:35:33Z cell CL:2000006 tonsil germinal center B cell Any germinal center B cell that is part of a tonsil. GOC:TermGenie Chondrocyte forming the hyaline cartilage found in the knee joint. TermGenie 2014-06-04T14:40:11Z cell CL:2000007 articular chondrocyte of knee joint Chondrocyte forming the hyaline cartilage found in the knee joint. GOC:TermGenie Any blood vessel endothelial cell that is part of a microvascular endothelium. TermGenie 2014-06-04T15:07:42Z cell CL:2000008 microvascular endothelial cell Any blood vessel endothelial cell that is part of a microvascular endothelium. GOC:TermGenie Any blood vessel endothelial cell that is part of a microvascular endothelium. CL:2000008 TermGenie 2014-06-04T15:09:18Z cell CL:2000009 obsolete microvascular endothelium blood vessel endothelial cell true Any blood vessel endothelial cell that is part of a microvascular endothelium. 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 endothelial cell of lymphatic vessel that is part of a dermis. TermGenie 2014-06-04T15:15:08Z cell CL:2000011 dermis lymphatic vessel endothelial cell Any endothelial cell of lymphatic vessel that is part of a dermis. GOC:TermGenie Any skin fibroblast that is part of a pedal digit skin. TermGenie 2014-06-04T15:16:44Z cell CL:2000012 fibroblast of pedal digit skin Any skin fibroblast that is part of a pedal digit skin. GOC:TermGenie Any skin fibroblast that is part of a skin of abdomen. TermGenie 2014-06-04T15:18:16Z cell CL:2000013 fibroblast of skin of abdomen Any skin fibroblast that is part of a skin of abdomen. GOC:TermGenie Any skin fibroblast that is part of a upper leg skin. TermGenie 2014-06-04T15:19:44Z cell CL:2000014 fibroblast of upper leg skin Any skin fibroblast that is part of a upper leg skin. GOC:TermGenie Any skin fibroblast that is part of a arm. TermGenie 2014-06-04T15:29:06Z cell CL:2000015 fibroblast of arm Any skin fibroblast that is part of a arm. GOC:TermGenie Any lung endothelial cell that is part of a microvascular endothelium. TermGenie 2014-06-04T16:00:56Z cell CL:2000016 lung microvascular endothelial cell Any lung endothelial cell that is part of a microvascular endothelium. GOC:TermGenie Any fibroblast that is part of a periodontal ligament. TermGenie 2014-06-04T16:50:33Z cell CL:2000017 fibroblast of peridontal ligament Any fibroblast that is part of a periodontal ligament. GOC:TermGenie Any endothelial cell of artery that is part of a coronary artery. TermGenie 2014-06-04T17:08:47Z cell CL:2000018 endothelial cell of coronary artery Any endothelial cell of artery that is part of a coronary artery. GOC:TermGenie Any photoreceptor cell that is part of a compound eye. TermGenie 2014-06-24T23:16:45Z cell CL:2000019 compound eye photoreceptor cell Any photoreceptor cell that is part of a compound eye. 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 interneuron that is part of a spinal cord ventral column. TermGenie 2014-06-25T00:23:36Z cell CL:2000023 spinal cord ventral column interneuron Any interneuron that is part of a spinal cord ventral column. GOC:TermGenie Any neuron that is part of a spinal cord medial motor column. TermGenie 2014-06-25T00:23:43Z cell CL:2000024 spinal cord medial motor column neuron Any neuron that is part of a spinal cord medial motor column. GOC:TermGenie Any oligodendrocyte that is part of a spinal cord. TermGenie 2014-06-25T00:23:50Z cell CL:2000025 spinal cord oligodendrocyte Any oligodendrocyte that is part of a spinal cord. GOC:TermGenie Any Golgi cell that is part of a cerebellum. TermGenie 2014-06-25T00:23:57Z cell CL:2000026 obsolete cerebellum Golgi cell true Any Golgi cell that is part of a cerebellum. GOC:TermGenie Any basket cell that is part of a cerebellum. TermGenie 2014-06-25T00:24:03Z cell CL:2000027 cerebellum basket cell Any basket cell that is part of a cerebellum. GOC:TermGenie Any glutamatergic neuron that is part of a cerebellum. TermGenie 2014-06-25T00:24:10Z cell CL:2000028 cerebellum glutamatergic neuron Any glutamatergic neuron that is part of a cerebellum. GOC:TermGenie Any neuron that is part of a central nervous system. TermGenie 2014-06-25T01:17:43Z cell CL:2000029 central nervous system neuron Any neuron that is part of a central nervous system. 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 neuron that is part of a lateral line ganglion. TermGenie 2014-06-25T01:17:57Z cell CL:2000031 lateral line ganglion neuron Any neuron that is part of a lateral line ganglion. GOC:TermGenie Any neuron that is part of a peripheral nervous system. TermGenie 2014-06-25T02:28:17Z cell CL:2000032 peripheral nervous system neuron Any neuron that is part of a peripheral nervous system. GOC:TermGenie Any basal cell of epidermis that is part of a limb. TermGenie 2014-06-25T02:28:25Z cell CL:2000033 limb basal cell of epidermis Any basal cell of epidermis that is part of a limb. GOC:TermGenie Any neuromast hair cell that is part of a anterior lateral line. TermGenie 2014-06-25T03:44:37Z cell CL:2000034 anterior lateral line neuromast hair cell Any neuromast hair cell that is part of a anterior lateral line. GOC:TermGenie Any neuromast mantle cell that is part of a anterior lateral line. TermGenie 2014-06-25T03:44:44Z cell CL:2000035 anterior lateral line neuromast mantle cell Any neuromast mantle cell that is part of a anterior lateral line. GOC:TermGenie Any neuromast support cell that is part of a anterior lateral line. TermGenie 2014-06-25T03:44:51Z cell CL:2000036 anterior lateral line neuromast support cell Any neuromast support cell that is part of a anterior lateral line. GOC:TermGenie Any neuromast hair cell that is part of a posterior lateral line. TermGenie 2014-06-25T03:44:57Z cell CL:2000037 posterior lateral line neuromast hair cell Any neuromast hair cell that is part of a posterior lateral line. GOC:TermGenie Any neuromast mantle cell that is part of a posterior lateral line. TermGenie 2014-06-25T03:45:04Z cell CL:2000038 posterior lateral line neuromast mantle cell Any neuromast mantle cell that is part of a posterior lateral line. GOC:TermGenie Any neuromast support cell that is part of a posterior lateral line. TermGenie 2014-06-25T03:45:11Z cell CL:2000039 posterior lateral line neuromast support cell Any neuromast support cell that is part of a posterior lateral line. GOC:TermGenie Any microvascular endothelial cell that is part of a urinary bladder. TermGenie 2014-07-09T00:04:47Z cell CL:2000040 bladder microvascular endothelial cell Any microvascular endothelial cell that is part of a urinary bladder. GOC:TermGenie Any dermis lymphatic vessel endothelial cell that is part of a microvascular endothelium. TermGenie 2014-07-09T00:09:54Z cell CL:2000041 dermis microvascular lymphatic vessel endothelial cell Any dermis lymphatic vessel endothelial cell that is part of a microvascular endothelium. GOC:TermGenie Any fibroblast that is part of a embryo. TermGenie 2014-07-09T00:12:00Z cell CL:2000042 embryonic fibroblast Any fibroblast that is part of a embryo. GOC:TermGenie Any pericyte cell that is part of a brain. TermGenie 2014-07-09T00:18:22Z cell CL:2000043 brain pericyte Any pericyte cell that is part of a brain. GOC:TermGenie Any microvascular endothelial cell that is part of a brain. TermGenie 2014-07-09T00:24:53Z cell CL:2000044 brain microvascular endothelial cell Any microvascular endothelial cell that is part of a brain. GOC:TermGenie Any melanocyte that is part of a prepuce of penis. TermGenie 2014-07-09T00:45:07Z cell CL:2000045 foreskin melanocyte Any melanocyte that is part of a prepuce of penis. GOC:TermGenie Any cardiac muscle cell that is part of a cardiac ventricle. TermGenie 2014-08-12T20:50:28Z cell CL:2000046 ventricular cardiac muscle cell Any cardiac muscle cell that is part of a cardiac ventricle. GOC:TermGenie Any motor neuron that is part of a brainstem. TermGenie 2014-10-02T23:52:53Z cell CL:2000047 brainstem motor neuron Any motor neuron that is part of a brainstem. GOC:TermGenie An lower motor neuron whose soma is located in one of the ventral horns of the spinal cord and innervates skeletal muscles of the trunk or head. TermGenie 2014-10-03T00:26:27Z NCIT:C12645 anterior horn cell ventral horn of spinal cord spinal cord motor neuron cell CL:2000048 Yang & Connolly (DOI:10.1016/B978-0-323-37101-8.00140-5) classify these as alpha motor neurons. Consider reflecting this if more references support this. anterior horn motor neuron An lower motor neuron whose soma is located in one of the ventral horns of the spinal cord and innervates skeletal muscles of the trunk or head. DOI:10.1016/B978-0-323-37101-8.00140-5 DOI:10.1016/B978-0-323-42876-7.00030-2 https://www.sciencedirect.com/topics/medicine-and-dentistry/anterior-horn-cell Any pyramidal cell that is part of a primary motor cortex. TermGenie 2014-10-06T17:39:04Z cell CL:2000049 http://www.ncbi.nlm.nih.gov/pubmed/12524689 primary motor cortex pyramidal cell Any pyramidal cell that is part of a primary motor cortex. GOC:TermGenie Any retinal ganglion cell that is part of a retina. TermGenie 2014-10-06T17:43:59Z cell CL:2000050 http://www.ncbi.nlm.nih.gov/pubmed/2889210 obsolete retina retinal ganglion cell true Any retinal ganglion cell that is part of a retina. GOC:TermGenie Any fibroblast that is part of a spleen. TermGenie 2014-10-06T18:58:47Z cell CL:2000051 splenic fibroblast Any fibroblast that is part of a spleen. 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 A large, granular, liver specific natural killer cell that adheres to the endothelial cells of the hepatic sinusoid. cell Pit cells are named for the presence of large cytoplasmic granules that resemble pits (pips) of fruit. hepatic pit cell A large, granular, liver specific natural killer cell that adheres to the endothelial cells of the hepatic sinusoid. GOC:dos PMID:9408963 Any dendritic cell that is part of a liver. TermGenie 2014-10-06T19:16:11Z hepatic dendritic cell cell CL:2000055 http://www.jleukbio.org/content/66/2/322.abstract liver dendritic cell Any dendritic cell that is part of a liver. GOC:TermGenie Any pyramidal cell that is part of a regional part of cerebral cortex. TermGenie 2014-10-06T19:20:41Z cell CL:2000056 Meynert cell Any pyramidal cell that is part of a regional part of cerebral cortex. GOC:TermGenie Any osteoblast that is part of a femur. TermGenie 2014-10-06T19:29:45Z cell CL:2000057 http://www.sciencellonline.com/site/productInformation.php?keyword=4610 femural osteoblast Any osteoblast that is part of a femur. GOC:TermGenie Any osteoblast that is part of a skull. TermGenie 2014-10-06T19:48:30Z cell CL:2000058 http://www.sciencellonline.com/site/productInformation.php?keyword=4600 calvarial osteoblast Any osteoblast that is part of a skull. GOC:TermGenie Any microvascular endothelial cell that is part of a prostate gland. TermGenie 2014-10-07T17:46:27Z cell CL:2000059 http://www.sciencellonline.com/site/productInformation.php?keyword=4400 prostate gland microvascular endothelial cell Any microvascular endothelial cell that is part of a prostate gland. GOC:TermGenie A trophoblast of placental villi. These cells fuse to form synctial trophoplast - the placental side of the interface between the placenta and maternal blood sinusoids in the decidua. TermGenie 2014-10-07T17:48:27Z BTO:0006119 BTO:0006208 vCTB villous cytotrophoblast cell CL:2000060 Same as synctial trophoblast? http://www.sciencellonline.com/site/productInformation.php?keyword=7120 placental villous trophoblast A trophoblast of placental villi. These cells fuse to form synctial trophoplast - the placental side of the interface between the placenta and maternal blood sinusoids in the decidua. PMID:31049600 vCTB PMID:31049600 Any mesenchymal stem cell that is part of a placenta. TermGenie 2014-10-07T17:51:11Z cell CL:2000061 http://www.sciencellonline.com/site/productInformation.php?keyword=7140 placental amniotic mesenchymal stromal cell Any mesenchymal stem cell that is part of a placenta. GOC:TermGenie Any capillary endothelial cell that is part of a placenta. TermGenie 2014-10-07T17:55:56Z cell CL:2000062 http://www.ncbi.nlm.nih.gov/books/NBK53245/ placental villus capillary endothelial cell Any capillary endothelial cell that is part of a placenta. GOC:TermGenie Any fibroblast that is part of a female gonad. TermGenie 2014-10-07T17:57:42Z cell CL:2000063 http://www.sciencellonline.com/site/productInformation.php?keyword=7330 ovarian fibroblast Any fibroblast that is part of a female gonad. 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 microvascular endothelial cell that is part of a female urethra. TermGenie 2014-10-07T18:18:01Z cell CL:2000065 http://www.sciencellonline.com/site/productInformation.php?keyword=7300 ovarian microvascular endothelial cell Any microvascular endothelial cell that is part of a female urethra. GOC:TermGenie Any fibroblast that is part of a cardiac ventricle. TermGenie 2014-10-07T18:35:38Z cell CL:2000066 http://www.sciencellonline.com/site/productInformation.php?keyword=6310 cardiac ventricle fibroblast Any fibroblast that is part of a cardiac ventricle. GOC:TermGenie Any fibroblast that is part of a cardiac atrium. TermGenie 2014-10-07T18:36:54Z cell CL:2000067 http://www.sciencellonline.com/site/productInformation.php?keyword=6320 cardiac atrium fibroblast Any fibroblast that is part of a cardiac atrium. GOC:TermGenie Any fibroblast that is part of a pericardium. TermGenie 2014-10-07T18:38:06Z cell CL:2000068 http://www.sciencellonline.com/site/productInformation.php?keyword=6430 pericardium fibroblast Any fibroblast that is part of a pericardium. GOC:TermGenie Any fibroblast that is part of a gallbladder. TermGenie 2014-10-07T18:41:43Z cell CL:2000069 http://www.sciencellonline.com/site/productInformation.php?keyword=5430 gallbladder fibroblast Any fibroblast that is part of a gallbladder. GOC:TermGenie Any fibroblast that is part of a optic choroid. TermGenie 2014-10-07T18:50:43Z cell CL:2000070 http://www.sciencellonline.com/site/productInformation.php?keyword=6620 optic choroid fibroblast Any fibroblast that is part of a optic choroid. GOC:TermGenie Any microvascular endothelial cell that is part of a breast. TermGenie 2014-10-07T19:55:30Z cell CL:2000071 http://www.sciencellonline.com/site/productInformation.php?keyword=7600 mammary microvascular endothelial cell Any microvascular endothelial cell that is part of a breast. GOC:TermGenie Any microvascular endothelial cell that is part of a adipose tissue. TermGenie 2014-10-07T22:13:45Z cell CL:2000072 http://www.sciencellonline.com/site/productInformation.php?keyword=7200 adipose microvascular endothelial cell Any microvascular endothelial cell that is part of a adipose tissue. GOC:TermGenie Any migratory neural crest cell that is part of a cardiac neural crest. TermGenie 2014-11-05T01:18:43Z cell CL:2000073 migratory cardiac neural crest cell Any migratory neural crest cell that is part of a cardiac neural crest. GOC:TermGenie Any leukocyte that is part of a spleen. TermGenie 2014-11-05T01:26:50Z cell CL:2000074 Splenocytes is a vague term that refers to any one of the different white blood cell types in the spleen. This name is seen many references as such and is not explained further, necessitating a need for this terminology. splenocyte Any leukocyte that is part of a spleen. GOC:TermGenie Any endodermal cell that is part of a anterior visceral endoderm. TermGenie 2014-11-05T01:34:13Z cell CL:2000075 anterior visceral endoderm cell Any endodermal cell that is part of a anterior visceral endoderm. 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 Any striated muscle cell that is part of a skeletal muscle tissue of pectoralis major. TermGenie 2014-12-02T18:48:17Z cell CL:2000077 skeletal muscle tissue of pectoralis major striated muscle cell Any striated muscle cell that is part of a skeletal muscle tissue of pectoralis major. GOC:TermGenie Any pericyte cell that is part of a placenta. TermGenie 2014-12-02T18:51:03Z cell CL:2000078 placental pericyte Any pericyte cell that is part of a placenta. GOC:TermGenie Any mesenchymal stem cell of the bone marrow that is part of a femur. TermGenie 2014-12-02T19:07:31Z cell CL:2000079 mesenchymal stem cell of femoral bone marrow Any mesenchymal stem cell of the bone marrow that is part of a femur. GOC:TermGenie Any mesenchymal stem cell of adipose that is part of a abdomen. TermGenie 2014-12-02T19:10:34Z cell CL:2000080 mesenchymal stem cell of abdominal adipose Any mesenchymal stem cell of adipose that is part of a abdomen. GOC:TermGenie Any melanocyte of skin that is part of a skin of face. TermGenie 2014-12-02T19:10:40Z cell CL:2000081 melanocyte of skin of face Any melanocyte of skin that is part of a skin of face. GOC:TermGenie Any melanocyte of skin that is part of a skin of prepuce of penis. TermGenie 2014-12-02T19:10:45Z cell CL:2000082 melanocyte of foreskin Any melanocyte of skin that is part of a skin of prepuce of penis. GOC:TermGenie Any hair follicle dermal papilla cell that is part of a scalp. TermGenie 2014-12-02T19:10:50Z cell CL:2000083 hair follicle dermal papilla cell of scalp Any hair follicle dermal papilla cell that is part of a scalp. GOC:TermGenie Any goblet cell that is part of a conjunctiva. TermGenie 2014-12-02T19:28:38Z cell CL:2000084 conjunctiva goblet cell Any goblet cell that is part of a conjunctiva. GOC:TermGenie Any mononuclear cell that is part of a umbilical cord. TermGenie 2014-12-02T20:14:16Z cell CL:2000085 mononuclear cell of umbilical cord Any mononuclear cell that is part of a umbilical cord. GOC:TermGenie Any basket cell that is part of a neocortex. TermGenie 2014-12-24T00:37:19Z cell CL:2000086 neocortex basket cell Any basket cell that is part of a neocortex. GOC:TermGenie Any basket cell that is part of a dentate gyrus of hippocampal formation. TermGenie 2014-12-24T00:37:24Z cell CL:2000087 dentate gyrus of hippocampal formation basket cell Any basket cell that is part of a dentate gyrus of hippocampal formation. GOC:TermGenie Any basket cell that is part of a Ammon's horn. TermGenie 2014-12-24T00:37:30Z cell CL:2000088 Ammon's horn basket cell Any basket cell that is part of a Ammon's horn. GOC:TermGenie The principal cell type of the dentate gyrus. TermGenie 2015-02-23T05:48:23Z cell CL:2000089 The granule cell has a characteristic cone-shaped tree of spiny apical dendrites. dentate gyrus of hippocampal formation granule cell The principal cell type of the dentate gyrus. GOC:TermGenie Any stellate cell that is part of a dentate gyrus of hippocampal formation. TermGenie 2015-02-23T05:48:40Z cell CL:2000090 dentate gyrus of hippocampal formation stellate cell Any stellate cell that is part of a dentate gyrus of hippocampal formation. GOC:TermGenie Any microvascular endothelial cell that is part of a endometrial blood vessel. TermGenie 2015-03-31T21:02:36Z cell CL:2000091 endometrial microvascular endothelial cells Any microvascular endothelial cell that is part of a endometrial blood vessel. GOC:TermGenie Any keratinocyte that is part of a hair follicle. TermGenie 2015-03-31T21:07:02Z cell CL:2000092 hair follicular keratinocyte Any keratinocyte that is part of a hair follicle. GOC:TermGenie Any fibroblast of lung that is part of a bronchus. TermGenie 2015-03-31T21:16:22Z cell CL:2000093 bronchus fibroblast of lung Any fibroblast of lung that is part of a bronchus. GOC:TermGenie Any epithelial cell of viscerocranial mucosa that is part of a nasal cavity respiratory epithelium. TermGenie 2015-03-31T22:25:17Z cell CL:2000094 nasal cavity respiratory epithelium epithelial cell of viscerocranial mucosa Any epithelial cell of viscerocranial mucosa that is part of a nasal cavity respiratory epithelium. GOC:TermGenie Any hematopoietic stem cell that is part of a umbilical cord blood. TermGenie 2015-05-26T18:58:34Z cell CL:2000095 cord blood hematopoietic stem cell Any hematopoietic stem cell that is part of a umbilical cord blood. GOC:TermGenie Any fibroblast that is part of a reticular layer of dermis. TermGenie 2015-08-11T16:28:16Z cell CL:2000096 reticular layer of dermis fibroblast Any fibroblast that is part of a reticular layer of dermis. GOC:TermGenie Any dopaminergic neuron that is part of a midbrain. TermGenie 2015-12-03T16:42:40Z cell CL:2000097 midbrain dopaminergic neuron Any dopaminergic neuron that is part of a midbrain. GOC:TermGenie A ciliated epithelial cell of the esophagus. CellBLAST 2019-02-09T16:40:30Z cell CL:3000000 ciliated epithelial cell of esophagus A ciliated epithelial cell of the esophagus. GOC:CellBLAST PMID:29802404 Oval eosinophilic histiocytes with granules and vacuoles found in placenta, which are of mesenchymal origin, in mesoderm of the chorionic villus, particularly numerous in early pregnancy. CellBLAST 2019-02-18T19:41:20Z cell CL:3000001 Hofbauer cell Oval eosinophilic histiocytes with granules and vacuoles found in placenta, which are of mesenchymal origin, in mesoderm of the chorionic villus, particularly numerous in early pregnancy. GOC:CellBLAST PMID:30429548 Sympathetic noradrenergic neuron. CellBLAST 2019-02-25T19:30:14Z cell CL:3000002 sympathetic noradrenergic neuron Sympathetic noradrenergic neuron. GOC:CellBLAST PMID:30096314 Sympathetic cholinergic neuron. CellBLAST 2019-02-25T19:32:20Z cell CL:3000003 sympathetic cholinergic neuron Sympathetic cholinergic neuron. GOC:CellBLAST PMID:30096314 Peripheral sensory neuron. CellBLAST 2019-02-25T19:34:33Z cell CL:3000004 peripheral sensory neuron Peripheral sensory neuron. GOC:CellBLAST PMID:30096314 A fibroblast that is part of the breast. breast fibroblast fibroblast of breast A fibroblast that is part of the skin of scalp. skin of scalp fibroblast fibroblast of skin of scalp A motor neuron that innervates both intrafusal and extrafusal muscle fibers. Low abundancy. They control both muscle contraction and responsiveness of the sensory feedback from muscle spindles. beta motor neuron A motor neuron that innervates both intrafusal and extrafusal muscle fibers. Low abundancy. They control both muscle contraction and responsiveness of the sensory feedback from muscle spindles. PMID:25346659 A beta motor neuron that innervates nuclear chain fibers. static beta motor neuron A beta motor neuron that innervates nuclear chain fibers. PMID:25346659 A beta motor neuron that innervates the nuclear bag fibers of muscle spindles. dynamic beta motor neuron A beta motor neuron that innervates the nuclear bag fibers of muscle spindles. PMID:25346659 A type of intrafusal muscle fiber that has nuclei arranged in a linear row. Unlike nuclear bag fibers, the equatorial region of these fibers (in the centre of the spindle) is not expanded. These fibers are responsible for the detection of changes in muscle length. They are innervated by static gamma motor neurons and are principally associated with type II sensory fibers. nuclear chain fiber A type of intrafusal muscle fiber that has nuclei arranged in a linear row. Unlike nuclear bag fibers, the equatorial region of these fibers (in the centre of the spindle) is not expanded. These fibers are responsible for the detection of changes in muscle length. They are innervated by static gamma motor neurons and are principally associated with type II sensory fibers. DOI:10.1016/B978-0-323-39632-5.00024-4 PMID:139469 A type of intrafusal muscle fiber that lies in the center of a muscle spindle. Nuclei are clustered centrally and give the equatorial region a swollen appearance. They are associated with associated with dynamic gamma motor neurons, and the stretching of the equatorial region of the nuclear bag fibers results in an increase in the firing rate of type Ia sensory fibers. nuclear bag fiber A type of intrafusal muscle fiber that lies in the center of a muscle spindle. Nuclei are clustered centrally and give the equatorial region a swollen appearance. They are associated with associated with dynamic gamma motor neurons, and the stretching of the equatorial region of the nuclear bag fibers results in an increase in the firing rate of type Ia sensory fibers. DOI:10.1016/B978-0-323-39632-5.00024-4 PMID:139469 A nuclear bag fiber that is sensitive mainly to the rate of change in muscle length. bag1 fiber nuclear bag1 intrafusal fiber dynamic nuclear bag fiber A nuclear bag fiber that is sensitive mainly to the rate of change in muscle length. DOI:10.1016/B978-0-323-39632-5.00024-4 A nuclear bag fiber that is sensitive only changes in muscle length but not the rate of that change. bag2 fiber nuclear bag2 intrafusal fiber static nuclear bag fiber A nuclear bag fiber that is sensitive only changes in muscle length but not the rate of that change. DOI:10.1016/B978-0-323-39632-5.00024-4 A Vip GABAergic cortical interneuron with bipolar morphology, with a soma found in L2/3. L2/3 bipolar Vip Cells have extending axons across all layers (with preferences for layers II/III and Va) and a dendritic tree that is vertically more restricted than deeper layer VIP cells and extend fewer dendrites into the layers outside their home layer (location of soma). L2/3 Bipolar Vip Cells have great variability in firing patterns, though most are continuous adapting. L2/3 Bipolar Vip Cells are more depolarized in their resting state, had less fast rectification, and had smaller after hyperpolarization than deeper Vip cells. L2/3 bipolar Vip (Mus) L2/3 bipolar Vip expressing GABAergic cortical interneuron (Mus musculus) A Vip GABAergic cortical interneuron with bipolar morphology, with a soma found in L2/3. L2/3 bipolar Vip Cells have extending axons across all layers (with preferences for layers II/III and Va) and a dendritic tree that is vertically more restricted than deeper layer VIP cells and extend fewer dendrites into the layers outside their home layer (location of soma). L2/3 Bipolar Vip Cells have great variability in firing patterns, though most are continuous adapting. L2/3 Bipolar Vip Cells are more depolarized in their resting state, had less fast rectification, and had smaller after hyperpolarization than deeper Vip cells. PMID:26420784 A glutamatergic neuron located in the cerebral cortex that projects to structures of telencephalic origins. ILX:0770100 IT projecting neuron intratelencephalic-projecting glutamatergic cortical neuron A glutamatergic neuron located in the cerebral cortex that projects to structures of telencephalic origins. DOI:10.1101/2020.10.19.343129 A glutamatergic neuron located in the cerebral cortex that projects to structures not derived from telencephalon. ILX:0770101 ET projecting neuron extratelencephalic-projecting glutamatergic cortical neuron A glutamatergic neuron located in the cerebral cortex that projects to structures not derived from telencephalon. DOI:10.1101/2020.10.19.343129 A GABAergic cortical interneuron that is strongly labelled for α7 nAChRs. These cells have soma found in L1 and have multipolar dendrites with vertically descending axonal collaterals that project deep into the column, usually branching and terminating in L5A. A7 cell (Mus) A7 cells have a transcriptomics signature that looks like Lamp5 GABAergic interneuron. Unlike typical Lamp5 electrophysiology, A7 cells have Vip- and Sst-like firing properties, with active depolarizing hump at near-threshold membrane potentials, and larger hyperpolarization sag, stronger burst, and rebound firing. alpha7 GABAergic cortical interneuron (Mus musculus) A GABAergic cortical interneuron that is strongly labelled for α7 nAChRs. These cells have soma found in L1 and have multipolar dendrites with vertically descending axonal collaterals that project deep into the column, usually branching and terminating in L5A. PMID:30413647 PMID:33184512 A7 cells have a transcriptomics signature that looks like Lamp5 GABAergic interneuron. DOI:10.1101/2020.10.19.343129 Unlike typical Lamp5 electrophysiology, A7 cells have Vip- and Sst-like firing properties, with active depolarizing hump at near-threshold membrane potentials, and larger hyperpolarization sag, stronger burst, and rebound firing. PMID:30413647 PMID:33184512 A GABAergic neuron located in the cerebral cortex that expresses Lamp5 ILX:0770149 Lamp5 GABAergic cortical interneuron A GABAergic neuron located in the cerebral cortex that expresses Lamp5 PMID:30382198 A glutamatergic neuron located in the cerebral cortex that projects axons locally rather than distantly. ILX:0770103 NP neuron near-projecting glutamatergic cortical neuron A glutamatergic neuron located in the cerebral cortex that projects axons locally rather than distantly. DOI:10.1101/2020.10.19.343129 A glutamatergic neuron located in the cerebral cortex that projects to the thalamus. CT projecting neuron corticothalamic-projecting glutamatergic cortical neuron A glutamatergic neuron located in the cerebral cortex that projects to the thalamus. DOI:10.1101/2020.10.19.343129 A Vip GABAergic cortical interneuron with a soma found in L5. L5 Vip cells have mostly local morphology with some deep-projecting axons. They show only moderate resistance, comparable to that of Sst subclass and unlike typical Vip subclass cells that tend to show high input resistance. L5 Vip cells show particularly low resting membrane potential. L5 VIP (Mus) L5 Vip expressing cortical GABAergic interneuron (Mus musculus) A Vip GABAergic cortical interneuron with a soma found in L5. L5 Vip cells have mostly local morphology with some deep-projecting axons. They show only moderate resistance, comparable to that of Sst subclass and unlike typical Vip subclass cells that tend to show high input resistance. L5 Vip cells show particularly low resting membrane potential. PMID:26420784 PMID:26612957 A GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein ILX:0770150 sncg GABAergic cortical interneuron A GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein PMID:33186530 A GABAergic neuron located in the cerebral cortex that expresses vasoactive intestinal polypeptide ILX:0770151 Vip GABAergic cortical interneuron A GABAergic neuron located in the cerebral cortex that expresses vasoactive intestinal polypeptide PMID:33186530 A GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst) ILX:0770152 sst GABAergic cortical interneuron A GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst) PMID:27477017 A GABAergic interneuron located in the cerebral cortex that expresses Parvalbumin. ILX:0770154 pvalb GABAergic cortical interneuron A GABAergic interneuron located in the cerebral cortex that expresses Parvalbumin. PMID:27477017 A Vip GABAergic cortical interneuron that expresses CCK. L5/6 CCK cells have soma found mainly in L5 and L6 and have large axonal arborization. L5/6 CCK Vip (Mus) L5/6 CCK and Vip expressing cortical GABAergic interneuron (Mus musculus) A Vip GABAergic cortical interneuron that expresses CCK. L5/6 CCK cells have soma found mainly in L5 and L6 and have large axonal arborization. PMID:33184512 A Lamp5 GABAergic cortical interneuron that has extended axons in the surface of L1. Canopy Lamp5 cells resemble neurogliaform cells in having elongated horizontal axonal arbors largely confined to L1; but the dendritic arbors are wider and have fewer branches, while the axon is less tortuous and extends further from the soma canopy Lamp5 GABAergic cortical interneuron (Mus musculus) A Lamp5 GABAergic cortical interneuron that has extended axons in the surface of L1. Canopy Lamp5 cells resemble neurogliaform cells in having elongated horizontal axonal arbors largely confined to L1; but the dendritic arbors are wider and have fewer branches, while the axon is less tortuous and extends further from the soma PMID:30413647 A Lamp 5 GABAergic cortical interneuron with neurogliaform morphology with a soma found in L5,6. L5,6 NGC Lamp5 have deep afterhyperpolarization (AHP) but narrow action potentials (APs). Unlike other deep neurogliaform cells (which are caudal ganglionic eminence (CGE) derived), L5,6 NGC Lamp5 cells are medial ganglionic eminence (MGE)-derived L5,6 NGC Lamp5 (mus) L5,6 Neurogliaform Lamp5 GABAergic cortical interneuron (Mus musculus) A Lamp 5 GABAergic cortical interneuron with neurogliaform morphology with a soma found in L5,6. L5,6 NGC Lamp5 have deep afterhyperpolarization (AHP) but narrow action potentials (APs). Unlike other deep neurogliaform cells (which are caudal ganglionic eminence (CGE) derived), L5,6 NGC Lamp5 cells are medial ganglionic eminence (MGE)-derived PMID:26727548 A Lamp5 GABAergic cortical interneuron with layer-adapting morphology. NGC Lamp5 cells have a small round soma, short dendrites, and a wide dense axonal arbor that tends to establish a dense axonal mesh with high connection probability both to themselves and L2 pyramidal cells. NGC Lamp5 cells have unique synaptic properties that distinguish them from other GABAergic interneurons, including the release of GABA to the extracellular space via volume transmission, and the ability to produce GABA-B responses in connected postsynaptic targets. NGC Lamp5 (mus) Neurogliaform Lamp5 GABAergic cortical interneuron (Mus musculus) A Lamp5 GABAergic cortical interneuron with layer-adapting morphology. NGC Lamp5 cells have a small round soma, short dendrites, and a wide dense axonal arbor that tends to establish a dense axonal mesh with high connection probability both to themselves and L2 pyramidal cells. NGC Lamp5 cells have unique synaptic properties that distinguish them from other GABAergic interneurons, including the release of GABA to the extracellular space via volume transmission, and the ability to produce GABA-B responses in connected postsynaptic targets. PMID:27477017 A Sst GABAergic cortical interneuron that is both an interneuron and a projecting neuron. They are found in all layers from upper L2/3 down to the bottom of L6. They have long-range projections, some with axons fading into white matter. These cells have low rebound potential, low hyperpolarization sag, and high variability in membrane time constant. LP SST (Mus) Long-range projecting Sst GABAergic cortical interneuron (Mus musculus) A Sst GABAergic cortical interneuron that is both an interneuron and a projecting neuron. They are found in all layers from upper L2/3 down to the bottom of L6. They have long-range projections, some with axons fading into white matter. These cells have low rebound potential, low hyperpolarization sag, and high variability in membrane time constant. PMID:26727548 A Sst GABAergic cortical interneuron with a soma found in L5 and possesses 'T-shaped' martinotti morphologies with local axonal plexus in L5a and translaminar axons restricted to the uppermost part of L1. They show low-threshold spiking patterns with strong rebound firing, and inhibit the L1 apical tuft of nearby pyramidal cells. L5 T Martinotti SST (Mus) L5 ‘T-shaped’ Martinotti Sst GABAergic cortical interneuron (Mus musculus) A Sst GABAergic cortical interneuron with a soma found in L5 and possesses 'T-shaped' martinotti morphologies with local axonal plexus in L5a and translaminar axons restricted to the uppermost part of L1. They show low-threshold spiking patterns with strong rebound firing, and inhibit the L1 apical tuft of nearby pyramidal cells. PMID:28254942 PMID:29326172 A Sst GABAergic cortical interneuron with a soma found in lower L5 with mostly local axonal arborization but with some sparse ascending axons. L5 non-Martinotti Sst cells show somatic localization and local axon plexus in L5b and L5b/6 and substantial innervation of L3 and L4, and receive thalamic input from the ventral posteromedial nucleus and specifically target L4 neurons, avoiding L5 pyramidal cells. L5 non-Martinotti Sst cells tend to show a higher input resistance and seem to be less stuttering. L5 non-Martinotti SST (Mus) L5 non-Martinotti Sst GABAergic cortical interneuron (Mus musculus) A Sst GABAergic cortical interneuron with a soma found in lower L5 with mostly local axonal arborization but with some sparse ascending axons. L5 non-Martinotti Sst cells show somatic localization and local axon plexus in L5b and L5b/6 and substantial innervation of L3 and L4, and receive thalamic input from the ventral posteromedial nucleus and specifically target L4 neurons, avoiding L5 pyramidal cells. L5 non-Martinotti Sst cells tend to show a higher input resistance and seem to be less stuttering. PMID:28254942 PMID:29326172 A Sst GABAergic cortical interneuron that has "fanning-out' Martinotti morphology that is found in layer 2/3/5 of the cerebral cortex. They have local axon arbor and long ascending axons that spreads horizontally and arborizes significantly in L1. L2/3/5 fan Martinotti SST (Mus) L2/3/5 fan Martionotti SST cells have an adapting firing pattern and non-zero afterdepolarization (ADP). L2/3/5 fan Martinotti Sst GABAergic cortical interneuron (Mus musculus) A Sst GABAergic cortical interneuron that has "fanning-out' Martinotti morphology that is found in layer 2/3/5 of the cerebral cortex. They have local axon arbor and long ascending axons that spreads horizontally and arborizes significantly in L1. PMID:27225074 PMID:27477017 PMID:28254942 PMID:29326172 L2/3/5 fan Martionotti SST cells have an adapting firing pattern and non-zero afterdepolarization (ADP). PMID:33184512 A Sst GABAergic cortical interneuron with a soma found in lower L2/3 and upper 5, L4 Sst cells have martinotti morphology with ascending axons but denser local axons and sparser ‘fanning-out’ projections to L1. L4 Sst cells have smaller membrane time constant to calb2 (L2/3/5 Fan Martinotti Cell) and non-zero afterdepolarization (ADP). L4 SST (Mus) L4 Sst GABAergic cortical interneuron (Mus musculus) A Sst GABAergic cortical interneuron with a soma found in lower L2/3 and upper 5, L4 Sst cells have martinotti morphology with ascending axons but denser local axons and sparser ‘fanning-out’ projections to L1. L4 Sst cells have smaller membrane time constant to calb2 (L2/3/5 Fan Martinotti Cell) and non-zero afterdepolarization (ADP). PMID:33184512 A Sst GABAergic cortical interneuron transcriptomically between the Sst and the Pvalb families with a soma found in L2/3. Some L2/3 PV-like SST cells have Martinotti morphology while some have basket cell morphology. L2/3 PV-like SST cells have lower AP width and higher firing rate than typical Sst subclass cells. L2/3 PV-like SST cells have high maximum firing rate variability, with many classified as belonging to the Pvalb subclass on the basis of electrophysiology. L2/3 PV-like SST Mus) L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) A Sst GABAergic cortical interneuron transcriptomically between the Sst and the Pvalb families with a soma found in L2/3. Some L2/3 PV-like SST cells have Martinotti morphology while some have basket cell morphology. L2/3 PV-like SST cells have lower AP width and higher firing rate than typical Sst subclass cells. L2/3 PV-like SST cells have high maximum firing rate variability, with many classified as belonging to the Pvalb subclass on the basis of electrophysiology. PMID:33184512 A Pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells have soma found in in upper L2/3, with some in deep L5. Chandelier PV cells exhibit fast-spiking but lower firing rate compared to basket cells, and have practically absent hyperpolarization sag. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner. ILX:0107356 Chandelier PV (Mus) Chandelier Pvalb GABAergic cortical interneuron (Mus musculus) A Pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells have soma found in in upper L2/3, with some in deep L5. Chandelier PV cells exhibit fast-spiking but lower firing rate compared to basket cells, and have practically absent hyperpolarization sag. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner. PMID:27477017 A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate. ILX:0770163 L6b glutamatergic cortical neuron A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate. DOI:10.1101/2020.10.19.34312 PMID:30382198 A intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layers L2/3-6 L2/3-6 IT projecting neuron L2/3-6 intratelencephalic projecting glutamatergic cortical neuron A intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layers L2/3-6 DOI:10.1101/2020.10.19.343129 A glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics. L5b neuron burst-firing layer 5 neuron pyramidal tract (PT) neuron subcerebral projection (SCPN) neuron thick-tufted layer 5 pyramidal neuron L5 extratelencephalic projecting glutamatergic cortical neuron A glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics. DOI:10.1101/2020.10.19.343129 A corticothalamic-projecting neuron with a soma found in cortical layer 6. L6 CT L6 corticothalamic-projecting glutamatergic cortical neuron A corticothalamic-projecting neuron with a soma found in cortical layer 6. DOI:10.1101/2020.10.19.343129 A near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex. ILX:0770161 L5/6 NP L5/6 near-projecting glutamatergic neuron of the primary motor cortex (Mus musculus) A near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex. DOI:10.1101/2020.10.19.343129 PMID:31209381 An extratelencephalic-projecting glutamatergic neuron located in layer 5b of the primary motor cortex that does not project to the medulla. Non-MY ET cells are large, big-tufted cells with the apical dendrite often bifurcating close to the soma, suggesting they are corticospinal cells. Non-MY ET cells have bigger hyperpolarization sag, lower input resistance, and smaller AP width, compared to L5 IT neurons. non-MY ET MOp (Mus) non-medulla-projecting extratelencephalic-projecting glutamatergic neuron of the primary motor cortex (Mus musculus) An extratelencephalic-projecting glutamatergic neuron located in layer 5b of the primary motor cortex that does not project to the medulla. Non-MY ET cells are large, big-tufted cells with the apical dendrite often bifurcating close to the soma, suggesting they are corticospinal cells. Non-MY ET cells have bigger hyperpolarization sag, lower input resistance, and smaller AP width, compared to L5 IT neurons. DOI:10.1101/2020.10.19.343129 PMID:24137110 PMID:9236245 An extratelencephalic-projecting glutamatergic neuron located in layer 5b of the primary motor cortex that projects to the medulla. MY ET cells are large, big-tufted cells with the apical dendrite often bifurcating close to the soma, suggesting they are corticospinal cells. MY ET cells have bigger hyperpolarization sag, lower input resistance, and smaller AP width, compared to L5 IT neurons. MY ET MOp (Mus) medulla-projecting extratelencephalic-projecting glutamatergic neuron of the primary motor cortex (Mus musculus) An extratelencephalic-projecting glutamatergic neuron located in layer 5b of the primary motor cortex that projects to the medulla. MY ET cells are large, big-tufted cells with the apical dendrite often bifurcating close to the soma, suggesting they are corticospinal cells. MY ET cells have bigger hyperpolarization sag, lower input resistance, and smaller AP width, compared to L5 IT neurons. DOI:10.1101/2020.10.19.343129 PMID:24137110 PMID:9236245 An excitatory glutamatergic neuron transcriptomically related to the CT subclass, with a soma preferentially located in the bottom of L6 of the primary motor cortex. L6b subplate glutamatergic neuron of the primary motor cortex (Mus musculus) An excitatory glutamatergic neuron transcriptomically related to the CT subclass, with a soma preferentially located in the bottom of L6 of the primary motor cortex. PMID:33184512 An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3. L2/3 IT MOp (Mus) L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex (Mus musculus) An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3. DOI:10.1101/2020.10.19.343129 An intratelencephalic-projecting glutamatergic with a soma located in upper L5 of the primary motor cortex. These cells have thin untufted apical dendrites. ILX:0770174 L4/5 IT MOp (Mus) L4/5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex (Mus musculus) An intratelencephalic-projecting glutamatergic with a soma located in upper L5 of the primary motor cortex. These cells have thin untufted apical dendrites. PMID:33184512 An intratelencephalic-projecting glutamatergic neuron with a soma found in L5 of the primary motor cortex. ILX:0770157 L5 IT MOp (Mus) L5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex (Mus musculus) An intratelencephalic-projecting glutamatergic neuron with a soma found in L5 of the primary motor cortex. PMID:33184512 An intratelencephalic-projecting glutamatergic neuron with a soma found in L6 of the primary motor cortex. These cells are short untufted pyramidal cells, which could be stellate or inverted. ILX:0770158 L6 IT MOp (Mus) L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex (Mus musculus) An intratelencephalic-projecting glutamatergic neuron with a soma found in L6 of the primary motor cortex. These cells are short untufted pyramidal cells, which could be stellate or inverted. PMID:9236245 A type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain. ILX:0770143 VLMC vascular leptomeningeal cell A type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain. PMID:27284195 PMID:29443965 PMID:30096314 A Betz cell that synapses with lower motor neurons directly. Betz upper motor neuron A Betz cell that synapses with lower motor neurons directly. DOI:10.1101/2020.03.31.016972 PMID:18558853 PMID:28751609 A Betz cell that syanpses with spinal interneurons. spinal interneuron synapsing Betz cell A Betz cell that syanpses with spinal interneurons. DOI:10.1101/2020.03.31.016972 PMID:18558853 A mesothelial cell that has undergone mesothelial-to-mesenchymal transition (MMT) to become a fibroblast cell. mesothelial fibroblast A mesothelial cell that has undergone mesothelial-to-mesenchymal transition (MMT) to become a fibroblast cell. PMID:26106328 A corticothalamic-projecting glutamatergic neuron that is located in L6 and lower L5 of the primary motor cortex, with a pyramidal morphology and mostly untufted apical dendrites terminating in midcortical layers. CT VAL/VM cells have a near tonic firing pattern and are distinguished from L6 IT neurons by a lower inter-spike interval adaptation index. CT VAL/VM MOp (Mus) corticothalamic VAL/VM projecting glutamatergic neuron of the primary motor cortex (Mus musculus) A corticothalamic-projecting glutamatergic neuron that is located in L6 and lower L5 of the primary motor cortex, with a pyramidal morphology and mostly untufted apical dendrites terminating in midcortical layers. CT VAL/VM cells have a near tonic firing pattern and are distinguished from L6 IT neurons by a lower inter-spike interval adaptation index. PMID:20556241 PMID:9236245 A type of mouse mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain. VLMC (Mus) vascular leptomeningeal cell (Mus musculus) PMID:30096314 PMID:30096314 PMID:30096314 A type of mouse mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain. PMID:30096314 A mesothelial fibroblast found in the leptomeninx. mesothelial fibroblast of the leptomeninx A mouse GABAergic cell located in the cerebral cortex that expresses meis2. meis2 expressing cortical GABAergic cell (Mus musculus) A mouse GABAergic cell located in the cerebral cortex that expresses meis2. PMID:33372656 A pyramidal neuron which has an apical tree which is oriented parallel to the pia. This is unlike typical pyramidal neurons which have its apical dendrite aligned vertically. horizontal pyramidal neuron A pyramidal neuron which has an apical tree which is oriented parallel to the pia. This is unlike typical pyramidal neurons which have its apical dendrite aligned vertically. PMID:30715238 A L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) that has Martinotti morphology. Martinotti L2/3 PV-like SST (Mus) Martinotti morphology L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) A L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) that has Martinotti morphology. PMID:33184512 A GABAergic cortical interneuron that develops from the medial ganglionic eminence and has migrated to the cerebral cortex. MGE cortical interneuron medial ganglionic eminence derived GABAergic cortical interneuron A GABAergic cortical interneuron that develops from the medial ganglionic eminence and has migrated to the cerebral cortex. PMID:12637172 A GABAergic cortical interneuron that develops from the caudal ganglionic eminence and has migrated to the cerebral cortex. CGE cortical interneuron caudal ganglionic eminence derived GABAergic cortical interneuron A GABAergic cortical interneuron that develops from the caudal ganglionic eminence and has migrated to the cerebral cortex. PMID:20130169 A GABAergic cortical interneuron that expresses CCK. L5/6 CCK cells have soma found mainly in L5 and L6 and have large axonal arborization. L5/6 CCK (Mus) L5/6 CCK expressing cortical GABAergic interneuron (Mus musculus) A GABAergic cortical interneuron that expresses CCK. L5/6 CCK cells have soma found mainly in L5 and L6 and have large axonal arborization. PMID:33184512 An interneuron that has Martinotti morphology. These interneurons are scattered throughout various layers of the cerebral cortex, sending their axons up to the cortical layer I where they form axonal arborization. ILX:0107375 nifext_55 Martinotti neuron An interneuron that has Martinotti morphology. These interneurons are scattered throughout various layers of the cerebral cortex, sending their axons up to the cortical layer I where they form axonal arborization. WikipediaVersioned:Martinotti_cell&oldid=9947732 A type of interneuron that has two clusters of dendritic branches that originate directly from the soma and extend in opposite directions and axons that form a plexus which spreads widely. Compared to bipolar neurons, bitufted neurons have branching that occur close to the soma. ILX:0777212 bitufted neuron A type of interneuron that has two clusters of dendritic branches that originate directly from the soma and extend in opposite directions and axons that form a plexus which spreads widely. Compared to bipolar neurons, bitufted neurons have branching that occur close to the soma. PMID:18568015 ILX:0777212 Interlex cross reference refers specifically to Markram 2015 rat bitufted cell. A L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) that has basket morphology. basket L2/3 PV-like SST (Mus) basket morphology L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) A L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) that has basket morphology. PMID:33184512 a L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex that has stellate pyramidal morphology. stellate L6 IT MOp (Mus) stellate L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex (Mus musculus) a L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex that has stellate pyramidal morphology. PMID:9236245 a L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex that has inverted pyramidal morphology. inverted L6 IT MOp (Mus) inverted L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex (Mus musculus) a L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex that has inverted pyramidal morphology. PMID:9236245 An interneuron that selectively innervates the axon initial segment of pyramidal cells. Their local axonal clusters are formed by high-frequency branching at shallow angles, often ramifying around, above or below their somata with a high bouton density. The characteristic terminal portions of the axon form short vertical rows of boutons, resembling a chandelier. Chandelier cells can be multipolar or bitufted. ILX:0777213 ChC chandelier cell An interneuron that selectively innervates the axon initial segment of pyramidal cells. Their local axonal clusters are formed by high-frequency branching at shallow angles, often ramifying around, above or below their somata with a high bouton density. The characteristic terminal portions of the axon form short vertical rows of boutons, resembling a chandelier. Chandelier cells can be multipolar or bitufted. PMID:27199673 PMID:15378039 ILX:0777213 Interlex cross reference refers specifically to Markram 2015 rat chandelier cell. ChC PMID:15378039 A Martinotti neuron that has axons that form a horizontal ramification, making it T-shaped. 'T-shaped' Martinotti neuron T Martinotti neuron A Martinotti neuron that has axons that form a horizontal ramification, making it T-shaped. doi:10.1016/b978-0-12-369497-3.10004-4 A Martinotti neuron that has axons that form a fan-like plexus. 'fanning-out' Martinotti neuron fan Martinotti neuron A Martinotti neuron that has axons that form a fan-like plexus. doi:10.1016/b978-0-12-369497-3.10004-4 A basket cell that is large, and typically ascends to give rise to many long horizontally and vertically projecting axon collaterals that traverse neighboring columns and can extend through all cortical layers. large basket cell A basket cell that is large, and typically ascends to give rise to many long horizontally and vertically projecting axon collaterals that traverse neighboring columns and can extend through all cortical layers. PMID:11884355 A basket cell which has simpler dendritic arbors (compared to small or large basket cells), and an axonal plexus of intermediate density, composed of a few long, smooth axonal branches. nest basket cell A basket cell which has simpler dendritic arbors (compared to small or large basket cells), and an axonal plexus of intermediate density, composed of a few long, smooth axonal branches. PMID:11884355 A basket cell with axonal arbors composed of frequent, short, curvy axonal branches that tend to be near their somata and within the same layer. small basket cell A basket cell with axonal arbors composed of frequent, short, curvy axonal branches that tend to be near their somata and within the same layer. PMID:11884355 A pyramidal neuron which has an apical tree which is oriented towards the white matter. inverted pyramidal neuron A pyramidal neuron which has an apical tree which is oriented towards the white matter. PMID:30715238 A pyramidal neuron which lacks a tuft formation but extends small radial distances forming a star-like shape. stellate pyramidal neuron A pyramidal neuron which lacks a tuft formation but extends small radial distances forming a star-like shape. PMID:30715238 A pyramidal neuron which has a distinctive tuft formation, distal from the soma. tufted pyramidal neuron A pyramidal neuron which has a distinctive tuft formation, distal from the soma. PMID:30715238 A pyramidal neuron which lacks a clear tuft formation but extends to large radial distances. untufted pyramidal neuron A pyramidal neuron which lacks a clear tuft formation but extends to large radial distances. PMID:30715238 Cytoplasm that exhibits a characteristic staining and color, pale-pink, with Wright-Giemsa stain. tmeehan 2010-05-25T01:36:34Z cell neutrophillic cytoplasm Cytoplasm that exhibits a characteristic staining and color, pale-pink, with Wright-Giemsa stain. GOC:add Nucleus with two or more lobes connected by a thin filament that contains no internal chromatin. http://purl.obolibrary.org/obo/GO_0098537 tmeehan 2009-12-22T03:54:43Z cell Obsoleted because duplicate with GO term. obsolete lobed nucleus https://github.com/obophenotype/cell-ontology/issues/734 true Nucleus with two or more lobes connected by a thin filament that contains no internal chromatin. GOC:tfm Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain. tmeehan 2009-12-22T04:23:25Z eosinophilic cell acidophilic cytoplasm Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain. GOC:add Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. tmeehan 2009-12-22T04:24:54Z cell basophilic cytoplasm Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. GOC:tfm Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions. tmeehan 2009-12-28T04:25:23Z cell polychromatophilic cytoplasm Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions. GOC:tfm 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 concave nuclear shape where the nucleus is indented to more than half the distance to the farthest nuclear margin, but in no area is the chromatin condensed to a single filament. tmeehan 2009-12-23T02:18:43Z cell banded nucleus A concave nuclear shape where the nucleus is indented to more than half the distance to the farthest nuclear margin, but in no area is the chromatin condensed to a single filament. GOC:tfm A concave nucleus shape where the indentation is smaller than half of the distance to the farthest nuclear margin. tmeehan 2009-12-23T02:31:25Z cell reniform nucleus A concave nucleus shape where the indentation is smaller than half of the distance to the farthest nuclear margin. GOC:tfm Heterochromatin that is arranged in a carthwheel pattern. tmeehan 2009-12-28T04:28:35Z cell cartwheel heterochromatin Heterochromatin that is arranged in a carthwheel pattern. GOC:tfm alobate nucleus The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GO:0019952 GO:0050876 Wikipedia:Reproduction reproductive physiological process biological_process GO:0000003 reproduction The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GOC:go_curators GOC:isa_complete GOC:jl ISBN:0198506732 Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. biological_process GO:0000018 regulation of DNA recombination Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. GOC:go_curators ISBN:0198506732 The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets. GO:0016359 mitotic chromosome segregation mitotic sister-chromatid adhesion release biological_process GO:0000070 mitotic sister chromatid segregation The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets. GOC:ai GOC:jl A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. microtubule cytoskeleton organisation microtubule dynamics biological_process microtubule cytoskeleton organization and biogenesis GO:0000226 microtubule cytoskeleton organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. GOC:mah microtubule cytoskeleton organisation GOC:mah microtubule dynamics GOC:dph GOC:tb microtubule cytoskeleton organization and biogenesis GOC:mah A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact. nuclear interphase chromosome cellular_component GO:0000228 nuclear chromosome A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact. GOC:dph GOC:mah A chromosome found in the cytoplasm. cytoplasmic interphase chromosome cellular_component GO:0000229 cytoplasmic chromosome A chromosome found in the cytoplasm. GOC:mah Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GO:0007067 Wikipedia:Mitosis biological_process mitosis GO:0000278 Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. mitotic cell cycle Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GOC:mah ISBN:0815316194 Reactome:69278 The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. biological_process karyokinesis GO:0000280 nuclear division The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. GOC:mah A ribosome contained within a subcellular membrane-bounded organelle. cellular_component GO:0000313 organellar ribosome A ribosome contained within a subcellular membrane-bounded organelle. GOC:mah GOC:mcc A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases. cellular_component GO:0000323 lytic vacuole A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases. GOC:krc The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. GO:0000789 GO:0000790 GO:0005717 NIF_Subcellular:sao1615953555 cytoplasmic chromatin nuclear chromatin cellular_component chromosome scaffold GO:0000785 Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. chromatin The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. GOC:elh PMID:20404130 A dispersed and relatively uncompacted form of chromatin. GO:0005719 NIF_Subcellular:sao445485807 Wikipedia:Euchromatin cellular_component nuclear euchromatin GO:0000791 euchromatin A dispersed and relatively uncompacted form of chromatin. GOC:elh A compact and highly condensed form of chromatin. GO:0005720 NIF_Subcellular:sao581845896 Wikipedia:Heterochromatin nuclear heterochromatin cellular_component GO:0000792 heterochromatin A compact and highly condensed form of chromatin. GOC:elh The cell cycle process in which sister chromatids are organized and then physically separated and apportioned to two or more sets. biological_process GO:0000819 sister chromatid segregation The cell cycle process in which sister chromatids are organized and then physically separated and apportioned to two or more sets. GOC:ai GOC:elh Any process that modulates levels of neurotransmitter. biological_process GO:0001505 regulation of neurotransmitter levels Any process that modulates levels of neurotransmitter. GOC:jl A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities. biological_process GO:0001508 Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so. action potential A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities. GOC:dph GOC:go_curators GOC:tb ISBN:978-0-07-139011-8 Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels. Wikipedia:Angiogenesis blood vessel formation from pre-existing blood vessels biological_process GO:0001525 angiogenesis Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels. ISBN:0878932453 blood vessel formation from pre-existing blood vessels Cell motility due to movement of eukaryotic cilia or bacterial-type flagella or archaeal-type flagella. ciliary/flagellar motility biological_process ciliary or bacterial-type flagellar motility GO:0001539 Note that we deem eukaryotic cilia and microtubule-based flagella to be equivalent, while the bacterial- and archaeal-type flagella have a different structure. The former are microtubule-based structures that lash back and forth and are present only in eukaryotes, while the latter achieve motility by rotation. Bacterial- and archaeal-type flagella are superficially similar but have a different molecular composition and fine structure. These three structures never co-exist in the same organism. Therefore, GO:0001539 'cilium or flagellum-dependent cell motility' is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term. Direct annotations to GO:0001539 'cilium or flagellum-dependent cell motility' may be amended during annotation QC. cilium or flagellum-dependent cell motility Cell motility due to movement of eukaryotic cilia or bacterial-type flagella or archaeal-type flagella. GOC:cilia GOC:hjd GOC:krc The set of processes resulting in differentiation of theca and granulosa cells into luteal cells and in the formation of a corpus luteum after ovulation. Wikipedia:Luteal_phase Wikipedia:Luteinization biological_process luteal phase GO:0001553 luteinization The set of processes resulting in differentiation of theca and granulosa cells into luteal cells and in the formation of a corpus luteum after ovulation. https://www.ncbi.nlm.nih.gov/books/NBK279054/ The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood. biological_process GO:0001568 blood vessel development The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood. GOC:hjd UBERON:0001981 A process that results in a parallel arrangement of microtubules. microtubule bundling biological_process GO:0001578 microtubule bundle formation A process that results in a parallel arrangement of microtubules. GOC:dph Cell migration that is accomplished by extension and retraction of a pseudopodium. ameboid cell migration amoeboid cell migration amoeboidal cell migration biological_process GO:0001667 Note that this term refers to a mode of migration rather than to any particular cell type. ameboidal-type cell migration Cell migration that is accomplished by extension and retraction of a pseudopodium. GOC:dph The formation of the acrosome from the spermatid Golgi. acrosome formation biological_process GO:0001675 acrosome assembly The formation of the acrosome from the spermatid Golgi. GOC:dph GOC:hjd GOC:tb acrosome formation GOC:dph GOC:tb The change in morphology and behavior of a dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor. biological_process GO:0001773 myeloid dendritic cell activation The change in morphology and behavior of a dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor. GOC:mgi_curators ISBN:0781735149 A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand. biological_process GO:0001775 cell activation A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand. GOC:mgi_curators The process of regulating the proliferation and elimination of cells of the immune system such that the total number of cells of a particular cell type within a whole or part of an organism is stable over time in the absence of an outside stimulus. immune cell homeostasis leucocyte homeostasis biological_process GO:0001776 Note that this term represents the return of immune system cell levels to stable numbers following an immune response as well as the proliferation and elimination of cells of the immune system required to maintain stable numbers in the absence of an outside stimulus. leukocyte homeostasis The process of regulating the proliferation and elimination of cells of the immune system such that the total number of cells of a particular cell type within a whole or part of an organism is stable over time in the absence of an outside stimulus. GOC:add ISBN:0781735149 The process of regulating the proliferation and elimination of B cells such that the total number of B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus. B lymphocyte homeostasis B-cell homeostasis B-lymphocyte homeostasis biological_process GO:0001782 Note that this term represents the return of B cell levels to stable numbers following an immune response as well as the proliferation and elimination of B cells required to maintain stable numbers in the absence of an outside stimulus. B cell homeostasis The process of regulating the proliferation and elimination of B cells such that the total number of B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus. GOC:add ISBN:0781735149 PMID:12956429 Any apoptotic process in a B cell, a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity. B cell programmed cell death by apoptosis B lymphocyte apoptosis B lymphocyte programmed cell death by apoptosis B-cell apoptosis B-cell programmed cell death by apoptosis B-lymphocyte apoptosis B-lymphocyte programmed cell death by apoptosis apoptosis of B cells apoptosis of B lymphocytes apoptosis of B-cells apoptosis of B-lymphocytes programmed cell death of B cells by apoptosis programmed cell death of B lymphocytes by apoptosis programmed cell death of B-cells by apoptosis programmed cell death of B-lymphocytes by apoptosis programmed cell death, B cells programmed cell death, B lymphocytes programmed cell death, B-cells programmed cell death, B-lymphocytes B cell apoptosis biological_process GO:0001783 B cell apoptotic process Any apoptotic process in a B cell, a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity. CL:0000236 GOC:add GOC:mtg_apoptosis ISBN:0781735149 The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. https://github.com/geneontology/go-ontology/issues/19116 GO:0042032 GO:0042089 GO:0042107 GO:0050663 cytokine biosynthetic process cytokine metabolic process cytokine secretion interferon production interferon secretion interleukin production interleukin secretion biological_process GO:0001816 Note that this term is intended for use when a gene product is seen to cause apparent increases in intracellular or extracellular cytokine levels, without specific regard as to whether the increase is due to increased biosynthesis, increased secretion of preexisting cytokine molecules, or increased conversion from precursor molecules. cytokine production The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:add ISBN:0781735149 interferon production GOC:add GOC:mah interferon secretion GOC:add GOC:mah interleukin production GOC:add GOC:mah http://wiki.geneontology.org/index.php/Why_isn%27t_interleukin_in_GO%3F interleukin secretion GOC:add GOC:mah http://wiki.geneontology.org/index.php/Why_isn%27t_interleukin_in_GO%3F Any process that modulates the frequency, rate, or extent of production of a cytokine. GO:0042035 GO:0050707 regulation of cytokine anabolism regulation of cytokine biosynthesis regulation of cytokine formation regulation of cytokine synthesis regulation of cytokine biosynthetic process regulation of cytokine secretion biological_process GO:0001817 regulation of cytokine production Any process that modulates the frequency, rate, or extent of production of a cytokine. GOC:add ISBN:0781735149 Any process that stops, prevents, or reduces the rate of production of a cytokine. GO:0042036 GO:0050710 down regulation of cytokine biosynthetic process down regulation of cytokine production down-regulation of cytokine biosynthetic process down-regulation of cytokine production downregulation of cytokine biosynthetic process downregulation of cytokine production negative regulation of cytokine anabolism negative regulation of cytokine biosynthesis negative regulation of cytokine formation negative regulation of cytokine synthesis inhibition of cytokine biosynthetic process inhibition of cytokine production negative regulation of cytokine biosynthetic process negative regulation of cytokine secretion biological_process GO:0001818 negative regulation of cytokine production Any process that stops, prevents, or reduces the rate of production of a cytokine. GOC:add ISBN:0781735149 Any process that activates or increases the frequency, rate or extent of production of a cytokine. GO:0042108 GO:0050715 up regulation of cytokine production up-regulation of cytokine production upregulation of cytokine production activation of cytokine production positive regulation of cytokine biosynthetic process positive regulation of cytokine secretion stimulation of cytokine production biological_process GO:0001819 positive regulation of cytokine production Any process that activates or increases the frequency, rate or extent of production of a cytokine. GOC:add ISBN:0781735149 The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells. 5-HT secretion 5-hydroxytryptamine secretion biological_process serotonin release GO:0001820 serotonin secretion The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells. GOC:ef ISBN:0198506732 ISBN:0781735149 serotonin release GOC:tb The regulated release of histamine by a cell or tissue. It is formed by decarboxylation of histidine and it acts through receptors in smooth muscle and in secretory systems. biological_process GO:0001821 histamine secretion The regulated release of histamine by a cell or tissue. It is formed by decarboxylation of histidine and it acts through receptors in smooth muscle and in secretory systems. GOC:mah ISBN:0198506732 ISBN:0781735149 A homeostatic process involved in the maintenance of an internal steady state within a defined tissue of an organism, including control of cellular proliferation and death and control of metabolic function. tissue maintenance biological_process GO:0001894 tissue homeostasis A homeostatic process involved in the maintenance of an internal steady state within a defined tissue of an organism, including control of cellular proliferation and death and control of metabolic function. GOC:add GOC:isa_complete tissue maintenance GOC:add Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions. biological_process necrosis GO:0001906 cell killing Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions. GOC:add The directed killing of a target cell by a leukocyte. immune cell mediated cell death immune cell mediated cell killing immune cell mediated cytotoxicity leucocyte mediated cytotoxicity biological_process GO:0001909 Note that this term and its children describe contact-dependent killing of target cells by lymphocytes and myeloid cells of the immune system. leukocyte mediated cytotoxicity The directed killing of a target cell by a leukocyte. GOC:add GO_REF:0000022 ISBN:0781735149 PMID:11911826 Any process that modulates the frequency, rate, or extent of leukocyte mediated cytotoxicity. regulation of immune cell mediated cell death regulation of immune cell mediated cell killing regulation of immune cell mediated cytotoxicity regulation of leucocyte mediated cytotoxicity biological_process GO:0001910 regulation of leukocyte mediated cytotoxicity Any process that modulates the frequency, rate, or extent of leukocyte mediated cytotoxicity. GOC:add ISBN:0781735149 PMID:11911826 Any process that stops, prevents, or reduces the rate of leukocyte mediated cytotoxicity. down regulation of leukocyte mediated cytotoxicity down-regulation of leukocyte mediated cytotoxicity downregulation of leukocyte mediated cytotoxicity negative regulation of immune cell mediated cytotoxicity negative regulation of leucocyte mediated cytotoxicity inhibition of leukocyte mediated cytotoxicity biological_process GO:0001911 negative regulation of leukocyte mediated cytotoxicity Any process that stops, prevents, or reduces the rate of leukocyte mediated cytotoxicity. GOC:add ISBN:0781735149 PMID:11911826 Any process that activates or increases the frequency, rate or extent of leukocyte mediated cytotoxicity. positive regulation of immune cell mediated cytotoxicity positive regulation of leucocyte mediated cytotoxicity up regulation of leukocyte mediated cytotoxicity up-regulation of leukocyte mediated cytotoxicity upregulation of leukocyte mediated cytotoxicity activation of leukocyte mediated cytotoxicity stimulation of leukocyte mediated cytotoxicity biological_process GO:0001912 positive regulation of leukocyte mediated cytotoxicity Any process that activates or increases the frequency, rate or extent of leukocyte mediated cytotoxicity. GOC:add ISBN:0781735149 PMID:11911826 The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. T cell mediated apoptosis T cell mediated cell death T cell mediated cell killing T lymphocyte mediated cytotoxicity T-cell mediated apoptosis T-cell mediated cell death T-cell mediated cell killing T-cell mediated cytotoxicity T-lymphocyte mediated cytotoxicity biological_process T cell mediated cytolysis GO:0001913 Note that either or both mechanisms mentioned in the definition may be used in this process. Note that both granule release and the engagement of death receptors on target cells result in the induction of apoptosis in the target cell. Note that both CD4 and CD8 positive T cells can mediate apoptosis of target cells, independently of their definition as 'helper' T cells or not. T cell mediated cytotoxicity The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. GOC:add GOC:pr ISBN:0781735149 PMID:11911826 Any process that modulates the frequency, rate, or extent of T cell mediated cytotoxicity. regulation of T cell mediated apoptosis regulation of T cell mediated cell death regulation of T cell mediated cell killing regulation of T lymphocyte mediated cytotoxicity regulation of T-cell mediated apoptosis regulation of T-cell mediated cell death regulation of T-cell mediated cell killing regulation of T-cell mediated cytotoxicity regulation of T-lymphocyte mediated cytotoxicity biological_process regulation of T cell mediated cytolysis regulation of T-cell mediated cytolysis GO:0001914 regulation of T cell mediated cytotoxicity Any process that modulates the frequency, rate, or extent of T cell mediated cytotoxicity. GOC:add ISBN:0781735149 Any process that stops, prevents, or reduces the rate of T cell mediated cytotoxicity. down regulation of T cell mediated cytotoxicity down-regulation of T cell mediated cytotoxicity downregulation of T cell mediated cytotoxicity negative regulation of T cell mediated apoptosis negative regulation of T cell mediated cell death negative regulation of T cell mediated cell killing negative regulation of T lymphocyte mediated cytotoxicity negative regulation of T-cell mediated apoptosis negative regulation of T-cell mediated cell death negative regulation of T-cell mediated cell killing negative regulation of T-cell mediated cytotoxicity negative regulation of T-lymphocyte mediated cytotoxicity inhibition of T cell mediated cytotoxicity biological_process negative regulation of T cell mediated cytolysis negative regulation of T-cell mediated cytolysis GO:0001915 negative regulation of T cell mediated cytotoxicity Any process that stops, prevents, or reduces the rate of T cell mediated cytotoxicity. GOC:add ISBN:0781735149 Any process that activates or increases the frequency, rate or extent of T cell mediated cytotoxicity. positive regulation of T cell mediated apoptosis positive regulation of T cell mediated cell death positive regulation of T cell mediated cell killing positive regulation of T lymphocyte mediated cytotoxicity positive regulation of T-cell mediated apoptosis positive regulation of T-cell mediated cell death positive regulation of T-cell mediated cell killing positive regulation of T-cell mediated cytotoxicity positive regulation of T-lymphocyte mediated cytotoxicity up regulation of T cell mediated cytotoxicity up-regulation of T cell mediated cytotoxicity upregulation of T cell mediated cytotoxicity activation of T cell mediated cytotoxicity stimulation of T cell mediated cytotoxicity biological_process positive regulation of T cell mediated cytolysis positive regulation of T-cell mediated cytolysis GO:0001916 positive regulation of T cell mediated cytotoxicity Any process that activates or increases the frequency, rate or extent of T cell mediated cytotoxicity. GOC:add ISBN:0781735149 The process whose specific outcome is the progression of the vasculature over time, from its formation to the mature structure. The vasculature is an interconnected tubular multi-tissue structure that contains fluid that is actively transported around the organism. biological_process vascular system development GO:0001944 vasculature development The process whose specific outcome is the progression of the vasculature over time, from its formation to the mature structure. The vasculature is an interconnected tubular multi-tissue structure that contains fluid that is actively transported around the organism. GOC:dph UBERON:0002409 Any process that activates or increases the frequency, rate or extent of the regulated release of a neurotransmitter. up regulation of neurotransmitter secretion up-regulation of neurotransmitter secretion upregulation of neurotransmitter secretion activation of neurotransmitter secretion stimulation of neurotransmitter secretion biological_process GO:0001956 positive regulation of neurotransmitter secretion Any process that activates or increases the frequency, rate or extent of the regulated release of a neurotransmitter. GOC:hjd The vesicular release of dopamine. from a presynapse, across a chemical synapse, the subsequent activation of dopamine receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. dopaminergic synaptic transmission biological_process GO:0001963 synaptic transmission, dopaminergic The vesicular release of dopamine. from a presynapse, across a chemical synapse, the subsequent activation of dopamine receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. GOC:dos GOC:dph The reorganization or renovation of existing blood vessels. biological_process GO:0001974 blood vessel remodeling The reorganization or renovation of existing blood vessels. GOC:hjd The regulation of blood pressure mediated by detection of stimuli and a neurological response. blood pressure regulation by neurological process neurological process involved in regulation of systemic arterial blood pressure neurological system process involved in regulation of systemic arterial blood pressure biological_process fast control of arterial pressure GO:0001976 nervous system process involved in regulation of systemic arterial blood pressure The regulation of blood pressure mediated by detection of stimuli and a neurological response. GOC:mtg_cardio ISBN:0721643949 neurological process involved in regulation of systemic arterial blood pressure GOC:dph GOC:tb The process in which hormones modulate the force with which blood passes through the circulatory system. A hormone is one of a group of substances 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 they have a specific regulatory action. blood pressure regulation by hormone hormonal regulation of blood pressure biological_process hormonal control of blood pressure GO:0001990 regulation of systemic arterial blood pressure by hormone The process in which hormones modulate the force with which blood passes through the circulatory system. A hormone is one of a group of substances 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 they have a specific regulatory action. GOC:mtg_cardio ISBN:0721643949 The process in which angiotensinogen metabolites in the bloodstream modulate the force with which blood passes through the circulatory system. The process begins when renin is released and cleaves angiotensinogen. circulatory renin-angiotensin blood pressure regulation circulatory renin-angiotensin regulation of blood pressure biological_process circulatory renin-angiotensin control of blood pressure control of blood pressure by circulatory renin-angiotensin renin-angiotensin blood pressure control GO:0001991 regulation of systemic arterial blood pressure by circulatory renin-angiotensin The process in which angiotensinogen metabolites in the bloodstream modulate the force with which blood passes through the circulatory system. The process begins when renin is released and cleaves angiotensinogen. ISBN:0721643949 The physiological response of the kidneys to a decrease in blood flow. biological_process renal response to blood flow during renin-angiotensin control of blood pressure GO:0001999 renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure The physiological response of the kidneys to a decrease in blood flow. GOC:dph The regulated release of renin into the blood stream by juxtoglomerular cells. renin release into blood stream biological_process GO:0002001 renin secretion into blood stream The regulated release of renin into the blood stream by juxtoglomerular cells. ISBN:0721643949 A process carried out by the nervous system that is required for the proper control of respiratory gaseous exchange. This process occurs in the respiratory center of the brain in vertebrates. neurological control of breathing regulation of respiratory gaseous exchange by neurological system process biological_process GO:0002087 regulation of respiratory gaseous exchange by nervous system process A process carried out by the nervous system that is required for the proper control of respiratory gaseous exchange. This process occurs in the respiratory center of the brain in vertebrates. GOC:dph GOC:tb PMID:12458206 neurological control of breathing GOC:dph GOC:tb The somatic process allowing for the production of immune receptors whose specificity is not encoded in the germline genomic sequences. biological_process GO:0002200 Note that this process covers somatic recombination, gene conversion, hypermutation, N-region addition, and alternate splicing processes of immune receptor diversification. somatic diversification of immune receptors The somatic process allowing for the production of immune receptors whose specificity is not encoded in the germline genomic sequences. GOC:add ISBN:0781735149 PMID:16102575 PMID:16166509 The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, also known as immunoglobulin gene segments, within a single locus following the induction of and contributing to an immune response. biological_process somatic recombination of antibody genes during immune response somatic recombination of immunoglobulin genes during immune response GO:0002204 somatic recombination of immunoglobulin genes involved in immune response The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, also known as immunoglobulin gene segments, within a single locus following the induction of and contributing to an immune response. GOC:add ISBN:0781735149 somatic recombination of immunoglobulin genes during immune response GOC:dph The somatic process that results in the generation of sequence diversity of immunoglobulins after induction, and contributes to an immune response. biological_process somatic diversification of antibodies during immune response somatic diversification of immunoglobulins during immune response GO:0002208 somatic diversification of immunoglobulins involved in immune response The somatic process that results in the generation of sequence diversity of immunoglobulins after induction, and contributes to an immune response. GOC:add ISBN:0781735149 PMID:14991701 somatic diversification of immunoglobulins during immune response GOC:dph A response to protect an organism from a directly detected or perceived external threat from a nematode or nematodes, which results in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. GO:0002216 physiological defense response to nematode biological_process GO:0002215 defense response to nematode A response to protect an organism from a directly detected or perceived external threat from a nematode or nematodes, which results in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. GOC:add PMID:11516579 PMID:14506883 Any process that activates or increases the frequency, rate, or extent of antimicrobial peptide production. antimicrobial peptide induction up regulation of antimicrobial peptide production up-regulation of antimicrobial peptide production upregulation of antimicrobial peptide production activation of antimicrobial peptide production stimulation of antimicrobial peptide production biological_process GO:0002225 positive regulation of antimicrobial peptide production Any process that activates or increases the frequency, rate, or extent of antimicrobial peptide production. GOC:add PMID:11807545 Any process of the innate immune response that takes place in the mucosal tissues. biological_process GO:0002227 innate immune response in mucosa Any process of the innate immune response that takes place in the mucosal tissues. GOC:add PMID:10719665 PMID:15971105 The promotion of an immune response by natural killer cells through direct recognition of target cells or through the release of cytokines. NK cell mediated immunity biological_process GO:0002228 natural killer cell mediated immunity The promotion of an immune response by natural killer cells through direct recognition of target cells or through the release of cytokines. GOC:add GO_REF:0000022 ISBN:0781735149 The movement of an immune cell in response to an external stimulus contributing to an inflammatory response. biological_process immune cell chemotaxis during inflammatory response leucocyte chemotaxis during inflammatory response leukocyte chemotaxis during inflammatory response GO:0002232 leukocyte chemotaxis involved in inflammatory response The movement of an immune cell in response to an external stimulus contributing to an inflammatory response. GOC:add ISBN:0781735149 leukocyte chemotaxis during inflammatory response GOC:dph The movement of an immune cell in response to an external stimulus a part of an immune response. immune cell chemotaxis during immune response leucocyte chemotaxis during immune response biological_process GO:0002233 leukocyte chemotaxis involved in immune response The movement of an immune cell in response to an external stimulus a part of an immune response. GOC:add ISBN:0781735149 The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells. haematopoietic progenitor cell differentiation haemopoietic progenitor cell differentiation hemopoietic progenitor cell differentiation biological_process GO:0002244 hematopoietic progenitor cell differentiation The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells. GOC:add GOC:rl ISBN:0781735149 PMID:16551251 The series of events that restore integrity to damaged tissue that contribute to an inflammatory response. biological_process healing during inflammatory response inflammatory response wound healing GO:0002246 wound healing involved in inflammatory response The series of events that restore integrity to damaged tissue that contribute to an inflammatory response. GOC:jal ISBN:0721601871 healing during inflammatory response GOC:dph inflammatory response wound healing GOC:dph Any process contributing to lymphocyte anergy, a state of functional inactivation. biological_process GO:0002249 lymphocyte anergy Any process contributing to lymphocyte anergy, a state of functional inactivation. GOC:add An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). Wikipedia:Adaptive_immune_system acquired immune response immune memory response biological_process GO:0002250 adaptive immune response An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). GOC:add GO_REF:0000022 ISBN:0781735149 acquired immune response ISBN:068340007X immune memory response GOC:add An immune response taking place in an organ or tissues such as the liver, brain, mucosa, or nervous system tissues. immune response in organ or tissue biological_process GO:0002251 organ or tissue specific immune response An immune response taking place in an organ or tissues such as the liver, brain, mucosa, or nervous system tissues. GOC:jal GO_REF:0000022 Any process of the immune system that executes a component of an immune response. An effector immune process takes place after its activation. https://github.com/geneontology/go-ontology/issues/18737 biological_process GO:0002252 immune effector process Any process of the immune system that executes a component of an immune response. An effector immune process takes place after its activation. GOC:add GO_REF:0000022 ISBN:0781735149 The process of regulating the proliferation and elimination of lymphocytes such that the total number of lymphocytes within a whole or part of an organism is stable over time in the absence of an outside stimulus. biological_process GO:0002260 lymphocyte homeostasis The process of regulating the proliferation and elimination of lymphocytes such that the total number of lymphocytes within a whole or part of an organism is stable over time in the absence of an outside stimulus. GOC:add PMID:15826826 PMID:16319493 PMID:16551252 PMID:16551262 The process of regulating the proliferation and elimination of myeloid cells such that the total number of myeloid cells within a whole or part of an organism is stable over time in the absence of an outside stimulus. biological_process GO:0002262 myeloid cell homeostasis The process of regulating the proliferation and elimination of myeloid cells such that the total number of myeloid cells within a whole or part of an organism is stable over time in the absence of an outside stimulus. CL:0000763 GOC:add A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an immune response. biological_process cell activation during immune response GO:0002263 cell activation involved in immune response A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an immune response. GOC:add GO_REF:0000022 ISBN:0781735149 cell activation during immune response GOC:tb A change in the morphology or behavior of a leukocyte resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an inflammatory response. biological_process immune cell activation during inflammatory response leukocyte activation during inflammatory response GO:0002269 leukocyte activation involved in inflammatory response A change in the morphology or behavior of a leukocyte resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an inflammatory response. GOC:add ISBN:0781735149 leukocyte activation during inflammatory response GOC:tb A change in the morphology or behavior of a myeloid leukocyte resulting from exposure to an activating factor such as a cellular or soluble ligand. myeloid leucocyte activation biological_process GO:0002274 myeloid leukocyte activation A change in the morphology or behavior of a myeloid leukocyte resulting from exposure to an activating factor such as a cellular or soluble ligand. GOC:add ISBN:0781735149 A change in the morphology or behavior of a myeloid cell resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an immune response. biological_process myeloid cell activation during immune response GO:0002275 myeloid cell activation involved in immune response A change in the morphology or behavior of a myeloid cell resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an immune response. GOC:add ISBN:0781735149 myeloid cell activation during immune response GOC:tb The change in morphology and behavior of a myeloid dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response. biological_process myeloid dendritic cell activation during immune response GO:0002277 myeloid dendritic cell activation involved in immune response The change in morphology and behavior of a myeloid dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response. GOC:add ISBN:0781735149 myeloid dendritic cell activation during immune response GOC:tb The process in which an immature myeloid dendritic cell acquires the specialized features of a mature myeloid dendritic cell as part of an immune response. biological_process myeloid dendritic cell differentiation during immune response GO:0002284 myeloid dendritic cell differentiation involved in immune response The process in which an immature myeloid dendritic cell acquires the specialized features of a mature myeloid dendritic cell as part of an immune response. GOC:add ISBN:0781735149 myeloid dendritic cell differentiation during immune response GOC:tb A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response. biological_process lymphocyte activation during immune response GO:0002285 lymphocyte activation involved in immune response A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response. GOC:add ISBN:0781735149 lymphocyte activation during immune response GOC:tb The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response. biological_process T cell activation during immune response T lymphocyte activation during immune response T-cell activation during immune response T-lymphocyte activation during immune response GO:0002286 T cell activation involved in immune response The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response. GOC:add ISBN:0781735149 T cell activation during immune response GOC:tb The change in morphology and behavior of an alpha-beta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response. biological_process alpha-beta T cell activation during immune response alpha-beta T lymphocyte activation during immune response alpha-beta T-cell activation during immune response alpha-beta T-lymphocyte activation during immune response GO:0002287 alpha-beta T cell activation involved in immune response The change in morphology and behavior of an alpha-beta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response. GOC:add ISBN:0781735149 alpha-beta T cell activation during immune response GOC:tb The change in morphology and behavior of a mature or immature natural killer T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response. biological_process NK T cell activation during immune response NK T lymphocyte activation during immune response NK T-cell activation during immune response NK T-lymphocyte activation during immune response natural killer T lymphocyte activation during immune response natural killer T-cell activation during immune response natural killer T-lymphocyte activation during immune response GO:0002288 NK T cell activation involved in immune response The change in morphology and behavior of a mature or immature natural killer T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response. GOC:add PMID:15771592 NK T cell activation during immune response GOC:tb The change in morphology and behavior of a gamma-delta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response. biological_process gamma-delta T cell activation during immune response gamma-delta T lymphocyte activation during immune response gamma-delta T-cell activation during immune response gamma-delta T-lymphocyte activation during immune response GO:0002290 gamma-delta T cell activation involved in immune response The change in morphology and behavior of a gamma-delta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response. GOC:add PMID:8717523 gamma-delta T cell activation during immune response GOC:tb The process in which an antigenically naive T cell acquires the specialized features of an effector, regulatory, or memory T cell as part of an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells. biological_process T cell development involved in immune response T cell differentiation during immune response T lymphocyte differentiation during immune response T-cell differentiation during immune response T-lymphocyte differentiation during immune response GO:0002292 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. T cell differentiation involved in immune response The process in which an antigenically naive T cell acquires the specialized features of an effector, regulatory, or memory T cell as part of an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells. GOC:add ISBN:0781735149 T cell development involved in immune response GOC:add T cell differentiation during immune response GOC:tb The process in which an antigenically naive alpha-beta T cell acquires the specialized features of an effector, regulatory, or memory T cell during an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells. biological_process alpha-beta T cell development involved in immune response alpha-beta T cell differentiation during immune response alpha-beta T lymphocyte differentiation during immune response alpha-beta T-cell differentiation during immune response alpha-beta T-lymphocyte differentiation during immune response GO:0002293 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. alpha-beta T cell differentiation involved in immune response The process in which an antigenically naive alpha-beta T cell acquires the specialized features of an effector, regulatory, or memory T cell during an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells. GOC:add ISBN:0781735149 alpha-beta T cell development involved in immune response GOC:add alpha-beta T cell differentiation during immune response GOC:tb The process in which an antigenically naive CD4-positive, alpha-beta T cell acquires the specialized features of an effector, regulatory, or memory T cell as part of an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells. biological_process CD4-positive, alpha-beta T cell development involved in immune response CD4-positive, alpha-beta T cell differentiation during immune response CD4-positive, alpha-beta T lymphocyte differentiation during immune response CD4-positive, alpha-beta T-cell differentiation during immune response CD4-positive, alpha-beta T-lymphocyte differentiation during immune response GO:0002294 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. CD4-positive, alpha-beta T cell differentiation involved in immune response The process in which an antigenically naive CD4-positive, alpha-beta T cell acquires the specialized features of an effector, regulatory, or memory T cell as part of an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells. GOC:add ISBN:0781735149 CD4-positive, alpha-beta T cell development involved in immune response GOC:add CD4-positive, alpha-beta T cell differentiation during immune response GOC:tb The process in which an antigenically naive gamma-delta T cell acquires the specialized features of an effector, regulatory, or memory T cell and contributes to an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells. biological_process gamma-delta T cell development involved in immune response gamma-delta T cell differentiation during immune response gamma-delta T lymphocyte differentiation during immune response gamma-delta T-cell differentiation during immune response gamma-delta T-lymphocyte differentiation during immune response GO:0002303 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. gamma-delta T cell differentiation involved in immune response The process in which an antigenically naive gamma-delta T cell acquires the specialized features of an effector, regulatory, or memory T cell and contributes to an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells. GOC:add gamma-delta T cell development involved in immune response GOC:add gamma-delta T cell differentiation during immune response GOC:dph The expansion of a T cell population by cell division as part of an immune response. biological_process T cell proliferation during immune response T lymphocyte proliferation during immune response T-cell proliferation during immune response T-lymphocyte proliferation during immune response GO:0002309 T cell proliferation involved in immune response The expansion of a T cell population by cell division as part of an immune response. GOC:add ISBN:0781735149 T cell proliferation during immune response GOC:tb The change in morphology and behavior of a mature or immature B cell during an immune response, resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. biological_process B cell activation during immune response B lymphocyte activation during immune response B-cell activation during immune response B-lymphocyte activation during immune response GO:0002312 B cell activation involved in immune response The change in morphology and behavior of a mature or immature B cell during an immune response, resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. GOC:jal B cell activation during immune response GOC:tb The process in which a naive B cell acquires the specialized features of a mature or memory B cell during an immune response. biological_process mature B cell development involved in immune response mature B cell differentiation during immune response mature B lymphocyte differentiation during immune response mature B-cell differentiation during immune response mature B-lymphocyte differentiation during immune response GO:0002313 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. mature B cell differentiation involved in immune response The process in which a naive B cell acquires the specialized features of a mature or memory B cell during an immune response. GOC:jal mature B cell development involved in immune response GOC:add mature B cell differentiation during immune response GOC:tb The process in which a B cell in the spleen acquires the specialized features of a germinal center B cell. Germinal center B cells are rapidly cycling B cells which have downregulated IgD expression and exhibit high levels of binding by peanut agglutinin (PNA). germinal center B lymphocyte differentiation germinal center B-cell differentiation germinal center B-lymphocyte differentiation biological_process germinal center B cell development GO:0002314 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. germinal center B cell differentiation The process in which a B cell in the spleen acquires the specialized features of a germinal center B cell. Germinal center B cells are rapidly cycling B cells which have downregulated IgD expression and exhibit high levels of binding by peanut agglutinin (PNA). GOC:jal ISBN:0781735149 germinal center B cell development GOC:add The change in morphology and behavior of a natural killer cell resulting from exposure a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response. biological_process NK cell activation during immune response natural killer cell activation during immune response GO:0002323 natural killer cell activation involved in immune response The change in morphology and behavior of a natural killer cell resulting from exposure a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response. GOC:add PMID:15032583 natural killer cell activation during immune response GOC:tb The process in which transitional stage B cells acquire the specialized features of mature B cells in the spleen. mature B lymphocyte differentiation mature B-cell differentiation mature B-lymphocyte differentiation biological_process mature cell development GO:0002335 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. mature B cell differentiation The process in which transitional stage B cells acquire the specialized features of mature B cells in the spleen. GOC:jal ISBN:0781735149 mature cell development GOC:add The process dependent upon B cell antigen receptor signaling in response to self or foreign antigen through which B cells are selected for survival. B lymphocyte selection B-cell selection B-lymphocyte selection biological_process GO:0002339 B cell selection The process dependent upon B cell antigen receptor signaling in response to self or foreign antigen through which B cells are selected for survival. GOC:jal Any B cell selection process that occurs in the periphery. peripheral B lymphocyte selection peripheral B-cell selection peripheral B-lymphocyte selection biological_process GO:0002343 peripheral B cell selection Any B cell selection process that occurs in the periphery. GOC:jal The process in which B cells produce antibodies with increased antigen affinity. This is accomplished by somatic hypermutation and selection for B cells which produce higher affinity antibodies to antigen. B lymphocyte affinity maturation B-cell affinity maturation B-lymphocyte affinity maturation biological_process GO:0002344 B cell affinity maturation The process in which B cells produce antibodies with increased antigen affinity. This is accomplished by somatic hypermutation and selection for B cells which produce higher affinity antibodies to antigen. GOC:jal GO_REF:0000022 ISBN:0781735149 The synthesis or release of histamine following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. histamine production involved in acute inflammatory response biological_process GO:0002349 histamine production involved in inflammatory response The synthesis or release of histamine following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. GOC:add ISBN:0781735149 PMID:16730260 The synthesis or release of serotonin following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. serotonin production involved in acute inflammatory response biological_process GO:0002351 serotonin production involved in inflammatory response The synthesis or release of serotonin following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. GOC:add ISBN:0781735149 PMID:16730260 A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response. biological_process immune cell activation during immune response leucocyte activation during immune response leukocyte activation during immune response GO:0002366 leukocyte activation involved in immune response A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response. GOC:add ISBN:0781735149 leukocyte activation during immune response GOC:tb The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels. GO:0002374 GO:0002375 cytokine biosynthetic process involved in immune response biological_process cytokine production during immune response cytokine secretion during immune response cytokine secretion involved in immune response GO:0002367 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. cytokine production involved in immune response The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels. GOC:add GO_REF:0000022 ISBN:0781735149 cytokine production during immune response GOC:dph cytokine secretion during immune response GOC:dph Any process that contributes to cytokine production by a T cell. T lymphocyte cytokine production T-cell cytokine production T-lymphocyte cytokine production biological_process GO:0002369 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. T cell cytokine production Any process that contributes to cytokine production by a T cell. GOC:add ISBN:0781735149 Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. Wikipedia:Immune_system biological_process GO:0002376 Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501). immune system process Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. GOC:add GO_REF:0000022 The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GO:0002378 GO:0048305 antibody production immunoglobulin biosynthetic process immunoglobulin secretion biological_process GO:0002377 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. immunoglobulin production The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:add ISBN:0781735149 The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus during an immune response, resulting in an increase in its intracellular or extracellular levels. GO:0002379 GO:0002380 immunoglobulin production involved in immunoglobulin mediated immune response immunoglobulin biosynthetic process involved in immune response immunoglobulin secretion involved in immune response biological_process antibody production during immune response antibody secretion during immune response immunoglobulin production during immune response immunoglobulin production involved in immune response GO:0002381 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. immunoglobulin production involved in immunoglobulin-mediated immune response The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus during an immune response, resulting in an increase in its intracellular or extracellular levels. GOC:add ISBN:0781735149 PMID:9185563 immunoglobulin production during immune response GOC:dph immunoglobulin production involved in immune response GOC:dph An immune response taking place in mucosal tissues, including those of the intestinal tract, nasal and upper respiratory tract, and genital tract. GO:0002386 GO:0002422 immune response in MALT immune response in mucosal-associated lymphoid tissue immune response in urogenital tract biological_process GO:0002385 mucosal immune response An immune response taking place in mucosal tissues, including those of the intestinal tract, nasal and upper respiratory tract, and genital tract. GOC:jal GO_REF:0000022 ISBN:0781735149 Immune response taking place in the gut-associated lymphoid tissue (GALT). GALT includes Peyer's patches, appendix, and solitary lymph nodules. immune response in GALT biological_process GO:0002387 immune response in gut-associated lymphoid tissue Immune response taking place in the gut-associated lymphoid tissue (GALT). GALT includes Peyer's patches, appendix, and solitary lymph nodules. GOC:jal ISBN:0781735149 An immune response taking place in the nasopharyngeal-associated lymphoid tissue (NALT). NALT includes the tonsils and adenoids. immune response in NALT biological_process GO:0002395 immune response in nasopharyngeal-associated lymphoid tissue An immune response taking place in the nasopharyngeal-associated lymphoid tissue (NALT). NALT includes the tonsils and adenoids. GOC:jal ISBN:0781735149 The formation of nodular inflammatory lesions, usually small or granular, firm, persistent, well-structured, and containing compactly grouped T lymphocytes and modified phagocytes such as epithelioid cells, giant cells, and other macrophages. Granuloma formation represents a chronic inflammatory response initiated by various infectious and noninfectious agents. The center of a granuloma consists of fused macrophages, which can become necrotic. biological_process GO:0002432 granuloma formation The formation of nodular inflammatory lesions, usually small or granular, firm, persistent, well-structured, and containing compactly grouped T lymphocytes and modified phagocytes such as epithelioid cells, giant cells, and other macrophages. Granuloma formation represents a chronic inflammatory response initiated by various infectious and noninfectious agents. The center of a granuloma consists of fused macrophages, which can become necrotic. GOC:add GO_REF:0000022 ISBN:068340007X ISBN:0721601464 ISBN:081533642X The synthesis or release of any molecular mediator of the immune response, resulting in an increase in its intracellular or extracellular levels. biological_process production of cellular mediator of immune response GO:0002440 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. production of molecular mediator of immune response The synthesis or release of any molecular mediator of the immune response, resulting in an increase in its intracellular or extracellular levels. GOC:add GO_REF:0000022 ISBN:0781735149 The regulated release of histamine by a cell as part of an inflammatory response. histamine secretion involved in acute inflammatory response biological_process GO:0002441 histamine secretion involved in inflammatory response The regulated release of histamine by a cell as part of an inflammatory response. GOC:add ISBN:0781735149 The regulated release of serotonin by a cell as part of an inflammatory response. serotonin secretion involved in acute inflammatory response biological_process serotonin release involved in inflammatory response GO:0002442 serotonin secretion involved in inflammatory response The regulated release of serotonin by a cell as part of an inflammatory response. GOC:add ISBN:0781735149 serotonin release involved in inflammatory response GOC:tb Any process involved in the carrying out of an immune response by a leukocyte. GO:0019723 GO:0042087 immune cell effector process immune cell mediated immunity leucocyte immune effector process leucocyte mediated immunity leukocyte immune effector process biological_process cell-mediated immune response cellular immune response GO:0002443 leukocyte mediated immunity Any process involved in the carrying out of an immune response by a leukocyte. GOC:add GO_REF:0000022 ISBN:0781735149 Any process involved in the carrying out of an immune response by a lymphocyte. cell-mediated immunity cellular immune response biological_process GO:0002449 lymphocyte mediated immunity Any process involved in the carrying out of an immune response by a lymphocyte. GOC:add GO_REF:0000022 ISBN:0781735149 Any process involved in the carrying out of an immune response by a T cell. cell-mediated immunity cellular immune response T lymphocyte mediated immunity T-cell mediated immunity T-lymphocyte mediated immunity biological_process GO:0002456 T cell mediated immunity Any process involved in the carrying out of an immune response by a T cell. GOC:add GO_REF:0000022 ISBN:0781735149 An immune response mediated by lymphocytes expressing specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains. Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies) produced by B cells. The first encounter with antigen elicits a primary immune response that is slow and not of great magnitude. T and B cells selected by antigen become activated and undergo clonal expansion. A fraction of antigen-reactive T and B cells become memory cells, whereas others differentiate into effector cells. The memory cells generated during the primary response enable a much faster and stronger secondary immune response upon subsequent exposures to the same antigen (immunological memory). An example of this is the adaptive immune response found in Mus musculus. biological_process GO:0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains An immune response mediated by lymphocytes expressing specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains. Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies) produced by B cells. The first encounter with antigen elicits a primary immune response that is slow and not of great magnitude. T and B cells selected by antigen become activated and undergo clonal expansion. A fraction of antigen-reactive T and B cells become memory cells, whereas others differentiate into effector cells. The memory cells generated during the primary response enable a much faster and stronger secondary immune response upon subsequent exposures to the same antigen (immunological memory). An example of this is the adaptive immune response found in Mus musculus. GOC:add GOC:mtg_sensu ISBN:0781735149 ISBN:1405196831 Tolerance induction dependent upon an immune response, typically a response by a mature T or B cell in the periphery resulting tolerance towards an antigen via induction of anergy, cellular deletion, or regulatory T cell activation. immune response-dependent tolerance induction biological_process GO:0002461 tolerance induction dependent upon immune response Tolerance induction dependent upon an immune response, typically a response by a mature T or B cell in the periphery resulting tolerance towards an antigen via induction of anergy, cellular deletion, or regulatory T cell activation. GOC:jal GO_REF:0000022 ISBN:0781735149 Tolerance induction in the peripheral lymphoid tissues: blood, lymph nodes, spleen, and mucosal-associated lymphoid tissues. biological_process GO:0002465 peripheral tolerance induction Tolerance induction in the peripheral lymphoid tissues: blood, lymph nodes, spleen, and mucosal-associated lymphoid tissues. GOC:jal GO_REF:0000022 ISBN:0781735149 The process in which germinal centers form. A germinal center is a specialized microenvironment formed when activated B cells enter lymphoid follicles. Germinal centers are the foci for B cell proliferation and somatic hypermutation. biological_process GO:0002467 germinal center formation The process in which germinal centers form. A germinal center is a specialized microenvironment formed when activated B cells enter lymphoid follicles. Germinal centers are the foci for B cell proliferation and somatic hypermutation. GOC:jal GO_REF:0000022 ISBN:081533642X The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules. peptide antigen processing and presentation via MHC class I biological_process GO:0002474 antigen processing and presentation of peptide antigen via MHC class I The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules. GOC:add ISBN:0781735149 PMID:15224092 PMID:15771591 The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC protein complex. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell. exogenous peptide antigen processing and presentation biological_process GO:0002478 antigen processing and presentation of exogenous peptide antigen The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC protein complex. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell. GOC:add ISBN:0781735149 The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein. peptide antigen processing and presentation via MHC class II biological_process GO:0002495 antigen processing and presentation of peptide antigen via MHC class II The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein. GOC:add ISBN:0781735149 PMID:15531770 PMID:15771591 The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex. peptide or polysaccharide antigen processing and presentation of via MHC class II biological_process GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex. GOC:add ISBN:0781735149 PMID:15531770 PMID:15771591 PMID:16153240 A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it. biological_process GO:0002507 tolerance induction A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it. GOC:jal GO_REF:0000022 ISBN:0781735149 A process involving any mechanism for tolerance induction in B cells. B lymphocyte tolerance induction B-cell tolerance induction B-lymphocyte tolerance induction biological_process GO:0002514 B cell tolerance induction A process involving any mechanism for tolerance induction in B cells. GOC:jal ISBN:0781735149 PMID:16460922 Any process contributing to anergy in B cells, a state of functional inactivation which is part of B cell tolerance induction. B lymphocyte anergy B-cell anergy B-lymphocyte anergy biological_process GO:0002515 B cell anergy Any process contributing to anergy in B cells, a state of functional inactivation which is part of B cell tolerance induction. GOC:jal ISBN:0781735149 The apoptotic death of B cells which is part of B cell tolerance induction. B lymphocyte deletion B-cell deletion B-lymphocyte deletion biological_process GO:0002516 B cell deletion The apoptotic death of B cells which is part of B cell tolerance induction. GOC:add GOC:jal ISBN:0781735149 The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, 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:0002520 immune system development The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, 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:add GOC:dph The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a leukocyte. A leukocyte is an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. immune cell differentiation leucocyte differentiation biological_process GO:0002521 leukocyte differentiation The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a leukocyte. A leukocyte is an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. CL:0000738 GOC:add PMID:16551264 The movement of a leukocyte within or between different tissues and organs of the body as part of an immune response. immune cell migration during immune response immune cell trafficking during immune response leucocyte migration during immune response leucocyte trafficking during immune response leukocyte trafficking during immune response biological_process GO:0002522 leukocyte migration involved in immune response The movement of a leukocyte within or between different tissues and organs of the body as part of an immune response. GOC:add ISBN:0781735149 PMID:14680625 PMID:14708592 PMID:7507411 PMID:8600538 The movement of a leukocyte within or between different tissues and organs of the body contributing to an inflammatory response. biological_process immune cell migration during inflammatory response immune cell trafficking during inflammatory response leucocyte migration during inflammatory response leucocyte trafficking during inflammatory response leukocyte migration during inflammatory response leukocyte trafficking during inflammatory response GO:0002523 leukocyte migration involved in inflammatory response The movement of a leukocyte within or between different tissues and organs of the body contributing to an inflammatory response. GOC:add ISBN:0781735149 PMID:14680625 PMID:14708592 PMID:7507411 PMID:8600538 leukocyte migration during inflammatory response GOC:dph Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response. biological_process GO:0002526 acute inflammatory response Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response. GOC:add GO_REF:0000022 ISBN:0781735149 The synthesis or release of any molecular mediator of the inflammatory response following an inflammatory stimulus, resulting in an increase in its intracellular or extracellular levels. production of molecular mediator involved in acute inflammatory response biological_process production of cellular mediator of acute inflammation GO:0002532 production of molecular mediator involved in inflammatory response The synthesis or release of any molecular mediator of the inflammatory response following an inflammatory stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:add GOC:dph GOC:tb ISBN:0781735149 The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. cytokine production involved in acute inflammatory response biological_process GO:0002534 cytokine production involved in inflammatory response The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. GOC:add ISBN:0781735149 A phase of elevated metabolic activity, during which oxygen consumption increases following a stimulus as part of an inflammatory response; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals, resulting in an increase in their intracellular or extracellular levels. oxidative burst during acute inflammatory response production of reactive oxygen species during acute inflammatory response respiratory burst involved in acute inflammatory response biological_process GO:0002536 respiratory burst involved in inflammatory response A phase of elevated metabolic activity, during which oxygen consumption increases following a stimulus as part of an inflammatory response; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals, resulting in an increase in their intracellular or extracellular levels. GOC:add ISBN:0781735149 The synthesis or release of nitric oxide following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. nitric oxide production involved in acute inflammatory response production of nitric oxide involved in acute inflammatory response production of nitric oxide involved in inflammatory response biological_process GO:0002537 nitric oxide production involved in inflammatory response The synthesis or release of nitric oxide following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. GOC:add ISBN:0781735149 nitric oxide production involved in acute inflammatory response GOC:mah The synthesis or release of products of arachidonic acid metabolism following a stimulus as part of an inflammatory response, resulting in an increase in their intracellular or extracellular levels. arachidonic acid metabolite production involved in acute inflammatory response production of arachidonic acid metabolites involved in acute inflammatory response production of arachidonic acid metabolites involved in inflammatory response biological_process GO:0002538 arachidonic acid metabolite production involved in inflammatory response The synthesis or release of products of arachidonic acid metabolism following a stimulus as part of an inflammatory response, resulting in an increase in their intracellular or extracellular levels. GOC:add ISBN:0781735149 arachidonic acid metabolite production involved in acute inflammatory response GOC:mah The synthesis or release of any prostaglandin following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. prostaglandin production involved in acute inflammatory response biological_process GO:0002539 prostaglandin production involved in inflammatory response The synthesis or release of any prostaglandin following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. GOC:add ISBN:0781735149 The synthesis or release of any leukotriene following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. leukotriene production involved in acute inflammatory response biological_process GO:0002540 leukotriene production involved in inflammatory response The synthesis or release of any leukotriene following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. GOC:add ISBN:0781735149 Inflammation of prolonged duration (weeks or months) in which active inflammation, tissue destruction, and attempts at repair are proceeding simultaneously. Although it may follow acute inflammation, chronic inflammation frequently begins insidiously, as a low-grade, smoldering, often asymptomatic response. biological_process GO:0002544 chronic inflammatory response Inflammation of prolonged duration (weeks or months) in which active inflammation, tissue destruction, and attempts at repair are proceeding simultaneously. Although it may follow acute inflammation, chronic inflammation frequently begins insidiously, as a low-grade, smoldering, often asymptomatic response. GOC:jal GO_REF:0000022 ISBN:0781735149 The movement of a monocyte in response to an external stimulus. biological_process GO:0002548 monocyte chemotaxis The movement of a monocyte in response to an external stimulus. GOC:add PMID:11696603 PMID:15173832 The process in which immune receptor genes are diversified through recombination of the germline genetic elements within a single genetic locus. biological_process GO:0002562 somatic diversification of immune receptors via germline recombination within a single locus The process in which immune receptor genes are diversified through recombination of the germline genetic elements within a single genetic locus. GOC:add ISBN:0781735149 PMID:16102575 PMID:16166509 The process in which immune receptor genes are diversified through somatic mutation. biological_process GO:0002566 somatic diversification of immune receptors via somatic mutation The process in which immune receptor genes are diversified through somatic mutation. ISBN:0781735149 PMID:16102575 The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage. myeloid leucocyte differentiation biological_process GO:0002573 myeloid leukocyte differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage. GOC:add PMID:16551251 The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a thrombocyte, a nucleated cell found in all vertebrates but mammals involved in hemostasis. biological_process GO:0002574 Note that platelets are the non-nucleated mammalian functional equivalent of the nucleated thrombocytes of non-mammalian vertebrates and are sometimes also referred to as thrombocytes. Platelet formation in mammals is covered by the biological_process term platelet formation ; GO:0030220. thrombocyte differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a thrombocyte, a nucleated cell found in all vertebrates but mammals involved in hemostasis. GOC:add Any process that modulates the frequency, rate, or extent of antigen processing and presentation. biological_process GO:0002577 regulation of antigen processing and presentation Any process that modulates the frequency, rate, or extent of antigen processing and presentation. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation. down regulation of antigen processing and presentation down-regulation of antigen processing and presentation downregulation of antigen processing and presentation inhibition of antigen processing and presentation biological_process GO:0002578 negative regulation of antigen processing and presentation Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation. GOC:add Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation. up regulation of antigen processing and presentation up-regulation of antigen processing and presentation upregulation of antigen processing and presentation activation of antigen processing and presentation stimulation of antigen processing and presentation biological_process GO:0002579 positive regulation of antigen processing and presentation Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation. GOC:add Any process that modulates the frequency, rate, or extent of antigen processing and presentation of antigen (peptide or polysaccharide) via MHC class II. regulation of peptide or polysaccharide antigen processing and presentation via MHC class II biological_process GO:0002580 regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II Any process that modulates the frequency, rate, or extent of antigen processing and presentation of antigen (peptide or polysaccharide) via MHC class II. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation of antigen (peptide or polysaccharide) via MHC class II. down regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II down-regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II downregulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II negative regulation of peptide or polysaccharide antigen processing and presentation via MHC class II inhibition of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II biological_process GO:0002581 negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation of antigen (peptide or polysaccharide) via MHC class II. GOC:add Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of antigen (peptide or polysaccharide) via MHC class II. positive regulation of peptide or polysaccharide antigen processing and presentation via MHC class II up regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II up-regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II upregulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II activation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II stimulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II biological_process GO:0002582 positive regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of antigen (peptide or polysaccharide) via MHC class II. GOC:add Any process that modulates the frequency, rate, or extent of antigen processing and presentation of peptide antigen. regulation of peptide antigen processing and presentation biological_process GO:0002583 regulation of antigen processing and presentation of peptide antigen Any process that modulates the frequency, rate, or extent of antigen processing and presentation of peptide antigen. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation of peptide antigen. down regulation of antigen processing and presentation of peptide antigen down-regulation of antigen processing and presentation of peptide antigen downregulation of antigen processing and presentation of peptide antigen negative regulation of peptide antigen processing and presentation inhibition of antigen processing and presentation of peptide antigen biological_process GO:0002584 negative regulation of antigen processing and presentation of peptide antigen Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation of peptide antigen. GOC:add Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of peptide antigen. positive regulation of peptide antigen processing and presentation up regulation of antigen processing and presentation of peptide antigen up-regulation of antigen processing and presentation of peptide antigen upregulation of antigen processing and presentation of peptide antigen activation of antigen processing and presentation of peptide antigen stimulation of antigen processing and presentation of peptide antigen biological_process GO:0002585 positive regulation of antigen processing and presentation of peptide antigen Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of peptide antigen. GOC:add Any process that modulates the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class II. regulation of peptide antigen processing and presentation via MHC class II biological_process GO:0002586 regulation of antigen processing and presentation of peptide antigen via MHC class II Any process that modulates the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class II. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class II. down regulation of antigen processing and presentation of peptide antigen via MHC class II down-regulation of antigen processing and presentation of peptide antigen via MHC class II downregulation of antigen processing and presentation of peptide antigen via MHC class II negative regulation of peptide antigen processing and presentation via MHC class II inhibition of antigen processing and presentation of peptide antigen via MHC class II biological_process GO:0002587 negative regulation of antigen processing and presentation of peptide antigen via MHC class II Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class II. GOC:add Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class II. positive regulation of peptide antigen processing and presentation via MHC class II up regulation of antigen processing and presentation of peptide antigen via MHC class II up-regulation of antigen processing and presentation of peptide antigen via MHC class II upregulation of antigen processing and presentation of peptide antigen via MHC class II activation of antigen processing and presentation of peptide antigen via MHC class II stimulation of antigen processing and presentation of peptide antigen via MHC class II biological_process GO:0002588 positive regulation of antigen processing and presentation of peptide antigen via MHC class II Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class II. GOC:add Any process that modulates the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class I. regulation of peptide antigen processing and presentation via MHC class I biological_process GO:0002589 regulation of antigen processing and presentation of peptide antigen via MHC class I Any process that modulates the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class I. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class I. down regulation of antigen processing and presentation of peptide antigen via MHC class I down-regulation of antigen processing and presentation of peptide antigen via MHC class I downregulation of antigen processing and presentation of peptide antigen via MHC class I negative regulation of peptide antigen processing and presentation via MHC class I inhibition of antigen processing and presentation of peptide antigen via MHC class I biological_process GO:0002590 negative regulation of antigen processing and presentation of peptide antigen via MHC class I Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class I. GOC:add Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class I. positive regulation of peptide antigen processing and presentation via MHC class I up regulation of antigen processing and presentation of peptide antigen via MHC class I up-regulation of antigen processing and presentation of peptide antigen via MHC class I upregulation of antigen processing and presentation of peptide antigen via MHC class I activation of antigen processing and presentation of peptide antigen via MHC class I stimulation of antigen processing and presentation of peptide antigen via MHC class I biological_process GO:0002591 positive regulation of antigen processing and presentation of peptide antigen via MHC class I Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class I. GOC:add Any process that modulates the frequency, rate, or extent of granuloma formation. biological_process GO:0002631 regulation of granuloma formation Any process that modulates the frequency, rate, or extent of granuloma formation. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of granuloma formation. down regulation of granuloma formation down-regulation of granuloma formation downregulation of granuloma formation inhibition of granuloma formation biological_process GO:0002632 negative regulation of granuloma formation Any process that stops, prevents, or reduces the frequency, rate, or extent of granuloma formation. GOC:add Any process that activates or increases the frequency, rate, or extent of granuloma formation. up regulation of granuloma formation up-regulation of granuloma formation upregulation of granuloma formation activation of granuloma formation stimulation of granuloma formation biological_process GO:0002633 positive regulation of granuloma formation Any process that activates or increases the frequency, rate, or extent of granuloma formation. GOC:add Any process that modulates the frequency, rate, or extent of germinal center formation. biological_process GO:0002634 regulation of germinal center formation Any process that modulates the frequency, rate, or extent of germinal center formation. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of germinal center formation. down regulation of germinal center formation down-regulation of germinal center formation downregulation of germinal center formation inhibition of germinal center formation biological_process GO:0002635 negative regulation of germinal center formation Any process that stops, prevents, or reduces the frequency, rate, or extent of germinal center formation. GOC:add Any process that activates or increases the frequency, rate, or extent of germinal center formation. up regulation of germinal center formation up-regulation of germinal center formation upregulation of germinal center formation activation of germinal center formation stimulation of germinal center formation biological_process GO:0002636 positive regulation of germinal center formation Any process that activates or increases the frequency, rate, or extent of germinal center formation. GOC:add Any process that modulates the frequency, rate, or extent of immunoglobulin production. GO:0002640 GO:0051023 regulation of antibody production regulation of immunoglobulin biosynthetic process regulation of immunoglobulin secretion biological_process GO:0002637 regulation of immunoglobulin production Any process that modulates the frequency, rate, or extent of immunoglobulin production. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of immunoglobulin production. GO:0002641 GO:0051025 down regulation of immunoglobulin production down-regulation of immunoglobulin production downregulation of immunoglobulin production inhibition of immunoglobulin production negative regulation of immunoglobulin biosynthetic process negative regulation of immunoglobulin secretion biological_process GO:0002638 negative regulation of immunoglobulin production Any process that stops, prevents, or reduces the frequency, rate, or extent of immunoglobulin production. GOC:add Any process that activates or increases the frequency, rate, or extent of immunoglobulin production. GO:0002642 GO:0051024 up regulation of immunoglobulin production up-regulation of immunoglobulin production upregulation of immunoglobulin production activation of immunoglobulin production positive regulation of immunoglobulin biosynthetic process positive regulation of immunoglobulin secretion stimulation of immunoglobulin production biological_process GO:0002639 positive regulation of immunoglobulin production Any process that activates or increases the frequency, rate, or extent of immunoglobulin production. GOC:add Any process that modulates the frequency, rate, or extent of tolerance induction. biological_process GO:0002643 regulation of tolerance induction Any process that modulates the frequency, rate, or extent of tolerance induction. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of tolerance induction. down regulation of tolerance induction down-regulation of tolerance induction downregulation of tolerance induction inhibition of tolerance induction biological_process GO:0002644 negative regulation of tolerance induction Any process that stops, prevents, or reduces the frequency, rate, or extent of tolerance induction. GOC:add Any process that activates or increases the frequency, rate, or extent of tolerance induction. up regulation of tolerance induction up-regulation of tolerance induction upregulation of tolerance induction activation of tolerance induction stimulation of tolerance induction biological_process GO:0002645 positive regulation of tolerance induction Any process that activates or increases the frequency, rate, or extent of tolerance induction. GOC:add Any process that modulates the frequency, rate, or extent of tolerance induction dependent upon immune response. regulation of immune response-dependent tolerance induction biological_process GO:0002652 regulation of tolerance induction dependent upon immune response Any process that modulates the frequency, rate, or extent of tolerance induction dependent upon immune response. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of tolerance induction dependent upon immune response. down regulation of tolerance induction dependent upon immune response down-regulation of tolerance induction dependent upon immune response downregulation of tolerance induction dependent upon immune response negative regulation of immune response-dependent tolerance induction inhibition of tolerance induction dependent upon immune response biological_process GO:0002653 negative regulation of tolerance induction dependent upon immune response Any process that stops, prevents, or reduces the frequency, rate, or extent of tolerance induction dependent upon immune response. GOC:add Any process that activates or increases the frequency, rate, or extent of tolerance induction dependent upon immune response. positive regulation of immune response-dependent tolerance induction up regulation of tolerance induction dependent upon immune response up-regulation of tolerance induction dependent upon immune response upregulation of tolerance induction dependent upon immune response activation of tolerance induction dependent upon immune response stimulation of tolerance induction dependent upon immune response biological_process GO:0002654 positive regulation of tolerance induction dependent upon immune response Any process that activates or increases the frequency, rate, or extent of tolerance induction dependent upon immune response. GOC:add Any process that modulates the frequency, rate, or extent of peripheral tolerance induction. biological_process GO:0002658 regulation of peripheral tolerance induction Any process that modulates the frequency, rate, or extent of peripheral tolerance induction. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of peripheral tolerance induction. down regulation of peripheral tolerance induction down-regulation of peripheral tolerance induction downregulation of peripheral tolerance induction inhibition of peripheral tolerance induction biological_process GO:0002659 negative regulation of peripheral tolerance induction Any process that stops, prevents, or reduces the frequency, rate, or extent of peripheral tolerance induction. GOC:add Any process that activates or increases the frequency, rate, or extent of peripheral tolerance induction. up regulation of peripheral tolerance induction up-regulation of peripheral tolerance induction upregulation of peripheral tolerance induction activation of peripheral tolerance induction stimulation of peripheral tolerance induction biological_process GO:0002660 positive regulation of peripheral tolerance induction Any process that activates or increases the frequency, rate, or extent of peripheral tolerance induction. GOC:add Any process that modulates the frequency, rate, or extent of B cell tolerance induction. regulation of B lymphocyte tolerance induction regulation of B-cell tolerance induction regulation of B-lymphocyte tolerance induction biological_process GO:0002661 regulation of B cell tolerance induction Any process that modulates the frequency, rate, or extent of B cell tolerance induction. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell tolerance induction. down regulation of B cell tolerance induction down-regulation of B cell tolerance induction downregulation of B cell tolerance induction negative regulation of B lymphocyte tolerance induction negative regulation of B-cell tolerance induction negative regulation of B-lymphocyte tolerance induction inhibition of B cell tolerance induction biological_process GO:0002662 negative regulation of B cell tolerance induction Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell tolerance induction. GOC:add Any process that activates or increases the frequency, rate, or extent of B cell tolerance induction. positive regulation of B lymphocyte tolerance induction positive regulation of B-cell tolerance induction positive regulation of B-lymphocyte tolerance induction up regulation of B cell tolerance induction up-regulation of B cell tolerance induction upregulation of B cell tolerance induction activation of B cell tolerance induction stimulation of B cell tolerance induction biological_process GO:0002663 positive regulation of B cell tolerance induction Any process that activates or increases the frequency, rate, or extent of B cell tolerance induction. GOC:add Any process that modulates the frequency, rate, or extent of B cell anergy. regulation of B lymphocyte anergy regulation of B-cell anergy regulation of B-lymphocyte anergy biological_process GO:0002670 regulation of B cell anergy Any process that modulates the frequency, rate, or extent of B cell anergy. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell anergy. down regulation of B cell anergy down-regulation of B cell anergy downregulation of B cell anergy negative regulation of B lymphocyte anergy negative regulation of B-cell anergy negative regulation of B-lymphocyte anergy inhibition of B cell anergy biological_process GO:0002671 negative regulation of B cell anergy Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell anergy. GOC:add Any process that activates or increases the frequency, rate, or extent of B cell anergy. positive regulation of B lymphocyte anergy positive regulation of B-cell anergy positive regulation of B-lymphocyte anergy up regulation of B cell anergy up-regulation of B cell anergy upregulation of B cell anergy activation of B cell anergy stimulation of B cell anergy biological_process GO:0002672 positive regulation of B cell anergy Any process that activates or increases the frequency, rate, or extent of B cell anergy. GOC:add Any process that modulates the frequency, rate, or extent of an acute inflammatory response. biological_process GO:0002673 regulation of acute inflammatory response Any process that modulates the frequency, rate, or extent of an acute inflammatory response. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of an acute inflammatory response. down regulation of acute inflammatory response down-regulation of acute inflammatory response downregulation of acute inflammatory response inhibition of acute inflammatory response biological_process GO:0002674 negative regulation of acute inflammatory response Any process that stops, prevents, or reduces the frequency, rate, or extent of an acute inflammatory response. GOC:add Any process that activates or increases the frequency, rate, or extent of an acute inflammatory response. up regulation of acute inflammatory response up-regulation of acute inflammatory response upregulation of acute inflammatory response activation of acute inflammatory response stimulation of acute inflammatory response biological_process GO:0002675 positive regulation of acute inflammatory response Any process that activates or increases the frequency, rate, or extent of an acute inflammatory response. GOC:add Any process that modulates the frequency, rate, or extent of a chronic inflammatory response. biological_process GO:0002676 regulation of chronic inflammatory response Any process that modulates the frequency, rate, or extent of a chronic inflammatory response. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of a chronic inflammatory response. down regulation of chronic inflammatory response down-regulation of chronic inflammatory response downregulation of chronic inflammatory response inhibition of chronic inflammatory response biological_process GO:0002677 negative regulation of chronic inflammatory response Any process that stops, prevents, or reduces the frequency, rate, or extent of a chronic inflammatory response. GOC:add Any process that activates or increases the frequency, rate, or extent of a chronic inflammatory response. up regulation of chronic inflammatory response up-regulation of chronic inflammatory response upregulation of chronic inflammatory response activation of chronic inflammatory response stimulation of chronic inflammatory response biological_process GO:0002678 positive regulation of chronic inflammatory response Any process that activates or increases the frequency, rate, or extent of a chronic inflammatory response. GOC:add A phase of elevated metabolic activity, during which oxygen consumption increases made as part of a defense response ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. biological_process GO:0002679 respiratory burst involved in defense response A phase of elevated metabolic activity, during which oxygen consumption increases made as part of a defense response ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. GOC:add ISBN:0781735149 PMID:12789499 Any process that modulates the frequency, rate, or extent of an immune system process. biological_process GO:0002682 regulation of immune system process Any process that modulates the frequency, rate, or extent of an immune system process. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process. down regulation of immune system process down-regulation of immune system process downregulation of immune system process inhibition of immune system process biological_process GO:0002683 negative regulation of immune system process Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process. GOC:add Any process that activates or increases the frequency, rate, or extent of an immune system process. up regulation of immune system process up-regulation of immune system process upregulation of immune system process activation of immune system process stimulation of immune system process biological_process GO:0002684 positive regulation of immune system process Any process that activates or increases the frequency, rate, or extent of an immune system process. GOC:add Any process that modulates the frequency, rate, or extent of leukocyte migration. regulation of immune cell migration regulation of leucocyte migration biological_process GO:0002685 regulation of leukocyte migration Any process that modulates the frequency, rate, or extent of leukocyte migration. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte migration. down regulation of leukocyte migration down-regulation of leukocyte migration downregulation of leukocyte migration negative regulation of immune cell migration negative regulation of leucocyte migration inhibition of leukocyte migration biological_process GO:0002686 negative regulation of leukocyte migration Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte migration. GOC:add Any process that activates or increases the frequency, rate, or extent of leukocyte migration. positive regulation of immune cell migration positive regulation of leucocyte migration up regulation of leukocyte migration up-regulation of leukocyte migration upregulation of leukocyte migration activation of leukocyte migration stimulation of leukocyte migration biological_process GO:0002687 positive regulation of leukocyte migration Any process that activates or increases the frequency, rate, or extent of leukocyte migration. GOC:add Any process that modulates the frequency, rate, or extent of leukocyte chemotaxis. regulation of immune cell chemotaxis regulation of leucocyte chemotaxis biological_process GO:0002688 regulation of leukocyte chemotaxis Any process that modulates the frequency, rate, or extent of leukocyte chemotaxis. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte chemotaxis. down regulation of leukocyte chemotaxis down-regulation of leukocyte chemotaxis downregulation of leukocyte chemotaxis negative regulation of immune cell chemotaxis negative regulation of leucocyte chemotaxis inhibition of leukocyte chemotaxis biological_process GO:0002689 negative regulation of leukocyte chemotaxis Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte chemotaxis. GOC:add Any process that activates or increases the frequency, rate, or extent of leukocyte chemotaxis. positive regulation of immune cell chemotaxis positive regulation of leucocyte chemotaxis up regulation of leukocyte chemotaxis up-regulation of leukocyte chemotaxis upregulation of leukocyte chemotaxis activation of leukocyte chemotaxis stimulation of leukocyte chemotaxis biological_process GO:0002690 positive regulation of leukocyte chemotaxis Any process that activates or increases the frequency, rate, or extent of leukocyte chemotaxis. GOC:add Any process that modulates the frequency, rate, or extent of leukocyte activation. regulation of immune cell activation regulation of leucocyte activation biological_process GO:0002694 regulation of leukocyte activation Any process that modulates the frequency, rate, or extent of leukocyte activation. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte activation. down regulation of leukocyte activation down-regulation of leukocyte activation downregulation of leukocyte activation negative regulation of immune cell activation negative regulation of leucocyte activation inhibition of leukocyte activation biological_process GO:0002695 negative regulation of leukocyte activation Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte activation. GOC:add Any process that activates or increases the frequency, rate, or extent of leukocyte activation. positive regulation of immune cell activation positive regulation of leucocyte activation up regulation of leukocyte activation up-regulation of leukocyte activation upregulation of leukocyte activation activation of leukocyte activation stimulation of leukocyte activation biological_process GO:0002696 positive regulation of leukocyte activation Any process that activates or increases the frequency, rate, or extent of leukocyte activation. GOC:add Any process that modulates the frequency, rate, or extent of an immune effector process. biological_process GO:0002697 regulation of immune effector process Any process that modulates the frequency, rate, or extent of an immune effector process. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune effector process. down regulation of immune effector process down-regulation of immune effector process downregulation of immune effector process inhibition of immune effector process biological_process GO:0002698 negative regulation of immune effector process Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune effector process. GOC:add Any process that activates or increases the frequency, rate, or extent of an immune effector process. up regulation of immune effector process up-regulation of immune effector process upregulation of immune effector process activation of immune effector process stimulation of immune effector process biological_process GO:0002699 positive regulation of immune effector process Any process that activates or increases the frequency, rate, or extent of an immune effector process. GOC:add Any process that modulates the frequency, rate, or extent of the production of molecular mediator of immune response. biological_process GO:0002700 regulation of production of molecular mediator of immune response Any process that modulates the frequency, rate, or extent of the production of molecular mediator of immune response. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of the production of molecular mediator of immune response. down regulation of production of molecular mediator of immune response down-regulation of production of molecular mediator of immune response downregulation of production of molecular mediator of immune response inhibition of production of molecular mediator of immune response biological_process GO:0002701 negative regulation of production of molecular mediator of immune response Any process that stops, prevents, or reduces the frequency, rate, or extent of the production of molecular mediator of immune response. GOC:add Any process that activates or increases the frequency, rate, or extent of the production of molecular mediator of immune response. up regulation of production of molecular mediator of immune response up-regulation of production of molecular mediator of immune response upregulation of production of molecular mediator of immune response activation of production of molecular mediator of immune response stimulation of production of molecular mediator of immune response biological_process GO:0002702 positive regulation of production of molecular mediator of immune response Any process that activates or increases the frequency, rate, or extent of the production of molecular mediator of immune response. GOC:add Any process that modulates the frequency, rate, or extent of leukocyte mediated immunity. regulation of immune cell mediated immunity regulation of leucocyte mediated immunity biological_process GO:0002703 regulation of leukocyte mediated immunity Any process that modulates the frequency, rate, or extent of leukocyte mediated immunity. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte mediated immunity. down regulation of leukocyte mediated immunity down-regulation of leukocyte mediated immunity downregulation of leukocyte mediated immunity negative regulation of immune cell mediated immunity negative regulation of leucocyte mediated immunity inhibition of leukocyte mediated immunity biological_process GO:0002704 negative regulation of leukocyte mediated immunity Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte mediated immunity. GOC:add Any process that activates or increases the frequency, rate, or extent of leukocyte mediated immunity. positive regulation of immune cell mediated immunity positive regulation of leucocyte mediated immunity up regulation of leukocyte mediated immunity up-regulation of leukocyte mediated immunity upregulation of leukocyte mediated immunity activation of leukocyte mediated immunity stimulation of leukocyte mediated immunity biological_process GO:0002705 positive regulation of leukocyte mediated immunity Any process that activates or increases the frequency, rate, or extent of leukocyte mediated immunity. GOC:add Any process that modulates the frequency, rate, or extent of lymphocyte mediated immunity. biological_process GO:0002706 regulation of lymphocyte mediated immunity Any process that modulates the frequency, rate, or extent of lymphocyte mediated immunity. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of lymphocyte mediated immunity. down regulation of lymphocyte mediated immunity down-regulation of lymphocyte mediated immunity downregulation of lymphocyte mediated immunity inhibition of lymphocyte mediated immunity biological_process GO:0002707 negative regulation of lymphocyte mediated immunity Any process that stops, prevents, or reduces the frequency, rate, or extent of lymphocyte mediated immunity. GOC:add Any process that activates or increases the frequency, rate, or extent of lymphocyte mediated immunity. up regulation of lymphocyte mediated immunity up-regulation of lymphocyte mediated immunity upregulation of lymphocyte mediated immunity activation of lymphocyte mediated immunity stimulation of lymphocyte mediated immunity biological_process GO:0002708 positive regulation of lymphocyte mediated immunity Any process that activates or increases the frequency, rate, or extent of lymphocyte mediated immunity. GOC:add Any process that modulates the frequency, rate, or extent of T cell mediated immunity. regulation of T lymphocyte mediated immunity regulation of T-cell mediated immunity regulation of T-lymphocyte mediated immunity biological_process GO:0002709 regulation of T cell mediated immunity Any process that modulates the frequency, rate, or extent of T cell mediated immunity. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of T cell mediated immunity. down regulation of T cell mediated immunity down-regulation of T cell mediated immunity downregulation of T cell mediated immunity negative regulation of T lymphocyte mediated immunity negative regulation of T-cell mediated immunity negative regulation of T-lymphocyte mediated immunity inhibition of T cell mediated immunity biological_process GO:0002710 negative regulation of T cell mediated immunity Any process that stops, prevents, or reduces the frequency, rate, or extent of T cell mediated immunity. GOC:add Any process that activates or increases the frequency, rate, or extent of T cell mediated immunity. positive regulation of T lymphocyte mediated immunity positive regulation of T-cell mediated immunity positive regulation of T-lymphocyte mediated immunity up regulation of T cell mediated immunity up-regulation of T cell mediated immunity upregulation of T cell mediated immunity activation of T cell mediated immunity stimulation of T cell mediated immunity biological_process GO:0002711 positive regulation of T cell mediated immunity Any process that activates or increases the frequency, rate, or extent of T cell mediated immunity. GOC:add Any process that modulates the frequency, rate, or extent of B cell mediated immunity. regulation of B lymphocyte mediated immunity regulation of B-cell mediated immunity regulation of B-lymphocyte mediated immunity biological_process GO:0002712 regulation of B cell mediated immunity Any process that modulates the frequency, rate, or extent of B cell mediated immunity. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell mediated immunity. down regulation of B cell mediated immunity down-regulation of B cell mediated immunity downregulation of B cell mediated immunity negative regulation of B lymphocyte mediated immunity negative regulation of B-cell mediated immunity negative regulation of B-lymphocyte mediated immunity inhibition of B cell mediated immunity biological_process GO:0002713 negative regulation of B cell mediated immunity Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell mediated immunity. GOC:add Any process that activates or increases the frequency, rate, or extent of B cell mediated immunity. positive regulation of B lymphocyte mediated immunity positive regulation of B-cell mediated immunity positive regulation of B-lymphocyte mediated immunity up regulation of B cell mediated immunity up-regulation of B cell mediated immunity upregulation of B cell mediated immunity activation of B cell mediated immunity stimulation of B cell mediated immunity biological_process GO:0002714 positive regulation of B cell mediated immunity Any process that activates or increases the frequency, rate, or extent of B cell mediated immunity. GOC:add Any process that modulates the frequency, rate, or extent of natural killer cell mediated immunity. GO:0045845 regulation of NK cell mediated immunity biological_process regulation of natural killer cell activity GO:0002715 regulation of natural killer cell mediated immunity Any process that modulates the frequency, rate, or extent of natural killer cell mediated immunity. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of natural killer cell mediated immunity. GO:0030102 down regulation of natural killer cell mediated immunity down-regulation of natural killer cell mediated immunity downregulation of natural killer cell mediated immunity negative regulation of NK cell mediated immunity inhibition of natural killer cell mediated immunity biological_process negative regulation of NK cell activity negative regulation of natural killer cell activity GO:0002716 negative regulation of natural killer cell mediated immunity Any process that stops, prevents, or reduces the frequency, rate, or extent of natural killer cell mediated immunity. GOC:add Any process that activates or increases the frequency, rate, or extent of natural killer cell mediated immunity. GO:0045846 positive regulation of NK cell mediated immunity up regulation of natural killer cell mediated immunity up-regulation of natural killer cell mediated immunity upregulation of natural killer cell mediated immunity activation of natural killer cell mediated immunity stimulation of natural killer cell mediated immunity biological_process positive regulation of NK cell activity positive regulation of natural killer cell activity GO:0002717 positive regulation of natural killer cell mediated immunity Any process that activates or increases the frequency, rate, or extent of natural killer cell mediated immunity. GOC:add Any process that modulates the frequency, rate, or extent of cytokine production that contributes to an immune response. GO:0002739 GO:0002742 regulation of cytokine biosynthetic process involved in immune response regulation of cytokine secretion involved in immune response biological_process regulation of cytokine production during immune response GO:0002718 regulation of cytokine production involved in immune response Any process that modulates the frequency, rate, or extent of cytokine production that contributes to an immune response. GOC:add regulation of cytokine production during immune response GOC:dph Any process that stops, prevents, or reduces the frequency, rate, or extent of cytokine production contributing to an immune response. GO:0002740 GO:0002743 down-regulation of cytokine production during immune response negative regulation of cytokine biosynthetic process involved in immune response negative regulation of cytokine secretion involved in immune response biological_process down regulation of cytokine production during immune response downregulation of cytokine production during immune response inhibition of cytokine production during immune response negative regulation of cytokine production during immune response GO:0002719 negative regulation of cytokine production involved in immune response Any process that stops, prevents, or reduces the frequency, rate, or extent of cytokine production contributing to an immune response. GOC:add negative regulation of cytokine production during immune response GOC:dph Any process that activates or increases the frequency, rate, or extent of cytokine production that contributes to an immune response. GO:0002741 GO:0002744 activation of cytokine production during immune response positive regulation of cytokine biosynthetic process involved in immune response positive regulation of cytokine secretion involved in immune response stimulation of cytokine production during immune response biological_process positive regulation of cytokine production during immune response up regulation of cytokine production during immune response up-regulation of cytokine production during immune response upregulation of cytokine production during immune response GO:0002720 positive regulation of cytokine production involved in immune response Any process that activates or increases the frequency, rate, or extent of cytokine production that contributes to an immune response. GOC:add positive regulation of cytokine production during immune response GOC:dph Any process that modulates the frequency, rate, or extent of T cell cytokine production. regulation of T lymphocyte cytokine production regulation of T-cell cytokine production regulation of T-lymphocyte cytokine production biological_process GO:0002724 regulation of T cell cytokine production Any process that modulates the frequency, rate, or extent of T cell cytokine production. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of T cell cytokine production. down regulation of T cell cytokine production down-regulation of T cell cytokine production downregulation of T cell cytokine production negative regulation of T lymphocyte cytokine production negative regulation of T-cell cytokine production negative regulation of T-lymphocyte cytokine production inhibition of T cell cytokine production biological_process GO:0002725 negative regulation of T cell cytokine production Any process that stops, prevents, or reduces the frequency, rate, or extent of T cell cytokine production. GOC:add Any process that activates or increases the frequency, rate, or extent of T cell cytokine production. positive regulation of T lymphocyte cytokine production positive regulation of T-cell cytokine production positive regulation of T-lymphocyte cytokine production up regulation of T cell cytokine production up-regulation of T cell cytokine production upregulation of T cell cytokine production activation of T cell cytokine production stimulation of T cell cytokine production biological_process GO:0002726 positive regulation of T cell cytokine production Any process that activates or increases the frequency, rate, or extent of T cell cytokine production. GOC:add Any process that modulates the frequency, rate, or extent of an antimicrobial humoral response. biological_process GO:0002759 regulation of antimicrobial humoral response Any process that modulates the frequency, rate, or extent of an antimicrobial humoral response. GOC:add Any process that activates or increases the frequency, rate, or extent of an antimicrobial humoral response. up regulation of antimicrobial humoral response up-regulation of antimicrobial humoral response upregulation of antimicrobial humoral response activation of antimicrobial humoral response stimulation of antimicrobial humoral response biological_process GO:0002760 positive regulation of antimicrobial humoral response Any process that activates or increases the frequency, rate, or extent of an antimicrobial humoral response. GOC:add Any process that modulates the frequency, rate, or extent of myeloid leukocyte differentiation. biological_process GO:0002761 regulation of myeloid leukocyte differentiation Any process that modulates the frequency, rate, or extent of myeloid leukocyte differentiation. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of myeloid leukocyte differentiation. down regulation of myeloid leukocyte differentiation down-regulation of myeloid leukocyte differentiation downregulation of myeloid leukocyte differentiation inhibition of myeloid leukocyte differentiation biological_process GO:0002762 negative regulation of myeloid leukocyte differentiation Any process that stops, prevents, or reduces the frequency, rate, or extent of myeloid leukocyte differentiation. GOC:add Any process that activates or increases the frequency, rate, or extent of myeloid leukocyte differentiation. up regulation of myeloid leukocyte differentiation up-regulation of myeloid leukocyte differentiation upregulation of myeloid leukocyte differentiation activation of myeloid leukocyte differentiation stimulation of myeloid leukocyte differentiation biological_process GO:0002763 positive regulation of myeloid leukocyte differentiation Any process that activates or increases the frequency, rate, or extent of myeloid leukocyte differentiation. GOC:add The synthesis or release of an antimicrobial peptide during an immune response, resulting in an increase in intracellular or extracellular levels. Such peptides may have protective properties against bacteria, fungi, viruses, or protozoa. biological_process GO:0002775 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. antimicrobial peptide production The synthesis or release of an antimicrobial peptide during an immune response, resulting in an increase in intracellular or extracellular levels. Such peptides may have protective properties against bacteria, fungi, viruses, or protozoa. GOC:add ISBN:0781735149 PMID:11807545 PMID:15638771 The regulated release of an antimicrobial peptide from a cell or a tissue. Such peptides may have protective properties against bacteria, fungi, viruses, or protozoa. biological_process GO:0002776 antimicrobial peptide secretion The regulated release of an antimicrobial peptide from a cell or a tissue. Such peptides may have protective properties against bacteria, fungi, viruses, or protozoa. GOC:add ISBN:0781735149 PMID:11807545 PMID:15638771 Any process that modulates the frequency, rate, or extent of antimicrobial peptide production. biological_process GO:0002784 regulation of antimicrobial peptide production Any process that modulates the frequency, rate, or extent of antimicrobial peptide production. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of antimicrobial peptide production. down regulation of antimicrobial peptide production down-regulation of antimicrobial peptide production downregulation of antimicrobial peptide production inhibition of antimicrobial peptide production biological_process GO:0002785 negative regulation of antimicrobial peptide production Any process that stops, prevents, or reduces the frequency, rate, or extent of antimicrobial peptide production. GOC:add 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 Any process that modulates the frequency, rate, or extent of antimicrobial peptide secretion. biological_process GO:0002794 regulation of antimicrobial peptide secretion Any process that modulates the frequency, rate, or extent of antimicrobial peptide secretion. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of antimicrobial peptide secretion. down regulation of antimicrobial peptide secretion down-regulation of antimicrobial peptide secretion downregulation of antimicrobial peptide secretion inhibition of antimicrobial peptide secretion biological_process GO:0002795 negative regulation of antimicrobial peptide secretion Any process that stops, prevents, or reduces the frequency, rate, or extent of antimicrobial peptide secretion. GOC:add Any process that activates or increases the frequency, rate, or extent of antimicrobial peptide secretion. up regulation of antimicrobial peptide secretion up-regulation of antimicrobial peptide secretion upregulation of antimicrobial peptide secretion activation of antimicrobial peptide secretion stimulation of antimicrobial peptide secretion biological_process GO:0002796 positive regulation of antimicrobial peptide secretion Any process that activates or increases the frequency, rate, or extent of antimicrobial peptide secretion. GOC:add Any process that modulates the frequency, rate, or extent of an adaptive immune response. biological_process GO:0002819 regulation of adaptive immune response Any process that modulates the frequency, rate, or extent of an adaptive immune response. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of an adaptive immune response. down regulation of adaptive immune response down-regulation of adaptive immune response downregulation of adaptive immune response inhibition of adaptive immune response biological_process GO:0002820 negative regulation of adaptive immune response Any process that stops, prevents, or reduces the frequency, rate, or extent of an adaptive immune response. GOC:add Any process that activates or increases the frequency, rate, or extent of an adaptive immune response. up regulation of adaptive immune response up-regulation of adaptive immune response upregulation of adaptive immune response activation of adaptive immune response stimulation of adaptive immune response biological_process GO:0002821 positive regulation of adaptive immune response Any process that activates or increases the frequency, rate, or extent of an adaptive immune response. GOC:add Any process that modulates the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata. biological_process GO:0002822 regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains Any process that modulates the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata. GOC:add GOC:mtg_sensu Any process that stops, prevents, or reduces the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata. biological_process GO:0002823 negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains Any process that stops, prevents, or reduces the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata. GOC:add GOC:mtg_sensu Any process that activates or increases the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata. biological_process GO:0002824 positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains Any process that activates or increases the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata. GOC:add GOC:mtg_sensu Any process that modulates the frequency, rate, or extent of a T-helper 1 type immune response. biological_process GO:0002825 regulation of T-helper 1 type immune response Any process that modulates the frequency, rate, or extent of a T-helper 1 type immune response. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of a T-helper 1 type immune response. down regulation of T-helper 1 type immune response down-regulation of T-helper 1 type immune response downregulation of T-helper 1 type immune response inhibition of T-helper 1 type immune response biological_process GO:0002826 negative regulation of T-helper 1 type immune response Any process that stops, prevents, or reduces the frequency, rate, or extent of a T-helper 1 type immune response. GOC:add Any process that activates or increases the frequency, rate, or extent of a T-helper 1 type immune response. up regulation of T-helper 1 type immune response up-regulation of T-helper 1 type immune response upregulation of T-helper 1 type immune response activation of T-helper 1 type immune response stimulation of T-helper 1 type immune response biological_process GO:0002827 positive regulation of T-helper 1 type immune response Any process that activates or increases the frequency, rate, or extent of a T-helper 1 type immune response. GOC:add Any process that modulates the frequency, rate, or extent of a type 2 immune response. regulation of T-helper 2 type immune response regulation of Th2 immune response biological_process GO:0002828 regulation of type 2 immune response Any process that modulates the frequency, rate, or extent of a type 2 immune response. GOC:add regulation of T-helper 2 type immune response GOC:add regulation of Th2 immune response GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of a type 2 immune response. down regulation of type 2 immune response down-regulation of type 2 immune response downregulation of type 2 immune response inhibition of type 2 immune response negative regulation of T-helper 2 type immune response negative regulation of Th2 immune response biological_process GO:0002829 negative regulation of type 2 immune response Any process that stops, prevents, or reduces the frequency, rate, or extent of a type 2 immune response. GOC:add negative regulation of T-helper 2 type immune response GOC:add negative regulation of Th2 immune response GOC:add Any process that activates or increases the frequency, rate, or extent of a type 2 immune response. up regulation of type 2 immune response up-regulation of type 2 immune response upregulation of type 2 immune response activation of type 2 immune response positive regulation of T-helper 2 type immune response positive regulation of Th2 immune response stimulation of type 2 immune response biological_process GO:0002830 positive regulation of type 2 immune response Any process that activates or increases the frequency, rate, or extent of a type 2 immune response. GOC:add positive regulation of T-helper 2 type immune response GOC:add positive regulation of Th2 immune response GOC:add Any process that modulates the frequency, rate, or extent of a response to biotic stimulus. biological_process GO:0002831 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 biotic stimulus Any process that modulates the frequency, rate, or extent of a response to biotic stimulus. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of a response to biotic stimulus. down regulation of response to biotic stimulus down-regulation of response to biotic stimulus downregulation of response to biotic stimulus inhibition of response to biotic stimulus biological_process GO:0002832 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 biotic stimulus Any process that stops, prevents, or reduces the frequency, rate, or extent of a response to biotic stimulus. GOC:add Any process that activates or increases the frequency, rate, or extent of a response to biotic stimulus. up regulation of response to biotic stimulus up-regulation of response to biotic stimulus upregulation of response to biotic stimulus activation of response to biotic stimulus stimulation of response to biotic stimulus biological_process GO:0002833 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 biotic stimulus Any process that activates or increases the frequency, rate, or extent of a response to biotic stimulus. GOC:add Any process that modulates the frequency, rate, or extent of B cell deletion. regulation of B lymphocyte deletion regulation of B-cell deletion regulation of B-lymphocyte deletion biological_process GO:0002867 regulation of B cell deletion Any process that modulates the frequency, rate, or extent of B cell deletion. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell deletion. down regulation of B cell deletion down-regulation of B cell deletion downregulation of B cell deletion negative regulation of B lymphocyte deletion negative regulation of B-cell deletion negative regulation of B-lymphocyte deletion inhibition of B cell deletion biological_process GO:0002868 negative regulation of B cell deletion Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell deletion. GOC:add Any process that activates or increases the frequency, rate, or extent of B cell deletion. positive regulation of B lymphocyte deletion positive regulation of B-cell deletion positive regulation of B-lymphocyte deletion up regulation of B cell deletion up-regulation of B cell deletion upregulation of B cell deletion activation of B cell deletion stimulation of B cell deletion biological_process GO:0002869 positive regulation of B cell deletion Any process that activates or increases the frequency, rate, or extent of B cell deletion. GOC:add Any process that modulates the frequency, rate, or extent of an immunoglobulin mediated immune response. biological_process GO:0002889 regulation of immunoglobulin mediated immune response Any process that modulates the frequency, rate, or extent of an immunoglobulin mediated immune response. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of an immunoglobulin mediated immune response. down regulation of immunoglobulin mediated immune response down-regulation of immunoglobulin mediated immune response downregulation of immunoglobulin mediated immune response inhibition of immunoglobulin mediated immune response biological_process GO:0002890 negative regulation of immunoglobulin mediated immune response Any process that stops, prevents, or reduces the frequency, rate, or extent of an immunoglobulin mediated immune response. GOC:add Any process that activates or increases the frequency, rate, or extent of an immunoglobulin mediated immune response. up regulation of immunoglobulin mediated immune response up-regulation of immunoglobulin mediated immune response upregulation of immunoglobulin mediated immune response activation of immunoglobulin mediated immune response stimulation of immunoglobulin mediated immune response biological_process GO:0002891 positive regulation of immunoglobulin mediated immune response Any process that activates or increases the frequency, rate, or extent of an immunoglobulin mediated immune response. GOC:add Any apoptotic process in a B cell that is mature, having left the bone marrow. apoptosis of mature B cells apoptosis of mature B lymphocytes apoptosis of mature B-cells apoptosis of mature B-lymphocytes mature B cell programmed cell death by apoptosis mature B lymphocyte apoptosis mature B lymphocyte programmed cell death by apoptosis mature B-cell apoptosis mature B-cell programmed cell death by apoptosis mature B-lymphocyte apoptosis mature B-lymphocyte programmed cell death by apoptosis programmed cell death of mature B cells by apoptosis programmed cell death of mature B lymphocytes by apoptosis programmed cell death of mature B-cells by apoptosis programmed cell death of mature B-lymphocytes by apoptosis programmed cell death, mature B cells programmed cell death, mature B lymphocytes programmed cell death, mature B-cells programmed cell death, mature B-lymphocytes mature B cell apoptosis biological_process GO:0002901 mature B cell apoptotic process Any apoptotic process in a B cell that is mature, having left the bone marrow. CL:0000785 GOC:add GOC:mtg_apoptosis ISBN:0781735149 Any process that modulates the frequency, rate, or extent of B cell apoptotic process. regulation of B cell apoptosis biological_process GO:0002902 regulation of B cell apoptotic process Any process that modulates the frequency, rate, or extent of B cell apoptotic process. GOC:add GOC:mtg_apoptosis Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell apoptotic process. down regulation of B cell apoptosis down-regulation of B cell apoptosis downregulation of B cell apoptosis inhibition of B cell apoptosis negative regulation of B cell apoptosis biological_process GO:0002903 negative regulation of B cell apoptotic process Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell apoptotic process. GOC:add GOC:mtg_apoptosis Any process that activates or increases the frequency, rate, or extent of B cell apoptotic process. up regulation of B cell apoptosis up-regulation of B cell apoptosis upregulation of B cell apoptosis activation of B cell apoptosis positive regulation of B cell apoptosis stimulation of B cell apoptosis biological_process GO:0002904 positive regulation of B cell apoptotic process Any process that activates or increases the frequency, rate, or extent of B cell apoptotic process. GOC:add GOC:mtg_apoptosis Any process that modulates the frequency, rate, or extent of mature B cell apoptotic process. regulation of mature B cell apoptosis biological_process GO:0002905 regulation of mature B cell apoptotic process Any process that modulates the frequency, rate, or extent of mature B cell apoptotic process. GOC:add GOC:mtg_apoptosis Any process that stops, prevents, or reduces the frequency, rate, or extent of mature B cell apoptotic process. down regulation of mature B cell apoptosis down-regulation of mature B cell apoptosis downregulation of mature B cell apoptosis inhibition of mature B cell apoptosis negative regulation of mature B cell apoptosis biological_process GO:0002906 negative regulation of mature B cell apoptotic process Any process that stops, prevents, or reduces the frequency, rate, or extent of mature B cell apoptotic process. GOC:add GOC:mtg_apoptosis Any process that activates or increases the frequency, rate, or extent of mature B cell apoptotic process. up regulation of mature B cell apoptosis up-regulation of mature B cell apoptosis upregulation of mature B cell apoptosis activation of mature B cell apoptosis positive regulation of mature B cell apoptosis stimulation of mature B cell apoptosis biological_process GO:0002907 positive regulation of mature B cell apoptotic process Any process that activates or increases the frequency, rate, or extent of mature B cell apoptotic process. GOC:add GOC:mtg_apoptosis Any process that modulates the frequency, rate, or extent of lymphocyte anergy. biological_process GO:0002911 regulation of lymphocyte anergy Any process that modulates the frequency, rate, or extent of lymphocyte anergy. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of lymphocyte anergy. down regulation of lymphocyte anergy down-regulation of lymphocyte anergy downregulation of lymphocyte anergy inhibition of lymphocyte anergy biological_process GO:0002912 negative regulation of lymphocyte anergy Any process that stops, prevents, or reduces the frequency, rate, or extent of lymphocyte anergy. GOC:add Any process that activates or increases the frequency, rate, or extent of lymphocyte anergy. up regulation of lymphocyte anergy up-regulation of lymphocyte anergy upregulation of lymphocyte anergy activation of lymphocyte anergy stimulation of lymphocyte anergy biological_process GO:0002913 positive regulation of lymphocyte anergy Any process that activates or increases the frequency, rate, or extent of lymphocyte anergy. GOC:add Any process that modulates the frequency, rate, or extent of a humoral immune response. biological_process GO:0002920 regulation of humoral immune response Any process that modulates the frequency, rate, or extent of a humoral immune response. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of a humoral immune response. down regulation of humoral immune response down-regulation of humoral immune response downregulation of humoral immune response inhibition of humoral immune response biological_process GO:0002921 negative regulation of humoral immune response Any process that stops, prevents, or reduces the frequency, rate, or extent of a humoral immune response. GOC:add Any process that activates or increases the frequency, rate, or extent of a humoral immune response. up regulation of humoral immune response up-regulation of humoral immune response upregulation of humoral immune response activation of humoral immune response stimulation of humoral immune response biological_process GO:0002922 positive regulation of humoral immune response Any process that activates or increases the frequency, rate, or extent of a humoral immune response. GOC:add A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring. puberty biological_process reproductive developmental process GO:0003006 developmental process involved in reproduction A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring. GOC:dph GOC:isa_complete puberty GOC:dph reproductive developmental process GOC:dph GOC:tb 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 at the level of a muscle. Muscle tissue is composed of contractile cells or fibers. biological_process muscle physiological process GO:0003012 muscle system process A organ system process carried out at the level of a muscle. Muscle tissue is composed of contractile cells or fibers. 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 organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila). excretory system process biological_process kidney system process GO:0003014 renal system process A organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila). GOC:cjm GOC:mtg_cardio GOC:mtg_kidney_jan10 A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. biological_process cardiac process GO:0003015 heart process A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. GOC:mtg_cardio A process carried out by the organs or tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange. GO:0010802 respiratory gaseous exchange biological_process GO:0003016 respiratory system process A process carried out by the organs or tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange. GOC:dph GOC:mtg_cardio GOC:tb The regulation of blood pressure mediated by biochemical signaling: hormonal, autocrine or paracrine. blood pressure regulation mediated by a chemical signal biological_process GO:0003044 regulation of systemic arterial blood pressure mediated by a chemical signal The regulation of blood pressure mediated by biochemical signaling: hormonal, autocrine or paracrine. GOC:mtg_cardio Renal process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure. renal control of blood pressure renal regulation of systemic arterial blood pressure biological_process GO:0003071 renal system process involved in regulation of systemic arterial blood pressure Renal process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure. GOC:dph GOC:mtg_cardio GOC:tb renal regulation of systemic arterial blood pressure GOC:dph GOC:tb The process that modulates the force with which blood travels through the systemic arterial circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure. biological_process GO:0003073 regulation of systemic arterial blood pressure The process that modulates the force with which blood travels through the systemic arterial circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure. GOC:mtg_cardio The process in which renin-angiotensin modulates the force with which blood passes through the circulatory system. blood pressure regulation by renin-angiotensin biological_process GO:0003081 regulation of systemic arterial blood pressure by renin-angiotensin The process in which renin-angiotensin modulates the force with which blood passes through the circulatory system. GOC:mtg_cardio Any process that modulates the rate, frequency, or extent of the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells. dph 2009-11-02T02:07:40Z biological_process GO:0003330 regulation of extracellular matrix constituent secretion Any process that modulates the rate, frequency, or extent of the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells. GOC:dph GOC:tb Any process that increases the rate, frequency, or extent of the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells. dph 2009-11-02T02:11:22Z biological_process GO:0003331 positive regulation of extracellular matrix constituent secretion Any process that increases the rate, frequency, or extent of the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells. GOC:dph GOC:tb Any process that decreases the rate, frequency, or extent the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells. dph 2009-11-02T02:13:49Z biological_process GO:0003332 negative regulation of extracellular matrix constituent secretion Any process that decreases the rate, frequency, or extent the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells. GOC:dph GOC:tb The directed, self-propelled movement of a cilium. dph 2009-11-24T09:56:26Z GO:0036142 microtubule-based flagellum movement flagellar movement flagellum movement biological_process ciliary motility cilium beating flagellar motility GO:0003341 Note that we deem cilium and microtubule-based flagellum to be equivalent. cilium movement The directed, self-propelled movement of a cilium. GOC:dph GOC:jl flagellar movement GOC:bf cilium beating GOC:ascb_2009 GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium. dph 2009-12-03T10:12:00Z GO:1900172 regulation of microtubule-based flagellum movement biological_process regulation of flagellar movement regulation of flagellum movement GO:0003352 Note that we deem cilium and microtubule-based flagellum to be equivalent. regulation of cilium movement Any process that modulates the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium. GOC:dph regulation of flagellar movement GOC:TermGenie Any process that increases the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium. dph 2009-12-03T10:16:10Z GO:1900174 positive regulation of microtubule-based flagellum movement biological_process positive regulation of flagellar movement positive regulation of flagellum movement GO:0003353 Note that we deem cilium and microtubule-based flagellum to be equivalent. positive regulation of cilium movement Any process that increases the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium. GOC:dph positive regulation of flagellar movement GOC:TermGenie Any process that decreases the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium. dph 2009-12-03T10:17:47Z GO:1900173 negative regulation of microtubule-based flagellum movement biological_process negative regulation of flagellum movement GO:0003354 Note that we deem cilium and microtubule-based flagellum to be equivalent. negative regulation of cilium movement Any process that decreases the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium. GOC:dph 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. 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 Binding to a nucleic acid. GO:0000496 base pairing molecular_function GO:0003676 nucleic acid binding Binding to a nucleic acid. GOC:jl Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0043566 plasmid binding molecular_function microtubule/chromatin interaction structure specific DNA binding structure-specific DNA binding GO:0003677 DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GOC:dph GOC:jl GOC:tb GOC:vw catalytic activity Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction. GO:0004926 GO:0099600 transmembrane receptor activity Reactome:R-HSA-193672 transmembrane signalling receptor activity molecular_function GO:0004888 This term includes intracellular membrane receptors, e.g. IP3 triggered release of Ca2+ from intracellular stores. transmembrane signaling receptor activity Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction. GOC:go_curators Wikipedia:Transmembrane_receptor transmembrane receptor activity GOC:bf GOC:signaling Reactome:R-HSA-193672 Sphingomyelinase is activated by the NGF:p75NTR complex transmembrane signalling receptor activity GOC:mah Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. EBV-induced receptor molecular_function GO:0004930 G protein-coupled receptor activity Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. GOC:bf Wikipedia:GPCR http://www.iuphar-db.org Combining with any modified low-density lipoprotein (LDL) or other polyanionic ligand and delivering the ligand into the cell via endocytosis. Ligands include acetylated and oxidized LDL, Gram-positive and Gram-negative bacteria, apoptotic cells, amyloid-beta fibrils, and advanced glycation end products (AGEs). macrophage receptor activity molecular_function GO:0005044 Note that many gene products that are called scavenger receptors have a broad range of potential ligands and also can be annotated to 'pattern recognition receptor activity ; GO:0038187' or its child terms, or to 'lipoprotein receptor activity ; GO:0030228' or its child terms. For receptors that transduce a signal rather than endocytose their ligand, consider instead the terms 'signaling receptor activity ; GO:0038023' and its children. scavenger receptor activity Combining with any modified low-density lipoprotein (LDL) or other polyanionic ligand and delivering the ligand into the cell via endocytosis. Ligands include acetylated and oxidized LDL, Gram-positive and Gram-negative bacteria, apoptotic cells, amyloid-beta fibrils, and advanced glycation end products (AGEs). GOC:bf PMID:11790542 PMID:12379907 PMID:12621157 PMID:20981357 Binding to 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 Binding to 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 Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells. GO:0005478 EC:7.-.-.- Reactome:R-HSA-168313 Reactome:R-HSA-178215 molecular_function carrier GO:0005215 Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules. transporter activity Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells. GOC:ai GOC:dgf Reactome:R-HSA-168313 Virion-associated M2 protein mediated ion infusion Reactome:R-HSA-178215 SMAD7:SMURF1 complex is exported to the cytosol Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size). molecular_function GO:0005216 ion channel activity Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size). GOC:cy GOC:mtg_transport GOC:pr ISBN:0815340729 Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded. voltage gated ion channel activity molecular_function GO:0005244 voltage-gated ion channel activity Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded. GOC:mtg_transport ISBN:0198506732 ISBN:0815340729 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 Binding to a protein. GO:0001948 GO:0045308 protein amino acid binding glycoprotein binding molecular_function GO:0005515 protein binding Binding to a protein. GOC:go_curators 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. 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 The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. Wikipedia:Extracellular extracellular cellular_component GO:0005576 Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'. extracellular region The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. GOC:go_curators That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. NIF_Subcellular:sao1425028079 cellular_component intercellular space GO:0005615 Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). Gene products from a multi-cellular organism that are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term. extracellular space That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. ISBN:0198547684 A component of a cell contained within (but not including) the plasma membrane. 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 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 nucleocytoplasm GOC:mah protoplast GOC:mah 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. 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 The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). GO:0005636 Wikipedia:Nuclear_envelope cellular_component GO:0005635 nuclear envelope The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). ISBN:0198547684 A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. Wikipedia:Chromosome interphase chromosome prophase chromosome cellular_component chromatid GO:0005694 Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. chromosome A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. ISBN:0198547684 A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. NIF_Subcellular:sao1820400233 Wikipedia:Nucleolus cellular_component GO:0005730 nucleolus A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. ISBN:0198506732 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 small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions. NIF_Subcellular:sao585356902 Wikipedia:Lysosome cellular_component GO:0005764 lysosome A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions. GOC:mah ISBN:0198506732 A lysosome before it has fused with a vesicle or vacuole. NIF_Subcellular:sao1140587416 cellular_component GO:0005766 primary lysosome A lysosome before it has fused with a vesicle or vacuole. GOC:jl ISBN:0815316194 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 volume enclosed within the vacuolar membrane. cellular_component GO:0005775 vacuolar lumen The volume enclosed within the vacuolar membrane. ISBN:0198506732 A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways. Golgi NIF_Subcellular:sao451912436 Wikipedia:Golgi_apparatus Golgi complex Golgi ribbon cellular_component GO:0005794 Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon. Golgi apparatus A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways. ISBN:0198506732 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. GO:0033279 NIF_Subcellular:sao1429207766 Wikipedia:Ribosome free ribosome membrane bound ribosome cellular_component ribosomal RNA GO:0005840 ribosome An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. ISBN:0198506732 free ribosome NIF_Subcellular:sao1139385046 membrane bound ribosome NIF_Subcellular:sao1291545653 Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. Wikipedia:Cytoskeleton cellular_component GO:0005856 cytoskeleton Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. GOC:mah ISBN:0198547684 PMID:16959967 A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane. FMA:63850 NIF_Subcellular:sao1588493326 Wikipedia:Actin microfilament cellular_component GO:0005884 actin filament A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane. GOC:mah ISBN:0198506732 PMID:10666339 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 component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. integral to plasma membrane cellular_component GO:0005887 integral component of plasma membrane The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. GOC:dos GOC:go_curators Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells. NIF_Subcellular:sao671419673 Wikipedia:Microvillus cellular_component microvilli GO:0005902 Note that this term refers to a projection from a single cell, and should not be confused with 'microvillus' as used to refer to a multicellular structure such as that found in the placenta. microvillus Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells. ISBN:0815316194 microvilli NIF_Subcellular:sao671419673 A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. GO:0072372 FMA:67181 NIF_Subcellular:sao787716553 Wikipedia:Cilium eukaryotic flagellum microtubule-based flagellum primary cilium cellular_component flagellum GO:0005929 Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms. cilium A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. GOC:cilia GOC:curators GOC:kmv GOC:vw ISBN:0198547684 PMID:16824949 PMID:17009929 PMID:20144998 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 aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages. aminoglycan metabolism biological_process GO:0006022 aminoglycan metabolic process The chemical reactions and pathways involving aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages. GOC:ai ISBN:0198506732 The chemical reactions and pathways resulting in the formation of aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages. aminoglycan anabolism aminoglycan biosynthesis aminoglycan formation aminoglycan synthesis biological_process GO:0006023 aminoglycan biosynthetic process The chemical reactions and pathways resulting in the formation of aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages. GOC:ai ISBN:0198506732 The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars. glycosaminoglycan anabolism glycosaminoglycan biosynthesis glycosaminoglycan formation glycosaminoglycan synthesis biological_process GO:0006024 glycosaminoglycan biosynthetic process The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars. ISBN:0192800981 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 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 cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. GO:0055132 DNA metabolism cellular DNA metabolism biological_process GO:0006259 DNA metabolic process Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. ISBN:0198506732 Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction. biological_process GO:0006310 DNA recombination Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction. ISBN:0198506732 Any process in which DNA and associated proteins are formed into a compact, orderly structure. DNA condensation DNA organisation DNA organization biological_process GO:0006323 DNA packaging Any process in which DNA and associated proteins are formed into a compact, orderly structure. GOC:mah ISBN:0815316194 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. protein anabolism biological_process GO:0006412 translation The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. GOC:go_curators 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 resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification. Wikipedia:Steroid_metabolisms#Steroid_biosynthesis steroid anabolism steroid biosynthesis steroid formation steroid synthesis steroidogenesis biological_process GO:0006694 steroid biosynthetic process The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification. GOC:go_curators The chemical reactions and pathways resulting in the formation of bile acids, any of a group of steroid carboxylic acids occurring in bile. bile acid anabolism bile acid biosynthesis bile acid formation bile acid synthesis biological_process GO:0006699 bile acid biosynthetic process The chemical reactions and pathways resulting in the formation of bile acids, any of a group of steroid carboxylic acids occurring in bile. GOC:go_curators 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 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 superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species. oxygen free radical metabolic process oxygen free radical metabolism superoxide free radical metabolic process superoxide free radical metabolism superoxide metabolism biological_process GO:0006801 superoxide metabolic process The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species. GOC:jl 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 cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0006819 GO:0015674 GO:0072512 di-, tri-valent inorganic cation transport trivalent inorganic cation transport biological_process GO:0006812 cation transport The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai di-, tri-valent inorganic cation transport GOC:mah 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 dicarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0006841 biological_process sodium:dicarboxylate transport GO:0006835 dicarboxylic acid transport The directed movement of dicarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:krc The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell. sodium:neurotransmitter transport biological_process GO:0006836 neurotransmitter transport The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell. GOC:ai The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems. biological_process GO:0006837 serotonin transport The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems. GOC:ai The transport of substances that occurs outside cells. biological_process GO:0006858 extracellular transport The transport of substances that occurs outside cells. GOC:go_curators The directed extracellular movement of amino acids. biological_process GO:0006860 extracellular amino acid transport The directed extracellular movement of amino acids. GOC:ai The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0006866 biological_process GO:0006865 amino acid transport The directed movement of amino acids, organic acids containing one or more amino substituents, 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 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 A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle. GO:0016193 GO:0016196 GO:0098701 Wikipedia:Endocytosis endocytic import into cell vesicle endocytosis plasma membrane invagination biological_process nonselective vesicle endocytosis GO:0006897 endocytosis A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle. GOC:mah ISBN:0198506732 ISBN:0716731363 The evagination of a membrane, resulting in formation of a vesicle. jl 2013-12-19T15:26:17Z GO:0006902 GO:1902591 membrane evagination vesicle biosynthesis vesicle formation biological_process nonselective vesicle assembly single organism membrane budding single-organism membrane budding vesicle budding GO:0006900 vesicle budding from membrane The evagination of a membrane, resulting in formation of a vesicle. GOC:jid GOC:tb single organism membrane budding GOC:TermGenie The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo. biological_process GO:0006903 vesicle targeting The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo. GOC:mah PMID:17335816 A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles. Wikipedia:Phagocytosis biological_process GO:0006909 phagocytosis A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles. ISBN:0198506732 A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. GO:0006917 GO:0008632 cell suicide cellular suicide Wikipedia:Apoptosis apoptotic cell death apoptotic programmed cell death programmed cell death by apoptosis activation of apoptosis apoptosis apoptosis signaling apoptotic program type I programmed cell death biological_process apoptosis activator activity caspase-dependent programmed cell death commitment to apoptosis induction of apoptosis induction of apoptosis by p53 signaling (initiator) caspase activity GO:0006915 apoptotic process A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. GOC:cjm GOC:dhl GOC:ecd GOC:go_curators GOC:mtg_apoptosis GOC:tb ISBN:0198506732 PMID:18846107 PMID:21494263 apoptotic cell death GOC:sl apoptotic program GOC:add The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis. cellular component disassembly involved in apoptotic process disassembly of cell structures cellular component disassembly involved in apoptosis biological_process GO:0006921 cellular component disassembly involved in execution phase of apoptosis The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis. GOC:dph GOC:mah GOC:mtg_apoptosis GOC:tb The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore. cellular component motion cellular component movement biological_process cell movement GO:0006928 Note that in GO cellular components include whole cells (cell is_a cellular component). movement of cell or subcellular component The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore. GOC:dgh GOC:dph GOC:jl GOC:mlg cellular component motion GOC:dph GOC:jl The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). Wikipedia:Chemotaxis taxis in response to chemical stimulus biological_process GO:0006935 chemotaxis The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). ISBN:0198506732 A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Wikipedia:Muscle_contraction biological_process GO:0006936 muscle contraction A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. GOC:ef GOC:mtg_muscle ISBN:0198506732 Any process that modulates the frequency, rate or extent of muscle contraction. biological_process GO:0006937 regulation of muscle contraction Any process that modulates the frequency, rate or extent of muscle contraction. GOC:go_curators A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. 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. visceral muscle contraction biological_process GO:0006939 smooth muscle contraction A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. 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. GOC:ef GOC:jl GOC:mtg_muscle ISBN:0198506732 Any process that modulates the frequency, rate or extent of smooth muscle contraction. biological_process GO:0006940 regulation of smooth muscle contraction Any process that modulates the frequency, rate or extent of smooth muscle contraction. GOC:go_curators 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 Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. biological_process GO:0006955 immune response Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. GOC:add GO_REF:0000022 An immune response mediated through a body fluid. Wikipedia:Humoral_immunity biological_process GO:0006959 humoral immune response An immune response mediated through a body fluid. GOC:hb 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 the nucleus. GO:0048287 nuclear organisation nuclear organization biological_process nuclear morphology nuclear organization and biogenesis nucleus organization and biogenesis GO:0006997 nucleus organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus. GOC:dph GOC:ems GOC:jl GOC:mah nuclear organization and biogenesis GOC:mah nucleus organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. cytoskeleton organisation biological_process cytoskeletal organization and biogenesis cytoskeletal regulator activity cytoskeleton organization and biogenesis GO:0007010 cytoskeleton organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. GOC:dph GOC:jl GOC:mah cytoskeletal organization and biogenesis GOC:mah cytoskeleton organization and biogenesis GOC:mah Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins. biological_process GO:0007017 microtubule-based process Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins. GOC:mah A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. biological_process GO:0007018 microtubule-based movement A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. GOC:cjm ISBN:0815316194 The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. Wikipedia:Cell_cycle cell-division cycle biological_process GO:0007049 cell cycle The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. GOC:go_curators GOC:mtg_cell_cycle The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. Wikipedia:Chromosome_segregation chromosome division biological_process chromosome transmission GO:0007059 chromosome segregation The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. GOC:jl GOC:mah GOC:mtg_cell_cycle GOC:vw The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells. biological_process GO:0007076 mitotic chromosome condensation The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells. GOC:mah ISBN:0815316194 Any process that modulates the frequency, rate or extent of mitosis. regulation of mitosis biological_process GO:0007088 regulation of mitotic nuclear division Any process that modulates the frequency, rate or extent of mitosis. GOC:go_curators A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell. Wikipedia:Mitosis#Endomitosis biological_process endomitosis GO:0007113 Note that this term should not be confused with 'abortive mitotic cell cycle ; GO:0033277'. Although abortive mitosis is sometimes called endomitosis, GO:0033277 refers to a process in which a mitotic spindle forms and chromosome separation begins. endomitotic cell cycle A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell. GOC:curators GOC:dos GOC:expert_vm The second nuclear division of meiosis, in which the two chromatids in each chromosome are separated, resulting in four daughter nuclei from the two nuclei produced in meiosis II. Wikipedia:Meiosis#Meiosis_II meiosis II nuclear division biological_process GO:0007135 meiosis II The second nuclear division of meiosis, in which the two chromatids in each chromosome are separated, resulting in four daughter nuclei from the two nuclei produced in meiosis II. GOC:dph GOC:mah ISBN:0198547684 A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline. male nuclear division biological_process male meiosis GO:0007140 male meiotic nuclear division A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline. GOC:dph GOC:mah GOC:vw A cell cycle process comprising the steps by which a cell progresses through male meiosis II, the second meiotic division in the male germline. male meiosis II nuclear division biological_process GO:0007142 male meiosis II A cell cycle process comprising the steps by which a cell progresses through male meiosis II, the second meiotic division in the male germline. GOC:dph GOC:mah A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the female germline. female meiosis female meiotic division biological_process GO:0007143 Note that female germ lines can be found in female or hermaphroditic organisms, so this term can be used to annotate gene products from hermaphrodites such as those of C. elegans. See also the biological process term 'meiotic nuclear division; GO:0140013'. female meiotic nuclear division A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the female germline. GOC:dph GOC:ems GOC:mah GOC:vw The cell cycle process in which the second meiotic division occurs in the female germline. female meiosis II nuclear division biological_process GO:0007147 female meiosis II The cell cycle process in which the second meiotic division occurs in the female germline. 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 attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. dos 2014-04-15T15:59:10Z GO:0098602 Wikipedia:Cell_adhesion biological_process cell adhesion molecule activity single organism cell adhesion GO:0007155 cell adhesion The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. GOC:hb GOC:pf The attachment of a leukocyte to another cell via adhesion molecules. leukocyte adhesion leukocyte cell adhesion biological_process GO:0007159 leukocyte cell-cell adhesion The attachment of a leukocyte to another cell via adhesion molecules. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion. down regulation of cell adhesion down-regulation of cell adhesion downregulation of cell adhesion inhibition of cell adhesion biological_process cell adhesion receptor inhibitor activity GO:0007162 negative regulation of cell adhesion Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion. GOC:go_curators 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:0023014 GO:0023015 GO:0023016 GO:0023033 GO:0023045 Wikipedia:Signal_transduction signal transduction by cis-phosphorylation signal transduction by conformational transition signal transduction by protein phosphorylation signal transduction by trans-phosphorylation 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 A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription. cell surface receptor linked signal transduction cell surface receptor linked signaling pathway cell surface receptor linked signalling pathway biological_process GO:0007166 cell surface receptor signaling pathway A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription. GOC:bf GOC:mah GOC:pr GOC:signaling cell surface receptor linked signaling pathway GOC:bf cell surface receptor linked 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 vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. signal transmission across a synapse synaptic transmission Wikipedia:Neurotransmission biological_process neurotransmission GO:0007268 chemical synaptic transmission The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. GOC:jl MeSH:D009435 neurotransmission GOC:dph The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium-regulated exocytosis during synaptic transmission. GO:0010554 neurotransmitter release neurotransmitter secretory pathway biological_process GO:0007269 A neurotransmitter is any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell. Among the many substances that have the properties of a neurotransmitter are acetylcholine, noradrenaline, adrenaline, dopamine, glycine, gamma-aminobutyrate, glutamic acid, substance P, enkephalins, endorphins and serotonin. neurotransmitter secretion The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium-regulated exocytosis during synaptic transmission. GOC:dph The vesicular release of acetylcholine from a presynapse, across a chemical synapse, the subsequent activation of dopamine receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. cholinergic synaptic transmission biological_process GO:0007271 synaptic transmission, cholinergic The vesicular release of acetylcholine from a presynapse, across a chemical synapse, the subsequent activation of dopamine receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. GOC:dos Wikipedia:Cholinergic 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). https://github.com/geneontology/go-ontology/issues/21234 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 generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell. GO:0009552 biological_process gametogenesis GO:0007276 gamete generation The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell. GOC:ems GOC:mtg_sensu The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism. germ-cell development primordial germ cell development biological_process GO:0007281 germ cell development The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism. GOC:go_curators The developmental process by which male germ line stem cells self renew or give rise to successive cell types resulting in the development of a spermatozoa. Wikipedia:Spermatogenesis generation of spermatozoa biological_process GO:0007283 spermatogenesis The developmental process by which male germ line stem cells self renew or give rise to successive cell types resulting in the development of a spermatozoa. GOC:jid ISBN:9780878933846 PMID:28073824 PMID:30990821 generation of spermatozoa The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure. Wikipedia:Spermiogenesis spermatid cell development spermiogenesis biological_process GO:0007286 spermatid development The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure. GOC:dph GOC:go_curators The assembly and organization of the sperm flagellar axoneme, the bundle of microtubules and associated proteins that forms the core of the eukaryotic sperm flagellum, and is responsible for movement. biological_process GO:0007288 sperm axoneme assembly The assembly and organization of the sperm flagellar axoneme, the bundle of microtubules and associated proteins that forms the core of the eukaryotic sperm flagellum, and is responsible for movement. GOC:bf GOC:cilia ISBN:0198547684 The specialization of the spermatid nucleus during the development of a spermatid into a mature male gamete competent for fertilization. spermatid nuclear differentiation biological_process GO:0007289 See also the Cell Ontology term 'spermatid ; CL:0000018'. spermatid nucleus differentiation The specialization of the spermatid nucleus during the development of a spermatid into a mature male gamete competent for fertilization. GOC:bf GOC:dph GOC:jl GOC:mah Generation of the female gamete; specialised haploid cells produced by meiosis and along with a male gamete takes part in sexual reproduction. biological_process GO:0007292 female gamete generation Generation of the female gamete; specialised haploid cells produced by meiosis and along with a male gamete takes part in sexual reproduction. GOC:dph ISBN:0198506732 The union of male and female gametes to form a zygote. biological_process zygote biosynthesis zygote formation GO:0007338 single fertilization The union of male and female gametes to form a zygote. GOC:ems GOC:mtg_sensu Any process that modulates the rate or extent of progress through the mitotic cell cycle. mitotic cell cycle modulation mitotic cell cycle regulation modulation of mitotic cell cycle progression regulation of mitotic cell cycle progression regulation of progression through mitotic cell cycle biological_process mitotic cell cycle regulator GO:0007346 regulation of mitotic cell cycle Any process that modulates the rate or extent of progress through the mitotic cell cycle. GOC:dph GOC:go_curators GOC:tb regulation of progression through mitotic cell cycle GOC:dph GOC:tb The establishment of the sex of an organism by physical differentiation. Wikipedia:Sexual_differentiation biological_process GO:0007548 sex differentiation The establishment of the sex of an organism by physical differentiation. GOC:ai Any process that modulates the frequency, rate or extent of the regulated release of ecdysteroid from a cell. biological_process GO:0007555 regulation of ecdysteroid secretion Any process that modulates the frequency, rate or extent of the regulated release of ecdysteroid from a cell. GOC:go_curators Any process that modulates the frequency, rate or extent of juvenile hormone secretion. biological_process GO:0007558 regulation of juvenile hormone secretion Any process that modulates the frequency, rate or extent of juvenile hormone secretion. GOC:go_curators The process of 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. breathing respiration biological_process GO:0007585 respiratory gaseous exchange by respiratory system The process of 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. ISBN:0198506732 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 controlled release of a fluid by a cell or tissue in an animal. biological_process GO:0007589 body fluid secretion The controlled release of a fluid by a cell or tissue in an animal. GOC:ai GOC:dph GOC:mah GOC:tb The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers. Wikipedia:Coagulation blood clotting biological_process GO:0007596 blood coagulation The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers. ISBN:0198506732 http://www.graylab.ac.uk/omd/ The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part. Wikipedia:Hemostasis biological_process GO:0007599 hemostasis The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part. ISBN:0198506732 The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. Wikipedia:Perception biological_process GO:0007600 sensory perception The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GOC:ai GOC:dph The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image. Wikipedia:Visual_perception sense of sight sensory visual perception vision biological_process GO:0007601 visual perception The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image. GOC:ai The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound. Wikipedia:Hearing_(sense) hearing perception of sound biological_process GO:0007605 sensory perception of sound The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound. GOC:ai The series of events required for an organism to receive a sensory chemical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. chemosensory perception biological_process GO:0007606 sensory perception of chemical stimulus The series of events required for an organism to receive a sensory chemical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GOC:ai The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process. Wikipedia:Olfaction olfaction scent perception sense of smell smell perception biological_process GO:0007608 sensory perception of smell The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process. GOC:ai 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 that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body. regulation of cardiac contraction biological_process GO:0008016 regulation of heart contraction Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body. GOC:dph GOC:go_curators GOC:tb 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. 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. 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. jl 2012-10-17T15:46:40Z GO:0044236 GO:0044710 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 bile acids, a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine. bile acid metabolism biological_process GO:0008206 bile acid metabolic process The chemical reactions and pathways involving bile acids, a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine. GOC:go_curators Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure. Wikipedia:Blood_pressure#Regulation blood pressure regulation biological_process blood pressure homeostasis control of blood pressure GO:0008217 regulation of blood pressure Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure. GOC:dph GOC:mtg_cardio ISBN:0721643949 Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538). biological_process accidental cell death necrosis GO:0008219 This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide) show that cell death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Also, if experimental data suggest that a gene product influences cell death indirectly, rather than being involved in the death process directly, consider annotating to a 'regulation' term. cell death Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538). GOC:mah GOC:mtg_apoptosis PMID:25236395 The multiplication or reproduction of cells, resulting in the expansion of a cell population. biological_process cell proliferation GO:0008283 This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms. cell population proliferation The multiplication or reproduction of cells, resulting in the expansion of a cell population. GOC:mah GOC:mb Any process that activates or increases the rate or extent of cell proliferation. up regulation of cell proliferation up-regulation of cell proliferation upregulation of cell proliferation activation of cell proliferation stimulation of cell proliferation biological_process positive regulation of cell proliferation GO:0008284 positive regulation of cell population proliferation Any process that activates or increases the rate or extent of cell proliferation. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of cell proliferation. down regulation of cell proliferation down-regulation of cell proliferation downregulation of cell proliferation inhibition of cell proliferation biological_process negative regulation of cell proliferation GO:0008285 negative regulation of cell population proliferation Any process that stops, prevents or reduces the rate or extent of cell proliferation. GOC:go_curators Binding to a lipid. molecular_function GO:0008289 lipid binding Binding to a lipid. GOC:ai The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence. DNA bending activity DNA bending involving DNA binding molecular_function GO:0008301 DNA binding, bending The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence. GOC:krc GOC:vw PMID:10710711 PMID:19037758 Any process that stops, prevents, or reduces the frequency, rate, or extent of an antimicrobial humoral response. GO:0042154 GO:0042155 attenuation of antimicrobial humoral response down regulation of antimicrobial humoral response down-regulation of antimicrobial humoral response downregulation of antimicrobial humoral response inhibition of antimicrobial humoral response biological_process GO:0008348 negative regulation of antimicrobial humoral response Any process that stops, prevents, or reduces the frequency, rate, or extent of an antimicrobial humoral response. GOC:go_curators The process whose specific outcome is the progression of the gonad over time, from its formation to the mature structure. The gonad is an animal organ that produces gametes; in some species it also produces hormones. gonadogenesis biological_process GO:0008406 gonad development The process whose specific outcome is the progression of the gonad over time, from its formation to the mature structure. The gonad is an animal organ that produces gametes; in some species it also produces hormones. GOC:ems ISBN:0198506732 gonadogenesis GOC:cjm Enables the transfer of a negatively charged ion from one side of a membrane to the other. Reactome:R-HSA-166214 anion transporter activity molecular_function GO:0008509 anion transmembrane transporter activity Enables the transfer of a negatively charged ion from one side of a membrane to the other. GOC:dgf GOC:mtg_transport ISBN:0815340729 Reactome:R-HSA-166214 FA anion flip-flops to the opposite surface Enables the transfer of organic anions from one side of a membrane to the other. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage. Reactome:R-HSA-2142859 molecular_function GO:0008514 organic anion transmembrane transporter activity Enables the transfer of organic anions from one side of a membrane to the other. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage. GOC:ai Reactome:R-HSA-2142859 Growing HA is extruded from the cell by ABCC5 The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure. GO:0061039 biological_process ovarian development ovary development GO:0008585 female gonad development The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure. GOC:dph GOC:jid GOC:tb ovarian development GOC:sl ovary development GOC:sl The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. lipid anabolism lipid biosynthesis lipid formation lipid synthesis lipogenesis biological_process GO:0008610 lipid biosynthetic process The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. GOC:go_curators lipogenesis GOC:sl 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 resulting in the formation of a macromolecule, any 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. GO:0043284 biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis macromolecule formation macromolecule synthesis biological_process GO:0009059 macromolecule biosynthetic process The chemical reactions and pathways resulting in the formation of a macromolecule, any 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. GOC:mah biopolymer biosynthetic process GOC:mtg_chebi_dec09 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 temperature stimulus. response to thermal stimulus biological_process GO:0009266 response to temperature 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 temperature stimulus. GOC:hb 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 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 electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation. response to electromagnetic radiation stimulus response to radiation stimulus biological_process GO:0009314 Note that 'radiation' refers to electromagnetic radiation of any wavelength. response to radiation 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 electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation. GOC:jl Wikipedia:Electromagnetic_radiation The process in which nitrogen is taken from its relatively inert molecular form (N2) in the atmosphere and converted into nitrogen compounds useful for other chemical processes, such as ammonia, nitrate and nitrogen dioxide. MetaCyc:N2FIX-PWY Wikipedia:Nitrogen_fixation biological_process GO:0009399 nitrogen fixation The process in which nitrogen is taken from its relatively inert molecular form (N2) in the atmosphere and converted into nitrogen compounds useful for other chemical processes, such as ammonia, nitrate and nitrogen dioxide. Wikipedia:Nitrogen_fixation 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 ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers. response to UV light stimulus response to UV radiation stimulus response to ultraviolet light stimulus response to ultraviolet radiation stimulus biological_process GO:0009411 response to UV 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 ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers. GOC:hb 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 light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light. biological_process GO:0009416 response to light 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 light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light. GOC:go_curators ISBN:0582227089 The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). https://github.com/geneontology/go-ontology/issues/20176 Wikipedia:Fertilisation syngamy biological_process GO:0009566 fertilization The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). GOC:tb ISBN:0198506732 The series of events in which an external stimulus is received by a cell and converted into a molecular signal. biological_process perception of external stimulus GO:0009581 detection of external stimulus The series of events in which an external stimulus is received by a cell and converted into a molecular signal. GOC:hb The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal. biological_process perception of abiotic stimulus GO:0009582 detection of abiotic stimulus The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal. GOC:hb The series of events in which a light stimulus (in the form of photons) is received and converted into a molecular signal. detection of light biological_process perception of light GO:0009583 detection of light stimulus The series of events in which a light stimulus (in the form of photons) is received and converted into a molecular signal. GOC:go_curators The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm. biological_process perception of visible light GO:0009584 detection of visible light The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm. GOC:go_curators ISBN:0198506732 The series of events in which an ultraviolet radiation (UV light) stimulus is received and converted into a molecular signal. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers. detection of UV light stimulus detection of UV radiation stimulus detection of ultraviolet light stimulus detection of ultraviolet radiation stimulus biological_process perception of UV GO:0009589 detection of UV The series of events in which an ultraviolet radiation (UV light) stimulus is received and converted into a molecular signal. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers. GOC:dos GOC:go_curators GOC:hb ISBN:0198506732 The series of events in which a gravitational stimulus is received and converted into a molecular signal. biological_process perception of gravity GO:0009590 detection of gravity The series of events in which a gravitational stimulus is received and converted into a molecular signal. GOC:dos GOC:hb The series of events in which a chemical stimulus is received by a cell and converted into a molecular signal. chemoperception detection of chemical substance biological_process chemoreception perception of chemical stimulus perception of chemical substance GO:0009593 detection of chemical stimulus The series of events in which a chemical stimulus is received by a cell and converted into a molecular signal. GOC:jl 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 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 biotic stimulus, a stimulus caused or produced by a living organism. response to biotic stress biological_process GO:0009607 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 biotic 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 biotic stimulus, a stimulus caused or produced by a living organism. GOC:hb 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 indicating damage to the organism. GO:0002245 physiological response to wounding biological_process GO:0009611 response to wounding 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 indicating damage to the organism. GOC:go_curators 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 mechanical stimulus. mechanical stimulus response biological_process chemi-mechanical coupling GO:0009612 response to mechanical 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 mechanical stimulus. GOC:hb 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 from a bacterium. GO:0009618 GO:0009680 response to bacteria biological_process GO:0009617 response to bacterium 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 from a bacterium. GOC:hb 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 abiotic (not derived from living organisms) stimulus. https://github.com/geneontology/go-ontology/issues/16572 response to abiotic stress biological_process GO:0009628 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 abiotic 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 abiotic (not derived from living organisms) stimulus. GOC:hb 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 gravitational stimulus. response to gravitational stimulus biological_process GO:0009629 response to gravity 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 gravitational stimulus. GOC:hb 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 toxic stimulus. detoxification response biological_process toxin resistance toxin susceptibility/resistance GO:0009636 response to toxic substance 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 toxic stimulus. GOC:lr 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. 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 Compaction of chromatin structure prior to meiosis in eukaryotic cells. chromosome condensation involved in meiotic cell cycle biological_process GO:0010032 meiotic chromosome condensation Compaction of chromatin structure prior to meiosis in eukaryotic cells. PMID:10072401 chromosome condensation involved in meiotic cell cycle GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of photosynthesis. biological_process GO:0010109 regulation of photosynthesis Any process that modulates the frequency, rate or extent of photosynthesis. GOC:sm A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system. endomembrane organization endomembrane system organisation biological_process GO:0010256 endomembrane system organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system. GOC:mah GOC:sm endomembrane system organisation GOC:mah The infolding of a membrane. jl 2013-12-02T13:58:34Z GO:1902534 biological_process single-organism membrane invagination GO:0010324 membrane invagination The infolding of a membrane. GOC:tb The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. Wikipedia:Gene_expression biological_process GO:0010467 gene expression The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. Wikipedia:Regulation_of_gene_expression regulation of protein expression biological_process regulation of gene product expression GO:0010468 This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation. regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of a signaling receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity. regulation of receptor activity regulation of signalling receptor activity biological_process GO:0010469 regulation of signaling receptor activity Any process that modulates the frequency, rate or extent of a signaling receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity. GOC:dph GOC:tb Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any 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. biological_process GO:0010556 regulation of macromolecule biosynthetic process Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any 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. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any 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. biological_process GO:0010557 positive regulation of macromolecule biosynthetic process Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any 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. GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any 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. biological_process GO:0010558 negative regulation of macromolecule biosynthetic process Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any 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. GOC:dph GOC:tb Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. biological_process GO:0010564 regulation of cell cycle process Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. 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 the chemical reactions and pathways involving macromolecules, any 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. biological_process GO:0010604 positive regulation of macromolecule metabolic process Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any 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. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any 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. biological_process GO:0010605 negative regulation of macromolecule metabolic process Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any 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. GOC:dph GOC:tb The activation of endogenous cellular processes that result in the death of a cell as part of its development. developmental programmed cell death programmed cell death involved in development biological_process GO:0010623 This process is part of the natural developmental program of some cell types, but it does not always happen as part of the development or shaping of a gross anatomical structure. programmed cell death involved in cell development The activation of endogenous cellular processes that result in the death of a cell as part of its development. GOC:dph GOC:mtg_apoptosis GOC:tb Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. biological_process GO:0010628 positive regulation of gene expression Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. biological_process GO:0010629 This term covers any process that negatively regulates the rate of production of a mature gene product, and so includes processes that negatively regulate that rate by reducing the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that reduces the level, stability or availability of mRNA or circRNA for translation and thereby reduces the rate of production of the encoded protein via translation. negative regulation of gene expression Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. 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 decreases the frequency, rate or extent of the regulated release of norepinephrine. biological_process GO:0010700 negative regulation of norepinephrine secretion Any process that decreases the frequency, rate or extent of the regulated release of norepinephrine. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of the regulated release of norepinephrine. biological_process GO:0010701 positive regulation of norepinephrine secretion Any process that increases the frequency, rate or extent of the regulated release of norepinephrine. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process GO:0010720 positive regulation of cell development Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:BHF GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process GO:0010721 negative regulation of cell development Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:BHF 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 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 that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. biological_process GO:0010893 positive regulation of steroid biosynthetic process Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. GOC:tb Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. biological_process GO:0010894 negative regulation of steroid biosynthetic process Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. GOC:BHF GOC:tb The cellular component assembly that is part of the initial shaping of the component during its developmental progression. biological_process GO:0010927 cellular component assembly involved in morphogenesis The cellular component assembly that is part of the initial shaping of the component during its developmental progression. GOC:dph GOC:tb Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. biological_process GO:0010941 regulation of cell death Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. GOC:dph GOC:tb Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. biological_process GO:0010942 positive regulation of cell death Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. tb 2009-04-27T09:53:22Z biological_process GO:0010948 negative regulation of cell cycle process Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. GOC:dph GOC:tb The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity. tb 2009-05-27T10:56:08Z microtubule-based transport establishment of localization by movement along microtubule movement along microtubule biological_process GO:0010970 transport along microtubule The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity. GOC:dph GOC:mah GOC:tb establishment of localization by movement along microtubule GOC:dph A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. GO:0016244 regulated cell death Wikipedia:Programmed_cell_death caspase-independent cell death non-apoptotic programmed cell death nonapoptotic programmed cell death biological_process PCD RCD caspase-independent apoptosis GO:0012501 Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children. programmed cell death A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. GOC:lr GOC:mtg_apoptosis 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 regulated release of dopamine by a cell. Dopamine is a catecholamine and a precursor of adrenaline and noradrenaline. It acts as a neurotransmitter in the central nervous system but it is also produced peripherally and acts as a hormone. biological_process GO:0014046 dopamine secretion The regulated release of dopamine by a cell. Dopamine is a catecholamine and a precursor of adrenaline and noradrenaline. It acts as a neurotransmitter in the central nervous system but it is also produced peripherally and acts as a hormone. GOC:ef The controlled release of glutamate by a cell. The glutamate is the most abundant excitatory neurotransmitter in the nervous system. biological_process GO:0014047 glutamate secretion The controlled release of glutamate by a cell. The glutamate is the most abundant excitatory neurotransmitter in the nervous system. GOC:ef Any process that modulates the frequency, rate or extent of the controlled release of glutamate. biological_process GO:0014048 regulation of glutamate secretion Any process that modulates the frequency, rate or extent of the controlled release of glutamate. GOC:ef Any process that activates or increases the frequency, rate or extent of the controlled release of glutamate. up regulation of glutamate secretion up-regulation of glutamate secretion upregulation of glutamate secretion activation of glutamate secretion stimulation of glutamate secretion biological_process GO:0014049 positive regulation of glutamate secretion Any process that activates or increases the frequency, rate or extent of the controlled release of glutamate. GOC:ef Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of glutamate. down regulation of glutamate secretion down-regulation of glutamate secretion downregulation of glutamate secretion inhibition of glutamate secretion biological_process GO:0014050 negative regulation of glutamate secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of glutamate. GOC:ef The regulated release of gamma-aminobutyric acid by a cell or a tissue. The gamma-aminobutyric acid is the principal inhibitory neurotransmitter in the brain but is also found in several extraneural tissues. GABA secretion biological_process GO:0014051 gamma-aminobutyric acid secretion The regulated release of gamma-aminobutyric acid by a cell or a tissue. The gamma-aminobutyric acid is the principal inhibitory neurotransmitter in the brain but is also found in several extraneural tissues. GOC:ef Any process that modulates the frequency, rate or extent of the regulated release of gamma-aminobutyric acid. regulation of GABA secretion biological_process GO:0014052 regulation of gamma-aminobutyric acid secretion Any process that modulates the frequency, rate or extent of the regulated release of gamma-aminobutyric acid. GOC:ef Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of gamma-aminobutyric acid. down regulation of gamma-aminobutyric acid secretion down-regulation of gamma-aminobutyric acid secretion downregulation of gamma-aminobutyric acid secretion negative regulation of GABA secretion inhibition of gamma-aminobutyric acid secretion biological_process GO:0014053 negative regulation of gamma-aminobutyric acid secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of gamma-aminobutyric acid. GOC:ef Any process that activates or increases the frequency, rate or extent of the regulated release of gamma-aminobutyric acid. positive regulation of GABA secretion up regulation of gamma-aminobutyric acid secretion up-regulation of gamma-aminobutyric acid secretion upregulation of gamma-aminobutyric acid secretion activation of gamma-aminobutyric acid secretion stimulation of gamma-aminobutyric acid secretion biological_process GO:0014054 positive regulation of gamma-aminobutyric acid secretion Any process that activates or increases the frequency, rate or extent of the regulated release of gamma-aminobutyric acid. GOC:ef The regulated release of acetylcholine by a cell. The acetylcholine acts as a neurotransmitter that acts in both the peripheral nervous system (PNS) and central nervous system (CNS). biological_process GO:0014055 acetylcholine secretion, neurotransmission The regulated release of acetylcholine by a cell. The acetylcholine acts as a neurotransmitter that acts in both the peripheral nervous system (PNS) and central nervous system (CNS). GOC:ef Any process that modulates the frequency, rate or extent of the regulated release of acetylcholine. biological_process GO:0014056 regulation of acetylcholine secretion, neurotransmission Any process that modulates the frequency, rate or extent of the regulated release of acetylcholine. GOC:ef Any process that activates or increases the frequency, rate or extent of the regulated release of acetylcholine. up regulation of acetylcholine secretion up-regulation of acetylcholine secretion upregulation of acetylcholine secretion activation of acetylcholine secretion stimulation of acetylcholine secretion biological_process GO:0014057 positive regulation of acetylcholine secretion, neurotransmission Any process that activates or increases the frequency, rate or extent of the regulated release of acetylcholine. GOC:ef Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of acetylcholine. down regulation of acetylcholine secretion down-regulation of acetylcholine secretion downregulation of acetylcholine secretion inhibition of acetylcholine secretion biological_process GO:0014058 negative regulation of acetylcholine secretion, neurotransmission Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of acetylcholine. GOC:ef Any process that modulates the frequency, rate or extent of the regulated release of dopamine. biological_process GO:0014059 regulation of dopamine secretion Any process that modulates the frequency, rate or extent of the regulated release of dopamine. GOC:ef Any process that modulates the frequency, rate or extent of the regulated release of epinephrine. regulation of adrenaline secretion biological_process GO:0014060 regulation of epinephrine secretion Any process that modulates the frequency, rate or extent of the regulated release of epinephrine. GOC:ef Any process that modulates the frequency, rate or extent of the regulated release of norepinephrine. regulation of noradrenaline secretion biological_process GO:0014061 regulation of norepinephrine secretion Any process that modulates the frequency, rate or extent of the regulated release of norepinephrine. GOC:ef Any process that modulates the frequency, rate or extent of the regulated release of serotonin. biological_process regulation of serotonin release GO:0014062 regulation of serotonin secretion Any process that modulates the frequency, rate or extent of the regulated release of serotonin. GOC:ef regulation of serotonin release GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of serotonin. down regulation of serotonin secretion down-regulation of serotonin secretion downregulation of serotonin secretion inhibition of serotonin secretion biological_process positive regulation of serotonin release GO:0014063 negative regulation of serotonin secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of serotonin. GOC:ef positive regulation of serotonin release GOC:tb Any process that activates or increases the frequency, rate or extent of the regulated release of serotonin. up regulation of serotonin secretion up-regulation of serotonin secretion upregulation of serotonin secretion activation of serotonin secretion stimulation of serotonin secretion biological_process positive regulation of serotonin release GO:0014064 positive regulation of serotonin secretion Any process that activates or increases the frequency, rate or extent of the regulated release of serotonin. GOC:ef positive regulation of serotonin release GOC:tb 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 Enables the transfer of an ion from one side of a membrane to the other. ion transporter activity molecular_function GO:0015075 ion transmembrane transporter activity Enables the transfer of an ion from one side of a membrane to the other. GOC:dgf GOC:mtg_transport ISBN:0815340729 Enables the transfer of bicarbonate from one side of a membrane to the other. Bicarbonate is the hydrogencarbonate ion, HCO3-. RHEA:28695 Reactome:R-HSA-2752067 molecular_function GO:0015106 bicarbonate transmembrane transporter activity Enables the transfer of bicarbonate from one side of a membrane to the other. Bicarbonate is the hydrogencarbonate ion, HCO3-. GOC:ai Reactome:R-HSA-2752067 BESTs transport cytosolic HCO3- to extracellular region Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules. molecular_function alpha-type channel activity GO:0015267 channel activity Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules. GOC:mtg_transport ISBN:0815340729 TC:1.-.-.-.- Enables the transmembrane transfer of an ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts. ionotropic receptor activity molecular_function GO:0015276 ligand-gated ion channel activity Enables the transmembrane transfer of an ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts. GOC:mtg_transport ISBN:0815340729 ionotropic receptor activity GOC:bf GOC:sart The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes. cellular_component GO:0015629 actin cytoskeleton The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes. GOC:jl ISBN:0395825172 ISBN:0815316194 The directed movement of substances that are gaseous in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015669 gas transport The directed movement of substances that are gaseous in normal living conditions 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 oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015671 oxygen transport The directed movement of oxygen (O2) 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 organic cations into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic cations are atoms or small molecules with a positive charge which contain carbon in covalent linkage. biological_process GO:0015695 organic cation transport The directed movement of organic cations into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic cations are atoms or small molecules with a positive charge which contain carbon in covalent linkage. GOC:ai The directed movement of bicarbonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015701 bicarbonate transport The directed movement of bicarbonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:krc The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage. biological_process GO:0015711 organic anion transport The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage. GOC:ai GOC:krc The directed movement of monocarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015718 monocarboxylic acid transport The directed movement of monocarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:krc The directed movement of acidic amino acids, amino acids with a pH below 7, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015800 acidic amino acid transport The directed movement of acidic amino acids, amino acids with a pH below 7, 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 neutral amino acids, amino acids with no net 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:0015804 neutral amino acid transport The directed movement of neutral amino acids, amino acids with no net 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 gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. 4-aminobutanoate transport 4-aminobutyrate transport GABA transport biological_process GO:0015812 See also the biological process term 'neurotransmitter transport ; GO:0006836'. gamma-aminobutyric acid transport The directed movement of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:go_curators ISBN:0198506732 The directed movement of glycine, aminoethanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015816 glycine transport The directed movement of glycine, aminoethanoic acid, 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 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 The directed movement of amines, including polyamines, organic compounds containing one or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process amine/polyamine transport GO:0015837 amine transport The directed movement of amines, including polyamines, organic compounds containing one or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai ISBN:0198506732 The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0015873 biological_process GO:0015844 monoamine transport The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015849 organic acid transport The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. ISBN:0198506732 The directed movement of an organic hydroxy compound (organic alcohol) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. An organic hydroxy compound is an organic compound having at least one hydroxy group attached to a carbon atom. organic alcohol transport biological_process GO:0015850 organic hydroxy compound transport The directed movement of an organic hydroxy compound (organic alcohol) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. An organic hydroxy compound is an organic compound having at least one hydroxy group attached to a carbon atom. GOC:ai The directed movement of acetylcholine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Acetylcholine is an acetic acid ester of the organic base choline and functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions. biological_process GO:0015870 acetylcholine transport The directed movement of acetylcholine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Acetylcholine is an acetic acid ester of the organic base choline and functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions. GOC:ai The directed movement of dopamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Dopamine is a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline. biological_process GO:0015872 dopamine transport The directed movement of dopamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Dopamine is a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline. GOC:ai The directed movement of norepinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Norepinephrine (3,4-dihydroxyphenyl-2-aminoethanol) is a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine. levarterenol transport noradrenaline transport biological_process GO:0015874 norepinephrine transport The directed movement of norepinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Norepinephrine (3,4-dihydroxyphenyl-2-aminoethanol) is a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine. GOC:ai ISBN:0198506732 The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds. Wikipedia:Photosynthesis biological_process GO:0015979 photosynthesis The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds. ISBN:0198547684 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 A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. GOC:dos GOC:mah ISBN:0815316194 The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. Wikipedia:Transmembrane_protein integral to membrane cellular_component transmembrane GO:0016021 integral component of membrane The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. GOC:dos GOC:go_curators transmembrane GOC:mah 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 series of events in which a temperature stimulus (hot or cold) is received and converted into a molecular signal. detection of temperature detection of thermal stimulus biological_process perception of temperature GO:0016048 detection of temperature stimulus The series of events in which a temperature stimulus (hot or cold) is received and converted into a molecular signal. GOC:hb A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle. vesicle organisation biological_process vesicle organization and biogenesis GO:0016050 vesicle organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle. GOC:mah vesicle organization and biogenesis GOC:mah The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage. organic acid anabolism organic acid biosynthesis organic acid formation organic acid synthesis biological_process GO:0016053 organic acid biosynthetic process The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage. ISBN:0198506732 An immune response mediated by immunoglobulins, whether cell-bound or in solution. antibody-mediated immune response biological_process GO:0016064 immunoglobulin mediated immune response An immune response mediated by immunoglobulins, whether cell-bound or in solution. GOC:add GO_REF:0000022 ISBN:0781735149 A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. GO:0006899 vesicle transport vesicular transport nonselective vesicle transport biological_process protein sorting along secretory pathway vesicle trafficking GO:0016192 vesicle-mediated transport A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. GOC:ai GOC:mah ISBN:08789310662000 vesicular transport GOC:mah true kinase activity The cell cycle process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets during the meiotic cell cycle in a female. biological_process GO:0016321 female meiosis chromosome segregation The cell cycle process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets during the meiotic cell cycle in a female. GOC:ai Recombination occurring within or between DNA molecules in somatic cells. biological_process GO:0016444 somatic cell DNA recombination Recombination occurring within or between DNA molecules in somatic cells. GOC:ma The somatic process that results in the generation of sequence diversity of immunoglobulins. somatic diversification of antibodies biological_process GO:0016445 somatic diversification of immunoglobulins The somatic process that results in the generation of sequence diversity of immunoglobulins. GOC:add GOC:ma ISBN:0781735149 Mutations occurring somatically that result in amino acid changes in the rearranged V regions of immunoglobulins. somatic hypermutation of antibody genes biological_process GO:0016446 somatic hypermutation of immunoglobulin genes Mutations occurring somatically that result in amino acid changes in the rearranged V regions of immunoglobulins. GOC:add ISBN:0781735149 PMID:11205330 PMID:11205333 PMID:14975236 PMID:7813007 The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, as known as immunoglobulin gene segments, within a single locus. somatic recombination of antibody gene segments biological_process GO:0016447 somatic recombination of immunoglobulin gene segments The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, as known as immunoglobulin gene segments, within a single locus. GOC:add ISBN:0781735149 The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms. Wikipedia:Cell_migration biological_process GO:0016477 cell migration The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms. GOC:cjm GOC:dph GOC:ems GOC:pf Wikipedia:Cell_migration Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis. down regulation of angiogenesis down-regulation of angiogenesis downregulation of angiogenesis inhibition of angiogenesis biological_process GO:0016525 negative regulation of angiogenesis Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis. GOC:go_curators transferase activity transferase activity, transferring phosphorus-containing groups The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. stem cell renewal biological_process GO:0017145 stem cell division The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. GOC:jid ISBN:0582227089 The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle anabolism heterocycle biosynthesis heterocycle formation heterocycle synthesis biological_process GO:0018130 heterocycle biosynthetic process The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). ISBN:0198547684 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 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 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 The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission. conduction of nerve impulse signal transmission along a neuron biological_process GO:0019226 transmission of nerve impulse The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission. GOC:curators ISBN:0815316194 conduction of nerve impulse GOC:dph The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring. aromatic compound anabolism aromatic compound biosynthesis aromatic compound formation aromatic compound synthesis aromatic hydrocarbon biosynthesis aromatic hydrocarbon biosynthetic process biological_process GO:0019438 aromatic compound biosynthetic process The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring. GOC:ai Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells. B lymphocyte mediated immune effector process B lymphocyte mediated immunity B-cell mediated immune effector process B-cell mediated immunity B-lymphocyte mediated immune effector process B-lymphocyte mediated immunity biological_process GO:0019724 B cell mediated immunity Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells. GOC:add GO_REF:0000022 ISBN:0781735149 An immune response against microbes mediated through a body fluid. Examples of this process are seen in the antimicrobial humoral response of Drosophila melanogaster and Mus musculus. GO:0006960 GO:0019735 biological_process GO:0019730 antimicrobial humoral response An immune response against microbes mediated through a body fluid. Examples of this process are seen in the antimicrobial humoral response of Drosophila melanogaster and Mus musculus. GOC:go_curators GOC:mtg_sensu 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 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. antibody cellular_component GO:0019814 Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. 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. GOC:add GOC:jl ISBN:0781765196 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. GO:0042570 B lymphocyte receptor complex B-cell receptor complex B-lymphocyte receptor complex BCR complex immunoglobulin complex, membrane bound cellular_component B cell receptor accessory molecule complex antibody GO:0019815 Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. 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. GOC:add ISBN:0781735149 antibody GOC:mah The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. GO:0030333 Wikipedia:Antigen_presentation antigen presentation antigen processing biological_process GO:0019882 antigen processing and presentation The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. GOC:add GO_REF:0000022 ISBN:0781735149 PMID:15771591 PMID:15928678 The process in which an antigen-presenting cell expresses antigen (peptide or lipid) of exogenous origin on its cell surface in association with an MHC protein complex. antigen presentation, exogenous antigen biological_process GO:0019884 antigen processing and presentation of exogenous antigen The process in which an antigen-presenting cell expresses antigen (peptide or lipid) of exogenous origin on its cell surface in association with an MHC protein complex. GOC:add ISBN:0781735149 PMID:15771591 PMID:15928678 A reproduction process that creates a new organism by combining the genetic material of two gametes, which may come from two organisms or from a single organism, in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. It occurs both in eukaryotes and prokaryotes: in multicellular eukaryotic organisms, an individual is created anew; in prokaryotes, the initial cell has additional or transformed genetic material. In a process called genetic recombination, genetic material (DNA) originating from two gametes join up so that homologous sequences are aligned with each other, and this is followed by exchange of genetic information. After the new recombinant chromosome is formed, it is passed on to progeny. Wikipedia:Sexual_reproduction biological_process GO:0019953 Sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times. sexual reproduction A reproduction process that creates a new organism by combining the genetic material of two gametes, which may come from two organisms or from a single organism, in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. It occurs both in eukaryotes and prokaryotes: in multicellular eukaryotic organisms, an individual is created anew; in prokaryotes, the initial cell has additional or transformed genetic material. In a process called genetic recombination, genetic material (DNA) originating from two gametes join up so that homologous sequences are aligned with each other, and this is followed by exchange of genetic information. After the new recombinant chromosome is formed, it is passed on to progeny. GOC:jl GOC:kmv GOC:krc GOC:tb ISBN:0387520546 Wikipedia:Sexual_reproduction The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. biological_process GO:0022402 cell cycle process The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. GOC:isa_complete GOC:mtg_cell_cycle Any process that modulates the frequency, rate or extent of attachment of a cell to another cell. biological_process GO:0022407 regulation of cell-cell adhesion Any process that modulates the frequency, rate or extent of attachment of a cell to another cell. GOC:isa_complete Any process that stops, prevents or reduces the rate or extent of cell adhesion to another cell. down regulation of cell-cell adhesion down-regulation of cell-cell adhesion downregulation of cell-cell adhesion inhibition of cell-cell adhesion biological_process GO:0022408 negative regulation of cell-cell adhesion Any process that stops, prevents or reduces the rate or extent of cell adhesion to another cell. GOC:isa_complete Any process that activates or increases the rate or extent of cell adhesion to another cell. up regulation of cell-cell adhesion up-regulation of cell-cell adhesion upregulation of cell-cell adhesion activation of cell-cell adhesion stimulation of cell-cell adhesion biological_process GO:0022409 positive regulation of cell-cell adhesion Any process that activates or increases the rate or extent of cell adhesion to another cell. GOC:isa_complete A cellular process that results in the breakdown of a cellular component. GO:0071845 cell structure disassembly cellular component disassembly at cellular level biological_process GO:0022411 cellular component disassembly A cellular process that results in the breakdown of a cellular component. GOC:isa_complete A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism. reproductive cellular process in multicellular organism biological_process GO:0022412 cellular process involved in reproduction in multicellular organism A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism. GOC:isa_complete A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. jl 2012-09-19T15:56:06Z GO:0044702 biological_process single organism reproductive process GO:0022414 reproductive process A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GOC:dph GOC:isa_complete 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 A process involved in the sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years. biological_process estrous cycle process menstrual cycle process GO:0022602 ovulation cycle process A process involved in the sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years. GOC:isa_complete 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 The aggregation, arrangement and bonding together of a cellular component. GO:0071844 cell structure assembly cellular component assembly at cellular level biological_process GO:0022607 cellular component assembly The aggregation, arrangement and bonding together of a cellular component. GOC:isa_complete The attachment of a cell or organism to a substrate, another cell, or other organism. Biological adhesion includes intracellular attachment between membrane regions. biological_process GO:0022610 biological adhesion The attachment of a cell or organism to a substrate, another cell, or other organism. Biological adhesion includes intracellular attachment between membrane regions. GOC:isa_complete Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other. GO:0005386 GO:0015563 GO:0015646 GO:0022891 GO:0022892 Reactome:R-HSA-1236947 Reactome:R-HSA-429036 Reactome:R-HSA-5638209 Reactome:R-HSA-5671707 Reactome:R-HSA-6784434 Reactome:R-HSA-6784436 molecular_function substrate-specific transmembrane transporter activity substrate-specific transporter activity uptake permease activity uptake transmembrane transporter activity GO:0022857 transmembrane transporter activity Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other. GOC:jid GOC:mtg_transport ISBN:0815340729 Reactome:R-HSA-1236947 Egress of internalized antigen to the cytosol via sec61 Reactome:R-HSA-429036 SLC2A9 transports Fru, Glc, urate Reactome:R-HSA-5638209 Defective SLC2A9 does not transport Fru, Glc, urate Reactome:R-HSA-5671707 Fe3+ dissociates from SLC22A17:LCN2:2,5DHBA Reactome:R-HSA-6784434 An unknown carrier transports cytosolic glyoxylate to the peroxisome Reactome:R-HSA-6784436 An unknown carrier transports mitochondrial glyoxylate to the cytosol Any process that modulates the frequency, rate or extent of transmembrane transporter activity. biological_process GO:0022898 regulation of transmembrane transporter activity Any process that modulates the frequency, rate or extent of transmembrane transporter activity. GOC:dph GOC:mtg_cardio GOC:mtg_transport Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another. 2010-02-16T09:30:50Z biological_process regulation of gene expression as a consequence of signal transmission GO:0023019 signal transduction involved in regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another. GOC:mtg_signal regulation of gene expression as a consequence of signal transmission GOC:bf Binding to a major histocompatibility complex class Ib molecules. 2010-02-16T09:30:50Z molecular_function GO:0023029 MHC class Ib protein binding Binding to a major histocompatibility complex class Ib molecules. GOC:mtg_signal GOC:vw 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. 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 The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism. Wikipedia:Myofibril cellular_component GO:0030016 myofibril The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism. ISBN:0815316194 The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. Wikipedia:Sarcomere cellular_component GO:0030017 sarcomere The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. ISBN:0815316194 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. cell projection organisation biological_process cell projection organization and biogenesis cell surface structure organization and biogenesis GO:0030030 cell projection organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah http://www.cogsci.princeton.edu/~wn/ cell projection organization and biogenesis GOC:mah cell surface structure organization and biogenesis GOC:mah Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon. formation of a cell surface projection biological_process cell projection biogenesis GO:0030031 cell projection assembly Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah http://www.cogsci.princeton.edu/~wn/ cell projection biogenesis GOC:mah A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella. Wikipedia:Cell_junction cellular_component GO:0030054 cell junction A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella. GOC:aruk GOC:bc GOC:mah ISBN:0198506732 PMID:26820516 PMID:28096264 http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html The regulated release of a peptide hormone from a cell. biological_process GO:0030072 peptide hormone secretion The regulated release of a peptide hormone from a cell. GOC:mah The regulated release of proinsulin from secretory granules accompanied by cleavage of proinsulin to form mature insulin. In vertebrates, insulin is secreted from B granules in the B cells of the vertebrate pancreas and from insulin-producing cells in insects. https://github.com/geneontology/go-ontology/issues/11255#issuecomment-426191045 biological_process GO:0030073 insulin secretion The regulated release of proinsulin from secretory granules accompanied by cleavage of proinsulin to form mature insulin. In vertebrates, insulin is secreted from B granules in the B cells of the vertebrate pancreas and from insulin-producing cells in insects. GOC:mah ISBN:0198506732 The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates. Wikipedia:Haematopoiesis blood cell biosynthesis blood cell formation haemopoiesis hematopoiesis biological_process GO:0030097 hemopoiesis The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates. GOC:dgh ISBN:0198506732 The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. GO:0046650 lymphocyte cell differentiation lymphocytic blood cell differentiation biological_process lymphocyte development GO:0030098 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. lymphocyte differentiation The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. CL:0000542 GOC:go_curators lymphocyte development GOC:add The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages. biological_process GO:0030099 myeloid cell differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages. GOC:add ISBN:0781735149 Any process that modulates the frequency, rate or extent of endocytosis. biological_process GO:0030100 regulation of endocytosis Any process that modulates the frequency, rate or extent of endocytosis. GOC:go_curators The change in morphology and behavior of a natural killer cell in response to a cytokine, chemokine, cellular ligand, or soluble factor. NK cell activation biological_process GO:0030101 natural killer cell activation The change in morphology and behavior of a natural killer cell in response to a cytokine, chemokine, cellular ligand, or soluble factor. GOC:mgi_curators ISBN:0781735149 The regulated release of vasopressin from secretory granules into the blood. biological_process GO:0030103 vasopressin secretion The regulated release of vasopressin from secretory granules into the blood. 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 The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. Wikipedia:Cellular_differentiation biological_process GO:0030154 cell differentiation The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. ISBN:0198506732 Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix. biological_process cell adhesion receptor regulator activity GO:0030155 regulation of cell adhesion Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix. GOC:mah The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity. GO:0042115 B lymphocyte differentiation B-cell differentiation B-lymphocyte differentiation biological_process B cell development GO:0030183 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. B cell differentiation The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity. GOC:mah GO_REF:0000022 B cell development GOC:add The chemical reactions and pathways involving melatonin (N-acetyl-5-methoxytryptamine). melatonin metabolism biological_process GO:0030186 melatonin metabolic process The chemical reactions and pathways involving melatonin (N-acetyl-5-methoxytryptamine). GOC:mah ISBN:0198506732 The chemical reactions and pathways resulting in the formation of melatonin (N-acetyl-5-methoxytryptamine). melatonin anabolism melatonin biosynthesis melatonin formation melatonin synthesis biological_process GO:0030187 melatonin biosynthetic process The chemical reactions and pathways resulting in the formation of melatonin (N-acetyl-5-methoxytryptamine). GOC:mah ISBN:0198506732 Any process that modulates the frequency, rate or extent of blood coagulation. biological_process GO:0030193 regulation of blood coagulation Any process that modulates the frequency, rate or extent of blood coagulation. GOC:mah Any process that activates or increases the frequency, rate or extent of blood coagulation. up regulation of blood coagulation up-regulation of blood coagulation upregulation of blood coagulation activation of blood coagulation stimulation of blood coagulation biological_process GO:0030194 positive regulation of blood coagulation Any process that activates or increases the frequency, rate or extent of blood coagulation. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation. down regulation of blood coagulation down-regulation of blood coagulation downregulation of blood coagulation inhibition of blood coagulation biological_process GO:0030195 negative regulation of blood coagulation Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation. GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix. extracellular matrix organisation biological_process extracellular matrix organization and biogenesis GO:0030198 extracellular matrix organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix. GOC:mah extracellular matrix organization and biogenesis GOC:mah The chemical reactions and pathways involving heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells. They are similar to heparan sulfates but are of somewhat higher average Mr (6000-20000) and contain fewer N-acetyl groups and more N-sulfate and O-sulfate groups; they may be attached in the same manner to protein, forming proteoglycans. They consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues. heparin metabolism biological_process heparan sulfate metabolic process GO:0030202 heparin metabolic process The chemical reactions and pathways involving heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells. They are similar to heparan sulfates but are of somewhat higher average Mr (6000-20000) and contain fewer N-acetyl groups and more N-sulfate and O-sulfate groups; they may be attached in the same manner to protein, forming proteoglycans. They consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues. GOC:mah ISBN:0198506732 The chemical reactions and pathways involving glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars. Formerly known as mucopolysaccharides, they include hyaluronic acid and chondroitin, which provide lubrication in joints and form part of the matrix of cartilage. The three-dimensional structure of these molecules enables them to trap water, which forms a gel and gives glycosaminoglycans their elastic properties. glycosaminoglycan metabolism biological_process GO:0030203 glycosaminoglycan metabolic process The chemical reactions and pathways involving glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars. Formerly known as mucopolysaccharides, they include hyaluronic acid and chondroitin, which provide lubrication in joints and form part of the matrix of cartilage. The three-dimensional structure of these molecules enables them to trap water, which forms a gel and gives glycosaminoglycans their elastic properties. ISBN:0192800981 The chemical reactions and pathways resulting in the formation of heparin, any member of a group of glycosaminoglycans of average Mr (6000-20000), consisting predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues. heparin anabolism heparin biosynthesis heparin formation heparin synthesis biological_process heparan sulfate biosynthetic process GO:0030210 heparin biosynthetic process The chemical reactions and pathways resulting in the formation of heparin, any member of a group of glycosaminoglycans of average Mr (6000-20000), consisting predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues. GOC:mah ISBN:0198506732 The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex. GO:0042112 GO:0046652 T lymphocyte differentiation T-cell differentiation T-lymphocyte differentiation biological_process T cell development GO:0030217 Note that the term 'thymocyte differentiation' was merged into this term because thymocytes are T cells, and thus the term was essentially redundant. Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. T cell differentiation The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex. GOC:jid GOC:mah GO_REF:0000022 T cell development GOC:add The process in which a myeloid precursor cell acquires specializes features of an erythrocyte. Wikipedia:Erythropoiesis RBC differentiation erythrocyte cell differentiation erythropoiesis red blood cell differentiation biological_process GO:0030218 erythrocyte differentiation The process in which a myeloid precursor cell acquires specializes features of an erythrocyte. GOC:mah RBC differentiation CL:0000232 erythropoiesis GOC:add GOC:dph red blood cell differentiation CL:0000232 The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte. megakaryocyte cell differentiation biological_process GO:0030219 megakaryocyte differentiation The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte. GOC:mah The process in which a relatively unspecialized myeloid precursor cell acquires specialized features of a basophil cell. basophil cell differentiation biological_process GO:0030221 basophil differentiation The process in which a relatively unspecialized myeloid precursor cell acquires specialized features of a basophil cell. GOC:jid GOC:mah The process in which a relatively unspecialized myeloid precursor cell acquires the specializes features of an eosinophil. GO:0035856 eosinophil cell differentiation biological_process eosinophil cell development eosinophil development GO:0030222 eosinophil differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specializes features of an eosinophil. GOC:add GOC:mah eosinophil cell development GOC:bf The process in which a myeloid precursor cell acquires the specialized features of a neutrophil. neutrophil cell differentiation neutrophil granulocyte differentiation neutrophil granulocytopoiesis biological_process GO:0030223 neutrophil differentiation The process in which a myeloid precursor cell acquires the specialized features of a neutrophil. GOC:mah neutrophil granulocyte differentiation GOC:yaf neutrophil granulocytopoiesis GOC:yaf The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte. monocyte cell differentiation biological_process GO:0030224 monocyte differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte. GOC:mah The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage. macrophage cell differentiation biological_process GO:0030225 macrophage differentiation The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage. GOC:add ISBN:0781735149 The regulated release of growth hormone from secretory granules into the blood. somatotropin secretion biological_process GO:0030252 growth hormone secretion The regulated release of growth hormone from secretory granules into the blood. GOC:mah somatotropin secretion GOC:mah The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. GO:0000068 DNA condensation eukaryotic chromosome condensation nuclear chromosome condensation biological_process GO:0030261 chromosome condensation The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. GOC:mah ISBN:0815316194 DNA condensation Wikipedia:DNA_condensation eukaryotic chromosome condensation GOC:bf nuclear chromosome condensation GOC:bf Alterations undergone by nuclei at the molecular and morphological level as part of the execution phase of apoptosis. apoptotic nuclear change biological_process GO:0030262 apoptotic nuclear changes Alterations undergone by nuclei at the molecular and morphological level as part of the execution phase of apoptosis. GOC:mah GOC:mtg_apoptosis The compaction of chromatin during apoptosis. Wikipedia:Pyknosis pyknosis biological_process GO:0030263 apoptotic chromosome condensation The compaction of chromatin during apoptosis. GOC:mah The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue. osteoclast cell differentiation biological_process GO:0030316 osteoclast differentiation The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue. CL:0000092 GOC:add ISBN:0781735149 PMID:12161749 The directed, self-propelled movement of a cilium (aka flagellum) that contributes to the movement of a flagellated sperm. GO:0097724 GO:1905419 sperm motility sperm movement Wikipedia:Sperm_motility flagellated sperm movement sperm flagellum movement sperm flagellum movement involved in flagellated sperm motility sperm flagellum movement involved in flagellated sperm movement biological_process GO:0030317 flagellated sperm motility The directed, self-propelled movement of a cilium (aka flagellum) that contributes to the movement of a flagellated sperm. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000060 PMID:26680031 sperm flagellum movement GOC:cilia GOC:krc sperm flagellum movement involved in flagellated sperm movement GOC:TermGenie Any process that modulates the frequency, rate or extent of cell migration. biological_process GO:0030334 regulation of cell migration Any process that modulates the frequency, rate or extent of cell migration. GOC:go_curators Any process that activates or increases the frequency, rate or extent of cell migration. up regulation of cell migration up-regulation of cell migration upregulation of cell migration activation of cell migration stimulation of cell migration biological_process GO:0030335 positive regulation of cell migration Any process that activates or increases the frequency, rate or extent of cell migration. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration. down regulation of cell migration down-regulation of cell migration downregulation of cell migration inhibition of cell migration biological_process GO:0030336 negative regulation of cell migration Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration. GOC:go_curators The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter. NIF_Subcellular:sao1770195789 Wikipedia:Axon cellular_component GO:0030424 axon The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter. GOC:nln ISBN:0198506732 The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding. biological_process GO:0030593 neutrophil chemotaxis The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding. GOC:jl ISBN:0198506732 The movement of a leukocyte in response to an external stimulus. immune cell chemotaxis leucocyte chemotaxis biological_process GO:0030595 leukocyte chemotaxis The movement of a leukocyte in response to an external stimulus. GOC:add GOC:jl 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 The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell. biological_process GO:0030705 cytoskeleton-dependent intracellular transport The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell. GOC:mah The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils. granulocyte cell differentiation biological_process GO:0030851 granulocyte differentiation The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils. GOC:ecd http://life.nthu.edu.tw/~g864204/dict-search1.htm Any process that modulates the frequency, rate or extent of granulocyte differentiation. biological_process GO:0030852 regulation of granulocyte differentiation Any process that modulates the frequency, rate or extent of granulocyte differentiation. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of granulocyte differentiation. down regulation of granulocyte differentiation down-regulation of granulocyte differentiation downregulation of granulocyte differentiation inhibition of granulocyte differentiation biological_process GO:0030853 negative regulation of granulocyte differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of granulocyte differentiation. GOC:mah Any process that activates or increases the frequency, rate or extent of granulocyte differentiation. up regulation of granulocyte differentiation up-regulation of granulocyte differentiation upregulation of granulocyte differentiation activation of granulocyte differentiation stimulation of granulocyte differentiation biological_process GO:0030854 positive regulation of granulocyte differentiation Any process that activates or increases the frequency, rate or extent of granulocyte differentiation. GOC:mah Any process that modulates the frequency or rate of myeloid dendritic cell activation. biological_process GO:0030885 regulation of myeloid dendritic cell activation Any process that modulates the frequency or rate of myeloid dendritic cell activation. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid dendritic cell activation. down regulation of myeloid dendritic cell activation down-regulation of myeloid dendritic cell activation downregulation of myeloid dendritic cell activation inhibition of myeloid dendritic cell activation biological_process GO:0030886 negative regulation of myeloid dendritic cell activation Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid dendritic cell activation. GOC:mah Any process that stimulates, induces or increases the rate of myeloid dendritic cell activation. up regulation of myeloid dendritic cell activation up-regulation of myeloid dendritic cell activation upregulation of myeloid dendritic cell activation activation of myeloid dendritic cell activation stimulation of myeloid dendritic cell activation biological_process GO:0030887 positive regulation of myeloid dendritic cell activation Any process that stimulates, induces or increases the rate of myeloid dendritic cell activation. GOC:mah A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules. intraflagellar transport complex intraflagellar transport particle cellular_component IFT complex GO:0030990 Note that we deem cilia and microtubule-based flagella to be equivalent. intraciliary transport particle A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules. GOC:cilia GOC:kmv PMID:14570576 PMID:22118932 PMID:23945166 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 The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass). Wikipedia:Regeneration_(biology) biological_process GO:0031099 regeneration The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass). GOC:mah GOC:pr The component of a membrane consisting of the gene products having some covalently attached portion, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, which spans or is embedded in one or both leaflets of the membrane. intrinsic to membrane cellular_component GO:0031224 Note that proteins intrinsic to membranes cannot be removed without disrupting the membrane, e.g. by detergent. intrinsic component of membrane The component of a membrane consisting of the gene products having some covalently attached portion, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, which spans or is embedded in one or both leaflets of the membrane. GOC:mah The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane. intrinsic to plasma membrane cellular_component GO:0031226 intrinsic component of plasma membrane The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane. GOC:dos 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 pseudopodium, a temporary protrusion or retractile process of a cell, associated with cellular movement. pseudopodium organisation biological_process pseudopodium organization and biogenesis GO:0031268 pseudopodium organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pseudopodium, a temporary protrusion or retractile process of a cell, associated with cellular movement. GOC:pg pseudopodium organization and biogenesis GOC:mah The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the B- or T cell receptor to augment B- or T cell activation. lymphocyte co-stimulation biological_process GO:0031294 lymphocyte costimulation The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the B- or T cell receptor to augment B- or T cell activation. ISBN:0781735149 The component of the organelle membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane. intrinsic to organelle membrane cellular_component GO:0031300 intrinsic component of organelle membrane The component of the organelle membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane. GOC:dos GOC:mah The component of the organelle membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. integral to organelle membrane cellular_component GO:0031301 integral component of organelle membrane The component of the organelle membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. GOC:dos GOC:mah 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 cell killing, the process in which a cell brings about the death of another cell, either in the same or a different organism. biological_process GO:0031341 regulation of cell killing Any process that modulates the frequency, rate or extent of cell killing, the process in which a cell brings about the death of another cell, either in the same or a different organism. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of cell killing. down regulation of cell killing down-regulation of cell killing downregulation of cell killing inhibition of cell killing biological_process GO:0031342 negative regulation of cell killing Any process that stops, prevents, or reduces the frequency, rate or extent of cell killing. GOC:mah Any process that activates or increases the frequency, rate or extent of cell killing. up regulation of cell killing up-regulation of cell killing upregulation of cell killing activation of cell killing stimulation of cell killing biological_process GO:0031343 positive regulation of cell killing Any process that activates or increases the frequency, rate or extent of cell killing. 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 cell projections. regulation of cell projection organisation biological_process regulation of cell projection organization and biogenesis GO:0031344 regulation of cell projection 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 projections. GOC:mah regulation of cell projection 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 projections. down regulation of cell projection organization down-regulation of cell projection organization downregulation of cell projection organization negative regulation of cell projection organisation inhibition of cell projection organization biological_process negative regulation of cell projection organization and biogenesis GO:0031345 negative regulation of cell projection 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 projections. GOC:mah down regulation of cell projection organization GOC:mah negative regulation of cell projection organization and biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of the process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. positive regulation of cell projection organisation up regulation of cell projection organization up-regulation of cell projection organization upregulation of cell projection organization activation of cell projection organization stimulation of cell projection organization biological_process positive regulation of cell projection organization and biogenesis GO:0031346 positive regulation of cell projection organization Any process that activates or increases the frequency, rate or extent of the process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. GOC:mah positive regulation of cell projection organization and biogenesis 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 A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location. establishment and maintenance of protein complex localization protein complex localisation biological_process protein complex localization GO:0031503 protein-containing complex localization A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location. GOC:mah protein complex localisation GOC:mah Any process that modulates the frequency, rate or extent of a neurophysiological process, an organ system process carried out by any of the organs or tissues of the nervous system. regulation of neurological process regulation of neurological system process regulation of neurophysiological process biological_process GO:0031644 regulation of nervous system process Any process that modulates the frequency, rate or extent of a neurophysiological process, an organ system process carried out by any of the organs or tissues of the nervous system. GOC:dph GOC:mah GOC:tb regulation of neurological process GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of a neurophysiological process. down regulation of neurological process down-regulation of neurological process downregulation of neurological process negative regulation of neurological process negative regulation of neurological system process negative regulation of neurophysiological process inhibition of neurological process biological_process GO:0031645 negative regulation of nervous system process Any process that stops, prevents, or reduces the frequency, rate or extent of a neurophysiological process. GOC:dph GOC:mah GOC:tb negative regulation of neurological process GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of a neurophysiological process. positive regulation of neurological process positive regulation of neurological system process positive regulation of neurophysiological process up regulation of neurological process up-regulation of neurological process upregulation of neurological process activation of neurological process stimulation of neurological process biological_process GO:0031646 positive regulation of nervous system process Any process that activates or increases the frequency, rate or extent of a neurophysiological process. GOC:dph GOC:mah GOC:tb positive regulation of neurological process GOC:dph GOC:tb Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. NIF_Subcellular:sao1687101204 cellular_component GO:0031965 nuclear membrane Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. GOC:mah GOC:pz A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. cellular_component GO:0031967 organelle envelope A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. GOC:mah GOC:pz The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen. cellular_component GO:0031974 membrane-enclosed lumen The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen. GOC:add GOC:mah A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. cellular_component GO:0031975 envelope A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. GOC:mah GOC:pz The volume enclosed by the nuclear inner membrane. cellular_component GO:0031981 nuclear lumen The volume enclosed by the nuclear inner membrane. GOC:mah GOC:pz 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 activates or increases the frequency, rate or extent of the regulated release of insulin. up regulation of insulin secretion up-regulation of insulin secretion upregulation of insulin secretion activation of insulin secretion stimulation of insulin secretion biological_process GO:0032024 positive regulation of insulin secretion Any process that activates or increases the frequency, rate or extent of the regulated release of insulin. GOC:mah The assembly of a bleb, a cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Plasma membrane blebbing occurs during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses. blebbing membrane blebbing cell blebbing plasma membrane bleb assembly plasma membrane blebbing biological_process GO:0032060 bleb assembly The assembly of a bleb, a cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Plasma membrane blebbing occurs during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses. GOC:mah GOC:mtg_apoptosis PMID:12083798 PMID:16624291 Wikipedia:Bleb_(cell_biology) blebbing GOC:pr membrane blebbing GOC:pr plasma membrane bleb assembly GOC:pr plasma membrane blebbing GOC:pr 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 cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine. biological_process GO:0032222 regulation of synaptic transmission, cholinergic Any process that modulates the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine. down regulation of synaptic transmission, cholinergic down-regulation of synaptic transmission, cholinergic downregulation of synaptic transmission, cholinergic inhibition of synaptic transmission, cholinergic biological_process GO:0032223 negative regulation of synaptic transmission, cholinergic Any process that stops, prevents, or reduces the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine. GOC:mah Any process that activates, maintains or increases the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine. up regulation of synaptic transmission, cholinergic up-regulation of synaptic transmission, cholinergic upregulation of synaptic transmission, cholinergic activation of synaptic transmission, cholinergic stimulation of synaptic transmission, cholinergic biological_process GO:0032224 positive regulation of synaptic transmission, cholinergic Any process that activates, maintains or increases the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine. GOC:mah Any process that modulates the frequency, rate or extent of dopaminergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter dopamine. biological_process GO:0032225 regulation of synaptic transmission, dopaminergic Any process that modulates the frequency, rate or extent of dopaminergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter dopamine. GOC:mah Any process that activates, maintains or increases the frequency, rate or extent of dopaminergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter dopamine. up regulation of synaptic transmission, dopaminergic up-regulation of synaptic transmission, dopaminergic upregulation of synaptic transmission, dopaminergic activation of synaptic transmission, dopaminergic stimulation of synaptic transmission, dopaminergic biological_process GO:0032226 positive regulation of synaptic transmission, dopaminergic Any process that activates, maintains or increases the frequency, rate or extent of dopaminergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter dopamine. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of dopaminergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter dopamine. down regulation of synaptic transmission, dopaminergic down-regulation of synaptic transmission, dopaminergic downregulation of synaptic transmission, dopaminergic inhibition of synaptic transmission, dopaminergic biological_process GO:0032227 negative regulation of synaptic transmission, dopaminergic Any process that stops, prevents, or reduces the frequency, rate or extent of dopaminergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter dopamine. GOC:mah Any process that modulates the frequency, rate or extent of GABAergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter gamma-aminobutyric acid (GABA). biological_process GO:0032228 regulation of synaptic transmission, GABAergic Any process that modulates the frequency, rate or extent of GABAergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter gamma-aminobutyric acid (GABA). GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of GABAergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter gamma-aminobutyric acid (GABA). down regulation of synaptic transmission, GABAergic down-regulation of synaptic transmission, GABAergic downregulation of synaptic transmission, GABAergic inhibition of synaptic transmission, GABAergic biological_process GO:0032229 negative regulation of synaptic transmission, GABAergic Any process that stops, prevents, or reduces the frequency, rate or extent of GABAergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter gamma-aminobutyric acid (GABA). GOC:mah Any process that activates, maintains or increases the frequency, rate or extent of GABAergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter gamma-aminobutyric acid (GABA). up regulation of synaptic transmission, GABAergic up-regulation of synaptic transmission, GABAergic upregulation of synaptic transmission, GABAergic activation of synaptic transmission, GABAergic stimulation of synaptic transmission, GABAergic biological_process GO:0032230 positive regulation of synaptic transmission, GABAergic Any process that activates, maintains or increases the frequency, rate or extent of GABAergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter gamma-aminobutyric acid (GABA). GOC:mah The regulated release of a gonadotropin, any hormone that stimulates the gonads, especially follicle-stimulating hormone and luteinizing hormone. gonadotrophin secretion biological_process GO:0032274 gonadotropin secretion The regulated release of a gonadotropin, any hormone that stimulates the gonads, especially follicle-stimulating hormone and luteinizing hormone. GOC:mah ISBN:0721662544 The regulated release of luteinizing hormone, a gonadotropic glycoprotein hormone secreted by the anterior pituitary. biological_process GO:0032275 luteinizing hormone secretion The regulated release of luteinizing hormone, a gonadotropic glycoprotein hormone secreted by the anterior pituitary. ISBN:0198506732 Any process that modulates the frequency, rate or extent of the regulated release of a gonadotropin. regulation of gonadotrophin secretion biological_process GO:0032276 regulation of gonadotropin secretion Any process that modulates the frequency, rate or extent of the regulated release of a gonadotropin. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a gonadotropin. down regulation of gonadotropin secretion down-regulation of gonadotropin secretion downregulation of gonadotropin secretion negative regulation of gonadotrophin secretion inhibition of gonadotropin secretion biological_process GO:0032277 negative regulation of gonadotropin secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a gonadotropin. GOC:mah negative regulation of gonadotrophin secretion GOC:dph Any process that activates or increases the frequency, rate or extent of the regulated release of a gonadotropin. positive regulation of gonadotrophin secretion up regulation of gonadotropin secretion up-regulation of gonadotropin secretion upregulation of gonadotropin secretion activation of gonadotropin secretion stimulation of gonadotropin secretion biological_process GO:0032278 positive regulation of gonadotropin secretion Any process that activates or increases the frequency, rate or extent of the regulated release of a gonadotropin. GOC:mah positive regulation of gonadotrophin secretion GOC:dph Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving any hormone. regulation of hormone metabolism biological_process GO:0032350 regulation of hormone metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving any hormone. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving any hormone. down regulation of hormone metabolic process down-regulation of hormone metabolic process downregulation of hormone metabolic process negative regulation of hormone metabolism inhibition of hormone metabolic process biological_process GO:0032351 negative regulation of hormone metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving any hormone. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving any hormone. positive regulation of hormone metabolism up regulation of hormone metabolic process up-regulation of hormone metabolic process upregulation of hormone metabolic process activation of hormone metabolic process stimulation of hormone metabolic process biological_process GO:0032352 positive regulation of hormone metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving any hormone. 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 hormones. down regulation of hormone biosynthetic process down-regulation of hormone biosynthetic process downregulation of hormone biosynthetic process inhibition of hormone biosynthetic process biological_process GO:0032353 negative regulation of hormone 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 hormones. GOC:ai 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 Combining with an MHC class Ib protein complex and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. Class Ib here refers to non-classical class I molecules, such as those of the CD1 or HLA-E gene families. molecular_function T cell receptor activity alpha-beta T cell receptor activity gamma-delta T cell receptor activity GO:0032394 Note that this term is intended for annotation of gene products that act as receptors for MHC class Ib protein complexes, not for components of the MHC class Ib protein complexes themselves. MHC class Ib receptor activity Combining with an MHC class Ib protein complex and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. Class Ib here refers to non-classical class I molecules, such as those of the CD1 or HLA-E gene families. GOC:add GOC:signaling ISBN:0781735149 Any process that modulates the activity of a transporter. biological_process GO:0032409 regulation of transporter activity Any process that modulates the activity of a transporter. GOC:mah Any process that stops or reduces the activity of a transporter. down regulation of transporter activity down-regulation of transporter activity downregulation of transporter activity inhibition of transporter activity biological_process GO:0032410 negative regulation of transporter activity Any process that stops or reduces the activity of a transporter. GOC:mah Any process that activates or increases the activity of a transporter. up regulation of transporter activity up-regulation of transporter activity upregulation of transporter activity activation of transporter activity stimulation of transporter activity biological_process GO:0032411 positive regulation of transporter activity Any process that activates or increases the activity of a transporter. GOC:mah Any process that modulates the activity of an ion transporter. regulation of ion transporter activity biological_process GO:0032412 regulation of ion transmembrane transporter activity Any process that modulates the activity of an ion transporter. GOC:mah GOC:tb regulation of ion transporter activity GOC:tb Any process that stops or reduces the activity of an ion transporter. down regulation of ion transporter activity down-regulation of ion transporter activity downregulation of ion transporter activity negative regulation of ion transporter activity inhibition of ion transporter activity biological_process GO:0032413 negative regulation of ion transmembrane transporter activity Any process that stops or reduces the activity of an ion transporter. GOC:mah GOC:tb negative regulation of ion transporter activity GOC:tb Any process that activates or increases the activity of an ion transporter. positive regulation of ion transporter activity up regulation of ion transporter activity up-regulation of ion transporter activity upregulation of ion transporter activity activation of ion transporter activity stimulation of ion transporter activity biological_process GO:0032414 positive regulation of ion transmembrane transporter activity Any process that activates or increases the activity of an ion transporter. GOC:mah GOC:tb positive regulation of ion transporter activity GOC:tb An assembly of actin filaments that are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness. GO:0000141 GO:0030482 cellular_component actin cable GO:0032432 actin filament bundle An assembly of actin filaments that are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness. GOC:mah actin cable GOC:mah Any process that modulates the frequency, rate, or extent of interferon type I production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. regulation of type I IFN production biological_process GO:0032479 regulation of type I interferon production Any process that modulates the frequency, rate, or extent of interferon type I production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. GOC:add GOC:mah Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. down regulation of type I interferon production down-regulation of type I interferon production downregulation of type I interferon production negative regulation of type I IFN production inhibition of type I interferon production biological_process GO:0032480 negative regulation of type I interferon production Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. GOC:add GOC:mah Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. positive regulation of type I IFN production up regulation of type I interferon production up-regulation of type I interferon production upregulation of type I interferon production activation of type I interferon production stimulation of type I interferon production biological_process GO:0032481 positive regulation of type I interferon production Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. GOC:add 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 biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. biological_process GO:0032504 multicellular organism reproduction The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GOC:isa_complete GOC:jid 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 appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. GO:0045351 GO:0072641 interferon type I production type I IFN production type I interferon biosynthetic process type I interferon secretion biological_process GO:0032606 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. type I interferon production The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. GOC:add ISBN:0126896631 PMID:15546383 PMID:16681834 type I IFN production GOC:mah The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon. GO:0042095 GO:0072643 type II IFN production type II interferon production IFNG production interferon-gamma biosynthetic process interferon-gamma secretion biological_process GO:0032609 interferon-gamma production The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon. GOC:add GOC:mah PMID:15546383 type II IFN production GOC:mah IFNG production GOC:mah The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GO:0050702 GO:0050720 IL-1 beta production interleukin-1 beta biosynthetic process interleukin-1 beta secretion biological_process GO:0032611 interleukin-1 beta production The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GO:0042222 GO:0050701 IL-1 production interleukin-1 biosynthetic process interleukin-1 secretion biological_process GO:0032612 interleukin-1 production The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GO:0042091 GO:0072608 IL-10 production interleukin-10 biosynthetic process interleukin-10 secretion biological_process GO:0032613 interleukin-10 production The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GO:0042231 GO:0072611 IL-13 production interleukin-13 biosynthetic process interleukin-13 secretion biological_process GO:0032616 interleukin-13 production The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GO:0042235 GO:0072615 CTLA-8 production Cytotoxic T-lymphocyte-associated antigen 8 production IL-17 production interleukin-17 biosynthetic process interleukin-17 secretion biological_process GO:0032620 interleukin-17 production The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah GOC:rv Wikipedia:Interleukin_17 CTLA-8 production GOC:BHF Cytotoxic T-lymphocyte-associated antigen 8 production GOC:BHF The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GO:0042094 GO:0070970 IL-2 production interleukin-2 biosynthetic process interleukin-2 secretion biological_process GO:0032623 interleukin-2 production The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GO:0042239 GO:0072620 IL-22 production IL22 production ILTIF production ZCYTO18 production interleukin-22 biosynthetic process interleukin-22 secretion biological_process GO:0032626 interleukin-22 production The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah IL22 production GOC:BHF ILTIF production GOC:BHF ZCYTO18 production GOC:BHF The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GO:0042097 GO:0042224 GO:0072602 IL-4 production interleukin-4 biosynthetic process interleukin-4 secretion biological_process GO:0032633 interleukin-4 production The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GO:0042225 GO:0072603 IL-5 production interleukin-5 biosynthetic process interleukin-5 secretion biological_process GO:0032634 interleukin-5 production The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GO:0042226 GO:0072604 IL-6 production interleukin-6 biosynthetic process interleukin-6 secretion biological_process GO:0032635 interleukin-6 production The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GO:0042228 GO:0072606 IL-8 production interleukin-8 biosynthetic process interleukin-8 secretion biological_process GO:0032637 interleukin-8 production The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GO:0042229 GO:0072607 IL-9 production interleukin-9 biosynthetic process interleukin-9 secretion biological_process GO:0032638 interleukin-9 production The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Tumor necrosis factor is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis. sl 2015-06-15T22:59:26Z GO:0042533 GO:1990774 TNF production cachectin production TNF alpha biosynthesis TNF biosynthesis TNF biosynthetic process TNF-alpha biosynthesis TNF-alpha biosynthetic process tumor necrosis factor anabolism tumor necrosis factor biosynthesis tumor necrosis factor biosynthetic process tumor necrosis factor formation tumor necrosis factor secretion tumor necrosis factor synthesis biological_process TNF-alpha production Tnfa production tumor necrosis factor-alpha production GO:0032640 Note that this term refers only to the specific, original 'tumor necrosis factor' protein (TNF) and not other members of the tumor necrosis factor superfamily (those with the gene symbol root 'TNFSF'). That this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. tumor necrosis factor production The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Tumor necrosis factor is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis. GOC:mah PMID:10891884 PMID:15560120 Any process that modulates the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon. GO:0045072 GO:1902713 regulation of type II interferon production regulation of interferon-gamma biosynthetic process regulation of interferon-gamma secretion biological_process GO:0032649 regulation of interferon-gamma production Any process that modulates the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon. GOC:add GOC:mah PMID:15546383 Any process that modulates the frequency, rate, or extent of interleukin-1 beta production. GO:0050706 GO:0050722 regulation of IL-1 beta production regulation of interleukin-1 beta biosynthetic process regulation of interleukin-1 beta secretion biological_process GO:0032651 regulation of interleukin-1 beta production Any process that modulates the frequency, rate, or extent of interleukin-1 beta production. GOC:mah Any process that modulates the frequency, rate, or extent of interleukin-1 production. GO:0045360 GO:0050704 regulation of IL-1 production regulation of interleukin-1 biosynthetic process regulation of interleukin-1 secretion biological_process GO:0032652 regulation of interleukin-1 production Any process that modulates the frequency, rate, or extent of interleukin-1 production. GOC:mah Any process that modulates the frequency, rate, or extent of interleukin-10 production. GO:0045074 GO:2001179 regulation of IL-10 production regulation of interleukin-10 biosynthetic process regulation of interleukin-10 secretion biological_process GO:0032653 regulation of interleukin-10 production Any process that modulates the frequency, rate, or extent of interleukin-10 production. GOC:mah Any process that modulates the frequency, rate, or extent of interleukin-13 production. GO:0045366 GO:2000665 regulation of IL-13 production regulation of interleukin-13 biosynthetic process regulation of interleukin-13 secretion biological_process GO:0032656 regulation of interleukin-13 production Any process that modulates the frequency, rate, or extent of interleukin-13 production. GOC:mah Any process that modulates the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines. GO:0045378 GO:1905076 regulation of CTLA-8 production regulation of Cytotoxic T-lymphocyte-associated antigen 8 secretion regulation of IL-17 production regulation of interleukin-17 biosynthetic process regulation of interleukin-17 secretion biological_process GO:0032660 regulation of interleukin-17 production Any process that modulates the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines. GOC:add GOC:mah PMID:16482511 regulation of CTLA-8 production GOC:TermGenie Any process that modulates the frequency, rate, or extent of interleukin-2 production. GO:0045076 GO:1900040 regulation of IL-2 production regulation of interleukin-2 biosynthetic process regulation of interleukin-2 secretion biological_process GO:0032663 regulation of interleukin-2 production Any process that modulates the frequency, rate, or extent of interleukin-2 production. GOC:mah Any process that modulates the frequency, rate, or extent of interleukin-22 production. GO:0045393 regulation of IL-22 production regulation of interleukin-22 biosynthetic process biological_process GO:0032666 regulation of interleukin-22 production Any process that modulates the frequency, rate, or extent of interleukin-22 production. GOC:mah Any process that modulates the frequency, rate, or extent of interleukin-4 production. GO:0045402 GO:0150133 regulation of IL-4 production regulation of interleukin-4 biosynthetic process regulation of interleukin-4 secretion biological_process GO:0032673 regulation of interleukin-4 production Any process that modulates the frequency, rate, or extent of interleukin-4 production. GOC:mah PMID:29778524 Any process that modulates the frequency, rate, or extent of interleukin-5 production. GO:0045405 GO:2000662 regulation of IL-5 production regulation of interleukin-5 biosynthetic process regulation of interleukin-5 secretion biological_process GO:0032674 regulation of interleukin-5 production Any process that modulates the frequency, rate, or extent of interleukin-5 production. GOC:mah Any process that modulates the frequency, rate, or extent of interleukin-6 production. GO:0045408 regulation of IL-6 production regulation of interleukin-6 biosynthetic process biological_process GO:0032675 regulation of interleukin-6 production Any process that modulates the frequency, rate, or extent of interleukin-6 production. GOC:mah Any process that modulates the frequency, rate, or extent of interleukin-8 production. GO:0045414 GO:2000482 regulation of IL-8 production regulation of interleukin-8 biosynthetic process regulation of interleukin-8 secretion biological_process GO:0032677 regulation of interleukin-8 production Any process that modulates the frequency, rate, or extent of interleukin-8 production. GOC:mah Any process that modulates the frequency, rate, or extent of interleukin-9 production. GO:0045417 regulation of IL-9 production regulation of interleukin-9 biosynthetic process biological_process GO:0032678 regulation of interleukin-9 production Any process that modulates the frequency, rate, or extent of interleukin-9 production. GOC:mah Any process that modulates the frequency, rate or extent of tumor necrosis factor production. sl 2015-07-09T19:50:02Z GO:0042534 GO:1904467 regulation of TNF production regulation of TNF-alpha production regulation of cachectin production regulation of tumor necrosis factor-alpha production regulation of tumor necrosis factor biosynthetic process regulation of tumor necrosis factor secretion biological_process GO:0032680 Note that this term refers only to the specific, original 'tumor necrosis factor' protein (TNF) and not other members of the tumor necrosis factor superfamily (those with the gene symbol root 'TNFSF'). regulation of tumor necrosis factor production Any process that modulates the frequency, rate or extent of tumor necrosis factor production. GOC:mah PMID:10891884 PMID:15560120 regulation of cachectin production GOC:TermGenie Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon. GO:0045077 GO:1902714 negative regulation of type II interferon production down regulation of interferon-gamma production down-regulation of interferon-gamma production downregulation of interferon-gamma production inhibition of interferon-gamma production negative regulation of interferon-gamma biosynthetic process negative regulation of interferon-gamma secretion biological_process GO:0032689 negative regulation of interferon-gamma production Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon. GOC:add GOC:mah PMID:15546383 Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-1 beta production. GO:0050713 GO:0050724 down regulation of interleukin-1 beta production down-regulation of interleukin-1 beta production downregulation of interleukin-1 beta production negative regulation of IL-1 beta production inhibition of interleukin-1 beta production negative regulation of interleukin-1 beta biosynthetic process negative regulation of interleukin-1 beta secretion biological_process GO:0032691 negative regulation of interleukin-1 beta production Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-1 beta production. GOC:mah Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-1 production. GO:0045361 GO:0050711 down regulation of interleukin-1 production down-regulation of interleukin-1 production downregulation of interleukin-1 production negative regulation of IL-1 production inhibition of interleukin-1 production negative regulation of interleukin-1 biosynthetic process negative regulation of interleukin-1 secretion biological_process GO:0032692 negative regulation of interleukin-1 production Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-1 production. GOC:mah Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-10 production. GO:0045081 GO:2001180 down regulation of interleukin-10 production down-regulation of interleukin-10 production downregulation of interleukin-10 production negative regulation of IL-10 production inhibition of interleukin-10 production negative regulation of interleukin-10 biosynthetic process negative regulation of interleukin-10 secretion biological_process GO:0032693 negative regulation of interleukin-10 production Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-10 production. GOC:mah Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-13 production. GO:0045367 GO:2000666 down regulation of interleukin-13 production down-regulation of interleukin-13 production downregulation of interleukin-13 production negative regulation of IL-13 production inhibition of interleukin-13 production negative regulation of interleukin-13 biosynthetic process negative regulation of interleukin-13 secretion biological_process GO:0032696 negative regulation of interleukin-13 production Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-13 production. GOC:mah Any process that stops, prevents, or reduces the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines. GO:0045379 GO:1905077 down regulation of interleukin-17 production downregulation of interleukin-17 production negative regulation of Cytotoxic T-lymphocyte-associated antigen 8 secretion negative regulation of IL-17 production inhibition of interleukin-17 production negative regulation of CTLA-8 production negative regulation of interleukin-17 biosynthetic process negative regulation of interleukin-17 secretion biological_process GO:0032700 negative regulation of interleukin-17 production Any process that stops, prevents, or reduces the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines. GOC:add GOC:mah PMID:16482511 negative regulation of Cytotoxic T-lymphocyte-associated antigen 8 secretion GOC:TermGenie negative regulation of CTLA-8 production GOC:TermGenie Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-2 production. GO:0045085 GO:1900041 down regulation of interleukin-2 production down-regulation of interleukin-2 production downregulation of interleukin-2 production negative regulation of IL-2 production inhibition of interleukin-2 production negative regulation of interleukin-2 biosynthetic process negative regulation of interleukin-2 secretion biological_process GO:0032703 negative regulation of interleukin-2 production Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-2 production. GOC:mah Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-22 production. GO:0045394 down regulation of interleukin-22 production down-regulation of interleukin-22 production downregulation of interleukin-22 production negative regulation of IL-22 production inhibition of interleukin-22 production negative regulation of interleukin-22 biosynthetic process biological_process GO:0032706 negative regulation of interleukin-22 production Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-22 production. GOC:mah Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-4 production. bc GO:0045403 GO:0150134 down regulation of interleukin-4 production down-regulation of interleukin-4 production downregulation of interleukin-4 production negative regulation of IL-4 production inhibition of interleukin-4 production negative regulation of interleukin-4 biosynthetic process negative regulation of interleukin-4 secretion biological_process GO:0032713 negative regulation of interleukin-4 production Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-4 production. GOC:mah PMID:29778524 Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-5 production. GO:0045406 GO:2000663 down regulation of interleukin-5 production down-regulation of interleukin-5 production downregulation of interleukin-5 production negative regulation of IL-5 production inhibition of interleukin-5 production negative regulation of interleukin-5 biosynthetic process negative regulation of interleukin-5 secretion biological_process GO:0032714 negative regulation of interleukin-5 production Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-5 production. GOC:mah Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-6 production. GO:0045409 GO:1900165 down regulation of interleukin-6 production down-regulation of interleukin-6 production downregulation of interleukin-6 production negative regulation of IL-6 production inhibition of interleukin-6 production negative regulation of interleukin-6 biosynthetic process negative regulation of interleukin-6 secretion biological_process GO:0032715 negative regulation of interleukin-6 production Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-6 production. GOC:mah Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-8 production. GO:0045415 GO:2000483 down regulation of interleukin-8 production down-regulation of interleukin-8 production downregulation of interleukin-8 production negative regulation of IL-8 production inhibition of interleukin-8 production negative regulation of interleukin-8 biosynthetic process negative regulation of interleukin-8 secretion biological_process GO:0032717 negative regulation of interleukin-8 production Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-8 production. GOC:mah Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-9 production. GO:0045418 down regulation of interleukin-9 production down-regulation of interleukin-9 production downregulation of interleukin-9 production negative regulation of IL-9 production inhibition of interleukin-9 production negative regulation of interleukin-9 biosynthetic process biological_process GO:0032718 negative regulation of interleukin-9 production Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-9 production. GOC:mah Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production. sl 2015-07-09T19:50:08Z GO:0042536 GO:1904468 down regulation of tumor necrosis factor production down-regulation of tumor necrosis factor production downregulation of tumor necrosis factor production negative regulation TNF production negative regulation TNF-alpha production negative regulation tumor necrosis factor-alpha production inhibition of cachectin production inhibition of tumor necrosis factor production negative regulation of tumor necrosis factor biosynthetic process negative regulation of tumor necrosis factor secretion biological_process GO:0032720 Note that this term refers only to the specific, original 'tumor necrosis factor' protein (TNF) and not other members of the tumor necrosis factor superfamily (those with the gene symbol root 'TNFSF'). negative regulation of tumor necrosis factor production Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production. GOC:mah PMID:10891884 PMID:15560120 inhibition of cachectin production GOC:TermGenie Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon. GO:0045078 GO:1902715 positive regulation of type II interferon production up regulation of interferon-gamma production up-regulation of interferon-gamma production upregulation of interferon-gamma production activation of interferon-gamma production positive regulation of interferon-gamma biosynthetic process positive regulation of interferon-gamma secretion stimulation of interferon-gamma production biological_process GO:0032729 positive regulation of interferon-gamma production Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon. GOC:add GOC:mah PMID:15546383 Any process that activates or increases the frequency, rate, or extent of interleukin-1 beta production. GO:0050718 GO:0050725 positive regulation of IL-1 beta production up regulation of interleukin-1 beta production up-regulation of interleukin-1 beta production upregulation of interleukin-1 beta production activation of interleukin-1 beta production positive regulation of interleukin-1 beta biosynthetic process positive regulation of interleukin-1 beta secretion stimulation of interleukin-1 beta production biological_process GO:0032731 positive regulation of interleukin-1 beta production Any process that activates or increases the frequency, rate, or extent of interleukin-1 beta production. GOC:mah Any process that activates or increases the frequency, rate, or extent of interleukin-1 production. GO:0045362 GO:0050716 positive regulation of IL-1 production up regulation of interleukin-1 production up-regulation of interleukin-1 production upregulation of interleukin-1 production activation of interleukin-1 production positive regulation of interleukin-1 biosynthetic process positive regulation of interleukin-1 secretion stimulation of interleukin-1 production biological_process GO:0032732 positive regulation of interleukin-1 production Any process that activates or increases the frequency, rate, or extent of interleukin-1 production. GOC:mah Any process that activates or increases the frequency, rate, or extent of interleukin-10 production. GO:0045082 GO:2001181 positive regulation of IL-10 production up regulation of interleukin-10 production up-regulation of interleukin-10 production upregulation of interleukin-10 production activation of interleukin-10 production positive regulation of interleukin-10 biosynthetic process positive regulation of interleukin-10 secretion stimulation of interleukin-10 production biological_process GO:0032733 positive regulation of interleukin-10 production Any process that activates or increases the frequency, rate, or extent of interleukin-10 production. GOC:mah Any process that activates or increases the frequency, rate, or extent of interleukin-13 production. GO:0045368 GO:2000667 positive regulation of IL-13 production up regulation of interleukin-13 production up-regulation of interleukin-13 production upregulation of interleukin-13 production activation of interleukin-13 production positive regulation of interleukin-13 biosynthetic process positive regulation of interleukin-13 secretion stimulation of interleukin-13 production biological_process GO:0032736 positive regulation of interleukin-13 production Any process that activates or increases the frequency, rate, or extent of interleukin-13 production. GOC:mah Any process that activates or increases the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines. GO:0045380 GO:1905078 positive regulation of CTLA-8 production positive regulation of Cytotoxic T-lymphocyte-associated antigen 8 production positive regulation of IL-17 production up regulation of interleukin-17 production up-regulation of interleukin-17 production upregulation of interleukin-17 production activation of interleukin-17 production positive regulation of interleukin-17 biosynthetic process positive regulation of interleukin-17 secretion stimulation of interleukin-17 production biological_process GO:0032740 positive regulation of interleukin-17 production Any process that activates or increases the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines. GOC:add GOC:mah PMID:16482511 positive regulation of CTLA-8 production GOC:TermGenie positive regulation of Cytotoxic T-lymphocyte-associated antigen 8 production GOC:TermGenie Any process that activates or increases the frequency, rate, or extent of interleukin-2 production. GO:0045086 GO:1900042 positive regulation of IL-2 production up regulation of interleukin-2 production up-regulation of interleukin-2 production upregulation of interleukin-2 production activation of interleukin-2 production positive regulation of interleukin-2 biosynthetic process positive regulation of interleukin-2 secretion stimulation of interleukin-2 production biological_process GO:0032743 positive regulation of interleukin-2 production Any process that activates or increases the frequency, rate, or extent of interleukin-2 production. GOC:mah Any process that activates or increases the frequency, rate, or extent of interleukin-22 production. GO:0045395 positive regulation of IL-22 production up regulation of interleukin-22 production up-regulation of interleukin-22 production upregulation of interleukin-22 production activation of interleukin-22 production positive regulation of interleukin-22 biosynthetic process stimulation of interleukin-22 production biological_process GO:0032746 positive regulation of interleukin-22 production Any process that activates or increases the frequency, rate, or extent of interleukin-22 production. GOC:mah Any process that activates or increases the frequency, rate, or extent of interleukin-4 production. GO:0045404 GO:0150135 positive regulation of IL-4 production up regulation of interleukin-4 production up-regulation of interleukin-4 production upregulation of interleukin-4 production activation of interleukin-4 production positive regulation of interleukin-4 biosynthetic process positive regulation of interleukin-4 secretion stimulation of interleukin-4 production biological_process GO:0032753 positive regulation of interleukin-4 production Any process that activates or increases the frequency, rate, or extent of interleukin-4 production. GOC:mah Any process that activates or increases the frequency, rate, or extent of interleukin-5 production. GO:0045407 GO:2000664 positive regulation of IL-5 production up regulation of interleukin-5 production up-regulation of interleukin-5 production upregulation of interleukin-5 production activation of interleukin-5 production positive regulation of interleukin-5 biosynthetic process positive regulation of interleukin-5 secretion stimulation of interleukin-5 production biological_process GO:0032754 positive regulation of interleukin-5 production Any process that activates or increases the frequency, rate, or extent of interleukin-5 production. GOC:mah Any process that activates or increases the frequency, rate, or extent of interleukin-6 production. GO:0045410 GO:2000778 positive regulation of IL-6 production up regulation of interleukin-6 production up-regulation of interleukin-6 production upregulation of interleukin-6 production activation of interleukin-6 production positive regulation of interleukin-6 biosynthetic process positive regulation of interleukin-6 secretion stimulation of interleukin-6 production biological_process GO:0032755 positive regulation of interleukin-6 production Any process that activates or increases the frequency, rate, or extent of interleukin-6 production. GOC:mah Any process that activates or increases the frequency, rate, or extent of interleukin-8 production. GO:0045416 GO:2000484 positive regulation of IL-8 production up regulation of interleukin-8 production up-regulation of interleukin-8 production upregulation of interleukin-8 production activation of interleukin-8 production positive regulation of interleukin-8 biosynthetic process positive regulation of interleukin-8 secretion stimulation of interleukin-8 production biological_process GO:0032757 positive regulation of interleukin-8 production Any process that activates or increases the frequency, rate, or extent of interleukin-8 production. GOC:mah Any process that activates or increases the frequency, rate, or extent of interleukin-9 production. GO:0045419 positive regulation of IL-9 production up regulation of interleukin-9 production up-regulation of interleukin-9 production upregulation of interleukin-9 production activation of interleukin-9 production positive regulation of interleukin-9 biosynthetic process stimulation of interleukin-9 production biological_process GO:0032758 positive regulation of interleukin-9 production Any process that activates or increases the frequency, rate, or extent of interleukin-9 production. GOC:mah Any process that activates or increases the frequency, rate or extent of tumor necrosis factor production. sl 2015-07-09T19:50:14Z GO:0042535 GO:1904469 positive regulation of TNF production positive regulation of TNF-alpha production positive regulation of tumor necrosis factor-alpha production up regulation of tumor necrosis factor production up-regulation of tumor necrosis factor production upregulation of tumor necrosis factor production activation of tumor necrosis factor production positive regulation of TNF secretion positive regulation of cachectin secretion positive regulation of tumor necrosis factor biosynthesis positive regulation of tumor necrosis factor biosynthetic process positive regulation of tumor necrosis factor formation positive regulation of tumor necrosis factor secretion stimulation of tumor necrosis factor production biological_process GO:0032760 Note that this term refers only to the specific, original 'tumor necrosis factor' protein (TNF) and not other members of the tumor necrosis factor superfamily (those with the gene symbol root 'TNFSF'). positive regulation of tumor necrosis factor production Any process that activates or increases the frequency, rate or extent of tumor necrosis factor production. GOC:TermGenie GO_REF:0000058 PMID:10891884 PMID:15560120 positive regulation of TNF secretion GOC:TermGenie positive regulation of cachectin secretion GOC:TermGenie The regulated release of bile acid, composed of any of a group of steroid carboxylic acids occurring in bile, by a cell or a tissue. biological_process GO:0032782 bile acid secretion The regulated release of bile acid, composed of any of a group of steroid carboxylic acids occurring in bile, by a cell or a tissue. GOC:ecd 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 stops, prevents, or reduces the frequency, rate or extent of the regulated release of epinephrine. down regulation of epinephrine secretion down-regulation of epinephrine secretion downregulation of epinephrine secretion negative regulation of adrenaline secretion inhibition of epinephrine secretion biological_process GO:0032811 negative regulation of epinephrine secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of epinephrine. GOC:vk Any process that activates or increases the frequency, rate or extent of the regulated release of epinephrine. positive regulation of adrenaline secretion up regulation of epinephrine secretion up-regulation of epinephrine secretion upregulation of epinephrine secretion activation of epinephrine secretion stimulation of epinephrine secretion biological_process GO:0032812 positive regulation of epinephrine secretion Any process that activates or increases the frequency, rate or extent of the regulated release of epinephrine. GOC:vk Any process that modulates the frequency, rate or extent of natural killer cell activation. regulation of NK cell activation biological_process GO:0032814 regulation of natural killer cell activation Any process that modulates the frequency, rate or extent of natural killer cell activation. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of natural killer cell activation. down regulation of natural killer cell activation down-regulation of natural killer cell activation downregulation of natural killer cell activation negative regulation of NK cell activation inhibition of natural killer cell activation biological_process GO:0032815 negative regulation of natural killer cell activation Any process that stops, prevents, or reduces the frequency, rate or extent of natural killer cell activation. GOC:mah Any process that activates or increases the frequency, rate or extent of natural killer cell activation. positive regulation of NK cell activation up regulation of natural killer cell activation up-regulation of natural killer cell activation upregulation of natural killer cell activation activation of natural killer cell activation stimulation of natural killer cell activation biological_process GO:0032816 positive regulation of natural killer cell activation Any process that activates or increases the frequency, rate or extent of natural killer cell activation. GOC:mah All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection. cellular_component GO:0032838 plasma membrane bounded cell projection cytoplasm All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection. GOC:krc GOC:mah 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 Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the microtubule cytoskeleton. biological_process GO:0032886 regulation of microtubule-based process Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the microtubule cytoskeleton. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0032890 regulation of organic acid transport Any process that modulates the frequency, rate or extent of the directed movement of organic acids 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 organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of organic acid transport down-regulation of organic acid transport downregulation of organic acid transport inhibition of organic acid transport biological_process GO:0032891 negative regulation of organic acid transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of organic acids 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 organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of organic acid transport up-regulation of organic acid transport upregulation of organic acid transport activation of organic acid transport stimulation of organic acid transport biological_process GO:0032892 positive regulation of organic acid transport Any process that activates or increases the frequency, rate or extent of the directed movement of organic acids 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 enzymatic generation of superoxide by a cell. regulation of superoxide release biological_process GO:0032928 regulation of superoxide anion generation Any process that modulates the frequency, rate or extent of enzymatic generation of superoxide by a cell. GOC:mah regulation of superoxide release GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of enzymatic generation of superoxide by a cell. down regulation of superoxide release down-regulation of superoxide release downregulation of superoxide release negative regulation of superoxide release inhibition of superoxide release biological_process GO:0032929 negative regulation of superoxide anion generation Any process that stops, prevents, or reduces the frequency, rate or extent of enzymatic generation of superoxide by a cell. GOC:mah negative regulation of superoxide release GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of enzymatic generation of superoxide by a cell. positive regulation of superoxide release up regulation of superoxide release up-regulation of superoxide release upregulation of superoxide release activation of superoxide release stimulation of superoxide release biological_process GO:0032930 positive regulation of superoxide anion generation Any process that activates or increases the frequency, rate or extent of enzymatic generation of superoxide by a cell. GOC:mah positive regulation of superoxide release GOC:dph GOC:tb 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 The controlled release of a substance by a tissue. tissue secretion biological_process expulsion of gland contents GO:0032941 secretion by tissue The controlled release of a substance by a tissue. GOC:mah expulsion of gland contents GOC:mah The expansion of a mononuclear cell population by cell division. A mononuclear cell is a leukocyte with a single non-segmented nucleus in the mature form. PBMC proliferation peripheral blood mononuclear cell proliferation biological_process GO:0032943 mononuclear cell proliferation The expansion of a mononuclear cell population by cell division. A mononuclear cell is a leukocyte with a single non-segmented nucleus in the mature form. GOC:add Any process that modulates the frequency, rate or extent of mononuclear cell proliferation. regulation of PBMC proliferation regulation of peripheral blood mononuclear cell proliferation biological_process GO:0032944 regulation of mononuclear cell proliferation Any process that modulates the frequency, rate or extent of mononuclear cell proliferation. GOC:add Any process that stops, prevents, or reduces the frequency, rate or extent of mononuclear cell proliferation. negative regulation of PBMC proliferation negative regulation of peripheral blood mononuclear cell proliferation biological_process GO:0032945 negative regulation of mononuclear cell proliferation Any process that stops, prevents, or reduces the frequency, rate or extent of mononuclear cell proliferation. GOC:add Any process that activates or increases the frequency, rate or extent of mononuclear cell proliferation. up regulation of mononuclear cell proliferation up-regulation of mononuclear cell proliferation upregulation of mononuclear cell proliferation activation of mononuclear cell proliferation positive regulation of PBMC proliferation positive regulation of peripheral blood mononuclear cell proliferation stimulation of mononuclear cell proliferation biological_process GO:0032946 positive regulation of mononuclear cell proliferation Any process that activates or increases the frequency, rate or extent of mononuclear cell proliferation. GOC:add The process in which cellular structures, including whole cells or cell parts, are generated and organized. cellular structure morphogenesis biological_process GO:0032989 cellular component morphogenesis The process in which cellular structures, including whole cells or cell parts, are generated and organized. GOC:dph GOC:mah GOC:tb cellular structure morphogenesis GOC:dph GOC:tb 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. Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or carbohydrate groups. GO:0043234 macromolecular complex macromolecule complex protein containing complex protein-protein complex protein complex protein-protein complex cellular_component GO:0032991 A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. Note that although at some level almost all cellular components can be thought of as protein complexes, this term is intended to exclude structures composed of the same repeating subunit or subunits, for example microtubules. Protein complexes encompassed by this term are generally not structural, and usually have a defined set of subunits. protein-containing 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. GOC:dos GOC:mah Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or carbohydrate groups. GOC:go_curators A protein complex composed of a subunit or subunits capable of binding the Fc portion of an immunoglobulin with additional signaling components. The complex functions as a receptor for immunoglobulin. immunoglobulin receptor complex Fc-receptor complex FcR complex cellular_component GO:0032997 Fc receptor complex A protein complex composed of a subunit or subunits capable of binding the Fc portion of an immunoglobulin with additional signaling components. The complex functions as a receptor for immunoglobulin. GOC:add ISBN:0781735149 A protein complex composed of an Fc-gamma RIII alpha chain and an Fc-epsilon RI gamma chain dimer with or without an Fc-epsilon RI beta chain and additional signaling components. The complex functions primarily as an activating receptor for IgG. IgG receptor complex immunoglobulin G receptor complex FcgRIII complex cellular_component GO:0033001 Fc-gamma receptor III complex A protein complex composed of an Fc-gamma RIII alpha chain and an Fc-epsilon RI gamma chain dimer with or without an Fc-epsilon RI beta chain and additional signaling components. The complex functions primarily as an activating receptor for IgG. GOC:add ISBN:0781735149 PMID:11244038 PMID:12413532 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 a process involved in the formation, arrangement of constituent parts, or disassembly of a chromosome. regulation of chromosome organisation biological_process regulation of chromosome organization and biogenesis GO:0033044 regulation of chromosome 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 chromosome. GOC:mah regulation of chromosome organisation GOC:mah regulation of chromosome organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of sister chromatid segregation. biological_process GO:0033045 regulation of sister chromatid segregation Any process that modulates the frequency, rate or extent of sister chromatid segregation. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation. biological_process GO:0033046 negative regulation of sister chromatid segregation Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation. GOC:mah Any process that modulates the frequency, rate or extent of sister chromatid segregation during mitosis. biological_process GO:0033047 regulation of mitotic sister chromatid segregation Any process that modulates the frequency, rate or extent of sister chromatid segregation during mitosis. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation during mitosis. biological_process GO:0033048 negative regulation of mitotic sister chromatid segregation Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation during mitosis. GOC:mah The process in which immune receptor V, D, and J, or V and J gene segments, depending on the specific receptor, are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). Wikipedia:V(D)J_recombination V(D)J joining V-D-J joining V-D-J recombination V-J joining V-J recombination biological_process GO:0033151 V(D)J recombination The process in which immune receptor V, D, and J, or V and J gene segments, depending on the specific receptor, are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). GOC:add ISBN:0781700221 ISBN:0781735149 The process in which immunoglobulin gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). For immunoglobulin heavy chains V, D, and J gene segments are joined, and for immunoglobulin light chains V and J gene segments are joined. immunoglobulin V(D)J joining immunoglobulin V-D-J joining immunoglobulin V-D-J recombination immunoglobulin V-J joining immunoglobulin V-J recombination biological_process GO:0033152 immunoglobulin V(D)J recombination The process in which immunoglobulin gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). For immunoglobulin heavy chains V, D, and J gene segments are joined, and for immunoglobulin light chains V and J gene segments are joined. GOC:add ISBN:0781735149 immunoglobulin V(D)J joining GOC:add immunoglobulin V-D-J joining GOC:add immunoglobulin V-D-J recombination GOC:add immunoglobulin V-J joining GOC:add immunoglobulin V-J recombination GOC:add 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 The regulated release of cerebrospinal fluid (CSF) from the choroid plexus of the lateral, third and fourth ventricles. The cerebrospinal fluid is a clear liquid that located within the ventricles, spinal canal, and subarachnoid spaces. CSF secretion biological_process GO:0033326 cerebrospinal fluid secretion The regulated release of cerebrospinal fluid (CSF) from the choroid plexus of the lateral, third and fourth ventricles. The cerebrospinal fluid is a clear liquid that located within the ventricles, spinal canal, and subarachnoid spaces. GOC:ln PMID:10716451 http://users.ahsc.arizona.edu/davis/csf.htm A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a secretory granule. A secretory granule is 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 granule organisation biological_process secretory granule organization and biogenesis GO:0033363 secretory granule organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a secretory granule. A secretory granule is a small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. GOC:mah secretory granule organisation GOC:mah secretory granule organization and biogenesis GOC:mah A process in which a protein is transported to, or maintained in, a location within an organelle. protein localisation to organelle protein localization in organelle biological_process GO:0033365 protein localization to organelle A process in which a protein is transported to, or maintained in, a location within an organelle. GOC:mah protein localisation to organelle GOC:mah protein localization in organelle GOC:mah A process in which a protein is transported to, or maintained in, a location within a secretory granule. protein localisation in secretory granule protein localization in secretory granule biological_process GO:0033366 protein localization to secretory granule A process in which a protein is transported to, or maintained in, a location within a secretory granule. GOC:mah protein localisation in secretory granule 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 secretory granule in a T cell. A secretory granule is a small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. T cell secretory granule organisation T lymphocyte secretory granule organization T-cell secretory granule organization T-lymphocyte secretory granule organization biological_process T cell secretory granule organization and biogenesis T-lymphocyte secretory granule maturation GO:0033371 T cell secretory granule organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a secretory granule in a T cell. A secretory granule is a small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. GOC:mah T cell secretory granule organisation GOC:mah T cell secretory granule organization and biogenesis GOC:mah A process in which a protein is transported to, or maintained in, a location within a secretory granule in a T cell. protein localisation in T cell secretory granule protein localization in T cell secretory granule protein localization in T lymphocyte secretory granule protein localization in T-cell secretory granule protein localization in T-lymphocyte secretory granule biological_process GO:0033374 protein localization to T cell secretory granule A process in which a protein is transported to, or maintained in, a location within a secretory granule in a T cell. GOC:mah protein localisation in T cell secretory granule GOC:mah Any process in which a protease is transported to, or maintained in, a location within a secretory granule in a T cell. protease localisation in T cell secretory granule protease localization in T cell secretory granule protease localization in T lymphocyte secretory granule protease localization in T-cell secretory granule protease localization in T-lymphocyte secretory granule biological_process GO:0033375 protease localization to T cell secretory granule Any process in which a protease is transported to, or maintained in, a location within a secretory granule in a T cell. GOC:mah protease localisation in T cell secretory granule GOC:mah Any process in which the protease granzyme B is transported to, or maintained in, a location within a secretory granule in a T cell. granzyme B localisation in T cell secretory granule granzyme B localization in T cell secretory granule granzyme B localization in T lymphocyte secretory granule granzyme B localization in T-cell secretory granule granzyme B localization in T-lymphocyte secretory granule biological_process GO:0033380 granzyme B localization to T cell secretory granule Any process in which the protease granzyme B is transported to, or maintained in, a location within a secretory granule in a T cell. GOC:mah granzyme B localisation in T cell secretory granule GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of dopamine. down regulation of dopamine secretion down-regulation of dopamine secretion downregulation of dopamine secretion inhibition of dopamine secretion biological_process GO:0033602 negative regulation of dopamine secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of dopamine. GOC:sl Any process that activates or increases the frequency, rate or extent of the regulated release of dopamine. up regulation of dopamine secretion up-regulation of dopamine secretion upregulation of dopamine secretion activation of dopamine secretion stimulation of dopamine secretion biological_process GO:0033603 positive regulation of dopamine secretion Any process that activates or increases the frequency, rate or extent of the regulated release of dopamine. GOC:sl Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a catecholamine. down regulation of catecholamine secretion down-regulation of catecholamine secretion downregulation of catecholamine secretion inhibition of catecholamine secretion biological_process GO:0033604 negative regulation of catecholamine secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a catecholamine. GOC:mah Any process that activates or increases the frequency, rate or extent of the regulated release of a catecholamine. up regulation of catecholamine secretion up-regulation of catecholamine secretion upregulation of catecholamine secretion activation of catecholamine secretion stimulation of catecholamine secretion biological_process GO:0033605 positive regulation of catecholamine secretion Any process that activates or increases the frequency, rate or extent of the regulated release of a catecholamine. GOC:mah Any process that modulates the frequency, rate or extent of the regulated release of luteinizing hormone. biological_process GO:0033684 regulation of luteinizing hormone secretion Any process that modulates the frequency, rate or extent of the regulated release of luteinizing hormone. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of luteinizing hormone. down regulation of luteinizing hormone secretion down-regulation of luteinizing hormone secretion downregulation of luteinizing hormone secretion inhibition of luteinizing hormone secretion biological_process GO:0033685 negative regulation of luteinizing hormone secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of luteinizing hormone. GOC:mah Any process that activates or increases the frequency, rate or extent of the regulated release of luteinizing hormone. up regulation of luteinizing hormone secretion up-regulation of luteinizing hormone secretion upregulation of luteinizing hormone secretion activation of luteinizing hormone secretion stimulation of luteinizing hormone secretion biological_process GO:0033686 positive regulation of luteinizing hormone secretion Any process that activates or increases the frequency, rate or extent of the regulated release of luteinizing hormone. GOC:mah Any process of regulating the production and elimination of erythrocytes within an organism. RBC homeostasis red blood cell homeostasis biological_process GO:0034101 erythrocyte homeostasis Any process of regulating the production and elimination of erythrocytes within an organism. GOC:add PMID:10694114 PMID:14754397 RBC homeostasis CL:0000232 red blood cell homeostasis CL:0000232 The selective elimination of erythrocytes from the body by autoregulatory mechanisms. RBC clearance red blood cell clearance neocytolysis biological_process GO:0034102 Note that this term is intended for annotation of self-gene products that lead to elimination of erythrocytes without the involvement of a symbiont. erythrocyte clearance The selective elimination of erythrocytes from the body by autoregulatory mechanisms. GOC:add PMID:12905029 PMID:14754397 RBC clearance CL:0000232 red blood cell clearance CL:0000232 neocytolysis PMID:14754397 Any process that modulates the frequency, rate, or extent of tissue remodeling. biological_process GO:0034103 regulation of tissue remodeling Any process that modulates the frequency, rate, or extent of tissue remodeling. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of tissue remodeling. biological_process GO:0034104 negative regulation of tissue remodeling Any process that stops, prevents, or reduces the frequency, rate, or extent of tissue remodeling. GOC:add Any process that activates or increases the frequency, rate, or extent of tissue remodeling. biological_process GO:0034105 positive regulation of tissue remodeling Any process that activates or increases the frequency, rate, or extent of tissue remodeling. GOC:add Any process that modulates the frequency, rate, or extent of erythrocyte clearance. regulation of RBC clearance regulation of red blood cell clearance regulation of neocytolysis biological_process GO:0034106 regulation of erythrocyte clearance Any process that modulates the frequency, rate, or extent of erythrocyte clearance. GOC:add PMID:12905029 PMID:14754397 regulation of RBC clearance CL:0000232 regulation of red blood cell clearance CL:0000232 regulation of neocytolysis PMID:14754397 Any process that stops, prevents, or reduces the frequency, rate, or extent of erythrocyte clearance. negative regulation of RBC clearance negative regulation of red blood cell clearance negative regulation of neocytolysis biological_process GO:0034107 negative regulation of erythrocyte clearance Any process that stops, prevents, or reduces the frequency, rate, or extent of erythrocyte clearance. GOC:add PMID:12905029 PMID:14754397 negative regulation of RBC clearance CL:0000232 negative regulation of red blood cell clearance CL:0000232 negative regulation of neocytolysis PMID:14754397 Any process that activates or increases the frequency, rate, or extent of erythrocyte clearance. positive regulation of RBC clearance positive regulation of red blood cell clearance positive regulation of neocytolysis biological_process GO:0034108 positive regulation of erythrocyte clearance Any process that activates or increases the frequency, rate, or extent of erythrocyte clearance. GOC:add PMID:12905029 PMID:14754397 positive regulation of RBC clearance CL:0000232 positive regulation of red blood cell clearance CL:0000232 positive regulation of neocytolysis PMID:14754397 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 that modulates the frequency, rate or extent of the chemical reactions and pathways involving amides. regulation of amide metabolism biological_process GO:0034248 regulation of cellular amide metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amides. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amides. negative regulation of amide metabolism biological_process GO:0034249 negative regulation of cellular amide metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amides. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amides. positive regulation of amide metabolism biological_process GO:0034250 positive regulation of cellular amide metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amides. GOC:mah 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 The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone, as carried out by individual cells. biological_process GO:0034754 cellular hormone metabolic process The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone, 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 Events resulting in the formation of a multilayered cellular sheath surrounding an invader and thus preventing its development. This defense mechanism is often seen in insects in response to nematodes or parasitoids, which are too large to be phagocytosed by individual hemocytes. In some organisms the capsule is blackened due to melanization. biological_process GO:0035010 encapsulation of foreign target Events resulting in the formation of a multilayered cellular sheath surrounding an invader and thus preventing its development. This defense mechanism is often seen in insects in response to nematodes or parasitoids, which are too large to be phagocytosed by individual hemocytes. In some organisms the capsule is blackened due to melanization. GOC:bf GO_REF:0000022 PMID:11846478 PMID:12225920 The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. GO:0035083 GO:0035084 ciliary axoneme assembly cilium axoneme assembly flagellar axoneme assembly flagellum axoneme assembly biological_process axoneme biogenesis cilium axoneme biogenesis GO:0035082 Note that cilia and eukaryotic flagella are deemed to be equivalent. axoneme assembly The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. GOC:bf GOC:cilia GOC:jl ISBN:0815316194 axoneme biogenesis GOC:mah cilium axoneme biogenesis GOC:mah The process in which the anatomical structures of a tube are generated and organized. Epithelial and endothelial 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. biological_process GO:0035239 tube morphogenesis The process in which the anatomical structures of a tube are generated and organized. Epithelial and endothelial 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. GOC:bf PMID:14624839 The vesicular release of glutamate from a presynapse, across a chemical synapse, the subsequent activation of glutamate receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. glutamatergic synaptic transmission biological_process GO:0035249 synaptic transmission, glutamatergic The vesicular release of glutamate from a presynapse, across a chemical synapse, the subsequent activation of glutamate receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. GOC:dos The process whose specific outcome is the progression of a tube over time, from its initial formation to a mature structure. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts. biological_process GO:0035295 tube development The process whose specific outcome is the progression of a tube over time, from its initial formation to a mature structure. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts. PMID:12526790 An immunoglobulin-like complex that is present in at least the plasma membrane of pre-B cells, and that is composed of two identical immunoglobulin heavy chains and two surrogate light chains, each composed of the lambda-5 and VpreB proteins, and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. bf 2010-03-11T10:46:10Z pre-BCR cellular_component GO:0035369 Despite its name, the pre-BCR is not a receptor complex, as it appears to provide a low level of signal not dependent on a ligand, but rather simply on correct assembly of the complex as a measure for correct Ig heavy chain recombination and folding. A significant proportion of pre-BCR complexes fail to reach the cell surface, and in some cases may provide their signaling function from the trans-Golgi network or lysosome. pre-B cell receptor complex An immunoglobulin-like complex that is present in at least the plasma membrane of pre-B cells, and that is composed of two identical immunoglobulin heavy chains and two surrogate light chains, each composed of the lambda-5 and VpreB proteins, and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. GOC:add ISBN:0781765196 PMID:16464608 PMID:17306522 Any process that modulates the rate, frequency or extent of the synthesis or release of any leukotriene following a stimulus as part of an inflammatory response. bf 2010-04-26T10:49:22Z biological_process GO:0035490 regulation of leukotriene production involved in inflammatory response Any process that modulates the rate, frequency or extent of the synthesis or release of any leukotriene following a stimulus as part of an inflammatory response. GOC:bf Any process that increases the rate, frequency or extent of the synthesis or release of any leukotriene following a stimulus as part of an inflammatory response. bf 2010-04-26T10:50:14Z biological_process GO:0035491 positive regulation of leukotriene production involved in inflammatory response Any process that increases the rate, frequency or extent of the synthesis or release of any leukotriene following a stimulus as part of an inflammatory response. GOC:bf Any process that decreases the rate, frequency or extent of the synthesis or release of any leukotriene following a stimulus as part of an inflammatory response. bf 2010-04-26T10:50:55Z biological_process GO:0035492 negative regulation of leukotriene production involved in inflammatory response Any process that decreases the rate, frequency or extent of the synthesis or release of any leukotriene following a stimulus as part of an inflammatory response. GOC:bf 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. bf 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 transfer of information occurring at the level of a multicellular organism. bf 2011-01-14T10:13:50Z multicellular organismal signalling biological_process GO:0035637 multicellular organismal signaling The transfer of information occurring at the level of a multicellular organism. GOC:go_curators multicellular organismal signalling GOC:bf The change in morphology and behavior of a CD4-positive, alpha-beta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. bf 2011-03-02T03:04:11Z biological_process GO:0035710 CD4-positive, alpha-beta T cell activation The change in morphology and behavior of a CD4-positive, alpha-beta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. CL:0000624 GOC:BHF The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly. bf 2011-03-17T10:55:42Z intraflagellar transport Reactome:R-HSA-5620924.2 biological_process intraciliary transport involved in cilium morphogenesis intraflagellar transport involved in cilium morphogenesis GO:0035735 intraciliary transport involved in cilium assembly The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly. GOC:bf GOC:cilia Reactome:R-HSA-5620924.2 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 The regulated release of any corticosteroid hormone into the circulatory system. bf 2011-07-20T01:03:22Z corticosteroid secretion biological_process GO:0035930 corticosteroid hormone secretion The regulated release of any corticosteroid hormone into the circulatory system. GOC:sl corticosteroid secretion GOC:bf The regulated release of any mineralocorticoid into the circulatory system. Mineralocorticoids are a class of steroid hormones that regulate water and electrolyte metabolism. bf 2011-07-20T01:04:59Z biological_process GO:0035931 mineralocorticoid secretion The regulated release of any mineralocorticoid into the circulatory system. Mineralocorticoids are a class of steroid hormones that regulate water and electrolyte metabolism. GOC:sl The regulated release of any glucocorticoid hormone into the circulatory system. Glucocorticoids are a class of steroid hormones that regulate a variety of physiological processes, in particular control of the concentration of glucose in blood. bf 2011-07-20T01:08:37Z biological_process GO:0035933 glucocorticoid secretion The regulated release of any glucocorticoid hormone into the circulatory system. Glucocorticoids are a class of steroid hormones that regulate a variety of physiological processes, in particular control of the concentration of glucose in blood. GOC:sl The regulated release of an androgen into the circulatory system. Androgens are steroid hormones that stimulate or control the development and maintenance of masculine characteristics in vertebrates. bf 2011-07-20T01:11:31Z biological_process GO:0035935 androgen secretion The regulated release of an androgen into the circulatory system. Androgens are steroid hormones that stimulate or control the development and maintenance of masculine characteristics in vertebrates. GOC:sl The regulated release of testosterone into the circulatory system. Testosterone is an androgen having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5. bf 2011-07-20T01:13:13Z biological_process GO:0035936 testosterone secretion The regulated release of testosterone into the circulatory system. Testosterone is an androgen having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5. GOC:sl PMID:12606499 The regulated release of estradiol into the circulatory system. bf 2011-07-20T01:16:45Z oestradiol secretion biological_process GO:0035938 estradiol secretion The regulated release of estradiol into the circulatory system. GOC:sl PMID:21632818 The regulated release of a melanocyte-stimulating hormone, any of a group of peptide hormones that are produced by cells in the intermediate lobe of the pituitary gland, and stimulate the production of melanin to increase pigmentation. bf 2012-03-26T01:16:55Z MSH secretion biological_process GO:0036160 melanocyte-stimulating hormone secretion The regulated release of a melanocyte-stimulating hormone, any of a group of peptide hormones that are produced by cells in the intermediate lobe of the pituitary gland, and stimulate the production of melanin to increase pigmentation. GOC:cjm Wikipedia:Melanocyte-stimulating_hormone MSH secretion GOC:cjm The regulated release of calcitonin, a peptide hormone that participates in calcium and phosphorus metabolism, from a cell. bf 2012-03-26T01:30:32Z biological_process GO:0036161 calcitonin secretion The regulated release of calcitonin, a peptide hormone that participates in calcium and phosphorus metabolism, from a cell. GOC:cjm The regulated release of ghrelin from a cell. Ghrelin is a 28 amino acid hunger-stimulating peptide hormone. bf 2012-09-04T14:16:43Z pancreatic ghrelin secretion biological_process GO:0036321 ghrelin secretion The regulated release of ghrelin from a cell. Ghrelin is a 28 amino acid hunger-stimulating peptide hormone. GOC:cjm PMID:14610293 Wikipedia:Ghrelin pancreatic ghrelin secretion GOC:cjm Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. bf 2011-08-01T02:45:27Z GO:0004872 GO:0019041 receptor activity receptor activity involved in signal transduction signalling receptor activity molecular_function GO:0038023 signaling receptor activity Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. GOC:bf GOC:signaling receptor activity involved in signal transduction GOC:bf Binding specifically to a substance (cargo) to deliver it to a transport vesicle. Cargo receptors span a membrane (either the plasma membrane or a vesicle membrane), binding simultaneously to cargo molecules and coat adaptors, to efficiently recruit soluble proteins to nascent vesicles. bf 2011-08-01T02:50:45Z receptor activity transport receptor activity Reactome:R-HSA-3000122 Reactome:R-HSA-350168 endocytic receptor activity receptor activity involved in receptor-mediated endocytosis molecular_function GO:0038024 Notes: (1) this term and its child terms are intended for receptors that bind to and internalize molecules by receptor-mediated endocytosis. For receptors that are coupled to a signal transduction pathway, consider instead the term 'signaling receptor activity ; GO:0038023' and its children. (2) Cargo receptors transport substances by vesicular transport, not by transmembrane transport. For transmembrane transporters, consider instead the term 'transmembrane transporter activity ; GO:0022857. cargo receptor activity Binding specifically to a substance (cargo) to deliver it to a transport vesicle. Cargo receptors span a membrane (either the plasma membrane or a vesicle membrane), binding simultaneously to cargo molecules and coat adaptors, to efficiently recruit soluble proteins to nascent vesicles. PMID:15239958 PMID:27903609 transport receptor activity GOC:signaling Reactome:R-HSA-3000122 CD320 transports extracellular TCII:Cbl to endosome Reactome:R-HSA-350168 LRP2-mediated uptake of extracellular CUBN:GC:25(OH)D endocytic receptor activity GOC:signaling ISBN:0123645387 PMID:12671190 receptor activity involved in receptor-mediated endocytosis GOC:bf 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 Self-propelled movement of a cell or organism from one location to another. biological_process GO:0040011 locomotion Self-propelled movement of a cell or organism from one location to another. GOC:dgh Any process that modulates the frequency, rate or extent of locomotion of a cell or organism. biological_process GO:0040012 regulation of locomotion Any process that modulates the frequency, rate or extent of locomotion of a cell or organism. GOC:ems Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism. down regulation of locomotion down-regulation of locomotion downregulation of locomotion inhibition of locomotion biological_process GO:0040013 negative regulation of locomotion Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism. GOC:go_curators Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism. up regulation of locomotion up-regulation of locomotion upregulation of locomotion activation of locomotion stimulation of locomotion biological_process GO:0040017 positive regulation of locomotion Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism. GOC:go_curators Any process that modulates the frequency, rate or extent of meiotic nuclear division, the process in which the nucleus of a diploid cell divides twice forming four haploid cells, one or more of which usually function as gametes. regulation of meiosis biological_process GO:0040020 regulation of meiotic nuclear division Any process that modulates the frequency, rate or extent of meiotic nuclear division, the process in which the nucleus of a diploid cell divides twice forming four haploid cells, one or more of which usually function as gametes. GOC:ems GOC:ma regulation of meiosis GOC:vw The series of events that restore integrity to a damaged tissue, following an injury. Wikipedia:Wound_healing biological_process GO:0042060 wound healing The series of events that restore integrity to a damaged tissue, following an injury. GOC:bf PMID:15269788 The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins. GO:0035734 Wikipedia:Intraflagellar_transport intraflagellar transport intraflagellar transport involved in cilium organization intraflagellar transport involved in microtubule-based flagellum organisation biological_process IFT GO:0042073 Note that we deem cilium and microtubule-based flagellum to be equivalent. intraciliary transport The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins. GOC:cilia GOC:kmv PMID:17981739 PMID:18180368 PMID:22869374 Reactome:R-HSA-5620924.2 An immune response which is associated with resistance to intracellular bacteria, fungi, and protozoa, and pathological conditions such as arthritis, and which is typically orchestrated by the production of particular cytokines by T-helper 1 cells, most notably interferon-gamma, IL-2, and lymphotoxin. Th1 immune response biological_process GO:0042088 T-helper 1 type immune response An immune response which is associated with resistance to intracellular bacteria, fungi, and protozoa, and pathological conditions such as arthritis, and which is typically orchestrated by the production of particular cytokines by T-helper 1 cells, most notably interferon-gamma, IL-2, and lymphotoxin. GOC:add ISBN:0781735149 An immune response which is associated with resistance to extracellular organisms such as helminths and pathological conditions such as allergy, which is orchestrated by the production of particular cytokines, most notably IL-4, IL-5, IL-10, and IL-13, by any of a variety of cell types including T-helper 2 cells, eosinophils, basophils, mast cells, and nuocytes, resulting in enhanced production of certain antibody isotypes and other effects. T-helper 2 type immune response Th2 immune response biological_process GO:0042092 type 2 immune response An immune response which is associated with resistance to extracellular organisms such as helminths and pathological conditions such as allergy, which is orchestrated by the production of particular cytokines, most notably IL-4, IL-5, IL-10, and IL-13, by any of a variety of cell types including T-helper 2 cells, eosinophils, basophils, mast cells, and nuocytes, resulting in enhanced production of certain antibody isotypes and other effects. GOC:add ISBN:0781735149 PMID:18000958 PMID:18007680 PMID:20065995 PMID:20200518 T-helper 2 type immune response GOC:add Th2 immune response GOC:add The process in which a relatively unspecialized thymocyte acquires specialized features of a T-helper cell. helper T cell differentiation biological_process T-helper cell development GO:0042093 T-helper cell differentiation The process in which a relatively unspecialized thymocyte acquires specialized features of a T-helper cell. GOC:ebc helper T cell differentiation CL:0000912 T-helper cell development GOC:add The expansion of a T cell population by cell division. Follows T cell activation. GO:0042111 T lymphocyte proliferation T-cell proliferation T-lymphocyte proliferation biological_process GO:0042098 T cell proliferation The expansion of a T cell population by cell division. Follows T cell activation. GOC:jl 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. Wikipedia:T_cell_receptor T lymphocyte receptor complex T-cell receptor complex T-lymphocyte receptor complex TCR complex cellular_component TCR GO:0042101 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. GOC:mah ISBN:0781735149 TCR complex GOC:bf Any process that activates or increases the rate or extent of T cell proliferation. positive regulation of T lymphocyte proliferation positive regulation of T-lymphocyte proliferation up regulation of T cell proliferation up-regulation of T cell proliferation upregulation of T cell proliferation activation of T cell proliferation stimulation of T cell proliferation biological_process GO:0042102 positive regulation of T cell proliferation Any process that activates or increases the rate or extent of T cell proliferation. GOC:ai A T cell receptor complex in which the TCR heterodimer comprises alpha and beta chains, associated with the CD3 complex; recognizes a complex consisting of an antigen-derived peptide bound to a class I or class II MHC protein. alpha-beta T lymphocyte receptor complex alpha-beta T-cell receptor complex alpha-beta T-lymphocyte receptor complex alpha-beta TCR complex cellular_component GO:0042105 alpha-beta T cell receptor complex A T cell receptor complex in which the TCR heterodimer comprises alpha and beta chains, associated with the CD3 complex; recognizes a complex consisting of an antigen-derived peptide bound to a class I or class II MHC protein. GOC:mah ISBN:0781735149 A T cell receptor complex in which the TCR heterodimer comprises gamma and delta chains, associated with the CD3 complex; recognizes antigen directly, without a requirement for processing and presentation by an MHC protein. gamma-delta T lymphocyte receptor complex gamma-delta T-cell receptor complex gamma-delta T-lymphocyte receptor complex gamma-delta TCR complex cellular_component GO:0042106 gamma-delta T cell receptor complex A T cell receptor complex in which the TCR heterodimer comprises gamma and delta chains, associated with the CD3 complex; recognizes antigen directly, without a requirement for processing and presentation by an MHC protein. GOC:mah ISBN:0781735149 The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. T lymphocyte activation T-cell activation T-lymphocyte activation biological_process GO:0042110 T cell activation The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. GOC:mgi_curators ISBN:0781735149 The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. B lymphocyte activation B-cell activation B-lymphocyte activation biological_process GO:0042113 B cell activation The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. GOC:mgi_curators ISBN:0781735149 Any process that modulates the frequency, rate or extent of cell proliferation. biological_process regulation of cell proliferation GO:0042127 regulation of cell population proliferation Any process that modulates the frequency, rate or extent of cell proliferation. GOC:jl Any process that modulates the frequency, rate or extent of T cell proliferation. regulation of T lymphocyte proliferation regulation of T-cell proliferation regulation of T-lymphocyte proliferation biological_process GO:0042129 regulation of T cell proliferation Any process that modulates the frequency, rate or extent of T cell proliferation. GOC:jl Any process that stops, prevents or reduces the rate or extent of T cell proliferation. down regulation of T cell proliferation down-regulation of T cell proliferation downregulation of T cell proliferation negative regulation of T lymphocyte proliferation negative regulation of T-cell proliferation negative regulation of T-lymphocyte proliferation inhibition of T cell proliferation biological_process GO:0042130 negative regulation of T cell proliferation Any process that stops, prevents or reduces the rate or extent of T cell proliferation. GOC:jl 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 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 chemical stimulus. response to chemical stimulus response to chemical substance biological_process GO:0042221 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 chemical 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 chemical stimulus. GOC:jl response to chemical stimulus GOC:dos The regrowth of lost or destroyed tissues. biological_process GO:0042246 tissue regeneration The regrowth of lost or destroyed tissues. GOC:curators The directed killing of a target cell by a natural killer cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. NK cell mediated cell death NK cell mediated cell killing NK cell mediated cytotoxicity natural killer cell mediated cell death natural killer cell mediated cell killing biological_process NK cell mediated cytolysis killer activity natural killer cell mediated cytolysis natural killer-cell mediated cytolysis GO:0042267 Note that either or both mechanisms mentioned in the definition may be used in this process. Note that both granule release and the engagement of death receptors on target cells result in induction of apoptosis in the target cell. natural killer cell mediated cytotoxicity The directed killing of a target cell by a natural killer cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. GOC:add GOC:pr Any process that modulates the frequency, rate, or extent of natural killer cell mediated cytotoxicity. regulation of NK cell mediated cell death regulation of NK cell mediated cell killing regulation of natural killer cell mediated cell death regulation of natural killer cell mediated cell killing biological_process regulation of NK cell mediated cytolysis regulation of NK cell mediated cytotoxicity regulation of natural killer cell mediated cytolysis regulation of natural killer-cell mediated cytolysis GO:0042269 regulation of natural killer cell mediated cytotoxicity Any process that modulates the frequency, rate, or extent of natural killer cell mediated cytotoxicity. GOC:add ISBN:0781735149 Binding to a major histocompatibility complex molecule; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation. major histocompatibility complex binding major histocompatibility complex ligand molecular_function GO:0042287 Note that this term does not include binding to the antigen peptide bound to the MHC protein, for this also annotate to 'peptide antigen binding ; GO:0042605' or one of its children. MHC protein binding Binding to a major histocompatibility complex molecule; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation. GOC:jl The directed movement of a motile cell or organism in response to an external stimulus. Wikipedia:Taxis directed movement in response to stimulus biological_process GO:0042330 taxis The directed movement of a motile cell or organism in response to an external stimulus. GOC:jl ISBN:0192801023 Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. biological_process GO:0042391 regulation of membrane potential Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. GOC:jl GOC:mtg_cardio GOC:tb ISBN:0198506732 The chemical reactions and pathways involving compounds that contain an indole (2,3-benzopyrrole) skeleton. GO:0042434 indole and derivative metabolic process indole and derivative metabolism indole-containing compound metabolism ketole metabolic process ketole metabolism indole derivative metabolic process indole derivative metabolism biological_process GO:0042430 indole-containing compound metabolic process The chemical reactions and pathways involving compounds that contain an indole (2,3-benzopyrrole) skeleton. GOC:jl GOC:mah The chemical reactions and pathways resulting in the formation of compounds that contain an indole (2,3-benzopyrrole) skeleton. indole derivative biosynthesis indole derivative biosynthetic process indole-containing compound anabolism indole-containing compound biosynthesis indole-containing compound formation indole-containing compound synthesis biological_process GO:0042435 indole-containing compound biosynthetic process The chemical reactions and pathways resulting in the formation of compounds that contain an indole (2,3-benzopyrrole) skeleton. GOC:jl The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. hormone metabolism biological_process GO:0042445 hormone metabolic process The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. GOC:jl The chemical reactions and pathways resulting in the formation of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. hormone anabolism hormone biosynthesis hormone formation hormone synthesis biological_process GO:0042446 hormone biosynthetic process The chemical reactions and pathways resulting in the formation of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. GOC:jl A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells. Wikipedia:Melanosome cellular_component GO:0042470 melanosome A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells. GOC:jl PMID:11584301 The process whose specific outcome is the progression of a dentin-containing tooth over time, from its formation to the mature structure. A dentin-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and is composed mainly of dentin, a dense calcified substance, covered by a layer of enamel. odontogeny odontosis tooth development odontogenesis of dentine-containing teeth odontogenesis of dentine-containing tooth biological_process GO:0042475 Note that placoid scales found in the cartilaginous fishes presumably develop through the same processes, but are found on the dermis, rather than in the mouth or pharynx. See Wikipedia:Placoid_scale#Placoid_scales. odontogenesis of dentin-containing tooth The process whose specific outcome is the progression of a dentin-containing tooth over time, from its formation to the mature structure. A dentin-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and is composed mainly of dentin, a dense calcified substance, covered by a layer of enamel. GOC:cjm GOC:mah GOC:mtg_sensu PMID:10333884 PMID:15355794 odontogenesis of dentine-containing tooth GOC:mah The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food. GO:0042477 Wikipedia:Odontogenesis odontogeny odontosis tooth morphogenesis odontogenesis of calcareous or chitinous tooth biological_process tooth development GO:0042476 odontogenesis The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food. GOC:jl GOC:mah Any process that modulates the frequency, rate or extent of the formation and development of a tooth or teeth. GO:0042484 regulation of tooth development regulation of odontogenesis of calcareous or chitinous tooth biological_process GO:0042481 regulation of odontogenesis Any process that modulates the frequency, rate or extent of the formation and development of a tooth or teeth. GOC:jl Any process that activates or increases the frequency, rate or extent of the formation and development of a tooth or teeth. GO:0042485 positive regulation of tooth development up regulation of odontogenesis up-regulation of odontogenesis upregulation of odontogenesis activation of odontogenesis positive regulation of odontogenesis of calcareous or chitinous tooth stimulation of odontogenesis biological_process GO:0042482 positive regulation of odontogenesis Any process that activates or increases the frequency, rate or extent of the formation and development of a tooth or teeth. GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of the formation and development of a tooth or teeth. GO:0042486 down regulation of odontogenesis down-regulation of odontogenesis downregulation of odontogenesis negative regulation of tooth development inhibition of odontogenesis negative regulation of odontogenesis of calcareous or chitinous tooth biological_process GO:0042483 negative regulation of odontogenesis Any process that stops, prevents, or reduces the frequency, rate or extent of the formation and development of a tooth or teeth. GOC:jl Any process that modulates the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages which are borne on the jaws, or on other bones in the walls of the mouth or pharynx of most vertebrates. regulation of odontogenesis of dentine-containing teeth regulation of odontogenesis of dentine-containing tooth biological_process GO:0042487 regulation of odontogenesis of dentin-containing tooth Any process that modulates the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages which are borne on the jaws, or on other bones in the walls of the mouth or pharynx of most vertebrates. GOC:jl GOC:mtg_sensu PMID:15355794 regulation of odontogenesis of dentine-containing tooth GOC:mah Any process that activates or increases the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages that are borne on the jaws, or on other bones in the walls of the mouth or pharynx of most vertebrates. activation of odontogenesis stimulation of odontogenesis up regulation of odontogenesis up-regulation of odontogenesis upregulation of odontogenesis positive regulation of odontogenesis of dentine-containing teeth biological_process positive regulation of odontogenesis of dentine-containing tooth GO:0042488 positive regulation of odontogenesis of dentin-containing tooth Any process that activates or increases the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages that are borne on the jaws, or on other bones in the walls of the mouth or pharynx of most vertebrates. GOC:jl PMID:15355794 Any process that stops, prevents, or reduces the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages which are borne on the jaws, or on other bones in the walls of the mouth or pharynx. down regulation of odontogenesis down-regulation of odontogenesis downregulation of odontogenesis inhibition of odontogenesis negative regulation of odontogenesis negative regulation of odontogenesis of dentine-containing teeth biological_process negative regulation of odontogenesis of dentine-containing tooth GO:0042489 negative regulation of odontogenesis of dentin-containing tooth Any process that stops, prevents, or reduces the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages which are borne on the jaws, or on other bones in the walls of the mouth or pharynx. GOC:jl GOC:mtg_sensu PMID:15355794 The process in which a relatively unspecialized hemopoietic cell acquires specialized features of a gamma-delta T cell. A gamma-delta T cell is a T cell that expresses a gamma-delta T cell receptor complex. gamma-delta T lymphocyte differentiation gamma-delta T-cell differentiation gamma-delta T-lymphocyte differentiation biological_process gamma-delta T cell development GO:0042492 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. gamma-delta T cell differentiation The process in which a relatively unspecialized hemopoietic cell acquires specialized features of a gamma-delta T cell. A gamma-delta T cell is a T cell that expresses a gamma-delta T cell receptor complex. CL:0000798 GOC:jl gamma-delta T cell development GOC:add The enzymatic generation of superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species, by a cell in response to environmental stress, thereby mediating the activation of various stress-inducible signaling pathways. superoxide release biological_process GO:0042554 superoxide anion generation The enzymatic generation of superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species, by a cell in response to environmental stress, thereby mediating the activation of various stress-inducible signaling pathways. GOC:jl PMID:12359750 superoxide release GOC:hjd GOC:mah 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. Wikipedia:Antibody antibody cellular_component GO:0042571 Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. 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. GOC:add ISBN:0781735149 antibody GOC:add Primary lysosomal granule found in neutrophil granulocytes. Contains a wide range of hydrolytic enzymes and is released into the extracellular fluid. primary granule cellular_component GO:0042582 azurophil granule Primary lysosomal granule found in neutrophil granulocytes. Contains a wide range of hydrolytic enzymes and is released into the extracellular fluid. GOC:jl PMID:17152095 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 The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex. The peptide antigen is typically, but not always, processed from a whole protein. Class I here refers to classical class I molecules. cross presentation cross priming cross-presentation cross-priming antigen presentation, exogenous antigen via MHC class I antigen presentation, exogenous antigen via major histocompatibility complex class I exogenous peptide antigen processing and presentation via MHC class I biological_process GO:0042590 antigen processing and presentation of exogenous peptide antigen via MHC class I The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex. The peptide antigen is typically, but not always, processed from a whole protein. Class I here refers to classical class I molecules. GOC:add ISBN:0781735149 PMID:15771591 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 A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen. cellular_component GO:0042611 MHC protein complex A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen. GOC:add GOC:jl ISBN:0781735149 PMID:15928678 PMID:16153240 A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen. cellular_component GO:0042613 MHC class II protein complex A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen. GOC:add GOC:jl ISBN:0120781859 PMID:15928678 The type of sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years. biological_process GO:0042698 ovulation cycle The type of sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years. ISBN:0721662544 The regulated release of progesterone, a steroid hormone, by the corpus luteum of the ovary and by the placenta. biological_process GO:0042701 progesterone secretion The regulated release of progesterone, a steroid hormone, by the corpus luteum of the ovary and by the placenta. GOC:jl ISBN:0395825172 Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism. GO:0009816 GO:0042830 defence response to bacteria defence response to bacterium defense response to bacteria defense response to bacterium, incompatible interaction resistance response to pathogenic bacteria resistance response to pathogenic bacterium biological_process antibacterial peptide activity GO:0042742 defense response to bacterium Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism. GOC:jl 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 modulates the occurrence or rate of cell death by apoptotic process. regulation of apoptosis biological_process apoptosis regulator activity GO:0042981 This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. regulation of apoptotic process Any process that modulates the occurrence or rate of cell death by apoptotic process. GOC:jl GOC:mtg_apoptosis A prolongation or process extending from a cell, e.g. a flagellum or axon. cell process cellular process cellular projection cellular_component GO:0042995 cell projection A prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl http://www.cogsci.princeton.edu/~wn/ A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. NIF_Subcellular:sao867568886 neuron process neuron protrusion neuronal cell projection neurite cellular_component nerve fiber GO:0043005 neuron projection A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. GOC:jl http://www.cogsci.princeton.edu/~wn/ neuron protrusion NIF_Subcellular:sao250931889 nerve fiber GOC:dph The process in which a monocyte acquires the specialized features of a dendritic cell, an immunocompetent cell of the lymphoid and hemopoietic systems and skin. Wikipedia:Dendritic_cell biological_process GO:0043011 myeloid dendritic cell differentiation The process in which a monocyte acquires the specialized features of a dendritic cell, an immunocompetent cell of the lymphoid and hemopoietic systems and skin. CL:0000782 GOC:jl A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite. extracellular structure organisation extracellular structure organization and biogenesis biological_process GO:0043062 extracellular structure organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite. GOC:ai GOC:dph GOC:jl GOC:mah extracellular structure organization and biogenesis GOC:dph GOC:jl GOC:mah Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. up regulation of apoptosis up-regulation of apoptosis upregulation of apoptosis activation of apoptosis positive regulation of apoptosis stimulation of apoptosis biological_process pro-apoptosis GO:0043065 This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is positively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. positive regulation of apoptotic process Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. GOC:jl GOC:mtg_apoptosis Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. GO:0006916 anti-apoptosis down regulation of apoptosis down-regulation of apoptosis downregulation of apoptosis inhibition of apoptosis negative regulation of apoptosis biological_process apoptosis inhibitor activity pro-survival GO:0043066 This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is negatively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. negative regulation of apoptotic process Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. GOC:jl GOC:mtg_apoptosis Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GO:0043070 regulation of non-apoptotic programmed cell death biological_process GO:0043067 regulation of programmed cell death Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GOC:jl Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GO:0043071 up regulation of programmed cell death up-regulation of programmed cell death upregulation of programmed cell death activation of programmed cell death positive regulation of non-apoptotic programmed cell death stimulation of programmed cell death biological_process GO:0043068 positive regulation of programmed cell death Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GO:0043072 down regulation of programmed cell death down-regulation of programmed cell death downregulation of programmed cell death inhibition of programmed cell death negative regulation of non-apoptotic programmed cell death biological_process GO:0043069 negative regulation of programmed cell death Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GOC:jl Any process involved in the maintenance of a steady-state level of the surface-active lipoprotein mixture which coats the alveoli. biological_process GO:0043129 surfactant homeostasis Any process involved in the maintenance of a steady-state level of the surface-active lipoprotein mixture which coats the alveoli. PMID:9751757 A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the hindgut. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The hindgut is the posterior part of the alimentary canal, including the rectum, and the large intestine. biological_process GO:0043133 hindgut contraction A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the hindgut. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The hindgut is the posterior part of the alimentary canal, including the rectum, and the large intestine. GOC:jl GOC:mtg_muscle UBERON:0001046 Any process that modulates the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine. biological_process GO:0043134 regulation of hindgut contraction Any process that modulates the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine. GOC:jl UBERON:0001046 The chemical reactions and pathways involving macromolecules, any 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. GO:0043283 GO:0044259 biopolymer metabolic process macromolecule metabolism organismal macromolecule metabolism multicellular organismal macromolecule metabolic process biological_process GO:0043170 macromolecule metabolic process The chemical reactions and pathways involving macromolecules, any 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. GOC:mah biopolymer metabolic process GOC:mtg_chebi_dec09 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 biotic stimulus, an external stimulus caused by, or produced by living things. biological_process GO:0043207 response to external biotic 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 biotic stimulus, an external stimulus caused by, or produced by living things. GOC:go_curators Binding to glycosphingolipid, a compound with residues of sphingoid and at least one monosaccharide. molecular_function GO:0043208 glycosphingolipid binding Binding to glycosphingolipid, a compound with residues of sphingoid and at least one monosaccharide. GOC:jl 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, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. NIF_Subcellular:sao1456184038 non-membrane-enclosed organelle cellular_component GO:0043228 non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. 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, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi. cellular_component GO:0043230 extracellular organelle Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi. GOC:jl PMID:9914479 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 Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. intracellular non-membrane-enclosed organelle cellular_component GO:0043232 intracellular non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. GOC:go_curators The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen. cellular_component GO:0043233 organelle lumen The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen. GOC:jl GOC:mah Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. cellular_component GO:0043235 receptor complex Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. GOC:go_curators Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring outside the cell. extracellular non-membrane-enclosed organelle cellular_component GO:0043264 extracellular non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring outside the cell. GOC:jl 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 The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte. apoptotic cell removal efferocytosis programmed cell clearance biological_process GO:0043277 Note that unlike mammals or Drosophila, C. elegans (and many lower organisms) do not have professional macrophages/phagocytes, instead cell corpses are engulfed by neighboring cells. Cell types that can function as engulfing cells include hypodermal cells, gonadal sheath cells, pharyngeal muscle cells, and intestinal cells. apoptotic cell clearance The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte. GOC:rk PMID:14685684 efferocytosis PMID:17548650 Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle. contractile fibre cellular_component GO:0043292 contractile fiber Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle. GOC:go_curators ISBN:0815316194 The process in which a relatively unspecialized T cell acquires specialized features of a mature CD4-positive, alpha-beta T cell. CD4-positive, alpha beta T cell differentiation CD4-positive, alpha-beta T lymphocyte differentiation CD4-positive, alpha-beta T-cell differentiation CD4-positive, alpha-beta T-lymphocyte differentiation biological_process CD4-positive, alpha beta T cell development GO:0043367 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. CD4-positive, alpha-beta T cell differentiation The process in which a relatively unspecialized T cell acquires specialized features of a mature CD4-positive, alpha-beta T cell. CL:0000624 ISBN:0781735149 CD4-positive, alpha beta T cell differentiation GOC:bf CD4-positive, alpha beta T cell development GOC:add The process of sparing immature T cells which react with self-MHC protein complexes with low affinity levels from apoptotic death. positive T lymphocyte selection positive T-cell selection positive T-lymphocyte selection biological_process GO:0043368 positive T cell selection The process of sparing immature T cells which react with self-MHC protein complexes with low affinity levels from apoptotic death. ISBN:0781735149 PMID:12414722 Any process that modulates the frequency, rate, or extent of CD4-positive, alpha-beta T cell differentiation. regulation of CD4-positive T lymphocyte differentiation regulation of CD4-positive T-cell differentiation regulation of CD4-positive T-lymphocyte differentiation regulation of CD4-positive, alpha beta T cell differentiation regulation of CD4-positive, alpha beta T lymphocyte differentiation regulation of CD4-positive, alpha beta T-cell differentiation regulation of CD4-positive, alpha beta T-lymphocyte differentiation biological_process regulation of CD4-positive, alpha beta T cell development GO:0043370 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. regulation of CD4-positive, alpha-beta T cell differentiation Any process that modulates the frequency, rate, or extent of CD4-positive, alpha-beta T cell differentiation. GOC:add GOC:pr ISBN:0781735149 regulation of CD4-positive, alpha beta T cell differentiation GOC:bf regulation of CD4-positive, alpha beta T cell development GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of CD4-positive, alpha-beta T cell differentiation. down regulation of CD4-positive, alpha beta T cell differentiation down-regulation of CD4-positive, alpha beta T cell differentiation downregulation of CD4-positive, alpha beta T cell differentiation negative regulation of CD4-positive T-cell differentiation negative regulation of CD4-positive T-lymphocyte differentiation negative regulation of CD4-positive, alpha beta T lymphocyte differentiation negative regulation of CD4-positive, alpha beta T-cell differentiation negative regulation of CD4-positive, alpha beta T-lymphocyte differentiation inhibition of CD4-positive, alpha beta T cell differentiation biological_process negative regulation of CD4-positive, alpha beta T cell development GO:0043371 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. negative regulation of CD4-positive, alpha-beta T cell differentiation Any process that stops, prevents, or reduces the frequency, rate, or extent of CD4-positive, alpha-beta T cell differentiation. GOC:add GOC:pr ISBN:0781735149 negative regulation of CD4-positive, alpha beta T cell development GOC:add Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell differentiation. positive regulation of CD4-positive T lymphocyte differentiation positive regulation of CD4-positive T-cell differentiation positive regulation of CD4-positive T-lymphocyte differentiation positive regulation of CD4-positive, alpha beta T cell differentiation positive regulation of CD4-positive, alpha beta T lymphocyte differentiation positive regulation of CD4-positive, alpha beta T-cell differentiation positive regulation of CD4-positive, alpha beta T-lymphocyte differentiation up regulation of CD4-positive, alpha beta T cell differentiation up-regulation of CD4-positive, alpha beta T cell differentiation upregulation of CD4-positive, alpha beta T cell differentiation activation of CD4-positive, alpha beta T cell differentiation stimulation of CD4-positive, alpha beta T cell differentiation biological_process positive regulation of CD4-positive, alpha beta T cell development GO:0043372 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. positive regulation of CD4-positive, alpha-beta T cell differentiation Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell differentiation. GOC:add GOC:pr ISBN:0781735149 positive regulation of CD4-positive, alpha beta T cell differentiation GOC:bf positive regulation of CD4-positive, alpha beta T cell development GOC:add The process in which a newly activated T cell acquires specialized features of a memory T cell. memory T lymphocyte differentiation memory T-cell differentiation memory T-lymphocyte differentiation biological_process memory T cell development GO:0043379 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. memory T cell differentiation The process in which a newly activated T cell acquires specialized features of a memory T cell. ISBN:0781735149 memory T cell development GOC:add Any process that modulates the frequency, rate, or extent of memory T cell differentiation. regulation of memory T lymphocyte differentiation regulation of memory T-cell differentiation regulation of memory T-lymphocyte differentiation biological_process regulation of memory T cell development GO:0043380 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. regulation of memory T cell differentiation Any process that modulates the frequency, rate, or extent of memory T cell differentiation. ISBN:0781735149 regulation of memory T cell development GOC:add Any process that stops, prevents, or reduces the rate of memory T cell differentiation. down regulation of memory T cell differentiation down-regulation of memory T cell differentiation downregulation of memory T cell differentiation negative regulation of memory T lymphocyte differentiation negative regulation of memory T-cell differentiation negative regulation of memory T-lymphocyte differentiation inhibition of memory T cell differentiation biological_process negative regulation of memory T cell development GO:0043381 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. negative regulation of memory T cell differentiation Any process that stops, prevents, or reduces the rate of memory T cell differentiation. ISBN:0781735149 negative regulation of memory T cell development GOC:add Any process that activates or increases the frequency, rate or extent of memory T cell differentiation. positive regulation of memory T lymphocyte differentiation positive regulation of memory T-cell differentiation positive regulation of memory T-lymphocyte differentiation up regulation of memory T cell differentiation up-regulation of memory T cell differentiation upregulation of memory T cell differentiation activation of memory T cell differentiation stimulation of memory T cell differentiation biological_process positive regulation of memory T cell development GO:0043382 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. positive regulation of memory T cell differentiation Any process that activates or increases the frequency, rate or extent of memory T cell differentiation. ISBN:0781735149 positive regulation of memory T cell development GOC:add A receptor complex found on immature T cells consisting of a T cell receptor beta chain and the pre-TCR-alpha chain, along with additional signaling components including CD3 family members and additional signaling proteins. pre-T lymphocyte receptor complex pre-T-cell receptor complex pre-T-lymphocyte receptor complex pre-TCR complex cellular_component GO:0043384 pre-T cell receptor complex A receptor complex found on immature T cells consisting of a T cell receptor beta chain and the pre-TCR-alpha chain, along with additional signaling components including CD3 family members and additional signaling proteins. ISBN:0781735149 PMID:12220932 Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid). up regulation of DNA binding up-regulation of DNA binding upregulation of DNA binding activation of DNA binding stimulation of DNA binding biological_process GO:0043388 positive regulation of DNA binding Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid). GOC:dph GOC:jl GOC:tb Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid). down regulation of DNA binding down-regulation of DNA binding downregulation of DNA binding inhibition of DNA binding biological_process GO:0043392 negative regulation of DNA binding Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid). GOC:dph GOC:jl GOC:tb 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 process of gaseous exchange between an organism and its environment. biological_process GO:0043576 regulation of respiratory gaseous exchange Any process that modulates the frequency, rate or extent of the process of gaseous exchange between an organism and its environment. GOC:jl The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells. amide metabolism biological_process GO:0043603 cellular amide metabolic process The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells. GOC:curators The chemical reactions and pathways resulting in the formation of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group. biological_process GO:0043604 amide biosynthetic process The chemical reactions and pathways resulting in the formation of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group. GOC:curators 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 a respiratory system process, an organ system process carried out by any of the organs or tissues of the respiratory system. biological_process GO:0044065 regulation of respiratory system process Any process that modulates the frequency, rate or extent of a respiratory system process, an organ system process carried out by any of the organs or tissues of the respiratory 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 A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 cellular component biogenesis A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. GOC:jl GOC:mah Any process that modulates the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. biological_process GO:0044087 regulation of cellular component biogenesis Any process that modulates the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. GOC:jl Any process that activates or increases the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. biological_process GO:0044089 positive regulation of cellular component biogenesis Any process that activates or increases the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. 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. 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. 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 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 macromolecules, any 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, as carried out by individual cells. GO:0034960 cellular biopolymer metabolic process cellular macromolecule metabolism biological_process GO:0044260 cellular macromolecule metabolic process The chemical reactions and pathways involving macromolecules, any 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, as carried out by individual cells. GOC:mah cellular biopolymer metabolic process GOC:mtg_chebi_dec09 The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds. nitrogen compound anabolism nitrogen compound biosynthesis nitrogen compound formation nitrogen compound synthesis biological_process GO:0044271 cellular nitrogen compound biosynthetic process The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds. GOC:jl ISBN:0198506732 The chemical reactions and pathways resulting in the formation of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. sulfur compound anabolism sulfur compound biosynthesis sulfur compound formation sulfur compound synthesis sulfur biosynthesis sulfur biosynthetic process biological_process GO:0044272 sulfur compound biosynthetic process The chemical reactions and pathways resulting in the formation of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. 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 Any process evolved to enable an interaction with an organism of a different species. https://github.com/geneontology/go-ontology/issues/20191 interaction with another species interspecies interaction interspecies interaction between organisms interspecies interaction with other organisms biological_process GO:0044419 biological process involved in interspecies interaction between organisms Any process evolved to enable an interaction with an organism of a different species. GOC:cc The aggregation, arrangement and bonding together of a set of components to form a motile cilium. krc 2015-02-06T17:23:23Z GO:1903887 biological_process motile primary cilia assembly motile primary cilia formation motile primary cilium assembly motile primary cilium formation nodal cilium assembly nodal cilium formation GO:0044458 motile cilium assembly The aggregation, arrangement and bonding together of a set of components to form a motile cilium. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000079 PMID:19776033 PMID:21129373 ZFIN:dsf motile primary cilia assembly GOC:TermGenie motile primary cilia formation GOC:TermGenie motile primary cilium formation GOC:TermGenie nodal cilium assembly GOC:TermGenie nodal cilium formation GOC:TermGenie cell part A biological process that directly contributes to the process of producing new individuals, involving another organism. jl 2012-09-19T15:56:30Z biological_process GO:0044703 multi-organism reproductive process A biological process that directly contributes to the process of producing new individuals, involving another organism. GOC:jl A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. jl 2013-03-27T15:09:58Z microtubule-based flagellum organization biological_process GO:0044782 Note that we deem cilium and microtubule-based flagellum to be equivalent. cilium organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. GOC:cilia GOC:jl The process in which T cells that express T cell receptors that are restricted by self MHC protein complexes and tolerant to self antigens are selected for further maturation. Wikipedia:Thymocyte T lymphocyte selection T-cell selection T-lymphocyte selection biological_process GO:0045058 T cell selection The process in which T cells that express T cell receptors that are restricted by self MHC protein complexes and tolerant to self antigens are selected for further maturation. ISBN:0781735149 PMID:12414722 The process in which a relatively unspecialized T cell acquires the specialized features of a T-helper 1 (Th1) cell. A Th1 cell is a CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive and produces interferon-gamma. biological_process T-helper 1 cell development GO:0045063 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. T-helper 1 cell differentiation The process in which a relatively unspecialized T cell acquires the specialized features of a T-helper 1 (Th1) cell. A Th1 cell is a CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive and produces interferon-gamma. CL:0000545 GOC:ebc T-helper 1 cell development GOC:add The process in which a relatively unspecialized T cell acquires specialized features of a T-helper 2 (Th2) cell. A Th2 cell is a CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive and produces interleukin-4. biological_process T-helper 2 cell development GO:0045064 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. T-helper 2 cell differentiation The process in which a relatively unspecialized T cell acquires specialized features of a T-helper 2 (Th2) cell. A Th2 cell is a CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive and produces interleukin-4. CL:0000546 GOC:ebc T-helper 2 cell development GOC:add Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. GO:0002226 Wikipedia:Innate_immune_system innate immunity nonspecific immune response biological_process GO:0045087 innate immune response Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. GOC:add GOC:ebc GOC:mtg_sensu GO_REF:0000022 innate immunity GOC:pg Any process that modulates the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection. biological_process GO:0045088 regulation of innate immune response Any process that modulates the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection. GOC:ebc Any process that activates or increases the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection. up regulation of innate immune response up-regulation of innate immune response upregulation of innate immune response stimulation of innate immune response biological_process GO:0045089 positive regulation of innate immune response Any process that activates or increases the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection. GOC:ebc Any process that modulates the frequency, rate or extent of bone tissue loss (resorption). biological_process GO:0045124 regulation of bone resorption Any process that modulates the frequency, rate or extent of bone tissue loss (resorption). GOC:ai The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets during M phase of the meiotic cell cycle. biological_process GO:0045132 meiotic chromosome segregation The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets during M phase of the meiotic cell cycle. GOC:ai GOC:mah The process whose specific outcome is the progression of the primary sexual characteristics over time, from their formation to the mature structures. The primary sexual characteristics are the testes in males and the ovaries in females and they develop in response to sex hormone secretion. biological_process GO:0045137 development of primary sexual characteristics The process whose specific outcome is the progression of the primary sexual characteristics over time, from their formation to the mature structures. The primary sexual characteristics are the testes in males and the ovaries in females and they develop in response to sex hormone secretion. GOC:ai The cell cycle process in which sister chromatids are organized and then physically separated and randomly apportioned to two sets during the second division of the meiotic cell cycle. meiosis II, chromosome segregation biological_process GO:0045144 meiotic sister chromatid segregation The cell cycle process in which sister chromatids are organized and then physically separated and randomly apportioned to two sets during the second division of the meiotic cell cycle. GOC:ai ISBN:0815316194 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 The switching of activated B cells from IgM biosynthesis to biosynthesis of other isotypes of immunoglobulin, accomplished through a recombination process involving an intrachromosomal deletion involving switch regions that reside 5' of each constant region gene segment in the immunoglobulin heavy chain locus. Wikipedia:Immunoglobulin_class_switching class switch recombination class switching isotype switch recombination biological_process GO:0045190 Note that IgM and IgD can be coexpressed by B cells via an alternate splicing mechanism, but true recombinational isotype switching to IgD has been demonstrated as well. Note that this term is best used to annotate gene products which are involved in the mechanism of DNA recombination used in isotype switching, like the B cell specific Swap70 factor in the mouse, rather than gene products which promote isotype switching such as cytokines or co-stimulatory molecules, which should instead be annotated to 'regulation of isotype switching ; GO:0045191'. isotype switching The switching of activated B cells from IgM biosynthesis to biosynthesis of other isotypes of immunoglobulin, accomplished through a recombination process involving an intrachromosomal deletion involving switch regions that reside 5' of each constant region gene segment in the immunoglobulin heavy chain locus. ISBN:0781735149 Any process that modulates the frequency, rate or extent of isotype switching. regulation of class switch recombination regulation of class switching regulation of isotype switch recombination biological_process GO:0045191 regulation of isotype switching Any process that modulates the frequency, rate or extent of isotype switching. GOC:ai The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. NIF_Subcellular:sao914572699 Wikipedia:Chemical_synapse synaptic junction mixed synapse cellular_component electrotonic synapse GO:0045202 synapse The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. GOC:aruk ISBN:0198506732 PMID:24619342 PMID:29383328 PMID:31998110 mixed synapse NIF_Subcellular:sao1506103497 electrotonic synapse NIF_Subcellular:sao1311109124 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of external structures that lie outside the plasma membrane and surround the entire cell. external encapsulating structure organisation external encapsulating structure organization and biogenesis biological_process GO:0045229 external encapsulating structure organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of external structures that lie outside the plasma membrane and surround the entire cell. GOC:ai GOC:dph GOC:jl GOC:mah external encapsulating structure organization and biogenesis GOC:dph GOC:jl GOC:mah A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor. Wikipedia:Immunologic_activation immune cell activation leucocyte activation biological_process GO:0045321 leukocyte activation A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor. GOC:add The regulated release of juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis. biological_process GO:0045443 juvenile hormone secretion The regulated release of juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis. GOC:go_curators ISBN:0198547684 The process in which specialized cells known as osteoclasts degrade the organic and inorganic portions of bone, and endocytose and transport the degradation products. Wikipedia:Bone_resorption biological_process GO:0045453 bone resorption The process in which specialized cells known as osteoclasts degrade the organic and inorganic portions of bone, and endocytose and transport the degradation products. GOC:mah PMID:10968780 The regulated release of ecdysteroids, a group of polyhydroxylated ketosteroids which initiate post-embryonic development. biological_process GO:0045457 ecdysteroid secretion The regulated release of ecdysteroids, a group of polyhydroxylated ketosteroids which initiate post-embryonic development. GOC:go_curators Any process that modulates the frequency, rate or extent of B cell differentiation. regulation of B lymphocyte differentiation regulation of B-cell differentiation regulation of B-lymphocyte differentiation biological_process regulation of B cell development GO:0045577 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. regulation of B cell differentiation Any process that modulates the frequency, rate or extent of B cell differentiation. GOC:go_curators regulation of B cell development GOC:add Any process that stops, prevents, or reduces the frequency, rate or extent of B cell differentiation. down regulation of B cell differentiation down-regulation of B cell differentiation downregulation of B cell differentiation negative regulation of B lymphocyte differentiation negative regulation of B-cell differentiation negative regulation of B-lymphocyte differentiation inhibition of B cell differentiation biological_process negative regulation of B cell development GO:0045578 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. negative regulation of B cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of B cell differentiation. GOC:go_curators negative regulation of B cell development GOC:add Any process that activates or increases the frequency, rate or extent of B cell differentiation. positive regulation of B lymphocyte differentiation positive regulation of B-cell differentiation positive regulation of B-lymphocyte differentiation up regulation of B cell differentiation up-regulation of B cell differentiation upregulation of B cell differentiation activation of B cell differentiation stimulation of B cell differentiation biological_process positive regulation of B cell development GO:0045579 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. positive regulation of B cell differentiation Any process that activates or increases the frequency, rate or extent of B cell differentiation. GOC:go_curators positive regulation of B cell development GOC:add Any process that modulates the frequency, rate or extent of T cell differentiation. regulation of T lymphocyte differentiation regulation of T-cell differentiation regulation of T-lymphocyte differentiation biological_process regulation of T cell development GO:0045580 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. regulation of T cell differentiation Any process that modulates the frequency, rate or extent of T cell differentiation. GOC:go_curators regulation of T cell development GOC:add Any process that stops, prevents, or reduces the frequency, rate or extent of T cell differentiation. down regulation of T cell differentiation down-regulation of T cell differentiation downregulation of T cell differentiation negative regulation of T lymphocyte differentiation negative regulation of T-cell differentiation negative regulation of T-lymphocyte differentiation inhibition of T cell differentiation biological_process negative regulation of T cell development GO:0045581 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. negative regulation of T cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of T cell differentiation. GOC:go_curators negative regulation of T cell development GOC:add Any process that activates or increases the frequency, rate or extent of T cell differentiation. positive regulation of T lymphocyte differentiation positive regulation of T-cell differentiation positive regulation of T-lymphocyte differentiation up regulation of T cell differentiation up-regulation of T cell differentiation upregulation of T cell differentiation activation of T cell differentiation stimulation of T cell differentiation biological_process positive regulation of T cell development GO:0045582 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. positive regulation of T cell differentiation Any process that activates or increases the frequency, rate or extent of T cell differentiation. GOC:go_curators positive regulation of T cell development GOC:add Any process that modulates the frequency, rate or extent of gamma-delta T cell differentiation. regulation of gamma-delta T lymphocyte differentiation regulation of gamma-delta T-cell differentiation regulation of gamma-delta T-lymphocyte differentiation biological_process regulation of gamma-delta T cell development GO:0045586 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. regulation of gamma-delta T cell differentiation Any process that modulates the frequency, rate or extent of gamma-delta T cell differentiation. GOC:go_curators regulation of gamma-delta T cell development GOC:add Any process that stops, prevents, or reduces the frequency, rate or extent of gamma-delta T cell differentiation. down regulation of gamma-delta T cell differentiation down-regulation of gamma-delta T cell differentiation downregulation of gamma-delta T cell differentiation negative regulation of gamma-delta T lymphocyte differentiation negative regulation of gamma-delta T-cell differentiation negative regulation of gamma-delta T-lymphocyte differentiation inhibition of gamma-delta T cell differentiation biological_process negative regulation of gamma-delta T cell development GO:0045587 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. negative regulation of gamma-delta T cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of gamma-delta T cell differentiation. GOC:go_curators negative regulation of gamma-delta T cell development GOC:add Any process that activates or increases the frequency, rate or extent of gamma-delta T cell differentiation. positive regulation of gamma-delta T lymphocyte differentiation positive regulation of gamma-delta T-cell differentiation positive regulation of gamma-delta T-lymphocyte differentiation up regulation of gamma-delta T cell differentiation up-regulation of gamma-delta T cell differentiation upregulation of gamma-delta T cell differentiation activation of gamma-delta T cell differentiation stimulation of gamma-delta T cell differentiation biological_process positive regulation of gamma-delta T cell development GO:0045588 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. positive regulation of gamma-delta T cell differentiation Any process that activates or increases the frequency, rate or extent of gamma-delta T cell differentiation. GOC:go_curators positive regulation of gamma-delta T cell development GOC:add Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features. biological_process GO:0045595 regulation of cell differentiation Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation. down regulation of cell differentiation down-regulation of cell differentiation downregulation of cell differentiation inhibition of cell differentiation biological_process GO:0045596 negative regulation of cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of cell differentiation. up regulation of cell differentiation up-regulation of cell differentiation upregulation of cell differentiation activation of cell differentiation stimulation of cell differentiation biological_process GO:0045597 positive regulation of cell differentiation Any process that activates or increases the frequency, rate or extent of cell differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of lymphocyte differentiation. biological_process regulation of lymphocyte development GO:0045619 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. regulation of lymphocyte differentiation Any process that modulates the frequency, rate or extent of lymphocyte differentiation. GOC:go_curators regulation of lymphocyte development GOC:add Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte differentiation. down regulation of lymphocyte differentiation down-regulation of lymphocyte differentiation downregulation of lymphocyte differentiation inhibition of lymphocyte differentiation biological_process negative regulation of lymphocyte development GO:0045620 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. negative regulation of lymphocyte differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte differentiation. GOC:go_curators negative regulation of lymphocyte development GOC:add Any process that activates or increases the frequency, rate or extent of lymphocyte differentiation. up regulation of lymphocyte differentiation up-regulation of lymphocyte differentiation upregulation of lymphocyte differentiation activation of lymphocyte differentiation stimulation of lymphocyte differentiation biological_process positive regulation of lymphocyte development GO:0045621 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. positive regulation of lymphocyte differentiation Any process that activates or increases the frequency, rate or extent of lymphocyte differentiation. GOC:go_curators positive regulation of lymphocyte development GOC:add Any process that modulates the frequency, rate or extent of T-helper cell differentiation. biological_process regulation of T-helper cell development GO:0045622 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. regulation of T-helper cell differentiation Any process that modulates the frequency, rate or extent of T-helper cell differentiation. GOC:go_curators regulation of T-helper cell development GOC:add Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper cell differentiation. down regulation of T-helper cell differentiation down-regulation of T-helper cell differentiation downregulation of T-helper cell differentiation inhibition of T-helper cell differentiation biological_process negative regulation of T-helper cell development GO:0045623 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. negative regulation of T-helper cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper cell differentiation. GOC:go_curators negative regulation of T-helper cell development GOC:add Any process that activates or increases the frequency, rate or extent of T-helper cell differentiation. up regulation of T-helper cell differentiation up-regulation of T-helper cell differentiation upregulation of T-helper cell differentiation activation of T-helper cell differentiation stimulation of T-helper cell differentiation biological_process positive regulation of T-helper cell development GO:0045624 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. positive regulation of T-helper cell differentiation Any process that activates or increases the frequency, rate or extent of T-helper cell differentiation. GOC:go_curators positive regulation of T-helper cell development GOC:add Any process that modulates the frequency, rate or extent of T-helper 1 cell differentiation. biological_process regulation of T-helper 1 cell development GO:0045625 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. regulation of T-helper 1 cell differentiation Any process that modulates the frequency, rate or extent of T-helper 1 cell differentiation. GOC:go_curators regulation of T-helper 1 cell development GOC:add Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper 1 cell differentiation. down regulation of T-helper 1 cell differentiation down-regulation of T-helper 1 cell differentiation downregulation of T-helper 1 cell differentiation inhibition of T-helper 1 cell differentiation biological_process negative regulation of T-helper 1 cell development GO:0045626 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. negative regulation of T-helper 1 cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper 1 cell differentiation. GOC:go_curators negative regulation of T-helper 1 cell development GOC:add Any process that activates or increases the frequency, rate or extent of T-helper 1 cell differentiation. up regulation of T-helper 1 cell differentiation up-regulation of T-helper 1 cell differentiation upregulation of T-helper 1 cell differentiation activation of T-helper 1 cell differentiation stimulation of T-helper 1 cell differentiation biological_process positive regulation of T-helper 1 cell development GO:0045627 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. positive regulation of T-helper 1 cell differentiation Any process that activates or increases the frequency, rate or extent of T-helper 1 cell differentiation. GOC:go_curators positive regulation of T-helper 1 cell development GOC:add Any process that modulates the frequency, rate or extent of T-helper 2 cell differentiation. biological_process regulation of T-helper 2 cell development GO:0045628 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. regulation of T-helper 2 cell differentiation Any process that modulates the frequency, rate or extent of T-helper 2 cell differentiation. GOC:go_curators regulation of T-helper 2 cell development GOC:add Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper 2 cell differentiation. down regulation of T-helper 2 cell differentiation down-regulation of T-helper 2 cell differentiation downregulation of T-helper 2 cell differentiation inhibition of T-helper 2 cell differentiation biological_process negative regulation of T-helper 2 cell development GO:0045629 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. negative regulation of T-helper 2 cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper 2 cell differentiation. GOC:go_curators negative regulation of T-helper 2 cell development GOC:add Any process that activates or increases the frequency, rate or extent of T-helper 2 cell differentiation. up regulation of T-helper 2 cell differentiation up-regulation of T-helper 2 cell differentiation upregulation of T-helper 2 cell differentiation activation of T-helper 2 cell differentiation stimulation of T-helper 2 cell differentiation biological_process positive regulation of T-helper 2 cell development GO:0045630 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. positive regulation of T-helper 2 cell differentiation Any process that activates or increases the frequency, rate or extent of T-helper 2 cell differentiation. GOC:go_curators positive regulation of T-helper 2 cell development GOC:add Any process that modulates the frequency, rate or extent of myeloid cell differentiation. biological_process GO:0045637 regulation of myeloid cell differentiation Any process that modulates the frequency, rate or extent of myeloid cell differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid cell differentiation. down regulation of myeloid cell differentiation down-regulation of myeloid cell differentiation downregulation of myeloid cell differentiation inhibition of myeloid cell differentiation biological_process GO:0045638 negative regulation of myeloid cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid cell differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of myeloid cell differentiation. up regulation of myeloid cell differentiation up-regulation of myeloid cell differentiation upregulation of myeloid cell differentiation activation of myeloid cell differentiation stimulation of myeloid cell differentiation biological_process GO:0045639 positive regulation of myeloid cell differentiation Any process that activates or increases the frequency, rate or extent of myeloid cell differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of basophil differentiation. biological_process GO:0045640 regulation of basophil differentiation Any process that modulates the frequency, rate or extent of basophil differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of basophil differentiation. down regulation of basophil differentiation down-regulation of basophil differentiation downregulation of basophil differentiation inhibition of basophil differentiation biological_process GO:0045641 negative regulation of basophil differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of basophil differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of basophil differentiation. up regulation of basophil differentiation up-regulation of basophil differentiation upregulation of basophil differentiation activation of basophil differentiation stimulation of basophil differentiation biological_process GO:0045642 positive regulation of basophil differentiation Any process that activates or increases the frequency, rate or extent of basophil differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of eosinophil differentiation. biological_process GO:0045643 regulation of eosinophil differentiation Any process that modulates the frequency, rate or extent of eosinophil differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of eosinophil differentiation. down regulation of eosinophil differentiation down-regulation of eosinophil differentiation downregulation of eosinophil differentiation inhibition of eosinophil differentiation biological_process GO:0045644 negative regulation of eosinophil differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of eosinophil differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of eosinophil differentiation. up regulation of eosinophil differentiation up-regulation of eosinophil differentiation upregulation of eosinophil differentiation activation of eosinophil differentiation stimulation of eosinophil differentiation biological_process GO:0045645 positive regulation of eosinophil differentiation Any process that activates or increases the frequency, rate or extent of eosinophil differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of erythrocyte differentiation. regulation of RBC differentiation regulation of red blood cell differentiation biological_process GO:0045646 regulation of erythrocyte differentiation Any process that modulates the frequency, rate or extent of erythrocyte differentiation. GOC:go_curators regulation of RBC differentiation CL:0000232 regulation of red blood cell differentiation CL:0000232 Any process that stops, prevents, or reduces the frequency, rate or extent of erythrocyte differentiation. down regulation of erythrocyte differentiation down-regulation of erythrocyte differentiation downregulation of erythrocyte differentiation negative regulation of RBC differentiation negative regulation of red blood cell differentiation inhibition of erythrocyte differentiation biological_process GO:0045647 negative regulation of erythrocyte differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of erythrocyte differentiation. GOC:go_curators negative regulation of RBC differentiation CL:0000232 negative regulation of red blood cell differentiation CL:0000232 Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation. positive regulation of RBC differentiation positive regulation of red blood cell differentiation up regulation of erythrocyte differentiation up-regulation of erythrocyte differentiation upregulation of erythrocyte differentiation activation of erythrocyte differentiation stimulation of erythrocyte differentiation biological_process GO:0045648 positive regulation of erythrocyte differentiation Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation. GOC:go_curators positive regulation of RBC differentiation CL:0000232 positive regulation of red blood cell differentiation CL:0000232 Any process that modulates the frequency, rate or extent of macrophage differentiation. biological_process GO:0045649 regulation of macrophage differentiation Any process that modulates the frequency, rate or extent of macrophage differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of macrophage differentiation. down regulation of macrophage differentiation down-regulation of macrophage differentiation downregulation of macrophage differentiation inhibition of macrophage differentiation biological_process GO:0045650 negative regulation of macrophage differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of macrophage differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of macrophage differentiation. up regulation of macrophage differentiation up-regulation of macrophage differentiation upregulation of macrophage differentiation activation of macrophage differentiation stimulation of macrophage differentiation biological_process GO:0045651 positive regulation of macrophage differentiation Any process that activates or increases the frequency, rate or extent of macrophage differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of megakaryocyte differentiation. biological_process GO:0045652 regulation of megakaryocyte differentiation Any process that modulates the frequency, rate or extent of megakaryocyte differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation. down regulation of megakaryocyte differentiation down-regulation of megakaryocyte differentiation downregulation of megakaryocyte differentiation inhibition of megakaryocyte differentiation biological_process GO:0045653 negative regulation of megakaryocyte differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of megakaryocyte differentiation. up regulation of megakaryocyte differentiation up-regulation of megakaryocyte differentiation upregulation of megakaryocyte differentiation activation of megakaryocyte differentiation stimulation of megakaryocyte differentiation biological_process GO:0045654 positive regulation of megakaryocyte differentiation Any process that activates or increases the frequency, rate or extent of megakaryocyte differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of monocyte differentiation. biological_process GO:0045655 regulation of monocyte differentiation Any process that modulates the frequency, rate or extent of monocyte differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of monocyte differentiation. down regulation of monocyte differentiation down-regulation of monocyte differentiation downregulation of monocyte differentiation inhibition of monocyte differentiation biological_process GO:0045656 negative regulation of monocyte differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of monocyte differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of monocyte differentiation. up regulation of monocyte differentiation up-regulation of monocyte differentiation upregulation of monocyte differentiation activation of monocyte differentiation stimulation of monocyte differentiation biological_process GO:0045657 positive regulation of monocyte differentiation Any process that activates or increases the frequency, rate or extent of monocyte differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of neutrophil differentiation. biological_process GO:0045658 regulation of neutrophil differentiation Any process that modulates the frequency, rate or extent of neutrophil differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of neutrophil differentiation. down regulation of neutrophil differentiation down-regulation of neutrophil differentiation downregulation of neutrophil differentiation inhibition of neutrophil differentiation biological_process GO:0045659 negative regulation of neutrophil differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of neutrophil differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of neutrophil differentiation. up regulation of neutrophil differentiation up-regulation of neutrophil differentiation upregulation of neutrophil differentiation activation of neutrophil differentiation stimulation of neutrophil differentiation biological_process GO:0045660 positive regulation of neutrophil differentiation Any process that activates or increases the frequency, rate or extent of neutrophil differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of osteoclast differentiation. biological_process GO:0045670 regulation of osteoclast differentiation Any process that modulates the frequency, rate or extent of osteoclast differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of osteoclast differentiation. down regulation of osteoclast differentiation down-regulation of osteoclast differentiation downregulation of osteoclast differentiation inhibition of osteoclast differentiation biological_process GO:0045671 negative regulation of osteoclast differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of osteoclast differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of osteoclast differentiation. up regulation of osteoclast differentiation up-regulation of osteoclast differentiation upregulation of osteoclast differentiation activation of osteoclast differentiation stimulation of osteoclast differentiation biological_process GO:0045672 positive regulation of osteoclast differentiation Any process that activates or increases the frequency, rate or extent of osteoclast differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of spermatid nuclear differentiation. biological_process GO:0045700 regulation of spermatid nuclear differentiation Any process that modulates the frequency, rate or extent of spermatid nuclear differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of spermatid nuclear differentiation. down regulation of spermatid nuclear differentiation down-regulation of spermatid nuclear differentiation downregulation of spermatid nuclear differentiation inhibition of spermatid nuclear differentiation biological_process GO:0045701 negative regulation of spermatid nuclear differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of spermatid nuclear differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of spermatid nuclear differentiation. up regulation of spermatid nuclear differentiation up-regulation of spermatid nuclear differentiation upregulation of spermatid nuclear differentiation activation of spermatid nuclear differentiation stimulation of spermatid nuclear differentiation biological_process GO:0045702 positive regulation of spermatid nuclear differentiation Any process that activates or increases the frequency, rate or extent of spermatid nuclear differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the formation of a cilium. positive regulation of flagellum assembly up regulation of cilium assembly up-regulation of cilium assembly upregulation of cilium assembly activation of cilium assembly stimulation of cilium assembly biological_process positive regulation of flagellum biogenesis GO:0045724 positive regulation of cilium assembly Any process that activates or increases the frequency, rate or extent of the formation of a cilium. GOC:cilia GOC:go_curators positive regulation of flagellum biogenesis GOC:mah The phase of elevated metabolic activity, during which oxygen consumption increases, that occurs at fertilization. An enhanced uptake of oxygen leads to the production of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. Capacitation, a necessary prerequisite event to successful fertilization, can be induced by reactive oxygen species in vitro; hydrogen peroxide is used as an extracellular oxidant to cross-link the protective surface envelopes. metabolic burst at fertilization oxidative burst at fertilization biological_process GO:0045729 respiratory burst at fertilization The phase of elevated metabolic activity, during which oxygen consumption increases, that occurs at fertilization. An enhanced uptake of oxygen leads to the production of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. Capacitation, a necessary prerequisite event to successful fertilization, can be induced by reactive oxygen species in vitro; hydrogen peroxide is used as an extracellular oxidant to cross-link the protective surface envelopes. ISBN:0198506732 PMID:2537493 PMID:9013127 A phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. Wikipedia:Respiratory_burst metabolic burst oxidative burst biological_process GO:0045730 respiratory burst A phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. ISBN:0198506732 Any process that stops, prevents, or reduces the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. down regulation of action potential down-regulation of action potential downregulation of action potential inhibition of action potential biological_process GO:0045759 negative regulation of action potential Any process that stops, prevents, or reduces the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. GOC:go_curators Any process that activates or increases the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. up regulation of action potential up-regulation of action potential upregulation of action potential activation of action potential stimulation of action potential biological_process GO:0045760 positive regulation of action potential Any process that activates or increases the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. GOC:go_curators Any process that modulates the frequency, rate or extent of angiogenesis. biological_process GO:0045765 regulation of angiogenesis Any process that modulates the frequency, rate or extent of angiogenesis. GOC:go_curators Any process that activates or increases angiogenesis. up regulation of angiogenesis up-regulation of angiogenesis upregulation of angiogenesis activation of angiogenesis stimulation of angiogenesis biological_process GO:0045766 positive regulation of angiogenesis Any process that activates or increases angiogenesis. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of bone resorption. down regulation of bone resorption down-regulation of bone resorption downregulation of bone resorption inhibition of bone resorption biological_process GO:0045779 negative regulation of bone resorption Any process that stops, prevents, or reduces the frequency, rate or extent of bone resorption. GOC:go_curators Any process that activates or increases the frequency, rate or extent of bone resorption. up regulation of bone resorption up-regulation of bone resorption upregulation of bone resorption activation of bone resorption stimulation of bone resorption biological_process GO:0045780 positive regulation of bone resorption Any process that activates or increases the frequency, rate or extent of bone resorption. GOC:go_curators Any process that activates or increases the frequency, rate or extent of cell adhesion. up regulation of cell adhesion up-regulation of cell adhesion upregulation of cell adhesion activation of cell adhesion stimulation of cell adhesion biological_process GO:0045785 positive regulation of cell adhesion Any process that activates or increases the frequency, rate or extent of cell adhesion. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle. down regulation of progression through cell cycle down-regulation of progression through cell cycle downregulation of progression through cell cycle negative regulation of cell cycle progression negative regulation of progression through cell cycle inhibition of progression through cell cycle biological_process GO:0045786 negative regulation of cell cycle Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle. GOC:dph GOC:go_curators GOC:tb Any process that activates or increases the rate or extent of progression through the cell cycle. positive regulation of cell cycle progression positive regulation of progression through cell cycle up regulation of progression through cell cycle up-regulation of progression through cell cycle upregulation of progression through cell cycle activation of progression through cell cycle stimulation of progression through cell cycle biological_process GO:0045787 positive regulation of cell cycle Any process that activates or increases the rate or extent of progression through the cell cycle. GOC:go_curators positive regulation of progression through cell cycle GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis. down regulation of endocytosis down-regulation of endocytosis downregulation of endocytosis inhibition of endocytosis biological_process GO:0045806 negative regulation of endocytosis Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis. GOC:go_curators Any process that activates or increases the frequency, rate or extent of endocytosis. up regulation of endocytosis up-regulation of endocytosis upregulation of endocytosis activation of endocytosis stimulation of endocytosis biological_process GO:0045807 positive regulation of endocytosis Any process that activates or increases the frequency, rate or extent of endocytosis. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction. down regulation of heart contraction down-regulation of heart contraction downregulation of heart contraction inhibition of heart contraction biological_process negative regulation of cardiac contraction GO:0045822 negative regulation of heart contraction Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction. GOC:go_curators Any process that activates or increases the frequency, rate or extent of heart contraction. positive regulation of cardiac contraction up regulation of heart contraction up-regulation of heart contraction upregulation of heart contraction activation of heart contraction stimulation of heart contraction biological_process GO:0045823 positive regulation of heart contraction Any process that activates or increases the frequency, rate or extent of heart contraction. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the innate immune response. down regulation of innate immune response down-regulation of innate immune response downregulation of innate immune response inhibition of innate immune response biological_process GO:0045824 negative regulation of innate immune response Any process that stops, prevents, or reduces the frequency, rate or extent of the innate immune response. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of isotype switching. down regulation of isotype switching down-regulation of isotype switching downregulation of isotype switching negative regulation of class switch recombination negative regulation of class switching negative regulation of isotype switch recombination inhibition of isotype switching biological_process GO:0045829 negative regulation of isotype switching Any process that stops, prevents, or reduces the frequency, rate or extent of isotype switching. GOC:go_curators Any process that activates or increases the frequency, rate or extent of isotype switching. positive regulation of class switch recombination positive regulation of class switching positive regulation of isotype switch recombination up regulation of isotype switching up-regulation of isotype switching upregulation of isotype switching activation of isotype switching stimulation of isotype switching biological_process GO:0045830 positive regulation of isotype switching Any process that activates or increases the frequency, rate or extent of isotype switching. 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 meiosis. down regulation of meiosis down-regulation of meiosis downregulation of meiosis negative regulation of meiosis inhibition of meiosis biological_process GO:0045835 negative regulation of meiotic nuclear division Any process that stops, prevents, or reduces the frequency, rate or extent of meiosis. GOC:go_curators Any process that activates or increases the frequency, rate or extent of meiosis. positive regulation of meiosis up regulation of meiosis up-regulation of meiosis upregulation of meiosis activation of meiosis stimulation of meiosis biological_process GO:0045836 positive regulation of meiotic nuclear division Any process that activates or increases the frequency, rate or extent of meiosis. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of mitosis. Mitosis is the division of the eukaryotic cell nucleus to produce two daughter nuclei that, usually, contain the identical chromosome complement to their mother. down regulation of mitosis down-regulation of mitosis downregulation of mitosis negative regulation of mitosis inhibition of mitosis biological_process GO:0045839 negative regulation of mitotic nuclear division Any process that stops, prevents or reduces the rate or extent of mitosis. Mitosis is the division of the eukaryotic cell nucleus to produce two daughter nuclei that, usually, contain the identical chromosome complement to their mother. GOC:dph GOC:go_curators GOC:tb Any process that activates or increases the frequency, rate or extent of mitosis. positive regulation of mitosis up regulation of mitosis up-regulation of mitosis upregulation of mitosis activation of mitosis mitogenic activity stimulation of mitosis biological_process GO:0045840 positive regulation of mitotic nuclear division Any process that activates or increases the frequency, rate or extent of mitosis. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of DNA recombination. down regulation of DNA recombination down-regulation of DNA recombination downregulation of DNA recombination inhibition of DNA recombination biological_process GO:0045910 negative regulation of DNA recombination Any process that stops, prevents, or reduces the frequency, rate or extent of DNA recombination. GOC:go_curators Any process that activates or increases the frequency, rate or extent of DNA recombination. up regulation of DNA recombination up-regulation of DNA recombination upregulation of DNA recombination activation of DNA recombination stimulation of DNA recombination biological_process GO:0045911 positive regulation of DNA recombination Any process that activates or increases the frequency, rate or extent of DNA recombination. 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 process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle. down regulation of progression through mitotic cell cycle down-regulation of progression through mitotic cell cycle downregulation of progression through mitotic cell cycle negative regulation of mitotic cell cycle progression negative regulation of progression through mitotic cell cycle inhibition of progression through mitotic cell cycle biological_process GO:0045930 negative regulation of mitotic cell cycle Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle. GOC:dph GOC:go_curators GOC:tb negative regulation of progression through mitotic cell cycle GOC:dph GOC:tb Any process that activates or increases the rate or extent of progression through the mitotic cell cycle. positive regulation of mitotic cell cycle progression positive regulation of progression through mitotic cell cycle up regulation of progression through mitotic cell cycle up-regulation of progression through mitotic cell cycle upregulation of progression through mitotic cell cycle activation of progression through mitotic cell cycle stimulation of progression through mitotic cell cycle biological_process GO:0045931 positive regulation of mitotic cell cycle Any process that activates or increases the rate or extent of progression through the mitotic cell cycle. GOC:dph GOC:go_curators GOC:tb positive regulation of progression through mitotic cell cycle GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of muscle contraction. down regulation of muscle contraction down-regulation of muscle contraction downregulation of muscle contraction inhibition of muscle contraction biological_process GO:0045932 negative regulation of muscle contraction Any process that stops, prevents, or reduces the frequency, rate or extent of muscle contraction. GOC:go_curators Any process that activates or increases the frequency, rate or extent of muscle contraction. up regulation of muscle contraction up-regulation of muscle contraction upregulation of muscle contraction activation of muscle contraction stimulation of muscle contraction biological_process GO:0045933 positive regulation of muscle contraction Any process that activates or increases the frequency, rate or extent of muscle contraction. 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 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 rate of natural killer mediated cytotoxicity. down regulation of natural killer cell mediated cytotoxicity down-regulation of natural killer cell mediated cytotoxicity downregulation of natural killer cell mediated cytotoxicity negative regulation of NK cell mediated cell death negative regulation of NK cell mediated cell killing negative regulation of NK cell mediated cytotoxicity negative regulation of natural killer cell mediated cell death negative regulation of natural killer cell mediated cell killing inhibition of natural killer cell mediated cytotoxicity biological_process negative regulation of NK cell mediated cytolysis negative regulation of natural killer cell mediated cytolysis GO:0045953 negative regulation of natural killer cell mediated cytotoxicity Any process that stops, prevents, or reduces the rate of natural killer mediated cytotoxicity. GOC:add ISBN:0781735149 Any process that activates or increases the frequency, rate or extent of natural killer cell mediated cytotoxicity. positive regulation of NK cell mediated cell death positive regulation of NK cell mediated cell killing positive regulation of NK cell mediated cytotoxicity positive regulation of natural killer cell mediated cell death positive regulation of natural killer cell mediated cell killing up regulation of natural killer cell mediated cytotoxicity up-regulation of natural killer cell mediated cytotoxicity upregulation of natural killer cell mediated cytotoxicity activation of natural killer cell mediated cytotoxicity stimulation of natural killer cell mediated cytotoxicity biological_process positive regulation of NK cell mediated cytolysis positive regulation of natural killer cell mediated cytolysis GO:0045954 positive regulation of natural killer cell mediated cytotoxicity Any process that activates or increases the frequency, rate or extent of natural killer cell mediated cytotoxicity. GOC:add ISBN:0781735149 Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of juvenile hormone. down regulation of juvenile hormone secretion down-regulation of juvenile hormone secretion downregulation of juvenile hormone secretion inhibition of juvenile hormone secretion biological_process GO:0045972 negative regulation of juvenile hormone secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of juvenile hormone. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the regulated release of juvenile hormone. up regulation of juvenile hormone secretion up-regulation of juvenile hormone secretion upregulation of juvenile hormone secretion activation of juvenile hormone secretion stimulation of juvenile hormone secretion biological_process GO:0045973 positive regulation of juvenile hormone secretion Any process that activates or increases the frequency, rate or extent of the regulated release of juvenile hormone. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle contraction. down regulation of smooth muscle contraction down-regulation of smooth muscle contraction downregulation of smooth muscle contraction inhibition of smooth muscle contraction biological_process smooth muscle relaxation GO:0045986 negative regulation of smooth muscle contraction Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle contraction. GOC:go_curators Any process that activates or increases the frequency, rate or extent of smooth muscle contraction. up regulation of smooth muscle contraction up-regulation of smooth muscle contraction upregulation of smooth muscle contraction activation of smooth muscle contraction stimulation of smooth muscle contraction biological_process GO:0045987 positive regulation of smooth muscle contraction Any process that activates or increases the frequency, rate or extent of smooth muscle contraction. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of ecdysteroid. down regulation of ecdysteroid secretion down-regulation of ecdysteroid secretion downregulation of ecdysteroid secretion inhibition of ecdysteroid secretion biological_process GO:0045999 negative regulation of ecdysteroid secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of ecdysteroid. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the regulated release of ecdysteroid. up regulation of ecdysteroid secretion up-regulation of ecdysteroid secretion upregulation of ecdysteroid secretion activation of ecdysteroid secretion stimulation of ecdysteroid secretion biological_process GO:0046000 positive regulation of ecdysteroid secretion Any process that activates or increases the frequency, rate or extent of the regulated release of ecdysteroid. GOC:go_curators The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups. carboxylic acid anabolism carboxylic acid biosynthesis carboxylic acid formation carboxylic acid synthesis biological_process GO:0046394 carboxylic acid biosynthetic process The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups. ISBN:0198506732 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 The process whose specific outcome is the progression of the primary female sexual characteristics over time, from their formation to the mature structure. The primary female sexual characteristics are the ovaries, and they develop in response to sex hormone secretion. biological_process GO:0046545 development of primary female sexual characteristics The process whose specific outcome is the progression of the primary female sexual characteristics over time, from their formation to the mature structure. The primary female sexual characteristics are the ovaries, and they develop in response to sex hormone secretion. GOC:ai Binding to a sphingolipid, a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid). molecular_function GO:0046625 sphingolipid binding Binding to a sphingolipid, a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid). ISBN:0198506732 The change in morphology and behavior of a gamma-delta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. gamma-delta T lymphocyte activation gamma-delta T-cell activation gamma-delta T-lymphocyte activation biological_process GO:0046629 gamma-delta T cell activation The change in morphology and behavior of a gamma-delta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. GOC:add The change in morphology and behavior of an alpha-beta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. alpha-beta T lymphocyte activation alpha-beta T-cell activation alpha-beta T-lymphocyte activation biological_process GO:0046631 alpha-beta T cell activation The change in morphology and behavior of an alpha-beta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. GOC:add The process in which a precursor cell type acquires the specialized features of an alpha-beta T cell. An alpha-beta T cell is a T cell that expresses an alpha-beta T cell receptor complex. alpha-beta T lymphocyte differentiation alpha-beta T-cell differentiation alpha-beta T-lymphocyte differentiation biological_process alpha-beta T cell development GO:0046632 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. alpha-beta T cell differentiation The process in which a precursor cell type acquires the specialized features of an alpha-beta T cell. An alpha-beta T cell is a T cell that expresses an alpha-beta T cell receptor complex. CL:0000789 GOC:ai alpha-beta T cell development GOC:add Any process that modulates the frequency, rate or extent of alpha-beta T cell activation. regulation of alpha-beta T lymphocyte activation regulation of alpha-beta T-cell activation regulation of alpha-beta T-lymphocyte activation biological_process GO:0046634 regulation of alpha-beta T cell activation Any process that modulates the frequency, rate or extent of alpha-beta T cell activation. GOC:ai Any process that activates or increases the frequency, rate or extent of alpha-beta T cell activation. positive regulation of alpha-beta T lymphocyte activation positive regulation of alpha-beta T-cell activation positive regulation of alpha-beta T-lymphocyte activation up regulation of alpha-beta T cell activation up-regulation of alpha-beta T cell activation upregulation of alpha-beta T cell activation activation of alpha-beta T cell activation stimulation of alpha-beta T cell activation biological_process GO:0046635 positive regulation of alpha-beta T cell activation Any process that activates or increases the frequency, rate or extent of alpha-beta T cell activation. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of alpha-beta T cell activation. down regulation of alpha-beta T cell activation down-regulation of alpha-beta T cell activation downregulation of alpha-beta T cell activation negative regulation of alpha-beta T lymphocyte activation negative regulation of alpha-beta T-cell activation negative regulation of alpha-beta T-lymphocyte activation inhibition of alpha-beta T cell activation biological_process GO:0046636 negative regulation of alpha-beta T cell activation Any process that stops, prevents, or reduces the frequency, rate or extent of alpha-beta T cell activation. GOC:ai Any process that modulates the frequency, rate or extent of alpha-beta T cell differentiation. regulation of alpha-beta T lymphocyte differentiation regulation of alpha-beta T-cell differentiation regulation of alpha-beta T-lymphocyte differentiation biological_process regulation of alpha-beta T cell development GO:0046637 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. regulation of alpha-beta T cell differentiation Any process that modulates the frequency, rate or extent of alpha-beta T cell differentiation. GOC:ai regulation of alpha-beta T cell development GOC:add Any process that activates or increases the frequency, rate or extent of alpha-beta T cell differentiation. positive regulation of alpha-beta T lymphocyte differentiation positive regulation of alpha-beta T-cell differentiation positive regulation of alpha-beta T-lymphocyte differentiation up regulation of alpha-beta T cell differentiation up-regulation of alpha-beta T cell differentiation upregulation of alpha-beta T cell differentiation activation of alpha-beta T cell differentiation stimulation of alpha-beta T cell differentiation biological_process positive regulation of alpha-beta T cell development GO:0046638 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. positive regulation of alpha-beta T cell differentiation Any process that activates or increases the frequency, rate or extent of alpha-beta T cell differentiation. GOC:ai positive regulation of alpha-beta T cell development GOC:add Any process that stops, prevents, or reduces the frequency, rate or extent of alpha-beta T cell differentiation. down regulation of alpha-beta T cell differentiation down-regulation of alpha-beta T cell differentiation downregulation of alpha-beta T cell differentiation negative regulation of alpha-beta T lymphocyte differentiation negative regulation of alpha-beta T-cell differentiation negative regulation of alpha-beta T-lymphocyte differentiation inhibition of alpha-beta T cell differentiation biological_process negative regulation of alpha-beta T cell development GO:0046639 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. negative regulation of alpha-beta T cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of alpha-beta T cell differentiation. GOC:ai negative regulation of alpha-beta T cell development GOC:add Any process that modulates the frequency, rate or extent of gamma-delta T cell activation. regulation of gamma-delta T lymphocyte activation regulation of gamma-delta T-cell activation regulation of gamma-delta T-lymphocyte activation biological_process GO:0046643 regulation of gamma-delta T cell activation Any process that modulates the frequency, rate or extent of gamma-delta T cell activation. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of gamma-delta T cell activation. down regulation of gamma-delta T cell activation down-regulation of gamma-delta T cell activation downregulation of gamma-delta T cell activation negative regulation of gamma-delta T lymphocyte activation negative regulation of gamma-delta T-cell activation negative regulation of gamma-delta T-lymphocyte activation inhibition of gamma-delta T cell activation biological_process GO:0046644 negative regulation of gamma-delta T cell activation Any process that stops, prevents, or reduces the frequency, rate or extent of gamma-delta T cell activation. GOC:ai Any process that activates or increases the frequency, rate or extent of gamma-delta T cell activation. positive regulation of gamma-delta T lymphocyte activation positive regulation of gamma-delta T-cell activation positive regulation of gamma-delta T-lymphocyte activation up regulation of gamma-delta T cell activation up-regulation of gamma-delta T cell activation upregulation of gamma-delta T cell activation activation of gamma-delta T cell activation stimulation of gamma-delta T cell activation biological_process GO:0046645 positive regulation of gamma-delta T cell activation Any process that activates or increases the frequency, rate or extent of gamma-delta T cell activation. GOC:ai A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor. biological_process GO:0046649 lymphocyte activation A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor. GOC:mgi_curators ISBN:0781735149 The expansion of a lymphocyte population by cell division. biological_process GO:0046651 lymphocyte proliferation The expansion of a lymphocyte population by cell division. GOC:ai The establishment of the sex of a female organism by physical differentiation. biological_process GO:0046660 female sex differentiation The establishment of the sex of a female organism by physical differentiation. GOC:bf Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of insulin. down regulation of insulin secretion down-regulation of insulin secretion downregulation of insulin secretion inhibition of insulin secretion biological_process GO:0046676 negative regulation of insulin secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of insulin. GOC:ai The controlled release of acid by a cell or a tissue. biological_process GO:0046717 acid secretion The controlled release of acid by a cell or a tissue. GOC:ai The continuous turnover of bone matrix and mineral that involves first, an increase in resorption (osteoclastic activity) and later, reactive bone formation (osteoblastic activity). The process of bone remodeling takes place in the adult skeleton at discrete foci. The process ensures the mechanical integrity of the skeleton throughout life and plays an important role in calcium homeostasis. An imbalance in the regulation of bone resorption and bone formation results in many of the metabolic bone diseases, such as osteoporosis. Wikipedia:Bone_remodeling bone remodelling biological_process GO:0046849 bone remodeling The continuous turnover of bone matrix and mineral that involves first, an increase in resorption (osteoclastic activity) and later, reactive bone formation (osteoblastic activity). The process of bone remodeling takes place in the adult skeleton at discrete foci. The process ensures the mechanical integrity of the skeleton throughout life and plays an important role in calcium homeostasis. An imbalance in the regulation of bone resorption and bone formation results in many of the metabolic bone diseases, such as osteoporosis. GOC:curators Any process that modulates the frequency, rate or extent of bone remodeling, the processes of bone formation and resorption that combine to maintain skeletal integrity. biological_process GO:0046850 regulation of bone remodeling Any process that modulates the frequency, rate or extent of bone remodeling, the processes of bone formation and resorption that combine to maintain skeletal integrity. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of bone remodeling. down regulation of bone remodeling down-regulation of bone remodeling downregulation of bone remodeling inhibition of bone remodeling biological_process GO:0046851 negative regulation of bone remodeling Any process that stops, prevents, or reduces the frequency, rate or extent of bone remodeling. GOC:ai Any process that activates or increases the frequency, rate or extent of bone remodeling. up regulation of bone remodeling up-regulation of bone remodeling upregulation of bone remodeling activation of bone remodeling stimulation of bone remodeling biological_process GO:0046852 positive regulation of bone remodeling Any process that activates or increases the frequency, rate or extent of bone remodeling. GOC:ai The directed movement of isoprenoids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Isoprenoids comprise a group of compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues. biological_process GO:0046864 isoprenoid transport The directed movement of isoprenoids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Isoprenoids comprise a group of compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues. GOC:ai The directed movement of terpenoids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Terpenoids are a class of compounds characterized by an isoprenoid chemical structure and include derivatives with various functional groups. biological_process GO:0046865 terpenoid transport The directed movement of terpenoids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Terpenoids are a class of compounds characterized by an isoprenoid chemical structure and include derivatives with various functional groups. GOC:ai 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 modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones. regulation of hormone anabolism regulation of hormone biosynthesis regulation of hormone formation regulation of hormone synthesis biological_process GO:0046885 regulation of hormone biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones. positive regulation of hormone anabolism positive regulation of hormone biosynthesis positive regulation of hormone formation positive regulation of hormone synthesis up regulation of hormone biosynthetic process up-regulation of hormone biosynthetic process upregulation of hormone biosynthetic process activation of hormone biosynthetic process stimulation of hormone biosynthetic process biological_process GO:0046886 positive regulation of hormone biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones. 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 Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. positive regulation of lipid anabolism positive regulation of lipid biosynthesis positive regulation of lipid formation positive regulation of lipid synthesis positive regulation of lipogenesis up regulation of lipid biosynthetic process up-regulation of lipid biosynthetic process upregulation of lipid biosynthetic process activation of lipid biosynthetic process stimulation of lipid biosynthetic process biological_process GO:0046889 positive regulation of lipid biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. GOC:ai positive regulation of lipogenesis GOC:sl Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. regulation of lipid anabolism regulation of lipid biosynthesis regulation of lipid formation regulation of lipid synthesis regulation of lipogenesis biological_process GO:0046890 regulation of lipid biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. GOC:ai regulation of lipogenesis GOC:sl 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 Any process that modulates the frequency, rate or extent of the regulated release of a neurotransmitter from a cell. biological_process GO:0046928 regulation of neurotransmitter secretion Any process that modulates the frequency, rate or extent of the regulated release of a neurotransmitter from a cell. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a neurotransmitter. down regulation of neurotransmitter secretion down-regulation of neurotransmitter secretion downregulation of neurotransmitter secretion conotoxin activity inhibition of neurotransmitter secretion biological_process GO:0046929 negative regulation of neurotransmitter secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a neurotransmitter. GOC:ai The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-). biological_process GO:0046942 carboxylic acid transport The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-). GOC:ai The process in which an antigen-presenting cell expresses peptide antigen in association with an MHC protein complex on its cell surface, including proteolysis and transport steps for the peptide antigen both prior to and following assembly with the MHC protein complex. The peptide antigen is typically, but not always, processed from an endogenous or exogenous protein. antigen presentation, peptide antigen peptide antigen processing and presentation biological_process GO:0048002 antigen processing and presentation of peptide antigen The process in which an antigen-presenting cell expresses peptide antigen in association with an MHC protein complex on its cell surface, including proteolysis and transport steps for the peptide antigen both prior to and following assembly with the MHC protein complex. The peptide antigen is typically, but not always, processed from an endogenous or exogenous protein. GOC:add ISBN:0781735149 PMID:15771591 The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line. somatic stem cell renewal biological_process GO:0048103 somatic stem cell division The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line. GOC:jid ISBN:0582227089 The meiotic divisions undergone by the primary and secondary spermatocytes to produce haploid spermatids. spermatocyte cell division biological_process GO:0048137 spermatocyte division The meiotic divisions undergone by the primary and secondary spermatocytes to produce haploid spermatids. GOC:jid GOC:pr ISBN:0879694238 The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles. biological_process Golgi-derived vesicle transport GO:0048193 Golgi vesicle transport The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles. GOC:jid ISBN:0716731363 PMID:10219233 The process in which vesicles are directed to specific destination membranes during transport to, from or within the Golgi apparatus; mediated by the addition of specific coat proteins, including COPI and COPII proteins and clathrin, to the membrane during vesicle formation. Golgi vesicle targeting dictyosome vesicle targeting vesicle targeting, to, from or within dictyosome biological_process GO:0048199 vesicle targeting, to, from or within Golgi The process in which vesicles are directed to specific destination membranes during transport to, from or within the Golgi apparatus; mediated by the addition of specific coat proteins, including COPI and COPII proteins and clathrin, to the membrane during vesicle formation. GOC:jid GOC:mah ISBN:0716731363 PMID:10219233 Any process that modulates the frequency, rate, or destination of vesicle-mediated transport to, from or within the Golgi apparatus. regulation of Golgi vesicle targeting biological_process GO:0048209 regulation of vesicle targeting, to, from or within Golgi Any process that modulates the frequency, rate, or destination of vesicle-mediated transport to, from or within the Golgi apparatus. GOC:jid GOC:mah ISBN:0716731363 PMID:10219233 Generation of the male gamete; specialised haploid cells produced by meiosis and along with a female gamete takes part in sexual reproduction. biological_process GO:0048232 male gamete generation Generation of the male gamete; specialised haploid cells produced by meiosis and along with a female gamete takes part in sexual reproduction. GOC:dph GOC:jid The directed movement of epinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. adrenaline transport biological_process GO:0048241 epinephrine transport The directed movement of epinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:jid The regulated release of epinephrine by a cell. Epinephrine is a catecholamine hormone secreted by the adrenal medulla and a neurotransmitter, released by certain neurons and active in the central nervous system. adrenaline secretion biological_process GO:0048242 epinephrine secretion The regulated release of epinephrine by a cell. Epinephrine is a catecholamine hormone secreted by the adrenal medulla and a neurotransmitter, released by certain neurons and active in the central nervous system. GOC:ef GOC:jid The regulated release of norepinephrine by a cell. Norepinephrine is a catecholamine and it acts as a hormone and as a neurotransmitter of most of the sympathetic nervous system. noradrenaline secretion biological_process GO:0048243 norepinephrine secretion The regulated release of norepinephrine by a cell. Norepinephrine is a catecholamine and it acts as a hormone and as a neurotransmitter of most of the sympathetic nervous system. GOC:ef GOC:jid The creation of two or more organelles by division of one organelle. biological_process GO:0048285 organelle fission The creation of two or more organelles by division of one organelle. GOC:jid The switching of activated B cells from IgM biosynthesis to IgE biosynthesis, accomplished through a recombination process involving an intrachromosomal deletion between switch regions that reside 5' of the IgM and IgE constant region gene segments in the immunoglobulin heavy chain locus. class switch recombination to IgE isotypes class switching to IgE isotypes isotype switch recombination to IgE isotypes biological_process GO:0048289 isotype switching to IgE isotypes The switching of activated B cells from IgM biosynthesis to IgE biosynthesis, accomplished through a recombination process involving an intrachromosomal deletion between switch regions that reside 5' of the IgM and IgE constant region gene segments in the immunoglobulin heavy chain locus. ISBN:0781735149 PMID:12370374 PMID:2113175 PMID:9186655 Any process that modulates the frequency, rate or extent of isotype switching to IgE isotypes. regulation of class switch recombination to IgE isotypes regulation of class switching to IgE isotypes regulation of isotype switch recombination to IgE isotypes biological_process GO:0048293 regulation of isotype switching to IgE isotypes Any process that modulates the frequency, rate or extent of isotype switching to IgE isotypes. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of isotype switching to IgE isotypes. down regulation of isotype switching to IgE isotypes down-regulation of isotype switching to IgE isotypes downregulation of isotype switching to IgE isotypes negative regulation of class switch recombination to IgE isotypes negative regulation of class switching to IgE isotypes negative regulation of isotype switch recombination to IgE isotypes inhibition of isotype switching to IgE isotypes biological_process GO:0048294 negative regulation of isotype switching to IgE isotypes Any process that stops, prevents, or reduces the frequency, rate or extent of isotype switching to IgE isotypes. GOC:jid Any process that activates or increases the frequency, rate or extent of isotype switching to IgE isotypes. positive regulation of class switch recombination to IgE isotypes positive regulation of class switching to IgE isotypes positive regulation of isotype switch recombination to IgE isotypes up regulation of isotype switching to IgE isotypes up-regulation of isotype switching to IgE isotypes upregulation of isotype switching to IgE isotypes activation of isotype switching to IgE isotypes stimulation of isotype switching to IgE isotypes biological_process GO:0048295 positive regulation of isotype switching to IgE isotypes Any process that activates or increases the frequency, rate or extent of isotype switching to IgE isotypes. GOC:jid The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process terminal differentiation GO:0048468 cell development The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:go_curators terminal differentiation GOC:dph GOC:tb The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster. GO:0009993 GO:0048157 Wikipedia:Oogenesis ovum development biological_process GO:0048477 oogenesis The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster. GOC:kmv GOC:mtg_sensu GOC:pr ovum development Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism. biological_process rhythm GO:0048511 rhythmic process Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism. GOC:jid 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 The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood. biological_process GO:0048514 blood vessel morphogenesis The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood. GOC:jid The process whose specific outcome is the progression of a spermatid over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. spermatid cell differentiation biological_process GO:0048515 spermatid differentiation The process whose specific outcome is the progression of a spermatid over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. 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 The process whose specific outcome is the progression of any organ involved in hematopoiesis (also known as hemopoiesis) or lymphoid cell activation over time, from its formation to the mature structure. Such development includes differentiation of resident cell types (stromal cells) and of migratory cell types dependent on the unique microenvironment afforded by the organ for their proper differentiation. haematopoietic or lymphoid organ development haemopoietic or lymphoid organ development hemopoietic or lymphoid organ development biological_process GO:0048534 hematopoietic or lymphoid organ development The process whose specific outcome is the progression of any organ involved in hematopoiesis (also known as hemopoiesis) or lymphoid cell activation over time, from its formation to the mature structure. Such development includes differentiation of resident cell types (stromal cells) and of migratory cell types dependent on the unique microenvironment afforded by the organ for their proper differentiation. GOC:add GOC:rl ISBN:0781735149 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 The reproductive developmental process whose specific outcome is the progression of somatic structures that will be used in the process of creating new individuals from one or more parents, from their formation to the mature structures. biological_process GO:0048608 reproductive structure development The reproductive developmental process whose specific outcome is the progression of somatic structures that will be used in the process of creating new individuals from one or more parents, from their formation to the mature structures. GOC:dph GOC:isa_complete GOC:jid The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs. organismal reproductive process reproductive process in a multicellular organism biological_process GO:0048609 multicellular organismal reproductive process The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs. GOC:dph GOC:jid GOC:tb 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 developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. 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. formation of an anatomical structure involved in morphogenesis biological_process GO:0048646 Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense. anatomical structure formation involved in morphogenesis The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. 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. GOC:dph GOC:jid GOC:tb formation of an anatomical structure involved in 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 A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes. cellular_component GO:0048770 pigment granule A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes. GOC:jid GOC:mh The reorganization or renovation of existing tissues. This process can either change the characteristics of a tissue such as in blood vessel remodeling, or result in the dynamic equilibrium of a tissue such as in bone remodeling. biological_process GO:0048771 tissue remodeling The reorganization or renovation of existing tissues. This process can either change the characteristics of a tissue such as in blood vessel remodeling, or result in the dynamic equilibrium of a tissue such as in bone remodeling. GOC:ebc 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 A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. biological_process GO:0048869 cellular developmental process A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. GOC:isa_complete Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. cell locomotion movement of a cell biological_process cell movement GO:0048870 cell motility Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. GOC:dgh GOC:dph GOC:isa_complete GOC:mlg 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 the steady-state number of cells within a population of cells. cell population homeostasis homeostasis of cell number biological_process GO:0048872 homeostasis of number of cells Any biological process involved in the maintenance of the steady-state number of cells within a population of cells. GOC:isa_complete homeostasis of cell number GOC:dph Any biological process involved in the maintenance of the steady-state number of cells within a population of cells in a tissue. biological_process GO:0048873 homeostasis of number of cells within a tissue Any biological process involved in the maintenance of the steady-state number of cells within a population of cells in a tissue. GOC:isa_complete Any process involved in the maintenance of the internal steady state of the amount of a chemical at the level of the tissue. biological_process GO:0048875 chemical homeostasis within a tissue Any process involved in the maintenance of the internal steady state of the amount of a chemical at the level of the tissue. 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 The regulated release of catecholamines by a cell. The catecholamines are a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. biological_process GO:0050432 catecholamine secretion The regulated release of catecholamines by a cell. The catecholamines are a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. GOC:ai GOC:ef Any process that modulates the frequency, rate or extent of the regulated release of catecholamines. biological_process GO:0050433 regulation of catecholamine secretion Any process that modulates the frequency, rate or extent of the regulated release of catecholamines. GOC:ai Any process that modulates the frequency, rate or extent of lymphocyte proliferation. biological_process GO:0050670 regulation of lymphocyte proliferation Any process that modulates the frequency, rate or extent of lymphocyte proliferation. GOC:ai Any process that activates or increases the rate or extent of lymphocyte proliferation. up regulation of lymphocyte proliferation up-regulation of lymphocyte proliferation upregulation of lymphocyte proliferation activation of lymphocyte proliferation stimulation of lymphocyte proliferation biological_process GO:0050671 positive regulation of lymphocyte proliferation Any process that activates or increases the rate or extent of lymphocyte proliferation. GOC:ai Any process that stops, prevents or reduces the rate or extent of lymphocyte proliferation. down regulation of lymphocyte proliferation down-regulation of lymphocyte proliferation downregulation of lymphocyte proliferation inhibition of lymphocyte proliferation biological_process GO:0050672 negative regulation of lymphocyte proliferation Any process that stops, prevents or reduces the rate or extent of lymphocyte proliferation. GOC:ai The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population. Epithelial cells make up the epithelium, the covering of internal and external surfaces of the body, including the lining of vessels and other small cavities. It consists of cells joined by small amounts of cementing substances. biological_process GO:0050673 epithelial cell proliferation The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population. Epithelial cells make up the epithelium, the covering of internal and external surfaces of the body, including the lining of vessels and other small cavities. It consists of cells joined by small amounts of cementing substances. ISBN:0721662544 Any process that modulates the frequency, rate or extent of epithelial cell proliferation. biological_process GO:0050678 regulation of epithelial cell proliferation Any process that modulates the frequency, rate or extent of epithelial cell proliferation. GOC:ai Any process that activates or increases the rate or extent of epithelial cell proliferation. up regulation of epithelial cell proliferation up-regulation of epithelial cell proliferation upregulation of epithelial cell proliferation activation of epithelial cell proliferation stimulation of epithelial cell proliferation biological_process GO:0050679 positive regulation of epithelial cell proliferation Any process that activates or increases the rate or extent of epithelial cell proliferation. GOC:ai Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation. down regulation of epithelial cell proliferation down-regulation of epithelial cell proliferation downregulation of epithelial cell proliferation inhibition of epithelial cell proliferation biological_process GO:0050680 negative regulation of epithelial cell proliferation Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation. GOC:ai 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 phagocytosis, the process in which phagocytes engulf external particulate material. biological_process GO:0050764 regulation of phagocytosis Any process that modulates the frequency, rate or extent of phagocytosis, the process in which phagocytes engulf external particulate material. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of phagocytosis. down regulation of phagocytosis down-regulation of phagocytosis downregulation of phagocytosis inhibition of phagocytosis biological_process GO:0050765 negative regulation of phagocytosis Any process that stops, prevents, or reduces the frequency, rate or extent of phagocytosis. GOC:ai Any process that activates or increases the frequency, rate or extent of phagocytosis. up regulation of phagocytosis up-regulation of phagocytosis upregulation of phagocytosis activation of phagocytosis stimulation of phagocytosis biological_process GO:0050766 positive regulation of phagocytosis Any process that activates or increases the frequency, rate or extent of phagocytosis. GOC:ai Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. biological_process GO:0050776 regulation of immune response Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. down regulation of immune response down-regulation of immune response downregulation of immune response inhibition of immune response biological_process GO:0050777 negative regulation of immune response Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. GOC:ai Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. up regulation of immune response up-regulation of immune response upregulation of immune response stimulation of immune response biological_process GO:0050778 positive regulation of immune response Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. 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 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 that modulates the frequency, rate or extent of the regulated release of insulin. biological_process GO:0050796 regulation of insulin secretion Any process that modulates the frequency, rate or extent of the regulated release of insulin. GOC:ai Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission. modulation of synaptic transmission regulation of chemical synaptic transmission regulation of synaptic transmission biological_process GO:0050804 modulation of chemical synaptic transmission Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. down regulation of synaptic transmission down-regulation of synaptic transmission downregulation of synaptic transmission inhibition of synaptic transmission biological_process GO:0050805 negative regulation of synaptic transmission Any process that stops, prevents, or reduces the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. GOC:ai Any process that activates or increases the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. up regulation of synaptic transmission up-regulation of synaptic transmission upregulation of synaptic transmission activation of synaptic transmission stimulation of synaptic transmission biological_process GO:0050806 positive regulation of synaptic transmission Any process that activates or increases the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. regulation of steroid anabolism regulation of steroid biosynthesis regulation of steroid formation regulation of steroid synthesis regulation of steroidogenesis biological_process GO:0050810 regulation of steroid biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. GOC:ai The process in which a fluid solution, or part of it, changes into a solid or semisolid mass. clotting biological_process GO:0050817 coagulation The process in which a fluid solution, or part of it, changes into a solid or semisolid mass. ISBN:0198506732 Any process that modulates the frequency, rate or extent of coagulation, the process in which a fluid solution, or part of it, changes into a solid or semisolid mass. regulation of clotting biological_process GO:0050818 regulation of coagulation Any process that modulates the frequency, rate or extent of coagulation, the process in which a fluid solution, or part of it, changes into a solid or semisolid mass. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of coagulation. down regulation of coagulation down-regulation of coagulation downregulation of coagulation negative regulation of clotting inhibition of coagulation biological_process anticoagulant activity GO:0050819 negative regulation of coagulation Any process that stops, prevents, or reduces the frequency, rate or extent of coagulation. GOC:ai Any process that activates or increases the frequency, rate or extent of coagulation. positive regulation of clotting up regulation of coagulation up-regulation of coagulation upregulation of coagulation activation of coagulation stimulation of coagulation biological_process GO:0050820 positive regulation of coagulation Any process that activates or increases the frequency, rate or extent of coagulation. GOC:ai Binding to a cell adhesion molecule. CAM binding molecular_function adhesive extracellular matrix constituent cell adhesion molecule activity cell adhesion receptor activity GO:0050839 cell adhesion molecule binding Binding to a cell adhesion molecule. GOC:ai Any process that modulates the frequency, rate or extent of T cell activation. regulation of T lymphocyte activation regulation of T-cell activation regulation of T-lymphocyte activation biological_process GO:0050863 regulation of T cell activation Any process that modulates the frequency, rate or extent of T cell activation. GOC:ai Any process that modulates the frequency, rate or extent of B cell activation. regulation of B lymphocyte activation regulation of B-cell activation regulation of B-lymphocyte activation biological_process GO:0050864 regulation of B cell activation Any process that modulates the frequency, rate or extent of B cell activation. GOC:ai Any process that modulates the frequency, rate or extent of cell activation, the change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand. biological_process GO:0050865 regulation of cell activation Any process that modulates the frequency, rate or extent of cell activation, the change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of cell activation. down regulation of cell activation down-regulation of cell activation downregulation of cell activation inhibition of cell activation biological_process GO:0050866 negative regulation of cell activation Any process that stops, prevents, or reduces the frequency, rate or extent of cell activation. GOC:ai Any process that activates or increases the frequency, rate or extent of activation. up regulation of cell activation up-regulation of cell activation upregulation of cell activation activation of cell activation stimulation of cell activation biological_process GO:0050867 positive regulation of cell activation Any process that activates or increases the frequency, rate or extent of activation. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of T cell activation. down regulation of T cell activation down-regulation of T cell activation downregulation of T cell activation negative regulation of T lymphocyte activation negative regulation of T-cell activation negative regulation of T-lymphocyte activation inhibition of T cell activation biological_process GO:0050868 negative regulation of T cell activation Any process that stops, prevents, or reduces the frequency, rate or extent of T cell activation. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of B cell activation. down regulation of B cell activation down-regulation of B cell activation downregulation of B cell activation negative regulation of B lymphocyte activation negative regulation of B-cell activation negative regulation of B-lymphocyte activation inhibition of B cell activation biological_process GO:0050869 negative regulation of B cell activation Any process that stops, prevents, or reduces the frequency, rate or extent of B cell activation. GOC:ai Any process that activates or increases the frequency, rate or extent of T cell activation. positive regulation of T lymphocyte activation positive regulation of T-cell activation positive regulation of T-lymphocyte activation up regulation of T cell activation up-regulation of T cell activation upregulation of T cell activation activation of T cell activation stimulation of T cell activation biological_process GO:0050870 positive regulation of T cell activation Any process that activates or increases the frequency, rate or extent of T cell activation. GOC:ai Any process that activates or increases the frequency, rate or extent of B cell activation. positive regulation of B lymphocyte activation positive regulation of B-cell activation positive regulation of B-lymphocyte activation up regulation of B cell activation up-regulation of B cell activation upregulation of B cell activation activation of B cell activation stimulation of B cell activation biological_process GO:0050871 positive regulation of B cell activation Any process that activates or increases the frequency, rate or extent of B cell activation. GOC:ai A organ system process carried out by any of the organs or tissues of neurological system. https://github.com/geneontology/go-ontology/issues/13824 neurological system process neurophysiological process biological_process pan-neural process GO:0050877 nervous system process A organ system process carried out by any of the organs or tissues of neurological system. GOC:ai GOC:mtg_cardio 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 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 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 The movement of a leukocyte within or between different tissues and organs of the body. immune cell migration immune cell trafficking leucocyte migration leucocyte trafficking leukocyte trafficking biological_process GO:0050900 leukocyte migration The movement of a leukocyte within or between different tissues and organs of the body. GOC:add ISBN:0781735149 PMID:14680625 PMID:14708592 PMID:7507411 PMID:8600538 The series of events involved in sensory perception in which a sensory stimulus is received and converted into a molecular signal. Wikipedia:Transduction_(physiology) sensory detection of stimulus sensory perception, sensory transduction of stimulus sensory perception, stimulus detection sensory transduction biological_process GO:0050906 detection of stimulus involved in sensory perception The series of events involved in sensory perception in which a sensory stimulus is received and converted into a molecular signal. GOC:ai GOC:dos GOC:dph The series of events in which a chemical stimulus is received and converted into a molecular signal as part of sensory perception. sensory detection of chemical stimulus sensory detection of chemical stimulus during sensory perception sensory perception, sensory detection of chemical stimulus sensory perception, sensory transduction of chemical stimulus sensory transduction of chemical stimulus sensory transduction of chemical stimulus during sensory perception biological_process GO:0050907 detection of chemical stimulus involved in sensory perception The series of events in which a chemical stimulus is received and converted into a molecular signal as part of sensory perception. GOC:ai GOC:dos The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal. sensory detection of light during visual perception sensory detection of light stimulus during visual perception sensory transduction of light during visual perception sensory transduction of light stimulus during visual perception visual perception, detection of light stimulus visual perception, sensory transduction during perception of light visual perception, sensory transduction of light stimulus biological_process GO:0050908 detection of light stimulus involved in visual perception The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal. GOC:ai GOC:dos The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells. This is a neurological process. Wikipedia:Taste gustation sense of taste taste taste perception biological_process GO:0050909 sensory perception of taste The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells. This is a neurological process. GOC:ai The series of events involved in the perception of sound vibration in which the vibration is received and converted into a molecular signal. GO:0009592 GO:0055128 detection of sound hearing, sensory transduction of sound perception of sound, detection of mechanical stimulus perception of sound, sensory detection of mechanical stimulus perception of sound, sensory transduction of mechanical stimulus sensory detection of mechanical stimulus during perception of sound sensory transduction of mechanical stimulus during perception of sound sensory transduction of sound biological_process GO:0050910 detection of mechanical stimulus involved in sensory perception of sound The series of events involved in the perception of sound vibration in which the vibration is received and converted into a molecular signal. GOC:ai The series of events involved in the perception of smell in which an olfactory chemical stimulus is received and converted into a molecular signal. perception of smell, detection of chemical stimulus perception of smell, sensory detection of chemical stimulus perception of smell, sensory transduction of chemical stimulus sensory detection of chemical stimulus during perception of smell sensory detection of scent sensory detection of smell sensory transduction of chemical stimulus during perception of smell sensory transduction of scent sensory transduction of smell biological_process GO:0050911 detection of chemical stimulus involved in sensory perception of smell The series of events involved in the perception of smell in which an olfactory chemical stimulus is received and converted into a molecular signal. GOC:ai The series of events involved in the perception of taste in which a gustatory chemical stimulus is received and converted into a molecular signal. taste perception perception of taste, detection of chemical stimulus perception of taste, sensory detection of chemical stimulus perception of taste, sensory transduction of chemical stimulus sensory detection of chemical stimulus during perception of taste sensory detection of taste sensory transduction of chemical stimulus during perception of taste sensory transduction of taste biological_process GO:0050912 detection of chemical stimulus involved in sensory perception of taste The series of events involved in the perception of taste in which a gustatory chemical stimulus is received and converted into a molecular signal. GOC:ai Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient. biological_process GO:0050920 regulation of chemotaxis Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient. GOC:ai Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient. up regulation of chemotaxis up-regulation of chemotaxis upregulation of chemotaxis activation of chemotaxis stimulation of chemotaxis biological_process GO:0050921 positive regulation of chemotaxis Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient. down regulation of chemotaxis down-regulation of chemotaxis downregulation of chemotaxis inhibition of chemotaxis biological_process GO:0050922 negative regulation of chemotaxis Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient. GOC:ai The series of events required for an organism to receive a sensory temperature stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. sensory perception of thermal stimulus biological_process GO:0050951 sensory perception of temperature stimulus The series of events required for an organism to receive a sensory temperature stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GOC:ai The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. biological_process GO:0050953 sensory perception of light stimulus The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GOC:ai The series of events required for an organism to receive a sensory mechanical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. mechanosensory perception perception of mechanical stimulus biological_process chemi-mechanical coupling GO:0050954 sensory perception of mechanical stimulus The series of events required for an organism to receive a sensory mechanical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GOC:ai The series of events required for an organism to receive a temperature stimulus, convert it to a molecular signal, and recognize and characterize the signal. Thermoception in larger animals is mainly done in the skin; mammals have at least two types of sensor, for detecting heat (temperatures above body temperature) and cold (temperatures below body temperature). Wikipedia:Thermoception thermoreception biological_process GO:0050955 thermoception The series of events required for an organism to receive a temperature stimulus, convert it to a molecular signal, and recognize and characterize the signal. Thermoception in larger animals is mainly done in the skin; mammals have at least two types of sensor, for detecting heat (temperatures above body temperature) and cold (temperatures below body temperature). GOC:ai Wikipedia:Thermoception The series of events in which a temperature stimulus is received and converted into a molecular signal as part of thermoception. sensory detection of temperature stimulus during thermoception sensory detection of thermal stimulus during thermoception sensory transduction of temperature stimulus during thermoception sensory transduction of thermal stimulus during thermoception thermoception, sensory detection of temperature stimulus thermoception, sensory detection of thermal stimulus thermoception, sensory transduction of temperature stimulus thermoception, sensory transduction of thermal stimulus biological_process GO:0050960 detection of temperature stimulus involved in thermoception The series of events in which a temperature stimulus is received and converted into a molecular signal as part of thermoception. GOC:ai GOC:dos The series of events in which a temperature stimulus is received and converted into a molecular signal as part of sensory perception. sensory detection of temperature stimulus sensory detection of temperature stimulus during sensory perception sensory detection of thermal stimulus during sensory perception sensory perception, sensory detection of temperature stimulus sensory perception, sensory detection of thermal stimulus sensory perception, sensory transduction of temperature stimulus sensory perception, sensory transduction of thermal stimulus sensory transduction of temperature stimulus sensory transduction of temperature stimulus during sensory perception sensory transduction of thermal stimulus during sensory perception sensory detection of heat stimulus during sensory perception sensory perception, sensory detection of heat stimulus sensory perception, sensory transduction of heat stimulus sensory transduction of heat stimulus during sensory perception biological_process GO:0050961 detection of temperature stimulus involved in sensory perception The series of events in which a temperature stimulus is received and converted into a molecular signal as part of sensory perception. GOC:ai GOC:dos The series of events in which a light stimulus is received by a cell and converted into a molecular signal as part of the sensory perception of light. sensory detection of light stimulus sensory detection of light stimulus during sensory perception sensory perception, sensory detection of light stimulus sensory perception, sensory transduction of light stimulus sensory transduction of light stimulus sensory transduction of light stimulus during sensory perception biological_process GO:0050962 detection of light stimulus involved in sensory perception The series of events in which a light stimulus is received by a cell and converted into a molecular signal as part of the sensory perception of light. GOC:ai GOC:dos The series of events in which a mechanical stimulus is received and converted into a molecular signal as part of sensory perception. sensory detection of mechanical stimulus sensory detection of mechanical stimulus during sensory perception sensory perception, sensory detection of mechanical stimulus sensory perception, sensory transduction of mechanical stimulus sensory transduction of mechanical stimulus sensory transduction of mechanical stimulus during sensory perception biological_process GO:0050974 detection of mechanical stimulus involved in sensory perception The series of events in which a mechanical stimulus is received and converted into a molecular signal as part of sensory perception. GOC:ai GOC:dos The series of events required for an organism to receive a touch stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. The perception of touch in animals is mediated by mechanoreceptors in the skin and mucous membranes and is the sense by which contact with objects gives evidence as to certain of their qualities. Different types of touch can be perceived (for example, light, coarse, pressure and tickling) and the stimulus may be external or internal (e.g. the feeling of a full stomach). Wikipedia:Touch perception of touch tactile sense taction tactition biological_process GO:0050975 sensory perception of touch The series of events required for an organism to receive a touch stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. The perception of touch in animals is mediated by mechanoreceptors in the skin and mucous membranes and is the sense by which contact with objects gives evidence as to certain of their qualities. Different types of touch can be perceived (for example, light, coarse, pressure and tickling) and the stimulus may be external or internal (e.g. the feeling of a full stomach). GOC:ai The series of events involved in the perception of touch in which a mechanical stimulus is received and converted into a molecular signal. perception of touch, detection of mechanical stimulus perception of touch, sensory detection of mechanical stimulus perception of touch, sensory transduction of mechanical stimulus sensory detection of mechanical stimulus during perception of touch sensory transduction of mechanical stimulus during perception of touch tactition, sensory detection of mechanical stimulus biological_process GO:0050976 detection of mechanical stimulus involved in sensory perception of touch The series of events involved in the perception of touch in which a mechanical stimulus is received and converted into a molecular signal. GOC:ai GOC:dos The series of events by which a mechanical stimulus is received and converted into a molecular signal. biological_process GO:0050982 detection of mechanical stimulus The series of events by which a mechanical stimulus is received and converted into a molecular signal. GOC:ai GOC:dos true 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 modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA. regulation of DNA metabolism biological_process GO:0051052 regulation of DNA metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving DNA. down regulation of DNA metabolic process down-regulation of DNA metabolic process downregulation of DNA metabolic process negative regulation of DNA metabolism inhibition of DNA metabolic process biological_process GO:0051053 negative regulation of DNA metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving DNA. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA. positive regulation of DNA metabolism up regulation of DNA metabolic process up-regulation of DNA metabolic process upregulation of DNA metabolic process activation of DNA metabolic process stimulation of DNA metabolic process biological_process GO:0051054 positive regulation of DNA metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. down regulation of lipid biosynthetic process down-regulation of lipid biosynthetic process downregulation of lipid biosynthetic process negative regulation of lipid anabolism negative regulation of lipid biosynthesis negative regulation of lipid formation negative regulation of lipid synthesis negative regulation of lipogenesis inhibition of lipid biosynthetic process biological_process GO:0051055 negative regulation of lipid 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 lipids. GOC:ai negative regulation of lipogenesis GOC:sl 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 DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid). biological_process GO:0051101 regulation of DNA binding Any process that modulates the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid). GOC:ai 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 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 The change in morphology and behavior of a mature or immature natural killer T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. NK T lymphocyte activation NK T-cell activation NK T-lymphocyte activation NKT cell activation NT cell activation natural T cell activation natural killer T cell activation biological_process GO:0051132 Note that NK T cells are a distinct lineage of T cells expressing natural killer cell markers and having T cell receptors characterized by the usage of a restricted repetoire of variable region gene segments. NK T cell activation The change in morphology and behavior of a mature or immature natural killer T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. ISBN:0781735149 PMID:12154375 PMID:9133426 Any process that modulates the frequency, rate or extent of natural killer T cell activation. regulation of NK T lymphocyte activation regulation of NK T-cell activation regulation of NK T-lymphocyte activation regulation of NKT cell activation regulation of NT cell activation regulation of natural T cell activation regulation of natural killer T cell activation biological_process GO:0051133 regulation of NK T cell activation Any process that modulates the frequency, rate or extent of natural killer T cell activation. ISBN:0781735149 PMID:12154375 PMID:9133426 Any process that stops, prevents, or reduces the frequency, rate or extent of natural killer T cell activation. down regulation of NK T cell activation down-regulation of NK T cell activation downregulation of NK T cell activation negative regulation of NK T lymphocyte activation negative regulation of NK T-cell activation negative regulation of NK T-lymphocyte activation negative regulation of NKT cell activation negative regulation of NT cell activation negative regulation of natural T cell activation negative regulation of natural killer T cell activation inhibition of NK T cell activation biological_process GO:0051134 negative regulation of NK T cell activation Any process that stops, prevents, or reduces the frequency, rate or extent of natural killer T cell activation. ISBN:0781735149 PMID:12154375 PMID:9133426 Any process that activates or increases the frequency, rate or extent of natural killer T cell activation. positive regulation of NK T lymphocyte activation positive regulation of NK T-cell activation positive regulation of NK T-lymphocyte activation positive regulation of NKT cell activation positive regulation of NT cell activation positive regulation of natural T cell activation positive regulation of natural killer T cell activation up regulation of NK T cell activation up-regulation of NK T cell activation upregulation of NK T cell activation activation of NK T cell activation stimulation of NK T cell activation biological_process GO:0051135 positive regulation of NK T cell activation Any process that activates or increases the frequency, rate or extent of natural killer T cell activation. ISBN:0781735149 PMID:12154375 PMID:9133426 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 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 lymphocyte activation. biological_process GO:0051249 regulation of lymphocyte activation Any process that modulates the frequency, rate or extent of lymphocyte activation. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte activation. down regulation of lymphocyte activation down-regulation of lymphocyte activation downregulation of lymphocyte activation inhibition of lymphocyte activation biological_process GO:0051250 negative regulation of lymphocyte activation Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte activation. GOC:ai Any process that activates or increases the frequency, rate or extent of lymphocyte activation. up regulation of lymphocyte activation up-regulation of lymphocyte activation upregulation of lymphocyte activation activation of lymphocyte activation stimulation of lymphocyte activation biological_process GO:0051251 positive regulation of lymphocyte activation Any process that activates or increases the frequency, rate or extent of lymphocyte activation. GOC:ai Any process that modulates the frequency, rate or extent of the movement of a cellular component. regulation of cellular component motion biological_process regulation of cell movement GO:0051270 regulation of cellular component movement Any process that modulates the frequency, rate or extent of the movement of a cellular component. GOC:ai GOC:dph GOC:jl regulation of cellular component motion GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of a cellular component. negative regulation of cellular component motion biological_process GO:0051271 negative regulation of cellular component movement Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of a cellular component. GOC:ai GOC:dph GOC:jl negative regulation of cellular component motion GOC:mah Any process that activates or increases the frequency, rate or extent of the movement of a cellular component. positive regulation of cellular component motion biological_process GO:0051272 positive regulation of cellular component movement Any process that activates or increases the frequency, rate or extent of the movement of a cellular component. GOC:ai GOC:dph GOC:jl positive regulation of cellular component motion GOC:mah A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. GO:0007001 GO:0051277 chromosome organisation biological_process chromosome organization and biogenesis maintenance of genome integrity nuclear genome maintenance GO:0051276 chromosome organization A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. GOC:ai GOC:dph GOC:jl GOC:mah chromosome organization and biogenesis GOC:mah The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. Wikipedia:Cell_division biological_process GO:0051301 Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division. cell division The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. GOC:di GOC:go_curators GOC:pr Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells. biological_process GO:0051302 regulation of cell division Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells. GOC:go_curators Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions. GO:0007126 Wikipedia:Meiosis biological_process meiosis GO:0051321 Note that this term should not be confused with 'GO:0140013 ; meiotic nuclear division'. 'GO:0051321 ; meiotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140013 meiotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. meiotic cell cycle Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions. GOC:ai Any process that modulates the rate or extent of progression through the meiotic cell cycle. meiotic cell cycle modulation meiotic cell cycle regulation modulation of meiotic cell cycle progression regulation of meiotic cell cycle progression regulation of progression through meiotic cell cycle biological_process meiotic cell cycle regulator GO:0051445 regulation of meiotic cell cycle Any process that modulates the rate or extent of progression through the meiotic cell cycle. GOC:ai GOC:dph GOC:tb regulation of progression through meiotic cell cycle GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of progression through the meiotic cell cycle. positive regulation of meiotic cell cycle progression positive regulation of progression through meiotic cell cycle up regulation of progression through meiotic cell cycle up-regulation of progression through meiotic cell cycle upregulation of progression through meiotic cell cycle activation of progression through meiotic cell cycle stimulation of progression through meiotic cell cycle biological_process GO:0051446 positive regulation of meiotic cell cycle Any process that activates or increases the frequency, rate or extent of progression through the meiotic cell cycle. GOC:ai GOC:dph GOC:tb positive regulation of progression through meiotic cell cycle GOC:dph GOC:tb Any process that stops, prevents or reduces the rate or extent of progression through the meiotic cell cycle. down regulation of progression through meiotic cell cycle down-regulation of progression through meiotic cell cycle downregulation of progression through meiotic cell cycle negative regulation of meiotic cell cycle progression negative regulation of progression through meiotic cell cycle inhibition of progression through meiotic cell cycle biological_process GO:0051447 negative regulation of meiotic cell cycle Any process that stops, prevents or reduces the rate or extent of progression through the meiotic cell cycle. GOC:ai GOC:dph GOC:tb negative regulation of progression through meiotic cell cycle GOC:dph GOC:tb The regulated release of corticotropin by a cell. Corticotropin hormone is a polypeptide hormone synthesized and secreted from corticotropes in the anterior lobe of the pituitary gland in response to corticotropin-releasing hormone (CRH) released by the hypothalamus. ACTH secretion adrenocorticotropic hormone secretion adrenotropic hormone secretion adrenotropin secretion corticotropic hormone secretion biological_process adrenocorticotropin secretion GO:0051458 corticotropin secretion The regulated release of corticotropin by a cell. Corticotropin hormone is a polypeptide hormone synthesized and secreted from corticotropes in the anterior lobe of the pituitary gland in response to corticotropin-releasing hormone (CRH) released by the hypothalamus. GOC:cjm PMID:11027914 adrenocorticotropin secretion GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the regulated release of corticotropic hormone from a cell. regulation of ACTH secretion regulation of adrenocorticotropic hormone secretion regulation of adrenocorticotropin secretion regulation of adrenotropin hormone secretion regulation of adrenotropin secretion regulation of corticotropic hormone secretion biological_process GO:0051459 regulation of corticotropin secretion Any process that modulates the frequency, rate or extent of the regulated release of corticotropic hormone from a cell. GOC:ai GOC:dph regulation of adrenocorticotropic hormone secretion GOC:dph Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of corticotropic hormone from a cell. down regulation of adrenocorticotropin secretion down-regulation of adrenocorticotropin secretion downregulation of adrenocorticotropin secretion negative regulation of ACTH secretion negative regulation of adrenocorticotropic hormone secretion negative regulation of adrenocorticotropin secretion negative regulation of adrenotropic hormone secretion negative regulation of adrenotropin secretion negative regulation of corticotropic hormone secretion inhibition of adrenocorticotropin secretion biological_process GO:0051460 negative regulation of corticotropin secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of corticotropic hormone from a cell. GOC:ai Any process that activates or increases the frequency, rate or extent of the regulated release of corticotropin hormone from a cell. positive regulation of ACTH secretion positive regulation of adrenocorticotropic hormone secretion positive regulation of adrenocorticotropin secretion positive regulation of adrenotropic hormone secretion positive regulation of adrenotropin secretion positive regulation of corticotropic hormone secretion up regulation of adrenocorticotropin secretion up-regulation of adrenocorticotropin secretion upregulation of adrenocorticotropin secretion activation of adrenocorticotropin secretion stimulation of adrenocorticotropin secretion biological_process GO:0051461 positive regulation of corticotropin secretion Any process that activates or increases the frequency, rate or extent of the regulated release of corticotropin hormone from a cell. GOC:ai positive regulation of adrenocorticotropin secretion GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. regulation of cytoskeleton organisation biological_process regulation of cytoskeleton organization and biogenesis GO:0051493 regulation of cytoskeleton organization Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. GOC:ai regulation of cytoskeleton organisation GOC:mah regulation of cytoskeleton organization and biogenesis GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. down regulation of cytoskeleton organization down-regulation of cytoskeleton organization downregulation of cytoskeleton organization negative regulation of cytoskeleton organisation inhibition of cytoskeleton organization biological_process negative regulation of cytoskeleton organization and biogenesis GO:0051494 negative regulation of cytoskeleton organization Any process that stops, prevents, or reduces the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. GOC:ai negative regulation of cytoskeleton organisation GOC:mah negative regulation of cytoskeleton organization and biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. positive regulation of cytoskeleton organisation up regulation of cytoskeleton organization up-regulation of cytoskeleton organization upregulation of cytoskeleton organization activation of cytoskeleton organization stimulation of cytoskeleton organization biological_process positive regulation of cytoskeleton organization and biogenesis GO:0051495 positive regulation of cytoskeleton organization Any process that activates or increases the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. GOC:ai positive regulation of cytoskeleton organisation GOC:mah positive regulation of cytoskeleton organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051588 regulation of neurotransmitter transport Any process that modulates the frequency, rate or extent of the directed movement of a neurotransmitter 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 neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of neurotransmitter transport down-regulation of neurotransmitter transport downregulation of neurotransmitter transport inhibition of neurotransmitter transport biological_process GO:0051589 negative regulation of neurotransmitter transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a neurotransmitter 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 a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of neurotransmitter transport up-regulation of neurotransmitter transport upregulation of neurotransmitter transport activation of neurotransmitter transport stimulation of neurotransmitter transport biological_process GO:0051590 positive regulation of neurotransmitter transport Any process that activates or increases the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal. stimulus detection biological_process perception of stimulus stimulus sensing GO:0051606 detection of stimulus The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal. GOC:add GOC:ai GOC:dph GOC:mah The directed movement of histamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Histamine is a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans. biological_process GO:0051608 histamine transport The directed movement of histamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Histamine is a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans. GOC:ai Any process in which an organelle is transported to, and/or maintained in, a specific location. establishment and maintenance of organelle localization organelle localisation biological_process GO:0051640 organelle localization Any process in which an organelle is transported to, and/or maintained in, a specific location. GOC:ai organelle localisation 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 in which a vesicle or vesicles are transported to, and/or maintained in, a specific location. cytoplasmic vesicle localization establishment and maintenance of vesicle localization vesicle localisation biological_process GO:0051648 vesicle localization Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location. GOC:ai vesicle localisation GOC:mah 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 The directed movement of a vesicle to a specific location. establishment of vesicle localisation biological_process GO:0051650 establishment of vesicle localization The directed movement of a vesicle to a specific location. GOC:ai establishment of vesicle localisation GOC:mah The directed movement of an organelle to a specific location. establishment of organelle localisation biological_process GO:0051656 establishment of organelle localization The directed movement of an organelle to a specific location. GOC:ai establishment of organelle localisation GOC:mah Any process in which a cell is transported to, and/or maintained in, a specific location. cell localization establishment and maintenance of cell localization establishment and maintenance of localization of cell localisation of cell biological_process GO:0051674 localization of cell Any process in which a cell is transported to, and/or maintained in, a specific location. GOC:ai localisation of cell GOC:mah A biological process which involves another organism of the same or different species. GO:0051706 interaction between organisms physiological interaction between organisms physiological interaction with other organism biological_process GO:0051704 multi-organism process A biological process which involves another organism of the same or different species. GOC:jl 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 from another living organism. GO:0009613 GO:0042828 biological_process GO:0051707 response to other organism 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 from another living organism. GOC:ai 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 that modulates the rate or extent of progression through the cell cycle. GO:0000074 GO:0007050 GO:0071156 GO:0071157 GO:0071158 GO:0071850 cell cycle modulation cell cycle regulation control of cell cycle progression modulation of cell cycle progression regulation of cell cycle progression regulation of progression through cell cycle arrest of mitotic cell cycle progression cell cycle arrest mitotic cell cycle arrest negative regulation of cell cycle arrest positive regulation of cell cycle arrest regulation of cell cycle arrest biological_process cell cycle regulator tumor suppressor GO:0051726 regulation of cell cycle Any process that modulates the rate or extent of progression through the cell cycle. GOC:ai GOC:dph GOC:tb arrest of mitotic cell cycle progression GOC:mah The chemical reactions and pathways resulting in the formation of a nitric-oxide synthase, an enzyme which catalyzes the reaction L-arginine + n NADPH + n H+ + m O2 = citrulline + nitric oxide + n NADP+. GO:0051768 NO synthase biosynthesis NO synthase biosynthetic process NOS biosynthesis NOS biosynthetic process NOS1 biosynthesis NOS2 biosynthesis NOS2 synthase biosynthesis NOS2 synthase biosynthetic process NOS3 biosynthesis brain nitric-oxide synthase biosynthetic process endothelial nitric-oxide synthase biosynthetic process inducible nitric-oxide synthase biosynthetic process nitric-oxide synthase (type 2) biosynthesis nitric-oxide synthase (type 2) biosynthetic process nitric-oxide synthase (type II) biosynthesis nitric-oxide synthase (type II) biosynthetic process nitric-oxide synthase 2 biosynthetic process nitric-oxide synthase-1 biosynthetic process nitric-oxide synthase-2 biosynthetic process nitric-oxide synthase-3 biosynthetic process biological_process GO:0051767 nitric-oxide synthase biosynthetic process The chemical reactions and pathways resulting in the formation of a nitric-oxide synthase, an enzyme which catalyzes the reaction L-arginine + n NADPH + n H+ + m O2 = citrulline + nitric oxide + n NADP+. EC:1.14.13.39 GOC:ai NOS1 biosynthesis GOC:bf NOS2 biosynthesis GOC:bf NOS3 biosynthesis GOC:bf brain nitric-oxide synthase biosynthetic process GOC:bf endothelial nitric-oxide synthase biosynthetic process GOC:bf inducible nitric-oxide synthase biosynthetic process GOC:bf nitric-oxide synthase-1 biosynthetic process GOC:bf nitric-oxide synthase-2 biosynthetic process GOC:bf nitric-oxide synthase-3 biosynthetic process GOC:bf Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric-oxide synthase enzyme. GO:0051772 regulation of NO synthase biosynthesis regulation of NO synthase biosynthetic process regulation of NOS biosynthesis regulation of NOS biosynthetic process regulation of NOS2 synthase biosynthesis regulation of NOS2 synthase biosynthetic process regulation of nitric-oxide synthase (type 2) biosynthesis regulation of nitric-oxide synthase (type 2) biosynthetic process regulation of nitric-oxide synthase (type II) biosynthesis regulation of nitric-oxide synthase (type II) biosynthetic process regulation of nitric-oxide synthase 2 biosynthetic process biological_process GO:0051769 regulation of nitric-oxide synthase biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric-oxide synthase enzyme. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric oxide synthase enzyme. GO:0051773 positive regulation of NO synthase biosynthesis positive regulation of NO synthase biosynthetic process positive regulation of NOS biosynthesis positive regulation of NOS biosynthetic process up regulation of nitric-oxide synthase biosynthetic process up-regulation of nitric-oxide synthase biosynthetic process upregulation of nitric-oxide synthase biosynthetic process activation of nitric-oxide synthase 2 biosynthetic process activation of nitric-oxide synthase biosynthetic process positive regulation of NOS2 synthase biosynthesis positive regulation of NOS2 synthase biosynthetic process positive regulation of nitric-oxide synthase (type 2) biosynthesis positive regulation of nitric-oxide synthase (type 2) biosynthetic process positive regulation of nitric-oxide synthase (type II) biosynthesis positive regulation of nitric-oxide synthase (type II) biosynthetic process positive regulation of nitric-oxide synthase 2 biosynthetic process stimulation of nitric-oxide synthase 2 biosynthetic process stimulation of nitric-oxide synthase biosynthetic process up regulation of nitric-oxide synthase 2 biosynthetic process up-regulation of nitric-oxide synthase 2 biosynthetic process upregulation of nitric-oxide synthase 2 biosynthetic process biological_process GO:0051770 positive regulation of nitric-oxide synthase biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric oxide synthase enzyme. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric-oxide synthase enzyme. GO:0051774 down regulation of nitric-oxide synthase biosynthetic process down-regulation of nitric-oxide synthase biosynthetic process downregulation of nitric-oxide synthase biosynthetic process negative regulation of NO synthase biosynthesis negative regulation of NO synthase biosynthetic process negative regulation of NOS biosynthesis negative regulation of NOS biosynthetic process down regulation of nitric-oxide synthase 2 biosynthetic process down-regulation of nitric-oxide synthase 2 biosynthetic process downregulation of nitric-oxide synthase 2 biosynthetic process inhibition of nitric-oxide synthase 2 biosynthetic process inhibition of nitric-oxide synthase biosynthetic process negative regulation of NOS2 synthase biosynthesis negative regulation of NOS2 synthase biosynthetic process negative regulation of nitric-oxide synthase (type 2) biosynthesis negative regulation of nitric-oxide synthase (type 2) biosynthetic process negative regulation of nitric-oxide synthase (type II) biosynthesis negative regulation of nitric-oxide synthase (type II) biosynthetic process negative regulation of nitric-oxide synthase 2 biosynthetic process biological_process GO:0051771 negative regulation of nitric-oxide synthase 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 a nitric-oxide synthase enzyme. GOC:ai Any process that activates or increases the frequency, rate or extent of cell division. up regulation of cell division up-regulation of cell division upregulation of cell division activation of cell division stimulation of cell division biological_process GO:0051781 positive regulation of cell division Any process that activates or increases the frequency, rate or extent of cell division. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of cell division. down regulation of cell division down-regulation of cell division downregulation of cell division inhibition of cell division biological_process GO:0051782 negative regulation of cell division Any process that stops, prevents, or reduces the frequency, rate or extent of cell division. GOC:ai Any process that modulates the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. biological_process GO:0051783 regulation of nuclear division Any process that modulates the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. down regulation of nuclear division down-regulation of nuclear division downregulation of nuclear division inhibition of nuclear division biological_process GO:0051784 negative regulation of nuclear division Any process that stops, prevents, or reduces the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. GOC:ai Any process that activates or increases the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. up regulation of nuclear division up-regulation of nuclear division upregulation of nuclear division activation of nuclear division stimulation of nuclear division biological_process GO:0051785 positive regulation of nuclear division Any process that activates or increases the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. GOC:ai Binding to a glycolipid, any compound containing one or more monosaccharide residues bound by a glycosidic linkage to a hydrophobic group such as an acylglycerol, a sphingoid, a ceramide (N-acylsphingoid) or a prenyl phosphate. molecular_function GO:0051861 glycolipid binding Binding to a glycolipid, any compound containing one or more monosaccharide residues bound by a glycosidic linkage to a hydrophobic group such as an acylglycerol, a sphingoid, a ceramide (N-acylsphingoid) or a prenyl phosphate. PMID:19635802 Any process that modulates the frequency, rate or extent of sensory perception, the series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. biological_process GO:0051931 regulation of sensory perception Any process that modulates the frequency, rate or extent of sensory perception, the series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. GOC:ai The vesicular release of gamma-aminobutyric acid (GABA). from a presynapse, across a chemical synapse, the subsequent activation of GABA receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. GABAergic synaptic transmission synaptic transmission, GABA mediated synaptic transmission, gamma-aminobutyric acid mediated synaptic transmission, gamma-aminobutyric acid-ergic biological_process GO:0051932 synaptic transmission, GABAergic The vesicular release of gamma-aminobutyric acid (GABA). from a presynapse, across a chemical synapse, the subsequent activation of GABA receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. GOC:dos ISBN:0126603030 The directed movement of catecholamines, a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. biological_process GO:0051937 catecholamine transport The directed movement of catecholamines, a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. GOC:ai ISBN:0198506732 Any process that modulates the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051952 regulation of amine transport Any process that modulates the frequency, rate or extent of the directed movement of amines 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 amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of amine transport down-regulation of amine transport downregulation of amine transport inhibition of amine transport biological_process GO:0051953 negative regulation of amine transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of amines 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, maintains or increases the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of amine transport up-regulation of amine transport upregulation of amine transport activation of amine transport stimulation of amine transport biological_process GO:0051954 positive regulation of amine transport Any process that activates, maintains or increases the frequency, rate or extent of the directed movement of amines 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 amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051955 regulation of amino acid transport Any process that modulates the frequency, rate or extent of the directed movement of amino acids 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 amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of amino acid transport down-regulation of amino acid transport downregulation of amino acid transport negative regulation of amino acid transmembrane transport inhibition of amino acid transport biological_process GO:0051956 negative regulation of amino acid transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai negative regulation of amino acid transmembrane transport GOC:mah Any process that activates, maintains or increases the frequency, rate or extent of the directed movement of amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. positive regulation of amino acid transmembrane transport up regulation of amino acid transport up-regulation of amino acid transport upregulation of amino acid transport activation of amino acid transport stimulation of amino acid transport biological_process GO:0051957 positive regulation of amino acid transport Any process that activates, maintains or increases the frequency, rate or extent of the directed movement of amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai positive regulation of amino acid transmembrane transport GOC:mah Any process that modulates the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate. biological_process GO:0051966 regulation of synaptic transmission, glutamatergic Any process that modulates the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate. down regulation of synaptic transmission, glutamatergic down-regulation of synaptic transmission, glutamatergic downregulation of synaptic transmission, glutamatergic inhibition of synaptic transmission, glutamatergic biological_process GO:0051967 negative regulation of synaptic transmission, glutamatergic Any process that stops, prevents, or reduces the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate. GOC:ai Any process that activates, maintains or increases the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate. up regulation of synaptic transmission, glutamatergic up-regulation of synaptic transmission, glutamatergic upregulation of synaptic transmission, glutamatergic activation of synaptic transmission, glutamatergic stimulation of synaptic transmission, glutamatergic biological_process GO:0051968 positive regulation of synaptic transmission, glutamatergic Any process that activates, maintains or increases the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate. GOC:ai Any process that modulates the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. regulation of conduction of nerve impulse biological_process GO:0051969 regulation of transmission of nerve impulse Any process that modulates the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. GOC:ai regulation of conduction of nerve impulse GOC:dph Any process that stops, prevents, or reduces the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. down regulation of transmission of nerve impulse down-regulation of transmission of nerve impulse downregulation of transmission of nerve impulse negative regulation of conduction of nerve impulse inhibition of transmission of nerve impulse biological_process GO:0051970 negative regulation of transmission of nerve impulse Any process that stops, prevents, or reduces the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. GOC:ai negative regulation of conduction of nerve impulse GOC:dph Any process that activates, maintains or increases the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. positive regulation of conduction of nerve impulse up regulation of transmission of nerve impulse up-regulation of transmission of nerve impulse upregulation of transmission of nerve impulse activation of transmission of nerve impulse stimulation of transmission of nerve impulse biological_process GO:0051971 positive regulation of transmission of nerve impulse Any process that activates, maintains or increases the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. GOC:ai positive regulation of conduction of nerve impulse GOC:dph Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. biological_process GO:0051983 regulation of chromosome segregation Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. GOC:ai Any process that activates or increases the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. up regulation of chromosome segregation up-regulation of chromosome segregation upregulation of chromosome segregation activation of chromosome segregation stimulation of chromosome segregation biological_process GO:0051984 positive regulation of chromosome segregation Any process that activates or increases the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. down regulation of chromosome segregation down-regulation of chromosome segregation downregulation of chromosome segregation inhibition of chromosome segregation biological_process GO:0051985 negative regulation of chromosome segregation Any process that stops, prevents, or reduces the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. GOC:ai 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 vesicular release of glycine from a presynapse, across a chemical synapse, the subsequent activation of glycine receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. glycinergic synaptic transmission biological_process GO:0060012 synaptic transmission, glycinergic The vesicular release of glycine from a presynapse, across a chemical synapse, the subsequent activation of glycine receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. GOC:dos The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body. heart beating biological_process cardiac contraction hemolymph circulation GO:0060047 heart contraction The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body. GOC:dph Any process that activates or increases the rate or extent of epithelial cell proliferation, contributing to the restoration of integrity to a damaged tissue following an injury. biological_process GO:0060054 positive regulation of epithelial cell proliferation involved in wound healing Any process that activates or increases the rate or extent of epithelial cell proliferation, contributing to the restoration of integrity to a damaged tissue following an injury. GOC:dph Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to a damaged tissue, following an injury. biological_process GO:0060055 angiogenesis involved in wound healing Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to a damaged tissue, following an injury. GOC:dph PMID:15039218 Any process that modulates the potential difference across a post-synaptic membrane. regulation of post-synaptic membrane potential biological_process GO:0060078 regulation of postsynaptic membrane potential Any process that modulates the potential difference across a post-synaptic membrane. GOC:dph GOC:ef A process that leads to a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential. regulation of excitatory post-synaptic membrane potential biological_process regulation of EPSP GO:0060079 excitatory postsynaptic potential A process that leads to a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential. GOC:dph GOC:ef A process that causes a temporary decrease in postsynaptic membrane potential due to the flow of negatively charged ions into the postsynaptic cell. The flow of ions that causes an IPSP is an inhibitory postsynaptic current (IPSC) and makes it more difficult for the neuron to fire an action potential. regulation of inhibitory post-synaptic membrane potential biological_process IPSP GO:0060080 inhibitory postsynaptic potential A process that causes a temporary decrease in postsynaptic membrane potential due to the flow of negatively charged ions into the postsynaptic cell. The flow of ions that causes an IPSP is an inhibitory postsynaptic current (IPSC) and makes it more difficult for the neuron to fire an action potential. GOC:dph GOC:ef A compound molecular function in which an effector function is controlled by one or more regulatory components. molecular_function GO:0060089 molecular transducer activity A compound molecular function in which an effector function is controlled by one or more regulatory components. GOC:dos GOC:pdt The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way. GO:0032947 binding, bridging molecular_function protein complex scaffold activity protein-containing complex scaffold activity GO:0060090 molecular adaptor activity The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way. GOC:mtg_MIT_16mar07 GOC:vw Any process that modulates the frequency, rate or extent of glycinergic synaptic transmission. Glycinergic synaptic transmission is the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glycine. biological_process GO:0060092 regulation of synaptic transmission, glycinergic Any process that modulates the frequency, rate or extent of glycinergic synaptic transmission. Glycinergic synaptic transmission is the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glycine. GOC:dms GOC:dph Any process that stops or decreases the frequency, rate or extent of glycinergic synaptic transmission. Glycinergic synaptic transmission is the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glycine. negative regulation of glycinergic synaptic transmission biological_process GO:0060093 negative regulation of synaptic transmission, glycinergic Any process that stops or decreases the frequency, rate or extent of glycinergic synaptic transmission. Glycinergic synaptic transmission is the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glycine. GOC:dms GOC:dph Any process that activates or increases the frequency, rate or extent of glycinergic synaptic transmission. Glycinergic synaptic transmission is the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glycine. positive regulation of glycinergic synaptic transmission biological_process GO:0060094 positive regulation of synaptic transmission, glycinergic Any process that activates or increases the frequency, rate or extent of glycinergic synaptic transmission. Glycinergic synaptic transmission is the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glycine. GOC:dms GOC:dph The regulated release of serotonin by a cell, in which released serotonin acts as a neurotransmitter. biological_process serotonin release, neurotransmission GO:0060096 serotonin secretion, neurotransmission The regulated release of serotonin by a cell, in which released serotonin acts as a neurotransmitter. GOC:dph serotonin release, neurotransmission GOC:tb Any process that modulates the frequency, rate or extent of the regulated release of growth hormone from a cell. biological_process GO:0060123 regulation of growth hormone secretion Any process that modulates the frequency, rate or extent of the regulated release of growth hormone from a cell. GOC:dph Any process that increases the frequency, rate or extent of the regulated release of growth hormone from a cell. biological_process GO:0060124 positive regulation of growth hormone secretion Any process that increases the frequency, rate or extent of the regulated release of growth hormone from a cell. GOC:dph Any process that decreases or stops the frequency, rate or extent of the regulated release of growth hormone from a cell. biological_process GO:0060125 negative regulation of growth hormone secretion Any process that decreases or stops the frequency, rate or extent of the regulated release of growth hormone from a cell. GOC:dph A homeostatic process involved in the maintenance of an internal steady state within a defined anatomical structure of an organism, including control of cellular proliferation and death and control of metabolic function. 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. anatomical structure maintenance biological_process GO:0060249 anatomical structure homeostasis A homeostatic process involved in the maintenance of an internal steady state within a defined anatomical structure of an organism, including control of cellular proliferation and death and control of metabolic function. 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. GOC:dph anatomical structure maintenance GOC:dph Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any 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. biological_process GO:0060255 regulation of macromolecule metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any 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. GOC:dph GOC:tb Any process that modulates the rate frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. biological_process GO:0060263 regulation of respiratory burst Any process that modulates the rate frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. GOC:dph GOC:tb Any process that modulates the rate, frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases made as a defense response ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. regulation of respiratory burst involved in acute inflammatory response biological_process GO:0060264 regulation of respiratory burst involved in inflammatory response Any process that modulates the rate, frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases made as a defense response ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. GOC:BHF GOC:dph GOC:rl GOC:tb Any process that increases the rate, frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases made as a defense response ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. positive regulation of respiratory burst involved in acute inflammatory response biological_process GO:0060265 positive regulation of respiratory burst involved in inflammatory response Any process that increases the rate, frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases made as a defense response ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. GOC:BHF GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases made as a defense response ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. negative regulation of respiratory burst involved in acute inflammatory response biological_process GO:0060266 negative regulation of respiratory burst involved in inflammatory response Any process that decreases the rate, frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases made as a defense response ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. GOC:BHF GOC:dph GOC:tb Any process that increases the rate frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. biological_process GO:0060267 positive regulation of respiratory burst Any process that increases the rate frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. GOC:dph GOC:tb Any process that decreases the rate frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. biological_process GO:0060268 negative regulation of respiratory burst Any process that decreases the rate frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. GOC:dph GOC:tb The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. GO:0042384 Reactome:R-HSA-5617833.2 ciliogenesis cilium assembly cilium formation microtubule-based flagellum assembly biological_process cilium biogenesis cilium morphogenesis cilium organization GO:0060271 Note that we deem cilium and microtubule-based flagellum to be equivalent. cilium assembly The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. GOC:BHF GOC:cilia GOC:dph GOC:kmv GOC:pr GOC:vw ISBN:0198506732 PMID:13978319 PMID:27350441 Reactome:R-HSA-5617833.2 cilium biogenesis GOC:mah cilium organization GOC:dph Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process GO:0060284 regulation of cell development Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:dph GOC:tb Cell motility due to the motion of one or more eukaryotic cilia. A eukaryotic cilium is a specialized organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. GO:0071974 cilium cell motility microtubule-based flagellar cell motility biological_process ciliary cell motility GO:0060285 Note that we deem eukaryotic cilia and microtubule-based flagella to be equivalent. cilium-dependent cell motility Cell motility due to the motion of one or more eukaryotic cilia. A eukaryotic cilium is a specialized organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. GOC:cilia GOC:dgh GOC:dph GOC:krc GOC:mlg GOC:mtg_cambridge_2013 Movement of cilia mediated by motor proteins that contributes to the movement of a cell. biological_process GO:0060294 cilium movement involved in cell motility Movement of cilia mediated by motor proteins that contributes to the movement of a cell. GOC:BHF GOC:dph GOC:tb Any process that modulates the rate frequency or extent of cilium movement involved in ciliary motility. biological_process GO:0060295 regulation of cilium movement involved in cell motility Any process that modulates the rate frequency or extent of cilium movement involved in ciliary motility. GOC:BHF GOC:dph GOC:tb Any process that modulates the rate, frequency or extent of blood vessel remodeling, the reorganization or renovation of existing blood vessels. biological_process GO:0060312 regulation of blood vessel remodeling Any process that modulates the rate, frequency or extent of blood vessel remodeling, the reorganization or renovation of existing blood vessels. GOC:BHF GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of blood vessel remodeling, the reorganization or renovation of existing blood vessels. down-regulation of blood vessel remodeling inhibition of blood vessel remodeling biological_process GO:0060313 negative regulation of blood vessel remodeling Any process that decreases the rate, frequency or extent of blood vessel remodeling, the reorganization or renovation of existing blood vessels. GOC:BHF GOC:dph GOC:tb down-regulation of blood vessel remodeling GOC:dph GOC:tb inhibition of blood vessel remodeling GOC:dph GOC:tb The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). biological_process GO:0060326 cell chemotaxis The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). GOC:dph 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 in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. biological_process GO:0060374 mast cell differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. GOC:dph GOC:tb Any process that modulates the rate, frequency or extent of mast cell differentiation, the process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. biological_process GO:0060375 regulation of mast cell differentiation Any process that modulates the rate, frequency or extent of mast cell differentiation, the process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of mast cell differentiation, the process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. biological_process GO:0060376 positive regulation of mast cell differentiation Any process that increases the rate, frequency or extent of mast cell differentiation, the process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of mast cell differentiation, the process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. biological_process GO:0060377 negative regulation of mast cell differentiation Any process that decreases the rate, frequency or extent of mast cell differentiation, the process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine. biological_process GO:0060450 positive regulation of hindgut contraction Any process that increases the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine. biological_process GO:0060451 negative regulation of hindgut contraction Any process that decreases the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine. GOC:dph GOC:tb 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 Any process that decreases the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). biological_process GO:0060467 negative regulation of fertilization Any process that decreases the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). GOC:dph Any process that modulates the rate, frequency, or extent of cell projection assembly. biological_process regulation of cell projection formation GO:0060491 regulation of cell projection assembly Any process that modulates the rate, frequency, or extent of cell projection assembly. GOC:dph GOC:tb regulation of cell projection formation GOC:dph GOC:tb Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. dph 2009-04-13T01:56:10Z biological_process GO:0060548 negative regulation of cell death Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. GOC:BHF 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 Any apoptotic process that contributes to the shaping of an anatomical structure. dph 2009-04-28T09:17:27Z apoptosis involved in morphogenesis biological_process apoptosis involved in development morphogenetic apoptosis GO:0060561 apoptotic process involved in morphogenesis Any apoptotic process that contributes to the shaping of an anatomical structure. GOC:dph GOC:mtg_apoptosis morphogenetic apoptosis GOC:dph Any process that modulates the rate, frequency, or extent of chromosome condensation, the progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. dph 2009-05-18T02:12:13Z biological_process GO:0060623 regulation of chromosome condensation Any process that modulates the rate, frequency, or extent of chromosome condensation, the progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell. dph 2009-05-18T02:29:43Z biological_process GO:0060627 regulation of vesicle-mediated transport Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell. GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of microtubule-based movement, the movement of organelles, other microtubules and other particles along microtubules, mediated by motor proteins. dph 2009-05-18T03:07:02Z biological_process GO:0060632 regulation of microtubule-based movement Any process that modulates the rate, frequency, or extent of microtubule-based movement, the movement of organelles, other microtubules and other particles along microtubules, mediated by motor proteins. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of cell proliferation resulting in the maintenance of a steady-state number of cells within a tissue. dph 2009-07-31T01:46:28Z biological_process GO:0060784 regulation of cell proliferation involved in tissue homeostasis Any process that modulates the frequency, rate or extent of cell proliferation resulting in the maintenance of a steady-state number of cells within a tissue. GOC:dph Any process that modulates the occurrence or rate of cell death by apoptosis that results in the maintenance of the steady-state number of cells within a tissue. dph 2009-07-31T01:49:54Z biological_process GO:0060785 regulation of apoptosis involved in tissue homeostasis Any process that modulates the occurrence or rate of cell death by apoptosis that results in the maintenance of the steady-state number of cells within a tissue. GOC:dph Any process that modulates the frequency, rate or extent of cell differentiation that contributes to the maintenance of a steady state of a cell type within a tissue. dph 2009-07-31T01:55:19Z biological_process GO:0060786 regulation of cell differentiation involved in tissue homeostasis Any process that modulates the frequency, rate or extent of cell differentiation that contributes to the maintenance of a steady state of a cell type within a tissue. 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 the series of events that restore integrity to a damaged tissue, following an injury. dph 2010-02-25T10:14:37Z biological_process GO:0061041 regulation of wound healing Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury. GOC:BHF GOC:dph Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury. dph 2010-02-25T10:33:30Z biological_process GO:0061045 negative regulation of wound healing Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury. GOC:dph The progression of the reproductive system over time from its formation to the mature structure. The reproductive system consists of the organs that function in reproduction. dph 2012-08-22T17:47:53Z biological_process GO:0061458 reproductive system development The progression of the reproductive system over time from its formation to the mature structure. The reproductive system consists of the organs that function in reproduction. GOC:dph A process in which a protein is transported to, or maintained in, a location within a cilium. dph 2013-03-22T15:41:44Z biological_process GO:0061512 protein localization to cilium A process in which a protein is transported to, or maintained in, a location within a cilium. GOC:dph The regulated release of acetylcholine by a cell. dph 2013-06-21T15:40:39Z biological_process GO:0061526 acetylcholine secretion The regulated release of acetylcholine by a cell. GOC:dph The regulated release of dopamine by a cell in which the dopamine acts as a neurotransmitter. dph 2013-06-21T15:43:15Z biological_process GO:0061527 dopamine secretion, neurotransmission The regulated release of dopamine by a cell in which the dopamine acts as a neurotransmitter. GOC:dph The regulated release of norepinephrine by a cell, in which the norepinephrine acts as a neurotransmitter. dph 2013-06-21T16:05:08Z noradrenaline secretion, neurotransmission biological_process GO:0061533 norepinephrine secretion, neurotransmission The regulated release of norepinephrine by a cell, in which the norepinephrine acts as a neurotransmitter. GOC:dph noradrenaline secretion, neurotransmission GOC:dph The regulated release of gamma-aminobutyric acid by a cell, in which the gamma-aminobutyric acid acts as a neurotransmitter. dph 2013-06-21T16:10:50Z biological_process GO:0061534 gamma-aminobutyric acid secretion, neurotransmission The regulated release of gamma-aminobutyric acid by a cell, in which the gamma-aminobutyric acid acts as a neurotransmitter. GOC:dph The controlled release of glutamate by a cell, in which the glutamate acts as a neurotransmitter. dph 2013-06-21T16:14:47Z biological_process GO:0061535 glutamate secretion, neurotransmission The controlled release of glutamate by a cell, in which the glutamate acts as a neurotransmitter. GOC:dph The controlled release of glycine by a cell. dph 2013-06-21T16:18:23Z biological_process GO:0061536 glycine secretion The controlled release of glycine by a cell. GOC:dph The controlled release of glycine by a cell, in which glycine acts as a neurotransmitter. dph 2013-06-21T16:19:02Z biological_process GO:0061537 glycine secretion, neurotransmission The controlled release of glycine by a cell, in which glycine acts as a neurotransmitter. GOC:dph The controlled release of histamine by a cell, in which the histamine acts as a neurotransmitter. dph 2013-06-21T16:21:21Z biological_process GO:0061538 histamine secretion, neurotransmission The controlled release of histamine by a cell, in which the histamine acts as a neurotransmitter. GOC:dph The controlled release of a peptide from a cell in which the peptide acts as a neurotransmitter. dph 2013-06-25T09:10:10Z biological_process GO:0061544 peptide secretion, neurotransmission The controlled release of a peptide from a cell in which the peptide acts as a neurotransmitter. GOC:dph The controlled release of hypocretin from a cell or a tissue. dph 2013-12-26T10:07:38Z orexin secretion biological_process GO:0061584 hypocretin secretion The controlled release of hypocretin from a cell or a tissue. GOC:dph orexin secretion GOC:dph The controlled release of a peptide from a cell or a tissue in which the peptide acts as a neurotransmitter. dph 2013-12-26T10:09:37Z orexin secretion, neurotransmission biological_process GO:0061585 hypocretin secretion, neurotransmission The controlled release of a peptide from a cell or a tissue in which the peptide acts as a neurotransmitter. GOC:dph orexin secretion, neurotransmission GOC:dph An immune response against microbes mediated by anti-microbial peptides in body fluid. peptide-mediated antimicrobial humoral response antimicrobial peptide-mediated antimicrobial humoral response biological_process GO:0061844 antimicrobial humoral immune response mediated by antimicrobial peptide An immune response against microbes mediated by anti-microbial peptides in body fluid. PMID:15761415 PMID:24287494 A process that coontributes to the second meiotic division. The second meiotic division separates chromatids resulting in a haploid number of chromosomes. dph 2018-02-14T22:37:44Z second meiotic division biological_process GO:0061983 meiosis II cell cycle process A process that coontributes to the second meiotic division. The second meiotic division separates chromatids resulting in a haploid number of chromosomes. PMID:29385397 second meiotic division PMID:29385397 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 starts or increases the frequency, rate or extent of sister chromatid segregation during mitosis. dph 2018-04-23T14:32:23Z biological_process GO:0062033 positive regulation of mitotic sister chromatid segregation Any process that starts or increases the frequency, rate or extent of sister chromatid segregation during mitosis. PMID:12773390 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 Organized structure of distinctive morphology and function, bounded by a lipid bilayer membrane and occurring outside the cell. extracellular membrane-enclosed organelle cellular_component GO:0065010 extracellular membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a lipid bilayer membrane and occurring outside the cell. GOC:isa_complete An organelle lumen that is part of an intracellular organelle. cellular_component GO:0070013 intracellular organelle lumen An organelle lumen that is part of an intracellular organelle. GOC:mah The regulated release of glucagon from secretory granules in the A (alpha) cells of the pancreas (islets of Langerhans). biological_process GO:0070091 glucagon secretion The regulated release of glucagon from secretory granules in the A (alpha) cells of the pancreas (islets of Langerhans). GOC:BHF GOC:rl Any process that modulates the frequency, rate or extent of the regulated release of glucagon. biological_process GO:0070092 regulation of glucagon secretion Any process that modulates the frequency, rate or extent of the regulated release of glucagon. GOC:BHF GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of glucagon. down regulation of glucagon secretion down-regulation of glucagon secretion downregulation of glucagon secretion inhibition of glucagon secretion biological_process GO:0070093 negative regulation of glucagon secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of glucagon. GOC:BHF GOC:mah Any process that activates or increases the frequency, rate or extent of the regulated release of glucagon. up regulation of glucagon secretion up-regulation of glucagon secretion upregulation of glucagon secretion activation of glucagon secretion stimulation of glucagon secretion biological_process GO:0070094 positive regulation of glucagon secretion Any process that activates or increases the frequency, rate or extent of the regulated release of glucagon. GOC:BHF GOC:mah A process of chromosome organization that is involved in a meiotic cell cycle. chromosome organisation involved in meiosis meiotic chromosome organization biological_process GO:0070192 chromosome organization involved in meiotic cell cycle A process of chromosome organization that is involved in a meiotic cell cycle. GOC:mah chromosome organisation involved in meiosis GOC:mah meiotic chromosome organization GOC:mah 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 apoptotic process in a lymphocyte, a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. lymphocyte apoptosis biological_process GO:0070227 Note that a lymphocyte is a cell of the B cell, T cell, or natural killer cell lineage (CL:0000542). lymphocyte apoptotic process Any apoptotic process in a lymphocyte, a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. CL:0000542 GOC:add GOC:mtg_apoptosis ISBN:0781765196 Any process that modulates the occurrence or rate of lymphocyte death by apoptotic process. regulation of lymphocyte apoptosis biological_process GO:0070228 Note that a lymphocyte is a cell of the B cell, T cell, or natural killer cell lineage (CL:0000542). regulation of lymphocyte apoptotic process Any process that modulates the occurrence or rate of lymphocyte death by apoptotic process. GOC:add GOC:mtg_apoptosis ISBN:0781765196 Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte death by apoptotic process. down regulation of lymphocyte apoptosis down-regulation of lymphocyte apoptosis downregulation of lymphocyte apoptosis inhibition of lymphocyte apoptosis negative regulation of lymphocyte apoptosis biological_process GO:0070229 Note that a lymphocyte is a cell of the B cell, T cell, or natural killer cell lineage (CL:0000542). negative regulation of lymphocyte apoptotic process Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte death by apoptotic process. GOC:add GOC:mtg_apoptosis ISBN:0781765196 down regulation of lymphocyte apoptosis GOC:add down-regulation of lymphocyte apoptosis GOC:add downregulation of lymphocyte apoptosis GOC:add inhibition of lymphocyte apoptosis GOC:add Any process that activates or increases the frequency, rate or extent of lymphocyte death by apoptotic process. up regulation of lymphocyte apoptosis up-regulation of lymphocyte apoptosis upregulation of lymphocyte apoptosis activation of lymphocyte apoptosis positive regulation of lymphocyte apoptosis stimulation of lymphocyte apoptosis biological_process GO:0070230 Note that a lymphocyte is a cell of the B cell, T cell, or natural killer cell lineage (CL:0000542). positive regulation of lymphocyte apoptotic process Any process that activates or increases the frequency, rate or extent of lymphocyte death by apoptotic process. GOC:add GOC:mtg_apoptosis ISBN:0781765196 up regulation of lymphocyte apoptosis GOC:add up-regulation of lymphocyte apoptosis GOC:add upregulation of lymphocyte apoptosis GOC:add activation of lymphocyte apoptosis GOC:add stimulation of lymphocyte apoptosis GOC:add The regulated release of somatostatin from secretory granules in the D cells of the pancreas. biological_process GO:0070253 somatostatin secretion The regulated release of somatostatin from secretory granules in the D cells of the pancreas. GOC:mah The regulated release of mucus by the mucosa. Mucus is a viscous slimy secretion consisting of mucins and various inorganic salts dissolved in water, with suspended epithelial cells and leukocytes. The mucosa, or mucous membrane, is the membrane covered with epithelium that lines the tubular organs of the body. Mucins are carbohydrate-rich glycoproteins that have a lubricating and protective function. mucus production biological_process GO:0070254 mucus secretion The regulated release of mucus by the mucosa. Mucus is a viscous slimy secretion consisting of mucins and various inorganic salts dissolved in water, with suspended epithelial cells and leukocytes. The mucosa, or mucous membrane, is the membrane covered with epithelium that lines the tubular organs of the body. Mucins are carbohydrate-rich glycoproteins that have a lubricating and protective function. GOC:add ISBN:068340007X ISBN:0721662544 mucus production GOC:add Any process that modulates the frequency, rate or extent of the regulated release of mucus from a cell or a tissue. regulation of mucus production biological_process GO:0070255 regulation of mucus secretion Any process that modulates the frequency, rate or extent of the regulated release of mucus from a cell or a tissue. GOC:add regulation of mucus production GOC:add Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of mucus from a cell or a tissue. negative regulation of mucus production biological_process GO:0070256 negative regulation of mucus secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of mucus from a cell or a tissue. GOC:add negative regulation of mucus production GOC:add Any process that activates or increases the frequency, rate or extent of the regulated release of mucus from a cell or a tissue. positive regulation of mucus production biological_process GO:0070257 positive regulation of mucus secretion Any process that activates or increases the frequency, rate or extent of the regulated release of mucus from a cell or a tissue. GOC:add positive regulation of mucus production GOC:add The controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell. ECM constituent secretion ECM secretion biological_process GO:0070278 extracellular matrix constituent secretion The controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell. GOC:mah ECM constituent secretion GOC:mah ECM secretion GOC:mah The regulated release of prolactin, a peptide hormone that stimulates lactation, from secretory granules in the anterior pituitary. biological_process GO:0070459 prolactin secretion The regulated release of prolactin, a peptide hormone that stimulates lactation, from secretory granules in the anterior pituitary. GOC:mah ISBN:0198506732 The regulated release of thyroid-stimulating hormone, a peptide hormone that stimulates the activity of the thyroid gland, from secretory granules in the anterior pituitary. TSH secretion thyroid stimulating hormone secretion biological_process GO:0070460 thyroid-stimulating hormone secretion The regulated release of thyroid-stimulating hormone, a peptide hormone that stimulates the activity of the thyroid gland, from secretory granules in the anterior pituitary. GOC:mah ISBN:0198506732 thyroid stimulating hormone secretion GOC:mah Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. regulation of microtubule cytoskeleton organisation regulation of microtubule dynamics biological_process GO:0070507 regulation of microtubule cytoskeleton organization Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. GOC:mah regulation of microtubule cytoskeleton organisation GOC:mah regulation of microtubule dynamics GOC:dph GOC:tb The expansion of a leukocyte population by cell division. mah 2009-05-28T05:25:28Z biological_process GO:0070661 leukocyte proliferation The expansion of a leukocyte population by cell division. GOC:add Any process that modulates the frequency, rate or extent of leukocyte proliferation. mah 2009-05-28T05:30:39Z biological_process GO:0070663 regulation of leukocyte proliferation Any process that modulates the frequency, rate or extent of leukocyte proliferation. GOC:add GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte proliferation. mah 2009-05-28T05:34:50Z down regulation of leukocyte proliferation down-regulation of leukocyte proliferation downregulation of leukocyte proliferation inhibition of leukocyte proliferation biological_process GO:0070664 negative regulation of leukocyte proliferation Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte proliferation. GOC:add GOC:mah down regulation of leukocyte proliferation GOC:mah down-regulation of leukocyte proliferation GOC:mah downregulation of leukocyte proliferation GOC:mah inhibition of leukocyte proliferation GOC:mah Any process that activates or increases the frequency, rate or extent of leukocyte proliferation. mah 2009-05-28T05:36:46Z up regulation of leukocyte proliferation up-regulation of leukocyte proliferation upregulation of leukocyte proliferation activation of leukocyte proliferation stimulation of leukocyte proliferation biological_process GO:0070665 positive regulation of leukocyte proliferation Any process that activates or increases the frequency, rate or extent of leukocyte proliferation. GOC:add GOC:mah up regulation of leukocyte proliferation GOC:mah up-regulation of leukocyte proliferation GOC:mah upregulation of leukocyte proliferation GOC:mah activation of leukocyte proliferation GOC:mah stimulation of leukocyte proliferation 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 A secretory granule that contains cathepsin and gelatinase and is readily exocytosed upon cell activation; found primarily in mature neutrophil cells. mah 2009-07-20T03:57:00Z gelatinase granule cellular_component GO:0070820 tertiary granule A secretory granule that contains cathepsin and gelatinase and is readily exocytosed upon cell activation; found primarily in mature neutrophil cells. GOC:BHF GOC:mah GOC:rl PMID:12070036 gelatinase granule PMID:23650620 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids. mah 2009-08-14T03:09:02Z regulation of bile acid anabolism regulation of bile acid biosynthesis regulation of bile acid formation regulation of bile acid synthesis biological_process GO:0070857 regulation of bile acid biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids. GOC:BHF GOC:mah regulation of bile acid anabolism GOC:mah regulation of bile acid biosynthesis GOC:mah regulation of bile acid formation GOC:mah regulation of bile acid synthesis 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 bile acids. mah 2009-08-14T03:16:40Z down regulation of bile acid biosynthetic process down-regulation of bile acid biosynthetic process downregulation of bile acid biosynthetic process negative regulation of bile acid anabolism negative regulation of bile acid biosynthesis negative regulation of bile acid formation negative regulation of bile acid synthesis inhibition of bile acid biosynthetic process biological_process GO:0070858 negative regulation of bile acid 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 bile acids. GOC:BHF GOC:mah down regulation of bile acid biosynthetic process GOC:mah down-regulation of bile acid biosynthetic process GOC:mah downregulation of bile acid biosynthetic process GOC:mah negative regulation of bile acid anabolism GOC:mah negative regulation of bile acid biosynthesis GOC:mah negative regulation of bile acid formation GOC:mah negative regulation of bile acid synthesis GOC:mah inhibition of bile acid biosynthetic process GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids. mah 2009-08-14T03:22:58Z positive regulation of bile acid anabolism positive regulation of bile acid biosynthesis positive regulation of bile acid formation positive regulation of bile acid synthesis up regulation of bile acid biosynthetic process up-regulation of bile acid biosynthetic process upregulation of bile acid biosynthetic process activation of bile acid biosynthetic process stimulation of bile acid biosynthetic process biological_process GO:0070859 positive regulation of bile acid biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids. GOC:BHF GOC:mah positive regulation of bile acid anabolism GOC:mah positive regulation of bile acid biosynthesis GOC:mah positive regulation of bile acid formation GOC:mah positive regulation of bile acid synthesis GOC:mah up regulation of bile acid biosynthetic process GOC:mah up-regulation of bile acid biosynthetic process GOC:mah upregulation of bile acid biosynthetic process GOC:mah activation of bile acid biosynthetic process GOC:mah stimulation of bile acid biosynthetic process 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 chemical stimulus. mah 2009-08-27T04:41:45Z biological_process GO:0070887 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 chemical 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 chemical stimulus. GOC:mah The aggregation, arrangement and bonding together of a set of components to form an organelle. 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. mah 2009-09-15T03:00:51Z biological_process GO:0070925 organelle assembly The aggregation, arrangement and bonding together of a set of components to form an organelle. 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 The series of events required for an organism to receive a gravitational stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. mah 2009-11-03T03:25:12Z biological_process GO:0070998 sensory perception of gravity The series of events required for an organism to receive a gravitational stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GOC:mah The series of events involved in the perception of gravity in which a sensory mechanical stimulus is received and converted into a molecular signal. mah 2009-11-03T03:27:30Z biological_process GO:0070999 detection of mechanical stimulus involved in sensory perception of gravity The series of events involved in the perception of gravity in which a sensory mechanical stimulus is received and converted into a molecular signal. GOC:dos GOC:mah A cellular process that results in a change in the spatial configuration of a DNA molecule. A conformation change can bend DNA, or alter the, twist, writhe, or linking number of a DNA molecule. mah 2009-11-09T11:36:34Z DNA conformation modification biological_process GO:0071103 DNA conformation change A cellular process that results in a change in the spatial configuration of a DNA molecule. A conformation change can bend DNA, or alter the, twist, writhe, or linking number of a DNA molecule. GOC:mah DNA conformation modification GOC:mah The movement of a granulocyte in response to an external stimulus. mah 2010-02-09T04:08:17Z biological_process GO:0071621 granulocyte chemotaxis The movement of a granulocyte in response to an external stimulus. GOC:rph Any process that modulates the rate, frequency or extent of granulocyte chemotaxis. Granulocyte chemotaxis is the movement of a granulocyte in response to an external stimulus. mah 2010-02-09T04:09:24Z biological_process GO:0071622 regulation of granulocyte chemotaxis Any process that modulates the rate, frequency or extent of granulocyte chemotaxis. Granulocyte chemotaxis is the movement of a granulocyte in response to an external stimulus. GOC:mah Any process that decreases the rate, frequency or extent of granulocyte chemotaxis. Granulocyte chemotaxis is the movement of a granulocyte in response to an external stimulus. mah 2010-02-09T04:13:19Z biological_process GO:0071623 negative regulation of granulocyte chemotaxis Any process that decreases the rate, frequency or extent of granulocyte chemotaxis. Granulocyte chemotaxis is the movement of a granulocyte in response to an external stimulus. GOC:mah Any process that increases the rate, frequency or extent of granulocyte chemotaxis. Granulocyte chemotaxis is the movement of a granulocyte in response to an external stimulus. mah 2010-02-09T04:15:36Z biological_process GO:0071624 positive regulation of granulocyte chemotaxis Any process that increases the rate, frequency or extent of granulocyte chemotaxis. Granulocyte chemotaxis is the movement of a granulocyte in response to an external stimulus. GOC:mah The movement of a mononuclear cell within or between different tissues and organs of the body. mah 2010-02-16T02:11:00Z biological_process GO:0071674 mononuclear cell migration The movement of a mononuclear cell within or between different tissues and organs of the body. GOC:mah Any process that modulates the rate, frequency or extent of mononuclear cell migration. Mononuclear cell migration is the movement of a mononuclear cell within or between different tissues and organs of the body. mah 2010-02-16T02:11:53Z biological_process GO:0071675 regulation of mononuclear cell migration Any process that modulates the rate, frequency or extent of mononuclear cell migration. Mononuclear cell migration is the movement of a mononuclear cell within or between different tissues and organs of the body. GOC:mah Any process that decreases the rate, frequency or extent of mononuclear cell migration. Mononuclear cell migration is the movement of a mononuclear cell within or between different tissues and organs of the body. mah 2010-02-16T02:13:55Z down regulation of mononuclear cell migration down-regulation of mononuclear cell migration downregulation of mononuclear cell migration inhibition of mononuclear cell migration biological_process GO:0071676 negative regulation of mononuclear cell migration Any process that decreases the rate, frequency or extent of mononuclear cell migration. Mononuclear cell migration is the movement of a mononuclear cell within or between different tissues and organs of the body. GOC:mah down regulation of mononuclear cell migration GOC:mah down-regulation of mononuclear cell migration GOC:mah downregulation of mononuclear cell migration GOC:mah inhibition of mononuclear cell migration GOC:mah Any process that increases the rate, frequency or extent of mononuclear cell migration. Mononuclear cell migration is the movement of a mononuclear cell within or between different tissues and organs of the body. mah 2010-02-16T02:15:29Z up regulation of mononuclear cell migration up-regulation of mononuclear cell migration upregulation of mononuclear cell migration activation of mononuclear cell migration stimulation of mononuclear cell migration biological_process GO:0071677 positive regulation of mononuclear cell migration Any process that increases the rate, frequency or extent of mononuclear cell migration. Mononuclear cell migration is the movement of a mononuclear cell within or between different tissues and organs of the body. GOC:mah up regulation of mononuclear cell migration GOC:mah up-regulation of mononuclear cell migration GOC:mah upregulation of mononuclear cell migration GOC:mah activation of mononuclear cell migration GOC:mah stimulation of mononuclear cell migration 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 The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. mah 2010-03-09T02:40:35Z TNFSF cytokine production biological_process TNF superfamily production GO:0071706 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. tumor necrosis factor superfamily cytokine production The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:add TNFSF cytokine production GOC:add TNF superfamily production GOC:rv The process in which immunoglobulin heavy chain V, D, and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). mah 2010-03-09T04:20:31Z immunoglobulin V(D)J joining immunoglobulin V(D)J recombination immunoglobulin V-D-J joining biological_process GO:0071707 immunoglobulin heavy chain V-D-J recombination The process in which immunoglobulin heavy chain V, D, and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). GOC:add ISBN:0781735149 immunoglobulin V(D)J joining GOC:add immunoglobulin V(D)J recombination GOC:add immunoglobulin V-D-J joining GOC:add The process in which immunoglobulin light chain V and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). mah 2010-03-09T04:22:29Z immunoglobulin V(D)J joining immunoglobulin V(D)J recombination immunoglobulin V-J joining biological_process GO:0071708 immunoglobulin light chain V-J recombination The process in which immunoglobulin light chain V and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). GOC:add ISBN:0781735149 immunoglobulin V(D)J joining GOC:add immunoglobulin V(D)J recombination GOC:add immunoglobulin V-J joining GOC:add A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgG 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. mah 2010-03-24T01:44:53Z IgG1 IgG2 IgG2a IgG2b IgG2c IgG3 IgG4 cellular_component GO:0071735 Note that an IgG immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Also, IgG isotypes vary by species. IgG immunoglobulin complex A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgG 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. GOC:add ISBN:0781765196 IgG1 GOC:add IgG2 GOC:add IgG2a GOC:add IgG2b GOC:add IgG2c GOC:add IgG3 GOC:add IgG4 GOC:add A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. mah 2010-03-24T01:44:53Z IgG antibody IgG1 antibody IgG2 antibody IgG2a antibody IgG2b antibody IgG2c antibody IgG3 antibody IgG4 antibody cellular_component GO:0071736 Note that an IgG immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Also, IgG isotypes vary by species. IgG immunoglobulin complex, circulating A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. GOC:add ISBN:0781765196 IgG antibody GOC:add IgG1 antibody GOC:add IgG2 antibody GOC:add IgG2a antibody GOC:add IgG2b antibody GOC:add IgG2c antibody GOC:add IgG3 antibody GOC:add IgG4 antibody GOC:add A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgD 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. mah 2010-03-24T01:44:53Z cellular_component GO:0071738 Note that an IgD immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgD immunoglobulin complex A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgD 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. GOC:add ISBN:0781765196 PMID:11282392 A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. mah 2010-03-24T01:44:53Z IgD antibody cellular_component GO:0071739 Note that an IgD immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgD immunoglobulin complex, circulating A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. GOC:add ISBN:0781765196 PMID:11282392 IgD antibody GOC:add A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgE 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. mah 2010-03-24T01:44:53Z cellular_component GO:0071742 Note that an IgE immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgE immunoglobulin complex A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgE 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. GOC:add ISBN:0781765196 A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. mah 2010-03-24T01:44:53Z IgE antibody cellular_component GO:0071743 Note that an IgE immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgE immunoglobulin complex, circulating A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. GOC:add ISBN:0781765196 IgE antibody GOC:add A protein complex composed of two identical immunoglobulin heavy chains of the IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and sometimes complexed with J chain or J chain and secretory component. An IgA 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. mah 2010-03-24T01:44:53Z IgA1 antibody IgA2 antibody cellular_component GO:0071745 Note that an IgA immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgA immunoglobulin complex A protein complex composed of two identical immunoglobulin heavy chains of the IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and sometimes complexed with J chain or J chain and secretory component. An IgA 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. GOC:add ISBN:0781765196 PMID:16362985 IgA1 antibody GOC:add IgA2 antibody GOC:add A protein complex composed of two identical immunoglobulin heavy chains of an IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, sometimes complexed with J chain or J chain and secretory component, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. mah 2010-03-24T01:44:53Z IgA antibody IgA1 antibody IgA2 antibody cellular_component GO:0071746 Note that an IgA immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgA immunoglobulin complex, circulating A protein complex composed of two identical immunoglobulin heavy chains of an IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, sometimes complexed with J chain or J chain and secretory component, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. GOC:add ISBN:0781765196 PMID:16362985 IgA antibody GOC:add IgA1 antibody GOC:add IgA2 antibody GOC:add A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM 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. mah 2010-03-24T01:44:53Z cellular_component GO:0071753 Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgM immunoglobulin complex A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM 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. GOC:add ISBN:0781765196 PMID:20176268 A polymer of five or six IgM core units each composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds; the individual IgM core units are held together via disulfide bonds with a single J chain polypeptide acting as a bridge between two of the polymeric units. Circulating IgM is present in the extracellular space, in mucosal areas or other tissues, or in the blood or lymph. mah 2010-03-24T01:44:53Z IgM antibody cellular_component GO:0071754 Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgM immunoglobulin complex, circulating A polymer of five or six IgM core units each composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds; the individual IgM core units are held together via disulfide bonds with a single J chain polypeptide acting as a bridge between two of the polymeric units. Circulating IgM is present in the extracellular space, in mucosal areas or other tissues, or in the blood or lymph. GOC:add ISBN:0781765196 PMID:20176268 IgM antibody GOC:add 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 Any apoptotic process in a leukocyte, an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. mah 2010-09-14T12:44:09Z leukocyte apoptosis biological_process GO:0071887 Note that a lymphocyte is a cell of the B cell, T cell, or natural killer cell lineage (CL:0000542). leukocyte apoptotic process Any apoptotic process in a leukocyte, an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. CL:0000738 GOC:BHF GOC:mah GOC:mtg_apoptosis A nitrogen compound metabolic process that contributes to the nitrogen cycle. The nitrogen cycle is a series of metabolic pathways by which nitrogen is converted between various forms and redox states; it encompasses pathways in which nitrogen is acted upon directly, such as nitrification, denitrification, nitrogen fixation, and mineralization. mah 2010-09-30T05:21:03Z Wikipedia:Nitrogen_cycle biological_process GO:0071941 nitrogen cycle metabolic process A nitrogen compound metabolic process that contributes to the nitrogen cycle. The nitrogen cycle is a series of metabolic pathways by which nitrogen is converted between various forms and redox states; it encompasses pathways in which nitrogen is acted upon directly, such as nitrification, denitrification, nitrogen fixation, and mineralization. GOC:mah PMID:16675690 Wikipedia:Nitrogen_cycle 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 The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Exosomes are defined by their size, which generally ranges from 30 nm to 100 nm. mah 2010-10-18T03:44:18Z extracellular vesicular exosome assembly biological_process GO:0071971 extracellular exosome assembly The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Exosomes are defined by their size, which generally ranges from 30 nm to 100 nm. GOC:mah GOC:tfm PMID:19442504 PMID:27462458 extracellular vesicular exosome assembly GOC:vesicles The chemical reactions and pathways resulting in the formation of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group. mah 2010-11-02T04:51:32Z monocarboxylic acid anabolism monocarboxylic acid biosynthesis monocarboxylic acid formation monocarboxylic acid synthesis biological_process GO:0072330 monocarboxylic acid biosynthetic process The chemical reactions and pathways resulting in the formation of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group. GOC:mah monocarboxylic acid anabolism GOC:mah monocarboxylic acid biosynthesis GOC:mah monocarboxylic acid formation GOC:mah monocarboxylic acid synthesis GOC:mah The process whose specific outcome is the progression of the circulatory system over time, from its formation to the mature structure. The circulatory system is the 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. mah 2010-11-16T11:27:39Z GO:0072358 cardiovascular system development biological_process GO:0072359 circulatory system development The process whose specific outcome is the progression of the circulatory system over time, from its formation to the mature structure. The circulatory system is the 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. GOC:mah UBERON:0001009 The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers. mah 2011-02-11T10:50:06Z ROS metabolic process reactive oxygen species metabolism biological_process GO:0072593 reactive oxygen species metabolic process The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers. GOC:mah ROS metabolic process CHEBI:26523 GOC:mah reactive oxygen species 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 rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). dhl 2010-09-01T03:44:27Z biological_process GO:0080154 regulation of fertilization Any process that modulates the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). GOC:DHL PMID:20478994 Any process that modulates the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding. tb 2009-08-03T10:09:34Z biological_process GO:0090022 regulation of neutrophil chemotaxis Any process that modulates the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding. GOC:dph GOC:tb Any process that increases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding. tb 2009-08-03T10:12:23Z biological_process GO:0090023 positive regulation of neutrophil chemotaxis Any process that increases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding. GOC:dph GOC:tb Any process that decreases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding. tb 2009-08-03T10:13:09Z biological_process GO:0090024 negative regulation of neutrophil chemotaxis Any process that decreases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding. GOC:dph GOC:tb Any process that modulates the frequency, rate, or extent of monocyte chemotaxis. tb 2009-08-03T10:17:03Z biological_process GO:0090025 regulation of monocyte chemotaxis Any process that modulates the frequency, rate, or extent of monocyte chemotaxis. GOC:dph GOC:tb Any process that increases the frequency, rate, or extent of monocyte chemotaxis. tb 2009-08-03T10:18:54Z biological_process GO:0090026 positive regulation of monocyte chemotaxis Any process that increases the frequency, rate, or extent of monocyte chemotaxis. GOC:dph GOC:tb Any process that decreases the frequency, rate, or extent of monocyte chemotaxis. tb 2009-08-03T10:19:40Z biological_process GO:0090027 negative regulation of monocyte chemotaxis Any process that decreases the frequency, rate, or extent of monocyte chemotaxis. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. tb 2009-09-09T11:39:52Z biological_process GO:0090068 positive regulation of cell cycle process Any process that increases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. GOC:dph GOC:tb 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 frequency, rate or extent of a muscle system process, a multicellular organismal process carried out by any of the organs or tissues in a muscle system. tb 2010-02-03T11:48:13Z biological_process GO:0090257 regulation of muscle system process Any process that modulates the frequency, rate or extent of a muscle system process, a multicellular organismal process carried out by any of the organs or tissues in a muscle system. GOC:dph GOC:tb Any process that modulates the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas. tb 2010-02-05T02:54:14Z biological_process GO:0090273 regulation of somatostatin secretion Any process that modulates the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas. GOC:BHF Any process that increases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas. tb 2010-02-05T02:54:14Z biological_process GO:0090274 positive regulation of somatostatin secretion Any process that increases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas. GOC:BHF Any process that decreases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas. tb 2010-02-05T02:54:14Z biological_process GO:0090275 negative regulation of somatostatin secretion Any process that decreases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas. GOC:BHF Any process that modulates the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules. tb 2010-02-05T02:56:39Z biological_process GO:0090276 regulation of peptide hormone secretion Any process that modulates the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules. GOC:tb Any process that increases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules. tb 2010-02-05T02:56:39Z biological_process GO:0090277 positive regulation of peptide hormone secretion Any process that increases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules. GOC:tb Any process that decreases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules. tb 2010-02-05T02:56:39Z biological_process GO:0090278 negative regulation of peptide hormone secretion Any process that decreases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules. GOC:tb Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury. tb 2010-03-22T02:12:03Z biological_process GO:0090303 positive regulation of wound healing Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury. GOC:BHF Any cellular metabolic process involving nucleic acids. tb 2010-04-07T10:18:47Z biological_process GO:0090304 nucleic acid metabolic process Any cellular metabolic process involving nucleic acids. GOC:dph 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 superoxide metabolism, the chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species. tb 2010-05-06T02:29:05Z regulation of superoxide metabolism biological_process GO:0090322 regulation of superoxide metabolic process Any process that modulates the rate, frequency, or extent of superoxide metabolism, the chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species. GOC:tb regulation of superoxide metabolism GOC:tb Any process that prevents the establishment or decreases the extent of the excitatory postsynaptic potential (EPSP) which is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential. tb 2010-12-15T01:43:12Z negative regulation of excitatory post-synaptic membrane potential reduction of excitatory postsynaptic membrane potential biological_process negative regulation of EPSP GO:0090394 negative regulation of excitatory postsynaptic potential Any process that prevents the establishment or decreases the extent of the excitatory postsynaptic potential (EPSP) which is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential. GOC:BHF reduction of excitatory postsynaptic membrane potential GOC:bf The immediate defensive reaction by vertebrate tissue to injury caused by chemical or physical agents. tb 2014-08-12T12:13:53Z biological_process GO:0090594 inflammatory response to wounding The immediate defensive reaction by vertebrate tissue to injury caused by chemical or physical agents. GOC:add Any process of the immune system that can contribute to the formation of immunological memory or an immune response based upon activation of immunological memory. tb 2016-11-11T12:20:30Z biological_process GO:0090713 immunological memory process Any process of the immune system that can contribute to the formation of immunological memory or an immune response based upon activation of immunological memory. GOC:add PMID:26086132 PMID:26831526 Any immunological memory process that can contribute to the formation of immunological memory. tb 2016-11-11T12:25:47Z biological_process GO:0090715 immunological memory formation process Any immunological memory process that can contribute to the formation of immunological memory. GOC:add PMID:26086132 PMID:26831526 All of the contents of a cilium, excluding the plasma membrane surrounding the cilium. pr 2011-03-23T01:52:31Z cilium plasm microtubule-based flagellar matrix microtubule-based flagellum matrix cellular_component cilial cytoplasm ciliary cytoplasm cilium cytoplasm microtubule-based flagellar cytoplasm microtubule-based flagellum cytoplasm GO:0097014 Note that we deem cilium and microtubule-based flagellum to be equivalent. Also, researchers consider the composition of both the plasm and the membrane of the cilium to be detectably different from that in the non-ciliary cytosol and plasma membrane (e.g. in terms of calcium ion concentration, membrane lipid composition, and more). For this reason, the term "ciliary plasm" is not linked to "cytoplasm". ciliary plasm All of the contents of a cilium, excluding the plasma membrane surrounding the cilium. GOC:BHF GOC:cilia GOC:dos PMID:17895364 The process in which a precursor cell type acquires the specialized features of a dendritic cell. A dendritic cell is a leukocyte of dendritic lineage specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. pr 2011-04-01T10:08:42Z biological_process GO:0097028 Note that immunologists typically use the word 'maturation' to refer to dendritic cells undergoing the process that GO describes as 'cell differentiation'. dendritic cell differentiation The process in which a precursor cell type acquires the specialized features of a dendritic cell. A dendritic cell is a leukocyte of dendritic lineage specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. CL:0000451 GOC:pr A specialized area of membrane on either the presynaptic or the postsynaptic side of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell. pr 2011-06-07T11:22:09Z cellular_component GO:0097060 synaptic membrane A specialized area of membrane on either the presynaptic or the postsynaptic side of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell. GOC:BHF PMID:20410104 Any process that activates or increases the frequency, rate or extent of inhibitory postsynaptic potential (IPSP). IPSP is a temporary decrease in postsynaptic membrane potential due to the flow of negatively charged ions into the postsynaptic cell. The flow of ions that causes an IPSP is an inhibitory postsynaptic current (IPSC) and makes it more difficult for the neuron to fire an action potential. pr 2011-08-12T10:07:45Z positive regulation of IPSP positive regulation of inhibitory post-synaptic membrane potential biological_process GO:0097151 positive regulation of inhibitory postsynaptic potential Any process that activates or increases the frequency, rate or extent of inhibitory postsynaptic potential (IPSP). IPSP is a temporary decrease in postsynaptic membrane potential due to the flow of negatively charged ions into the postsynaptic cell. The flow of ions that causes an IPSP is an inhibitory postsynaptic current (IPSC) and makes it more difficult for the neuron to fire an action potential. GOC:BHF GOC:sjp PMID:18550748 Binding to an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure. pr 2011-09-23T02:31:01Z molecular_function GO:0097159 organic cyclic compound binding Binding to an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure. GOC:sjw PMID:7583672 The process whose specific outcome is the formation of tooth enamel, occurring in two stages: secretory stage and maturation stage. pr 2011-11-21T09:01:24Z enamel development biological_process GO:0097186 amelogenesis The process whose specific outcome is the formation of tooth enamel, occurring in two stages: secretory stage and maturation stage. GOC:cjm GOC:sl PMID:10206335 PMID:21196346 A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. pr 2011-11-23T09:45:24Z execution phase of apoptotic process apoptosis biological_process GO:0097194 execution phase of apoptosis A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. GOC:mtg_apoptosis PMID:21760595 Binding to a carbohydrate derivative. pr 2012-08-02T13:03:39Z molecular_function GO:0097367 carbohydrate derivative binding Binding to a carbohydrate derivative. GOC:pr The movement of a myeloid leukocyte within or between different tissues and organs of the body. pr 2013-11-11T13:59:43Z biological_process GO:0097529 myeloid leukocyte migration The movement of a myeloid leukocyte within or between different tissues and organs of the body. GOC:cvs PMID:22342843 PMID:24157461 The movement of a granulocyte within or between different tissues and organs of the body. pr 2013-11-11T14:00:44Z biological_process GO:0097530 granulocyte migration The movement of a granulocyte within or between different tissues and organs of the body. GOC:cvs PMID:24163421 PMID:24193336 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 process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces. pr 2016-08-05T16:16:28Z biological_process GO:0097712 vesicle targeting, trans-Golgi to periciliary membrane compartment The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces. GOC:cilia PMID:20106869 PMID:23351793 PMID:24814148 PMID:26485645 Reactome:R-HSA-5620920.1 Any process involved in the controlled movement of a sperm cell. pr 2016-09-01T12:00:45Z sperm movement biological_process GO:0097722 sperm motility Any process involved in the controlled movement of a sperm cell. GOC:cilia GOC:krc The assembly and secretion of an extracellular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. pr 2016-10-03T14:35:25Z exosome assembly or secretion exosome biogenesis exosome production biological_process ILV assembly intraluminal vesicle assembly GO:0097734 extracellular exosome biogenesis The assembly and secretion of an extracellular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. GOC:PARL GOC:bf PMID:19442504 PMID:25392495 OBSOLETE. Nucleus with two or more lobes connected by a thin filament that contains no internal chromatin. Examples include the nuclei of mature basophils, eosinophils and neutrophils in mice and humans. https://github.com/geneontology/go-ontology/issues/20764 dos 2013-10-22T18:31:36Z cellular_component GO:0098537 This term was obsoleted because it does not correspond to a specific type of nucleus, it is a morphologically different nucleus present in certain cell types. obsolete lobed nucleus true OBSOLETE. Nucleus with two or more lobes connected by a thin filament that contains no internal chromatin. Examples include the nuclei of mature basophils, eosinophils and neutrophils in mice and humans. GOC:dos GOC:tfm Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism. https://github.com/geneontology/go-ontology/issues/18737 dos 2013-11-11T12:59:11Z GO:0009814 defence response incompatible interaction defence response to pathogen, incompatible interaction defense response, incompatible interaction resistance response to pathogen biological_process GO:0098542 defense response to other organism Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism. GOC:dos 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 attachment of one cell to another cell via adhesion molecules. dos 2014-04-16T13:40:03Z GO:0016337 biological_process single organismal cell-cell adhesion GO:0098609 cell-cell adhesion The attachment of one cell to another cell via adhesion molecules. GOC:dos The binding by a cell-adhesion protein on a cell surface to an adhesion molecule on another cell surface, to mediate adhesion of the cell to the external substrate or to another cell. cell adhesion molecule protein binding involved in cell adhesion molecular_function GO:0098631 cell adhesion mediator activity The binding by a cell-adhesion protein on a cell surface to an adhesion molecule on another cell surface, to mediate adhesion of the cell to the external substrate or to another cell. GOC:vw Wikipedia:Cell_adhesion The binding by a cell-adhesion protein on the cell surface to an extracellular matrix component, to mediate adhesion of the cell to another cell. cell-cell adhesion molecule protein binding involved in cell-cell adhesion molecular_function GO:0098632 cell-cell adhesion mediator activity The binding by a cell-adhesion protein on the cell surface to an extracellular matrix component, to mediate adhesion of the cell to another cell. Wikipedia:Cell_adhesion 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 that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance. biological_process GO:0098754 detoxification Any process that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance. GOC:dos The part of a synapse that is part of the presynaptic cell. presynaptic terminal cellular_component GO:0098793 presynapse The part of a synapse that is part of the presynaptic cell. GOC:dos The part of a synapse that is part of the post-synaptic cell. cellular_component GO:0098794 postsynapse The part of a synapse that is part of the post-synaptic cell. GOC:dos Any protein complex that is part of a membrane. cellular_component GO:0098796 membrane protein complex Any protein complex that is part of a membrane. GOC:dos Any protein complex that is part of the plasma membrane. cellular_component GO:0098797 plasma membrane protein complex Any protein complex that is part of the plasma membrane. GOC:dos Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by the renal system. biological_process GO:0098801 regulation of renal system process Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by the renal system. GOC:dos Any protein complex that is part of the plasma membrane and which functions as a signaling receptor. cellular_component GO:0098802 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. plasma membrane signaling receptor complex Any protein complex that is part of the plasma membrane and which functions as a signaling receptor. GOC:dos The process in which genetic material, in the form of nuclear chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. Nuclear chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. biological_process GO:0098813 nuclear chromosome segregation The process in which genetic material, in the form of nuclear chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. Nuclear chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. GOC:dos Any process that modulates the frequency, rate or extent of excitatory postsynaptic potential (EPSP). EPSP is a process that leads to a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential. biological_process GO:0098815 modulation of excitatory postsynaptic potential Any process that modulates the frequency, rate or extent of excitatory postsynaptic potential (EPSP). EPSP is a process that leads to a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential. GOC:dos Any process that modulates the frequency, rate or extent of inhibitory postsynaptic potential (IPSP). IPSP is a temporary decrease in postsynaptic membrane potential due to the flow of negatively charged ions into the postsynaptic cell. The flow of ions that causes an IPSP is an inhibitory postsynaptic current (IPSC) and makes it more difficult for the neuron to fire an action potential. regulation of inhibitory postsynaptic potential biological_process GO:0098828 modulation of inhibitory postsynaptic potential Any process that modulates the frequency, rate or extent of inhibitory postsynaptic potential (IPSP). IPSP is a temporary decrease in postsynaptic membrane potential due to the flow of negatively charged ions into the postsynaptic cell. The flow of ions that causes an IPSP is an inhibitory postsynaptic current (IPSC) and makes it more difficult for the neuron to fire an action potential. GOC:dos A cell projection supported by an assembly of actin filaments, and which lacks microtubules. cellular_component GO:0098858 actin-based cell projection A cell projection supported by an assembly of actin filaments, and which lacks microtubules. PMID:15661519 The actin cytoskeleton that is part of a postsynapse. cellular_component GO:0098871 postsynaptic actin cytoskeleton The actin cytoskeleton that is part of a postsynapse. GOC:dos Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. biological_process GO:0098900 The ion channels through which current flows during an action potential should be annotated to the process 'action potential'. Gene products involved in modulating the characteristics of an action potential via changing the expression levels or the activity of these channels (e.g. modulating their kinetics or voltage sensitivity) should be annotated to this regulation term. regulation of action potential Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. GOC:dos GOC:dph GOC:go_curators GOC:tb ISBN:978-0-07-139011-8 Cell-cell signaling from pre to post-synapse, across the synaptic cleft. biological_process GO:0098916 anterograde trans-synaptic signaling Cell-cell signaling from pre to post-synapse, across the synaptic cleft. GOC:dos Synaptic transmission that results in an excitatory postsynaptic potential. biological_process GO:0098976 excitatory chemical synaptic transmission Synaptic transmission that results in an excitatory postsynaptic potential. GOC:dos Synaptic transmission that results in an inhibitory postsynaptic potential. biological_process GO:0098977 inhibitory chemical synaptic transmission Synaptic transmission that results in an inhibitory postsynaptic potential. GOC:dos Any vesicle-mediated transport that occurs in a synapse. biological_process GO:0099003 vesicle-mediated transport in synapse Any vesicle-mediated transport that occurs in a synapse. GOC:dos A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber. cellular_component GO:0099080 supramolecular complex A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber. GOC:dos A polymeric supramolecular structure. cellular_component GO:0099081 supramolecular polymer A polymeric supramolecular structure. GOC:dos A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. biological_process GO:0099111 microtubule-based transport A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. GOC:cjm ISBN:0815316194 The regulated release of dopamine from an axon. axonal DA release axonal dopamine release biological_process GO:0099124 axonal dopamine secretion The regulated release of dopamine from an axon. GOC:PARL GOC:bf PMID:21576241 axonal DA release PMID:21576241 axonal dopamine release PMID:21576241 The actin cytoskeleton that is part of a presynapse. dos 2017-06-09T18:36:19Z cellular_component GO:0099143 presynaptic actin cytoskeleton The actin cytoskeleton that is part of a presynapse. GOC:dos Any process, acting in the postsynapse that results in modulation of chemical synaptic transmission. dos 2017-09-11T17:09:17Z biological_process GO:0099170 postsynaptic modulation of chemical synaptic transmission Any process, acting in the postsynapse that results in modulation of chemical synaptic transmission. GOC:dos Any process, acting in the presynapse that results in modulation of chemical synaptic transmission. dos 2017-09-11T17:09:31Z biological_process GO:0099171 presynaptic modulation of chemical synaptic transmission Any process, acting in the presynapse that results in modulation of chemical synaptic transmission. GOC:dos Any process that modulates the frequency, rate or extent of trans-synaptic signaling. biological_process GO:0099177 regulation of trans-synaptic signaling Any process that modulates the frequency, rate or extent of trans-synaptic signaling. GOC:dos The component of the synaptic membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane. dos 2017-05-25T17:23:21Z intrinsic to synaptic membrane cellular_component GO:0099240 intrinsic component of synaptic membrane The component of the synaptic membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane. GOC:dos GOC:mah 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 A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. GO:0043205 cellular_component fibril GO:0099512 supramolecular fiber A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. GOC:dos A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits. cellular_component GO:0099513 polymeric cytoskeletal fiber A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits. GOC:dos The pathway leading to secretion of a neurotransmitter from the presynapse as part of synaptic transmission. biological_process GO:0099531 presynaptic process involved in chemical synaptic transmission The pathway leading to secretion of a neurotransmitter from the presynapse as part of synaptic transmission. GOC:dos Cell-cell signaling to, from or within a synapse. biological_process GO:0099536 synaptic signaling Cell-cell signaling to, from or within a synapse. GOC:dos Cell-cell signaling in either direction across the synaptic cleft. biological_process GO:0099537 trans-synaptic signaling Cell-cell signaling in either direction across the synaptic cleft. GOC:dos Cell-cell signaling between presynapse and postsynapse, across the synaptic cleft, that modulates the synaptic transmission properties of the synapse. biological_process GO:0099550 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. trans-synaptic signaling, modulating synaptic transmission Cell-cell signaling between presynapse and postsynapse, across the synaptic cleft, that modulates the synaptic transmission properties of the synapse. GOC:dos The part of synaptic transmission occurring in the post-synapse: a signal transduction pathway consisting of neurotransmitter receptor activation and its effects on postsynaptic membrane potential and the ionic composition of the postsynaptic cytosol. biological_process postsynaptic process involved in chemical synaptic transmission GO:0099565 chemical synaptic transmission, postsynaptic The part of synaptic transmission occurring in the post-synapse: a signal transduction pathway consisting of neurotransmitter receptor activation and its effects on postsynaptic membrane potential and the ionic composition of the postsynaptic cytosol. GOC:dos postsynaptic process involved in chemical synaptic transmission 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 portion of the cytoskeleton contained within the presynapse. cellular_component GO:0099569 presynaptic cytoskeleton The portion of the cytoskeleton contained within the presynapse. GOC:dos The portion of the cytoskeleton contained within the postsynapse. cellular_component GO:0099571 postsynaptic cytoskeleton The portion of the cytoskeleton contained within the postsynapse. GOC:dos PMID:19889835 Any signal release from a synapse. biological_process GO:0099643 signal release from synapse Any signal release from a synapse. GOC:dos The component of the synaptic membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. dos 2017-05-25T17:22:18Z cellular_component GO:0099699 integral component of synaptic membrane The component of the synaptic membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. 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 inflammatory response to wounding. hjd 2017-04-28T20:03:14Z biological_process GO:0106014 regulation of inflammatory response to wounding Any process that modulates the frequency, rate or extent of the inflammatory response to wounding. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:26022821 Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response to wounding. hjd 2017-04-28T20:09:46Z biological_process GO:0106015 negative regulation of inflammatory response to wounding Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response to wounding. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:26022821 Any process that activates or increases the frequency, rate or extent of the inflammatory response to wounding. hjd 2017-04-28T20:16:31Z biological_process GO:0106016 positive regulation of inflammatory response to wounding Any process that activates or increases the frequency, rate or extent of the inflammatory response to wounding. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:26022821 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 A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13193 krc 2017-03-21T17:26:07Z cellular_component GO:0120025 plasma membrane bounded cell projection A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. GOC:krc Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-24T23:56:08Z eupodium biological_process GO:0120031 plasma membrane bounded cell projection assembly Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. GOC:krc eupodium GOC:krc GOC:rjd PMID:10328951 PMID:9096956 Any process that modulates the rate, frequency, or extent of plasma membrane bounded cell projection assembly. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-26T04:27:04Z biological_process GO:0120032 regulation of plasma membrane bounded cell projection assembly Any process that modulates the rate, frequency, or extent of plasma membrane bounded cell projection assembly. GOC:krc Any process that stops, prevents or reduces the frequency, rate or extent of plasma membrane bounded cell projection assembly. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-26T04:34:31Z biological_process GO:0120033 negative regulation of plasma membrane bounded cell projection assembly Any process that stops, prevents or reduces the frequency, rate or extent of plasma membrane bounded cell projection assembly. GOC:krc Any process that activates or increases the frequency, rate or extent of plasma membrane bounded cell projection assembly. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-26T04:34:45Z biological_process GO:0120034 positive regulation of plasma membrane bounded cell projection assembly Any process that activates or increases the frequency, rate or extent of plasma membrane bounded cell projection assembly. GOC:krc Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of plasma membrane bounded cell projections. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-26T16:02:06Z biological_process GO:0120035 regulation of plasma membrane bounded cell projection organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of plasma membrane bounded cell projections. GOC:krc A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-26T16:07:02Z biological_process GO:0120036 plasma membrane bounded cell projection organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon. GOC:krc All of the contents of a plasma membrane bounded neuron projection, excluding the plasma membrane surrounding the projection. krc 2017-11-01T18:58:12Z cellular_component GO:0120111 neuron projection cytoplasm All of the contents of a plasma membrane bounded neuron projection, excluding the plasma membrane surrounding the projection. GOC:ha Any process that modulates the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue. krc 2018-07-16T22:28:58Z biological_process GO:0120188 regulation of bile acid secretion Any process that modulates the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:22767443 Any process that activates or increases the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue. krc 2018-07-16T22:36:17Z biological_process GO:0120189 positive regulation of bile acid secretion Any process that activates or increases the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:22767443 Any process that stops, prevents or reduces the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue. krc 2018-07-16T22:38:34Z biological_process GO:0120190 negative regulation of bile acid secretion Any process that stops, prevents or reduces the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:22767443 The assembly and organization of the sperm flagellum, the microtubule-based axoneme and associated structures that are part of a sperm flagellum (or cilium). krc 2021-04-29T01:27:27Z biological_process GO:0120316 sperm flagellum assembly The assembly and organization of the sperm flagellum, the microtubule-based axoneme and associated structures that are part of a sperm flagellum (or cilium). GOC:krc PMID:32791035 One of the two nuclear divisions that occur as part of the meiotic cell cycle. https://github.com/geneontology/go-ontology/issues/19910 pg 2017-03-23T09:40:00Z meiosis biological_process GO:0140013 meiotic nuclear division One of the two nuclear divisions that occur as part of the meiotic cell cycle. PMID:9334324 A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. https://github.com/geneontology/go-ontology/issues/19910 pg 2017-03-23T14:44:23Z mitosis biological_process GO:0140014 mitotic nuclear division A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. ISBN:0198547684 The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content. https://github.com/geneontology/go-ontology/issues/14256 pg 2017-10-23T11:53:42Z extracellular vesicle assembly biological_process GO:0140112 extracellular vesicle biogenesis The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content. PMID:28736435 A vesicle-mediated transport process in which the presynapse take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle. https://github.com/geneontology/synapse/issues/230 pg 2018-07-15T07:33:55Z biological_process GO:0140238 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. presynaptic endocytosis A vesicle-mediated transport process in which the presynapse take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle. PMID:24719103 A vesicle-mediated transport process in which the postsynapse take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle. https://github.com/geneontology/synapse/issues/230 pg 2018-07-15T07:38:27Z biological_process GO:0140239 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. postsynaptic endocytosis A vesicle-mediated transport process in which the postsynapse take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle. PMID:12839988 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 Receiving a signal and transmitting it in a cell to initiate an immune response. pg 2019-10-18T14:11:15Z molecular_function GO:0140375 immune receptor activity Receiving a signal and transmitting it in a cell to initiate an immune response. PMID:31415752 Wikipedia:Immune_receptor 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 in the nucleus. pg 2020-09-09T05:12:38Z nuclear complex cellular_component GO:0140513 nuclear protein-containing 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 in the nucleus. GOC:pg Any process that modulates the frequency, rate or extent of cytokine production involved in inflammatory response. rph 2012-01-11T09:34:27Z regulation of cytokine production involved in acute inflammatory response biological_process GO:1900015 regulation of cytokine production involved in inflammatory response Any process that modulates the frequency, rate or extent of cytokine production involved in inflammatory response. GOC:TermGenie regulation of cytokine production involved in acute inflammatory response GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cytokine production involved in inflammatory response. rph 2012-01-11T09:34:31Z down regulation of cytokine production involved in acute inflammatory response negative regulation of cytokine production involved in acute inflammatory response biological_process down regulation of cytokine production involved in inflammatory response GO:1900016 negative regulation of cytokine production involved in inflammatory response Any process that stops, prevents or reduces the frequency, rate or extent of cytokine production involved in inflammatory response. GOC:TermGenie down regulation of cytokine production involved in acute inflammatory response GOC:TermGenie negative regulation of cytokine production involved in acute inflammatory response GOC:TermGenie down regulation of cytokine production involved in inflammatory response GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cytokine production involved in inflammatory response. rph 2012-01-11T09:34:35Z up regulation of cytokine production involved in acute inflammatory response positive regulation of cytokine production involved in acute inflammatory response biological_process up regulation of cytokine production involved in inflammatory response GO:1900017 positive regulation of cytokine production involved in inflammatory response Any process that activates or increases the frequency, rate or extent of cytokine production involved in inflammatory response. GOC:TermGenie up regulation of cytokine production involved in acute inflammatory response GOC:TermGenie positive regulation of cytokine production involved in acute inflammatory response GOC:TermGenie up regulation of cytokine production involved in inflammatory response GOC:TermGenie Any process that modulates the frequency, rate or extent of hemostasis. jl 2012-01-19T03:23:38Z biological_process GO:1900046 regulation of hemostasis Any process that modulates the frequency, rate or extent of hemostasis. GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of hemostasis. jl 2012-01-19T03:23:42Z down regulation of hemostasis down-regulation of hemostasis downregulation of hemostasis inhibition of hemostasis biological_process GO:1900047 negative regulation of hemostasis Any process that stops, prevents or reduces the frequency, rate or extent of hemostasis. GOC:TermGenie down regulation of hemostasis GOC:TermGenie down-regulation of hemostasis GOC:TermGenie downregulation of hemostasis GOC:TermGenie inhibition of hemostasis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of hemostasis. jl 2012-01-19T03:23:45Z up regulation of hemostasis up-regulation of hemostasis upregulation of hemostasis activation of hemostasis biological_process GO:1900048 positive regulation of hemostasis Any process that activates or increases the frequency, rate or extent of hemostasis. GOC:TermGenie up regulation of hemostasis GOC:TermGenie up-regulation of hemostasis GOC:TermGenie upregulation of hemostasis GOC:TermGenie activation of hemostasis GOC:TermGenie Any regulation of signal transduction that takes place in the extracellular region. bf 2012-02-22T10:21:48Z regulation of signaling pathway in extracellular region regulation of signalling pathway in extracellular region biological_process GO:1900115 extracellular regulation of signal transduction Any regulation of signal transduction that takes place in the extracellular region. GOC:TermGenie GOC:signaling regulation of signaling pathway in extracellular region GOC:TermGenie regulation of signalling pathway in extracellular region GOC:TermGenie Any negative regulation of signal transduction that takes place in extracellular region. bf 2012-02-22T10:27:56Z down regulation of signal transduction in extracellular region down-regulation of signal transduction in extracellular region downregulation of signal transduction in extracellular region negative regulation of signaling pathway in extracellular region negative regulation of signalling pathway in extracellular region extracellular inhibition of signaling pathway inhibition of signal transduction in extracellular region biological_process GO:1900116 extracellular negative regulation of signal transduction Any negative regulation of signal transduction that takes place in extracellular region. GOC:TermGenie GOC:signaling down regulation of signal transduction in extracellular region GOC:TermGenie down-regulation of signal transduction in extracellular region GOC:TermGenie downregulation of signal transduction in extracellular region GOC:TermGenie negative regulation of signaling pathway in extracellular region GOC:TermGenie negative regulation of signalling pathway in extracellular region GOC:TermGenie extracellular inhibition of signaling pathway GOC:bf inhibition of signal transduction in extracellular region GOC:TermGenie Any process that modulates the frequency, rate or extent of execution phase of apoptosis. pr 2012-02-22T11:26:20Z biological_process GO:1900117 regulation of execution phase of apoptosis Any process that modulates the frequency, rate or extent of execution phase of apoptosis. GOC:TermGenie GOC:mtg_apoptosis Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis. pr 2012-02-22T11:26:24Z down regulation of execution phase of apoptosis down-regulation of execution phase of apoptosis downregulation of execution phase of apoptosis inhibition of execution phase of apoptosis biological_process GO:1900118 negative regulation of execution phase of apoptosis Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis. GOC:TermGenie GOC:mtg_apoptosis down regulation of execution phase of apoptosis GOC:TermGenie down-regulation of execution phase of apoptosis GOC:TermGenie downregulation of execution phase of apoptosis GOC:TermGenie inhibition of execution phase of apoptosis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis. pr 2012-02-22T11:26:27Z up regulation of execution phase of apoptosis up-regulation of execution phase of apoptosis upregulation of execution phase of apoptosis activation of execution phase of apoptosis biological_process GO:1900119 positive regulation of execution phase of apoptosis Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis. GOC:TermGenie GOC:mtg_apoptosis up regulation of execution phase of apoptosis GOC:TermGenie up-regulation of execution phase of apoptosis GOC:TermGenie upregulation of execution phase of apoptosis GOC:TermGenie activation of execution phase of apoptosis GOC:TermGenie 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 Any process that modulates the frequency, rate or extent of lipid binding. pm 2012-02-23T04:05:03Z biological_process GO:1900130 regulation of lipid binding Any process that modulates the frequency, rate or extent of lipid binding. GOC:TermGenie GOC:pm Any process that stops, prevents or reduces the frequency, rate or extent of lipid binding. pm 2012-02-23T04:05:07Z down regulation of lipid binding down-regulation of lipid binding downregulation of lipid binding inhibition of lipid binding biological_process GO:1900131 negative regulation of lipid binding Any process that stops, prevents or reduces the frequency, rate or extent of lipid binding. GOC:TermGenie GOC:pm down regulation of lipid binding GOC:TermGenie down-regulation of lipid binding GOC:TermGenie downregulation of lipid binding GOC:TermGenie inhibition of lipid binding GOC:TermGenie Any process that activates or increases the frequency, rate or extent of lipid binding. pm 2012-02-23T04:05:11Z up regulation of lipid binding up-regulation of lipid binding upregulation of lipid binding activation of lipid binding biological_process GO:1900132 positive regulation of lipid binding Any process that activates or increases the frequency, rate or extent of lipid binding. GOC:TermGenie GOC:pm up regulation of lipid binding GOC:TermGenie up-regulation of lipid binding GOC:TermGenie upregulation of lipid binding GOC:TermGenie activation of lipid binding GOC:TermGenie Any process that modulates the frequency, rate or extent of renin secretion into blood stream. rph 2012-02-27T10:32:01Z regulation of renin release into blood stream biological_process GO:1900133 regulation of renin secretion into blood stream Any process that modulates the frequency, rate or extent of renin secretion into blood stream. GOC:TermGenie regulation of renin release into blood stream GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of renin secretion into blood stream. rph 2012-02-27T10:32:05Z down regulation of renin release into blood stream down regulation of renin secretion into blood stream down-regulation of renin release into blood stream down-regulation of renin secretion into blood stream downregulation of renin release into blood stream downregulation of renin secretion into blood stream negative regulation of renin release into blood stream inhibition of renin release into blood stream inhibition of renin secretion into blood stream biological_process GO:1900134 negative regulation of renin secretion into blood stream Any process that stops, prevents or reduces the frequency, rate or extent of renin secretion into blood stream. GOC:TermGenie down regulation of renin release into blood stream GOC:TermGenie down regulation of renin secretion into blood stream GOC:TermGenie down-regulation of renin release into blood stream GOC:TermGenie down-regulation of renin secretion into blood stream GOC:TermGenie downregulation of renin release into blood stream GOC:TermGenie downregulation of renin secretion into blood stream GOC:TermGenie negative regulation of renin release into blood stream GOC:TermGenie inhibition of renin release into blood stream GOC:TermGenie inhibition of renin secretion into blood stream GOC:TermGenie Any process that activates or increases the frequency, rate or extent of renin secretion into blood stream. rph 2012-02-27T10:32:08Z positive regulation of renin release into blood stream up regulation of renin release into blood stream up regulation of renin secretion into blood stream up-regulation of renin release into blood stream up-regulation of renin secretion into blood stream upregulation of renin release into blood stream upregulation of renin secretion into blood stream activation of renin release into blood stream activation of renin secretion into blood stream biological_process GO:1900135 positive regulation of renin secretion into blood stream Any process that activates or increases the frequency, rate or extent of renin secretion into blood stream. GOC:TermGenie positive regulation of renin release into blood stream GOC:TermGenie up regulation of renin release into blood stream GOC:TermGenie up regulation of renin secretion into blood stream GOC:TermGenie up-regulation of renin release into blood stream GOC:TermGenie up-regulation of renin secretion into blood stream GOC:TermGenie upregulation of renin release into blood stream GOC:TermGenie upregulation of renin secretion into blood stream GOC:TermGenie activation of renin release into blood stream GOC:TermGenie activation of renin secretion into blood stream GOC:TermGenie Any process that modulates the frequency, rate or extent of defense response to bacterium. dhl 2012-04-24T10:12:43Z GO:1902477 regulation of defence response to bacteria regulation of defence response to bacterium regulation of defense response to bacteria regulation of defence response to bacterium, incompatible interaction regulation of defence response to pathogenic bacteria, incompatible interaction regulation of defence response to pathogenic bacterium, incompatible interaction regulation of defense response to bacterium, incompatible interaction regulation of resistance response to pathogenic bacteria regulation of resistance response to pathogenic bacterium biological_process regulation of antibacterial peptide activity GO:1900424 regulation of defense response to bacterium Any process that modulates the frequency, rate or extent of defense response to bacterium. GOC:TermGenie PMID:22346749 regulation of defence response to bacteria GOC:TermGenie regulation of defence response to bacterium GOC:TermGenie regulation of defense response to bacteria GOC:TermGenie regulation of defence response to bacterium, incompatible interaction GOC:TermGenie regulation of defence response to pathogenic bacteria, incompatible interaction GOC:TermGenie regulation of defence response to pathogenic bacterium, incompatible interaction GOC:TermGenie regulation of resistance response to pathogenic bacteria GOC:TermGenie regulation of resistance response to pathogenic bacterium GOC:TermGenie regulation of antibacterial peptide activity GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of defense response to bacterium. dhl 2012-04-24T10:12:54Z GO:1902478 down regulation of defence response to bacteria down regulation of defence response to bacterium down regulation of defense response to bacteria down regulation of defense response to bacterium down-regulation of defence response to bacteria down-regulation of defence response to bacterium down-regulation of defense response to bacteria down-regulation of defense response to bacterium downregulation of defence response to bacteria downregulation of defence response to bacterium downregulation of defense response to bacteria downregulation of defense response to bacterium inhibition of defence response to bacteria inhibition of defence response to bacterium inhibition of defense response to bacteria negative regulation of defence response to bacteria negative regulation of defence response to bacterium negative regulation of defense response to bacteria inhibition of defence response to pathogenic bacteria, incompatible interaction inhibition of defence response to pathogenic bacterium, incompatible interaction inhibition of defense response to bacterium inhibition of defense response to bacterium, incompatible interaction inhibition of resistance response to pathogenic bacteria inhibition of resistance response to pathogenic bacterium inhibition of response to pathogenic bacteria (incompatible interaction) inhibition of response to pathogenic bacterium (incompatible interaction) negative regulation of defense response to bacterium, incompatible interaction biological_process down regulation of antibacterial peptide activity down-regulation of antibacterial peptide activity downregulation of antibacterial peptide activity inhibition of antibacterial peptide activity negative regulation of antibacterial peptide activity GO:1900425 negative regulation of defense response to bacterium Any process that stops, prevents or reduces the frequency, rate or extent of defense response to bacterium. GOC:TermGenie PMID:22346749 down regulation of defence response to bacteria GOC:TermGenie down regulation of defence response to bacterium GOC:TermGenie down regulation of defense response to bacteria GOC:TermGenie down regulation of defense response to bacterium GOC:TermGenie down-regulation of defence response to bacteria GOC:TermGenie down-regulation of defence response to bacterium GOC:TermGenie down-regulation of defense response to bacteria GOC:TermGenie down-regulation of defense response to bacterium GOC:TermGenie downregulation of defence response to bacteria GOC:TermGenie downregulation of defence response to bacterium GOC:TermGenie downregulation of defense response to bacteria GOC:TermGenie downregulation of defense response to bacterium GOC:TermGenie inhibition of defence response to bacteria GOC:TermGenie inhibition of defence response to bacterium GOC:TermGenie inhibition of defense response to bacteria GOC:TermGenie negative regulation of defence response to bacteria GOC:TermGenie negative regulation of defence response to bacterium GOC:TermGenie negative regulation of defense response to bacteria GOC:TermGenie inhibition of defence response to pathogenic bacteria, incompatible interaction GOC:TermGenie inhibition of defence response to pathogenic bacterium, incompatible interaction GOC:TermGenie inhibition of defense response to bacterium GOC:TermGenie inhibition of defense response to bacterium, incompatible interaction GOC:TermGenie inhibition of resistance response to pathogenic bacteria GOC:TermGenie inhibition of resistance response to pathogenic bacterium GOC:TermGenie inhibition of response to pathogenic bacteria (incompatible interaction) GOC:TermGenie inhibition of response to pathogenic bacterium (incompatible interaction) GOC:TermGenie down regulation of antibacterial peptide activity GOC:TermGenie down-regulation of antibacterial peptide activity GOC:TermGenie downregulation of antibacterial peptide activity GOC:TermGenie inhibition of antibacterial peptide activity GOC:TermGenie negative regulation of antibacterial peptide activity GOC:TermGenie Any process that activates or increases the frequency, rate or extent of defense response to bacterium. dhl 2012-04-24T10:13:13Z GO:1902479 activation of defence response to bacteria activation of defence response to bacterium activation of defense response to bacteria positive regulation of defence response to bacteria positive regulation of defence response to bacterium positive regulation of defense response to bacteria up regulation of defence response to bacteria up regulation of defence response to bacterium up regulation of defense response to bacteria up regulation of defense response to bacterium up-regulation of defence response to bacteria up-regulation of defence response to bacterium up-regulation of defense response to bacteria up-regulation of defense response to bacterium upregulation of defence response to bacteria upregulation of defence response to bacterium upregulation of defense response to bacteria upregulation of defense response to bacterium activation of defense response to bacterium activation of resistance response to pathogenic bacteria activation of resistance response to pathogenic bacterium positive regulation of defense response to bacterium, incompatible interaction biological_process activation of antibacterial peptide activity positive regulation of antibacterial peptide activity up regulation of antibacterial peptide activity up-regulation of antibacterial peptide activity upregulation of antibacterial peptide activity GO:1900426 positive regulation of defense response to bacterium Any process that activates or increases the frequency, rate or extent of defense response to bacterium. GOC:TermGenie PMID:22346749 activation of defence response to bacteria GOC:TermGenie activation of defence response to bacterium GOC:TermGenie activation of defense response to bacteria GOC:TermGenie positive regulation of defence response to bacteria GOC:TermGenie positive regulation of defence response to bacterium GOC:TermGenie positive regulation of defense response to bacteria GOC:TermGenie up regulation of defence response to bacteria GOC:TermGenie up regulation of defence response to bacterium GOC:TermGenie up regulation of defense response to bacteria GOC:TermGenie up regulation of defense response to bacterium GOC:TermGenie up-regulation of defence response to bacteria GOC:TermGenie up-regulation of defence response to bacterium GOC:TermGenie up-regulation of defense response to bacteria GOC:TermGenie up-regulation of defense response to bacterium GOC:TermGenie upregulation of defence response to bacteria GOC:TermGenie upregulation of defence response to bacterium GOC:TermGenie upregulation of defense response to bacteria GOC:TermGenie upregulation of defense response to bacterium GOC:TermGenie activation of defense response to bacterium GOC:TermGenie activation of resistance response to pathogenic bacteria GOC:TermGenie activation of resistance response to pathogenic bacterium GOC:TermGenie activation of antibacterial peptide activity GOC:TermGenie positive regulation of antibacterial peptide activity GOC:TermGenie up regulation of antibacterial peptide activity GOC:TermGenie up-regulation of antibacterial peptide activity GOC:TermGenie upregulation of antibacterial peptide activity GOC:TermGenie The chemical reactions and pathways involving carbohydrate derivative. bf 2012-07-12T04:05:09Z carbohydrate derivative metabolism biological_process GO:1901135 carbohydrate derivative metabolic process The chemical reactions and pathways involving carbohydrate derivative. GOC:TermGenie carbohydrate derivative metabolism GOC:TermGenie The chemical reactions and pathways resulting in the formation of carbohydrate derivative. bf 2012-07-12T04:05:39Z carbohydrate derivative anabolism carbohydrate derivative biosynthesis carbohydrate derivative formation carbohydrate derivative synthesis biological_process GO:1901137 carbohydrate derivative biosynthetic process The chemical reactions and pathways resulting in the formation of carbohydrate derivative. GOC:TermGenie carbohydrate derivative anabolism GOC:TermGenie carbohydrate derivative biosynthesis GOC:TermGenie carbohydrate derivative formation GOC:TermGenie carbohydrate derivative synthesis GOC:TermGenie Any gene expression that is involved in extracellular matrix organization. Gene expression includes both transcription to produce an RNA transcript, and the translation of that mRNA into protein. Protein maturation is included in gene expression when required to form an active form of a product from an inactive precursor form. bf 2012-07-16T03:29:30Z expression of extracellular matrix proteins biological_process extracellular matrix protein production GO:1901148 gene expression involved in extracellular matrix organization Any gene expression that is involved in extracellular matrix organization. Gene expression includes both transcription to produce an RNA transcript, and the translation of that mRNA into protein. Protein maturation is included in gene expression when required to form an active form of a product from an inactive precursor form. GOC:TermGenie GOC:pg PMID:18668558 expression of extracellular matrix proteins GOC:bf extracellular matrix protein production GOC:pg Any process that modulates the frequency, rate or extent of flagellated sperm motility. hjd 2012-08-22T20:50:14Z regulation of sperm motility regulation of sperm movement biological_process GO:1901317 regulation of flagellated sperm motility Any process that modulates the frequency, rate or extent of flagellated sperm motility. GOC:TermGenie GOC:cilia GOC:krc regulation of sperm movement GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of flagellated sperm motility. hjd 2012-08-22T20:50:35Z down regulation of sperm motility down regulation of sperm movement down-regulation of sperm motility down-regulation of sperm movement downregulation of sperm motility downregulation of sperm movement inhibition of sperm movement negative regulation of sperm motility negative regulation of sperm movement inhibition of sperm motility biological_process GO:1901318 negative regulation of flagellated sperm motility Any process that stops, prevents or reduces the frequency, rate or extent of flagellated sperm motility. GOC:TermGenie GOC:cilia GOC:krc down regulation of sperm motility GOC:TermGenie down regulation of sperm movement GOC:TermGenie down-regulation of sperm motility GOC:TermGenie down-regulation of sperm movement GOC:TermGenie downregulation of sperm motility GOC:TermGenie downregulation of sperm movement GOC:TermGenie inhibition of sperm movement GOC:TermGenie negative regulation of sperm movement GOC:TermGenie inhibition of sperm motility GOC:TermGenie Any process that modulates the frequency, rate or extent of vasculature development. bf 2012-09-06T09:16:15Z biological_process regulation of vascular system development GO:1901342 regulation of vasculature development Any process that modulates the frequency, rate or extent of vasculature development. GOC:TermGenie regulation of vascular system development GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of vasculature development. bf 2012-09-06T09:17:24Z down regulation of vasculature development down-regulation of vasculature development downregulation of vasculature development inhibition of vasculature development biological_process down regulation of vascular system development down-regulation of vascular system development downregulation of vascular system development inhibition of vascular system development negative regulation of vascular system development GO:1901343 negative regulation of vasculature development Any process that stops, prevents or reduces the frequency, rate or extent of vasculature development. GOC:TermGenie down regulation of vasculature development GOC:TermGenie down-regulation of vasculature development GOC:TermGenie downregulation of vasculature development GOC:TermGenie inhibition of vasculature development GOC:TermGenie down regulation of vascular system development GOC:TermGenie down-regulation of vascular system development GOC:TermGenie downregulation of vascular system development GOC:TermGenie inhibition of vascular system development GOC:TermGenie negative regulation of vascular system development 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 The chemical reactions and pathways resulting in the formation of organic cyclic compound. bf 2012-09-14T09:05:22Z organic cyclic compound anabolism organic cyclic compound biosynthesis organic cyclic compound formation organic cyclic compound synthesis biological_process GO:1901362 organic cyclic compound biosynthetic process The chemical reactions and pathways resulting in the formation of organic cyclic compound. GOC:TermGenie organic cyclic compound anabolism GOC:TermGenie organic cyclic compound biosynthesis GOC:TermGenie organic cyclic compound formation GOC:TermGenie organic cyclic compound synthesis GOC:TermGenie Binding to heterocyclic compound. bf 2012-09-14T13:53:50Z molecular_function GO:1901363 heterocyclic compound binding Binding to heterocyclic compound. GOC:TermGenie The directed movement of an acetate ester into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. bf 2012-09-28T10:42:13Z biological_process GO:1901374 acetate ester transport The directed movement of an acetate ester into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:TermGenie Any process that modulates the frequency, rate or extent of hematopoietic progenitor cell differentiation. vk 2012-10-24T11:23:01Z regulation of haematopoietic progenitor cell differentiation regulation of haemopoietic progenitor cell differentiation regulation of hemopoietic progenitor cell differentiation biological_process GO:1901532 regulation of hematopoietic progenitor cell differentiation Any process that modulates the frequency, rate or extent of hematopoietic progenitor cell differentiation. GOC:BHF GOC:TermGenie GOC:rl regulation of haematopoietic progenitor cell differentiation GOC:TermGenie regulation of haemopoietic progenitor cell differentiation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic progenitor cell differentiation. vk 2012-10-24T11:23:06Z down regulation of haematopoietic progenitor cell differentiation down regulation of haemopoietic progenitor cell differentiation down regulation of hemopoietic progenitor cell differentiation down-regulation of haematopoietic progenitor cell differentiation down-regulation of haemopoietic progenitor cell differentiation down-regulation of hemopoietic progenitor cell differentiation downregulation of haematopoietic progenitor cell differentiation downregulation of haemopoietic progenitor cell differentiation downregulation of hemopoietic progenitor cell differentiation inhibition of haematopoietic progenitor cell differentiation inhibition of haemopoietic progenitor cell differentiation negative regulation of haematopoietic progenitor cell differentiation negative regulation of haemopoietic progenitor cell differentiation negative regulation of hemopoietic progenitor cell differentiation inhibition of hemopoietic progenitor cell differentiation biological_process down regulation of hematopoietic progenitor cell differentiation down-regulation of hematopoietic progenitor cell differentiation downregulation of hematopoietic progenitor cell differentiation inhibition of hematopoietic progenitor cell differentiation GO:1901533 negative regulation of hematopoietic progenitor cell differentiation Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic progenitor cell differentiation. GOC:BHF GOC:TermGenie GOC:rl down regulation of haematopoietic progenitor cell differentiation GOC:TermGenie down regulation of haemopoietic progenitor cell differentiation GOC:TermGenie down regulation of hemopoietic progenitor cell differentiation GOC:TermGenie down-regulation of haematopoietic progenitor cell differentiation GOC:TermGenie down-regulation of haemopoietic progenitor cell differentiation GOC:TermGenie down-regulation of hemopoietic progenitor cell differentiation GOC:TermGenie downregulation of haematopoietic progenitor cell differentiation GOC:TermGenie downregulation of haemopoietic progenitor cell differentiation GOC:TermGenie downregulation of hemopoietic progenitor cell differentiation GOC:TermGenie inhibition of haematopoietic progenitor cell differentiation GOC:TermGenie inhibition of haemopoietic progenitor cell differentiation GOC:TermGenie negative regulation of haematopoietic progenitor cell differentiation GOC:TermGenie negative regulation of haemopoietic progenitor cell differentiation GOC:TermGenie inhibition of hemopoietic progenitor cell differentiation GOC:TermGenie down regulation of hematopoietic progenitor cell differentiation GOC:TermGenie down-regulation of hematopoietic progenitor cell differentiation GOC:TermGenie downregulation of hematopoietic progenitor cell differentiation GOC:TermGenie inhibition of hematopoietic progenitor cell differentiation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of hematopoietic progenitor cell differentiation. vk 2012-10-24T11:23:14Z activation of haematopoietic progenitor cell differentiation activation of haemopoietic progenitor cell differentiation positive regulation of haematopoietic progenitor cell differentiation positive regulation of haemopoietic progenitor cell differentiation positive regulation of hemopoietic progenitor cell differentiation up regulation of haematopoietic progenitor cell differentiation up regulation of haemopoietic progenitor cell differentiation up regulation of hemopoietic progenitor cell differentiation up-regulation of haematopoietic progenitor cell differentiation up-regulation of haemopoietic progenitor cell differentiation up-regulation of hemopoietic progenitor cell differentiation upregulation of haematopoietic progenitor cell differentiation upregulation of haemopoietic progenitor cell differentiation upregulation of hemopoietic progenitor cell differentiation activation of hemopoietic progenitor cell differentiation biological_process activation of hematopoietic progenitor cell differentiation up regulation of hematopoietic progenitor cell differentiation up-regulation of hematopoietic progenitor cell differentiation upregulation of hematopoietic progenitor cell differentiation GO:1901534 positive regulation of hematopoietic progenitor cell differentiation Any process that activates or increases the frequency, rate or extent of hematopoietic progenitor cell differentiation. GOC:BHF GOC:TermGenie GOC:rl activation of haematopoietic progenitor cell differentiation GOC:TermGenie activation of haemopoietic progenitor cell differentiation GOC:TermGenie positive regulation of haematopoietic progenitor cell differentiation GOC:TermGenie positive regulation of haemopoietic progenitor cell differentiation GOC:TermGenie up regulation of haematopoietic progenitor cell differentiation GOC:TermGenie up regulation of haemopoietic progenitor cell differentiation GOC:TermGenie up regulation of hemopoietic progenitor cell differentiation GOC:TermGenie up-regulation of haematopoietic progenitor cell differentiation GOC:TermGenie up-regulation of haemopoietic progenitor cell differentiation GOC:TermGenie up-regulation of hemopoietic progenitor cell differentiation GOC:TermGenie upregulation of haematopoietic progenitor cell differentiation GOC:TermGenie upregulation of haemopoietic progenitor cell differentiation GOC:TermGenie upregulation of hemopoietic progenitor cell differentiation GOC:TermGenie activation of hemopoietic progenitor cell differentiation GOC:TermGenie activation of hematopoietic progenitor cell differentiation GOC:TermGenie up regulation of hematopoietic progenitor cell differentiation GOC:TermGenie up-regulation of hematopoietic progenitor cell differentiation GOC:TermGenie upregulation of hematopoietic progenitor cell differentiation 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 resulting in the formation of organonitrogen compound. pr 2012-11-04T15:18:00Z organonitrogen compound anabolism organonitrogen compound biosynthesis organonitrogen compound formation organonitrogen compound synthesis biological_process GO:1901566 organonitrogen compound biosynthetic process The chemical reactions and pathways resulting in the formation of organonitrogen compound. GOC:TermGenie GOC:pr organonitrogen compound anabolism GOC:TermGenie organonitrogen compound biosynthesis GOC:TermGenie organonitrogen compound formation GOC:TermGenie organonitrogen compound 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 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 resulting in the formation of organic hydroxy compound. pr 2012-11-13T12:54:36Z organic hydroxy compound anabolism organic hydroxy compound biosynthesis organic hydroxy compound formation organic hydroxy compound synthesis biological_process GO:1901617 organic hydroxy compound biosynthetic process The chemical reactions and pathways resulting in the formation of organic hydroxy compound. GOC:TermGenie GOC:pr organic hydroxy compound anabolism GOC:TermGenie organic hydroxy compound biosynthesis GOC:TermGenie organic hydroxy compound formation GOC:TermGenie organic hydroxy compound synthesis GOC:TermGenie Any process that modulates the frequency, rate or extent of cilium assembly. dph 2013-03-26T18:10:51Z regulation of ciliogenesis biological_process regulation of cilium biogenesis GO:1902017 regulation of cilium assembly Any process that modulates the frequency, rate or extent of cilium assembly. GOC:TermGenie GOC:cilia GOC:dph PMID:17719545 regulation of ciliogenesis GOC:TermGenie regulation of cilium biogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cilium assembly. dph 2013-03-26T18:10:56Z down regulation of ciliogenesis down regulation of cilium assembly down-regulation of ciliogenesis down-regulation of cilium assembly downregulation of ciliogenesis downregulation of cilium assembly inhibition of ciliogenesis negative regulation of ciliogenesis inhibition of cilium assembly biological_process down regulation of cilium biogenesis down-regulation of cilium biogenesis downregulation of cilium biogenesis inhibition of cilium biogenesis negative regulation of cilium biogenesis GO:1902018 negative regulation of cilium assembly Any process that stops, prevents or reduces the frequency, rate or extent of cilium assembly. GOC:TermGenie GOC:cilia GOC:dph PMID:17719545 down regulation of ciliogenesis GOC:TermGenie down regulation of cilium assembly GOC:TermGenie down-regulation of ciliogenesis GOC:TermGenie down-regulation of cilium assembly GOC:TermGenie downregulation of ciliogenesis GOC:TermGenie downregulation of cilium assembly GOC:TermGenie inhibition of ciliogenesis GOC:TermGenie negative regulation of ciliogenesis GOC:TermGenie inhibition of cilium assembly GOC:TermGenie down regulation of cilium biogenesis GOC:TermGenie down-regulation of cilium biogenesis GOC:TermGenie downregulation of cilium biogenesis GOC:TermGenie inhibition of cilium biogenesis GOC:TermGenie negative regulation of cilium biogenesis GOC:TermGenie Any process that modulates the frequency, rate or extent of cilium-dependent cell motility. jl 2013-03-27T14:42:38Z regulation of cilium cell motility biological_process regulation of ciliary cell motility GO:1902019 regulation of cilium-dependent cell motility Any process that modulates the frequency, rate or extent of cilium-dependent cell motility. GOC:TermGenie GOC:cilia GOC:jl Any process that stops, prevents or reduces the frequency, rate or extent of cilium-dependent cell motility. jl 2013-03-27T14:42:42Z down regulation of ciliary cell motility down-regulation of ciliary cell motility downregulation of ciliary cell motility negative regulation of cilium cell motility inhibition of ciliary cell motility biological_process negative regulation of ciliary cell motility GO:1902020 negative regulation of cilium-dependent cell motility Any process that stops, prevents or reduces the frequency, rate or extent of cilium-dependent cell motility. GOC:TermGenie GOC:cilia GOC:jl down regulation of ciliary cell motility GOC:TermGenie down-regulation of ciliary cell motility GOC:TermGenie downregulation of ciliary cell motility GOC:TermGenie inhibition of ciliary cell motility GOC:TermGenie Any process that activates or increases the frequency, rate or extent of flagellated sperm motility. bf 2013-04-29T09:15:25Z activation of sperm movement positive regulation of sperm motility positive regulation of sperm movement up regulation of sperm motility up regulation of sperm movement up-regulation of sperm motility up-regulation of sperm movement upregulation of sperm motility upregulation of sperm movement activation of sperm motility biological_process GO:1902093 positive regulation of flagellated sperm motility Any process that activates or increases the frequency, rate or extent of flagellated sperm motility. GOC:TermGenie GOC:cilia GOC:jh2 GOC:krc PMID:7513657 activation of sperm movement GOC:TermGenie positive regulation of sperm movement GOC:TermGenie up regulation of sperm motility GOC:TermGenie up regulation of sperm movement GOC:TermGenie up-regulation of sperm motility GOC:TermGenie up-regulation of sperm movement GOC:TermGenie upregulation of sperm motility GOC:TermGenie upregulation of sperm movement GOC:TermGenie activation of sperm motility GOC:TermGenie Any process that modulates the frequency, rate or extent of leukocyte differentiation. pr 2013-05-02T17:32:42Z regulation of immune cell differentiation regulation of leucocyte differentiation biological_process GO:1902105 regulation of leukocyte differentiation Any process that modulates the frequency, rate or extent of leukocyte differentiation. GOC:TermGenie GOC:add regulation of immune cell differentiation GOC:TermGenie regulation of leucocyte differentiation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte differentiation. pr 2013-05-02T17:32:47Z down regulation of immune cell differentiation down regulation of leucocyte differentiation down regulation of leukocyte differentiation down-regulation of immune cell differentiation down-regulation of leucocyte differentiation down-regulation of leukocyte differentiation downregulation of immune cell differentiation downregulation of leucocyte differentiation downregulation of leukocyte differentiation negative regulation of immune cell differentiation negative regulation of leucocyte differentiation inhibition of immune cell differentiation inhibition of leucocyte differentiation inhibition of leukocyte differentiation biological_process GO:1902106 negative regulation of leukocyte differentiation Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte differentiation. GOC:TermGenie GOC:add down regulation of immune cell differentiation GOC:TermGenie down regulation of leucocyte differentiation GOC:TermGenie down regulation of leukocyte differentiation GOC:TermGenie down-regulation of immune cell differentiation GOC:TermGenie down-regulation of leucocyte differentiation GOC:TermGenie down-regulation of leukocyte differentiation GOC:TermGenie downregulation of immune cell differentiation GOC:TermGenie downregulation of leucocyte differentiation GOC:TermGenie downregulation of leukocyte differentiation GOC:TermGenie negative regulation of immune cell differentiation GOC:TermGenie negative regulation of leucocyte differentiation GOC:TermGenie inhibition of immune cell differentiation GOC:TermGenie inhibition of leucocyte differentiation GOC:TermGenie inhibition of leukocyte differentiation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of leukocyte differentiation. pr 2013-05-02T17:32:52Z positive regulation of immune cell differentiation positive regulation of leucocyte differentiation up regulation of immune cell differentiation up regulation of leucocyte differentiation up regulation of leukocyte differentiation up-regulation of immune cell differentiation up-regulation of leucocyte differentiation up-regulation of leukocyte differentiation upregulation of immune cell differentiation upregulation of leucocyte differentiation upregulation of leukocyte differentiation activation of immune cell differentiation activation of leucocyte differentiation activation of leukocyte differentiation biological_process GO:1902107 positive regulation of leukocyte differentiation Any process that activates or increases the frequency, rate or extent of leukocyte differentiation. GOC:TermGenie GOC:add positive regulation of immune cell differentiation GOC:TermGenie positive regulation of leucocyte differentiation GOC:TermGenie up regulation of immune cell differentiation GOC:TermGenie up regulation of leucocyte differentiation GOC:TermGenie up regulation of leukocyte differentiation GOC:TermGenie up-regulation of immune cell differentiation GOC:TermGenie up-regulation of leucocyte differentiation GOC:TermGenie up-regulation of leukocyte differentiation GOC:TermGenie upregulation of immune cell differentiation GOC:TermGenie upregulation of leucocyte differentiation GOC:TermGenie upregulation of leukocyte differentiation GOC:TermGenie activation of immune cell differentiation GOC:TermGenie activation of leucocyte differentiation GOC:TermGenie activation of leukocyte differentiation GOC:TermGenie Any process that modulates the frequency, rate or extent of organelle assembly. pr 2013-05-14T09:43:21Z biological_process GO:1902115 regulation of organelle assembly Any process that modulates the frequency, rate or extent of organelle assembly. GOC:TermGenie GOC:pr Any process that stops, prevents or reduces the frequency, rate or extent of organelle assembly. pr 2013-05-14T09:43:31Z down regulation of organelle assembly down-regulation of organelle assembly downregulation of organelle assembly inhibition of organelle assembly biological_process GO:1902116 negative regulation of organelle assembly Any process that stops, prevents or reduces the frequency, rate or extent of organelle assembly. GOC:TermGenie GOC:pr down regulation of organelle assembly GOC:TermGenie down-regulation of organelle assembly GOC:TermGenie downregulation of organelle assembly GOC:TermGenie inhibition of organelle assembly GOC:TermGenie Any process that activates or increases the frequency, rate or extent of organelle assembly. pr 2013-05-14T09:43:36Z up regulation of organelle assembly up-regulation of organelle assembly upregulation of organelle assembly activation of organelle assembly biological_process GO:1902117 positive regulation of organelle assembly Any process that activates or increases the frequency, rate or extent of organelle assembly. GOC:TermGenie GOC:pr up regulation of organelle assembly GOC:TermGenie up-regulation of organelle assembly GOC:TermGenie upregulation of organelle assembly GOC:TermGenie activation of organelle assembly GOC:TermGenie Any apoptotic process that is involved in blood vessel morphogenesis. dph 2013-06-25T16:16:00Z apoptotic cell death involved in patterning of blood vessels apoptotic programmed cell death involved in patterning of blood vessels programmed cell death by apoptosis involved in patterning of blood vessels apoptosis involved in patterning of blood vessels apoptotic program involved in patterning of blood vessels type I programmed cell death involved in patterning of blood vessels biological_process signaling (initiator) caspase activity involved in patterning of blood vessels GO:1902262 apoptotic process involved in blood vessel morphogenesis Any apoptotic process that is involved in blood vessel morphogenesis. GOC:TermGenie GOC:dph GOC:mtg_apoptosis PMID:16163358 apoptotic cell death involved in patterning of blood vessels GOC:TermGenie apoptotic programmed cell death involved in patterning of blood vessels GOC:TermGenie programmed cell death by apoptosis involved in patterning of blood vessels GOC:TermGenie apoptosis involved in patterning of blood vessels GOC:TermGenie apoptotic program involved in patterning of blood vessels GOC:TermGenie type I programmed cell death involved in patterning of blood vessels GOC:TermGenie signaling (initiator) caspase activity involved in patterning of blood vessels GOC:TermGenie Any process that modulates the frequency, rate or extent of apoptotic process involved in morphogenesis. sart 2013-07-29T15:03:16Z regulation of apoptosis involved in morphogenesis biological_process regulation of apoptosis involved in development regulation of morphogenetic apoptosis GO:1902337 regulation of apoptotic process involved in morphogenesis Any process that modulates the frequency, rate or extent of apoptotic process involved in morphogenesis. GOC:TermGenie GOC:sart PMID:12202035 regulation of apoptosis involved in morphogenesis GOC:TermGenie regulation of apoptosis involved in development GOC:TermGenie regulation of morphogenetic apoptosis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in morphogenesis. sart 2013-07-29T15:03:25Z down regulation of apoptotic process involved in morphogenesis down-regulation of apoptotic process involved in morphogenesis downregulation of apoptotic process involved in morphogenesis down regulation of apoptosis involved in morphogenesis down-regulation of apoptosis involved in morphogenesis downregulation of apoptosis involved in morphogenesis inhibition of apoptosis involved in morphogenesis inhibition of apoptotic process involved in morphogenesis negative regulation of apoptosis involved in morphogenesis biological_process down regulation of apoptosis involved in development down regulation of morphogenetic apoptosis down-regulation of apoptosis involved in development down-regulation of morphogenetic apoptosis downregulation of apoptosis involved in development downregulation of morphogenetic apoptosis inhibition of apoptosis involved in development inhibition of morphogenetic apoptosis negative regulation of apoptosis involved in development negative regulation of morphogenetic apoptosis GO:1902338 negative regulation of apoptotic process involved in morphogenesis Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in morphogenesis. GOC:TermGenie GOC:sart PMID:12202035 down regulation of apoptotic process involved in morphogenesis GOC:TermGenie down-regulation of apoptotic process involved in morphogenesis GOC:TermGenie downregulation of apoptotic process involved in morphogenesis GOC:TermGenie down regulation of apoptosis involved in morphogenesis GOC:TermGenie down-regulation of apoptosis involved in morphogenesis GOC:TermGenie downregulation of apoptosis involved in morphogenesis GOC:TermGenie inhibition of apoptosis involved in morphogenesis GOC:TermGenie inhibition of apoptotic process involved in morphogenesis GOC:TermGenie negative regulation of apoptosis involved in morphogenesis GOC:TermGenie down regulation of apoptosis involved in development GOC:TermGenie down regulation of morphogenetic apoptosis GOC:TermGenie down-regulation of apoptosis involved in development GOC:TermGenie down-regulation of morphogenetic apoptosis GOC:TermGenie downregulation of apoptosis involved in development GOC:TermGenie downregulation of morphogenetic apoptosis GOC:TermGenie inhibition of apoptosis involved in development GOC:TermGenie inhibition of morphogenetic apoptosis GOC:TermGenie negative regulation of apoptosis involved in development GOC:TermGenie negative regulation of morphogenetic apoptosis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of apoptotic process involved in morphogenesis. sart 2013-07-29T15:03:33Z up regulation of apoptotic process involved in morphogenesis up-regulation of apoptotic process involved in morphogenesis upregulation of apoptotic process involved in morphogenesis activation of apoptosis involved in morphogenesis activation of apoptotic process involved in morphogenesis positive regulation of apoptosis involved in morphogenesis up regulation of apoptosis involved in morphogenesis up-regulation of apoptosis involved in morphogenesis upregulation of apoptosis involved in morphogenesis biological_process activation of apoptosis involved in development activation of morphogenetic apoptosis positive regulation of apoptosis involved in development positive regulation of morphogenetic apoptosis up regulation of apoptosis involved in development up regulation of morphogenetic apoptosis up-regulation of apoptosis involved in development up-regulation of morphogenetic apoptosis upregulation of apoptosis involved in development upregulation of morphogenetic apoptosis GO:1902339 positive regulation of apoptotic process involved in morphogenesis Any process that activates or increases the frequency, rate or extent of apoptotic process involved in morphogenesis. GOC:TermGenie GOC:sart PMID:12202035 up regulation of apoptotic process involved in morphogenesis GOC:TermGenie up-regulation of apoptotic process involved in morphogenesis GOC:TermGenie upregulation of apoptotic process involved in morphogenesis GOC:TermGenie activation of apoptosis involved in morphogenesis GOC:TermGenie activation of apoptotic process involved in morphogenesis GOC:TermGenie positive regulation of apoptosis involved in morphogenesis GOC:TermGenie up regulation of apoptosis involved in morphogenesis GOC:TermGenie up-regulation of apoptosis involved in morphogenesis GOC:TermGenie upregulation of apoptosis involved in morphogenesis GOC:TermGenie activation of apoptosis involved in development GOC:TermGenie activation of morphogenetic apoptosis GOC:TermGenie positive regulation of apoptosis involved in development GOC:TermGenie positive regulation of morphogenetic apoptosis GOC:TermGenie up regulation of apoptosis involved in development GOC:TermGenie up regulation of morphogenetic apoptosis GOC:TermGenie up-regulation of apoptosis involved in development GOC:TermGenie up-regulation of morphogenetic apoptosis GOC:TermGenie upregulation of apoptosis involved in development GOC:TermGenie upregulation of morphogenetic apoptosis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of chromosome condensation. dgf 2013-07-29T20:54:14Z down regulation of chromosome condensation down regulation of eukaryotic chromosome condensation down regulation of nuclear chromosome condensation down-regulation of chromosome condensation down-regulation of eukaryotic chromosome condensation down-regulation of nuclear chromosome condensation downregulation of chromosome condensation downregulation of eukaryotic chromosome condensation downregulation of nuclear chromosome condensation negative regulation of eukaryotic chromosome condensation negative regulation of nuclear chromosome condensation inhibition of chromosome condensation inhibition of eukaryotic chromosome condensation inhibition of nuclear chromosome condensation biological_process GO:1902340 negative regulation of chromosome condensation Any process that stops, prevents or reduces the frequency, rate or extent of chromosome condensation. GOC:TermGenie PMID:23219725 down regulation of chromosome condensation GOC:TermGenie down regulation of eukaryotic chromosome condensation GOC:TermGenie down regulation of nuclear chromosome condensation GOC:TermGenie down-regulation of chromosome condensation GOC:TermGenie down-regulation of eukaryotic chromosome condensation GOC:TermGenie down-regulation of nuclear chromosome condensation GOC:TermGenie downregulation of chromosome condensation GOC:TermGenie downregulation of eukaryotic chromosome condensation GOC:TermGenie downregulation of nuclear chromosome condensation GOC:TermGenie negative regulation of eukaryotic chromosome condensation GOC:TermGenie negative regulation of nuclear chromosome condensation GOC:TermGenie inhibition of chromosome condensation GOC:TermGenie inhibition of eukaryotic chromosome condensation GOC:TermGenie inhibition of nuclear chromosome condensation 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 Any process that modulates the frequency, rate or extent of neutrophil migration. sl 2014-01-15T18:58:39Z biological_process GO:1902622 regulation of neutrophil migration Any process that modulates the frequency, rate or extent of neutrophil migration. GOC:TermGenie GO_REF:0000058 PMID:1826836 Any process that stops, prevents or reduces the frequency, rate or extent of neutrophil migration. sl 2014-01-15T18:58:49Z down regulation of neutrophil migration down-regulation of neutrophil migration downregulation of neutrophil migration inhibition of neutrophil migration biological_process GO:1902623 negative regulation of neutrophil migration Any process that stops, prevents or reduces the frequency, rate or extent of neutrophil migration. GOC:TermGenie GO_REF:0000058 PMID:1826836 down regulation of neutrophil migration GOC:TermGenie down-regulation of neutrophil migration GOC:TermGenie downregulation of neutrophil migration GOC:TermGenie inhibition of neutrophil migration GOC:TermGenie Any process that activates or increases the frequency, rate or extent of neutrophil migration. sl 2014-01-15T18:58:58Z up regulation of neutrophil migration up-regulation of neutrophil migration upregulation of neutrophil migration activation of neutrophil migration biological_process GO:1902624 positive regulation of neutrophil migration Any process that activates or increases the frequency, rate or extent of neutrophil migration. GOC:TermGenie GO_REF:0000058 PMID:1826836 up regulation of neutrophil migration GOC:TermGenie up-regulation of neutrophil migration GOC:TermGenie upregulation of neutrophil migration GOC:TermGenie activation of neutrophil migration GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of prolactin secretion. mr 2014-02-24T16:09:28Z down regulation of prolactin secretion down-regulation of prolactin secretion downregulation of prolactin secretion inhibition of prolactin secretion biological_process GO:1902721 negative regulation of prolactin secretion Any process that stops, prevents or reduces the frequency, rate or extent of prolactin secretion. GOC:TermGenie GO_REF:0000058 PMID:16159377 down regulation of prolactin secretion GOC:TermGenie down-regulation of prolactin secretion GOC:TermGenie downregulation of prolactin secretion GOC:TermGenie inhibition of prolactin secretion GOC:TermGenie Any process that activates or increases the frequency, rate or extent of prolactin secretion. mr 2014-02-24T16:09:37Z up regulation of prolactin secretion up-regulation of prolactin secretion upregulation of prolactin secretion activation of prolactin secretion biological_process GO:1902722 positive regulation of prolactin secretion Any process that activates or increases the frequency, rate or extent of prolactin secretion. GOC:TermGenie GO_REF:0000058 PMID:16159377 up regulation of prolactin secretion GOC:TermGenie up-regulation of prolactin secretion GOC:TermGenie upregulation of prolactin secretion GOC:TermGenie activation of prolactin secretion GOC:TermGenie Any apoptotic process that is involved in anatomical structure development. pr 2014-02-28T13:09:43Z apoptotic cell death involved in anatomical structure development apoptotic cell death involved in development of an anatomical structure apoptotic process involved in anatomical structure development apoptotic process involved in development of an anatomical structure apoptotic programmed cell death involved in anatomical structure development apoptotic programmed cell death involved in development of an anatomical structure programmed cell death by apoptosis involved in anatomical structure development programmed cell death by apoptosis involved in development of an anatomical structure activation of apoptosis involved in anatomical structure development activation of apoptosis involved in development of an anatomical structure apoptosis involved in anatomical structure development apoptosis involved in development of an anatomical structure apoptosis signaling involved in anatomical structure development apoptosis signaling involved in development of an anatomical structure apoptotic program involved in anatomical structure development apoptotic program involved in development of an anatomical structure type I programmed cell death involved in anatomical structure development type I programmed cell death involved in development of an anatomical structure biological_process apoptosis activator activity involved in anatomical structure development apoptosis activator activity involved in development of an anatomical structure commitment to apoptosis involved in anatomical structure development commitment to apoptosis involved in development of an anatomical structure induction of apoptosis by p53 involved in anatomical structure development induction of apoptosis by p53 involved in development of an anatomical structure induction of apoptosis involved in anatomical structure development induction of apoptosis involved in development of an anatomical structure signaling (initiator) caspase activity involved in anatomical structure development signaling (initiator) caspase activity involved in development of an anatomical structure GO:1902742 apoptotic process involved in development Any apoptotic process that is involved in anatomical structure development. GOC:TermGenie GOC:mtg_apoptosis GOC:pg GO_REF:0000060 apoptotic cell death involved in anatomical structure development GOC:TermGenie apoptotic cell death involved in development of an anatomical structure GOC:TermGenie apoptotic process involved in development of an anatomical structure GOC:TermGenie apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie activation of apoptosis involved in anatomical structure development GOC:TermGenie activation of apoptosis involved in development of an anatomical structure GOC:TermGenie apoptosis involved in anatomical structure development GOC:TermGenie apoptosis involved in development of an anatomical structure GOC:TermGenie apoptosis signaling involved in anatomical structure development GOC:TermGenie apoptosis signaling involved in development of an anatomical structure GOC:TermGenie apoptotic program involved in anatomical structure development GOC:TermGenie apoptotic program involved in development of an anatomical structure GOC:TermGenie type I programmed cell death involved in anatomical structure development GOC:TermGenie type I programmed cell death involved in development of an anatomical structure GOC:TermGenie apoptosis activator activity involved in anatomical structure development GOC:TermGenie apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie commitment to apoptosis involved in anatomical structure development GOC:TermGenie commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie induction of apoptosis involved in anatomical structure development GOC:TermGenie induction of apoptosis involved in development of an anatomical structure GOC:TermGenie signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie Any microtubule cytoskeleton organization that is involved in mitosis. vw 2014-04-02T14:19:38Z microtubule cytoskeleton organisation involved in mitosis microtubule dynamics involved in mitosis biological_process microtubule cytoskeleton organization and biogenesis involved in mitosis GO:1902850 microtubule cytoskeleton organization involved in mitosis Any microtubule cytoskeleton organization that is involved in mitosis. GOC:TermGenie GO_REF:0000060 PMID:18799626 microtubule cytoskeleton organisation involved in mitosis GOC:TermGenie microtubule dynamics involved in mitosis GOC:TermGenie microtubule cytoskeleton organization and biogenesis involved in mitosis GOC:TermGenie Any process that modulates the frequency, rate or extent of response to wounding. kmv 2014-05-18T01:28:46Z regulation of physiological response to wounding biological_process GO:1903034 regulation of response to wounding Any process that modulates the frequency, rate or extent of response to wounding. GOC:TermGenie GOC:kmv GO_REF:0000058 pmid:19164535 regulation of physiological response to wounding GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of response to wounding. kmv 2014-05-18T01:28:52Z down regulation of physiological response to wounding down regulation of response to wounding down-regulation of physiological response to wounding down-regulation of response to wounding downregulation of physiological response to wounding downregulation of response to wounding negative regulation of physiological response to wounding inhibition of physiological response to wounding inhibition of response to wounding biological_process GO:1903035 negative regulation of response to wounding Any process that stops, prevents or reduces the frequency, rate or extent of response to wounding. GOC:TermGenie GOC:kmv GO_REF:0000058 pmid:19164535 down regulation of physiological response to wounding GOC:TermGenie down regulation of response to wounding GOC:TermGenie down-regulation of physiological response to wounding GOC:TermGenie down-regulation of response to wounding GOC:TermGenie downregulation of physiological response to wounding GOC:TermGenie downregulation of response to wounding GOC:TermGenie negative regulation of physiological response to wounding GOC:TermGenie inhibition of physiological response to wounding GOC:TermGenie inhibition of response to wounding GOC:TermGenie Any process that activates or increases the frequency, rate or extent of response to wounding. kmv 2014-05-18T01:28:58Z positive regulation of physiological response to wounding up regulation of physiological response to wounding up regulation of response to wounding up-regulation of physiological response to wounding up-regulation of response to wounding upregulation of physiological response to wounding upregulation of response to wounding activation of physiological response to wounding activation of response to wounding biological_process GO:1903036 positive regulation of response to wounding Any process that activates or increases the frequency, rate or extent of response to wounding. GOC:TermGenie GOC:kmv GO_REF:0000058 pmid:19164535 positive regulation of physiological response to wounding GOC:TermGenie up regulation of physiological response to wounding GOC:TermGenie up regulation of response to wounding GOC:TermGenie up-regulation of physiological response to wounding GOC:TermGenie up-regulation of response to wounding GOC:TermGenie upregulation of physiological response to wounding GOC:TermGenie upregulation of response to wounding GOC:TermGenie activation of physiological response to wounding GOC:TermGenie activation of response to wounding GOC:TermGenie Any process that modulates the frequency, rate or extent of leukocyte cell-cell adhesion. rl 2014-05-19T15:29:58Z regulation of leukocyte adhesion regulation of leukocyte cell adhesion biological_process GO:1903037 Exogenous expression of ASS1 or NOS3 in HUVECs enhances NO production and inhibits monocyte adhesion regulation of leukocyte cell-cell adhesion Any process that modulates the frequency, rate or extent of leukocyte cell-cell adhesion. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:21106532 regulation of leukocyte adhesion GOC:TermGenie regulation of leukocyte cell adhesion GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte cell-cell adhesion. rl 2014-05-19T15:30:05Z down regulation of leukocyte adhesion down regulation of leukocyte cell adhesion down regulation of leukocyte cell-cell adhesion down-regulation of leukocyte adhesion down-regulation of leukocyte cell adhesion down-regulation of leukocyte cell-cell adhesion downregulation of leukocyte adhesion downregulation of leukocyte cell adhesion downregulation of leukocyte cell-cell adhesion negative regulation of leukocyte adhesion negative regulation of leukocyte cell adhesion inhibition of leukocyte adhesion inhibition of leukocyte cell adhesion inhibition of leukocyte cell-cell adhesion biological_process GO:1903038 Exogenous expression of ASS1 or NOS3 in HUVECs enhances NO production and inhibits monocyte adhesion negative regulation of leukocyte cell-cell adhesion Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte cell-cell adhesion. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:21106532 down regulation of leukocyte adhesion GOC:TermGenie down regulation of leukocyte cell adhesion GOC:TermGenie down regulation of leukocyte cell-cell adhesion GOC:TermGenie down-regulation of leukocyte adhesion GOC:TermGenie down-regulation of leukocyte cell adhesion GOC:TermGenie down-regulation of leukocyte cell-cell adhesion GOC:TermGenie downregulation of leukocyte adhesion GOC:TermGenie downregulation of leukocyte cell adhesion GOC:TermGenie downregulation of leukocyte cell-cell adhesion GOC:TermGenie negative regulation of leukocyte adhesion GOC:TermGenie negative regulation of leukocyte cell adhesion GOC:TermGenie inhibition of leukocyte adhesion GOC:TermGenie inhibition of leukocyte cell adhesion GOC:TermGenie inhibition of leukocyte cell-cell adhesion GOC:TermGenie Any process that activates or increases the frequency, rate or extent of leukocyte cell-cell adhesion. rl 2014-05-19T15:30:15Z positive regulation of leukocyte adhesion positive regulation of leukocyte cell adhesion up regulation of leukocyte adhesion up regulation of leukocyte cell adhesion up regulation of leukocyte cell-cell adhesion up-regulation of leukocyte adhesion up-regulation of leukocyte cell adhesion up-regulation of leukocyte cell-cell adhesion upregulation of leukocyte adhesion upregulation of leukocyte cell adhesion upregulation of leukocyte cell-cell adhesion activation of leukocyte adhesion activation of leukocyte cell adhesion activation of leukocyte cell-cell adhesion biological_process GO:1903039 Exogenous expression of ASS1 or NOS3 in HUVECs enhances NO production and inhibits monocyte adhesion positive regulation of leukocyte cell-cell adhesion Any process that activates or increases the frequency, rate or extent of leukocyte cell-cell adhesion. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:21106532 positive regulation of leukocyte adhesion GOC:TermGenie positive regulation of leukocyte cell adhesion GOC:TermGenie up regulation of leukocyte adhesion GOC:TermGenie up regulation of leukocyte cell adhesion GOC:TermGenie up regulation of leukocyte cell-cell adhesion GOC:TermGenie up-regulation of leukocyte adhesion GOC:TermGenie up-regulation of leukocyte cell adhesion GOC:TermGenie up-regulation of leukocyte cell-cell adhesion GOC:TermGenie upregulation of leukocyte adhesion GOC:TermGenie upregulation of leukocyte cell adhesion GOC:TermGenie upregulation of leukocyte cell-cell adhesion GOC:TermGenie activation of leukocyte adhesion GOC:TermGenie activation of leukocyte cell adhesion GOC:TermGenie activation of leukocyte cell-cell adhesion GOC:TermGenie A process that is part of the meiotic cell cycle. jl 2014-05-22T14:22:28Z biological_process GO:1903046 meiotic cell cycle process A process that is part of the meiotic cell cycle. GOC:TermGenie GOC:mtg_cell_cycle GO_REF:0000060 A process that is part of the mitotic cell cycle. jl 2014-05-22T14:22:34Z biological_process GO:1903047 mitotic cell cycle process A process that is part of the mitotic cell cycle. GOC:TermGenie GOC:mtg_cell_cycle GO_REF:0000060 Any process that modulates the frequency, rate or extent of extracellular matrix organization. rl 2014-05-23T17:15:41Z regulation of extracellular matrix organisation biological_process regulation of extracellular matrix organization and biogenesis GO:1903053 regulation of extracellular matrix organization Any process that modulates the frequency, rate or extent of extracellular matrix organization. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:22357537 regulation of extracellular matrix organisation GOC:TermGenie regulation of extracellular matrix organization and biogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of extracellular matrix organization. rl 2014-05-23T17:15:47Z down regulation of extracellular matrix organisation down regulation of extracellular matrix organization down-regulation of extracellular matrix organisation down-regulation of extracellular matrix organization downregulation of extracellular matrix organisation downregulation of extracellular matrix organization negative regulation of extracellular matrix organisation inhibition of extracellular matrix organisation inhibition of extracellular matrix organization biological_process down regulation of extracellular matrix organization and biogenesis down-regulation of extracellular matrix organization and biogenesis downregulation of extracellular matrix organization and biogenesis inhibition of extracellular matrix organization and biogenesis negative regulation of extracellular matrix organization and biogenesis GO:1903054 negative regulation of extracellular matrix organization Any process that stops, prevents or reduces the frequency, rate or extent of extracellular matrix organization. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:22357537 down regulation of extracellular matrix organisation GOC:TermGenie down regulation of extracellular matrix organization GOC:TermGenie down-regulation of extracellular matrix organisation GOC:TermGenie down-regulation of extracellular matrix organization GOC:TermGenie downregulation of extracellular matrix organisation GOC:TermGenie downregulation of extracellular matrix organization GOC:TermGenie negative regulation of extracellular matrix organisation GOC:TermGenie inhibition of extracellular matrix organisation GOC:TermGenie inhibition of extracellular matrix organization GOC:TermGenie down regulation of extracellular matrix organization and biogenesis GOC:TermGenie down-regulation of extracellular matrix organization and biogenesis GOC:TermGenie downregulation of extracellular matrix organization and biogenesis GOC:TermGenie inhibition of extracellular matrix organization and biogenesis GOC:TermGenie negative regulation of extracellular matrix organization and biogenesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of extracellular matrix organization. rl 2014-05-23T17:15:53Z positive regulation of extracellular matrix organisation up regulation of extracellular matrix organisation up regulation of extracellular matrix organization up-regulation of extracellular matrix organisation up-regulation of extracellular matrix organization upregulation of extracellular matrix organisation upregulation of extracellular matrix organization activation of extracellular matrix organisation activation of extracellular matrix organization biological_process activation of extracellular matrix organization and biogenesis positive regulation of extracellular matrix organization and biogenesis up regulation of extracellular matrix organization and biogenesis up-regulation of extracellular matrix organization and biogenesis upregulation of extracellular matrix organization and biogenesis GO:1903055 positive regulation of extracellular matrix organization Any process that activates or increases the frequency, rate or extent of extracellular matrix organization. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:22357537 positive regulation of extracellular matrix organisation GOC:TermGenie up regulation of extracellular matrix organisation GOC:TermGenie up regulation of extracellular matrix organization GOC:TermGenie up-regulation of extracellular matrix organisation GOC:TermGenie up-regulation of extracellular matrix organization GOC:TermGenie upregulation of extracellular matrix organisation GOC:TermGenie upregulation of extracellular matrix organization GOC:TermGenie activation of extracellular matrix organisation GOC:TermGenie activation of extracellular matrix organization GOC:TermGenie activation of extracellular matrix organization and biogenesis GOC:TermGenie positive regulation of extracellular matrix organization and biogenesis GOC:TermGenie up regulation of extracellular matrix organization and biogenesis GOC:TermGenie up-regulation of extracellular matrix organization and biogenesis GOC:TermGenie upregulation of extracellular matrix organization and biogenesis GOC:TermGenie The process in which a relatively unspecialized cell acquires the specialized features of a mononuclear cell. cls 2014-06-25T15:47:09Z biological_process GO:1903131 mononuclear cell differentiation The process in which a relatively unspecialized cell acquires the specialized features of a mononuclear cell. CL:0000842 GOC:TermGenie GO_REF:0000086 PMID:24759906 Any process that modulates the frequency, rate or extent of glutamate secretion, neurotransmission. pad 2014-08-13T13:54:15Z biological_process GO:1903294 An example of this is Rab3gap1 in mouse (Q80UJ7) in PMID:16782817 inferred from mutant phenotype regulation of glutamate secretion, neurotransmission Any process that modulates the frequency, rate or extent of glutamate secretion, neurotransmission. GOC:TermGenie GO_REF:0000058 PMID:16782817 Any process that stops, prevents or reduces the frequency, rate or extent of glutamate secretion, neurotransmission. pad 2014-08-13T13:54:23Z down regulation of glutamate secretion, neurotransmission down-regulation of glutamate secretion, neurotransmission downregulation of glutamate secretion, neurotransmission inhibition of glutamate secretion, neurotransmission biological_process GO:1903295 An example of this is Rab3gap1 in mouse (Q80UJ7) in PMID:16782817 inferred from mutant phenotype negative regulation of glutamate secretion, neurotransmission Any process that stops, prevents or reduces the frequency, rate or extent of glutamate secretion, neurotransmission. GOC:TermGenie GO_REF:0000058 PMID:16782817 down regulation of glutamate secretion, neurotransmission GOC:TermGenie down-regulation of glutamate secretion, neurotransmission GOC:TermGenie downregulation of glutamate secretion, neurotransmission GOC:TermGenie inhibition of glutamate secretion, neurotransmission GOC:TermGenie Any process that activates or increases the frequency, rate or extent of glutamate secretion, where glutamate acts as a neurotransmitter. pad 2014-08-13T13:54:31Z up regulation of glutamate secretion, neurotransmission up-regulation of glutamate secretion, neurotransmission upregulation of glutamate secretion, neurotransmission activation of glutamate secretion, neurotransmission biological_process GO:1903296 An example of this is Rab3gap1 in mouse (Q80UJ7) in PMID:16782817 inferred from mutant phenotype positive regulation of glutamate secretion, neurotransmission Any process that activates or increases the frequency, rate or extent of glutamate secretion, where glutamate acts as a neurotransmitter. GOC:TermGenie GO_REF:0000058 PMID:16782817 up regulation of glutamate secretion, neurotransmission GOC:TermGenie up-regulation of glutamate secretion, neurotransmission GOC:TermGenie upregulation of glutamate secretion, neurotransmission GOC:TermGenie activation of glutamate secretion, neurotransmission GOC:TermGenie Any process that modulates the frequency, rate or extent of nitrogen cycle metabolic process. vw 2014-08-18T12:57:34Z biological_process GO:1903314 regulation of nitrogen cycle metabolic process Any process that modulates the frequency, rate or extent of nitrogen cycle metabolic process. GOC:TermGenie GOC:vw GO_REF:0000058 Any process that stops, prevents or reduces the frequency, rate or extent of nitrogen cycle metabolic process. vw 2014-08-18T12:57:42Z down regulation of nitrogen cycle metabolic process down-regulation of nitrogen cycle metabolic process downregulation of nitrogen cycle metabolic process inhibition of nitrogen cycle metabolic process biological_process GO:1903315 negative regulation of nitrogen cycle metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of nitrogen cycle metabolic process. GOC:TermGenie GOC:vw GO_REF:0000058 down regulation of nitrogen cycle metabolic process GOC:TermGenie down-regulation of nitrogen cycle metabolic process GOC:TermGenie downregulation of nitrogen cycle metabolic process GOC:TermGenie inhibition of nitrogen cycle metabolic process GOC:TermGenie Any process that activates or increases the frequency, rate or extent of nitrogen cycle metabolic process. vw 2014-08-18T12:57:50Z up regulation of nitrogen cycle metabolic process up-regulation of nitrogen cycle metabolic process upregulation of nitrogen cycle metabolic process activation of nitrogen cycle metabolic process biological_process GO:1903316 positive regulation of nitrogen cycle metabolic process Any process that activates or increases the frequency, rate or extent of nitrogen cycle metabolic process. GOC:TermGenie GOC:vw GO_REF:0000058 up regulation of nitrogen cycle metabolic process GOC:TermGenie up-regulation of nitrogen cycle metabolic process GOC:TermGenie upregulation of nitrogen cycle metabolic process GOC:TermGenie activation of nitrogen cycle metabolic process GOC:TermGenie Any process that modulates the frequency, rate or extent of nucleus organization. hjd 2014-08-20T19:36:16Z regulation of nuclear organisation regulation of nuclear organization biological_process regulation of nuclear morphology regulation of nuclear organization and biogenesis regulation of nucleus organization and biogenesis GO:1903353 regulation of nucleus organization Any process that modulates the frequency, rate or extent of nucleus organization. GOC:TermGenie GO_REF:0000058 PMID:16943282 regulation of nuclear organisation GOC:TermGenie regulation of nuclear organization GOC:TermGenie regulation of nuclear morphology GOC:TermGenie regulation of nuclear organization and biogenesis GOC:TermGenie regulation of nucleus organization and biogenesis GOC:TermGenie Any process that modulates the frequency, rate or extent of mitotic chromosome condensation. al 2014-08-26T13:57:13Z biological_process GO:1903379 regulation of mitotic chromosome condensation Any process that modulates the frequency, rate or extent of mitotic chromosome condensation. GOC:TermGenie GO_REF:0000058 PMID:9490640 Any process that activates or increases the frequency, rate or extent of mitotic chromosome condensation. al 2014-08-26T13:57:29Z up regulation of mitotic chromosome condensation up-regulation of mitotic chromosome condensation upregulation of mitotic chromosome condensation activation of mitotic chromosome condensation biological_process GO:1903380 positive regulation of mitotic chromosome condensation Any process that activates or increases the frequency, rate or extent of mitotic chromosome condensation. GOC:TermGenie GO_REF:0000058 PMID:9490640 up regulation of mitotic chromosome condensation GOC:TermGenie up-regulation of mitotic chromosome condensation GOC:TermGenie upregulation of mitotic chromosome condensation GOC:TermGenie activation of mitotic chromosome condensation GOC:TermGenie The chemical reactions and pathways involving mucopolysaccharide. dph 2014-10-01T21:55:47Z mucopolysaccharide metabolism biological_process GO:1903510 mucopolysaccharide metabolic process The chemical reactions and pathways involving mucopolysaccharide. GOC:TermGenie GOC:dph GO_REF:0000068 PMID:4236091 mucopolysaccharide metabolism 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 modulates the frequency, rate or extent of extracellular vesicular exosome assembly. pga 2014-10-20T15:37:25Z regulation of extracellular vesicular exosome assembly biological_process GO:1903551 regulation of extracellular exosome assembly Any process that modulates the frequency, rate or extent of extracellular vesicular exosome assembly. GOC:TermGenie GO_REF:0000058 PMID:24105262 regulation of extracellular vesicular exosome assembly GOC:vesicles Any process that stops, prevents or reduces the frequency, rate or extent of extracellular vesicular exosome assembly. pga 2014-10-20T15:37:33Z down regulation of extracellular vesicular exosome assembly down-regulation of extracellular vesicular exosome assembly downregulation of extracellular vesicular exosome assembly negative regulation of extracellular vesicular exosome assembly inhibition of extracellular vesicular exosome assembly biological_process GO:1903552 negative regulation of extracellular exosome assembly Any process that stops, prevents or reduces the frequency, rate or extent of extracellular vesicular exosome assembly. GOC:TermGenie GO_REF:0000058 PMID:24105262 down regulation of extracellular vesicular exosome assembly GOC:TermGenie down-regulation of extracellular vesicular exosome assembly GOC:TermGenie downregulation of extracellular vesicular exosome assembly GOC:TermGenie negative regulation of extracellular vesicular exosome assembly GOC:vesicles inhibition of extracellular vesicular exosome assembly GOC:TermGenie Any process that activates or increases the frequency, rate or extent of extracellular vesicular exosome assembly. pga 2014-10-20T15:37:42Z up regulation of extracellular vesicular exosome assembly up-regulation of extracellular vesicular exosome assembly upregulation of extracellular vesicular exosome assembly activation of extracellular vesicular exosome assembly biological_process positive regulation of extracellular vesicular exosome assembly GO:1903553 positive regulation of extracellular exosome assembly Any process that activates or increases the frequency, rate or extent of extracellular vesicular exosome assembly. GOC:TermGenie GO_REF:0000058 PMID:24105262 up regulation of extracellular vesicular exosome assembly GOC:TermGenie up-regulation of extracellular vesicular exosome assembly GOC:TermGenie upregulation of extracellular vesicular exosome assembly GOC:TermGenie activation of extracellular vesicular exosome assembly GOC:TermGenie positive regulation of extracellular vesicular exosome assembly GOC:vesicles Any process that modulates the frequency, rate or extent of tumor necrosis factor superfamily cytokine production. pga 2014-10-21T10:26:05Z regulation of TNFSF cytokine production biological_process regulation of TNF superfamily production GO:1903555 regulation of tumor necrosis factor superfamily cytokine production Any process that modulates the frequency, rate or extent of tumor necrosis factor superfamily cytokine production. GOC:TermGenie GO_REF:0000058 PMID:24187568 regulation of TNFSF cytokine production GOC:TermGenie regulation of TNF superfamily production GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of tumor necrosis factor superfamily cytokine production. pga 2014-10-21T10:26:14Z down regulation of TNFSF cytokine production down regulation of tumor necrosis factor superfamily cytokine production down-regulation of TNFSF cytokine production down-regulation of tumor necrosis factor superfamily cytokine production downregulation of TNFSF cytokine production downregulation of tumor necrosis factor superfamily cytokine production negative regulation of TNFSF cytokine production inhibition of TNFSF cytokine production inhibition of tumor necrosis factor superfamily cytokine production biological_process down regulation of TNF superfamily production down-regulation of TNF superfamily production downregulation of TNF superfamily production inhibition of TNF superfamily production negative regulation of TNF superfamily production GO:1903556 negative regulation of tumor necrosis factor superfamily cytokine production Any process that stops, prevents or reduces the frequency, rate or extent of tumor necrosis factor superfamily cytokine production. GOC:TermGenie GO_REF:0000058 PMID:24187568 down regulation of TNFSF cytokine production GOC:TermGenie down regulation of tumor necrosis factor superfamily cytokine production GOC:TermGenie down-regulation of TNFSF cytokine production GOC:TermGenie down-regulation of tumor necrosis factor superfamily cytokine production GOC:TermGenie downregulation of TNFSF cytokine production GOC:TermGenie downregulation of tumor necrosis factor superfamily cytokine production GOC:TermGenie negative regulation of TNFSF cytokine production GOC:TermGenie inhibition of TNFSF cytokine production GOC:TermGenie inhibition of tumor necrosis factor superfamily cytokine production GOC:TermGenie down regulation of TNF superfamily production GOC:TermGenie down-regulation of TNF superfamily production GOC:TermGenie downregulation of TNF superfamily production GOC:TermGenie inhibition of TNF superfamily production GOC:TermGenie negative regulation of TNF superfamily production GOC:TermGenie Any process that activates or increases the frequency, rate or extent of tumor necrosis factor superfamily cytokine production. pga 2014-10-21T10:26:23Z positive regulation of TNFSF cytokine production up regulation of TNFSF cytokine production up regulation of tumor necrosis factor superfamily cytokine production up-regulation of TNFSF cytokine production up-regulation of tumor necrosis factor superfamily cytokine production upregulation of TNFSF cytokine production upregulation of tumor necrosis factor superfamily cytokine production activation of TNFSF cytokine production activation of tumor necrosis factor superfamily cytokine production biological_process activation of TNF superfamily production positive regulation of TNF superfamily production up regulation of TNF superfamily production up-regulation of TNF superfamily production upregulation of TNF superfamily production GO:1903557 positive regulation of tumor necrosis factor superfamily cytokine production Any process that activates or increases the frequency, rate or extent of tumor necrosis factor superfamily cytokine production. GOC:TermGenie GO_REF:0000058 PMID:24187568 positive regulation of TNFSF cytokine production GOC:TermGenie up regulation of TNFSF cytokine production GOC:TermGenie up regulation of tumor necrosis factor superfamily cytokine production GOC:TermGenie up-regulation of TNFSF cytokine production GOC:TermGenie up-regulation of tumor necrosis factor superfamily cytokine production GOC:TermGenie upregulation of TNFSF cytokine production GOC:TermGenie upregulation of tumor necrosis factor superfamily cytokine production GOC:TermGenie activation of TNFSF cytokine production GOC:TermGenie activation of tumor necrosis factor superfamily cytokine production GOC:TermGenie activation of TNF superfamily production GOC:TermGenie positive regulation of TNF superfamily production GOC:TermGenie up regulation of TNF superfamily production GOC:TermGenie up-regulation of TNF superfamily production GOC:TermGenie upregulation of TNF superfamily production GOC:TermGenie Any vesicle that is part of the extracellular region. jl 2014-10-22T14:26:11Z cellular_component microparticle GO:1903561 extracellular vesicle Any vesicle that is part of the extracellular region. GOC:TermGenie GOC:pm GO_REF:0000064 PMID:24769233 microparticle GOC:vesicles Any process that modulates the frequency, rate or extent of protein localization to cilium. krc 2014-10-24T20:58:11Z biological_process GO:1903564 regulation of protein localization to cilium Any process that modulates the frequency, rate or extent of protein localization to cilium. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000058 PMID:22072986 Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cilium. krc 2014-10-24T20:58:20Z down regulation of protein localization to cilium down-regulation of protein localization to cilium downregulation of protein localization to cilium inhibition of protein localization to cilium biological_process GO:1903565 negative regulation of protein localization to cilium Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cilium. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000058 PMID:22072986 down regulation of protein localization to cilium GOC:TermGenie down-regulation of protein localization to cilium GOC:TermGenie downregulation of protein localization to cilium GOC:TermGenie inhibition of protein localization to cilium GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein localization to cilium. krc 2014-10-24T20:58:28Z up regulation of protein localization to cilium up-regulation of protein localization to cilium upregulation of protein localization to cilium activation of protein localization to cilium biological_process GO:1903566 positive regulation of protein localization to cilium Any process that activates or increases the frequency, rate or extent of protein localization to cilium. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000058 PMID:22072986 up regulation of protein localization to cilium GOC:TermGenie up-regulation of protein localization to cilium GOC:TermGenie upregulation of protein localization to cilium GOC:TermGenie activation of protein localization to cilium GOC:TermGenie Any process that modulates the frequency, rate or extent of hemopoiesis. pad 2014-12-04T15:34:13Z regulation of blood cell biosynthesis regulation of blood cell formation regulation of haemopoiesis regulation of hematopoiesis biological_process GO:1903706 An example of this is Atg7 in mouse (UniProt symbol, Q9D906) in PMID:20080761, inferred from mutant phenotype. regulation of hemopoiesis Any process that modulates the frequency, rate or extent of hemopoiesis. GOC:PARL GOC:TermGenie GOC:pad GO_REF:0000058 PMID:20080761 regulation of blood cell biosynthesis GOC:TermGenie regulation of blood cell formation GOC:TermGenie regulation of haemopoiesis GOC:TermGenie regulation of hematopoiesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of hemopoiesis. pad 2014-12-04T15:34:21Z down regulation of blood cell biosynthesis down regulation of blood cell formation down regulation of haemopoiesis down regulation of hematopoiesis down regulation of hemopoiesis down-regulation of blood cell biosynthesis down-regulation of blood cell formation down-regulation of haemopoiesis down-regulation of hematopoiesis down-regulation of hemopoiesis downregulation of blood cell biosynthesis downregulation of blood cell formation downregulation of haemopoiesis downregulation of hematopoiesis downregulation of hemopoiesis negative regulation of blood cell biosynthesis negative regulation of blood cell formation negative regulation of haemopoiesis negative regulation of hematopoiesis inhibition of blood cell biosynthesis inhibition of blood cell formation inhibition of haemopoiesis inhibition of hematopoiesis inhibition of hemopoiesis biological_process GO:1903707 An example of this is Atg7 in mouse (UniProt symbol, Q9D906) in PMID:20080761, inferred from mutant phenotype. negative regulation of hemopoiesis Any process that stops, prevents or reduces the frequency, rate or extent of hemopoiesis. GOC:PARL GOC:TermGenie GOC:pad GO_REF:0000058 PMID:20080761 down regulation of blood cell biosynthesis GOC:TermGenie down regulation of blood cell formation GOC:TermGenie down regulation of haemopoiesis GOC:TermGenie down regulation of hematopoiesis GOC:TermGenie down regulation of hemopoiesis GOC:TermGenie down-regulation of blood cell biosynthesis GOC:TermGenie down-regulation of blood cell formation GOC:TermGenie down-regulation of haemopoiesis GOC:TermGenie down-regulation of hematopoiesis GOC:TermGenie down-regulation of hemopoiesis GOC:TermGenie downregulation of blood cell biosynthesis GOC:TermGenie downregulation of blood cell formation GOC:TermGenie downregulation of haemopoiesis GOC:TermGenie downregulation of hematopoiesis GOC:TermGenie downregulation of hemopoiesis GOC:TermGenie negative regulation of blood cell biosynthesis GOC:TermGenie negative regulation of blood cell formation GOC:TermGenie negative regulation of haemopoiesis GOC:TermGenie negative regulation of hematopoiesis GOC:TermGenie inhibition of blood cell biosynthesis GOC:TermGenie inhibition of blood cell formation GOC:TermGenie inhibition of haemopoiesis GOC:TermGenie inhibition of hematopoiesis GOC:TermGenie inhibition of hemopoiesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of hemopoiesis. pad 2014-12-04T15:34:30Z positive regulation of blood cell biosynthesis positive regulation of blood cell formation positive regulation of haemopoiesis positive regulation of hematopoiesis up regulation of blood cell biosynthesis up regulation of blood cell formation up regulation of haemopoiesis up regulation of hematopoiesis up regulation of hemopoiesis up-regulation of blood cell biosynthesis up-regulation of blood cell formation up-regulation of haemopoiesis up-regulation of hematopoiesis up-regulation of hemopoiesis upregulation of blood cell biosynthesis upregulation of blood cell formation upregulation of haemopoiesis upregulation of hematopoiesis upregulation of hemopoiesis activation of blood cell biosynthesis activation of blood cell formation activation of haemopoiesis activation of hematopoiesis activation of hemopoiesis biological_process GO:1903708 An example of this is Atg7 in mouse (UniProt symbol, Q9D906) in PMID:20080761, inferred from mutant phenotype. positive regulation of hemopoiesis Any process that activates or increases the frequency, rate or extent of hemopoiesis. GOC:PARL GOC:TermGenie GOC:pad GO_REF:0000058 PMID:20080761 positive regulation of blood cell biosynthesis GOC:TermGenie positive regulation of blood cell formation GOC:TermGenie positive regulation of haemopoiesis GOC:TermGenie positive regulation of hematopoiesis GOC:TermGenie up regulation of blood cell biosynthesis GOC:TermGenie up regulation of blood cell formation GOC:TermGenie up regulation of haemopoiesis GOC:TermGenie up regulation of hematopoiesis GOC:TermGenie up regulation of hemopoiesis GOC:TermGenie up-regulation of blood cell biosynthesis GOC:TermGenie up-regulation of blood cell formation GOC:TermGenie up-regulation of haemopoiesis GOC:TermGenie up-regulation of hematopoiesis GOC:TermGenie up-regulation of hemopoiesis GOC:TermGenie upregulation of blood cell biosynthesis GOC:TermGenie upregulation of blood cell formation GOC:TermGenie upregulation of haemopoiesis GOC:TermGenie upregulation of hematopoiesis GOC:TermGenie upregulation of hemopoiesis GOC:TermGenie activation of blood cell biosynthesis GOC:TermGenie activation of blood cell formation GOC:TermGenie activation of haemopoiesis GOC:TermGenie activation of hematopoiesis GOC:TermGenie activation of hemopoiesis 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 stops, prevents or reduces the frequency, rate or extent of respiratory gaseous exchange. sl 2015-02-17T20:26:24Z down regulation of respiratory gaseous exchange down-regulation of respiratory gaseous exchange downregulation of respiratory gaseous exchange inhibition of respiratory gaseous exchange biological_process GO:1903941 negative regulation of respiratory gaseous exchange Any process that stops, prevents or reduces the frequency, rate or extent of respiratory gaseous exchange. GOC:TermGenie GO_REF:0000058 PMID:22819705 down regulation of respiratory gaseous exchange GOC:TermGenie down-regulation of respiratory gaseous exchange GOC:TermGenie downregulation of respiratory gaseous exchange GOC:TermGenie inhibition of respiratory gaseous exchange GOC:TermGenie Any process that activates or increases the frequency, rate or extent of respiratory gaseous exchange. sl 2015-02-17T20:26:35Z up regulation of respiratory gaseous exchange up-regulation of respiratory gaseous exchange upregulation of respiratory gaseous exchange activation of respiratory gaseous exchange biological_process GO:1903942 positive regulation of respiratory gaseous exchange Any process that activates or increases the frequency, rate or extent of respiratory gaseous exchange. GOC:TermGenie GO_REF:0000058 PMID:22819705 up regulation of respiratory gaseous exchange GOC:TermGenie up-regulation of respiratory gaseous exchange GOC:TermGenie upregulation of respiratory gaseous exchange GOC:TermGenie activation of respiratory gaseous exchange 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 activates or increases the frequency, rate or extent of vasculature development. sl 2015-03-06T22:17:04Z up regulation of vasculature development up-regulation of vasculature development upregulation of vasculature development activation of vasculature development biological_process activation of vascular system development positive regulation of vascular system development up regulation of vascular system development up-regulation of vascular system development upregulation of vascular system development GO:1904018 positive regulation of vasculature development Any process that activates or increases the frequency, rate or extent of vasculature development. GOC:TermGenie GO_REF:0000058 PMID:21472453 up regulation of vasculature development GOC:TermGenie up-regulation of vasculature development GOC:TermGenie upregulation of vasculature development GOC:TermGenie activation of vasculature development GOC:TermGenie activation of vascular system development GOC:TermGenie positive regulation of vascular system development GOC:TermGenie up regulation of vascular system development GOC:TermGenie up-regulation of vascular system development GOC:TermGenie upregulation of vascular system development GOC:TermGenie Any cytoplasm that is part of a axon. sl 2015-04-06T18:13:14Z axoplasm cellular_component GO:1904115 axon cytoplasm Any cytoplasm that is part of a axon. GOC:TermGenie GO_REF:0000064 PMID:18667152 Any process that modulates the frequency, rate or extent of bleb assembly. als 2015-04-23T09:32:19Z regulation of cell blebbing biological_process GO:1904170 regulation of bleb assembly Any process that modulates the frequency, rate or extent of bleb assembly. GOC:TermGenie GOC:als GO_REF:0000058 PMID:25651887 regulation of cell blebbing GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of bleb assembly. als 2015-04-23T09:32:25Z down regulation of bleb assembly down regulation of cell blebbing down-regulation of bleb assembly down-regulation of cell blebbing downregulation of bleb assembly downregulation of cell blebbing negative regulation of cell blebbing inhibition of bleb assembly inhibition of cell blebbing biological_process GO:1904171 negative regulation of bleb assembly Any process that stops, prevents or reduces the frequency, rate or extent of bleb assembly. GOC:TermGenie GOC:als GO_REF:0000058 PMID:25651887 down regulation of bleb assembly GOC:TermGenie down regulation of cell blebbing GOC:TermGenie down-regulation of bleb assembly GOC:TermGenie down-regulation of cell blebbing GOC:TermGenie downregulation of bleb assembly GOC:TermGenie downregulation of cell blebbing GOC:TermGenie negative regulation of cell blebbing GOC:TermGenie inhibition of bleb assembly GOC:TermGenie inhibition of cell blebbing GOC:TermGenie Any process that activates or increases the frequency, rate or extent of bleb assembly. als 2015-04-23T09:32:31Z positive regulation of cell blebbing up regulation of bleb assembly up regulation of cell blebbing up-regulation of bleb assembly up-regulation of cell blebbing upregulation of bleb assembly upregulation of cell blebbing activation of bleb assembly activation of cell blebbing biological_process GO:1904172 positive regulation of bleb assembly Any process that activates or increases the frequency, rate or extent of bleb assembly. GOC:TermGenie GOC:als GO_REF:0000058 PMID:25651887 positive regulation of cell blebbing GOC:TermGenie up regulation of bleb assembly GOC:TermGenie up regulation of cell blebbing GOC:TermGenie up-regulation of bleb assembly GOC:TermGenie up-regulation of cell blebbing GOC:TermGenie upregulation of bleb assembly GOC:TermGenie upregulation of cell blebbing GOC:TermGenie activation of bleb assembly GOC:TermGenie activation of cell blebbing GOC:TermGenie Any process that modulates the frequency, rate or extent of bile acid metabolic process. bf 2015-05-20T11:04:28Z regulation of bile acid metabolism biological_process GO:1904251 regulation of bile acid metabolic process Any process that modulates the frequency, rate or extent of bile acid metabolic process. GOC:TermGenie GOC:bf GO_REF:0000058 regulation of bile acid metabolism GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of bile acid metabolic process. bf 2015-05-20T11:04:35Z down regulation of bile acid metabolic process down regulation of bile acid metabolism down-regulation of bile acid metabolic process down-regulation of bile acid metabolism downregulation of bile acid metabolic process downregulation of bile acid metabolism negative regulation of bile acid metabolism inhibition of bile acid metabolic process inhibition of bile acid metabolism biological_process GO:1904252 negative regulation of bile acid metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of bile acid metabolic process. GOC:TermGenie GOC:bf GO_REF:0000058 down regulation of bile acid metabolic process GOC:TermGenie down regulation of bile acid metabolism GOC:TermGenie down-regulation of bile acid metabolic process GOC:TermGenie down-regulation of bile acid metabolism GOC:TermGenie downregulation of bile acid metabolic process GOC:TermGenie downregulation of bile acid metabolism GOC:TermGenie negative regulation of bile acid metabolism GOC:TermGenie inhibition of bile acid metabolic process GOC:TermGenie inhibition of bile acid metabolism GOC:TermGenie Any process that activates or increases the frequency, rate or extent of bile acid metabolic process. bf 2015-05-20T11:04:40Z positive regulation of bile acid metabolism up regulation of bile acid metabolic process up regulation of bile acid metabolism up-regulation of bile acid metabolic process up-regulation of bile acid metabolism upregulation of bile acid metabolic process upregulation of bile acid metabolism activation of bile acid metabolic process activation of bile acid metabolism biological_process GO:1904253 positive regulation of bile acid metabolic process Any process that activates or increases the frequency, rate or extent of bile acid metabolic process. GOC:TermGenie GOC:bf GO_REF:0000058 positive regulation of bile acid metabolism GOC:TermGenie up regulation of bile acid metabolic process GOC:TermGenie up regulation of bile acid metabolism GOC:TermGenie up-regulation of bile acid metabolic process GOC:TermGenie up-regulation of bile acid metabolism GOC:TermGenie upregulation of bile acid metabolic process GOC:TermGenie upregulation of bile acid metabolism GOC:TermGenie activation of bile acid metabolic process GOC:TermGenie activation of bile acid metabolism GOC:TermGenie Any process that modulates the frequency, rate or extent of calcitonin secretion. sl 2015-06-15T17:54:52Z biological_process GO:1904362 regulation of calcitonin secretion Any process that modulates the frequency, rate or extent of calcitonin secretion. GOC:TermGenie GO_REF:0000058 PMID:11278900 Any process that stops, prevents or reduces the frequency, rate or extent of calcitonin secretion. sl 2015-06-15T17:54:58Z down regulation of calcitonin secretion down-regulation of calcitonin secretion downregulation of calcitonin secretion inhibition of calcitonin secretion biological_process GO:1904363 negative regulation of calcitonin secretion Any process that stops, prevents or reduces the frequency, rate or extent of calcitonin secretion. GOC:TermGenie GO_REF:0000058 PMID:11278900 down regulation of calcitonin secretion GOC:TermGenie down-regulation of calcitonin secretion GOC:TermGenie downregulation of calcitonin secretion GOC:TermGenie inhibition of calcitonin secretion GOC:TermGenie Any process that activates or increases the frequency, rate or extent of calcitonin secretion. sl 2015-06-15T17:55:05Z up regulation of calcitonin secretion up-regulation of calcitonin secretion upregulation of calcitonin secretion activation of calcitonin secretion biological_process GO:1904364 positive regulation of calcitonin secretion Any process that activates or increases the frequency, rate or extent of calcitonin secretion. GOC:TermGenie GO_REF:0000058 PMID:11278900 up regulation of calcitonin secretion GOC:TermGenie up-regulation of calcitonin secretion GOC:TermGenie upregulation of calcitonin secretion GOC:TermGenie activation of calcitonin secretion GOC:TermGenie Any process that modulates the frequency, rate or extent of secretory granule organization. sl 2015-06-25T19:40:42Z regulation of secretory granule organisation biological_process regulation of secretory granule organization and biogenesis GO:1904409 regulation of secretory granule organization Any process that modulates the frequency, rate or extent of secretory granule organization. GOC:TermGenie GO_REF:0000058 PMID:15039777 regulation of secretory granule organisation GOC:TermGenie regulation of secretory granule organization and biogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of secretory granule organization. sl 2015-06-25T19:40:49Z down regulation of secretory granule organisation down regulation of secretory granule organization down-regulation of secretory granule organisation down-regulation of secretory granule organization downregulation of secretory granule organisation downregulation of secretory granule organization negative regulation of secretory granule organisation inhibition of secretory granule organisation inhibition of secretory granule organization biological_process down regulation of secretory granule organization and biogenesis down-regulation of secretory granule organization and biogenesis downregulation of secretory granule organization and biogenesis inhibition of secretory granule organization and biogenesis negative regulation of secretory granule organization and biogenesis GO:1904410 negative regulation of secretory granule organization Any process that stops, prevents or reduces the frequency, rate or extent of secretory granule organization. GOC:TermGenie GO_REF:0000058 PMID:15039777 down regulation of secretory granule organisation GOC:TermGenie down regulation of secretory granule organization GOC:TermGenie down-regulation of secretory granule organisation GOC:TermGenie down-regulation of secretory granule organization GOC:TermGenie downregulation of secretory granule organisation GOC:TermGenie downregulation of secretory granule organization GOC:TermGenie negative regulation of secretory granule organisation GOC:TermGenie inhibition of secretory granule organisation GOC:TermGenie inhibition of secretory granule organization GOC:TermGenie down regulation of secretory granule organization and biogenesis GOC:TermGenie down-regulation of secretory granule organization and biogenesis GOC:TermGenie downregulation of secretory granule organization and biogenesis GOC:TermGenie inhibition of secretory granule organization and biogenesis GOC:TermGenie negative regulation of secretory granule organization and biogenesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of secretory granule organization. sl 2015-06-25T19:40:55Z positive regulation of secretory granule organisation up regulation of secretory granule organisation up regulation of secretory granule organization up-regulation of secretory granule organisation up-regulation of secretory granule organization upregulation of secretory granule organisation upregulation of secretory granule organization activation of secretory granule organisation activation of secretory granule organization biological_process activation of secretory granule organization and biogenesis positive regulation of secretory granule organization and biogenesis up regulation of secretory granule organization and biogenesis up-regulation of secretory granule organization and biogenesis upregulation of secretory granule organization and biogenesis GO:1904411 positive regulation of secretory granule organization Any process that activates or increases the frequency, rate or extent of secretory granule organization. GOC:TermGenie GO_REF:0000058 PMID:15039777 positive regulation of secretory granule organisation GOC:TermGenie up regulation of secretory granule organisation GOC:TermGenie up regulation of secretory granule organization GOC:TermGenie up-regulation of secretory granule organisation GOC:TermGenie up-regulation of secretory granule organization GOC:TermGenie upregulation of secretory granule organisation GOC:TermGenie upregulation of secretory granule organization GOC:TermGenie activation of secretory granule organisation GOC:TermGenie activation of secretory granule organization GOC:TermGenie activation of secretory granule organization and biogenesis GOC:TermGenie positive regulation of secretory granule organization and biogenesis GOC:TermGenie up regulation of secretory granule organization and biogenesis GOC:TermGenie up-regulation of secretory granule organization and biogenesis GOC:TermGenie upregulation of secretory granule organization and biogenesis GOC:TermGenie Any process that modulates the frequency, rate or extent of glycine secretion, neurotransmission. hjd 2015-08-27T20:03:38Z biological_process GO:1904624 regulation of glycine secretion, neurotransmission Any process that modulates the frequency, rate or extent of glycine secretion, neurotransmission. GOC:TermGenie GO_REF:0000058 PMID:22988142 Any process that stops, prevents or reduces the frequency, rate or extent of glycine secretion, neurotransmission. hjd 2015-08-27T20:03:44Z down regulation of glycine secretion, neurotransmission down-regulation of glycine secretion, neurotransmission downregulation of glycine secretion, neurotransmission inhibition of glycine secretion, neurotransmission biological_process GO:1904625 negative regulation of glycine secretion, neurotransmission Any process that stops, prevents or reduces the frequency, rate or extent of glycine secretion, neurotransmission. GOC:TermGenie GO_REF:0000058 PMID:22988142 down regulation of glycine secretion, neurotransmission GOC:TermGenie down-regulation of glycine secretion, neurotransmission GOC:TermGenie downregulation of glycine secretion, neurotransmission GOC:TermGenie inhibition of glycine secretion, neurotransmission GOC:TermGenie Any process that activates or increases the frequency, rate or extent of glycine secretion, neurotransmission. hjd 2015-08-27T20:03:49Z up regulation of glycine secretion, neurotransmission up-regulation of glycine secretion, neurotransmission upregulation of glycine secretion, neurotransmission activation of glycine secretion, neurotransmission biological_process GO:1904626 positive regulation of glycine secretion, neurotransmission Any process that activates or increases the frequency, rate or extent of glycine secretion, neurotransmission. GOC:TermGenie GO_REF:0000058 PMID:22988142 up regulation of glycine secretion, neurotransmission GOC:TermGenie up-regulation of glycine secretion, neurotransmission GOC:TermGenie upregulation of glycine secretion, neurotransmission GOC:TermGenie activation of glycine secretion, neurotransmission GOC:TermGenie Any process that modulates the frequency, rate or extent of somatic stem cell division. rph 2015-09-14T08:47:22Z regulation of somatic stem cell renewal biological_process GO:1904675 regulation of somatic stem cell division Any process that modulates the frequency, rate or extent of somatic stem cell division. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:19409607 regulation of somatic stem cell renewal GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of somatic stem cell division. rph 2015-09-14T08:47:28Z down regulation of somatic stem cell division down regulation of somatic stem cell renewal down-regulation of somatic stem cell division down-regulation of somatic stem cell renewal downregulation of somatic stem cell division downregulation of somatic stem cell renewal negative regulation of somatic stem cell renewal inhibition of somatic stem cell division inhibition of somatic stem cell renewal biological_process GO:1904676 negative regulation of somatic stem cell division Any process that stops, prevents or reduces the frequency, rate or extent of somatic stem cell division. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:19409607 down regulation of somatic stem cell division GOC:TermGenie down regulation of somatic stem cell renewal GOC:TermGenie down-regulation of somatic stem cell division GOC:TermGenie down-regulation of somatic stem cell renewal GOC:TermGenie downregulation of somatic stem cell division GOC:TermGenie downregulation of somatic stem cell renewal GOC:TermGenie negative regulation of somatic stem cell renewal GOC:TermGenie inhibition of somatic stem cell division GOC:TermGenie inhibition of somatic stem cell renewal GOC:TermGenie Any process that activates or increases the frequency, rate or extent of somatic stem cell division. rph 2015-09-14T08:47:34Z positive regulation of somatic stem cell renewal up regulation of somatic stem cell division up regulation of somatic stem cell renewal up-regulation of somatic stem cell division up-regulation of somatic stem cell renewal upregulation of somatic stem cell division upregulation of somatic stem cell renewal activation of somatic stem cell division activation of somatic stem cell renewal biological_process GO:1904677 positive regulation of somatic stem cell division Any process that activates or increases the frequency, rate or extent of somatic stem cell division. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:19409607 positive regulation of somatic stem cell renewal GOC:TermGenie up regulation of somatic stem cell division GOC:TermGenie up regulation of somatic stem cell renewal GOC:TermGenie up-regulation of somatic stem cell division GOC:TermGenie up-regulation of somatic stem cell renewal GOC:TermGenie upregulation of somatic stem cell division GOC:TermGenie upregulation of somatic stem cell renewal GOC:TermGenie activation of somatic stem cell division GOC:TermGenie activation of somatic stem cell renewal GOC:TermGenie Any membrane-enclosed lumen that is part of a tertiary granule. mec 2015-10-12T12:53:10Z membrane-enclosed lumen of gelatinase granule membrane-enclosed lumen of tertiary granule tertiary granule membrane-enclosed lumen cellular_component gelatinase granule membrane-enclosed lumen GO:1904724 tertiary granule lumen Any membrane-enclosed lumen that is part of a tertiary granule. GOC:TermGenie GO_REF:0000064 PMID:23650620 membrane-enclosed lumen of gelatinase granule GOC:TermGenie membrane-enclosed lumen of tertiary granule GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in development. es 2015-10-19T14:12:27Z down regulation of apoptotic cell death involved in anatomical structure development down regulation of apoptotic cell death involved in development of an anatomical structure down regulation of apoptotic process involved in anatomical structure development down regulation of apoptotic process involved in development down regulation of apoptotic process involved in development of an anatomical structure down regulation of apoptotic programmed cell death involved in anatomical structure development down regulation of apoptotic programmed cell death involved in development of an anatomical structure down regulation of programmed cell death by apoptosis involved in anatomical structure development down regulation of programmed cell death by apoptosis involved in development of an anatomical structure down-regulation of apoptotic cell death involved in anatomical structure development down-regulation of apoptotic cell death involved in development of an anatomical structure down-regulation of apoptotic process involved in anatomical structure development down-regulation of apoptotic process involved in development down-regulation of apoptotic process involved in development of an anatomical structure down-regulation of apoptotic programmed cell death involved in anatomical structure development down-regulation of apoptotic programmed cell death involved in development of an anatomical structure down-regulation of programmed cell death by apoptosis involved in anatomical structure development down-regulation of programmed cell death by apoptosis involved in development of an anatomical structure downregulation of apoptotic cell death involved in anatomical structure development downregulation of apoptotic cell death involved in development of an anatomical structure downregulation of apoptotic process involved in anatomical structure development downregulation of apoptotic process involved in development downregulation of apoptotic process involved in development of an anatomical structure downregulation of apoptotic programmed cell death involved in anatomical structure development downregulation of apoptotic programmed cell death involved in development of an anatomical structure downregulation of programmed cell death by apoptosis involved in anatomical structure development downregulation of programmed cell death by apoptosis involved in development of an anatomical structure negative regulation of apoptotic cell death involved in anatomical structure development negative regulation of apoptotic cell death involved in development of an anatomical structure negative regulation of apoptotic process involved in anatomical structure development negative regulation of apoptotic process involved in development of an anatomical structure negative regulation of apoptotic programmed cell death involved in anatomical structure development negative regulation of apoptotic programmed cell death involved in development of an anatomical structure negative regulation of programmed cell death by apoptosis involved in anatomical structure development negative regulation of programmed cell death by apoptosis involved in development of an anatomical structure down regulation of activation of apoptosis involved in anatomical structure development down regulation of activation of apoptosis involved in development of an anatomical structure down regulation of apoptosis involved in anatomical structure development down regulation of apoptosis involved in development of an anatomical structure down regulation of apoptosis signaling involved in anatomical structure development down regulation of apoptosis signaling involved in development of an anatomical structure down regulation of apoptotic program involved in anatomical structure development down regulation of apoptotic program involved in development of an anatomical structure down regulation of type I programmed cell death involved in anatomical structure development down regulation of type I programmed cell death involved in development of an anatomical structure down-regulation of activation of apoptosis involved in anatomical structure development down-regulation of activation of apoptosis involved in development of an anatomical structure down-regulation of apoptosis involved in anatomical structure development down-regulation of apoptosis involved in development of an anatomical structure down-regulation of apoptosis signaling involved in anatomical structure development down-regulation of apoptosis signaling involved in development of an anatomical structure down-regulation of apoptotic program involved in anatomical structure development down-regulation of apoptotic program involved in development of an anatomical structure down-regulation of type I programmed cell death involved in anatomical structure development down-regulation of type I programmed cell death involved in development of an anatomical structure downregulation of activation of apoptosis involved in anatomical structure development downregulation of activation of apoptosis involved in development of an anatomical structure downregulation of apoptosis involved in anatomical structure development downregulation of apoptosis involved in development of an anatomical structure downregulation of apoptosis signaling involved in anatomical structure development downregulation of apoptosis signaling involved in development of an anatomical structure downregulation of apoptotic program involved in anatomical structure development downregulation of apoptotic program involved in development of an anatomical structure downregulation of type I programmed cell death involved in anatomical structure development downregulation of type I programmed cell death involved in development of an anatomical structure inhibition of activation of apoptosis involved in anatomical structure development inhibition of activation of apoptosis involved in development of an anatomical structure inhibition of apoptosis involved in anatomical structure development inhibition of apoptosis involved in development of an anatomical structure inhibition of apoptosis signaling involved in anatomical structure development inhibition of apoptosis signaling involved in development of an anatomical structure inhibition of apoptotic cell death involved in anatomical structure development inhibition of apoptotic cell death involved in development of an anatomical structure inhibition of apoptotic process involved in anatomical structure development inhibition of apoptotic process involved in development inhibition of apoptotic process involved in development of an anatomical structure inhibition of apoptotic program involved in anatomical structure development inhibition of apoptotic program involved in development of an anatomical structure inhibition of apoptotic programmed cell death involved in anatomical structure development inhibition of apoptotic programmed cell death involved in development of an anatomical structure inhibition of programmed cell death by apoptosis involved in anatomical structure development inhibition of programmed cell death by apoptosis involved in development of an anatomical structure inhibition of type I programmed cell death involved in anatomical structure development inhibition of type I programmed cell death involved in development of an anatomical structure negative regulation of activation of apoptosis involved in anatomical structure development negative regulation of activation of apoptosis involved in development of an anatomical structure negative regulation of apoptosis involved in anatomical structure development negative regulation of apoptosis involved in development of an anatomical structure negative regulation of apoptosis signaling involved in anatomical structure development negative regulation of apoptosis signaling involved in development of an anatomical structure negative regulation of apoptotic program involved in anatomical structure development negative regulation of apoptotic program involved in development of an anatomical structure negative regulation of type I programmed cell death involved in anatomical structure development negative regulation of type I programmed cell death involved in development of an anatomical structure biological_process down regulation of apoptosis activator activity involved in anatomical structure development down regulation of apoptosis activator activity involved in development of an anatomical structure down regulation of commitment to apoptosis involved in anatomical structure development down regulation of commitment to apoptosis involved in development of an anatomical structure down regulation of induction of apoptosis by p53 involved in anatomical structure development down regulation of induction of apoptosis by p53 involved in development of an anatomical structure down regulation of induction of apoptosis involved in anatomical structure development down regulation of induction of apoptosis involved in development of an anatomical structure down regulation of signaling (initiator) caspase activity involved in anatomical structure development down regulation of signaling (initiator) caspase activity involved in development of an anatomical structure down-regulation of apoptosis activator activity involved in anatomical structure development down-regulation of apoptosis activator activity involved in development of an anatomical structure down-regulation of commitment to apoptosis involved in anatomical structure development down-regulation of commitment to apoptosis involved in development of an anatomical structure down-regulation of induction of apoptosis by p53 involved in anatomical structure development down-regulation of induction of apoptosis by p53 involved in development of an anatomical structure down-regulation of induction of apoptosis involved in anatomical structure development down-regulation of induction of apoptosis involved in development of an anatomical structure down-regulation of signaling (initiator) caspase activity involved in anatomical structure development down-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure downregulation of apoptosis activator activity involved in anatomical structure development downregulation of apoptosis activator activity involved in development of an anatomical structure downregulation of commitment to apoptosis involved in anatomical structure development downregulation of commitment to apoptosis involved in development of an anatomical structure downregulation of induction of apoptosis by p53 involved in anatomical structure development downregulation of induction of apoptosis by p53 involved in development of an anatomical structure downregulation of induction of apoptosis involved in anatomical structure development downregulation of induction of apoptosis involved in development of an anatomical structure downregulation of signaling (initiator) caspase activity involved in anatomical structure development downregulation of signaling (initiator) caspase activity involved in development of an anatomical structure inhibition of apoptosis activator activity involved in anatomical structure development inhibition of apoptosis activator activity involved in development of an anatomical structure inhibition of commitment to apoptosis involved in anatomical structure development inhibition of commitment to apoptosis involved in development of an anatomical structure inhibition of induction of apoptosis by p53 involved in anatomical structure development inhibition of induction of apoptosis by p53 involved in development of an anatomical structure inhibition of induction of apoptosis involved in anatomical structure development inhibition of induction of apoptosis involved in development of an anatomical structure inhibition of signaling (initiator) caspase activity involved in anatomical structure development inhibition of signaling (initiator) caspase activity involved in development of an anatomical structure negative regulation of apoptosis activator activity involved in anatomical structure development negative regulation of apoptosis activator activity involved in development of an anatomical structure negative regulation of commitment to apoptosis involved in anatomical structure development negative regulation of commitment to apoptosis involved in development of an anatomical structure negative regulation of induction of apoptosis by p53 involved in anatomical structure development negative regulation of induction of apoptosis by p53 involved in development of an anatomical structure negative regulation of induction of apoptosis involved in anatomical structure development negative regulation of induction of apoptosis involved in development of an anatomical structure negative regulation of signaling (initiator) caspase activity involved in anatomical structure development negative regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GO:1904746 U4PR86 in PMID:22801495 inferred from mutant phenotype negative regulation of apoptotic process involved in development Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in development. GOC:TermGenie GO_REF:0000058 PMID:22801495 down regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie down regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie down regulation of apoptotic process involved in anatomical structure development GOC:TermGenie down regulation of apoptotic process involved in development GOC:TermGenie down regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie down regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie down regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie down regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie down regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie down-regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptotic process involved in anatomical structure development GOC:TermGenie down-regulation of apoptotic process involved in development GOC:TermGenie down-regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie down-regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie down-regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie downregulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie downregulation of apoptotic process involved in anatomical structure development GOC:TermGenie downregulation of apoptotic process involved in development GOC:TermGenie downregulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie downregulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie downregulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie downregulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie downregulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie negative regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptotic process involved in anatomical structure development GOC:TermGenie negative regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie negative regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie negative regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie down regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of apoptosis involved in anatomical structure development GOC:TermGenie down regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie down regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie down regulation of apoptotic program involved in anatomical structure development GOC:TermGenie down regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie down regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie down regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie down-regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie down-regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptotic program involved in anatomical structure development GOC:TermGenie down-regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie down-regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie down-regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie downregulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie downregulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of apoptosis involved in anatomical structure development GOC:TermGenie downregulation of apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie downregulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie downregulation of apoptotic program involved in anatomical structure development GOC:TermGenie downregulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie downregulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie downregulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie inhibition of activation of apoptosis involved in anatomical structure development GOC:TermGenie inhibition of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of apoptosis involved in anatomical structure development GOC:TermGenie inhibition of apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of apoptosis signaling involved in anatomical structure development GOC:TermGenie inhibition of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie inhibition of apoptotic cell death involved in anatomical structure development GOC:TermGenie inhibition of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie inhibition of apoptotic process involved in anatomical structure development GOC:TermGenie inhibition of apoptotic process involved in development GOC:TermGenie inhibition of apoptotic process involved in development of an anatomical structure GOC:TermGenie inhibition of apoptotic program involved in anatomical structure development GOC:TermGenie inhibition of apoptotic program involved in development of an anatomical structure GOC:TermGenie inhibition of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie inhibition of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie inhibition of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie inhibition of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of type I programmed cell death involved in anatomical structure development GOC:TermGenie inhibition of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie negative regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie negative regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptotic program involved in anatomical structure development GOC:TermGenie negative regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie negative regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie negative regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie down regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie down regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie down regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie down regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie down regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie down regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie down regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie down regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie down-regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie down-regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie down-regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie down-regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie down-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie downregulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie downregulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie downregulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie downregulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie downregulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie downregulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie downregulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie downregulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie inhibition of apoptosis activator activity involved in anatomical structure development GOC:TermGenie inhibition of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie inhibition of commitment to apoptosis involved in anatomical structure development GOC:TermGenie inhibition of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie inhibition of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie inhibition of induction of apoptosis involved in anatomical structure development GOC:TermGenie inhibition of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie inhibition of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie negative regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie negative regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie negative regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie negative regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie negative regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie Any process that activates or increases the frequency, rate or extent of apoptotic process involved in development. es 2015-10-19T14:12:34Z positive regulation of apoptotic cell death involved in anatomical structure development positive regulation of apoptotic cell death involved in development of an anatomical structure positive regulation of apoptotic process involved in anatomical structure development positive regulation of apoptotic process involved in development of an anatomical structure positive regulation of apoptotic programmed cell death involved in anatomical structure development positive regulation of apoptotic programmed cell death involved in development of an anatomical structure positive regulation of programmed cell death by apoptosis involved in anatomical structure development positive regulation of programmed cell death by apoptosis involved in development of an anatomical structure up regulation of apoptotic cell death involved in anatomical structure development up regulation of apoptotic cell death involved in development of an anatomical structure up regulation of apoptotic process involved in anatomical structure development up regulation of apoptotic process involved in development up regulation of apoptotic process involved in development of an anatomical structure up regulation of apoptotic programmed cell death involved in anatomical structure development up regulation of apoptotic programmed cell death involved in development of an anatomical structure up regulation of programmed cell death by apoptosis involved in anatomical structure development up regulation of programmed cell death by apoptosis involved in development of an anatomical structure up-regulation of apoptotic cell death involved in anatomical structure development up-regulation of apoptotic cell death involved in development of an anatomical structure up-regulation of apoptotic process involved in anatomical structure development up-regulation of apoptotic process involved in development up-regulation of apoptotic process involved in development of an anatomical structure up-regulation of apoptotic programmed cell death involved in anatomical structure development up-regulation of apoptotic programmed cell death involved in development of an anatomical structure up-regulation of programmed cell death by apoptosis involved in anatomical structure development up-regulation of programmed cell death by apoptosis involved in development of an anatomical structure upregulation of apoptotic cell death involved in anatomical structure development upregulation of apoptotic cell death involved in development of an anatomical structure upregulation of apoptotic process involved in anatomical structure development upregulation of apoptotic process involved in development upregulation of apoptotic process involved in development of an anatomical structure upregulation of apoptotic programmed cell death involved in anatomical structure development upregulation of apoptotic programmed cell death involved in development of an anatomical structure upregulation of programmed cell death by apoptosis involved in anatomical structure development upregulation of programmed cell death by apoptosis involved in development of an anatomical structure activation of activation of apoptosis involved in anatomical structure development activation of activation of apoptosis involved in development of an anatomical structure activation of apoptosis involved in anatomical structure development activation of apoptosis involved in development of an anatomical structure activation of apoptosis signaling involved in anatomical structure development activation of apoptosis signaling involved in development of an anatomical structure activation of apoptotic cell death involved in anatomical structure development activation of apoptotic cell death involved in development of an anatomical structure activation of apoptotic process involved in anatomical structure development activation of apoptotic process involved in development activation of apoptotic process involved in development of an anatomical structure activation of apoptotic program involved in anatomical structure development activation of apoptotic program involved in development of an anatomical structure activation of apoptotic programmed cell death involved in anatomical structure development activation of apoptotic programmed cell death involved in development of an anatomical structure activation of programmed cell death by apoptosis involved in anatomical structure development activation of programmed cell death by apoptosis involved in development of an anatomical structure activation of type I programmed cell death involved in anatomical structure development activation of type I programmed cell death involved in development of an anatomical structure positive regulation of activation of apoptosis involved in anatomical structure development positive regulation of activation of apoptosis involved in development of an anatomical structure positive regulation of apoptosis involved in anatomical structure development positive regulation of apoptosis involved in development of an anatomical structure positive regulation of apoptosis signaling involved in anatomical structure development positive regulation of apoptosis signaling involved in development of an anatomical structure positive regulation of apoptotic program involved in anatomical structure development positive regulation of apoptotic program involved in development of an anatomical structure positive regulation of type I programmed cell death involved in anatomical structure development positive regulation of type I programmed cell death involved in development of an anatomical structure up regulation of activation of apoptosis involved in anatomical structure development up regulation of activation of apoptosis involved in development of an anatomical structure up regulation of apoptosis involved in anatomical structure development up regulation of apoptosis involved in development of an anatomical structure up regulation of apoptosis signaling involved in anatomical structure development up regulation of apoptosis signaling involved in development of an anatomical structure up regulation of apoptotic program involved in anatomical structure development up regulation of apoptotic program involved in development of an anatomical structure up regulation of type I programmed cell death involved in anatomical structure development up regulation of type I programmed cell death involved in development of an anatomical structure up-regulation of activation of apoptosis involved in anatomical structure development up-regulation of activation of apoptosis involved in development of an anatomical structure up-regulation of apoptosis involved in anatomical structure development up-regulation of apoptosis involved in development of an anatomical structure up-regulation of apoptosis signaling involved in anatomical structure development up-regulation of apoptosis signaling involved in development of an anatomical structure up-regulation of apoptotic program involved in anatomical structure development up-regulation of apoptotic program involved in development of an anatomical structure up-regulation of type I programmed cell death involved in anatomical structure development up-regulation of type I programmed cell death involved in development of an anatomical structure upregulation of activation of apoptosis involved in anatomical structure development upregulation of activation of apoptosis involved in development of an anatomical structure upregulation of apoptosis involved in anatomical structure development upregulation of apoptosis involved in development of an anatomical structure upregulation of apoptosis signaling involved in anatomical structure development upregulation of apoptosis signaling involved in development of an anatomical structure upregulation of apoptotic program involved in anatomical structure development upregulation of apoptotic program involved in development of an anatomical structure upregulation of type I programmed cell death involved in anatomical structure development upregulation of type I programmed cell death involved in development of an anatomical structure biological_process activation of apoptosis activator activity involved in anatomical structure development activation of apoptosis activator activity involved in development of an anatomical structure activation of commitment to apoptosis involved in anatomical structure development activation of commitment to apoptosis involved in development of an anatomical structure activation of induction of apoptosis by p53 involved in anatomical structure development activation of induction of apoptosis by p53 involved in development of an anatomical structure activation of induction of apoptosis involved in anatomical structure development activation of induction of apoptosis involved in development of an anatomical structure activation of signaling (initiator) caspase activity involved in anatomical structure development activation of signaling (initiator) caspase activity involved in development of an anatomical structure positive regulation of apoptosis activator activity involved in anatomical structure development positive regulation of apoptosis activator activity involved in development of an anatomical structure positive regulation of commitment to apoptosis involved in anatomical structure development positive regulation of commitment to apoptosis involved in development of an anatomical structure positive regulation of induction of apoptosis by p53 involved in anatomical structure development positive regulation of induction of apoptosis by p53 involved in development of an anatomical structure positive regulation of induction of apoptosis involved in anatomical structure development positive regulation of induction of apoptosis involved in development of an anatomical structure positive regulation of signaling (initiator) caspase activity involved in anatomical structure development positive regulation of signaling (initiator) caspase activity involved in development of an anatomical structure up regulation of apoptosis activator activity involved in anatomical structure development up regulation of apoptosis activator activity involved in development of an anatomical structure up regulation of commitment to apoptosis involved in anatomical structure development up regulation of commitment to apoptosis involved in development of an anatomical structure up regulation of induction of apoptosis by p53 involved in anatomical structure development up regulation of induction of apoptosis by p53 involved in development of an anatomical structure up regulation of induction of apoptosis involved in anatomical structure development up regulation of induction of apoptosis involved in development of an anatomical structure up regulation of signaling (initiator) caspase activity involved in anatomical structure development up regulation of signaling (initiator) caspase activity involved in development of an anatomical structure up-regulation of apoptosis activator activity involved in anatomical structure development up-regulation of apoptosis activator activity involved in development of an anatomical structure up-regulation of commitment to apoptosis involved in anatomical structure development up-regulation of commitment to apoptosis involved in development of an anatomical structure up-regulation of induction of apoptosis by p53 involved in anatomical structure development up-regulation of induction of apoptosis by p53 involved in development of an anatomical structure up-regulation of induction of apoptosis involved in anatomical structure development up-regulation of induction of apoptosis involved in development of an anatomical structure up-regulation of signaling (initiator) caspase activity involved in anatomical structure development up-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure upregulation of apoptosis activator activity involved in anatomical structure development upregulation of apoptosis activator activity involved in development of an anatomical structure upregulation of commitment to apoptosis involved in anatomical structure development upregulation of commitment to apoptosis involved in development of an anatomical structure upregulation of induction of apoptosis by p53 involved in anatomical structure development upregulation of induction of apoptosis by p53 involved in development of an anatomical structure upregulation of induction of apoptosis involved in anatomical structure development upregulation of induction of apoptosis involved in development of an anatomical structure upregulation of signaling (initiator) caspase activity involved in anatomical structure development upregulation of signaling (initiator) caspase activity involved in development of an anatomical structure GO:1904747 U4PR86 in PMID:22801495 inferred from mutant phenotype positive regulation of apoptotic process involved in development Any process that activates or increases the frequency, rate or extent of apoptotic process involved in development. GOC:TermGenie GO_REF:0000058 PMID:22801495 positive regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie positive regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptotic process involved in anatomical structure development GOC:TermGenie positive regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie positive regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie positive regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie up regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie up regulation of apoptotic process involved in anatomical structure development GOC:TermGenie up regulation of apoptotic process involved in development GOC:TermGenie up regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie up regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie up regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie up regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie up regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie up-regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptotic process involved in anatomical structure development GOC:TermGenie up-regulation of apoptotic process involved in development GOC:TermGenie up-regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie up-regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie up-regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie upregulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie upregulation of apoptotic process involved in anatomical structure development GOC:TermGenie upregulation of apoptotic process involved in development GOC:TermGenie upregulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie upregulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie upregulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie upregulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie upregulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie activation of activation of apoptosis involved in anatomical structure development GOC:TermGenie activation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie activation of apoptosis involved in anatomical structure development GOC:TermGenie activation of apoptosis involved in development of an anatomical structure GOC:TermGenie activation of apoptosis signaling involved in anatomical structure development GOC:TermGenie activation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie activation of apoptotic cell death involved in anatomical structure development GOC:TermGenie activation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie activation of apoptotic process involved in anatomical structure development GOC:TermGenie activation of apoptotic process involved in development GOC:TermGenie activation of apoptotic process involved in development of an anatomical structure GOC:TermGenie activation of apoptotic program involved in anatomical structure development GOC:TermGenie activation of apoptotic program involved in development of an anatomical structure GOC:TermGenie activation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie activation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie activation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie activation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie activation of type I programmed cell death involved in anatomical structure development GOC:TermGenie activation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie positive regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie positive regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptotic program involved in anatomical structure development GOC:TermGenie positive regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie positive regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie positive regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie up regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie up regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of apoptosis involved in anatomical structure development GOC:TermGenie up regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie up regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie up regulation of apoptotic program involved in anatomical structure development GOC:TermGenie up regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie up regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie up regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie up-regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie up-regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptotic program involved in anatomical structure development GOC:TermGenie up-regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie up-regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie up-regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie upregulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie upregulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of apoptosis involved in anatomical structure development GOC:TermGenie upregulation of apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie upregulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie upregulation of apoptotic program involved in anatomical structure development GOC:TermGenie upregulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie upregulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie upregulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie activation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie activation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie activation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie activation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie activation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie activation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie activation of induction of apoptosis involved in anatomical structure development GOC:TermGenie activation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie activation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie activation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie positive regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie positive regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie positive regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie positive regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie positive regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie positive regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie positive regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie up regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie up regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie up regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie up regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie up regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie up regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie up regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie up regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie up-regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie up-regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie up-regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie up-regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie up-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie upregulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie upregulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie upregulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie upregulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie upregulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie upregulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie upregulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie upregulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie Any process that modulates the frequency, rate or extent of apoptotic process involved in development. es 2015-10-19T15:02:28Z regulation of apoptotic cell death involved in anatomical structure development regulation of apoptotic cell death involved in development of an anatomical structure regulation of apoptotic process involved in anatomical structure development regulation of apoptotic process involved in development of an anatomical structure regulation of apoptotic programmed cell death involved in anatomical structure development regulation of apoptotic programmed cell death involved in development of an anatomical structure regulation of programmed cell death by apoptosis involved in anatomical structure development regulation of programmed cell death by apoptosis involved in development of an anatomical structure regulation of activation of apoptosis involved in anatomical structure development regulation of activation of apoptosis involved in development of an anatomical structure regulation of apoptosis involved in anatomical structure development regulation of apoptosis involved in development of an anatomical structure regulation of apoptosis signaling involved in anatomical structure development regulation of apoptosis signaling involved in development of an anatomical structure regulation of apoptotic program involved in anatomical structure development regulation of apoptotic program involved in development of an anatomical structure regulation of type I programmed cell death involved in anatomical structure development regulation of type I programmed cell death involved in development of an anatomical structure biological_process regulation of apoptosis activator activity involved in anatomical structure development regulation of apoptosis activator activity involved in development of an anatomical structure regulation of commitment to apoptosis involved in anatomical structure development regulation of commitment to apoptosis involved in development of an anatomical structure regulation of induction of apoptosis by p53 involved in anatomical structure development regulation of induction of apoptosis by p53 involved in development of an anatomical structure regulation of induction of apoptosis involved in anatomical structure development regulation of induction of apoptosis involved in development of an anatomical structure regulation of signaling (initiator) caspase activity involved in anatomical structure development regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GO:1904748 Q10943 in PMID:22801495, inferred from mutant phenotype regulation of apoptotic process involved in development Any process that modulates the frequency, rate or extent of apoptotic process involved in development. GOC:TermGenie GO_REF:0000058 PMID:22801495 regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie regulation of apoptotic process involved in anatomical structure development GOC:TermGenie regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of apoptosis involved in anatomical structure development GOC:TermGenie regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie regulation of apoptotic program involved in anatomical structure development GOC:TermGenie regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie 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 cell surface receptor signaling pathway that is involved in cell-cell signaling. dos 2016-04-06T16:59:57Z cell surface receptor linked signal transduction involved in cell-cell signaling cell surface receptor linked signal transduction involved in cell-cell signalling cell surface receptor linked signaling pathway involved in cell-cell signaling cell surface receptor linked signaling pathway involved in cell-cell signalling cell surface receptor linked signalling pathway involved in cell-cell signaling cell surface receptor linked signalling pathway involved in cell-cell signalling cell surface receptor signaling pathway involved in cell-cell signalling biological_process GO:1905114 cell surface receptor signaling pathway involved in cell-cell signaling Any cell surface receptor signaling pathway that is involved in cell-cell signaling. GOC:TermGenie GO_REF:0000060 ISBN:0-7167-3051-0 cell surface receptor linked signal transduction involved in cell-cell signaling GOC:TermGenie cell surface receptor linked signal transduction involved in cell-cell signalling GOC:TermGenie cell surface receptor linked signaling pathway involved in cell-cell signaling GOC:TermGenie cell surface receptor linked signaling pathway involved in cell-cell signalling GOC:TermGenie cell surface receptor linked signalling pathway involved in cell-cell signaling GOC:TermGenie cell surface receptor linked signalling pathway involved in cell-cell signalling GOC:TermGenie cell surface receptor signaling pathway involved in cell-cell signalling GOC:TermGenie Any process that modulates the frequency, rate or extent of membrane invagination. bf 2016-04-18T15:43:54Z biological_process GO:1905153 regulation of membrane invagination Any process that modulates the frequency, rate or extent of membrane invagination. GOC:PARL GOC:TermGenie GOC:bf GO_REF:0000058 PMID:26589353 Any process that stops, prevents or reduces the frequency, rate or extent of membrane invagination. bf 2016-04-18T15:44:04Z down regulation of membrane invagination down-regulation of membrane invagination downregulation of membrane invagination inhibition of membrane invagination biological_process GO:1905154 negative regulation of membrane invagination Any process that stops, prevents or reduces the frequency, rate or extent of membrane invagination. GOC:PARL GOC:TermGenie GOC:bf GO_REF:0000058 PMID:26589353 down regulation of membrane invagination GOC:TermGenie down-regulation of membrane invagination GOC:TermGenie downregulation of membrane invagination GOC:TermGenie inhibition of membrane invagination GOC:TermGenie Any process that activates or increases the frequency, rate or extent of membrane invagination. bf 2016-04-18T15:44:12Z up regulation of membrane invagination up-regulation of membrane invagination upregulation of membrane invagination activation of membrane invagination biological_process GO:1905155 positive regulation of membrane invagination Any process that activates or increases the frequency, rate or extent of membrane invagination. GOC:PARL GOC:TermGenie GOC:bf GO_REF:0000058 up regulation of membrane invagination GOC:TermGenie up-regulation of membrane invagination GOC:TermGenie upregulation of membrane invagination GOC:TermGenie activation of membrane invagination GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of photosynthesis. tb 2016-04-19T16:12:29Z down regulation of photosynthesis down-regulation of photosynthesis downregulation of photosynthesis inhibition of photosynthesis biological_process GO:1905156 negative regulation of photosynthesis Any process that stops, prevents or reduces the frequency, rate or extent of photosynthesis. GOC:TermGenie GO_REF:0000058 PMID:7592491 down regulation of photosynthesis GOC:TermGenie down-regulation of photosynthesis GOC:TermGenie downregulation of photosynthesis GOC:TermGenie inhibition of photosynthesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of photosynthesis. tb 2016-04-19T16:12:39Z up regulation of photosynthesis up-regulation of photosynthesis upregulation of photosynthesis activation of photosynthesis biological_process GO:1905157 positive regulation of photosynthesis Any process that activates or increases the frequency, rate or extent of photosynthesis. GOC:TermGenie GO_REF:0000058 PMID:7592491 up regulation of photosynthesis GOC:TermGenie up-regulation of photosynthesis GOC:TermGenie upregulation of photosynthesis GOC:TermGenie activation of photosynthesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of mitotic chromosome condensation. vw 2016-06-03T08:41:08Z biological_process GO:1905213 negative regulation of mitotic chromosome condensation Any process that stops, prevents or reduces the frequency, rate or extent of mitotic chromosome condensation. GOC:TermGenie GO_REF:0000058 PMID:23219725 The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone. pr 2016-08-04T14:49:43Z cilial transition zone assembly cilial transition zone formation ciliary transition zone formation cilium transition zone assembly cilium transition zone formation biological_process GO:1905349 ciliary transition zone assembly The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone. GOC:TermGenie GOC:cilia GO_REF:0000079 PMID:21725307 PMID:23644468 PMID:24448408 PMID:26595381 PMID:26982032 cilial transition zone assembly GOC:TermGenie cilial transition zone formation GOC:TermGenie ciliary transition zone formation GOC:TermGenie cilium transition zone assembly GOC:TermGenie cilium transition zone formation GOC:TermGenie Any process that modulates the frequency, rate or extent of motile cilium assembly. krc 2016-09-27T18:27:47Z biological_process regulation of motile primary cilia assembly regulation of motile primary cilia formation regulation of motile primary cilium assembly regulation of motile primary cilium formation regulation of nodal cilium assembly regulation of nodal cilium formation GO:1905503 regulation of motile cilium assembly Any process that modulates the frequency, rate or extent of motile cilium assembly. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000058 PMID:25294941 regulation of motile primary cilia assembly GOC:TermGenie regulation of motile primary cilia formation GOC:TermGenie regulation of motile primary cilium formation GOC:TermGenie regulation of nodal cilium assembly GOC:TermGenie regulation of nodal cilium formation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of motile cilium assembly. krc 2016-09-27T18:27:55Z inhibition of motile primary cilia assembly inhibition of motile primary cilia formation inhibition of motile primary cilium assembly inhibition of motile primary cilium formation biological_process down regulation of motile primary cilia assembly down regulation of motile primary cilia formation down regulation of motile primary cilium assembly down regulation of motile primary cilium formation down regulation of nodal cilium assembly down regulation of nodal cilium formation down-regulation of motile primary cilia assembly down-regulation of motile primary cilia formation down-regulation of motile primary cilium assembly down-regulation of motile primary cilium formation down-regulation of nodal cilium assembly down-regulation of nodal cilium formation downregulation of motile primary cilia assembly downregulation of motile primary cilia formation downregulation of motile primary cilium assembly downregulation of motile primary cilium formation downregulation of nodal cilium assembly downregulation of nodal cilium formation inhibition of nodal cilium assembly inhibition of nodal cilium formation negative regulation of motile primary cilia assembly negative regulation of motile primary cilia formation negative regulation of motile primary cilium assembly negative regulation of motile primary cilium formation negative regulation of nodal cilium assembly negative regulation of nodal cilium formation GO:1905504 negative regulation of motile cilium assembly Any process that stops, prevents or reduces the frequency, rate or extent of motile cilium assembly. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000058 PMID:25294941 inhibition of motile primary cilia assembly GOC:TermGenie inhibition of motile primary cilia formation GOC:TermGenie inhibition of motile primary cilium assembly GOC:TermGenie inhibition of motile primary cilium formation GOC:TermGenie down regulation of motile primary cilia assembly GOC:TermGenie down regulation of motile primary cilia formation GOC:TermGenie down regulation of motile primary cilium assembly GOC:TermGenie down regulation of motile primary cilium formation GOC:TermGenie down regulation of nodal cilium assembly GOC:TermGenie down regulation of nodal cilium formation GOC:TermGenie down-regulation of motile primary cilia assembly GOC:TermGenie down-regulation of motile primary cilia formation GOC:TermGenie down-regulation of motile primary cilium assembly GOC:TermGenie down-regulation of motile primary cilium formation GOC:TermGenie down-regulation of nodal cilium assembly GOC:TermGenie down-regulation of nodal cilium formation GOC:TermGenie downregulation of motile primary cilia assembly GOC:TermGenie downregulation of motile primary cilia formation GOC:TermGenie downregulation of motile primary cilium assembly GOC:TermGenie downregulation of motile primary cilium formation GOC:TermGenie downregulation of nodal cilium assembly GOC:TermGenie downregulation of nodal cilium formation GOC:TermGenie inhibition of nodal cilium assembly GOC:TermGenie inhibition of nodal cilium formation GOC:TermGenie negative regulation of motile primary cilia assembly GOC:TermGenie negative regulation of motile primary cilia formation GOC:TermGenie negative regulation of motile primary cilium formation GOC:TermGenie negative regulation of nodal cilium assembly GOC:TermGenie negative regulation of nodal cilium formation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of motile cilium assembly. krc 2016-09-27T18:28:03Z activation of motile primary cilia assembly activation of motile primary cilia formation activation of motile primary cilium assembly activation of motile primary cilium formation biological_process activation of nodal cilium assembly activation of nodal cilium formation positive regulation of motile primary cilia assembly positive regulation of motile primary cilia formation positive regulation of motile primary cilium assembly positive regulation of motile primary cilium formation positive regulation of nodal cilium assembly positive regulation of nodal cilium formation up regulation of motile primary cilia assembly up regulation of motile primary cilia formation up regulation of motile primary cilium assembly up regulation of motile primary cilium formation up regulation of nodal cilium assembly up regulation of nodal cilium formation up-regulation of motile primary cilia assembly up-regulation of motile primary cilia formation up-regulation of motile primary cilium assembly up-regulation of motile primary cilium formation up-regulation of nodal cilium assembly up-regulation of nodal cilium formation upregulation of motile primary cilia assembly upregulation of motile primary cilia formation upregulation of motile primary cilium assembly upregulation of motile primary cilium formation upregulation of nodal cilium assembly upregulation of nodal cilium formation GO:1905505 positive regulation of motile cilium assembly Any process that activates or increases the frequency, rate or extent of motile cilium assembly. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000058 PMID:25294941 activation of motile primary cilia assembly GOC:TermGenie activation of motile primary cilia formation GOC:TermGenie activation of motile primary cilium assembly GOC:TermGenie activation of motile primary cilium formation GOC:TermGenie activation of nodal cilium assembly GOC:TermGenie activation of nodal cilium formation GOC:TermGenie positive regulation of motile primary cilia assembly GOC:TermGenie positive regulation of motile primary cilia formation GOC:TermGenie positive regulation of motile primary cilium formation GOC:TermGenie positive regulation of nodal cilium assembly GOC:TermGenie positive regulation of nodal cilium formation GOC:TermGenie up regulation of motile primary cilia assembly GOC:TermGenie up regulation of motile primary cilia formation GOC:TermGenie up regulation of motile primary cilium assembly GOC:TermGenie up regulation of motile primary cilium formation GOC:TermGenie up regulation of nodal cilium assembly GOC:TermGenie up regulation of nodal cilium formation GOC:TermGenie up-regulation of motile primary cilia assembly GOC:TermGenie up-regulation of motile primary cilia formation GOC:TermGenie up-regulation of motile primary cilium assembly GOC:TermGenie up-regulation of motile primary cilium formation GOC:TermGenie up-regulation of nodal cilium assembly GOC:TermGenie up-regulation of nodal cilium formation GOC:TermGenie upregulation of motile primary cilia assembly GOC:TermGenie upregulation of motile primary cilia formation GOC:TermGenie upregulation of motile primary cilium assembly GOC:TermGenie upregulation of motile primary cilium formation GOC:TermGenie upregulation of nodal cilium assembly GOC:TermGenie upregulation of nodal cilium formation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of fertilization. pr 2016-09-30T14:32:32Z positive regulation of syngamy up regulation of fertilization up regulation of syngamy up-regulation of fertilization up-regulation of syngamy upregulation of fertilization upregulation of syngamy activation of fertilization activation of syngamy biological_process GO:1905516 positive regulation of fertilization Any process that activates or increases the frequency, rate or extent of fertilization. GOC:TermGenie GOC:hbye GO_REF:0000058 PMID:27564576 positive regulation of syngamy GOC:TermGenie up regulation of fertilization GOC:TermGenie up regulation of syngamy GOC:TermGenie up-regulation of fertilization GOC:TermGenie up-regulation of syngamy GOC:TermGenie upregulation of fertilization GOC:TermGenie upregulation of syngamy GOC:TermGenie activation of fertilization GOC:TermGenie activation of syngamy GOC:TermGenie Any process that modulates the frequency, rate or extent of detection of mechanical stimulus involved in sensory perception of touch. hbye 2017-01-09T15:11:04Z regulation of perception of touch, detection of mechanical stimulus regulation of perception of touch, sensory detection of mechanical stimulus regulation of perception of touch, sensory transduction of mechanical stimulus regulation of sensory detection of mechanical stimulus during perception of touch regulation of sensory transduction of mechanical stimulus during perception of touch regulation of tactition, sensory detection of mechanical stimulus biological_process GO:1905787 regulation of detection of mechanical stimulus involved in sensory perception of touch Any process that modulates the frequency, rate or extent of detection of mechanical stimulus involved in sensory perception of touch. GOC:TermGenie GO_REF:0000058 PMID:8692859 regulation of perception of touch, detection of mechanical stimulus GOC:TermGenie regulation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie regulation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie regulation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie regulation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie regulation of tactition, sensory detection of mechanical stimulus GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of detection of mechanical stimulus involved in sensory perception of touch. hbye 2017-01-09T15:11:14Z down regulation of detection of mechanical stimulus involved in sensory perception of touch down regulation of perception of touch, detection of mechanical stimulus down regulation of perception of touch, sensory detection of mechanical stimulus down regulation of perception of touch, sensory transduction of mechanical stimulus down regulation of sensory detection of mechanical stimulus during perception of touch down regulation of sensory transduction of mechanical stimulus during perception of touch down regulation of tactition, sensory detection of mechanical stimulus down-regulation of detection of mechanical stimulus involved in sensory perception of touch down-regulation of perception of touch, detection of mechanical stimulus down-regulation of perception of touch, sensory detection of mechanical stimulus down-regulation of perception of touch, sensory transduction of mechanical stimulus down-regulation of sensory detection of mechanical stimulus during perception of touch down-regulation of sensory transduction of mechanical stimulus during perception of touch down-regulation of tactition, sensory detection of mechanical stimulus downregulation of detection of mechanical stimulus involved in sensory perception of touch downregulation of perception of touch, detection of mechanical stimulus downregulation of perception of touch, sensory detection of mechanical stimulus downregulation of perception of touch, sensory transduction of mechanical stimulus downregulation of sensory detection of mechanical stimulus during perception of touch downregulation of sensory transduction of mechanical stimulus during perception of touch downregulation of tactition, sensory detection of mechanical stimulus negative regulation of perception of touch, detection of mechanical stimulus negative regulation of perception of touch, sensory detection of mechanical stimulus negative regulation of perception of touch, sensory transduction of mechanical stimulus negative regulation of sensory detection of mechanical stimulus during perception of touch negative regulation of sensory transduction of mechanical stimulus during perception of touch negative regulation of tactition, sensory detection of mechanical stimulus inhibition of detection of mechanical stimulus involved in sensory perception of touch inhibition of perception of touch, detection of mechanical stimulus inhibition of perception of touch, sensory detection of mechanical stimulus inhibition of perception of touch, sensory transduction of mechanical stimulus inhibition of sensory detection of mechanical stimulus during perception of touch inhibition of sensory transduction of mechanical stimulus during perception of touch inhibition of tactition, sensory detection of mechanical stimulus biological_process GO:1905788 negative regulation of detection of mechanical stimulus involved in sensory perception of touch Any process that stops, prevents or reduces the frequency, rate or extent of detection of mechanical stimulus involved in sensory perception of touch. GOC:TermGenie GO_REF:0000058 PMID:8692859 down regulation of detection of mechanical stimulus involved in sensory perception of touch GOC:TermGenie down regulation of perception of touch, detection of mechanical stimulus GOC:TermGenie down regulation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie down regulation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie down regulation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie down regulation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie down regulation of tactition, sensory detection of mechanical stimulus GOC:TermGenie down-regulation of detection of mechanical stimulus involved in sensory perception of touch GOC:TermGenie down-regulation of perception of touch, detection of mechanical stimulus GOC:TermGenie down-regulation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie down-regulation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie down-regulation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie down-regulation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie down-regulation of tactition, sensory detection of mechanical stimulus GOC:TermGenie downregulation of detection of mechanical stimulus involved in sensory perception of touch GOC:TermGenie downregulation of perception of touch, detection of mechanical stimulus GOC:TermGenie downregulation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie downregulation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie downregulation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie downregulation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie downregulation of tactition, sensory detection of mechanical stimulus GOC:TermGenie negative regulation of perception of touch, detection of mechanical stimulus GOC:TermGenie negative regulation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie negative regulation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie negative regulation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie negative regulation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie negative regulation of tactition, sensory detection of mechanical stimulus GOC:TermGenie inhibition of detection of mechanical stimulus involved in sensory perception of touch GOC:TermGenie inhibition of perception of touch, detection of mechanical stimulus GOC:TermGenie inhibition of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie inhibition of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie inhibition of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie inhibition of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie inhibition of tactition, sensory detection of mechanical stimulus GOC:TermGenie Any process that activates or increases the frequency, rate or extent of detection of mechanical stimulus involved in sensory perception of touch. hbye 2017-01-09T15:11:23Z positive regulation of perception of touch, detection of mechanical stimulus positive regulation of perception of touch, sensory detection of mechanical stimulus positive regulation of perception of touch, sensory transduction of mechanical stimulus positive regulation of sensory detection of mechanical stimulus during perception of touch positive regulation of sensory transduction of mechanical stimulus during perception of touch positive regulation of tactition, sensory detection of mechanical stimulus up regulation of detection of mechanical stimulus involved in sensory perception of touch up regulation of perception of touch, detection of mechanical stimulus up regulation of perception of touch, sensory detection of mechanical stimulus up regulation of perception of touch, sensory transduction of mechanical stimulus up regulation of sensory detection of mechanical stimulus during perception of touch up regulation of sensory transduction of mechanical stimulus during perception of touch up regulation of tactition, sensory detection of mechanical stimulus up-regulation of detection of mechanical stimulus involved in sensory perception of touch up-regulation of perception of touch, detection of mechanical stimulus up-regulation of perception of touch, sensory detection of mechanical stimulus up-regulation of perception of touch, sensory transduction of mechanical stimulus up-regulation of sensory detection of mechanical stimulus during perception of touch up-regulation of sensory transduction of mechanical stimulus during perception of touch up-regulation of tactition, sensory detection of mechanical stimulus upregulation of detection of mechanical stimulus involved in sensory perception of touch upregulation of perception of touch, detection of mechanical stimulus upregulation of perception of touch, sensory detection of mechanical stimulus upregulation of perception of touch, sensory transduction of mechanical stimulus upregulation of sensory detection of mechanical stimulus during perception of touch upregulation of sensory transduction of mechanical stimulus during perception of touch upregulation of tactition, sensory detection of mechanical stimulus activation of detection of mechanical stimulus involved in sensory perception of touch activation of perception of touch, detection of mechanical stimulus activation of perception of touch, sensory detection of mechanical stimulus activation of perception of touch, sensory transduction of mechanical stimulus activation of sensory detection of mechanical stimulus during perception of touch activation of sensory transduction of mechanical stimulus during perception of touch activation of tactition, sensory detection of mechanical stimulus biological_process GO:1905789 positive regulation of detection of mechanical stimulus involved in sensory perception of touch Any process that activates or increases the frequency, rate or extent of detection of mechanical stimulus involved in sensory perception of touch. GOC:TermGenie GO_REF:0000058 PMID:8692859 positive regulation of perception of touch, detection of mechanical stimulus GOC:TermGenie positive regulation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie positive regulation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie positive regulation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie positive regulation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie positive regulation of tactition, sensory detection of mechanical stimulus GOC:TermGenie up regulation of detection of mechanical stimulus involved in sensory perception of touch GOC:TermGenie up regulation of perception of touch, detection of mechanical stimulus GOC:TermGenie up regulation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie up regulation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie up regulation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie up regulation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie up regulation of tactition, sensory detection of mechanical stimulus GOC:TermGenie up-regulation of detection of mechanical stimulus involved in sensory perception of touch GOC:TermGenie up-regulation of perception of touch, detection of mechanical stimulus GOC:TermGenie up-regulation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie up-regulation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie up-regulation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie up-regulation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie up-regulation of tactition, sensory detection of mechanical stimulus GOC:TermGenie upregulation of detection of mechanical stimulus involved in sensory perception of touch GOC:TermGenie upregulation of perception of touch, detection of mechanical stimulus GOC:TermGenie upregulation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie upregulation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie upregulation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie upregulation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie upregulation of tactition, sensory detection of mechanical stimulus GOC:TermGenie activation of detection of mechanical stimulus involved in sensory perception of touch GOC:TermGenie activation of perception of touch, detection of mechanical stimulus GOC:TermGenie activation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie activation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie activation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie activation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie activation of tactition, sensory detection of mechanical stimulus GOC:TermGenie Any process that activates or increases the frequency, rate or extent of chromosome condensation. bhm 2017-01-13T14:13:44Z positive regulation of eukaryotic chromosome condensation positive regulation of nuclear chromosome condensation up regulation of chromosome condensation up regulation of eukaryotic chromosome condensation up regulation of nuclear chromosome condensation up-regulation of chromosome condensation up-regulation of eukaryotic chromosome condensation up-regulation of nuclear chromosome condensation upregulation of chromosome condensation upregulation of eukaryotic chromosome condensation upregulation of nuclear chromosome condensation activation of chromosome condensation activation of eukaryotic chromosome condensation activation of nuclear chromosome condensation biological_process GO:1905821 positive regulation of chromosome condensation Any process that activates or increases the frequency, rate or extent of chromosome condensation. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:17268547 positive regulation of eukaryotic chromosome condensation GOC:TermGenie positive regulation of nuclear chromosome condensation GOC:TermGenie up regulation of chromosome condensation GOC:TermGenie up regulation of eukaryotic chromosome condensation GOC:TermGenie up regulation of nuclear chromosome condensation GOC:TermGenie up-regulation of chromosome condensation GOC:TermGenie up-regulation of eukaryotic chromosome condensation GOC:TermGenie up-regulation of nuclear chromosome condensation GOC:TermGenie upregulation of chromosome condensation GOC:TermGenie upregulation of eukaryotic chromosome condensation GOC:TermGenie upregulation of nuclear chromosome condensation GOC:TermGenie activation of chromosome condensation GOC:TermGenie activation of eukaryotic chromosome condensation GOC:TermGenie activation of nuclear chromosome condensation GOC:TermGenie Any process that modulates the frequency, rate or extent of oogenesis. hbye 2017-01-31T09:31:05Z regulation of ovum development biological_process GO:1905879 regulation of oogenesis Any process that modulates the frequency, rate or extent of oogenesis. GOC:TermGenie GO_REF:0000058 PMID:26434723 regulation of ovum development GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of oogenesis. hbye 2017-01-31T09:31:15Z down regulation of oogenesis down regulation of ovum development down-regulation of oogenesis down-regulation of ovum development downregulation of oogenesis downregulation of ovum development negative regulation of ovum development inhibition of oogenesis inhibition of ovum development biological_process GO:1905880 negative regulation of oogenesis Any process that stops, prevents or reduces the frequency, rate or extent of oogenesis. GOC:TermGenie GO_REF:0000058 PMID:26434723 down regulation of oogenesis GOC:TermGenie down regulation of ovum development GOC:TermGenie down-regulation of oogenesis GOC:TermGenie down-regulation of ovum development GOC:TermGenie downregulation of oogenesis GOC:TermGenie downregulation of ovum development GOC:TermGenie negative regulation of ovum development GOC:TermGenie inhibition of oogenesis GOC:TermGenie inhibition of ovum development GOC:TermGenie Any process that activates or increases the frequency, rate or extent of oogenesis. hbye 2017-01-31T09:31:23Z positive regulation of ovum development up regulation of oogenesis up regulation of ovum development up-regulation of oogenesis up-regulation of ovum development upregulation of oogenesis upregulation of ovum development activation of oogenesis activation of ovum development biological_process GO:1905881 positive regulation of oogenesis Any process that activates or increases the frequency, rate or extent of oogenesis. GOC:TermGenie GO_REF:0000058 PMID:26434723 positive regulation of ovum development GOC:TermGenie up regulation of oogenesis GOC:TermGenie up regulation of ovum development GOC:TermGenie up-regulation of oogenesis GOC:TermGenie up-regulation of ovum development GOC:TermGenie upregulation of oogenesis GOC:TermGenie upregulation of ovum development GOC:TermGenie activation of oogenesis GOC:TermGenie activation of ovum development GOC:TermGenie Any process that modulates the frequency, rate or extent of gonad development. hbye 2017-02-09T17:01:50Z regulation of gonadogenesis biological_process GO:1905939 regulation of gonad development Any process that modulates the frequency, rate or extent of gonad development. GOC:TermGenie GO_REF:0000058 PMID:15342467 regulation of gonadogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of gonad development. hbye 2017-02-09T17:01:59Z down regulation of gonad development down regulation of gonadogenesis down-regulation of gonad development down-regulation of gonadogenesis downregulation of gonad development downregulation of gonadogenesis negative regulation of gonadogenesis inhibition of gonad development inhibition of gonadogenesis biological_process GO:1905940 negative regulation of gonad development Any process that stops, prevents or reduces the frequency, rate or extent of gonad development. GOC:TermGenie GO_REF:0000058 PMID:15342467 down regulation of gonad development GOC:TermGenie down regulation of gonadogenesis GOC:TermGenie down-regulation of gonad development GOC:TermGenie down-regulation of gonadogenesis GOC:TermGenie downregulation of gonad development GOC:TermGenie downregulation of gonadogenesis GOC:TermGenie negative regulation of gonadogenesis GOC:TermGenie inhibition of gonad development GOC:TermGenie inhibition of gonadogenesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of gonad development. hbye 2017-02-09T17:02:08Z positive regulation of gonadogenesis up regulation of gonad development up regulation of gonadogenesis up-regulation of gonad development up-regulation of gonadogenesis upregulation of gonad development upregulation of gonadogenesis activation of gonad development activation of gonadogenesis biological_process GO:1905941 positive regulation of gonad development Any process that activates or increases the frequency, rate or extent of gonad development. GOC:TermGenie GO_REF:0000058 PMID:15342467 positive regulation of gonadogenesis GOC:TermGenie up regulation of gonad development GOC:TermGenie up regulation of gonadogenesis GOC:TermGenie up-regulation of gonad development GOC:TermGenie up-regulation of gonadogenesis GOC:TermGenie upregulation of gonad development GOC:TermGenie upregulation of gonadogenesis GOC:TermGenie activation of gonad development GOC:TermGenie activation of gonadogenesis 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 The movement of a neutrophil within or between different tissues and organs of the body. sl 2014-01-10T00:17:47Z biological_process GO:1990266 neutrophil migration The movement of a neutrophil within or between different tissues and organs of the body. PMID:1826836 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 stem cell division. tb 2010-08-05T11:34:53Z regulation of stem cell renewal biological_process GO:2000035 regulation of stem cell division Any process that modulates the frequency, rate or extent of stem cell division. GOC:obol regulation of stem cell renewal GOC:obol Any process that modulates the frequency, rate or extent of leukocyte apoptotic process. mah 2010-09-15T01:42:05Z regulation of leukocyte apoptosis biological_process GO:2000106 regulation of leukocyte apoptotic process Any process that modulates the frequency, rate or extent of leukocyte apoptotic process. GOC:BHF GOC:mtg_apoptosis Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte apoptotic process. mah 2010-09-15T01:42:09Z negative regulation of leukocyte apoptosis biological_process GO:2000107 negative regulation of leukocyte apoptotic process Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte apoptotic process. GOC:BHF GOC:mtg_apoptosis Any process that activates or increases the frequency, rate or extent of leukocyte apoptotic process. mah 2010-09-15T01:42:12Z positive regulation of leukocyte apoptosis biological_process GO:2000108 positive regulation of leukocyte apoptotic process Any process that activates or increases the frequency, rate or extent of leukocyte apoptotic process. GOC:BHF GOC:mtg_apoptosis Any process that modulates the frequency, rate or extent of cell motility. mah 2010-10-01T09:41:21Z regulation of cell locomotion regulation of movement of a cell biological_process regulation of cell movement GO:2000145 regulation of cell motility Any process that modulates the frequency, rate or extent of cell motility. GOC:mah regulation of cell locomotion GOC:obol regulation of movement of a cell GOC:obol regulation of cell movement GOC:obol Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility. mah 2010-10-01T09:41:26Z negative regulation of cell locomotion negative regulation of movement of a cell biological_process negative regulation of cell movement GO:2000146 negative regulation of cell motility Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility. GOC:mah negative regulation of cell locomotion GOC:obol negative regulation of movement of a cell GOC:obol negative regulation of cell movement GOC:obol Any process that activates or increases the frequency, rate or extent of cell motility. mah 2010-10-01T09:41:30Z positive regulation of cell locomotion positive regulation of movement of a cell biological_process positive regulation of cell movement GO:2000147 positive regulation of cell motility Any process that activates or increases the frequency, rate or extent of cell motility. GOC:mah positive regulation of cell locomotion GOC:obol positive regulation of movement of a cell GOC:obol positive regulation of cell movement GOC:obol Any process that activates or increases the frequency, rate or extent of cilium-dependent cell motility. mah 2010-10-04T12:41:05Z biological_process positive regulation of ciliary cell motility GO:2000155 positive regulation of cilium-dependent cell motility Any process that activates or increases the frequency, rate or extent of cilium-dependent cell motility. GOC:cilia GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of blood vessel morphogenesis. dph 2010-10-13T12:46:31Z biological_process GO:2000181 negative regulation of blood vessel morphogenesis Any process that stops, prevents, or reduces the frequency, rate or extent of blood vessel morphogenesis. GOC:dph GOC:yaf Any process that modulates the frequency, rate or extent of female gonad development. yaf 2010-10-19T10:45:34Z regulation of ovarian development regulation of ovary development biological_process GO:2000194 regulation of female gonad development Any process that modulates the frequency, rate or extent of female gonad development. GOC:obol regulation of ovarian development GOC:obol regulation of ovary development GOC:obol Any process that stops, prevents, or reduces the frequency, rate or extent of female gonad development. yaf 2010-10-19T10:45:38Z negative regulation of ovarian development negative regulation of ovary development biological_process GO:2000195 negative regulation of female gonad development Any process that stops, prevents, or reduces the frequency, rate or extent of female gonad development. GOC:obol negative regulation of ovarian development GOC:obol negative regulation of ovary development GOC:obol Any process that activates or increases the frequency, rate or extent of female gonad development. yaf 2010-10-19T10:45:41Z positive regulation of ovarian development positive regulation of ovary development biological_process GO:2000196 positive regulation of female gonad development Any process that activates or increases the frequency, rate or extent of female gonad development. GOC:obol positive regulation of ovarian development GOC:obol positive regulation of ovary development GOC:obol Any process that modulates the frequency, rate or extent of reproductive process. mah 2010-11-10T02:44:02Z biological_process GO:2000241 regulation of reproductive process Any process that modulates the frequency, rate or extent of reproductive process. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of reproductive process. mah 2010-11-10T02:44:05Z biological_process GO:2000242 negative regulation of reproductive process Any process that stops, prevents, or reduces the frequency, rate or extent of reproductive process. GOC:mah Any process that activates or increases the frequency, rate or extent of reproductive process. mah 2010-11-10T02:44:08Z biological_process GO:2000243 positive regulation of reproductive process Any process that activates or increases the frequency, rate or extent of reproductive process. GOC:mah Any process that stops, prevents or reduces the frequency, rate or extent of a signaling receptor activity. bf 2010-12-02T09:28:47Z negative regulation of receptor activity negative regulation of signalling receptor activity biological_process GO:2000272 negative regulation of signaling receptor activity Any process that stops, prevents or reduces the frequency, rate or extent of a signaling receptor activity. GOC:obol Any process that activates or increases the frequency, rate or extent of signaling receptor activity. bf 2010-12-02T09:28:50Z positive regulation of signalling receptor activity biological_process GO:2000273 positive regulation of signaling receptor activity Any process that activates or increases the frequency, rate or extent of signaling receptor activity. GOC:obol Any process that modulates the frequency, rate or extent of reactive oxygen species metabolic process. mah 2011-02-11T02:06:36Z regulation of ROS metabolic process regulation of reactive oxygen species metabolism biological_process GO:2000377 regulation of reactive oxygen species metabolic process Any process that modulates the frequency, rate or extent of reactive oxygen species metabolic process. GOC:mah regulation of ROS metabolic process GOC:obol regulation of reactive oxygen species metabolism GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of reactive oxygen species metabolic process. mah 2011-02-11T02:06:49Z negative regulation of ROS metabolic process negative regulation of reactive oxygen species metabolism biological_process GO:2000378 negative regulation of reactive oxygen species metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of reactive oxygen species metabolic process. GOC:mah negative regulation of ROS metabolic process GOC:obol negative regulation of reactive oxygen species metabolism GOC:obol Any process that activates or increases the frequency, rate or extent of reactive oxygen species metabolic process. mah 2011-02-11T02:06:57Z positive regulation of ROS metabolic process positive regulation of reactive oxygen species metabolism biological_process GO:2000379 positive regulation of reactive oxygen species metabolic process Any process that activates or increases the frequency, rate or extent of reactive oxygen species metabolic process. GOC:mah positive regulation of ROS metabolic process GOC:obol positive regulation of reactive oxygen species metabolism GOC:obol Any process that modulates the frequency, rate or extent of apoptotic cell clearance. bf 2011-02-25T11:50:11Z regulation of apoptotic cell removal regulation of efferocytosis regulation of programmed cell clearance biological_process GO:2000425 regulation of apoptotic cell clearance Any process that modulates the frequency, rate or extent of apoptotic cell clearance. GOC:obol regulation of apoptotic cell removal GOC:obol regulation of efferocytosis GOC:obol regulation of programmed cell clearance GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic cell clearance. bf 2011-02-25T11:50:39Z negative regulation of apoptotic cell removal negative regulation of efferocytosis negative regulation of programmed cell clearance biological_process GO:2000426 negative regulation of apoptotic cell clearance Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic cell clearance. GOC:obol negative regulation of apoptotic cell removal GOC:obol negative regulation of efferocytosis GOC:obol negative regulation of programmed cell clearance GOC:obol Any process that activates or increases the frequency, rate or extent of apoptotic cell clearance. bf 2011-02-25T11:50:59Z positive regulation of apoptotic cell removal positive regulation of efferocytosis positive regulation of programmed cell clearance biological_process GO:2000427 positive regulation of apoptotic cell clearance Any process that activates or increases the frequency, rate or extent of apoptotic cell clearance. GOC:obol positive regulation of apoptotic cell removal GOC:obol positive regulation of efferocytosis GOC:obol positive regulation of programmed cell clearance GOC:obol Any process that enhances the establishment or increases the extent of the excitatory postsynaptic potential (EPSP) which is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential. rl 2011-03-04T02:43:32Z positive regulation of excitatory post-synaptic membrane potential biological_process positive regulation of EPSP GO:2000463 positive regulation of excitatory postsynaptic potential Any process that enhances the establishment or increases the extent of the excitatory postsynaptic potential (EPSP) which is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential. GOC:BHF GOC:bf positive regulation of EPSP GOC:bf GOC:obol Any process that activates or increases the frequency, rate or extent of blood vessel remodeling. pr 2011-03-21T10:33:20Z biological_process GO:2000504 positive regulation of blood vessel remodeling Any process that activates or increases the frequency, rate or extent of blood vessel remodeling. GOC:obol Any process that modulates the frequency, rate or extent of CD4-positive, alpha-beta T cell activation. ebc 2011-03-22T10:36:56Z biological_process GO:2000514 regulation of CD4-positive, alpha-beta T cell activation Any process that modulates the frequency, rate or extent of CD4-positive, alpha-beta T cell activation. GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of CD4-positive, alpha-beta T cell activation. ebc 2011-03-22T10:37:02Z biological_process GO:2000515 negative regulation of CD4-positive, alpha-beta T cell activation Any process that stops, prevents or reduces the frequency, rate or extent of CD4-positive, alpha-beta T cell activation. GOC:obol Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell activation. ebc 2011-03-22T10:37:06Z biological_process GO:2000516 positive regulation of CD4-positive, alpha-beta T cell activation Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell activation. GOC:obol Any process that modulates the frequency, rate or extent of thyroid-stimulating hormone secretion. yaf 2011-04-18T12:56:16Z regulation of TSH secretion regulation of thyroid stimulating hormone secretion biological_process GO:2000612 regulation of thyroid-stimulating hormone secretion Any process that modulates the frequency, rate or extent of thyroid-stimulating hormone secretion. GOC:obol regulation of TSH secretion GOC:obol regulation of thyroid stimulating hormone secretion GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of thyroid-stimulating hormone secretion. yaf 2011-04-18T12:56:20Z negative regulation of TSH secretion negative regulation of thyroid stimulating hormone secretion biological_process GO:2000613 negative regulation of thyroid-stimulating hormone secretion Any process that stops, prevents or reduces the frequency, rate or extent of thyroid-stimulating hormone secretion. GOC:obol negative regulation of TSH secretion GOC:obol negative regulation of thyroid stimulating hormone secretion GOC:obol Any process that activates or increases the frequency, rate or extent of thyroid-stimulating hormone secretion. yaf 2011-04-18T12:56:22Z positive regulation of TSH secretion positive regulation of thyroid stimulating hormone secretion biological_process GO:2000614 positive regulation of thyroid-stimulating hormone secretion Any process that activates or increases the frequency, rate or extent of thyroid-stimulating hormone secretion. GOC:obol positive regulation of TSH secretion GOC:obol positive regulation of thyroid stimulating hormone secretion 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 Any process that modulates the frequency, rate or extent of androgen secretion. bf 2011-07-26T08:39:45Z biological_process GO:2000834 regulation of androgen secretion Any process that modulates the frequency, rate or extent of androgen secretion. GOC:sl Any process that stops, prevents or reduces the frequency, rate or extent of androgen secretion. bf 2011-07-26T08:39:48Z biological_process GO:2000835 negative regulation of androgen secretion Any process that stops, prevents or reduces the frequency, rate or extent of androgen secretion. GOC:sl Any process that activates or increases the frequency, rate or extent of androgen secretion. bf 2011-07-26T08:39:51Z biological_process GO:2000836 positive regulation of androgen secretion Any process that activates or increases the frequency, rate or extent of androgen secretion. GOC:sl Any process that modulates the frequency, rate or extent of testosterone secretion. bf 2011-07-26T08:42:29Z biological_process GO:2000843 regulation of testosterone secretion Any process that modulates the frequency, rate or extent of testosterone secretion. GOC:sl Any process that stops, prevents or reduces the frequency, rate or extent of testosterone secretion. bf 2011-07-26T08:42:33Z biological_process GO:2000844 negative regulation of testosterone secretion Any process that stops, prevents or reduces the frequency, rate or extent of testosterone secretion. GOC:sl Any process that activates or increases the frequency, rate or extent of testosterone secretion. bf 2011-07-26T08:42:36Z biological_process GO:2000845 positive regulation of testosterone secretion Any process that activates or increases the frequency, rate or extent of testosterone secretion. GOC:sl Any process that modulates the frequency, rate or extent of corticosteroid hormone secretion. bf 2011-07-26T08:43:38Z biological_process regulation of corticosteroid secretion GO:2000846 regulation of corticosteroid hormone secretion Any process that modulates the frequency, rate or extent of corticosteroid hormone secretion. GOC:sl regulation of corticosteroid secretion GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of corticosteroid hormone secretion. bf 2011-07-26T08:43:42Z biological_process negative regulation of corticosteroid secretion GO:2000847 negative regulation of corticosteroid hormone secretion Any process that stops, prevents or reduces the frequency, rate or extent of corticosteroid hormone secretion. GOC:sl negative regulation of corticosteroid secretion GOC:obol Any process that activates or increases the frequency, rate or extent of corticosteroid hormone secretion. bf 2011-07-26T08:43:45Z biological_process positive regulation of corticosteroid secretion GO:2000848 positive regulation of corticosteroid hormone secretion Any process that activates or increases the frequency, rate or extent of corticosteroid hormone secretion. GOC:sl positive regulation of corticosteroid secretion GOC:obol Any process that modulates the frequency, rate or extent of glucocorticoid secretion. bf 2011-07-26T08:44:43Z biological_process GO:2000849 regulation of glucocorticoid secretion Any process that modulates the frequency, rate or extent of glucocorticoid secretion. GOC:sl Any process that stops, prevents or reduces the frequency, rate or extent of glucocorticoid secretion. bf 2011-07-26T08:44:48Z biological_process GO:2000850 negative regulation of glucocorticoid secretion Any process that stops, prevents or reduces the frequency, rate or extent of glucocorticoid secretion. GOC:sl Any process that activates or increases the frequency, rate or extent of glucocorticoid secretion. bf 2011-07-26T08:44:51Z biological_process GO:2000851 positive regulation of glucocorticoid secretion Any process that activates or increases the frequency, rate or extent of glucocorticoid secretion. GOC:sl Any process that modulates the frequency, rate or extent of mineralocorticoid secretion. bf 2011-07-26T08:46:38Z biological_process GO:2000855 regulation of mineralocorticoid secretion Any process that modulates the frequency, rate or extent of mineralocorticoid secretion. GOC:sl Any process that stops, prevents or reduces the frequency, rate or extent of mineralocorticoid secretion. bf 2011-07-26T08:46:42Z biological_process GO:2000856 negative regulation of mineralocorticoid secretion Any process that stops, prevents or reduces the frequency, rate or extent of mineralocorticoid secretion. GOC:sl Any process that activates or increases the frequency, rate or extent of mineralocorticoid secretion. bf 2011-07-26T08:46:45Z biological_process GO:2000857 positive regulation of mineralocorticoid secretion Any process that activates or increases the frequency, rate or extent of mineralocorticoid secretion. GOC:sl Any process that modulates the frequency, rate or extent of estradiol secretion. bf 2011-07-26T08:49:13Z regulation of oestradiol secretion biological_process GO:2000864 regulation of estradiol secretion Any process that modulates the frequency, rate or extent of estradiol secretion. GOC:sl regulation of oestradiol secretion GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of estradiol secretion. bf 2011-07-26T08:49:17Z negative regulation of oestradiol secretion biological_process GO:2000865 negative regulation of estradiol secretion Any process that stops, prevents or reduces the frequency, rate or extent of estradiol secretion. GOC:sl negative regulation of oestradiol secretion GOC:obol Any process that activates or increases the frequency, rate or extent of estradiol secretion. bf 2011-07-26T08:49:20Z positive regulation of oestradiol secretion biological_process GO:2000866 positive regulation of estradiol secretion Any process that activates or increases the frequency, rate or extent of estradiol secretion. GOC:sl positive regulation of oestradiol secretion GOC:obol Any process that modulates the frequency, rate or extent of progesterone secretion. bf 2011-07-26T08:51:14Z biological_process GO:2000870 regulation of progesterone secretion Any process that modulates the frequency, rate or extent of progesterone secretion. GOC:sl Any process that stops, prevents or reduces the frequency, rate or extent of progesterone secretion. bf 2011-07-26T08:51:19Z biological_process GO:2000871 negative regulation of progesterone secretion Any process that stops, prevents or reduces the frequency, rate or extent of progesterone secretion. GOC:sl Any process that activates or increases the frequency, rate or extent of progesterone secretion. bf 2011-07-26T08:51:22Z biological_process GO:2000872 positive regulation of progesterone secretion Any process that activates or increases the frequency, rate or extent of progesterone secretion. GOC:sl Any process that modulates the frequency, rate or extent of gamma-delta T cell activation involved in immune response. yaf 2011-11-03T04:28:38Z biological_process regulation of gamma-delta T cell activation during immune response regulation of gamma-delta T lymphocyte activation during immune response regulation of gamma-delta T-cell activation during immune response regulation of gamma-delta T-lymphocyte activation during immune response GO:2001191 regulation of gamma-delta T cell activation involved in immune response Any process that modulates the frequency, rate or extent of gamma-delta T cell activation involved in immune response. GOC:obol regulation of gamma-delta T cell activation during immune response GOC:obol regulation of gamma-delta T lymphocyte activation during immune response GOC:obol regulation of gamma-delta T-cell activation during immune response GOC:obol regulation of gamma-delta T-lymphocyte activation during immune response GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of gamma-delta T cell activation involved in immune response. yaf 2011-11-03T04:28:44Z biological_process negative regulation of gamma-delta T cell activation during immune response negative regulation of gamma-delta T lymphocyte activation during immune response negative regulation of gamma-delta T-cell activation during immune response negative regulation of gamma-delta T-lymphocyte activation during immune response GO:2001192 negative regulation of gamma-delta T cell activation involved in immune response Any process that stops, prevents or reduces the frequency, rate or extent of gamma-delta T cell activation involved in immune response. GOC:obol negative regulation of gamma-delta T cell activation during immune response GOC:obol negative regulation of gamma-delta T lymphocyte activation during immune response GOC:obol negative regulation of gamma-delta T-cell activation during immune response GOC:obol negative regulation of gamma-delta T-lymphocyte activation during immune response GOC:obol Any process that activates or increases the frequency, rate or extent of gamma-delta T cell activation involved in immune response. yaf 2011-11-03T04:28:48Z biological_process positive regulation of gamma-delta T cell activation during immune response positive regulation of gamma-delta T lymphocyte activation during immune response positive regulation of gamma-delta T-cell activation during immune response positive regulation of gamma-delta T-lymphocyte activation during immune response GO:2001193 positive regulation of gamma-delta T cell activation involved in immune response Any process that activates or increases the frequency, rate or extent of gamma-delta T cell activation involved in immune response. GOC:obol positive regulation of gamma-delta T cell activation during immune response GOC:obol positive regulation of gamma-delta T lymphocyte activation during immune response GOC:obol positive regulation of gamma-delta T-cell activation during immune response GOC:obol positive regulation of gamma-delta T-lymphocyte activation during immune response GOC:obol Any process that modulates the frequency, rate or extent of dendritic cell differentiation. yaf 2011-11-04T02:01:27Z biological_process GO:2001198 regulation of dendritic cell differentiation Any process that modulates the frequency, rate or extent of dendritic cell differentiation. GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of dendritic cell differentiation. yaf 2011-11-04T02:01:33Z biological_process GO:2001199 negative regulation of dendritic cell differentiation Any process that stops, prevents or reduces the frequency, rate or extent of dendritic cell differentiation. GOC:obol Any process that activates or increases the frequency, rate or extent of dendritic cell differentiation. yaf 2011-11-04T02:01:36Z biological_process GO:2001200 positive regulation of dendritic cell differentiation Any process that activates or increases the frequency, rate or extent of dendritic cell differentiation. GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization. yaf 2011-12-02T02:01:20Z negative regulation of chromosome organisation biological_process negative regulation of chromosome organization and biogenesis negative regulation of maintenance of genome integrity negative regulation of nuclear genome maintenance GO:2001251 negative regulation of chromosome organization Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization. GOC:obol negative regulation of chromosome organisation GOC:obol negative regulation of chromosome organization and biogenesis GOC:obol negative regulation of maintenance of genome integrity GOC:obol negative regulation of nuclear genome maintenance GOC:obol Any process that activates or increases the frequency, rate or extent of chromosome organization. yaf 2011-12-02T02:01:26Z positive regulation of chromosome organisation biological_process positive regulation of chromosome organization and biogenesis positive regulation of maintenance of genome integrity positive regulation of nuclear genome maintenance GO:2001252 positive regulation of chromosome organization Any process that activates or increases the frequency, rate or extent of chromosome organization. GOC:obol positive regulation of chromosome organisation GOC:obol positive regulation of chromosome organization and biogenesis GOC:obol positive regulation of maintenance of genome integrity GOC:obol positive regulation of nuclear genome maintenance GOC:obol GlycoRes PSI-MOD MOD:00693 glycosylated residue GlycoRes PSI-MOD MOD:00764 glycoconjugated residue GC_ID:1 ncbi_taxonomy all root all GC_ID:1 PMID:15371245 ncbi_taxonomy Muridae GC_ID:1 Mus mice mouse ncbi_taxonomy Mus <genus> Mus mice mouse NCBITaxon:85055 GC_ID:1 house mouse mouse ncbi_taxonomy m mouse NCBITaxon:10090 Mus musculus house mouse mouse m PRO:DAN mouse GC_ID:1 ncbi_taxonomy Teleostomi NCBITaxon:40673 GC_ID:1 bony vertebrates ncbi_taxonomy Euteleostomi bony vertebrates GC_ID:1 ncbi_taxonomy Ecdysozoa GC_ID:1 ncbi_taxonomy Lophotrochozoa GC_ID:1 ncbi_taxonomy biota cellular organisms biota GC_ID:1 ncbi_taxonomy Dipnotetrapodomorpha GC_ID:1 PMID:11062127 PMID:9342353 ncbi_taxonomy Eumycetozoa Zopf, 1884 Mycetozoa mycetozoans Eumycetozoa Eumycetozoa Zopf, 1884 Mycetozoa mycetozoans GC_ID:1 PMID:11743200 PMID:11791233 ncbi_taxonomy Boreotheria Boreoeutheria Boreotheria GC_ID:1 mice and others ncbi_taxonomy Sciurognathi Myomorpha mice and others Sciurognathi GC_ID:1 ncbi_taxonomy Homo/Pan/Gorilla group Homininae Homo/Pan/Gorilla group GC_ID:1 ncbi_taxonomy Evosea GC_ID:1 ncbi_taxonomy Spiralia GC_ID:1 PMID:23020233 PMID:30257078 eucaryotes eukaryotes ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae euk- eukaryotes NCBITaxon:2759 Eukaryota eucaryotes eukaryotes Eucarya Eucaryotae Eukarya Eukaryotae euk- PRO:DAN eukaryotes GC_ID:1 PMID:11214318 PMID:11214319 PMID:12878460 ncbi_taxonomy Laurasiatheria GC_ID:1 PMID:11214319 PMID:12082125 PMID:12878460 PMID:15522813 ncbi_taxonomy Euarchontoglires GC_ID:1 PMID:11214319 PMID:12082125 PMID:15522813 Rodents and rabbits ncbi_taxonomy Glires Rodents and rabbits GC_ID:1 ncbi_taxonomy Anthropoidea Simiiformes Anthropoidea GC_ID:1 ape apes ncbi_taxonomy Hominoidea ape apes GC_ID:1 tetrapods ncbi_taxonomy Tetrapoda tetrapods GC_ID:1 amniotes ncbi_taxonomy Amniota amniotes GC_ID:1 Theria ncbi_taxonomy Theria <mammals> Theria GC_ID:1 ncbi_taxonomy Fungi/Metazoa group opisthokonts NCBITaxon:33154 Opisthokonta Fungi/Metazoa group opisthokonts GC_ID:1 metazoans multicellular animals ncbi_taxonomy Animalia animals metazoan- NCBITaxon:33208 Metazoa metazoans multicellular animals Animalia animals metazoan- PRO:DAN GC_ID:1 ncbi_taxonomy Bilateria GC_ID:1 ncbi_taxonomy Protostomia GC_ID:1 deuterostomes ncbi_taxonomy Deuterostomia deuterostomes GC_ID:1 carnivores ncbi_taxonomy carnivores Carnivora carnivores carnivores GC_ID:1 PMID:15019624 PMID:15371245 ncbi_taxonomy Muroidea GC_ID:1 ncbi_taxonomy Felinae GC_ID:1 ncbi_taxonomy Haplorrhini GC_ID:1 ncbi_taxonomy Feliformia NCBITaxon:109679 GC_ID:1 ncbi_taxonomy Murinae GC_ID:1 mammal mammals ncbi_taxonomy mammal- mammals NCBITaxon:40674 Mammalia mammal mammals mammal- PRO:DAN mammals GC_ID:1 PMID:11062127 PMID:12684019 ncbi_taxonomy Mycota fungal- fungi NCBITaxon:4751 Fungi Mycota fungal- PRO:DAN fungi fungi GC_ID:1 PMID:23020233 PMID:30257078 ncbi_taxonomy Amoebozoa GC_ID:1 ncbi_taxonomy Eumetazoa GC_ID:1 flatworm flatworms ncbi_taxonomy flatworms Platyhelminthes flatworm flatworms flatworms GC_ID:1 arthropods ncbi_taxonomy arthropods Arthropoda arthropods arthropods GC_ID:1 chordates ncbi_taxonomy chordates Chordata chordates chordates GC_ID:1 Vertebrata vertebrates ncbi_taxonomy vertebrates Vertebrata <vertebrates> Vertebrata vertebrates vertebrates GC_ID:1 Gnathostomata jawed vertebrates ncbi_taxonomy Gnathostomata <vertebrates> Gnathostomata jawed vertebrates GC_ID:1 ncbi_taxonomy Sarcopterygii GC_ID:1 Mus ncbi_taxonomy Mus <subgenus> Mus GC_ID:1 ncbi_taxonomy Panarthropoda GC_ID:1 Craniata ncbi_taxonomy Craniata <chordates> Craniata GC_ID:1 eutherian mammals placental mammals placentals ncbi_taxonomy Placentalia placentals Eutheria eutherian mammals placental mammals placentals Placentalia placentals GC_ID:1 primate ncbi_taxonomy Primata primates Primates primate Primata primates GC_ID:1 ncbi_taxonomy Catarrhini GC_ID:1 great apes ncbi_taxonomy Pongidae Hominidae great apes Pongidae GC_ID:1 humans ncbi_taxonomy Homo humans GC_ID:1 human man ncbi_taxonomy h human NCBITaxon:9606 Homo sapiens human man h PRO:DAN human PRO:DAN GC_ID:1 cat family ncbi_taxonomy Felidae cat family GC_ID:1 ncbi_taxonomy Felis NCBITaxon:36475 GC_ID:1 PMID:17600185 PMID:8581300 PMID:8603894 cat cats domestic cat ncbi_taxonomy Felis domesticus Felis silvestris catus NCBITaxon:9685 Felis catus cat cat cats domestic cat Felis domesticus Felis silvestris catus GC_ID:1 rodent ncbi_taxonomy rodents NCBITaxon:9989 Rodentia rodent rodent rodents obi OBI:0100026 Category=external. organism 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 time quality inhering in a bearer by virtue of the bearer's expected maximum age. quality PATO:0000050 life span A time quality inhering in a bearer by virtue of the bearer's expected maximum age. 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 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) A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. 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 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 in which events occur in sequence. quality PATO:0000165 time A quality in which events occur in sequence. PATOC:GVG A quality of a single physical entity which is held by a bearer when the latter exhibits a state of growth, differentiation, or development. quality PATO:0000261 maturity A quality of a single physical entity which is held by a bearer when the latter exhibits a state of growth, differentiation, or development. Merriam-Webster:Merriam-Webster A curvature quality inhering in a bearer by virtue of the bearer's having or being marked by a curve or smoothly rounded bend. bowing quality curled PATO:0000406 curved A curvature quality inhering in a bearer by virtue of the bearer's having or being marked by a curve or smoothly rounded bend. WordNet:WordNet A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center. quality round rounded PATO:0000411 circular A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center. thefreedictionary.com:thefreedictionary.com 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 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 spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section. ellipse-shaped ellipsoid elliptical quality oval ovoid PATO:0000947 elliptic A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section. 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 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 cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. quality PATO:0001374 ploidy A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. Wikipedia:http://en.wikipedia.org/wiki/Ploidy A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. quality PATO:0001375 haploid A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Haploid A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes. quality PATO:0001393 euploid A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Euploid A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father. quality PATO:0001394 The exact number may be one or two different from the 2n number and still be classified as diploidy (although with aneuploidy). Nearly all mammals are diploid organisms, although all individuals have some small fracton of cells that are polyploidy. diploid A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father. Wikipedia:http://en.wikipedia.org/wiki/Diploid 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 that arises by virtue of whether the bearer's disposition to differentiate into one or more mature cell types. quality PATO:0001397 cellular potency A cellular quality that arises by virtue of whether the bearer's disposition to differentiate into one or more mature cell types. PATOC:GVG A cellular potency that is the capacity to produce only one differentiated cell type. quality PATO:0001400 Unipotent cells have the quality of self-renewal which distinguishes them from non-stem cells. unipotent A cellular potency that is the capacity to produce only one differentiated cell type. Wikipedia:http://en.wikipedia.org/wiki/Unipotent A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity. quality PATO:0001401 Less potent than multipotent, often thought of as precursor or progenitor cell status. oligopotent A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity. PATOC:MAH A cellular potency that is the capacity to form multiple differentiated cell types. quality PATO:0001402 multipotent A cellular potency that is the capacity to form multiple differentiated cell types. Wikipedia:http://en.wikipedia.org/wiki/Multipotent 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 cellular quality inhering in a bearer by virtue of the bearer's having thin, tail-like projections extending outwards from the cell body. quality PATO:0001408 ciliatedness A cellular quality inhering in a bearer by virtue of the bearer's having thin, tail-like projections extending outwards from the cell body. Wikipedia:http://en.wikipedia.org/wiki/Ciliated A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel. quality PATO:0001410 striated A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel. Biology-online:Biology-online A quality inhering in a bearer by virtue of the bearer's lacking complete growth, differentiation, or development. quality underdeveloped PATO:0001501 immature A quality inhering in a bearer by virtue of the bearer's lacking complete growth, differentiation, or development. Merriam-Webster:Merriam-Webster A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending. quality PATO:0001591 curvature A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending. WordNet:WordNet A curvature which is relatively high. quality PATO:0001592 increased curvature A curvature which is relatively high. PATO:GVG A curvature which is relatively low. quality PATO:0001593 decreased curvature A curvature which is relatively low. PATO:GVG A life span which is relatively high. high life span quality PATO:0001603 increased life span A life span which is relatively high. PATO:GVG A life span which is relatively low. low life span quality PATO:0001604 decreased life span A life span which is relatively low. PATO:GVG A curvature quality inhering in a bearer by virtue of the bearer's having a shape resembling a dome. quality PATO:0001789 domed A curvature quality inhering in a bearer by virtue of the bearer's having a shape resembling a dome. 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 concave 3-D shape quality inhering in a bearer by virtue of the bearer's having the shape of a kidney. kidney-shaped quality bean shaped PATO:0001871 reniform A concave 3-D shape quality inhering in a bearer by virtue of the bearer's having the shape of a kidney. ISBN:0881923214 A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. PATO:0001203 rod-like rod-shaped tubulate quality PATO:0001873 cylindrical A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. PATOC:MAH A shape quality inhering in a bearer by virtue of the bearer's being cylindrical, in which the height is less than the diameter. disc-shaped disk-shaped quality PATO:0001874 discoid A shape quality inhering in a bearer by virtue of the bearer's being cylindrical, in which the height is less than the diameter. PATOC:cjm 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 A surface shape quality inhering in a bearer by virtue of the bearer's shape of features present on its surface or outer shell. quality PATO:0001925 This quality either inheres directly in the surface, or in the entity that has the surface. For example, to say that a particular fly wing is curved is shorthand for saying the wing has a surface which is curved. surface feature shape A surface shape quality inhering in a bearer by virtue of the bearer's shape of features present on its surface or outer shell. PATOC:CJM 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 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 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 complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png quality PATO:0002007 Use this term or an is_a child of this term when the entire shape of the object is known. convex 3-D shape A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. PATOC:CJM A complete three dimensional shape in which there is a line connecting pair of points on the object that lies outside the object. Or: a shape with cavities. Contrast: concave. Image:http://en.wikipedia.org/wiki/Image:Convex_polygon_illustration2.png quality PATO:0002008 concave 3-D shape A complete three dimensional shape in which there is a line connecting pair of points on the object that lies outside the object. Or: a shape with cavities. Contrast: concave. PATOC:CJM A structural quality which is held by a bearer when the latter's disposition the presence of abnormally proliferating masses of cells. tumorous quality PATO:0002011 neoplastic A structural quality which is held by a bearer when the latter's disposition the presence of abnormally proliferating masses of cells. PATOC:MAH A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces. quality PATO:0002039 biconcave A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces. PATOC:GVG A molecular quality that arises from the molecular attraction exerted between two atoms or compounds. George Gkoutos 2009-09-18T01:16:16Z quality PATO:0002070 affinity A molecular quality that arises from the molecular attraction exerted between two atoms or compounds. PATOC:GVG An affinity which is relatively high. George Gkoutos 2009-09-18T01:29:42Z quality PATO:0002071 increased affinity An affinity which is relatively high. PATOC:GVG An affinity which is relatively low. George Gkoutos 2009-09-18T01:30:11Z quality PATO:0002072 decreased affinity An affinity which is relatively low. PATOC:GVG An affinity inhering in a tissue constituent by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific ph conditions. george 2009-10-05T12:05:23Z quality PATO:0002094 basophilic An affinity inhering in a tissue constituent by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific ph conditions. PATOC:GVG A disposition inhering in a tumour by virtue of the bearer's disposition to progress, invade surrounding tissues or metastasize. george 2009-10-05T12:50:22Z quality PATO:0002097 neoplastic, malignant A disposition inhering in a tumour by virtue of the bearer's disposition to progress, invade surrounding tissues or metastasize. PATOC:GVG A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. George Gkoutos 2010-03-10T03:18:15Z PATO:0002061 relational molecular quality quality PATO:0002182 molecular quality A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. PATOC:GVG A shape that inheres in a 3 dimensional entity. george 2010-10-05T12:31:16Z quality PATO:0002266 3-D shape A shape that inheres in a 3 dimensional entity. PATOC:OREGON 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 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 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 shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt George Gkoutos 2011-10-12T12:45:16Z Lamé curve quality PATO:0002318 superelliptic A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt wiktionary:superellipse A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented transversely relative to the long axis of the bearer. gkoutos 2013-09-15T12:29:15Z quality PATO:0002478 transversely striated A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented transversely relative to the long axis of the bearer. PATOC:DS A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented obliquely relative to the long axis of the bearer. gkoutos 2013-09-15T12:29:42Z quality PATO:0002479 obliquely striated A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented obliquely relative to the long axis of the bearer. PATOC:DS 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 surface feature shape quality inhering in a bearer by virtue of the bearer's not having undulating edges forming lobes. gkoutos 2013-10-25T04:42:40Z quality PATO:0002506 alobate A surface feature shape quality inhering in a bearer by virtue of the bearer's not having undulating edges forming lobes. PATOC:DOS A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure. http://orcid.org/0000-0002-7073-9172 2021-01-23T11:31:53Z quality PATO:0010006 Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts. cell morphology A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure. ORCID:0000-0002-7073-9172 A quality of an object that has a value that is normal or average. Luke Slater 2017-12-21T14:11:01Z quality PATO:0045001 normal object quality An affinity which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045004 normal affinity A curvature which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045013 normal curvature A life span which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045026 normal life span A size quality which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045050 normal size A cell morphology that inheres in neurons which have a small round soma, a large number of short, smooth, or slightly beaded primary dendrites that give rise to only a few secondary branches, and a branched axon that establishes a dense axonal mesh with thin shafts. http://orcid.org/0000-0001-7258-9596 ilxtr:NeurogliaformPhenotype quality PATO:0070001 neurogliaform morphology A cell morphology that inheres in neurons which have a small round soma, a large number of short, smooth, or slightly beaded primary dendrites that give rise to only a few secondary branches, and a branched axon that establishes a dense axonal mesh with thin shafts. PMID:17122314 A cell morphology that inheres in multipolar neurons with densely branched terminal axonal arborizations that form basket-like structures surrounding and synapsing to the somas of target cells. http://orcid.org/0000-0001-7258-9596 ILX:0101123 ilxtr:BasketPhenotype nifext:3 quality PATO:0070002 basket cell morphology A cell morphology that inheres in multipolar neurons with densely branched terminal axonal arborizations that form basket-like structures surrounding and synapsing to the somas of target cells. WikipediaVersioned:Basket_cell&oldid=951703880 doi:10.1016/b978-0-12-369497-3.10004-4 A basket cell morphology that inheres in neurons with axonal arbors composed of frequent, short, curvy axonal branches that tend to be near their somata and within the same layer. http://orcid.org/0000-0001-7258-9596 ilxtr:SmallBasketPhenotype quality PATO:0070003 small basket cell morphology A basket cell morphology that inheres in neurons with axonal arbors composed of frequent, short, curvy axonal branches that tend to be near their somata and within the same layer. PMID:11884355 A basket cell morphology that inheres in neurons that are large, and typically ascend to give rise to many long horizontally and vertically projecting axon collaterals that traverse neighboring columns and can extend through all cortical layers. http://orcid.org/0000-0001-7258-9596 ilxtr:LargeBasketPhenotype quality PATO:0070004 large basket cell morphology A basket cell morphology that inheres in neurons that are large, and typically ascend to give rise to many long horizontally and vertically projecting axon collaterals that traverse neighboring columns and can extend through all cortical layers. PMID:11884355 A basket cell morphology that inheres in neurons which have simpler dendritic arbors (compared to small or large basket cell morphology), and an axonal plexus of intermediate density, composed of a few long, smooth axonal branches. http://orcid.org/0000-0001-7258-9596 ilxtr:NestBasketPhenotype quality PATO:0070005 nest basket cell morphology A basket cell morphology that inheres in neurons which have simpler dendritic arbors (compared to small or large basket cell morphology), and an axonal plexus of intermediate density, composed of a few long, smooth axonal branches. PMID:11884355 A cell morphology that inheres in neurons which have two principal fibres (dendrites or axon) that emerge from the soma and begin to branch some distance from it, have few spines, and branch in narrow fields. This is in contrast to bitufted morphology where branching occurs close to the soma. http://orcid.org/0000-0001-7258-9596 ILX:0101312 ilxtr:BipolarPhenotype nifext:2 quality PATO:0070006 bipolar morphology A cell morphology that inheres in neurons which have two principal fibres (dendrites or axon) that emerge from the soma and begin to branch some distance from it, have few spines, and branch in narrow fields. This is in contrast to bitufted morphology where branching occurs close to the soma. PMID:18568015 doi:10.1016/b978-0-12-369497-3.10004-4 A cell morphology that inheres in neurons which are large and non-spiny, with dendrites radiating in a multipolar or bitufted pattern, often favouring the descending side, and axons that ascend directly from the superficial side of the soma, and travel upward without branching. http://orcid.org/0000-0001-7258-9596 ilxtr:MartinottiPhenotype quality PATO:0070007 martinotti morphology A cell morphology that inheres in neurons which are large and non-spiny, with dendrites radiating in a multipolar or bitufted pattern, often favouring the descending side, and axons that ascend directly from the superficial side of the soma, and travel upward without branching. doi:10.1016/b978-0-12-369497-3.10004-4 A martinotti cell morphology that inheres in neurons which have axons that form a horizontal ramification, making it T-shaped. http://orcid.org/0000-0001-7258-9596 quality PATO:0070008 'T-shaped' martinotti morphology A martinotti cell morphology that inheres in neurons which have axons that form a horizontal ramification, making it T-shaped. doi:10.1016/b978-0-12-369497-3.10004-4 A martinotti cell morphology that inheres in neurons which have axons that form a fan-like plexus. http://orcid.org/0000-0001-7258-9596 quality PATO:0070009 'fanning-out' martinotti morphology A martinotti cell morphology that inheres in neurons which have axons that form a fan-like plexus. doi:10.1016/b978-0-12-369497-3.10004-4 A cell morphology that inheres in neurons that have dendritic processes radiating from the cell body forming a star-like shape. http://orcid.org/0000-0001-7258-9596 ILX:0111036 SAO:9271919883 quality PATO:0070010 stellate morphology A cell morphology that inheres in neurons that have dendritic processes radiating from the cell body forming a star-like shape. ISBN:9780123973481 A cell morphology that inheres in neurons which are small and round, and make highly specialized synapses with the axon initial segments of pyramidal neurons, wrapping them with candle-shaped synaptic “cartridges”. http://orcid.org/0000-0001-7258-9596 ILX:0102028 ilxtr:ChandelierPhenotype nifext:4 quality PATO:0070011 Chandelier cells can be bitufted or multipolar. chandelier cell morphology A cell morphology that inheres in neurons which are small and round, and make highly specialized synapses with the axon initial segments of pyramidal neurons, wrapping them with candle-shaped synaptic “cartridges”. doi:10.1016/b978-0-12-369497-3.10004-4 Chandelier cells can be bitufted or multipolar. DOI:10.1016/B978-0-12-369497-3.10004-4 A cell morphology that inheres in neurons which have two clusters of primary dendrites that originate directly and extend from opposite ends of the soma, and axons that form a plexus which spreads widely. Compared to the narrow vertical axonal projection of bipolar morphology, and the 'horse-tail' axonal cluster of double boquet cells, bitufted morphology has wide horizontal axonal spans, and branching that occur close to the soma. Their vertical projection is also less extensive and crosses mostly to neighboring layers. http://orcid.org/0000-0001-7258-9596 ilxtr:BituftedPhenotype quality PATO:0070012 bitufted cell morphology A cell morphology that inheres in neurons which have two clusters of primary dendrites that originate directly and extend from opposite ends of the soma, and axons that form a plexus which spreads widely. Compared to the narrow vertical axonal projection of bipolar morphology, and the 'horse-tail' axonal cluster of double boquet cells, bitufted morphology has wide horizontal axonal spans, and branching that occur close to the soma. Their vertical projection is also less extensive and crosses mostly to neighboring layers. PMID:15378039 PMID:18568015 doi:10.1016/b978-0-12-369497-3.10004-4 A cell morphology that inheres in neurons which have spiny basal dendrites and resemble pyramidal cells but lose their apical dendrites as they mature. Their axons nearly always emerge from the descending side of the soma, but often recurve and ascend with arc-like collaterals. http://orcid.org/0000-0001-7258-9596 ilxtr:SpinyStellatePhenotype quality PATO:0070013 spiny stellate cell morphology A cell morphology that inheres in neurons which have spiny basal dendrites and resemble pyramidal cells but lose their apical dendrites as they mature. Their axons nearly always emerge from the descending side of the soma, but often recurve and ascend with arc-like collaterals. doi:10.1016/b978-0-12-369497-3.10004-4 A cell morphology that inheres in neurons which have a pyramidal shaped soma, a single axon, a large apical dendrite and multiple basal dendrites. http://orcid.org/0000-0001-7258-9596 ILX:0109553 SAO:1465673360 quality PATO:0070015 pyramidal family morphology A cell morphology that inheres in neurons which have a pyramidal shaped soma, a single axon, a large apical dendrite and multiple basal dendrites. doi:10.1016/b978-0-12-369497-3.10004-4 A pyramidal family morphology that inheres in neurons which have an apical tree which is oriented parallel to the pia. http://orcid.org/0000-0001-7258-9596 ilxtr:HorizontalPyramidalPhenotype quality PATO:0070016 horizontal pyramidal morphology A pyramidal family morphology that inheres in neurons which have an apical tree which is oriented parallel to the pia. PMID:30715238 A pyramidal family morphology that inheres in neurons which have a standard pyramidal shape with its apical dendrite aligned vertically. http://orcid.org/0000-0001-7258-9596 ilxtr:PyramidalPhenotype pyramidal cell morphology vertical pyramidal morphology quality PATO:0070017 standard pyramidal morphology A pyramidal family morphology that inheres in neurons which have a standard pyramidal shape with its apical dendrite aligned vertically. doi:10.1016/b978-0-12-369497-3.10004-4 A pyramidal cell morphology that inheres in neurons which have a distinct tuft formation, distal from the soma. http://orcid.org/0000-0001-7258-9596 ilxtr:TuftedPyramidalPhenotype quality PATO:0070018 tufted pyramidal morphology A pyramidal cell morphology that inheres in neurons which have a distinct tuft formation, distal from the soma. PMID:30715238 A pyramidal cell morphology that inheres in neurons which lack a clear tuft formation but extend to large radial distances. http://orcid.org/0000-0001-7258-9596 ilxtr:UntuftedPyramidalPhenotype quality PATO:0070019 untufted pyramidal morphology A pyramidal cell morphology that inheres in neurons which lack a clear tuft formation but extend to large radial distances. PMID:30715238 A pyramidal cell morphology that inheres in neurons which lack a tuft formation but extend to small radial distances forming a star-like shape. http://orcid.org/0000-0001-7258-9596 ilxtr:StarPyramidalPhenotype quality PATO:0070020 stellate pyramidal morphology A pyramidal cell morphology that inheres in neurons which lack a tuft formation but extend to small radial distances forming a star-like shape. PMID:30715238 A pyramidal cell morphology that inheres in neurons which have an apical tree which is oriented towards the white matter. http://orcid.org/0000-0001-7258-9596 ilxtr:InvertedPyramidalPhenotype quality PATO:0070021 inverted pyramidal morphology A pyramidal cell morphology that inheres in neurons which have an apical tree which is oriented towards the white matter. PMID:30715238 A cell morphology that inheres in neurons which possess a single axon and many dendrites and dendritic branches. http://orcid.org/0000-0001-7258-9596 ILX:0107196 NLX:378 quality PATO:0070026 multipolar neuron morphology A cell morphology that inheres in neurons which possess a single axon and many dendrites and dendritic branches. WikipediaVersioned:Multipolar_neuron&oldid=1022942606 A neuron projection quality that is a characteristic of neurons whose soma is located in the telencephalon and that project to structures outside the telencephalon http://orcid.org/0000-0001-7258-9596 ILX:0770101 ET projecting quality PATO:0070028 extratelencephalic projecting A neuron projection quality that is a characteristic of neurons whose soma is located in the telencephalon and that project to structures outside the telencephalon DOI:10.1101/2020.10.19.343129 A neuron projection quality that is a characteristic of neurons with soma in the cerebral cortex and projections to the thalamus. http://orcid.org/0000-0001-7258-9596 ILX:0770102 CT projecting quality PATO:0070029 corticothalamic projecting A neuron projection quality that is a characteristic of neurons with soma in the cerebral cortex and projections to the thalamus. DOI:10.1101/2020.10.19.343129 A neuron projection quality that is a characteristic of neurons with projections that terminate locally rather than distantly. http://orcid.org/0000-0001-7258-9596 ILX:0770103 NP quality PATO:0070030 near projecting A neuron projection quality that is a characteristic of neurons with projections that terminate locally rather than distantly. DOI:10.1101/2020.10.19.343129 A neuron projection quality that is a characteristic of neurons that project to the medulla oblongata from other brain regions. http://orcid.org/0000-0001-7258-9596 MY projecting quality PATO:0070031 corticomedulla projecting A neuron projection quality that is a characteristic of neurons that project to the medulla oblongata from other brain regions. DOI:10.1101/2020.10.19.343129 A physical quality inhering in a neuron by virtue of the relative location of its soma and the regions to which it projects and makes synaptic contacts in. http://orcid.org/0000-0001-7258-9596 quality PATO:0070033 neuron projection quality A physical quality inhering in a neuron by virtue of the relative location of its soma and the regions to which it projects and makes synaptic contacts in. DOI:10.1101/2020.10.19.343129 A neuron projection quality that is a characteristic of neurons with both soma and projections entirely within the telencephalon. http://orcid.org/0000-0001-7258-9596 ILX:0770100 IT projecting quality PATO:0070034 intratelencephalic projecting A neuron projection quality that is a characteristic of neurons with both soma and projections entirely within the telencephalon. DOI:10.1101/2020.10.19.343129 An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. natural protein native protein protein PR:000000001 The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. protein An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. PRO:DAN PRO:WCB natural protein PRO:DAN native protein IEDB:BP A transient receptor potential channel protein that is a member of the subfamily C of the transient receptor potential cation channels (TRPs), with amino- and carboxyl-terminal intracellular domains separated by a domain (common with other ion channels) containing six transmembrane helices (S1-S6) in which the last two helices (S5 and S6) flank a loop, called the pore loop, which determines ion selectivity. The amino-terminal domain contains up to 4 detectable copies of Ankyrin repeat (Pfam:PF00023) followed by the Transient receptor ion channel II domain (Pfam:PF08344). Most TRPs are relatively non-selective. They may be modulated by voltage changes but channel gating is generally effected by other means. PIRSF:PIRSF005528 fam:TRPC protein PR:000000680 Category=family. transient receptor potential cation channel TRPC A transient receptor potential channel protein that is a member of the subfamily C of the transient receptor potential cation channels (TRPs), with amino- and carboxyl-terminal intracellular domains separated by a domain (common with other ion channels) containing six transmembrane helices (S1-S6) in which the last two helices (S5 and S6) flank a loop, called the pore loop, which determines ion selectivity. The amino-terminal domain contains up to 4 detectable copies of Ankyrin repeat (Pfam:PF00023) followed by the Transient receptor ion channel II domain (Pfam:PF08344). Most TRPs are relatively non-selective. They may be modulated by voltage changes but channel gating is generally effected by other means. PMID:16382100 PMID:16460286 PMID:17579562 PRO:WCB fam:TRPC PRO:DAN A transient receptor potential cation channel TRPC that is a member of a subgroup of subfamily C containing the very similar TRPC3, TRPC6, and TRPC7. They form homomeric or heteromeric nonselective cation channels that generate double-rectifying currents and are activated by diacylglycerol. PIRSF:PIRSF500999 fam:TRPC[3/6/7] protein DAG-sensitive TRPC PR:000000718 Category=family. transient receptor potential cation channel TRPC3/6/7 A transient receptor potential cation channel TRPC that is a member of a subgroup of subfamily C containing the very similar TRPC3, TRPC6, and TRPC7. They form homomeric or heteromeric nonselective cation channels that generate double-rectifying currents and are activated by diacylglycerol. PMID:16382100 PMID:16460286 PMID:17579562 fam:TRPC[3/6/7] PRO:DAN A transient receptor potential cation channel TRPC3/6/7 that is a translation product of the human TRPC3 gene or a 1:1 ortholog thereof. IUPHARobj:488 TRP-3 TRPC3 Trp-related protein 3 Trp3 TrpC3 receptor-activated cation channel TRP3 transient receptor protein 3 protein TRP3 Trrp3 PR:000000775 Category=gene. short transient receptor potential cation channel TRPC3 A transient receptor potential cation channel TRPC3/6/7 that is a translation product of the human TRPC3 gene or a 1:1 ortholog thereof. PRO:CNA TRPC3 PRO:DNx TRP3 Trrp3 A protein that is a translation product of the human CD19 gene or a 1:1 ortholog thereof. It is composed of an N-terminal extracellular domain containing two Ig-like C2-type (immunoglobulin-like) domains, followed by a single-pass transmembrane segment and a cytoplasmic C-terminal tail. CD19 expression is restricted to members of the B cell lineage. It functions as a co-receptor for B-cell antigen receptor (BCR), regulating signal transduction. IUPHARobj:2764 PIRSF:PIRSF016630 B-lymphocyte surface antigen B4 CD19 T-cell surface antigen Leu-12 differentiation antigen CD19 protein PR:000001002 Category=gene. Requested by=CL. CD19 molecule A protein that is a translation product of the human CD19 gene or a 1:1 ortholog thereof. It is composed of an N-terminal extracellular domain containing two Ig-like C2-type (immunoglobulin-like) domains, followed by a single-pass transmembrane segment and a cytoplasmic C-terminal tail. CD19 expression is restricted to members of the B cell lineage. It functions as a co-receptor for B-cell antigen receptor (BCR), regulating signal transduction. PMID:15778510 CD19 PRO:DNx A protein that is a translation product of the human CD34 gene or a 1:1 ortholog thereof. It is a leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. It contains a single-pass transmembrane domain and that show distinct expression on early hematopoietic precursors and vascular-associated tissue. Acts as a scaffold that presents selectin carbohydrate ligands in a clustered, tissue specific manner to allow for higher avidity interactions between leukocytes and endothelial cells during the inflammatory process. In common with related sialomucins (endoglycan and podocalyxin), the extracellular region is dominated by an N-terminal mucin-like domain, which is densely substituted with sialylated O-linked carbohydrates. The mucin-like region is followed by a cysteine-containing and presumably globular domain. This domain may fold into an immunoglobulin-like structure as the positions of 2 of the cysteines are conserved in the C2 set of the immunoglobulin superfamily. The cytoplasmic domain is around 73-76 residues long and highly conserved. PIRSF:PIRSF028749 CD34 hematopoietic progenitor cell antigen CD34 protein PR:000001003 Category=gene. Requested by=CL. CD34 molecule A protein that is a translation product of the human CD34 gene or a 1:1 ortholog thereof. It is a leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. It contains a single-pass transmembrane domain and that show distinct expression on early hematopoietic precursors and vascular-associated tissue. Acts as a scaffold that presents selectin carbohydrate ligands in a clustered, tissue specific manner to allow for higher avidity interactions between leukocytes and endothelial cells during the inflammatory process. In common with related sialomucins (endoglycan and podocalyxin), the extracellular region is dominated by an N-terminal mucin-like domain, which is densely substituted with sialylated O-linked carbohydrates. The mucin-like region is followed by a cysteine-containing and presumably globular domain. This domain may fold into an immunoglobulin-like structure as the positions of 2 of the cysteines are conserved in the C2 set of the immunoglobulin superfamily. The cytoplasmic domain is around 73-76 residues long and highly conserved. PMID:16720896 PMID:8983065 CD34 PRO:DNx A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. PIRSF:PIRSF001977 CD4 T-cell differentiation antigen L3T4 T-cell surface antigen T4/Leu-3 T-cell surface glycoprotein CD4 protein PR:000001004 Category=gene. Requested by=CL. CD4 molecule A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. PMID:15326605 CD4 PRO:DNx An integrin alpha that contains an A domain. A hallmark of this class is the presence of a von Willebrand factor type A domain (Pfam:PF00092) (I-domain) of approximately 200 amino acid residues at the N terminus, which confers divalent cation binding properties. Unlike other integrin alpha proteins, they do not undergo proteolytic cleavage. PIRSF:PIRSF002497 integrin alpha with I domain protein PR:000001005 Category=family. integrin alpha with A domain An integrin alpha that contains an A domain. A hallmark of this class is the presence of a von Willebrand factor type A domain (Pfam:PF00092) (I-domain) of approximately 200 amino acid residues at the N terminus, which confers divalent cation binding properties. Unlike other integrin alpha proteins, they do not undergo proteolytic cleavage. PIRSF:PIRSF002497 A protein that is a translation product of the human PTPRC gene or a 1:1 ortholog thereof. It is composed of an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic protein-tyrosine phosphatase domains. Contains 1 to 3 copies of the Fibronectin type III domain (Pfam:PF00041) followed by two copies of the Protein-tyrosine phosphatase (Pfam:PF00102) domain. Receptor-type tyrosine-protein phosphatase C (CD45) regulates signal transduction and lymphocyte activation by specific association with receptor molecules on T and B cells. Multiple isoforms of CD45 (180-235 kDa) can be generated asa result of alternative splicing of three variable exons 4(A), 5(B) and 6(C), encoding sequences at the N-terminal extracellular domain of the molecule. T200 IUPHARobj:1852 PIRSF:PIRSF002004 CD45 L-CA PTPRC leukocyte common antigen ly-5 lymphocyte antigen 5 protein PR:000001006 Category=gene. Requested by=CL. receptor-type tyrosine-protein phosphatase C A protein that is a translation product of the human PTPRC gene or a 1:1 ortholog thereof. It is composed of an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic protein-tyrosine phosphatase domains. Contains 1 to 3 copies of the Fibronectin type III domain (Pfam:PF00041) followed by two copies of the Protein-tyrosine phosphatase (Pfam:PF00102) domain. Receptor-type tyrosine-protein phosphatase C (CD45) regulates signal transduction and lymphocyte activation by specific association with receptor molecules on T and B cells. Multiple isoforms of CD45 (180-235 kDa) can be generated asa result of alternative splicing of three variable exons 4(A), 5(B) and 6(C), encoding sequences at the N-terminal extracellular domain of the molecule. PMID:1351092 PRO:CNA T200 PRO:DNx PTPRC PRO:DNx An integrin alpha with A domain that is a translation product of the human ITGA2 gene or a 1:1 ortholog thereof. IUPHARobj:2440 CD49 antigen-like family member B CD49b GPIa ITGA2 VLA-2 subunit alpha collagen receptor platelet membrane glycoprotein Ia protein CD49B PR:000001008 Category=gene. Requested by=CL. integrin alpha-2 An integrin alpha with A domain that is a translation product of the human ITGA2 gene or a 1:1 ortholog thereof. PRO:CNA ITGA2 PRO:DNx CD49B An integrin alpha with A domain that is a translation product of the human ITGAE gene or a 1:1 ortholog thereof. IUPHARobj:2450 CD103 HML-1 antigen ITGAE integrin alpha M290 integrin alpha-IEL mucosal lymphocyte 1 antigen protein PR:000001010 Category=gene. Requested by=CL. integrin alpha-E An integrin alpha with A domain that is a translation product of the human ITGAE gene or a 1:1 ortholog thereof. PRO:CNA ITGAE PRO:DNx An integrin alpha with A domain that is a translation product of the human ITGAM gene or a 1:1 ortholog thereof. They constitute subunits of the integrin alpha-M/beta-2 receptor. This receptor is implicated in various adhesive interactions of monocytes, macrophages and granulocytes as well as in mediating the uptake of complement-coated particles. It is also a receptor for fibrinogen, factor X and ICAM1. IUPHARobj:2452 CD11 antigen-like family member B CD11b CR-3 alpha chain ITGAM cell surface glycoprotein MAC-1 subunit alpha leukocyte adhesion receptor MO1 neutrophil adherence receptor protein CD11B CR3A PR:000001012 Category=gene. Requested by=CL. integrin alpha-M An integrin alpha with A domain that is a translation product of the human ITGAM gene or a 1:1 ortholog thereof. They constitute subunits of the integrin alpha-M/beta-2 receptor. This receptor is implicated in various adhesive interactions of monocytes, macrophages and granulocytes as well as in mediating the uptake of complement-coated particles. It is also a receptor for fibrinogen, factor X and ICAM1. UniProtKB:P11215 ITGAM PRO:DNx CD11B CR3A An integrin alpha with A domain that is a translation product of the human ITGAX gene or a 1:1 ortholog thereof. Integrin alpha-X complexed with beta-2 is a receptor for fibrinogen. It recognizes the sequence GPR in fibrinogen. It mediates cell-cell interaction during inflammatory responses. It is especially important in monocyte adhesion and chemotaxis. IUPHARobj:2454 CD11 antigen-like family member C CD11c ITGAX Leu M5 leukocyte adhesion glycoprotein p150,95 alpha chain leukocyte adhesion receptor p150,95 protein CD11C PR:000001013 Category=gene. Requested by=CL. integrin alpha-X An integrin alpha with A domain that is a translation product of the human ITGAX gene or a 1:1 ortholog thereof. Integrin alpha-X complexed with beta-2 is a receptor for fibrinogen. It recognizes the sequence GPR in fibrinogen. It mediates cell-cell interaction during inflammatory responses. It is especially important in monocyte adhesion and chemotaxis. UniProtKB:P20702 ITGAX PRO:DNx CD11C A receptor-type tyrosine-protein phosphatase C that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P08575-3 or a 1:1 ortholog thereof. CD45RABC PTPRC/iso:CD45RABC protein B220 CD45R PR:000001014 Category=sequence. Requested by=CL. Note: This isoform includes the region encoded by the variable exons 4(A), 5(B), and 6(C). receptor-type tyrosine-protein phosphatase C isoform CD45RABC A receptor-type tyrosine-protein phosphatase C that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P08575-3 or a 1:1 ortholog thereof. PMID:1351092 PRO:CNA PRO:DAN PTPRC/iso:CD45RABC PRO:DNx A receptor-type tyrosine-protein phosphatase C isoform CD45R that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P08575-8 or a 1:1 ortholog thereof. CD45RA PTPRC/iso:CD45RA protein PR:000001015 Category=sequence. Requested by=CL. Note: This isoform includes the region encoded by the variable exon 4(A), and lacks the region encoded by exons 5(B) and 6(C). receptor-type tyrosine-protein phosphatase C isoform CD45RA A receptor-type tyrosine-protein phosphatase C isoform CD45R that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P08575-8 or a 1:1 ortholog thereof. PMID:1351092 PRO:CNA PRO:DAN PTPRC/iso:CD45RA PRO:DNx A receptor-type tyrosine-protein phosphatase C that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P08575-4 or a 1:1 ortholog thereof. 180 kDa form CD45RO PTPRC/iso:CD45RO protein T200 PR:000001017 Category=sequence. Requested by=CL. Note: This isoform lacks the region encoded by the variable exons 4(A), 5(B), and 6(C). receptor-type tyrosine-protein phosphatase C isoform CD45RO A receptor-type tyrosine-protein phosphatase C that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P08575-4 or a 1:1 ortholog thereof. PMID:1351092 PRO:CNA PRO:DAN CD45RO GOC:add PRO:ADD PTPRC/iso:CD45RO PRO:DNx A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response. PIRSF:PIRSF001993 CD3 subunit with Ig-like domain protein PR:000001018 Category=family. CD3 subunit with immunoglobulin domain A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response. PMID:16473826 PMID:1724736 A CD3 subunit with immunoglobulin domain that is a translation product of the human CD3E gene or a 1:1 ortholog thereof. IUPHARobj:2742 CD3E CD3e T-cell surface antigen T3/Leu-4 epsilon chain protein T3E PR:000001020 Category=gene. Requested by=CL. CD3 epsilon A CD3 subunit with immunoglobulin domain that is a translation product of the human CD3E gene or a 1:1 ortholog thereof. PRO:CNA CD3E PRO:DNx T3E A protein with a domain composition consisting of a large extracellular domain, including five Ig-like C2-type domains followed by two copies of the Fibronectin type-III domain (Pfam:PF00041), a single-pass transmembrane domain and a short cytoplasmic C-terminal domain. PIRSF:PIRSF002507 protein PR:000001022 Category=family. neural cell adhesion molecule A protein with a domain composition consisting of a large extracellular domain, including five Ig-like C2-type domains followed by two copies of the Fibronectin type-III domain (Pfam:PF00041), a single-pass transmembrane domain and a short cytoplasmic C-terminal domain. PRO:CNA A neural cell adhesion molecule that is involved in neuronal development, synaptic plasticity, and regeneration. PIRSF:PIRSF501037 protein PR:000001023 Category=family. neural cell adhesion molecule NCAM A neural cell adhesion molecule that is involved in neuronal development, synaptic plasticity, and regeneration. PMID:17975827 A neural cell adhesion molecule NCAM that is a translation product of the human NCAM1 gene or a 1:1 ortholog thereof. IUPHARobj:2769 CD56 N-CAM-1 NCAM-1 NCAM1 protein NCAM PR:000001024 Category=gene. Requested by=CL. neural cell adhesion molecule 1 A neural cell adhesion molecule NCAM that is a translation product of the human NCAM1 gene or a 1:1 ortholog thereof. PRO:CNA NCAM1 PRO:DNx NCAM A protein that is a type I transmembrane receptor with an N-terminal cysteine-rich domain, a single Fibronectin type II (FNII) domain (Pfam:PF00040) and eight to ten copies of the Lectin C-type domain (Pfam:PF00059) (CTLDs). The presence of multiple copies of the CTLD domain is a hallmark of this class. PIRSF:PIRSF002427 protein PR:000001025 Category=family. C-type lectin with multiple lectin domains A protein that is a type I transmembrane receptor with an N-terminal cysteine-rich domain, a single Fibronectin type II (FNII) domain (Pfam:PF00040) and eight to ten copies of the Lectin C-type domain (Pfam:PF00059) (CTLDs). The presence of multiple copies of the CTLD domain is a hallmark of this class. PMID:12223280 A C-type lectin with multiple lectin domains that is a translation product of the human LY75 gene or a 1:1 ortholog thereof. It consists of 12 extracellular domains (an N-terminal cysteine-rich domain, a fibronectin type II domain and 10 C-type carbohydrate recognition domains), a transmembrane region and a small cytoplasmic C terminus containing a single Tyr residue, but no obvious kinase domain. Acts as an endocytic receptor to direct captured antigens from the extracellular space to a specialized antigen-processing compartment. C-type lectin domain family 13 member B CD205 DEC-205 LY75 gp200-MR6 ly-75 protein CLEC13B PR:000001026 Category=gene. Requested by=CL. lymphocyte antigen 75 A C-type lectin with multiple lectin domains that is a translation product of the human LY75 gene or a 1:1 ortholog thereof. It consists of 12 extracellular domains (an N-terminal cysteine-rich domain, a fibronectin type II domain and 10 C-type carbohydrate recognition domains), a transmembrane region and a small cytoplasmic C terminus containing a single Tyr residue, but no obvious kinase domain. Acts as an endocytic receptor to direct captured antigens from the extracellular space to a specialized antigen-processing compartment. PMID:9862343 LY75 PRO:DNx A protein that is a translation product of the human CD2 gene or a 1:1 ortholog thereof. IUPHARobj:2600 PIRSF:PIRSF001984 CD2 LFA-2 LFA-3 receptor T-cell surface antigen CD2 T-cell surface antigen T11/Leu-5 T-cell surface glycoprotein CD2 erythrocyte receptor ly-37 lymphocyte antigen 37 rosette receptor protein SRBC PR:000001083 Category=gene. Requested by=CL. CD2 molecule A protein that is a translation product of the human CD2 gene or a 1:1 ortholog thereof. PRO:CNA CD2 PRO:DNx SRBC A protein that is a translation product of the human CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain. PANTHER:PTHR10441:SF1 CD8A CD8a T-cell surface glycoprotein Lyt-2 T-lymphocyte differentiation antigen T8/Leu-2 protein Lyt-2 Lyt2 MAL PR:000001084 Category=gene. Requested by=CL. T-cell surface glycoprotein CD8 alpha chain A protein that is a translation product of the human CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain. PMID:11114424 PRO:CNA Wikipedia:CD8 CD8A PRO:DNx Lyt-2 Lyt2 MAL A protein that is a translation product of the human CD8B gene or a 1:1 ortholog thereof. CD8 is a transmembrane receptor that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain. PIRSF:PIRSF002020 CD8B T-cell membrane glycoprotein Ly-3 T-cell surface glycoprotein Lyt-3 lymphocyte antigen 3 protein CD8B1 Ly-3 Lyt-3 Lyt3 PR:000001085 Category=gene. T-cell surface glycoprotein CD8 beta chain A protein that is a translation product of the human CD8B gene or a 1:1 ortholog thereof. CD8 is a transmembrane receptor that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain. PRO:CNA Wikipedia:CD8 CD8B PRO:DNx CD8B1 Ly-3 Lyt-3 Lyt3 A G-protein coupled receptor with a 7 transmembrane (secretin family) domain (Pfam:PF00002) preceded by an amino-terminal region containing one or more functional domains with adhesion-like motifs. IUPHAR:GPCRListForward?class=adhesion IUPHARfam:17 adhesion class GPCR fam:adhesion subfamily B2 G-protein coupled receptor protein secretin receptor-like G-protein coupled receptor PR:000001087 Category=family. Classification based on GRAFS system. [PMID:12761335] adhesion G-protein coupled receptor A G-protein coupled receptor with a 7 transmembrane (secretin family) domain (Pfam:PF00002) preceded by an amino-terminal region containing one or more functional domains with adhesion-like motifs. PMID:12761335 PRO:DAN PRO:WCB adhesion class GPCR IUPHARfam:17 fam:adhesion PRO:DAN subfamily B2 G-protein coupled receptor PMID:11790261 A G-protein coupled receptor that contains the 7 transmembrane receptor (rhodopsin family) domain (Pfam:PF00001), which includes 7 transmembrane helices (TMI-TM7) with 3 intracellular loops (IL1-IL3) and 3 extracellular loops (EL1-EL3) between the helices. The amino-terminal region is extracellular and the carboxyl-terminal region is intracellular. Rhodopsin-like G-protein coupled receptors (GPCRs) are unique among the several classes of GPCRs in that most have a very short amino-terminal segment and several characteristic sequence motifs, particularly NSxxNPxxY in TM7 and D/E-R-Y/F between TM3 and loop IL2. Most bind their ligands within a cavity between the TM regions. IUPHAR:GPCRListForward?class=A PIRSF:PIRSF800006 class 1 G-protein coupled receptor class A G-protein coupled receptor fam:rhodopsin protein PR:000001094 Category=family. Classification based on GRAFS system. [PMID:12761335] rhodopsin-like G-protein coupled receptor A G-protein coupled receptor that contains the 7 transmembrane receptor (rhodopsin family) domain (Pfam:PF00001), which includes 7 transmembrane helices (TMI-TM7) with 3 intracellular loops (IL1-IL3) and 3 extracellular loops (EL1-EL3) between the helices. The amino-terminal region is extracellular and the carboxyl-terminal region is intracellular. Rhodopsin-like G-protein coupled receptors (GPCRs) are unique among the several classes of GPCRs in that most have a very short amino-terminal segment and several characteristic sequence motifs, particularly NSxxNPxxY in TM7 and D/E-R-Y/F between TM3 and loop IL2. Most bind their ligands within a cavity between the TM regions. PMID:12761335 PRO:DAN PRO:WCB class 1 G-protein coupled receptor PMID:15914470 class A G-protein coupled receptor IUPHAR:GPCRListForward?class=A fam:rhodopsin PRO:DAN A rhodopsin-like G-protein coupled receptor that in active form binds to one or more chemokines. IUPHARfam:14 PIRSF:PIRSF038545 protein PR:000001128 Category=family. Note: Only those that have been unequivocally shown to activate a G-protein coupled signaling pathway appear on the official IUPHAR list. chemokine receptor A rhodopsin-like G-protein coupled receptor that in active form binds to one or more chemokines. PMID:12037138 PRO:WCB PRO:XQ A chemokine receptor that is a translation product of the human CCR1 or CCR3 genes, the mouse CCR1L1 gene, 1:1 orthologs thereof, or a semi-ortholog thereof. PIRSF:PIRSF501024 protein PR:000001197 Category=family. chemokine receptor CCR1/3/1L A chemokine receptor that is a translation product of the human CCR1 or CCR3 genes, the mouse CCR1L1 gene, 1:1 orthologs thereof, or a semi-ortholog thereof. PRO:DAN PRO:WCB A chemokine receptor that is a translation product of the human CCR2 gene or a 1:1 ortholog thereof. The preferred ligands include CCL2, CCL7, CCL8, CCL13. IUPHARobj:59 C-C CKR-2 CC-CKR-2 CCR-2 CCR2 CD192 JE/FIC receptor MCP-1 receptor MCP-1-R chemokine receptor CCR2 monocyte chemoattractant protein 1 receptor protein CMKBR2 PR:000001199 Category=gene. Requested by=CL. C-C chemokine receptor type 2 A chemokine receptor that is a translation product of the human CCR2 gene or a 1:1 ortholog thereof. The preferred ligands include CCL2, CCL7, CCL8, CCL13. PMID:12037138 PRO:WCB CCR2 PRO:DNx CMKBR2 A chemokine receptor that is a translation product of the human CCR4 gene or a 1:1 ortholog thereof. The preferred ligands include CCL17 and CCL22. IUPHARobj:61 C-C CKR-4 CC-CKR-4 CCR-4 CCR4 CD194 K5-5 chemokine receptor CCR4 protein CMKBR4 PR:000001200 Category=gene. C-C chemokine receptor type 4 A chemokine receptor that is a translation product of the human CCR4 gene or a 1:1 ortholog thereof. The preferred ligands include CCL17 and CCL22. PMID:12037138 PRO:WCB CCR4 PRO:DNx CMKBR4 A chemokine receptor that is a translation product of the human CCR5 gene or a 1:1 ortholog thereof. The preferred ligands include CCL3, CCL4, CCL5, CCL8, CCL14. IUPHARobj:62 C-C CKR-5 CC-CKR-5 CCR-5 CCR5 CD195 CHEMR13 HIV-1 fusion coreceptor MIP-1 alpha receptor chemokine receptor CCR5 protein CMKBR5 PR:000001201 Category=gene. Requested by=CL. C-C chemokine receptor type 5 A chemokine receptor that is a translation product of the human CCR5 gene or a 1:1 ortholog thereof. The preferred ligands include CCL3, CCL4, CCL5, CCL8, CCL14. PMID:12037138 PRO:WCB CCR5 PRO:DNx CMKBR5 A chemokine receptor that is a translation product of the human CCR6 gene or a 1:1 ortholog thereof. The preferred ligand is CCL20. IUPHARobj:63 C-C CKR-6 CC-CKR-6 CCR-6 CCR6 CD196 CKR-L3 DRY6 G-protein coupled receptor 29 GPR-CY4 GPRCY4 KY411 LARC receptor chemokine receptor CCR6 chemokine receptor-like 3 protein CKRL3 CMKBR6 GPR29 STRL22 PR:000001202 Category=gene. Requested by=CL. C-C chemokine receptor type 6 A chemokine receptor that is a translation product of the human CCR6 gene or a 1:1 ortholog thereof. The preferred ligand is CCL20. PMID:12037138 PRO:WCB CCR6 PRO:DNx CKRL3 CMKBR6 GPR29 STRL22 A chemokine receptor that is a translation product of the human CCR7 gene or a 1:1 ortholog thereof. The preferred ligands are CCL19 and CCL21. IUPHARobj:64 BLR2 C-C CKR-7 CC-CKR-7 CCR-7 CCR7 CD197 CDw197 EBI1 EBV-induced G-protein coupled receptor 1 MIP-3 beta receptor chemokine receptor CCR7 epstein-Barr virus-induced G-protein coupled receptor 1 protein CMKBR7 EVI1 Ebi1h PR:000001203 Category=gene. Requested by=CL. C-C chemokine receptor type 7 A chemokine receptor that is a translation product of the human CCR7 gene or a 1:1 ortholog thereof. The preferred ligands are CCL19 and CCL21. PMID:12037138 PRO:WCB CCR7 PRO:DNx CMKBR7 EVI1 Ebi1h A chemokine receptor that is a translation product of the human CX3CR1 gene or a 1:1 ortholog thereof. The preferred ligand is CX3CL1. IUPHARobj:74 PIRSF:PIRSF501025 C-X3-C CKR-1 CMK-BRL-1 CMK-BRL1 CX3CR1 G-protein coupled receptor 13 V28 beta chemokine receptor-like 1 chemokine receptor CX3CR1 fractalkine receptor protein CMKBRL1 GPR13 PR:000001206 Category=gene. Requested by=CL. CX3C chemokine receptor 1 A chemokine receptor that is a translation product of the human CX3CR1 gene or a 1:1 ortholog thereof. The preferred ligand is CX3CL1. PMID:12037138 PRO:WCB CX3CR1 PRO:DNx CMKBRL1 GPR13 A chemokine receptor that is a translation product of the human CXCR3 gene or a 1:1 ortholog thereof. The preferred ligands include CXCL9, CXCL10, CXCL11. IUPHARobj:70 PIRSF:PIRSF501023 CD183 CKR-L2 CXC-R3 CXCR-3 CXCR3 G-protein coupled receptor 9 IP-10 receptor chemokine receptor CXCR3 interferon-inducible protein 10 receptor protein Cmkar3 GPR9 PR:000001207 Category=gene. C-X-C chemokine receptor type 3 A chemokine receptor that is a translation product of the human CXCR3 gene or a 1:1 ortholog thereof. The preferred ligands include CXCL9, CXCL10, CXCL11. PMID:12037138 PRO:WCB CXCR3 PRO:DNx Cmkar3 GPR9 A chemokine receptor that is a translation product of the human CXCR4 gene or a 1:1 ortholog thereof. The preferred ligand is CXCL12. IUPHARobj:71 PIRSF:PIRSF501021 CD184 CXC-R4 CXCR-4 CXCR4 FB22 HM89 LCR1 LESTR NPYRL PB-CKR SDF-1 receptor chemokine receptor CXCR4 fusin leukocyte-derived seven transmembrane domain receptor pre-B-cell-derived chemokine receptor stromal cell-derived factor 1 receptor protein Cmkar4 Sdf1r PR:000001208 Category=gene. Requested by=CL. C-X-C chemokine receptor type 4 A chemokine receptor that is a translation product of the human CXCR4 gene or a 1:1 ortholog thereof. The preferred ligand is CXCL12. PMID:12037138 PRO:WCB CXCR4 PRO:DNx Cmkar4 Sdf1r A chemokine receptor that is a translation product of the human CXCR5 gene or a 1:1 ortholog thereof. The preferred ligand is CXCL13. IUPHARobj:72 PANTHER:PTHR24227:SF213 CD185 CXC-R5 CXCR-5 CXCR5 MDR-15 burkitt lymphoma receptor 1 burkitt lymphoma receptor 1 homolog chemokine receptor CXCR5 monocyte-derived receptor 15 protein BLR1 Gpcr6 MDR15 PR:000001209 Category=gene. Requested by=CL. C-X-C chemokine receptor type 5 A chemokine receptor that is a translation product of the human CXCR5 gene or a 1:1 ortholog thereof. The preferred ligand is CXCL13. PMID:12037138 PRO:WCB CXCR5 PRO:DNx BLR1 Gpcr6 MDR15 A chemokine receptor whose active form binds interleukin-8 with high affinity. PIRSF:PIRSF501022 protein PR:000001226 Category=family. high affinity interleukin-8 receptor A chemokine receptor whose active form binds interleukin-8 with high affinity. PRO:WCB A chemokine receptor CCR1/3/1L that is a translation product of the human CCR1 gene or a 1:1 ortholog thereof. IUPHARobj:58 C-C CKR-1 CC-CKR-1 CCR-1 CCR1 CD191 HM145 LD78 receptor MIP-1alpha-R RANTES-R chemokine receptor CCR1 macrophage inflammatory protein 1-alpha receptor protein CMKBR1 CMKR1 SCYAR1 PR:000001254 Category=gene. Requested by=CL. C-C chemokine receptor type 1 A chemokine receptor CCR1/3/1L that is a translation product of the human CCR1 gene or a 1:1 ortholog thereof. PRO:WCB CCR1 PRO:DNx CMKBR1 CMKR1 SCYAR1 A chemokine receptor CCR1/3/1L that is a translation product of the human CCR3 gene or a 1:1 ortholog thereof. IUPHARobj:60 C-C CKR-3 CC-CKR-3 CCR-3 CCR3 CD193 CKR3 MIP-1 alpha RL2 chemokine receptor CCR3 eosinophil eotaxin receptor macrophage inflammatory protein 1-alpha receptor-like 2 protein CMKBR3 Cmkbr1l2 PR:000001255 Category=gene. Requested by=CL. C-C chemokine receptor type 3 A chemokine receptor CCR1/3/1L that is a translation product of the human CCR3 gene or a 1:1 ortholog thereof. PMID:12037138 PRO:WCB CCR3 PRO:DNx CMKBR3 Cmkbr1l2 A high affinity interleukin-8 receptor that is a translation product of the human CXCR1 gene or a 1:1 ortholog thereof. IUPHARobj:68 CD181 CDw128a CXC-R1 CXCR-1 CXCR1 IL-8 receptor type 1 IL-8R A high affinity interleukin-8 receptor A protein CMKAR1 IL8RA PR:000001256 Category=gene. Requested by=CL. C-X-C chemokine receptor type 1 A high affinity interleukin-8 receptor that is a translation product of the human CXCR1 gene or a 1:1 ortholog thereof. PRO:WCB CXCR1 PRO:DNx CMKAR1 IL8RA A high affinity interleukin-8 receptor that is a translation product of the human CXCR2 gene or a 1:1 ortholog thereof. IUPHARobj:69 CD182 CDw128b CXC-R2 CXCR-2 CXCR2 GRO/MGSA receptor IL-8 receptor type 2 IL-8R B high affinity interleukin-8 receptor B protein Cmkar2 Gpcr16 IL8RB PR:000001257 Category=gene. Requested by=CL. C-X-C chemokine receptor type 2 A high affinity interleukin-8 receptor that is a translation product of the human CXCR2 gene or a 1:1 ortholog thereof. PRO:WCB CXCR2 PRO:DNx Cmkar2 Gpcr16 IL8RB A protein that contains the ADP-ribosyl cyclase domain (Pfam:PF02267). PIRSF:PIRSF005736 protein PR:000001281 Category=family. ADP-ribosyl cyclase A protein that contains the ADP-ribosyl cyclase domain (Pfam:PF02267). PRO:WCB A protein that is a translation product of the human CD22 gene or a 1:1 ortholog thereof. IUPHARobj:2786 B-lymphocyte cell adhesion molecule BL-CAM CD22 T-cell surface antigen Leu-14 sialic acid-binding Ig-like lectin 2 siglec-2 protein Lyb-8 SIGLEC2 PR:000001288 Category=gene. Requested by=CL. B-cell receptor CD22 A protein that is a translation product of the human CD22 gene or a 1:1 ortholog thereof. PRO:WCB CD22 PRO:DNx Lyb-8 SIGLEC2 A protein that is a translation product of the human MS4A1 gene or a 1:1 ortholog thereof. IUPHARobj:2628 PIRSF:PIRSF001995 B-cell differentiation antigen Ly-44 B-cell surface antigen CD20 B-lymphocyte antigen CD20 B-lymphocyte surface antigen B1 Bp35 CD20 MS4A1 leukocyte surface antigen Leu-16 lymphocyte antigen 44 protein Ly-44 Ms4a2 PR:000001289 Category=gene. Requested by=CL. membrane-spanning 4-domains subfamily A member 1 A protein that is a translation product of the human MS4A1 gene or a 1:1 ortholog thereof. PRO:WCB MS4A1 PRO:DNx Ly-44 Ms4a2 A protein that is a member of a family that includes translation products of genes CD86, CD276, ICOSLG, and others. These are membrane-anchored proteins with a small intracellular domain and an extracellular domain with signal sequence, an Immunoglobulin V-set domain (Pfam:PF07686), and a CD80-like C2-set immunoglobulin domain (Pfam:PF08205). protein PR:000001290 Category=family. B7-related protein A protein that is a member of a family that includes translation products of genes CD86, CD276, ICOSLG, and others. These are membrane-anchored proteins with a small intracellular domain and an extracellular domain with signal sequence, an Immunoglobulin V-set domain (Pfam:PF07686), and a CD80-like C2-set immunoglobulin domain (Pfam:PF08205). PRO:WCB A protein that is a translation product of the human CLEC4C gene or a 1:1 ortholog thereof. BDCA-2 C-type lectin superfamily member 7 CD303 CLEC4C blood dendritic cell antigen 2 dendritic lectin protein BDCA2 CLECSF11 CLECSF7 DLEC HECL UNQ9361/PRO34150 PR:000001292 Category=gene. Requested by=CL. C-type lectin domain family 4 member C A protein that is a translation product of the human CLEC4C gene or a 1:1 ortholog thereof. PRO:WCB CLEC4C PRO:DNx BDCA2 CLECSF11 CLECSF7 DLEC HECL UNQ9361/PRO34150 A protein that is a translation product of the human CD207 gene or a 1:1 ortholog thereof. CD207 langerin protein CLEC4K PR:000001293 Category=gene. Requested by=CL. C-type lectin domain family 4 member K A protein that is a translation product of the human CD207 gene or a 1:1 ortholog thereof. PRO:WCB CD207 PRO:DNx CLEC4K A protein that is a translation product of the human CD209 gene or a 1:1 ortholog thereof. IUPHARobj:2930 C-type lectin domain family 4 member L CD209 CD209 antigen DC-SIGN1 dendritic cell-specific ICAM-3-grabbing non-integrin 1 protein CLEC4L DC-SIGN PR:000001300 Category=gene. This gene and CLEC4M are products of a recent gene duplication in the primate lineage. Independent duplications of an ancestral gene have given rise to several orthologs in rodents, including CD209A. Requested by=CL. CD209 molecule A protein that is a translation product of the human CD209 gene or a 1:1 ortholog thereof. PRO:WCB CD209 PRO:DNx CLEC4L A protein that is a translation product of the human CD44 gene or a 1:1 ortholog thereof. CD44 CD44 antigen CDw44 ECMR-III GP90 lymphocyte homing/adhesion receptor HUTCH-I PGP-1 epican extracellular matrix receptor III heparan sulfate proteoglycan hermes antigen hyaluronate receptor ly-24 lymphocyte antigen 24 phagocytic glycoprotein 1 phagocytic glycoprotein I protein LHR MDU2 MDU3 MIC4 PGP-I PR:000001307 Category=gene. Requested by=CL. CD44 molecule A protein that is a translation product of the human CD44 gene or a 1:1 ortholog thereof. PRO:WCB CD44 PRO:DNx LHR MDU2 MDU3 MIC4 A protein that is a translation product of the human CD48 gene or a 1:1 ortholog thereof. PANTHER:PTHR12080:SF3 PIRSF:PIRSF001973 B-lymphocyte activation marker BLAST-1 BCM1 surface antigen BLAST-1 CD48 CD48 antigen HM48-1 MRC OX-45 surface antigen SLAM family member 2 SLAMF2 TCT.1 leukocyte antigen MEM-102 sgp-60 signaling lymphocytic activation molecule 2 protein BCM1 BLAST1 Bcm-1 PR:000001308 Category=gene. Requested by=CL. CD48 molecule A protein that is a translation product of the human CD48 gene or a 1:1 ortholog thereof. PRO:WCB CD48 PRO:DNx BCM1 BLAST1 Bcm-1 A protein that is a translation product of the human CD83 gene or a 1:1 ortholog thereof. B-cell activation protein CD83 CD83 antigen cell surface protein HB15 protein PR:000001310 Category=gene. Requested by=CL. CD83 molecule A protein that is a translation product of the human CD83 gene or a 1:1 ortholog thereof. PRO:WCB CD83 PRO:DNx A protein that is a translation product of the human SELL gene or a 1:1 ortholog thereof. It is a leukocyte adhesion receptor that play an important role in regulating the inflammatory response by mediating leukocyte tethering and rolling on adherent leukocytes. PIRSF:PIRSF002421 CD62 antigen-like family member L CD62L LAM-1 LECAM1 SELL TQ1 gp90-MEL leukocyte adhesion molecule 1 leukocyte surface antigen Leu-8 leukocyte-endothelial cell adhesion molecule 1 ly-22 lymph node homing receptor lymphocyte antigen 22 lymphocyte surface MEL-14 antigen protein LNHR LYAM1 Ly22 PR:000001318 Category=gene. Requested by=CL. L-selectin A protein that is a translation product of the human SELL gene or a 1:1 ortholog thereof. It is a leukocyte adhesion receptor that play an important role in regulating the inflammatory response by mediating leukocyte tethering and rolling on adherent leukocytes. PMID:12403782 PRO:JAN SELL PRO:DNx LNHR LYAM1 Ly22 A protein that is a translation product of the human CD84 gene or a 1:1 ortholog thereof. PANTHER:PTHR12080:SF6 CD84 cell surface antigen MAX.3 hly9-beta leukocyte differentiation antigen CD84 signaling lymphocytic activation molecule 5 protein SLAMF5 PR:000001319 Category=gene. Requested by=CL. SLAM family member 5 A protein that is a translation product of the human CD84 gene or a 1:1 ortholog thereof. PRO:WCB CD84 PRO:DNx SLAMF5 A protein that is a stand alone version of the Glycosyltransferase family 10 (fucosyltransferase) (Pfam:PF00852) domain. Proteins in this class may catalyze alpha-1,3 glycosidic linkages. PIRSF:PIRSF005726 protein PR:000001320 Category=family. alpha-(1,3)-fucosyltransferase A protein that is a stand alone version of the Glycosyltransferase family 10 (fucosyltransferase) (Pfam:PF00852) domain. Proteins in this class may catalyze alpha-1,3 glycosidic linkages. PMID:9451017 A protein that is a translation product of the human BST2 gene or a 1:1 ortholog thereof. PIRSF:PIRSF023920 BST-2 BST2 CD317 HM1.24 antigen tetherin protein PR:000001326 Category=gene. Requested by=CL. bone marrow stromal antigen 2 A protein that is a translation product of the human BST2 gene or a 1:1 ortholog thereof. PRO:WCB BST2 PRO:DNx A protein that has a core domain structure of signal sequence, propeptide, five Cadherin domains (Pfam:PF00028), a transmembrane region, and a Cadherin cytoplasmic region (Pfam:PF01049). Cadherins function as adhesion molecules that mediate Ca2+-dependent cell-cell adhesion in solid tissues. PIRSF:PIRSF002504 protein PR:000001327 Category=family. cadherin A protein that has a core domain structure of signal sequence, propeptide, five Cadherin domains (Pfam:PF00028), a transmembrane region, and a Cadherin cytoplasmic region (Pfam:PF01049). Cadherins function as adhesion molecules that mediate Ca2+-dependent cell-cell adhesion in solid tissues. PRO:WCB A protein that is a translation product of the human CEACAM8 gene or a 1:1 ortholog thereof. CD66b CD67 antigen CEACAM8 carcinoembryonic antigen CGM6 non-specific cross-reacting antigen NCA-95 protein CGM6 PR:000001332 Category=gene. Requested by=CL. carcinoembryonic antigen-related cell adhesion molecule 8 A protein that is a translation product of the human CEACAM8 gene or a 1:1 ortholog thereof. PRO:CNA CEACAM8 PRO:DNx CGM6 A protein that is a translation product of the human CR1 gene or a 1:1 ortholog thereof. C3b/C4b receptor CD35 CR1 protein C3BR PR:000001337 Category=gene. Requested by=CL. Note: There is no counterpart in mouse. complement receptor type 1 A protein that is a translation product of the human CR1 gene or a 1:1 ortholog thereof. PRO:WCB CR1 PRO:DNx C3BR A protein that is a translation product of the human CR2 gene or a 1:1 ortholog thereof. PIRSF:PIRSF002484 CD21 CR2 Cr2 EBV receptor complement C3d receptor epstein-Barr virus receptor protein C3DR PR:000001338 Category=gene. Requested by=CL. complement receptor type 2 A protein that is a translation product of the human CR2 gene or a 1:1 ortholog thereof. PRO:WCB CR2 PRO:DNx C3DR A protein that is a translation product of the human CD69 gene or a 1:1 ortholog thereof. A type II transmembrane protein with a C-type lectin binding domain in the extracellular portion of the molecule. Involved in lymphocyte proliferation and functions as a signal transmitting receptor in lymphocytes, natural killer (NK) cells, and platelets. AIM BL-AC/P26 C-type lectin domain family 2 member C CD69 EA1 GP32/28 MLR-3 activation inducer molecule early T-cell activation antigen p60 early activation antigen CD69 leukocyte surface antigen Leu-23 protein CLEC2C PR:000001343 Category=gene. Requested by=CL. CD69 molecule A protein that is a translation product of the human CD69 gene or a 1:1 ortholog thereof. A type II transmembrane protein with a C-type lectin binding domain in the extracellular portion of the molecule. Involved in lymphocyte proliferation and functions as a signal transmitting receptor in lymphocytes, natural killer (NK) cells, and platelets. PMID:10466080 PRO:CNA UniProtKB:Q07108 CD69 PRO:DNx CLEC2C A protein that is a translation product of the human ENPP3 gene or a 1:1 ortholog thereof. CD203c E-NPP 3 ENPP3 PD-Ibeta ectonucleotide pyrophosphatase/phosphodiesterase 3 phosphodiesterase I beta phosphodiesterase I/nucleotide pyrophosphatase 3 protein PDNP3 PR:000001344 Category=gene. Requested by=CL. ectonucleotide pyrophosphatase/phosphodiesterase family member 3 A protein that is a translation product of the human ENPP3 gene or a 1:1 ortholog thereof. PRO:WCB ENPP3 PRO:DNx PDNP3 A protein that is a translation product of the human ENG gene or a 1:1 ortholog thereof. IUPHARobj:2895 PIRSF:PIRSF038746 CD105 ENG cell surface MJ7/18 antigen protein END Edg PR:000001345 Category=gene. Requested by=CL. endoglin A protein that is a translation product of the human ENG gene or a 1:1 ortholog thereof. PRO:CNA ENG PRO:DNx END Edg A protein that is a translation product of the human FOXP3 gene or a 1:1 ortholog thereof. FOXP3 scurfin protein IPEX JM2 PR:000001350 Category=gene. Requested by=CL. forkhead box protein P3 A protein that is a translation product of the human FOXP3 gene or a 1:1 ortholog thereof. PRO:CNA FOXP3 PRO:DNx IPEX JM2 A protein that contains an extracellular Glycophorin A domain (Pfam:PF01102), followed by a single-pass transmembrane region and a small intracellular domain. A protein that is an integral protein of the red cell membrane. Proteins in this class are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. PIRSF:PIRSF002466 protein PR:000001352 Category=family. glycophorin A protein that contains an extracellular Glycophorin A domain (Pfam:PF01102), followed by a single-pass transmembrane region and a small intracellular domain. A protein that is an integral protein of the red cell membrane. Proteins in this class are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. InterPro:IPR001195 PRO:CNA A protein with a core domain architecture consisting of an extracellular domain containing two copies of the Immunoglobulin domain (Pfam:PF00047), followed by a single-pass transmembrane region and a small intracellular domain. The active protein is a low affinity receptor for immunoglobulin gamma chain Fc region. Human II-a, II-b, and II-c represent a recent gene expansion and are equally related to mouse II, III, and IV. Human III-A and III-B are closely related and closer to mouse IV than to mouse III. PIRSF:PIRSF001980 protein PR:000001355 Category=family. immunoglobulin gamma Fc receptor II/III/IV A protein with a core domain architecture consisting of an extracellular domain containing two copies of the Immunoglobulin domain (Pfam:PF00047), followed by a single-pass transmembrane region and a small intracellular domain. The active protein is a low affinity receptor for immunoglobulin gamma chain Fc region. Human II-a, II-b, and II-c represent a recent gene expansion and are equally related to mouse II, III, and IV. Human III-A and III-B are closely related and closer to mouse IV than to mouse III. PRO:WCB A protein with a core domain architecture consisting of an extracellular domain containing two or three copies of the Immunoglobulin domain (Pfam:PF00047), followed by a single-pass transmembrane region and a small intracellular domain. PIRSF:PIRSF001981 protein Fc-gamma receptor PR:000001356 Category=family. Note: The active protein is a low affinity receptor for immunoglobulin gamma chain Fc region. It comprises the translation products of the FCGR1 gene (mouse) or one of the closely related FCGR1A, FCGR1B, or FCGR1C genes (human). FCGR1C may be a pseudogene in human. immunoglobulin gamma Fc receptor I A protein with a core domain architecture consisting of an extracellular domain containing two or three copies of the Immunoglobulin domain (Pfam:PF00047), followed by a single-pass transmembrane region and a small intracellular domain. PRO:CNA A protein that is a translation product of the human IL2RA gene or a 1:1 ortholog thereof. p55 IUPHARobj:1695 PIRSF:PIRSF001954 CD25 IL-2 receptor subunit alpha IL-2-RA IL-2R subunit alpha IL2-RA IL2RA TAC antigen protein Il2r PR:000001380 Category=gene. Requested by=CL. interleukin-2 receptor subunit alpha A protein that is a translation product of the human IL2RA gene or a 1:1 ortholog thereof. PRO:CNA p55 PRO:DNx IL2RA PRO:DNx Il2r A protein that is a translation product of the human IL2RB gene or a 1:1 ortholog thereof. p75 IUPHARobj:1696 CD122 IL-2 receptor subunit beta IL-2R subunit beta IL-2RB IL2RB high affinity IL-2 receptor subunit beta p70-75 protein IL15RB PR:000001381 Category=gene. Requested by=CL. interleukin-2 receptor subunit beta A protein that is a translation product of the human IL2RB gene or a 1:1 ortholog thereof. PRO:CNA p75 PRO:DNx IL2RB PRO:DNx IL15RB A leukocyte immunoglobulin-like receptor subfamily member that is a translation product of the human LILRA4 gene or a 1:1 ortholog thereof. This gene is a member of a lineage-specific gene expansion in primates. IUPHARobj:2896 CD85 antigen-like family member G CD85g ILT-7 LILRA4 immunoglobulin-like transcript 7 protein ILT7 PR:000001398 Category=gene. Requested by=CL. leukocyte immunoglobulin-like receptor subfamily A member 4 A leukocyte immunoglobulin-like receptor subfamily member that is a translation product of the human LILRA4 gene or a 1:1 ortholog thereof. This gene is a member of a lineage-specific gene expansion in primates. PRO:WCB LILRA4 PRO:DNx ILT7 A protein that is a translation product of the human KLRD1 gene or a 1:1 ortholog thereof. CD94 KLRD1 KP43 NK cell receptor natural killer cells antigen CD94 protein PR:000001402 Category=gene. Requested by=CL. killer cell lectin-like receptor subfamily D member 1 A protein that is a translation product of the human KLRD1 gene or a 1:1 ortholog thereof. PRO:WCB KLRD1 PRO:DNx A protein with four transmembrane domains, small intracellular amino- and carboxyl-terminal regions, and two extracellular loops, a small one (EC1) and a larger one (EC2) of about 100 residues. The EC2 loop contains at least 4 cysteine residues, including a highly conserved 'CCG' motif. PIRSF:PIRSF002419 protein PR:000001403 Category=family. tetraspanin A protein with four transmembrane domains, small intracellular amino- and carboxyl-terminal regions, and two extracellular loops, a small one (EC1) and a larger one (EC2) of about 100 residues. The EC2 loop contains at least 4 cysteine residues, including a highly conserved 'CCG' motif. PRO:WCB Wikipedia:Tetraspanin An ADP-ribosyl cyclase that is a translation product of the human CD38 gene or a 1:1 ortholog thereof. IUPHARobj:2766 2'-phospho-ADP-ribosyl cyclase 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase 2'-phospho-cyclic-ADP-ribose transferase ADP-ribosyl cyclase 1 ADPRC 1 CD38 I-19 NIM-R5 antigen T10 cADPr hydrolase 1 cyclic ADP-ribose hydrolase 1 protein PR:000001408 Category=gene. Requested by=CL. ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 An ADP-ribosyl cyclase that is a translation product of the human CD38 gene or a 1:1 ortholog thereof. PRO:WCB CD38 PRO:DNx A B7-related protein that is a translation product of the human CD86 gene or a 1:1 ortholog thereof. IUPHARobj:2745 PANTHER:PTHR25462:SF45 B70 BU63 CD86 CD86 antigen CTLA-4 counter-receptor B7.2 ETC-1 FUN-1 T-lymphocyte activation antigen CD86 activation B7-2 antigen early T-cell costimulatory molecule 1 protein CD28LG2 PR:000001412 Category=gene. Requested by=CL. CD86 molecule A B7-related protein that is a translation product of the human CD86 gene or a 1:1 ortholog thereof. PRO:WCB CD86 PRO:DNx CD28LG2 A rhodopsin-like G-protein coupled receptor that is a translation product of the human FPR1, FPR2, or FPR3 genes, 1:1 orthologs thereof, or a semi-ortholog thereof. The active form binds N-formyl methionyl peptides. IUPHARfam:23 PIRSF:PIRSF038561 formylpeptide receptor protein PR:000001431 Category=family. N-formyl peptide receptor A rhodopsin-like G-protein coupled receptor that is a translation product of the human FPR1, FPR2, or FPR3 genes, 1:1 orthologs thereof, or a semi-ortholog thereof. The active form binds N-formyl methionyl peptides. InterPro:IPR000826 PRO:DAN PRO:WCB PRO:XQ formylpeptide receptor IUPHARfam:23 A B7-related protein that is a translation product of the human CD80 gene or a 1:1 ortholog thereof. IUPHARobj:2744 B7 BB1 CD80 CTLA-4 counter-receptor B7.1 T-lymphocyte activation antigen CD80 activation B7-1 antigen protein CD28LG CD28LG1 LAB7 PR:000001438 Category=gene. Requested by=CL. CD80 molecule A B7-related protein that is a translation product of the human CD80 gene or a 1:1 ortholog thereof. PRO:WCB CD80 PRO:DNx CD28LG CD28LG1 LAB7 A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof. 7B4 antigen CD144 CDH5 VE-cadherin vascular endothelial cadherin protein PR:000001444 Category=gene. Requested by=CL. cadherin-5 A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof. PRO:WCB CDH5 PRO:DNx A cadherin that is a translation product of the human CDH1 gene or a 1:1 ortholog thereof. ARC-1 CAM 120/80 CD324 CDH1 E-cadherin epithelial cadherin uvomorulin protein CDHE UVO PR:000001447 Category=gene. Requested by=CL. cadherin-1 A cadherin that is a translation product of the human CDH1 gene or a 1:1 ortholog thereof. PRO:WCB CDH1 PRO:DNx CDHE UVO An alpha-(1,3)-fucosyltransferase that is a translation product of the human FUT4 gene or a 1:1 ortholog thereof. galactoside 3-L-fucosyltransferase CD15 ELAM-1 ligand fucosyltransferase FUT4 Fuc-TIV FucT-IV alpha-(1,3)-fucosyltransferase FUT4 fucosyltransferase 4 fucosyltransferase FUT4 fucosyltransferase IV protein ELFT FCT3A PR:000001456 Category=gene. Requested by=CL. alpha-(1,3)-fucosyltransferase 4 An alpha-(1,3)-fucosyltransferase that is a translation product of the human FUT4 gene or a 1:1 ortholog thereof. PRO:CNA galactoside 3-L-fucosyltransferase PRO:DNx FUT4 PRO:DNx ELFT FCT3A A glycophorin that is a translation product of the human GYPA gene or a 1:1 ortholog thereof. It is the major sialoglycoprotein of the erythrocyte membrane. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on Ser and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. CD235a GYPA MN sialoglycoprotein PAS-2 sialoglycoprotein alpha protein GPA PR:000001460 Category=gene. Requested by=CL. glycophorin-A A glycophorin that is a translation product of the human GYPA gene or a 1:1 ortholog thereof. It is the major sialoglycoprotein of the erythrocyte membrane. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on Ser and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. InterPro:IPR001195 PRO:CNA GYPA PRO:DNx GPA An immunoglobulin gamma Fc receptor I that is a translation product of the human FCGR1A gene or a 1:1 ortholog thereof. CD64 FCGR1A Fc-gamma RI FcRI IgG Fc receptor I protein FCG1 FCGR1 IGFR1 PR:000001465 Category=gene. The Fcgr1 gene in mouse is a 1:1 ortholog of FCGR1A, not FCGR1B. Requested by=CL. high affinity immunoglobulin gamma Fc receptor I An immunoglobulin gamma Fc receptor I that is a translation product of the human FCGR1A gene or a 1:1 ortholog thereof. PRO:CNA FCGR1A PRO:DNx FCG1 FCGR1 IGFR1 An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr2 gene or a 1:1 ortholog thereof. CD32 Fc gamma receptor IIB Fc-gamma RII Fc-gamma-RIIB FcRII Fcgr2 IgG Fc receptor II beta ly-17 lymphocyte antigen 17 protein Fcgr2b PR:000001479 Category=gene. Requested by=CL. low affinity immunoglobulin gamma Fc region receptor II An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr2 gene or a 1:1 ortholog thereof. PRO:CNA CD32 PRO:DNx Fcgr2 PRO:DNx Fcgr2b An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the human FCGR2B gene or a 1:1 ortholog thereof. CD32 CDw32 FCGR2B Fc-gamma RII-b Fc-gamma-RIIb FcRII-b IgG Fc receptor II-b protein FCG2 IGFR2 PR:000001481 Category=gene. Requested by=CL. low affinity immunoglobulin gamma Fc region receptor II-b An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the human FCGR2B gene or a 1:1 ortholog thereof. PRO:CNA CD32 PRO:DNx CDw32 PRO:DNx FCGR2B PRO:DNx FCG2 IGFR2 An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr3 gene or a 1:1 ortholog thereof. CD16 Fc-gamma RIII FcRIII Fcgr3 IgG Fc receptor III protein PR:000001483 Category=gene. Requested by=CL. low affinity immunoglobulin gamma Fc region receptor III An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr3 gene or a 1:1 ortholog thereof. PRO:CNA Fcgr3 PRO:DNx A prostanoid receptor that is a translation product of the human PTGDR2 gene or a 1:1 ortholog thereof. The preferred ligand is 11-dehydro-thromboxane B2. This receptor is not closely related to the prostaglandin D2 receptor encoded by PGD2. IUPHARobj:339 PIRSF:PIRSF038608 CD294 G-protein coupled receptor 44 PTGDR2 chemoattractant receptor-homologous molecule expressed on Th2 cells protein CRTH2 DL1R GPR44 PR:000001547 Category=gene. prostaglandin D2 receptor DP2 A prostanoid receptor that is a translation product of the human PTGDR2 gene or a 1:1 ortholog thereof. The preferred ligand is 11-dehydro-thromboxane B2. This receptor is not closely related to the prostaglandin D2 receptor encoded by PGD2. PRO:WCB PTGDR2 PRO:DNx CRTH2 DL1R GPR44 A rhodopsin-like G-protein coupled receptor that is a translation product of the human PTGDR, PTGDR2, PTGER1 to PTGER4, PTGFR, PTGIR, or TBXA2R genes, 1:1 orthologs thereof, or a semi-ortholog thereof. The active form binds prostanoids (prostaglandins and thromboxanes). IUPHARfam:58 PIRSF:PIRSF001962 protein PR:000001549 Category=family. prostanoid receptor A rhodopsin-like G-protein coupled receptor that is a translation product of the human PTGDR, PTGDR2, PTGER1 to PTGER4, PTGFR, PTGIR, or TBXA2R genes, 1:1 orthologs thereof, or a semi-ortholog thereof. The active form binds prostanoids (prostaglandins and thromboxanes). PMID:7938166 PRO:WCB PRO:XQ An N-formyl peptide receptor that is a translation product of the human FPR1 gene or a 1:1 ortholog thereof. The preferred ligand is the peptide fMet-Leu-Phe, a bacterial peptide that acts as a chemoattractant in various pathophysiological conditions. N-formyl peptide receptor IUPHARobj:222 FPR FPR1 N-formylpeptide chemoattractant receptor fMLP receptor protein PR:000001580 Category=gene. Requested by=CL. fMet-Leu-Phe receptor An N-formyl peptide receptor that is a translation product of the human FPR1 gene or a 1:1 ortholog thereof. The preferred ligand is the peptide fMet-Leu-Phe, a bacterial peptide that acts as a chemoattractant in various pathophysiological conditions. InterPro:IPR000826 PRO:WCB N-formyl peptide receptor PRO:DNx FPR1 PRO:DNx A protein with a core domain composition consisting of a Rel homology domain (RHD) (Pfam:PF00554), an IPT/TIG domain (Pfam:PF01833), six copies of the Ankyrin repeat (Pfam:PF00023), a Death domain (Pfam:PF00531) and a C-terminal PEST region. PIRSF:PIRSF036310 protein transcription factor NF-kappa-B PR:000001753 Category=family. transcription factor NF-kappa-B subunit A protein with a core domain composition consisting of a Rel homology domain (RHD) (Pfam:PF00554), an IPT/TIG domain (Pfam:PF01833), six copies of the Ankyrin repeat (Pfam:PF00023), a Death domain (Pfam:PF00531) and a C-terminal PEST region. PRO:JAN A protein with core architecture consisting of one Prominin (Pfam:PF05478) domain. The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and human prominin and prominin-like 1 are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. PANTHER:PTHR22730 PIRSF:PIRSF017831 protein PR:000001785 Category=family. prominin A protein with core architecture consisting of one Prominin (Pfam:PF05478) domain. The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and human prominin and prominin-like 1 are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. InterPro:IPR008795 PMID:11467842 A prominin that is a translation product of the human PROM1 gene or a 1:1 ortholog thereof. CD133 PROM1 antigen AC133 antigen AC133 homolog prominin-like protein 1 protein MSTP061 PROML1 Prom PR:000001786 Category=gene. Requested by=CL. prominin-1 A prominin that is a translation product of the human PROM1 gene or a 1:1 ortholog thereof. PRO:CNA PROM1 PRO:DNx MSTP061 PROML1 Prom A protein that is a translation product of the human CLEC6A gene or a 1:1 ortholog thereof. IUPHARobj:2928 C-type lectin superfamily member 10 CLEC6A DC-associated C-type lectin 2 dectin-2 dendritic cell-associated C-type lectin 2 protein CLECSF10 Clec4n DECTIN2 PR:000001806 Category=gene. Requested by=CL. C-type lectin domain family 6 member A A protein that is a translation product of the human CLEC6A gene or a 1:1 ortholog thereof. PRO:WCB CLEC6A PRO:DNx CLECSF10 Clec4n DECTIN2 A protein that is a translation product of the human CLEC7A gene or a 1:1 ortholog thereof. IUPHARobj:2927 C-type lectin superfamily member 12 CD369 CLEC7A DC-associated C-type lectin 1 beta-glucan receptor dectin-1 dendritic cell-associated C-type lectin 1 protein BGR CLECSF12 DECTIN1 UNQ539/PRO1082 PR:000001807 Category=gene. Requested by=CL. C-type lectin domain family 7 member A A protein that is a translation product of the human CLEC7A gene or a 1:1 ortholog thereof. PRO:WCB CLEC7A PRO:DNx BGR CLECSF12 DECTIN1 UNQ539/PRO1082 A protein that is a translation product of the human CD59 gene, a 1:1 ortholog thereof, or pro-orthologs thereof. This gene is present as a single copy in human and has undergone a lineage-specific duplication in mouse. CD59 antigen has a core architecture consisting of one UPAR/Ly-6 domain (Pfam:PF00021), a small domain of about 70 amino acids and containing 5 conserved disulfide bonds. It is both N- and O-glycosylated and is a GPI-anchored protein that releases soluble forms in some tissues. PIRSF:PIRSF038782 protein PR:000001809 Category=gene. Requested by=CL. Pro-orthology refers to, in this case, after-speciation gene duplication in the non-human species (aka 1:many orthology). CD59-like glycoprotein A protein that is a translation product of the human CD59 gene, a 1:1 ortholog thereof, or pro-orthologs thereof. This gene is present as a single copy in human and has undergone a lineage-specific duplication in mouse. CD59 antigen has a core architecture consisting of one UPAR/Ly-6 domain (Pfam:PF00021), a small domain of about 70 amino acids and containing 5 conserved disulfide bonds. It is both N- and O-glycosylated and is a GPI-anchored protein that releases soluble forms in some tissues. PRO:WCB A protein with core architecture consisting of asignal sequence, 5 Ig-like domains, followed by a transmembrane sequence, followed by a Protein tyrosine kinase domain (Pfam:PF07714). However, only 1-3 of the Ig domains are detected by the Pfam HMMs in most of the sequences. Pfam:PF00047 is most common, but other members of the Ig domain clan, Pfam:PF07679 and Pfam:PF07686 can be identified instead. The fourth Ig domain lacks the disulfide-bonded cysteines. PIRSF:PIRSF000615 protein PR:000001810 Category=family. CSF-1/PDGF receptor-type tyrosine-protein kinase A protein with core architecture consisting of asignal sequence, 5 Ig-like domains, followed by a transmembrane sequence, followed by a Protein tyrosine kinase domain (Pfam:PF07714). However, only 1-3 of the Ig domains are detected by the Pfam HMMs in most of the sequences. Pfam:PF00047 is most common, but other members of the Ig domain clan, Pfam:PF07679 and Pfam:PF07686 can be identified instead. The fourth Ig domain lacks the disulfide-bonded cysteines. PRO:WCB An adhesion G-protein coupled receptor that is a translation product of the human ADGRE1 gene or a 1:1 ortholog thereof. IUPHARobj:182 PIRSF:PIRSF038685 ADGRE1 EGF-like module receptor 1 EGF-like module-containing mucin-like hormone receptor-like 1 EMR1 EMR1 hormone receptor cell surface glycoprotein F4/80 protein Gpf480 TM7LN3 PR:000001813 Category=gene. Requested by=CL. adhesion G protein-coupled receptor E1 An adhesion G-protein coupled receptor that is a translation product of the human ADGRE1 gene or a 1:1 ortholog thereof. PRO:DAN PRO:WCB ADGRE1 PRO:DNx EMR1 PRO:DNx Gpf480 TM7LN3 A protein with core architecture consisting of a signal sequence, a Class II histocompatibility antigen, alpha domain (Pfam:PF00993) and an Immunoglobulin C1-set domain (Pfam:PF07654); these form the extracellular domain and are followed by a single-pass transmembrane region and a small cytoplasmic region. MHCcIIalpha protein PR:000001820 Category=family. Note: There are three major and two minor class II MHC (major histocompatability complex) alpha chain genes in human. Designations for the MHC complex loci are species specific: HLA (human leukocyte antigen) in human, H-2 in mouse. MHC class II loci are characterized by large numbers of allelic variants. In contrast to MHC Class I alpha chain genes, orthologies can be seen between some human and mouse genes. MHC class II alpha chains form heterodimers with MHLC class II beta chains. MHC class II histocompatibility antigen alpha chain A protein with core architecture consisting of a signal sequence, a Class II histocompatibility antigen, alpha domain (Pfam:PF00993) and an Immunoglobulin C1-set domain (Pfam:PF07654); these form the extracellular domain and are followed by a single-pass transmembrane region and a small cytoplasmic region. PRO:WCB Wikipedia:Human_leukocyte_antigen MHCcIIalpha PRO:DAN A protein with core architecture consisting of a signal sequence, one Immunoglobulin V-set domain (Pfam:PF07686), two Immunoglobulin C1-set domains (Pfam:PF07654), a single-pass transmembrane region and a very small cytoplasmic region. PIRSF:PIRSF038063 protein PR:000001832 Category=family. SIRP/SHPS-1 family protein A protein with core architecture consisting of a signal sequence, one Immunoglobulin V-set domain (Pfam:PF07686), two Immunoglobulin C1-set domains (Pfam:PF07654), a single-pass transmembrane region and a very small cytoplasmic region. PRO:WCB A protein that is a translation product of the human SLAMF1 gene or a 1:1 ortholog thereof. PANTHER:PTHR12080:SF1 CD150 CDw150 IPO-3 SLAMF1 protein SLAM PR:000001833 Category=gene. Requested by=CL. SLAM family member 1 A protein that is a translation product of the human SLAMF1 gene or a 1:1 ortholog thereof. PRO:WCB SLAMF1 PRO:DNx SLAM A protein that is a translation product of the human TBX21 gene or a 1:1 ortholog thereof. T-box protein 21 T-cell-specific T-box transcription factor T-bet TBX21 transcription factor TBLYM protein TBET TBLYM PR:000001835 Category=gene. Requested by=CL. T-box transcription factor TBX21 A protein that is a translation product of the human TBX21 gene or a 1:1 ortholog thereof. PRO:WCB TBX21 PRO:DNx TBET TBLYM A protein that is a translation product of the human CD7 gene or a 1:1 ortholog thereof. PIRSF:PIRSF038791 CD7 GP40 T-cell antigen CD7 T-cell leukemia antigen T-cell surface antigen Leu-9 TP41 protein PR:000001836 Category=gene. Requested by=CL. CD7 molecule A protein that is a translation product of the human CD7 gene or a 1:1 ortholog thereof. PRO:WCB CD7 PRO:DNx A protein with core architecture consisting of a signal sequence, an extracellular region with Class I Histocompatibility antigen, domains alpha 1 and alpha two (Pfam:PF00129) and an Immunoglobulin C1-set domain (Pfam:PF07654), a single-pass transmembrane region, and a very short cytoplasmic region. Forms a heterodimer with beta-2 microglobulin. PIRSF:PIRSF038798 CD1 protein PR:000001838 Category=family. T-cell surface glycoprotein CD1 A protein with core architecture consisting of a signal sequence, an extracellular region with Class I Histocompatibility antigen, domains alpha 1 and alpha two (Pfam:PF00129) and an Immunoglobulin C1-set domain (Pfam:PF07654), a single-pass transmembrane region, and a very short cytoplasmic region. Forms a heterodimer with beta-2 microglobulin. PRO:WCB CD1 PRO:DAN A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof. PANTHER:PTHR19331:SF6 CD5 Lyt-1 ly-1 lymphocyte antigen 1 lymphocyte antigen T1/Leu-1 protein LEU1 PR:000001839 Category=gene. Requested by=CL. T-cell surface glycoprotein CD5 A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof. PRO:WCB CD5 PRO:DNx LEU1 A protein that is a translation product of the human CD28 gene or a 1:1 ortholog thereof. IUPHARobj:2863 CD28 TP44 protein PR:000001841 Category=gene. Requested by=CL. T-cell-specific surface glycoprotein CD28 A protein that is a translation product of the human CD28 gene or a 1:1 ortholog thereof. PRO:WCB CD28 PRO:DNx A protein that is a translation product of the human THY1 gene or a 1:1 ortholog thereof. PIRSF:PIRSF038777 CD90 CDw90 THY1 Thy-1 antigen protein Thy-1 PR:000001843 Category=gene. Requested by=CL. Thy-1 membrane glycoprotein A protein that is a translation product of the human THY1 gene or a 1:1 ortholog thereof. PRO:WCB THY1 PRO:DNx Thy-1 A protein that is a translation product of the human ARG1 gene or a 1:1 ortholog thereof. IUPHARobj:1244 ARG1 liver-type arginase type I arginase protein PR:000001844 Category=gene. Requested by=CL. arginase-1 A protein that is a translation product of the human ARG1 gene or a 1:1 ortholog thereof. PRO:WCB ARG1 PRO:DNx A cathepsin-like protease that is a translation product of the human CTSK gene or a 1:1 ortholog thereof. IUPHARobj:2350 CTSK cathepsin O2 protein CTSO CTSO2 cathepsin O cathepsin X PR:000001850 Category=gene. Requested by=CL. cathepsin K A cathepsin-like protease that is a translation product of the human CTSK gene or a 1:1 ortholog thereof. PRO:DAN PRO:WCB CTSK PRO:DNx CTSO CTSO2 A protein that is a translation product of the human CTLA4 gene or a 1:1 ortholog thereof. IUPHARobj:2743 CD152 CTLA-4 CTLA4 cytotoxic T-lymphocyte-associated antigen 4 protein PR:000001852 Category=gene. Requested by=CL. cytotoxic T-lymphocyte protein 4 A protein that is a translation product of the human CTLA4 gene or a 1:1 ortholog thereof. PRO:WCB CTLA4 PRO:DNx A protein that is a translation product of the human VPREB1 gene or a 1:1 ortholog thereof. The gene is recently and independently duplicated in mouse and rabbit, giving rise to very closely related VPREB2 genes in those species. The protein associates with the Ig-mu chain to form a molecular complex that is expressed only on the surface of pre-B-cells. PIRSF:PIRSF038787 CD179 antigen-like family member A CD179a V(pre)B protein VPREB1 VpreB protein protein VPreB1 protein VPREB PR:000001858 Category=gene. Requested by=CL. immunoglobulin iota chain A protein that is a translation product of the human VPREB1 gene or a 1:1 ortholog thereof. The gene is recently and independently duplicated in mouse and rabbit, giving rise to very closely related VPREB2 genes in those species. The protein associates with the Ig-mu chain to form a molecular complex that is expressed only on the surface of pre-B-cells. PRO:WCB VPREB1 PRO:DNx VPREB A protein that is a translation product of the human IGLL1 gene or a 1:1 ortholog thereof. CD179 antigen-like family member B CD179b IGLL1 Ig lambda-5 immunoglobulin omega polypeptide immunoglobulin-related protein 14.1 protein IGL1 Igl-5 PR:000001859 Category=gene. Requested by=CL. immunoglobulin lambda-like polypeptide 1 A protein that is a translation product of the human IGLL1 gene or a 1:1 ortholog thereof. PRO:WCB IGLL1 PRO:DNx IGL1 A protein that is a translation product of the human ICOS gene or a 1:1 ortholog thereof. IUPHARobj:2939 CCLP CD278 CD28 and CTLA-4-like protein CD28-related protein 1 ICOS activation-inducible lymphocyte immunomediatory molecule protein AILIM CRP-1 PR:000001860 Category=gene. Requested by=CL. inducible T-cell costimulator A protein that is a translation product of the human ICOS gene or a 1:1 ortholog thereof. PRO:WCB ICOS PRO:DNx AILIM A protein with core architecture consisting of a large extracellular region containing one Integrin, beta chain domain (Pfam:PF00362), up to four EGF-like domains (Pfam:PF07974), and an Integrin beta tail domain (Pfam:PF07965), followed by a single-pass transmembrane region and a small cytoplasmic region often containing an Integrin beta cytoplasmic domain (Pfam:PF08725). PIRSF:PIRSF002512 protein PR:000001861 Category=family. integrin beta A protein with core architecture consisting of a large extracellular region containing one Integrin, beta chain domain (Pfam:PF00362), up to four EGF-like domains (Pfam:PF07974), and an Integrin beta tail domain (Pfam:PF07965), followed by a single-pass transmembrane region and a small cytoplasmic region often containing an Integrin beta cytoplasmic domain (Pfam:PF08725). PRO:WCB A protein that is a translation product of the human IL3RA gene or a 1:1 ortholog thereof. IUPHARobj:1705 CD123 IL-3 receptor subunit alpha IL-3R subunit alpha IL-3R-alpha IL-3RA IL3RA interleukin-3 receptor class II alpha chain protein IL3R Sut-1 PR:000001865 Category=gene. Requested by=CL. interleukin-3 receptor class 2 alpha chain A protein that is a translation product of the human IL3RA gene or a 1:1 ortholog thereof. PRO:WCB IL3RA PRO:DNx IL3R Sut-1 A protein that is a translation product of the human IL5RA gene or a 1:1 ortholog thereof. IUPHARobj:1706 PIRSF:PIRSF018419 CD125 CDw125 IL-5 receptor subunit alpha IL-5R subunit alpha IL-5R-alpha IL-5RA IL5RA protein IL5R PR:000001867 Category=gene. Requested by=CL. interleukin-5 receptor subunit alpha A protein that is a translation product of the human IL5RA gene or a 1:1 ortholog thereof. PRO:WCB IL5RA PRO:DNx IL5R A protein that is a translation product of the human IL7R gene or a 1:1 ortholog thereof. IUPHARobj:1698 PIRSF:PIRSF001960 CD127 CDw127 IL-7 receptor subunit alpha IL-7R subunit alpha IL-7R-alpha IL-7RA IL7R protein PR:000001869 Category=gene. Requested by=CL. interleukin-7 receptor subunit alpha A protein that is a translation product of the human IL7R gene or a 1:1 ortholog thereof. PRO:WCB IL7R PRO:DNx A protein that is a translation product of the KLRB1 gene or its closely related paralogs (KLRB1A-F). There are lineage-specific expansions in mouse and rat. PIRSF:PIRSF038804 protein PR:000001874 Category=family. Requested by=CL. KLRB1-like protein A protein that is a translation product of the KLRB1 gene or its closely related paralogs (KLRB1A-F). There are lineage-specific expansions in mouse and rat. PRO:WCB A protein that is a translation product of the human SPN gene or a 1:1 ortholog thereof. PIRSF:PIRSF001994 B-cell differentiation antigen LP-3 CD43 GALGP SPN galactoglycoprotein leukocyte sialoglycoprotein ly-48 lymphocyte antigen 48 sialophorin protein PR:000001879 Category=gene. Requested by=CL. leukosialin A protein that is a translation product of the human SPN gene or a 1:1 ortholog thereof. PRO:WCB SPN PRO:DNx A protein that is a translation product of the human FCER2 gene or a 1:1 ortholog thereof. IUPHARobj:2935 PIRSF:PIRSF002426 BLAST-2 C-type lectin domain family 4 member J CD23 FCER2 Fc-epsilon-RII immunoglobulin E-binding factor lymphocyte IgE receptor protein CD23A CLEC4J FCE2 Fcer2a IGEBF PR:000001880 Category=gene. Requested by=CL. low affinity immunoglobulin epsilon Fc receptor A protein that is a translation product of the human FCER2 gene or a 1:1 ortholog thereof. PRO:WCB FCER2 PRO:DNx CD23A CLEC4J FCE2 Fcer2a IGEBF A protein with core architecture consisting of a Lysosome-associated membrane glycoprotein (Pfam:PF01299) domain. It is a single-pass type I membrane protein that shuttles between lysosomes, endosomes, and the plasma membrane. PIRSF:PIRSF002462 protein PR:000001883 Category=family. lysosome-associated membrane protein A protein with core architecture consisting of a Lysosome-associated membrane glycoprotein (Pfam:PF01299) domain. It is a single-pass type I membrane protein that shuttles between lysosomes, endosomes, and the plasma membrane. PRO:WCB A protein that is a translation product of the human MARCO gene or a 1:1 ortholog thereof. MARCO macrophage receptor with collagenous structure scavenger receptor class A member 2 protein SCARA2 PR:000001884 Category=gene. Requested by=CL. macrophage receptor MARCO A protein that is a translation product of the human MARCO gene or a 1:1 ortholog thereof. PRO:WCB MARCO PRO:DNx SCARA2 A protein that is a translation product of the human MSR1 gene or a 1:1 ortholog thereof. CD204 MSR1 SR-A macrophage acetylated LDL receptor I and II scavenger receptor class A member 1 scavenger receptor type A protein SCARA1 Scvr PR:000001885 Category=gene. Requested by=CL. macrophage scavenger receptor types I and II A protein that is a translation product of the human MSR1 gene or a 1:1 ortholog thereof. PRO:WCB MSR1 PRO:DNx SCARA1 Scvr A protein with core architecture consisting of a Peptidase family M1 domain (Pfam:PF01433). PIRSF:PIRSF005502 protein PR:000001888 Category=family. membrane alanyl aminopeptidase-like metallopeptidase A protein with core architecture consisting of a Peptidase family M1 domain (Pfam:PF01433). PRO:WCB A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof. PIRSF:PIRSF002017 CD14 monocyte differentiation antigen CD14 myeloid cell-specific leucine-rich glycoprotein protein PR:000001889 Category=gene. Requested by=CL. CD14 molecule A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof. PRO:WCB CD14 PRO:DNx A protein that is a translation product of the human CD33 gene or a 1:1 ortholog thereof. IUPHARobj:2601 CD33 gp67 myeloid cell surface antigen CD33 sialic acid-binding Ig-like lectin 3 siglec-3 protein SIGLEC3 PR:000001892 Category=gene. Requested by=CL. CD33 molecule A protein that is a translation product of the human CD33 gene or a 1:1 ortholog thereof. PRO:WCB CD33 PRO:DNx SIGLEC3 A protein that is a translation product of the human NCR1 gene or a 1:1 ortholog thereof. NK cell-activating receptor AR-1 CD335 NCR1 NK-p46 NKp46 activating receptor 1 lymphocyte antigen 94 lymphocyte antigen 94 homolog natural killer cell p46-related protein protein LY94 PR:000001893 Category=gene. Requested by=CL. natural cytotoxicity triggering receptor 1 A protein that is a translation product of the human NCR1 gene or a 1:1 ortholog thereof. PRO:WCB NK cell-activating receptor PRO:DNx NCR1 PRO:DNx LY94 A protein that is a translation product of the human NCR2 gene or a 1:1 ortholog thereof. NK cell-activating receptor PIRSF:PIRSF037963 CD336 NCR2 NK-p44 NKp44 lymphocyte antigen 95 homolog natural killer cell p44-related protein protein LY95 PR:000001894 Category=gene. Not found in mouse. natural cytotoxicity triggering receptor 2 A protein that is a translation product of the human NCR2 gene or a 1:1 ortholog thereof. PRO:WCB NK cell-activating receptor PRO:DNx NCR2 PRO:DNx LY95 A protein that is a translation product of the human CD244 gene or a 1:1 ortholog thereof. CD244 NAIL NK cell activation-inducing ligand NK cell type I receptor protein 2B4 NKR2B4 SLAM family member 4 SLAMF4 non-MHC restricted killing associated signaling lymphocytic activation molecule 4 protein 2B4 Nmrk PR:000001896 Category=gene. Requested by=CL. natural killer cell receptor 2B4 A protein that is a translation product of the human CD244 gene or a 1:1 ortholog thereof. PRO:WCB CD244 PRO:DNx 2B4 Nmrk A protein with core architecture consisting of an as yet unnamed domain in the amino-terminal half and a carboxyl-terminal Lectin C-type domain (Pfam:PF00059). PIRSF:PIRSF005558 protein PR:000001897 Category=family. natural killer cell receptor NKG2 A protein with core architecture consisting of an as yet unnamed domain in the amino-terminal half and a carboxyl-terminal Lectin C-type domain (Pfam:PF00059). PRO:WCB A protein that is a translation product of the human MME gene or a 1:1 ortholog thereof. IUPHARobj:1611 PIRSF:PIRSF501074 CALLA CD10 MME NEP SFE atriopeptidase common acute lymphocytic leukemia antigen enkephalinase neutral endopeptidase neutral endopeptidase 24.11 skin fibroblast elastase protein EPN PR:000001898 Category=gene. Requested by=CL. neprilysin A protein that is a translation product of the human MME gene or a 1:1 ortholog thereof. PRO:WCB MME PRO:DNx EPN A protein that is a translation product of the human RORC gene or a 1:1 ortholog thereof. IUPHARobj:600 RAR-related orphan receptor C RORC TOR nuclear receptor RZR-gamma nuclear receptor subfamily 1 group F member 3 retinoid-related orphan receptor-gamma thymus orphan receptor protein NR1F3 RORG RZRG Thor PR:000001902 Category=gene. nuclear receptor ROR-gamma A protein that is a translation product of the human RORC gene or a 1:1 ortholog thereof. PRO:WCB RORC PRO:DNx NR1F3 RORG RZRG Thor A protein that is a translation product of the human PAX5 gene or a 1:1 ortholog thereof. B-cell-specific transcription factor BSAP PAX5 protein Pax-5 PR:000001903 Category=gene. Requested by=CL. paired box protein PAX-5 A protein that is a translation product of the human PAX5 gene or a 1:1 ortholog thereof. PRO:WCB PAX5 PRO:DNx Pax-5 A protein that is a translation product of the human CD36 gene or a 1:1 ortholog thereof. CD36 FAT GPIIIB GPIV PAS IV PAS-4 fatty acid translocase glycoprotein IIIb leukocyte differentiation antigen CD36 platelet collagen receptor platelet glycoprotein IV thrombospondin receptor protein GP3B GP4 PR:000001905 Category=gene. Requested by=CL. platelet glycoprotein 4 A protein that is a translation product of the human CD36 gene or a 1:1 ortholog thereof. PRO:WCB CD36 PRO:DNx GP3B GP4 A protein that is a translation product of the human GP1BA gene or a 1:1 ortholog thereof. PIRSF:PIRSF002493 CD42b GP-Ib alpha GP1BA GPIb-alpha GPIbA antigen CD42b-alpha glycoprotein Ibalpha protein PR:000001907 Category=gene. Requested by=CL. platelet glycoprotein Ib alpha chain A protein that is a translation product of the human GP1BA gene or a 1:1 ortholog thereof. PRO:WCB GP1BA PRO:DNx A protein that is a translation product of the human PDCD1 gene or a 1:1 ortholog thereof. IUPHARobj:2760 PIRSF:PIRSF018380 CD279 PD-1 PDCD1 protein PD-1 protein PD1 PR:000001919 Category=gene. Requested by=CL. programmed cell death protein 1 A protein that is a translation product of the human PDCD1 gene or a 1:1 ortholog thereof. PRO:WCB PDCD1 PRO:DNx PD1 A protein that is a translation product of the human CD163 gene or a 1:1 ortholog thereof. CD163 hemoglobin scavenger receptor protein M130 PR:000001925 Category=gene. Requested by=CL. scavenger receptor cysteine-rich type 1 protein M130 A protein that is a translation product of the human CD163 gene or a 1:1 ortholog thereof. PRO:WCB CD163 PRO:DNx M130 A protein that is a translation product of the human SIGLEC5 gene or a 1:1 ortholog thereof. CD170 CD33 antigen-like 2 OB-BP2 OB-binding protein 2 SIGLEC5 obesity-binding protein 2 sialic acid-binding Ig-like lectin F siglec-5 siglec-F protein CD33L2 OBBP2 Siglecf PR:000001927 Category=gene. Requested by=CL. sialic acid-binding Ig-like lectin 5 A protein that is a translation product of the human SIGLEC5 gene or a 1:1 ortholog thereof. PRO:WCB SIGLEC5 PRO:DNx CD33L2 OBBP2 A protein that is a translation product of the human SIGLEC1 gene or a 1:1 ortholog thereof. CD169 SER SIGLEC1 sheep erythrocyte receptor sialic acid-binding Ig-like lectin 1 siglec-1 protein SN Sa PR:000001931 Category=gene. Requested by=CL. sialoadhesin A protein that is a translation product of the human SIGLEC1 gene or a 1:1 ortholog thereof. PRO:WCB SIGLEC1 PRO:DNx SN Sa A protein that is a translation product of the human CD24 gene or a 1:1 ortholog thereof. CD24 HSA M1/69-J11D heat stable antigen R13-Ag X62 heat stable antigen ly-52 lymphocyte antigen 52 nectadrin small cell lung carcinoma cluster 4 antigen protein CD24A PR:000001932 Category=gene. The mouse ortholog is Cd24a. Mouse protein Cd24b likely also orthologous. Currently it is not in UniProt. Requested by=CL. signal transducer CD24 A protein that is a translation product of the human CD24 gene or a 1:1 ortholog thereof. PRO:WCB CD24 PRO:DNx CD24A A protein that is a translation product of the human SDC1 gene or a 1:1 ortholog thereof. PIRSF:PIRSF015854 CD138 SDC1 SYND1 protein SDC Synd-1 PR:000001935 Category=gene. Requested by=CL. syndecan-1 A protein that is a translation product of the human SDC1 gene or a 1:1 ortholog thereof. PRO:WCB SDC1 PRO:DNx SDC Synd-1 A protein that is a translation product of the human ACP5 gene or a 1:1 ortholog thereof. PIRSF:PIRSF000898 ACP5 TR-AP TrATPase tartrate-resistant acid ATPase type 5 acid phosphatase protein T5ap Trap PR:000001937 Category=gene. Requested by=CL. tartrate-resistant acid phosphatase type 5 A protein that is a translation product of the human ACP5 gene or a 1:1 ortholog thereof. PRO:WCB ACP5 PRO:DNx T5ap Trap A protein with core architecture consisting of a signal sequence, a Lectin C-type domain (Pfam:PF00059), 5 or 6 EGF-like domains (Pfam:PF00008, Pfam:PF09064, or Pfam:PF07645), a transmembrane region, and a small cytoplasmic region (36-51 amino acids). PIRSF:PIRSF001775 protein PR:000001938 Category=family. thrombomodulin-like receptor A protein with core architecture consisting of a signal sequence, a Lectin C-type domain (Pfam:PF00059), 5 or 6 EGF-like domains (Pfam:PF00008, Pfam:PF09064, or Pfam:PF07645), a transmembrane region, and a small cytoplasmic region (36-51 amino acids). PRO:WCB A protein that is a translation product of the human GATA3 gene or a 1:1 ortholog thereof. GATA-binding factor 3 GATA3 protein Gata-3 PR:000001941 Category=gene. Requested by=CL. trans-acting T-cell-specific transcription factor GATA-3 A protein that is a translation product of the human GATA3 gene or a 1:1 ortholog thereof. PRO:WCB GATA3 PRO:DNx Gata-3 A protein that is a translation product of the human SPI1 gene or a 1:1 ortholog thereof. 31 kDa-transforming protein SFFV proviral integration 1 protein SPI1 protein Sfpi-1 Sfpi1 PR:000001944 Category=gene. Requested by=CL. transcription factor PU.1 A protein that is a translation product of the human SPI1 gene or a 1:1 ortholog thereof. PRO:WCB SPI1 PRO:DNx Sfpi-1 Sfpi1 A protein that is a translation product of the human TFRC gene or a 1:1 ortholog thereof. p90 CD71 T9 TFRC TfR TfR1 Trfr protein TR PR:000001945 Category=gene. Requested by=CL. transferrin receptor protein 1 A protein that is a translation product of the human TFRC gene or a 1:1 ortholog thereof. PRO:WCB p90 PRO:DNx TFRC PRO:DNx A protein that is a translation product of the human CD40LG gene or a 1:1 ortholog thereof. TRAP PIRSF:PIRSF016527 CD154 CD40-L CD40LG T-cell antigen Gp39 TNF-related activation protein protein CD40L TNFSF5 PR:000001950 Category=gene. Requested by=CL. tumor necrosis factor ligand superfamily member 5 A protein that is a translation product of the human CD40LG gene or a 1:1 ortholog thereof. PRO:WCB TRAP PRO:DNx CD40LG PRO:DNx CD40L TNFSF5 A protein that is a translation product of the human TNFRSF11A gene or a 1:1 ortholog thereof. IUPHARobj:1881 PIRSF:PIRSF038806 CD265 ODFR TNFRSF11A osteoclast differentiation factor receptor receptor activator of NF-KB protein RANK PR:000001954 Category=gene. Requested by=CL. tumor necrosis factor receptor superfamily member 11A A protein that is a translation product of the human TNFRSF11A gene or a 1:1 ortholog thereof. PRO:WCB TNFRSF11A PRO:DNx RANK A protein that is a translation product of the human CD27 gene or a 1:1 ortholog thereof. IUPHARobj:1876 PIRSF:PIRSF001966 CD27 CD27L receptor T-cell activation antigen CD27 tumor necrosis factor receptor superfamily member 7 protein T14 TNFRSF7 PR:000001963 Category=gene. Requested by=CL. CD27 molecule A protein that is a translation product of the human CD27 gene or a 1:1 ortholog thereof. PRO:WCB CD27 PRO:DNx TNFRSF7 A SIRP/SHPS-1 family protein that is a translation product of the human SIRPA gene or a 1:1 ortholog thereof. p84 IUPHARobj:2942 Bit CD172 antigen-like family member A CD172a MyD-1 antigen SHP substrate 1 SHPS-1 SIRPA Sirp-alpha-1 Sirp-alpha-2 Sirp-alpha-3 brain Ig-like molecule with tyrosine-based activation motifs inhibitory receptor SHPS-1 macrophage fusion receptor signal-regulatory protein alpha-1 signal-regulatory protein alpha-2 signal-regulatory protein alpha-3 protein BIT MFR MYD1 PTPNS1 SHPS1 SIRP PR:000001968 Category=gene. Requested by=CL. tyrosine-protein phosphatase non-receptor type substrate 1 A SIRP/SHPS-1 family protein that is a translation product of the human SIRPA gene or a 1:1 ortholog thereof. PRO:WCB p84 PRO:DNx SIRPA PRO:DNx BIT MFR MYD1 PTPNS1 SHPS1 SIRP A protein that is a translation product of the human PLAUR gene or a 1:1 ortholog thereof. PIRSF:PIRSF002022 CD87 PLAUR U-PAR monocyte activation antigen Mo3 uPAR protein MO3 UPAR PR:000001969 Category=gene. Requested by=CL. urokinase plasminogen activator surface receptor A protein that is a translation product of the human PLAUR gene or a 1:1 ortholog thereof. PRO:WCB PLAUR PRO:DNx MO3 UPAR A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain. PIRSF:PIRSF038502 protein PR:000001971 Category=family. vascular endothelial growth factor receptor A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain. PRO:WCB A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human FLT3 gene or a 1:1 ortholog thereof. IUPHARobj:1807 PIRSF:PIRSF500949 CD135 FL cytokine receptor FLK-2 FLT-3 FLT3 Fms-like tyrosine kinase 3 fetal liver kinase 2 stem cell tyrosine kinase 1 tyrosine-protein kinase FLT3 tyrosine-protein kinase receptor FLT3 tyrosine-protein kinase receptor flk-2 protein FLK2 STK-1 STK1 PR:000002001 Category=gene. Requested by=CL. receptor-type tyrosine-protein kinase FLT3 A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human FLT3 gene or a 1:1 ortholog thereof. PRO:WCB FLT3 PRO:DNx FLK2 STK1 An MHC class II histocompatibility antigen alpha chain that is a translation product of the human HLA-DRA gene or a 1:1 ortholog thereof. H2-IE-alpha MHC class II antigen DRA MHCcIIalpha_DRA protein H2-Ea HLA-DRA HLA-DRA1 PR:000002015 Category=gene. The mouse ortholog is called H2-Ea. MHC class II histocompatibility antigen alpha chain DRA An MHC class II histocompatibility antigen alpha chain that is a translation product of the human HLA-DRA gene or a 1:1 ortholog thereof. PRO:WCB MHCcIIalpha_DRA PRO:DAN HLA-DRA HLA-DRA1 A natural killer cell receptor NKG2 that is a translation product of the human KLRC1 gene or a 1:1 ortholog thereof. IUPHARobj:2849 CD159 antigen-like family member A CD159a KLRC1 NK cell receptor A NKG2-A/B-activating NK receptor protein NKG2A PR:000002023 Category=gene. Requested by=CL. NKG2-A/NKG2-B type II integral membrane protein A natural killer cell receptor NKG2 that is a translation product of the human KLRC1 gene or a 1:1 ortholog thereof. PRO:WCB KLRC1 PRO:DNx NKG2A A T-cell surface glycoprotein CD1 that is a translation product of the human CD1A gene or a 1:1 ortholog thereof. CD1A CD1a T-cell surface antigen T6/Leu-6 Ta1 thymocyte antigen protein PR:000002025 Category=gene. Requested by=CL. T-cell surface glycoprotein CD1a A T-cell surface glycoprotein CD1 that is a translation product of the human CD1A gene or a 1:1 ortholog thereof. PRO:WCB CD1A PRO:DNx A T-cell surface glycoprotein CD1 that is a translation product of the human CD1C gene or a 1:1 ortholog thereof. CD1C CD1c protein PR:000002027 Category=gene. Requested by=CL. T-cell surface glycoprotein CD1c A T-cell surface glycoprotein CD1 that is a translation product of the human CD1C gene or a 1:1 ortholog thereof. PRO:WCB CD1C PRO:DNx A T-cell surface glycoprotein CD1 that is a translation product of the human CD1D gene or a 1:1 ortholog thereof. CD1D CD1d CD1d.1 R3G1 T-cell surface glycoprotein CD1d protein Cd1.1 Cd1d1 PR:000002028 Category=gene. Requested by=CL. antigen-presenting glycoprotein CD1d A T-cell surface glycoprotein CD1 that is a translation product of the human CD1D gene or a 1:1 ortholog thereof. PRO:WCB CD1D PRO:DNx Cd1.1 Cd1d1 A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human PDGFRA gene or a 1:1 ortholog thereof. IUPHARobj:1803 PANTHER:PTHR24416:SF207 PIRSF:PIRSF500950 CD140 antigen-like family member A CD140a CD140a antigen PDGF-R-alpha PDGFR-alpha PDGFRA alpha platelet-derived growth factor receptor platelet-derived growth factor alpha receptor protein PDGFR2 RHEPDGFRA PR:000002030 Category=gene. alpha-type platelet-derived growth factor receptor A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human PDGFRA gene or a 1:1 ortholog thereof. PRO:WCB PDGFRA PRO:DNx PDGFR2 RHEPDGFRA A membrane alanyl aminopeptidase-like metallopeptidase that is a translation product of the human ANPEP gene or a 1:1 ortholog thereof. IUPHARobj:1560 ANPEP AP-M AP-N CD13 alanyl aminopeptidase aminopeptidase M gp150 membrane protein p161 microsomal aminopeptidase myeloid plasma membrane glycoprotein CD13 protein APN Lap-1 Lap1 PEPN PR:000002031 Category=gene. Requested by=CL. aminopeptidase N A membrane alanyl aminopeptidase-like metallopeptidase that is a translation product of the human ANPEP gene or a 1:1 ortholog thereof. PRO:WCB ANPEP PRO:DNx APN Lap-1 Lap1 PEPN A thrombomodulin-like receptor that is a translation product of the human CD93 gene or a 1:1 ortholog thereof. C1q/MBL/SPA receptor C1qR C1qR(p) C1qRp CD93 CDw93 Ly-68 cell surface antigen AA4 complement component 1 q subcomponent receptor 1 lymphocyte antigen 68 matrix-remodeling-associated protein 4 protein Aa4 C1QR1 Ly68 MXRA4 PR:000002037 Category=gene. Requested by=CL. complement component C1q receptor A thrombomodulin-like receptor that is a translation product of the human CD93 gene or a 1:1 ortholog thereof. PRO:WCB CD93 PRO:DNx Aa4 C1QR1 Ly68 MXRA4 A membrane alanyl aminopeptidase-like metallopeptidase that is a translation product of the human ENPEP gene or a 1:1 ortholog thereof. IUPHARobj:1568 AP-A BP-1/6C3 antigen CD249 ENPEP aminopeptidase A differentiation antigen gp160 protein EAP PR:000002039 Category=gene. Requested by=CL. glutamyl aminopeptidase A membrane alanyl aminopeptidase-like metallopeptidase that is a translation product of the human ENPEP gene or a 1:1 ortholog thereof. PRO:WCB ENPEP PRO:DNx A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human CSF1R gene or a 1:1 ortholog thereof. IUPHARobj:1806 PIRSF:PIRSF500947 CD115 CSF-1 receptor CSF-1-R CSF-1R CSF1R M-CSF-R proto-oncogene c-Fms protein Csfmr FMS PR:000002062 Category=gene. Requested by=CL. macrophage colony-stimulating factor 1 receptor A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human CSF1R gene or a 1:1 ortholog thereof. PRO:WCB CSF1R PRO:DNx Csfmr FMS A lysosome-associated membrane protein that is a translation product of the human CD68 gene or a 1:1 ortholog thereof. CD68 protein gp110 PR:000002064 Category=gene. Requested by=CL. macrosialin A lysosome-associated membrane protein that is a translation product of the human CD68 gene or a 1:1 ortholog thereof. PRO:WCB CD68 PRO:DNx A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human KIT gene or a 1:1 ortholog thereof. IUPHARobj:1805 PIRSF:PIRSF500951 CD117 KIT SCFR proto-oncogene c-Kit tyrosine-protein kinase Kit protein Sl PR:000002065 Category=gene. Requested by=CL. mast/stem cell growth factor receptor A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human KIT gene or a 1:1 ortholog thereof. PRO:WCB KIT PRO:DNx Sl A thrombomodulin-like receptor that is a translation product of the human THBD gene or a 1:1 ortholog thereof. BDCA-3 BDCA3 CD141 THBD TM fetomodulin protein THRM PR:000002105 Category=gene. Requested by=CL. thrombomodulin A thrombomodulin-like receptor that is a translation product of the human THBD gene or a 1:1 ortholog thereof. PRO:WCB BDCA-3 Wikipedia:Thrombomodulin BDCA3 Wikipedia:Thrombomodulin THBD PRO:DNx THRM A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof. IUPHARobj:1813 CD309 FLK-1 KDR VEGFR-2 fetal liver kinase 1 kinase NYK kinase insert domain receptor protein-tyrosine kinase receptor flk-1 protein FLK1 VEGFR2 PR:000002112 Category=gene. Requested by=CL. vascular endothelial growth factor receptor 2 A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof. PRO:WCB KDR PRO:DNx FLK1 VEGFR2 A C-type lectin with multiple lectin domains that is a translation product of the human MRC1 gene or a 1:1 ortholog thereof. C-type lectin domain family 13 member D CD206 MMR MRC1 protein C-type lectin domain family 13 member D-like CLEC13D CLEC13DL MRC1L1 macrophage mannose receptor 1-like protein 1 PR:000002972 Category=gene. Requested by=CL. macrophage mannose receptor 1 A C-type lectin with multiple lectin domains that is a translation product of the human MRC1 gene or a 1:1 ortholog thereof. PMID:8297379 PRO:CNA MRC1 PRO:DNx CLEC13D CLEC13DL MRC1L1 A protein that is the translation product of any of the LY6 genes (LY6A-LY6I). PIRSF:PIRSF002021 protein PR:000002976 Category=family. Ly-6-like protein A protein that is the translation product of any of the LY6 genes (LY6A-LY6I). PRO:CNA A KLRB1-like protein that is a translation product of the mouse Klrb1c gene or a 1:1 ortholog thereof. CD161 antigen-like family member C CD161c Klrb1c NK1.1 NKR-P1 40 NKR-P1.9 NKR-P1C ly-55c lymphocyte antigen 55c natural killer cell surface protein P1-40 protein Ly55c Nkrp1c PR:000002977 Category=gene. Requested by=CL. killer cell lectin-like receptor subfamily B member 1C A KLRB1-like protein that is a translation product of the mouse Klrb1c gene or a 1:1 ortholog thereof. PRO:CNA Klrb1c PRO:DNx Ly55c Nkrp1c An Ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof. Ly-6G Ly-6G.1 Ly6g protein PR:000002978 Category=gene. Requested by=CL. lymphocyte antigen 6G An Ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof. PRO:CNA Ly6g PRO:DNx An Ly-6-like protein that is a translation product of the mouse Ly6a gene or a 1:1 ortholog thereof. Ly-6A.2/Ly-6E.1 Ly6a T-cell-activating protein stem cell antigen 1 protein Ly6 SCA-1 TAP PR:000002979 Category=gene. Requested by=CL. lymphocyte antigen 6A-2/6E-1 An Ly-6-like protein that is a translation product of the mouse Ly6a gene or a 1:1 ortholog thereof. PRO:CNA Ly6a PRO:DNx Ly6 An Ly-6-like protein that is a translation product of the mouse Ly6c2 gene or a 1:1 ortholog thereof. Ly-6C2 Ly6c2 protein Ly6c PR:000002980 Category=gene. Requested by=CL. lymphocyte antigen 6C2 An Ly-6-like protein that is a translation product of the mouse Ly6c2 gene or a 1:1 ortholog thereof. PRO:CNA Ly6c2 PRO:DNx Ly6c A protein that is a translation product of the Ly76 gene in mouse. mLy76 ter-119 ter119 protein PR:000002981 Category=organism-gene. Requested by=CL. lymphocyte antigen 76 (mouse) A protein that is a translation product of the Ly76 gene in mouse. PMID:10848813 PRO:DAN mLy76 PRO:DNx A protein that is a component of collagen. Collagens are trimeric molecules in which each chain comprises a repeating Gly-X-Y triplet, in which X and Y can be any residue but are usually proline and hydroxyproline, respectively. This results in a left-handed helix that combines with other two to form a triple-helical structure. protein PR:000003262 Category=family. collagen alpha chain A protein that is a component of collagen. Collagens are trimeric molecules in which each chain comprises a repeating Gly-X-Y triplet, in which X and Y can be any residue but are usually proline and hydroxyproline, respectively. This results in a left-handed helix that combines with other two to form a triple-helical structure. PMID:15788652 PMID:1639194 Pfam:PF01391 A collagen alpha chain that is a translation product of the human COL1A1 or COL1A2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof. protein PR:000003263 Category=family. collagen type I alpha chain A collagen alpha chain that is a translation product of the human COL1A1 or COL1A2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof. PRO:CNA PRO:DAN A collagen type I alpha chain that is a translation product of the human COL1A1 gene or a 1:1 ortholog thereof. COL1A1 alpha-1 type I collagen protein Cola1 PR:000003264 Category=gene. collagen alpha-1(I) chain A collagen type I alpha chain that is a translation product of the human COL1A1 gene or a 1:1 ortholog thereof. PRO:CNA COL1A1 PRO:DNx Cola1 A protein that is a translation product of the human BCL6 gene or a 1:1 ortholog thereof. IUPHARobj:2957 B-cell lymphoma 5 protein BCL-5 BCL-6 BCL6 protein LAZ-3 zinc finger and BTB domain-containing protein 27 zinc finger protein 51 protein BCL5 LAZ3 ZBTB27 ZNF51 PR:000003450 Category=gene. Requested by=CL. B-cell lymphoma 6 protein A protein that is a translation product of the human BCL6 gene or a 1:1 ortholog thereof. PRO:CNA BCL6 PRO:DNx BCL5 LAZ3 ZBTB27 ZNF51 A nuclear receptor ROR-gamma that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P51450-2 or a 1:1 ortholog thereof. RORC/iso:2 protein PR:000003455 Category=sequence. Requested by=CL. nuclear receptor ROR-gamma isoform 2 A nuclear receptor ROR-gamma that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P51450-2 or a 1:1 ortholog thereof. PRO:CNA RORC/iso:2 PRO:DNx A protein that is a translation product of the human RAG1 gene or a 1:1 ortholog thereof. RAG-1 RAG1 RING finger protein 74 protein RNF74 PR:000003457 Category=gene. Requested by=CL. V(D)J recombination-activating protein 1 A protein that is a translation product of the human RAG1 gene or a 1:1 ortholog thereof. PRO:CNA RAG1 PRO:DNx RNF74 A protein that is a translation product of the human RAG2 gene or a 1:1 ortholog thereof. RAG-2 RAG2 protein PR:000003460 Category=gene. Requested by=CL. V(D)J recombination-activating protein 2 A protein that is a translation product of the human RAG2 gene or a 1:1 ortholog thereof. PRO:CNA RAG2 PRO:DNx A T-brain transcription factor that is a translation product of the human EOMES gene or a 1:1 ortholog thereof. EOMES T-box brain protein 2 T-brain-2 TBR-2 protein TBR2 PR:000003463 Category=gene. Requested by=CL. eomesodermin A T-brain transcription factor that is a translation product of the human EOMES gene or a 1:1 ortholog thereof. PMID:10407135 PRO:CNA EOMES PRO:DNx TBR2 A protein that is a translation product of the human PRF1 gene or a 1:1 ortholog thereof. PFP PRF1 cytolysin lymphocyte pore-forming protein protein P1 PR:000003466 Category=gene. Requested by=CL. perforin-1 A protein that is a translation product of the human PRF1 gene or a 1:1 ortholog thereof. PRO:CNA PRF1 PRO:DNx A protein that is a translation product of the human EGR2 gene or a 1:1 ortholog thereof. AT591 E3 SUMO-protein transferase ERG2 EGR-2 EGR2 zinc finger protein Krox-20 protein KROX20 Krox-20 Zfp-25 PR:000003469 Category=gene. Requested by=CL. early growth response protein 2 A protein that is a translation product of the human EGR2 gene or a 1:1 ortholog thereof. PRO:CNA EGR2 PRO:DNx KROX20 Krox-20 Zfp-25 A leukocyte granule-associated proteinase that is a translation product of the human GZMB gene or a 1:1 ortholog thereof. CTLA-1 fragmentin-2 IUPHARobj:2369 C11 CTSGL1 GZMB SECT T-cell serine protease 1-3E cathepsin G-like 1 cytotoxic T-lymphocyte proteinase 2 granzyme-2 lymphocyte protease protein CGL1 CSPB CTLA1 GRB HLP PR:000003499 Category=gene. Requested by=CL. granzyme B A leukocyte granule-associated proteinase that is a translation product of the human GZMB gene or a 1:1 ortholog thereof. PRO:CNA CTLA-1 PRO:DNx fragmentin-2 PRO:DNx GZMB PRO:DNx CGL1 CSPB CTLA1 GRB A protein that is a serine protease of the granules from mast cells, cytotoxic T lymphocytes and/or natural killer cells. Leukocyte granule-associated proteinase is a component of the immune system that protect higher organisms against viral infection and cellular transformation. Members of this class have features that are strongly conserved including: consensus sequences at their N-termini and around the three catalytic residues, activation from zymogenic forms, and conserved disulphide bridges. protein PR:000003505 Category=family. leukocyte granule-associated proteinase A protein that is a serine protease of the granules from mast cells, cytotoxic T lymphocytes and/or natural killer cells. Leukocyte granule-associated proteinase is a component of the immune system that protect higher organisms against viral infection and cellular transformation. Members of this class have features that are strongly conserved including: consensus sequences at their N-termini and around the three catalytic residues, activation from zymogenic forms, and conserved disulphide bridges. PMID:11790262 PMID:7952649 PMID:8929545 A protein that contains one copy of the T-box domain (Pfam:PF00907) and it is involved in the anterior neural specification. Eomes/Tbr1/Tbx21 family protein protein PR:000003506 Category=family. T-brain transcription factor A protein that contains one copy of the T-box domain (Pfam:PF00907) and it is involved in the anterior neural specification. PMID:10750050 PMID:12210112 A protein that is a translation product of the human A4GALT gene or a 1:1 ortholog thereof. alpha-1,4-N-acetylglucosaminyltransferase A4GALT CD77 synthase Gb3 synthase P1/Pk synthase UDP-galactose:beta-D-galactosyl-beta1-R 4-alpha-D-galactosyltransferase alpha-1,4-galactosyltransferase alpha4Gal-T1 globotriaosylceramide synthase protein A14GALT A4GALT1 PR:000003516 Category=gene. Requested by=CL. lactosylceramide 4-alpha-galactosyltransferase A protein that is a translation product of the human A4GALT gene or a 1:1 ortholog thereof. PRO:DNx alpha-1,4-N-acetylglucosaminyltransferase PRO:DNx A4GALT PRO:DNx A14GALT A4GALT1 A protein that is a translation product of the human CCK gene or a 1:1 ortholog thereof. CCK protein PR:000005110 Category=gene. cholecystokinin A protein that is a translation product of the human CCK gene or a 1:1 ortholog thereof. PRO:DNx CCK PRO:DNx A tetraspanin that is a translation product of the human CD9 gene or a 1:1 ortholog thereof. p24 5H9 antigen CD9 CD9 antigen MRP-1 cell growth-inhibiting gene 2 protein leukocyte antigen MIC3 motility-related protein tetraspanin-29 tspan-29 protein GIG2 MIC3 TSPAN29 PR:000005178 Category=gene. Requested by=CL. CD9 molecule A tetraspanin that is a translation product of the human CD9 gene or a 1:1 ortholog thereof. PRO:DNx p24 PRO:DNx CD9 PRO:DNx GIG2 MIC3 TSPAN29 A protein that is a translation product of the human CEBPA gene or a 1:1 ortholog thereof. C/EBP alpha CEBPA protein CEBP PR:000005307 Category=gene. Requested by=CL. CCAAT/enhancer-binding protein alpha A protein that is a translation product of the human CEBPA gene or a 1:1 ortholog thereof. PRO:DNx CEBPA PRO:DNx CEBP A protein that is a translation product of the human CEBPE gene or a 1:1 ortholog thereof. C/EBP epsilon CEBPE protein Gm294 PR:000005310 Category=gene. Requested by=CL. CCAAT/enhancer-binding protein epsilon A protein that is a translation product of the human CEBPE gene or a 1:1 ortholog thereof. PRO:DNx CEBPE PRO:DNx Gm294 A nicotinic acetylcholine receptor protein that is a translation product of the human CHRNA7 gene or a 1:1 ortholog thereof. IUPHARobj:468 CHRNA7 protein Acra7 NACHRA7 PR:000005460 Category=gene. neuronal acetylcholine receptor subunit alpha-7 A nicotinic acetylcholine receptor protein that is a translation product of the human CHRNA7 gene or a 1:1 ortholog thereof. PRO:DNx CHRNA7 PRO:DNx Acra7 NACHRA7 A protein that is a translation product of the mouse Cd200r3 gene or a 1:1 ortholog thereof. CD200 cell surface glycoprotein receptor-like 3 CD200 cell surface glycoprotein receptor-like b CD200 receptor-like 3 CD200RLb Cd200r3 cell surface glycoprotein OX2 receptor 3 protein PR:000006169 Category=gene. Requested by=CL. cell surface glycoprotein CD200 receptor 3 A protein that is a translation product of the mouse Cd200r3 gene or a 1:1 ortholog thereof. PRO:DNx Cd200r3 PRO:DNx A protein that is a translation product of the mouse Cd209b gene or a 1:1 ortholog thereof. Cd209b DC-SIGN-related protein 1 DC-SIGNR1 OtB7 protein PR:000006172 Category=gene. Requested by=CL. CD209 molecule-like protein B A protein that is a translation product of the mouse Cd209b gene or a 1:1 ortholog thereof. PRO:DNx Cd209b PRO:DNx A protein that is a translation product of the human DNTT gene or a 1:1 ortholog thereof. DNTT TDT terminal addition enzyme terminal deoxynucleotidyltransferase terminal transferase protein PR:000006611 Category=gene. Requested by=CL. DNA nucleotidylexotransferase A protein that is a translation product of the human DNTT gene or a 1:1 ortholog thereof. PRO:DNx DNTT PRO:DNx A protein that is a translation product of the human EPX gene or a 1:1 ortholog thereof. EPO EPX protein EPER EPP PR:000007152 Category=gene. Requested by=CL. eosinophil peroxidase A protein that is a translation product of the human EPX gene or a 1:1 ortholog thereof. PRO:DNx EPO PRO:DNx EPX PRO:DNx EPER EPP An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the human FCER1A gene or a 1:1 ortholog thereof. IUPHARobj:2933 FCER1A Fc-epsilon RI-alpha IgE Fc receptor subunit alpha protein FCE1A FcERI PR:000007431 Category=gene. Requested by=CL. high affinity immunoglobulin epsilon receptor subunit alpha An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the human FCER1A gene or a 1:1 ortholog thereof. PRO:DNx FCER1A PRO:DNx FCE1A A protein that is a translation product of the human FOS gene or a 1:1 ortholog thereof. FOS G0/G1 switch regulatory protein 7 cellular oncogene fos proto-oncogene protein c-fos protein G0S7 PR:000007597 Category=gene. Requested by=CL. proto-oncogene c-Fos A protein that is a translation product of the human FOS gene or a 1:1 ortholog thereof. PRO:DNx FOS PRO:DNx G0S7 A protein that is a translation product of the human GATA1 gene or a 1:1 ortholog thereof. Eryf1 GATA-1 GATA-binding factor 1 GATA1 NF-E1 DNA-binding protein protein ERYF1 GF-1 GF1 PR:000007857 Category=gene. Requested by=CL. erythroid transcription factor A protein that is a translation product of the human GATA1 gene or a 1:1 ortholog thereof. PRO:DNx GATA1 PRO:DNx ERYF1 GF1 A protein that is a translation product of the human GATA2 gene or a 1:1 ortholog thereof. GATA-binding protein 2 GATA2 protein PR:000007858 Category=gene. Requested by=CL. endothelial transcription factor GATA-2 A protein that is a translation product of the human GATA2 gene or a 1:1 ortholog thereof. PRO:DNx GATA2 PRO:DNx A protein that is a translation product of the human GFAP gene or a 1:1 ortholog thereof. GFAP protein PR:000007939 Category=gene. Requested by=CL. glial fibrillary acidic protein A protein that is a translation product of the human GFAP gene or a 1:1 ortholog thereof. PRO:DNx GFAP PRO:DNx A hemoglobin subunit that is a translation product of the human HBB gene, a 1:1 ortholog thereof, or pro-orthologs thereof. b-globin protein PR:000008457 Category=gene. beta-globin A hemoglobin subunit that is a translation product of the human HBB gene, a 1:1 ortholog thereof, or pro-orthologs thereof. PRO:DAN b-globin PRO:DNx A hemoglobin subunit that is a translation product of the human HBZ gene or a 1:1 ortholog thereof. HBAZ HBZ alpha-like embryonic globin chain x hemoglobin zeta chain zeta-globin protein HBZ2 Hba-x Hbz1 PR:000008467 Category=gene. Requested by=CL. hemoglobin subunit zeta A hemoglobin subunit that is a translation product of the human HBZ gene or a 1:1 ortholog thereof. PRO:DNx HBZ PRO:DNx HBZ2 Hba-x Hbz1 A beta-globin that is a translation product of the mouse Hbb-b1 gene or a 1:1 ortholog thereof. Hbb-b1 beta-1-globin hemoglobin beta-1 chain hemoglobin beta-major chain protein PR:000008857 Category=gene. Requested by=CL. hemoglobin subunit beta-1 A beta-globin that is a translation product of the mouse Hbb-b1 gene or a 1:1 ortholog thereof. PRO:DNx Hbb-b1 PRO:DNx A protein that is a translation product of the human IL17RB gene or a 1:1 ortholog thereof. IUPHARobj:1739 IL-17 receptor B IL-17 receptor homolog 1 IL-17B receptor IL-17ER IL-17RB IL-17Rh1 IL17RB IL17Rh1 cytokine receptor-like 4 interleukin-17B receptor protein CRL4 EVI27 IL17BR UNQ2501/PRO19612 PR:000008982 Category=gene. Requested by=CL. interleukin-17 receptor B A protein that is a translation product of the human IL17RB gene or a 1:1 ortholog thereof. PRO:DNx IL17RB PRO:DNx CRL4 EVI27 IL17BR UNQ2501/PRO19612 A protein that is a translation product of the human IL1RL1 gene or a 1:1 ortholog thereof. IUPHARobj:1735 IL1RL1 lymphocyte antigen 84 protein ST2 protein T1 protein DER4 Ly84 ST2 Ste2 T1 PR:000008994 Category=gene. Requested by=CL. interleukin-1 receptor-like 1 A protein that is a translation product of the human IL1RL1 gene or a 1:1 ortholog thereof. PRO:DNx IL1RL1 PRO:DNx DER4 Ly84 ST2 Ste2 T1 An integrin alpha lacking A domain that is a translation product of the human ITGA2B gene or a 1:1 ortholog thereof. IUPHARobj:2441 CD41 GPIIb GPalpha IIb ITGA2B platelet membrane glycoprotein IIb protein GP2B ITGAB PR:000009127 Category=gene. Requested by=CL. integrin alpha-IIb An integrin alpha lacking A domain that is a translation product of the human ITGA2B gene or a 1:1 ortholog thereof. PRO:DNx ITGA2B PRO:DNx GP2B ITGAB An integrin alpha lacking A domain that is a translation product of the human ITGA4 gene or a 1:1 ortholog thereof. IUPHARobj:2443 CD49 antigen-like family member D CD49d ITGA4 LPAM subunit alpha VLA-4 subunit alpha integrin alpha-IV lymphocyte Peyer patch adhesion molecules subunit alpha protein CD49D PR:000009129 Category=gene. Requested by=CL. integrin alpha-4 An integrin alpha lacking A domain that is a translation product of the human ITGA4 gene or a 1:1 ortholog thereof. PRO:DNx ITGA4 PRO:DNx CD49D An integrin beta that is a translation product of the human ITGB7 gene or a 1:1 ortholog thereof. IUPHARobj:2461 Gut homing receptor beta subunit ITGB7 M290 IEL antigen integrin beta-P protein PR:000009143 Category=gene. Requested by=CL. integrin beta-7 An integrin beta that is a translation product of the human ITGB7 gene or a 1:1 ortholog thereof. PRO:DNx ITGB7 PRO:DNx A protein that is a translation product of the human KLRG1 gene or a 1:1 ortholog thereof. C-type lectin domain family 15 member A ITIM-containing receptor MAFA-L KLRG1 MAFA-like receptor mast cell function-associated antigen mast cell function-associated antigen 2F1 protein CLEC15A MAFA MAFAL PR:000009426 Category=gene. killer cell lectin-like receptor subfamily G member 1 A protein that is a translation product of the human KLRG1 gene or a 1:1 ortholog thereof. PRO:DNx KLRG1 PRO:DNx CLEC15A MAFA MAFAL A protein that is a translation product of the mouse Klra1 gene or a 1:1 ortholog thereof. Klra1 T lymphocyte antigen A1 ly-49a lymphocyte antigen 49a protein Ly-49 Ly49 Ly49A PR:000009616 Category=gene. Requested by=CL. T-cell surface glycoprotein YE1/48 A protein that is a translation product of the mouse Klra1 gene or a 1:1 ortholog thereof. PRO:DNx Klra1 PRO:DNx Ly-49 Ly49 Ly49A A protein that is a translation product of the mouse Klra3 gene or a 1:1 ortholog thereof. 5E6 Klra3 T-cell surface glycoprotein Ly-49C ly-49c lymphocyte antigen 49c protein Ly49C PR:000009618 Category=gene. Requested by=CL. killer cell lectin-like receptor 3 A protein that is a translation product of the mouse Klra3 gene or a 1:1 ortholog thereof. PRO:DNx Klra3 PRO:DNx Ly49C A protein that is a translation product of the mouse Klra4 gene or a 1:1 ortholog thereof. Klra4 T-cell surface glycoprotein Ly-49D ly-49d lymphocyte antigen 49d protein Ly49-d Ly49d PR:000009619 Category=gene. Requested by=CL. killer cell lectin-like receptor 4 A protein that is a translation product of the mouse Klra4 gene or a 1:1 ortholog thereof. PRO:DNx Klra4 PRO:DNx Ly49-d Ly49d A protein that is a translation product of the mouse Klra8 gene or a 1:1 ortholog thereof. Klra8 T-cell surface glycoprotein Ly-49H ly-49h lymphocyte antigen 49h protein Ly49-h Ly49H PR:000009623 Category=gene. Requested by=CL. killer cell lectin-like receptor 8 A protein that is a translation product of the mouse Klra8 gene or a 1:1 ortholog thereof. PRO:DNx Klra8 PRO:DNx Ly49-h Ly49H A protein that is a translation product of the human LCN2 gene or a 1:1 ortholog thereof. p25 25 kDa alpha-2-microglobulin-related subunit of MMP-9 LCN2 NGAL SV-40-induced 24P3 protein lipocalin-2 oncogene 24p3 protein HNL PR:000009725 Category=gene. Requested by=CL. neutrophil gelatinase-associated lipocalin A protein that is a translation product of the human LCN2 gene or a 1:1 ortholog thereof. PRO:DNx p25 PRO:DNx LCN2 PRO:DNx HNL A protein that is a translation product of the human LGALS1 gene or a 1:1 ortholog thereof. 14 kDa laminin-binding protein 14 kDa lectin HBL HLBP14 HPL LGALS1 S-Lac lectin 1 beta-galactoside-binding lectin L-14-I gal-1 galaptin lactose-binding lectin 1 lectin galactoside-binding soluble 1 putative MAPK-activating protein PM12 protein Gbp PR:000009766 Category=gene. Requested by=CL. galectin-1 A protein that is a translation product of the human LGALS1 gene or a 1:1 ortholog thereof. PRO:DNx LGALS1 PRO:DNx Gbp A protein that is a translation product of the human LHX3 gene or a 1:1 ortholog thereof. LHX3 LIM homeobox protein 3 homeobox protein LIM-3 homeobox protein P-LIM protein Lim-3 Lim3 Plim PR:000009793 Category=gene. LIM/homeobox protein Lhx3 A protein that is a translation product of the human LHX3 gene or a 1:1 ortholog thereof. PRO:DNx LHX3 PRO:DNx Lim-3 Lim3 Plim A protein that is a translation product of the human LTF gene or a 1:1 ortholog thereof. LTF lactoferrin talalactoferrin protein GIG12 LF PR:000009978 Category=gene. Requested by=CL. lactotransferrin A protein that is a translation product of the human LTF gene or a 1:1 ortholog thereof. PRO:DNx LTF PRO:DNx GIG12 LF A protein that is a translation product of the human LUM gene or a 1:1 ortholog thereof. KSPG lumican LUM keratan sulfate proteoglycan lumican protein LDC Lcn SLRR2D PR:000009981 Category=gene. lumican A protein that is a translation product of the human LUM gene or a 1:1 ortholog thereof. PRO:DNx LUM PRO:DNx LDC Lcn SLRR2D A protein that is a translation product of the human MEIS2 gene or a 1:1 ortholog thereof. MEIS2 Meis1-related protein 1 protein MRG1 Stra10 PR:000010317 Category=gene. homeobox protein Meis2 A protein that is a translation product of the human MEIS2 gene or a 1:1 ortholog thereof. PRO:DNx MEIS2 PRO:DNx MRG1 Stra10 A protein that is a translation product of the human MERTK gene or a 1:1 ortholog thereof. IUPHARobj:1837 MERTK proto-oncogene c-Mer proto-oncogene tyrosine-protein kinase MER receptor tyrosine kinase MerTK protein MER PR:000010329 Category=gene. Requested by=CL. tyrosine-protein kinase Mer A protein that is a translation product of the human MERTK gene or a 1:1 ortholog thereof. PRO:DNx MERTK PRO:DNx MER A protein that is a translation product of the human MPO gene or a 1:1 ortholog thereof. IUPHARobj:2789 MPO protein PR:000010543 Category=gene. Requested by=CL. myeloperoxidase A protein that is a translation product of the human MPO gene or a 1:1 ortholog thereof. PRO:DNx MPO PRO:DNx A protein that is a translation product of the human MYB gene or a 1:1 ortholog thereof. MYB proto-oncogene c-Myb protein PR:000010799 Category=gene. Requested by=CL. myb proto-oncogene protein A protein that is a translation product of the human MYB gene or a 1:1 ortholog thereof. PRO:DNx MYB PRO:DNx A protein that is a translation product of the human NETO1 gene or a 1:1 ortholog thereof. NETO1 brain-specific transmembrane protein containing 2 CUB and 1 LDL-receptor class A domains protein 1 protein BTCL1 PR:000011143 Category=gene. neuropilin and tolloid-like protein 1 A protein that is a translation product of the human NETO1 gene or a 1:1 ortholog thereof. PRO:DNx NETO1 PRO:DNx BTCL1 A transcription factor NF-kappa-B subunit that is a translation product of the human NFKB2 gene or a 1:1 ortholog thereof. DNA-binding factor KBF2 H2TF1 NFKB2 lymphocyte translocation chromosome 10 protein lyt10 nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 oncogene Lyt-10 protein LYT10 PR:000011178 Category=gene. Requested by=CL. nuclear factor NF-kappa-B p100 subunit A transcription factor NF-kappa-B subunit that is a translation product of the human NFKB2 gene or a 1:1 ortholog thereof. PRO:DNx NFKB2 PRO:DNx LYT10 A protein that is a translation product of the human NTNG1 gene or a 1:1 ortholog thereof. NTNG1 laminet-1 protein KIAA0976 LMNT1 UNQ571/PRO1133 PR:000011467 Category=gene. netrin-G1 A protein that is a translation product of the human NTNG1 gene or a 1:1 ortholog thereof. PRO:DNx NTNG1 PRO:DNx KIAA0976 LMNT1 UNQ571/PRO1133 A protein that is a translation product of the human PRG2 gene or a 1:1 ortholog thereof. BMPG PRG2 proteoglycan 2 protein MBP Mbp-1 PR:000013206 Category=gene. bone marrow proteoglycan A protein that is a translation product of the human PRG2 gene or a 1:1 ortholog thereof. PRO:DNx PRG2 PRO:DNx MBP Mbp-1 A protein that is a translation product of the human PVALB gene or a 1:1 ortholog thereof. PVALB protein Pva PR:000013502 Category=gene. parvalbumin alpha A protein that is a translation product of the human PVALB gene or a 1:1 ortholog thereof. PRO:DNx PVALB PRO:DNx Pva A protein that is a translation product of the human RNASE2 gene or a 1:1 ortholog thereof. MR-4 RNASE2 RNase 2 RNase UpI-2 eosinophil cationic-type ribonuclease 4 eosinophil-derived neurotoxin ribonuclease 2 ribonuclease US protein EDN Ear4 RNS2 PR:000014046 Category=gene. Requested by=CL. non-secretory ribonuclease A protein that is a translation product of the human RNASE2 gene or a 1:1 ortholog thereof. PRO:DNx RNASE2 PRO:DNx EDN RNS2 A protein that is a translation product of the human RNASE3 gene or a 1:1 ortholog thereof. ECP RNASE3 RNase 3 protein RNS3 ribonuclease 3 PR:000014047 Category=gene. Requested by=CL. eosinophil cationic protein A protein that is a translation product of the human RNASE3 gene or a 1:1 ortholog thereof. PRO:DNx RNASE3 PRO:DNx RNS3 A protein that is a translation product of the human RUNX1 gene or a 1:1 ortholog thereof. CBF-alpha-2 PEA2-alpha B PEBP2-alpha B RUNX1 SL3-3 enhancer factor 1 alpha B subunit SL3/AKV core-binding factor alpha B subunit acute myeloid leukemia 1 protein core-binding factor subunit alpha-2 oncogene AML-1 polyomavirus enhancer-binding protein 2 alpha B subunit protein AML1 CBFA2 Pebp2ab PR:000014362 Category=gene. Requested by=CL. runt-related transcription factor 1 A protein that is a translation product of the human RUNX1 gene or a 1:1 ortholog thereof. PRO:DNx RUNX1 PRO:DNx AML1 CBFA2 Pebp2ab A protein that is a translation product of the human SNCG gene or a 1:1 ortholog thereof. SNCG SR breast cancer-specific gene 1 protein persyn synoretin protein BCSG1 PERSYN PRSN PR:000015325 Category=gene. gamma-synuclein A protein that is a translation product of the human SNCG gene or a 1:1 ortholog thereof. PRO:DNx SNCG PRO:DNx BCSG1 PERSYN PRSN A protein that is a translation product of the human SST gene or a 1:1 ortholog thereof. SST growth hormone release-inhibiting factor protein Smst PR:000015665 Category=gene. somatostatin A protein that is a translation product of the human SST gene or a 1:1 ortholog thereof. PRO:DNx SST PRO:DNx Smst A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof. T-cell leukemia/lymphoma protein 5 TAL-1 TAL1 bHLHa17 class A basic helix-loop-helix protein 17 stem cell protein protein BHLHA17 SCL TCL5 PR:000016043 Category=gene. Requested by=CL. T-cell acute lymphocytic leukemia protein 1 A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof. PRO:DNx TAL1 PRO:DNx BHLHA17 SCL TCL5 A protein that is a translation product of the human TMED1 gene or a 1:1 ortholog thereof. TMED1 interleukin-1 receptor-like 1 ligand p24 family protein gamma-1 p24gamma1 putative T1/ST2 receptor-binding protein protein IL1RL1L IL1RL1LG PR:000016401 Category=gene. Requested by=CL. transmembrane emp24 domain-containing protein 1 A protein that is a translation product of the human TMED1 gene or a 1:1 ortholog thereof. PRO:DNx TMED1 PRO:DNx IL1RL1L IL1RL1LG A protein that is a translation product of the human VIP gene or a 1:1 ortholog thereof. VIP vasoactive intestinal peptides vasoactive intestinal polypeptides vasoactive intestinal polypeptides precursor protein PR:000017299 Category=gene. VIP peptides A protein that is a translation product of the human VIP gene or a 1:1 ortholog thereof. PRO:DNx VIP PRO:DNx vasoactive intestinal peptides PRO:DNx vasoactive intestinal polypeptides PRO:DNx An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. peptide polypeptide protein PR:000018263 Category=external. amino acid chain An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. PRO:DAN PRO:JSG peptide PRO:DAN polypeptide PRO:DAN A CD19 molecule that has had the signal peptide removed. CD19/SigPep- protein PR:000018300 Category=modification. CD19 molecule, signal peptide removed form A CD19 molecule that has had the signal peptide removed. PRO:DNx CD19/SigPep- PRO:DNx A CD34 molecule that has had the signal peptide removed. CD34/SigPep- protein PR:000018302 Category=modification. CD34 molecule, signal peptide removed form A CD34 molecule that has had the signal peptide removed. PRO:DNx CD34/SigPep- PRO:DNx A CD4 molecule that has had the signal peptide removed. CD4/SigPep- protein PR:000018304 Category=modification. CD4 molecule, signal peptide removed form A CD4 molecule that has had the signal peptide removed. PRO:DNx CD4/SigPep- PRO:DNx A receptor-type tyrosine-protein phosphatase C that has had the signal peptide removed. PTPRC/SigPep- protein PR:000018306 Category=modification. receptor-type tyrosine-protein phosphatase C, signal peptide removed form A receptor-type tyrosine-protein phosphatase C that has had the signal peptide removed. PRO:DNx PTPRC/SigPep- PRO:DNx An integrin alpha-2 that has had the signal peptide removed. ITGA2/SigPep- protein PR:000018308 Category=modification. integrin alpha-2, signal peptide removed form An integrin alpha-2 that has had the signal peptide removed. PRO:DNx ITGA2/SigPep- PRO:DNx An integrin alpha-E that has had the signal peptide removed. ITGAE/SigPep- protein PR:000018310 Category=modification. integrin alpha-E, signal peptide removed form An integrin alpha-E that has had the signal peptide removed. PRO:DNx ITGAE/SigPep- PRO:DNx An integrin alpha-M that has had the signal peptide removed. ITGAM/SigPep- protein PR:000018315 Category=modification. integrin alpha-M, signal peptide removed form An integrin alpha-M that has had the signal peptide removed. PRO:DNx ITGAM/SigPep- PRO:DNx An integrin alpha-X that has had the signal peptide removed. ITGAX/SigPep- protein PR:000018317 Category=modification. integrin alpha-X, signal peptide removed form An integrin alpha-X that has had the signal peptide removed. PRO:DNx ITGAX/SigPep- PRO:DNx A CD3 epsilon that has had the signal peptide removed. CD3E/SigPep- protein PR:000018321 Category=modification. CD3 epsilon, signal peptide removed form A CD3 epsilon that has had the signal peptide removed. PRO:DNx CD3E/SigPep- PRO:DNx A neural cell adhesion molecule 1 that has had the signal peptide removed. NCAM1/SigPep- protein PR:000018325 Category=modification. neural cell adhesion molecule 1, signal peptide removed form A neural cell adhesion molecule 1 that has had the signal peptide removed. PRO:DNx NCAM1/SigPep- PRO:DNx A lymphocyte antigen 75 that has had the signal peptide removed. LY75/SigPep- protein PR:000018327 Category=modification. lymphocyte antigen 75, signal peptide removed form A lymphocyte antigen 75 that has had the signal peptide removed. PRO:DNx LY75/SigPep- PRO:DNx A CD2 molecule that has had the signal peptide removed. CD2/SigPep- protein PR:000018333 Category=modification. CD2 molecule, signal peptide removed form A CD2 molecule that has had the signal peptide removed. PRO:DNx CD2/SigPep- PRO:DNx A T-cell surface glycoprotein CD8 alpha chain that has had the signal peptide removed. CD8A/SigPep- protein PR:000018335 Category=modification. T-cell surface glycoprotein CD8 alpha chain, signal peptide removed form A T-cell surface glycoprotein CD8 alpha chain that has had the signal peptide removed. PRO:DNx CD8A/SigPep- PRO:DNx A T-cell surface glycoprotein CD8 beta chain that has had the signal peptide removed. CD8B/SigPep- protein PR:000018337 Category=modification. T-cell surface glycoprotein CD8 beta chain, signal peptide removed form A T-cell surface glycoprotein CD8 beta chain that has had the signal peptide removed. PRO:DNx CD8B/SigPep- PRO:DNx A CD48 molecule that has had the signal peptide removed. CD48/SigPep- protein PR:000018380 Category=modification. CD48 molecule, signal peptide removed form A CD48 molecule that has had the signal peptide removed. PRO:DNx CD48/SigPep- PRO:DNx A CD83 molecule that has had the signal peptide removed. CD83/SigPep- protein PR:000018383 Category=modification. CD83 molecule, signal peptide removed form A CD83 molecule that has had the signal peptide removed. PRO:DNx CD83/SigPep- PRO:DNx An L-selectin that has had the signal peptide removed. SELL/SigPep- protein PR:000018389 Category=modification. L-selectin, signal peptide removed form An L-selectin that has had the signal peptide removed. PRO:DNx SELL/SigPep- PRO:DNx A SLAM family member 5 that has had the signal peptide removed. CD84/SigPep- protein PR:000018392 Category=modification. SLAM family member 5, signal peptide removed form A SLAM family member 5 that has had the signal peptide removed. PRO:DNx CD84/SigPep- PRO:DNx A carcinoembryonic antigen-related cell adhesion molecule 8 that has had the signal peptide removed. CEACAM8/SigPep- protein PR:000018405 Category=modification. carcinoembryonic antigen-related cell adhesion molecule 8, signal peptide removed form A carcinoembryonic antigen-related cell adhesion molecule 8 that has had the signal peptide removed. PRO:DNx CEACAM8/SigPep- PRO:DNx A complement receptor type 1 that has had the signal peptide removed. CR1/SigPep- protein PR:000018413 Category=modification. complement receptor type 1, signal peptide removed form A complement receptor type 1 that has had the signal peptide removed. PRO:DNx CR1/SigPep- PRO:DNx A complement receptor type 2 that has had the signal peptide removed. CR2/SigPep- protein PR:000018415 Category=modification. complement receptor type 2, signal peptide removed form A complement receptor type 2 that has had the signal peptide removed. PRO:DNx CR2/SigPep- PRO:DNx An endoglin that has had the signal peptide removed. ENG/SigPep- protein PR:000018420 Category=modification. endoglin, signal peptide removed form An endoglin that has had the signal peptide removed. PRO:DNx ENG/SigPep- PRO:DNx An interleukin-2 receptor subunit alpha that has had the signal peptide removed. IL2RA/SigPep- protein PR:000018444 Category=modification. interleukin-2 receptor subunit alpha, signal peptide removed form An interleukin-2 receptor subunit alpha that has had the signal peptide removed. PRO:DNx IL2RA/SigPep- PRO:DNx An interleukin-2 receptor subunit beta that has had the signal peptide removed. IL2RB/SigPep- protein PR:000018446 Category=modification. interleukin-2 receptor subunit beta, signal peptide removed form An interleukin-2 receptor subunit beta that has had the signal peptide removed. PRO:DNx IL2RB/SigPep- PRO:DNx A CD80 molecule that has had the signal peptide removed. CD80/SigPep- protein PR:000018477 Category=modification. CD80 molecule, signal peptide removed form A CD80 molecule that has had the signal peptide removed. PRO:DNx CD80/SigPep- PRO:DNx A glycophorin-A that has had the signal peptide removed. GYPA/SigPep- protein PR:000018492 Category=modification. glycophorin-A, signal peptide removed form A glycophorin-A that has had the signal peptide removed. PRO:DNx GYPA/SigPep- PRO:DNx A high affinity immunoglobulin gamma Fc receptor I that has had the signal peptide removed. FCGR1A/SigPep- protein PR:000018496 Category=modification. high affinity immunoglobulin gamma Fc receptor I, signal peptide removed form A high affinity immunoglobulin gamma Fc receptor I that has had the signal peptide removed. PRO:DNx FCGR1A/SigPep- PRO:DNx A low affinity immunoglobulin gamma Fc region receptor II that has had the signal peptide removed. Fcgr2/SigPep- protein PR:000018508 Category=modification. low affinity immunoglobulin gamma Fc region receptor II, signal peptide removed form A low affinity immunoglobulin gamma Fc region receptor II that has had the signal peptide removed. PRO:DNx Fcgr2/SigPep- PRO:DNx A CD7 molecule that has had the signal peptide removed. CD7/SigPep- protein PR:000018537 Category=modification. CD7 molecule, signal peptide removed form A CD7 molecule that has had the signal peptide removed. PRO:DNx CD7/SigPep- PRO:DNx A T-cell surface glycoprotein CD5 that has had the signal peptide removed. CD5/SigPep- protein PR:000018539 Category=modification. T-cell surface glycoprotein CD5, signal peptide removed form A T-cell surface glycoprotein CD5 that has had the signal peptide removed. PRO:DNx CD5/SigPep- PRO:DNx A T-cell-specific surface glycoprotein CD28 that has had the signal peptide removed. CD28/SigPep- protein PR:000018541 Category=modification. T-cell-specific surface glycoprotein CD28, signal peptide removed form A T-cell-specific surface glycoprotein CD28 that has had the signal peptide removed. PRO:DNx CD28/SigPep- PRO:DNx A Thy-1 membrane glycoprotein that has had the signal peptide removed. THY1/SigPep- protein PR:000018545 Category=modification. Thy-1 membrane glycoprotein, signal peptide removed form A Thy-1 membrane glycoprotein that has had the signal peptide removed. PRO:DNx THY1/SigPep- PRO:DNx An interleukin-5 receptor subunit alpha that has had the signal peptide removed. IL5RA/SigPep- protein PR:000018555 Category=modification. interleukin-5 receptor subunit alpha, signal peptide removed form An interleukin-5 receptor subunit alpha that has had the signal peptide removed. PRO:DNx IL5RA/SigPep- PRO:DNx An interleukin-7 receptor subunit alpha that has had the signal peptide removed. IL7R/SigPep- protein PR:000018559 Category=modification. interleukin-7 receptor subunit alpha, signal peptide removed form An interleukin-7 receptor subunit alpha that has had the signal peptide removed. PRO:DNx IL7R/SigPep- PRO:DNx A leukosialin that has had the signal peptide removed. SPN/SigPep- protein PR:000018567 Category=modification. leukosialin, signal peptide removed form A leukosialin that has had the signal peptide removed. PRO:DNx SPN/SigPep- PRO:DNx A CD14 molecule that has had the signal peptide removed. CD14/SigPep- protein PR:000018574 Category=modification. CD14 molecule, signal peptide removed form A CD14 molecule that has had the signal peptide removed. PRO:DNx CD14/SigPep- PRO:DNx A natural killer cell receptor 2B4 that has had the signal peptide removed. CD244/SigPep- protein PR:000018580 Category=modification. natural killer cell receptor 2B4, signal peptide removed form A natural killer cell receptor 2B4 that has had the signal peptide removed. PRO:DNx CD244/SigPep- PRO:DNx A platelet glycoprotein Ib alpha chain that has had the signal peptide removed. GP1BA/SigPep- protein PR:000018590 Category=modification. platelet glycoprotein Ib alpha chain, signal peptide removed form A platelet glycoprotein Ib alpha chain that has had the signal peptide removed. PRO:DNx GP1BA/SigPep- PRO:DNx A sialoadhesin that has had the signal peptide removed. SIGLEC1/SigPep- protein PR:000018596 Category=modification. sialoadhesin, signal peptide removed form A sialoadhesin that has had the signal peptide removed. PRO:DNx SIGLEC1/SigPep- PRO:DNx A signal transducer CD24 that has had the signal peptide removed. CD24/SigPep- protein PR:000018598 Category=modification. signal transducer CD24, signal peptide removed form A signal transducer CD24 that has had the signal peptide removed. PRO:DNx CD24/SigPep- PRO:DNx A tartrate-resistant acid phosphatase type 5 that has had the signal peptide removed. ACP5/SigPep- protein PR:000018600 Category=modification. tartrate-resistant acid phosphatase type 5, signal peptide removed form A tartrate-resistant acid phosphatase type 5 that has had the signal peptide removed. PRO:DNx ACP5/SigPep- PRO:DNx A CD27 molecule that has had the signal peptide removed. CD27/SigPep- protein PR:000018620 Category=modification. CD27 molecule, signal peptide removed form A CD27 molecule that has had the signal peptide removed. PRO:DNx CD27/SigPep- PRO:DNx A tyrosine-protein phosphatase non-receptor type substrate 1 that has had the signal peptide removed. SIRPA/SigPep- protein PR:000018626 Category=modification. tyrosine-protein phosphatase non-receptor type substrate 1, signal peptide removed form A tyrosine-protein phosphatase non-receptor type substrate 1 that has had the signal peptide removed. PRO:DNx SIRPA/SigPep- PRO:DNx A urokinase plasminogen activator surface receptor that has had the signal peptide removed. PLAUR/SigPep- protein PR:000018628 Category=modification. urokinase plasminogen activator surface receptor, signal peptide removed form A urokinase plasminogen activator surface receptor that has had the signal peptide removed. PRO:DNx PLAUR/SigPep- PRO:DNx An MHC class II histocompatibility antigen alpha chain DRA that has had the signal peptide removed. MHCcIIalpha_DRA/SigPep- protein HLA-DRA/SigPep- PR:000018678 Category=modification. MHC class II histocompatibility antigen alpha chain DRA, signal peptide removed form An MHC class II histocompatibility antigen alpha chain DRA that has had the signal peptide removed. PRO:DNx MHCcIIalpha_DRA/SigPep- PRO:DAN HLA-DRA/SigPep- PRO:DNx A T-cell surface glycoprotein CD1a that has had the signal peptide removed. CD1A/SigPep- protein PR:000018692 Category=modification. T-cell surface glycoprotein CD1a, signal peptide removed form A T-cell surface glycoprotein CD1a that has had the signal peptide removed. PRO:DNx CD1A/SigPep- PRO:DNx An antigen-presenting glycoprotein CD1d that has had the signal peptide removed. CD1D/SigPep- protein PR:000018694 Category=modification. antigen-presenting glycoprotein CD1d, signal peptide removed form An antigen-presenting glycoprotein CD1d that has had the signal peptide removed. PRO:DNx CD1D/SigPep- PRO:DNx An alpha-type platelet-derived growth factor receptor that has had the signal peptide removed. PDGFRA/SigPep- protein PR:000018697 Category=modification. alpha-type platelet-derived growth factor receptor, signal peptide removed form An alpha-type platelet-derived growth factor receptor that has had the signal peptide removed. PRO:DNx PDGFRA/SigPep- PRO:DNx A complement component C1q receptor that has had the signal peptide removed. CD93/SigPep- protein PR:000018704 Category=modification. complement component C1q receptor, signal peptide removed form A complement component C1q receptor that has had the signal peptide removed. PRO:DNx CD93/SigPep- PRO:DNx A thrombomodulin that has had the signal peptide removed. THBD/SigPep- protein PR:000018720 Category=modification. thrombomodulin, signal peptide removed form A thrombomodulin that has had the signal peptide removed. PRO:DNx THBD/SigPep- PRO:DNx A lymphocyte antigen 6A-2/6E-1 that has had the signal peptide removed. Ly6a/SigPep- protein PR:000018773 Category=modification. lymphocyte antigen 6A-2/6E-1, signal peptide removed form A lymphocyte antigen 6A-2/6E-1 that has had the signal peptide removed. PRO:DNx Ly6a/SigPep- PRO:DNx A lymphocyte antigen 6C2 that has had the signal peptide removed. Ly6c2/SigPep- protein PR:000018775 Category=modification. lymphocyte antigen 6C2, signal peptide removed form A lymphocyte antigen 6C2 that has had the signal peptide removed. PRO:DNx Ly6c2/SigPep- PRO:DNx A collagen alpha-1(I) chain that has had the signal peptide removed. COL1A1/SigPep- protein PR:000018797 Category=modification. collagen alpha-1(I) chain, signal peptide removed form A collagen alpha-1(I) chain that has had the signal peptide removed. PRO:DNx COL1A1/SigPep- PRO:DNx A perforin-1 that has had the signal peptide removed. PRF1/SigPep- protein PR:000018819 Category=modification. perforin-1, signal peptide removed form A perforin-1 that has had the signal peptide removed. PRO:DNx PRF1/SigPep- PRO:DNx A cholecystokinin that has had the signal peptide removed. CCK/SigPep- protein PR:000019254 Category=modification. cholecystokinin, signal peptide removed form A cholecystokinin that has had the signal peptide removed. PRO:DNx CCK/SigPep- PRO:DNx A high affinity immunoglobulin epsilon receptor subunit alpha that has had the signal peptide removed. FCER1A/SigPep- protein PR:000019856 Category=modification. high affinity immunoglobulin epsilon receptor subunit alpha, signal peptide removed form A high affinity immunoglobulin epsilon receptor subunit alpha that has had the signal peptide removed. PRO:DNx FCER1A/SigPep- PRO:DNx An interleukin-17 receptor B that has had the signal peptide removed. IL17RB/SigPep- protein PR:000020288 Category=modification. interleukin-17 receptor B, signal peptide removed form An interleukin-17 receptor B that has had the signal peptide removed. PRO:DNx IL17RB/SigPep- PRO:DNx An interleukin-1 receptor-like 1 that has had the signal peptide removed. IL1RL1/SigPep- protein PR:000020295 Category=modification. interleukin-1 receptor-like 1, signal peptide removed form An interleukin-1 receptor-like 1 that has had the signal peptide removed. PRO:DNx IL1RL1/SigPep- PRO:DNx An integrin alpha-IIb that has had the signal peptide removed. ITGA2B/SigPep- protein PR:000020328 Category=modification. integrin alpha-IIb, signal peptide removed form An integrin alpha-IIb that has had the signal peptide removed. PRO:DNx ITGA2B/SigPep- PRO:DNx An integrin alpha-4 that has had the signal peptide removed. ITGA4/SigPep- protein PR:000020333 Category=modification. integrin alpha-4, signal peptide removed form An integrin alpha-4 that has had the signal peptide removed. PRO:DNx ITGA4/SigPep- PRO:DNx An integrin beta-7 that has had the signal peptide removed. ITGB7/SigPep- protein PR:000020347 Category=modification. integrin beta-7, signal peptide removed form An integrin beta-7 that has had the signal peptide removed. PRO:DNx ITGB7/SigPep- PRO:DNx A neutrophil gelatinase-associated lipocalin that has had the signal peptide removed. LCN2/SigPep- protein PR:000020444 Category=modification. neutrophil gelatinase-associated lipocalin, signal peptide removed form A neutrophil gelatinase-associated lipocalin that has had the signal peptide removed. PRO:DNx LCN2/SigPep- PRO:DNx A lactotransferrin that has had the signal peptide removed. LTF/SigPep- protein PR:000020496 Category=modification. lactotransferrin, signal peptide removed form A lactotransferrin that has had the signal peptide removed. PRO:DNx LTF/SigPep- PRO:DNx A lumican that has had the signal peptide removed. LUM/SigPep- protein PR:000020499 Category=modification. lumican, signal peptide removed form A lumican that has had the signal peptide removed. PRO:DNx LUM/SigPep- PRO:DNx A myeloperoxidase that has had the signal peptide removed. MPO/SigPep- protein PR:000020630 Category=modification. myeloperoxidase, signal peptide removed form A myeloperoxidase that has had the signal peptide removed. PRO:DNx MPO/SigPep- PRO:DNx A netrin-G1 that has had the signal peptide removed. NTNG1/SigPep- protein PR:000020800 Category=modification. netrin-G1, signal peptide removed form A netrin-G1 that has had the signal peptide removed. PRO:DNx NTNG1/SigPep- PRO:DNx A bone marrow proteoglycan that has had the signal peptide removed. PRG2/SigPep- protein PR:000021081 Category=modification. bone marrow proteoglycan, signal peptide removed form A bone marrow proteoglycan that has had the signal peptide removed. PRO:DNx PRG2/SigPep- PRO:DNx A non-secretory ribonuclease that has had the signal peptide removed. RNASE2/SigPep- protein PR:000021271 Category=modification. non-secretory ribonuclease, signal peptide removed form A non-secretory ribonuclease that has had the signal peptide removed. PRO:DNx RNASE2/SigPep- PRO:DNx An eosinophil cationic protein that has had the signal peptide removed. RNASE3/SigPep- protein PR:000021273 Category=modification. eosinophil cationic protein, signal peptide removed form An eosinophil cationic protein that has had the signal peptide removed. PRO:DNx RNASE3/SigPep- PRO:DNx A somatostatin that has had the signal peptide removed. SST/SigPep- protein PR:000021577 Category=modification. somatostatin, signal peptide removed form A somatostatin that has had the signal peptide removed. PRO:DNx SST/SigPep- PRO:DNx A part of a protein that is removed during the protein maturation process. cleaved_peptide_region protein PR:000021935 immature protein part A part of a protein that is removed during the protein maturation process. PRO:DAN cleaved_peptide_region SO:0100011 A bone marrow proteoglycan that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P13727-1 or a 1:1 ortholog thereof. PRG2/iso:1 protein PR:000022003 Category=sequence. bone marrow proteoglycan isoform 1 A bone marrow proteoglycan that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P13727-1 or a 1:1 ortholog thereof. PRO:CNA PRG2/iso:1 PRO:DNx A bone marrow proteoglycan isoform 1, signal peptide removed form that has had the acidic propeptide removed. PRG2/iso:1/EMBP protein PR:000022006 Category=modification. Requested by=CL. eosinophil granule major basic protein A bone marrow proteoglycan isoform 1, signal peptide removed form that has had the acidic propeptide removed. PMID:9657764 PRO:CNA PRO:DAN PRG2/iso:1/EMBP PRO:DAN A protein-containing complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction. CD8alphabeta TCR co-receptor CD8 protein PR:000025402 Category=complex. Requested by=CL. T cell receptor co-receptor CD8 A protein-containing complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction. PMID:18275828 PMID:3264320 PRO:DAN A T-cell surface glycoprotein CD8 alpha chain that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P01732-1 or a 1:1 ortholog thereof. Having a single-pass transmembrane domain, this form is membrane bound. CD8A/iso:1 mCD8alpha protein PR:000025403 Category=sequence. Requested by=CL. T-cell surface glycoprotein CD8 alpha chain isoform 1 A T-cell surface glycoprotein CD8 alpha chain that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P01732-1 or a 1:1 ortholog thereof. Having a single-pass transmembrane domain, this form is membrane bound. PRO:DAN CD8A/iso:1 PRO:DNx A T-cell surface glycoprotein CD8 beta chain that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P10966-1 or a 1:1 ortholog thereof. CD8B/iso:1 CD8beta isoform M-1 protein PR:000025405 Category=sequence. T-cell surface glycoprotein CD8 beta chain isoform 1 A T-cell surface glycoprotein CD8 beta chain that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P10966-1 or a 1:1 ortholog thereof. PRO:DAN CD8B/iso:1 PRO:DNx CD8beta isoform M-1 PMID:1541829 A T-cell surface glycoprotein CD8 alpha chain isoform 1 that has had the signal peptide removed to yield the mature form. CD8A/iso:1/SigPep- protein PR:000025406 Category=modification. T-cell surface glycoprotein CD8 alpha chain isoform 1, signal peptide removed form A T-cell surface glycoprotein CD8 alpha chain isoform 1 that has had the signal peptide removed to yield the mature form. PRO:DAN CD8A/iso:1/SigPep- PRO:DNx A T-cell surface glycoprotein CD8 beta chain isoform 1 that has had the signal peptide removed to yield the mature form. CD8B/iso:1/SigPep- protein PR:000025407 Category=modification. T-cell surface glycoprotein CD8 beta chain isoform 1, signal peptide removed form A T-cell surface glycoprotein CD8 beta chain isoform 1 that has had the signal peptide removed to yield the mature form. PRO:DAN CD8B/iso:1/SigPep- PRO:DNx A T-cell surface glycoprotein CD8 alpha chain isoform 1, signal peptide removed form that includes at least one glycosylated residue. CD8A/iso:1/SigPep-/GlycoRes+ protein PR:000025408 Category=modification. T-cell surface glycoprotein CD8 alpha chain isoform 1, signal peptide removed glycosylated form A T-cell surface glycoprotein CD8 alpha chain isoform 1, signal peptide removed form that includes at least one glycosylated residue. PRO:DAN CD8A/iso:1/SigPep-/GlycoRes+ PRO:DNx A T-cell surface glycoprotein CD8 beta chain isoform 1, signal peptide removed form that includes at least one glycosylated residue. CD8B/iso:1/SigPep-/GlycoRes+ protein PR:000025409 Category=modification. T-cell surface glycoprotein CD8 beta chain isoform 1, signal peptide removed glycosylated form A T-cell surface glycoprotein CD8 beta chain isoform 1, signal peptide removed form that includes at least one glycosylated residue. PRO:DAN CD8B/iso:1/SigPep-/GlycoRes+ PRO:DNx A bone marrow proteoglycan isoform 1 that has had the signal peptide removed. PRG2/iso:1/SigPep- protein PR:000025466 Category=modification. bone marrow proteoglycan isoform 1, signal peptide removed form A bone marrow proteoglycan isoform 1 that has had the signal peptide removed. PRO:DAN PRG2/iso:1/SigPep- PRO:DNx An organic group that results from covalent modification or chemical alteration to the side chain or backbone atoms of an amino acid residue or derivative thereof, where such alteration maintains the integrity of the amino acid chain containing the residue. modified amino acid chain residue modified protein residue protein PR:000025513 Category=external. Note: This entity is distinct from MOD:00000 "protein modification" in that the latter includes proteolytic cleavages. [PRO:DAN, PRO:JSG] modified amino-acid residue An organic group that results from covalent modification or chemical alteration to the side chain or backbone atoms of an amino acid residue or derivative thereof, where such alteration maintains the integrity of the amino acid chain containing the residue. PRO:DAN PRO:JSG modified amino acid chain residue PRO:DAN modified protein residue PRO:DAN A KLRB1-like protein that is a translation product of the human KLRB1 gene or a 1:1 ortholog thereof. NKR-P1A C-type lectin domain family 5 member B CD antigen CD161 CD161 HNKR-P1a KLRB1 Natural killer cell surface protein P1A protein CLEC5B NKRP1A PR:000025670 Category=gene. killer cell lectin-like receptor subfamily B member 1 A KLRB1-like protein that is a translation product of the human KLRB1 gene or a 1:1 ortholog thereof. PRO:DAN NKR-P1A PRO:DNx KLRB1 PRO:DNx CLEC5B NKRP1A A protein that is composed of a long N-terminal extracellular domain, a transmembrane domain and a short cytoplasmic C-terminal domain. The N-terminal domain contains beta-propeller repeats (interrupted by an A domain in a subset of integrins alpha), while the C-terminal domain contains a GFFxR motif. protein PR:000025796 Category=family. Integrins are heterodimeric complexes of an alpha and a beta subunit. They are a structurally elaborate family of adhesion molecules that transmit signals bidirectionally across the plasma membrane by undergoing large-scale structural rearrangements. By regulating cell-cell and cell-matrix contacts, integrins participate in a wide-range of biological interactions including development, tissue repair, angiogenesis, inflammation and hemostasis. [PMID:10402956, PMID:11988479, PMID:9676575]. integrin alpha A protein that is composed of a long N-terminal extracellular domain, a transmembrane domain and a short cytoplasmic C-terminal domain. The N-terminal domain contains beta-propeller repeats (interrupted by an A domain in a subset of integrins alpha), while the C-terminal domain contains a GFFxR motif. PMID:19693543 An integrin alpha that lacks an A domain. This type of integrin is often cleaved into heavy and light chains. PIRSF:PIRSF005666 protein PR:000025797 Category=family. integrin alpha lacking A domain An integrin alpha that lacks an A domain. This type of integrin is often cleaved into heavy and light chains. PRO:DAN A receptor-type tyrosine-protein phosphatase C isoform CD45RABC that has had the signal peptide removed. PTPRC/iso:CD45RABC/SigPep- protein PR:000025805 Category=modification. receptor-type tyrosine-protein phosphatase C isoform CD45RABC, signal peptide removed form A receptor-type tyrosine-protein phosphatase C isoform CD45RABC that has had the signal peptide removed. PRO:DAN PTPRC/iso:CD45RABC/SigPep- PRO:DNx A receptor-type tyrosine-protein phosphatase C isoform CD45RA that has had the signal peptide removed. PTPRC/iso:CD45RA/SigPep- protein PR:000025806 Category=modification. receptor-type tyrosine-protein phosphatase C isoform CD45RA, signal peptide removed form A receptor-type tyrosine-protein phosphatase C isoform CD45RA that has had the signal peptide removed. PMID:1351092 PRO:CNA PTPRC/iso:CD45RA/SigPep- PRO:DNx A receptor-type tyrosine-protein phosphatase C isoform CD45RO that has had the signal peptide removed. PTPRC/iso:CD45RO/SigPep- protein PR:000025808 Category=modification. receptor-type tyrosine-protein phosphatase C isoform CD45RO, signal peptide removed form A receptor-type tyrosine-protein phosphatase C isoform CD45RO that has had the signal peptide removed. PRO:DAN PTPRC/iso:CD45RO/SigPep- PRO:DNx A receptor-type tyrosine-protein phosphatase C isoform CD45RABC, signal peptide removed form that includes at least one glycosylated residue. B220 PTPRC/iso:CD45R/SigPep-/GlycoRes+ protein PR:000025813 Category=modification. receptor-type tyrosine-protein phosphatase C isoform CD45RABC, signal peptide removed glycosylated form A receptor-type tyrosine-protein phosphatase C isoform CD45RABC, signal peptide removed form that includes at least one glycosylated residue. PRO:DAN PTPRC/iso:CD45R/SigPep-/GlycoRes+ PRO:DNx A receptor-type tyrosine-protein phosphatase C isoform CD45RA, signal peptide removed form that includes at least one glycosylated residue. PTPRC/iso:CD45RA/SigPep-/GlycoRes+ protein PR:000025814 Category=modification. receptor-type tyrosine-protein phosphatase C isoform CD45RA, signal peptide removed glycosylated form A receptor-type tyrosine-protein phosphatase C isoform CD45RA, signal peptide removed form that includes at least one glycosylated residue. PMID:1351092 PRO:CNA PTPRC/iso:CD45RA/SigPep-/GlycoRes+ PRO:DNx A receptor-type tyrosine-protein phosphatase C isoform CD45RO, signal peptide removed form that includes at least one glycosylated residue. T200 PTPRC/iso:CD45RO/SigPep-/GlycoRes+ protein PR:000025816 Category=modification. receptor-type tyrosine-protein phosphatase C isoform CD45RO, signal peptide removed glycosylated form A receptor-type tyrosine-protein phosphatase C isoform CD45RO, signal peptide removed form that includes at least one glycosylated residue. PRO:DAN T200 PRO:DNx PTPRC/iso:CD45RO/SigPep-/GlycoRes+ PRO:DNx A transmembrane emp24 domain-containing protein 1 that has had the signal peptide removed. TMED1/SigPep- protein PR:000026631 Category=modification. transmembrane emp24 domain-containing protein 1, signal peptide removed form A transmembrane emp24 domain-containing protein 1 that has had the signal peptide removed. PRO:DNx TMED1/SigPep- PRO:DNx A granzyme B that has had the signal peptide removed. GZMB/SigPep- protein PR:000026712 Category=modification. granzyme B, signal peptide removed form A granzyme B that has had the signal peptide removed. PRO:DNx GZMB/SigPep- PRO:DNx An integrin alpha-E, signal peptide removed form in human. UniProtKB:P38570, 19-1179. Reactome:R-HSA-265403 PRO_0000016283 UniProtKB:P38570, 19-1179 hITGAE/SigPep- protein PR:000026869 Category=organism-modification. integrin alpha-E, signal peptide removed form (human) An integrin alpha-E, signal peptide removed form in human. UniProtKB:P38570, 19-1179. PRO:CNA Reactome:R-HSA-265403 Reactome:R-HSA-265403 PR:000026869 located_in GO:0005886 PRO_0000016283 PRO:DNx UniProtKB:P38570, 19-1179 PRO:DNx hITGAE/SigPep- PRO:DNx A T-cell-specific surface glycoprotein CD28, signal peptide removed form in human. Example: UniProtKB:P10747-1, 19-220. Reactome:R-HSA-167628 Reactome:R-HSA-167632 hCD28/SigPep- PRO_0000014652 UniProtKB:P10747-1, 19-220 protein PR:000026870 Category=organism-modification. T-cell-specific surface glycoprotein CD28, signal peptide removed form (human) A T-cell-specific surface glycoprotein CD28, signal peptide removed form in human. Example: UniProtKB:P10747-1, 19-220. PRO:CNA Reactome:R-HSA-167628 Reactome:R-HSA-167632 Reactome:R-HSA-167628 PR:000026870 located_in GO:0005829 Reactome:R-HSA-167632 PR:000026870 located_in GO:0005886 hCD28/SigPep- PRO:DNx PRO_0000014652 PRO:DNx UniProtKB:P10747-1, 19-220 PRO:DNx An integrin alpha-M, signal peptide removed form in human. Example: UniProtKB:P11215-1, 17-1152. Reactome:R-HSA-202757 Reactome:R-HSA-6799647 Reactome:R-HSA-6800979 hITGAM/SigPep- PRO_0000016289 UniProtKB:P11215-1, 17-1152 protein PR:000027393 Category=organism-modification. integrin alpha-M, signal peptide removed form (human) An integrin alpha-M, signal peptide removed form in human. Example: UniProtKB:P11215-1, 17-1152. PRO:DNx Reactome:R-HSA-202757 PR:000027393 located_in GO:0005886 Reactome:R-HSA-6799647 PR:000027393 located_in GO:0035579 Reactome:R-HSA-6800979 PR:000027393 located_in GO:0070821 hITGAM/SigPep- PRO:DNx PRO_0000016289 PRO:DNx UniProtKB:P11215-1, 17-1152 PRO:DNx An integrin alpha-IIb, signal peptide removed form in human. Example: UniProtKB:P08514-1, 32-1039. Reactome:R-HSA-57578 hITGA2B/SigPep- PRO_0000016276 UniProtKB:P08514-1, 32-1039 protein PR:000028409 Category=organism-modification. integrin alpha-IIb, signal peptide removed form (human) An integrin alpha-IIb, signal peptide removed form in human. Example: UniProtKB:P08514-1, 32-1039. PRO:DNx Reactome:R-HSA-57578 PR:000028409 located_in GO:0005886 hITGA2B/SigPep- PRO:DNx PRO_0000016276 PRO:DNx UniProtKB:P08514-1, 32-1039 PRO:DNx A CD4 molecule, signal peptide removed form in human. UniProtKB:P01730, 26-458. Reactome:R-HSA-167542 Reactome:R-HSA-180575 Reactome:R-HSA-182147 Reactome:R-HSA-8869082 PRO_0000014621 UniProtKB:P01730, 26-458 hCD4/SigPep- protein PR:000028418 Category=organism-modification. CD4 molecule, signal peptide removed form (human) A CD4 molecule, signal peptide removed form in human. UniProtKB:P01730, 26-458. PRO:DNx Reactome:R-HSA-167542 PR:000028418 located_in GO:0005886 Reactome:R-HSA-180575 PR:000028418 located_in GO:0005789 Reactome:R-HSA-182147 PR:000028418 located_in GO:0005769 Reactome:R-HSA-8869082 PR:000028418 located_in GO:0030665 PRO_0000014621 PRO:DNx UniProtKB:P01730, 26-458 PRO:DNx hCD4/SigPep- PRO:DNx A protein that is encoded in the genome of Mus musculus. mouse protein protein PR:000029032 Mus musculus protein A protein that is encoded in the genome of Mus musculus. PRO:DAN mouse protein PRO:DAN A protein that is encoded in the genome of Homo sapiens. human protein protein PR:000029067 Homo sapiens protein A protein that is encoded in the genome of Homo sapiens. PRO:DAN human protein PRO:DAN A protein that is a translation product of the human IRX6 gene or a 1:1 ortholog thereof. IRX6 homeodomain protein IRXB3 iroquois homeobox protein 6 protein IRX7 IRXB3 PR:000029562 Category=gene. iroquois-class homeodomain protein IRX-6 A protein that is a translation product of the human IRX6 gene or a 1:1 ortholog thereof. PRO:DNx IRX6 PRO:DNx IRX7 IRXB3 A protein that has G protein-coupled receptor (GPCR) activity. Each GPCR consists of a single polypeptide with an extracellular N-terminus, an intracellular C-terminus and seven hydrophobic transmembrane domains (TM1-TM7) linked by three extracellular loops (ECL1-ECL3) and three intracellular loops (ICL1-ICL3). GPCRs function as part of a heterotrimeric complex to transmit an extracellular signal across the membrane by activating an associated G-protein via the exchange of GDP for GTP on the alpha subunit. 7TM receptor seven-transmembrane receptor IUPHARfam:694 fam:GPCR protein PR:000030035 Category=family. Classification based on GRAFS system. [PMID:12761335] G-protein coupled receptor A protein that has G protein-coupled receptor (GPCR) activity. Each GPCR consists of a single polypeptide with an extracellular N-terminus, an intracellular C-terminus and seven hydrophobic transmembrane domains (TM1-TM7) linked by three extracellular loops (ECL1-ECL3) and three intracellular loops (ICL1-ICL3). GPCRs function as part of a heterotrimeric complex to transmit an extracellular signal across the membrane by activating an associated G-protein via the exchange of GDP for GTP on the alpha subunit. IUPHARfam:694 PRO:DAN Wikipedia:GPCR 7TM receptor IUPHARfam:694 seven-transmembrane receptor IUPHARfam:694 fam:GPCR PRO:DAN A protein that is a translation product of the human LAMP5 gene or a 1:1 ortholog thereof. BAD-LAMP LAMP-5 LAMP5 brain and dendritic cell-associated LAMP brain-associated LAMP-like protein lysosome-associated membrane protein 5 protein C20orf103 PR:000032148 Category=gene. lysosome-associated membrane glycoprotein 5 A protein that is a translation product of the human LAMP5 gene or a 1:1 ortholog thereof. PRO:DNx LAMP5 PRO:DNx C20orf103 A lymphocyte antigen 75 that is encoded in the genome of human. C-type lectin domain family 13 member B (human) CD205 (human) CLEC13B (human) DEC-205 (human) gp200-MR6 (human) hLY75 ly-75 (human) protein PR:000034294 Category=organism-gene. lymphocyte antigen 75 (human) A lymphocyte antigen 75 that is encoded in the genome of human. PRO:DAN UniProtKB:O60449 C-type lectin domain family 13 member B (human) UniProtKB:O60449 CD205 (human) UniProtKB:O60449 CLEC13B (human) UniProtKB:O60449 DEC-205 (human) UniProtKB:O60449 gp200-MR6 (human) UniProtKB:O60449 hLY75 PRO:DNx ly-75 (human) UniProtKB:O60449 A protein that is encoded in the genome of some Eukaryota. Eukaryota protein protein PR:000036194 eukaryotic protein A protein that is encoded in the genome of some Eukaryota. PRO:DAN Eukaryota protein PRO:DAN A T-cell surface glycoprotein CD1 that is encoded in the genome of human. MRO:0000634 HLA-CD1 chain hCD1 protein PR:000036947 Category=organism-family. Requested by=IEDB. Requested by=ImmPort. T-cell surface glycoprotein CD1 (human) A T-cell surface glycoprotein CD1 that is encoded in the genome of human. PRO:DAN HLA-CD1 chain MRO:0000634 hCD1 PRO:DAN A protein that includes at least one glycosylated residue. Prot/GlycoRes+ glycated protein glycosylated protein protein PR:000037069 Category=modification. glycoprotein A protein that includes at least one glycosylated residue. PRO:DAN Prot/GlycoRes+ PRO:DAN glycated protein PRO:DAN glycosylated protein PRO:DAN A protein that is a translation product of some metazoan gene that encodes a signal peptide followed by a single Cathepsin propeptide inhibitor domain (Pfam:PF08246) followed by a single Papain family cysteine protease (Pfam:PF00112) domain at the C terminus. fam:CTS cathepsin protein PR:000040662 Category=family. cathepsin-like protease A protein that is a translation product of some metazoan gene that encodes a signal peptide followed by a single Cathepsin propeptide inhibitor domain (Pfam:PF08246) followed by a single Papain family cysteine protease (Pfam:PF00112) domain at the C terminus. PRO:DAN fam:CTS PRO:DNx cathepsin PRO:DAN A neuronal acetylcholine receptor subunit alpha-7 that has had the signal peptide removed. CHRNA7/SigPep- protein PR:000044062 Category=modification. neuronal acetylcholine receptor subunit alpha-7, signal peptide removed form A neuronal acetylcholine receptor subunit alpha-7 that has had the signal peptide removed. PRO:DAN CHRNA7/SigPep- PRO:DAN A neuronal acetylcholine receptor subunit alpha-7, signal peptide removed form in human. Example: UniProtKB:P36544-1, 23-502. Reactome:R-HSA-507830 hCHRNA7/SigPep- PRO_0000000366 UniProtKB:P36544-1, 23-502 protein PR:000044063 Category=organism-modification. neuronal acetylcholine receptor subunit alpha-7, signal peptide removed form (human) A neuronal acetylcholine receptor subunit alpha-7, signal peptide removed form in human. Example: UniProtKB:P36544-1, 23-502. PRO:DAN Reactome:R-HSA-507830 PR:000044063 located_in GO:0005886 hCHRNA7/SigPep- PRO:DAN PRO_0000000366 PRO:DNx UniProtKB:P36544-1, 23-502 PRO:DNx An ion channel protein that has voltage-gated ion channel activity. A voltage-gated ion channel enables the transmembrane transfer of a solute by a channel whose open state is dependent on the voltage across the membrane in which it is embedded. IUPHARfam:696 fam:vgate_ion_chan protein PR:000044628 Category=family. voltage-gated ion channel protein An ion channel protein that has voltage-gated ion channel activity. A voltage-gated ion channel enables the transmembrane transfer of a solute by a channel whose open state is dependent on the voltage across the membrane in which it is embedded. GO:0022832 PRO:XQ fam:vgate_ion_chan PRO:DAN A voltage-gated ion channel protein that is a translation product of the human TRPC1, TRPM1, TRPV1, TRPA1, TRPP1 or TRPML1 gene, paralogs thereof, 1:1 orthologs thereof, a semi-ortholog thereof, or pro-orthologs thereof. IUPHARfam:78 fam:TRP_chan protein PR:000044657 Category=family. transient receptor potential channel protein A voltage-gated ion channel protein that is a translation product of the human TRPC1, TRPM1, TRPV1, TRPA1, TRPP1 or TRPML1 gene, paralogs thereof, 1:1 orthologs thereof, a semi-ortholog thereof, or pro-orthologs thereof. PRO:XQ fam:TRP_chan PRO:DAN A ligand-gated ion channel protein that is a translation product of the human CHRNA1-7, CHRNA9-10, CHRNB1-4, CHRNG, CHRND, or CHRNE genes, 1:1 orthologs thereof, or a semi-ortholog thereof. IUPHARfam:76 protein PR:000044668 Category=family. nicotinic acetylcholine receptor protein A ligand-gated ion channel protein that is a translation product of the human CHRNA1-7, CHRNA9-10, CHRNB1-4, CHRNG, CHRND, or CHRNE genes, 1:1 orthologs thereof, or a semi-ortholog thereof. PRO:XQ An ion channel protein that has ligand-gated ion channel activity. The ligand-gated ion channel opens when a specific ligand has been bound by the channel complex or one of its constituent parts. IUPHARfam:697 ionotropic receptor protein PR:000044671 Category=family. ligand-gated ion channel protein An ion channel protein that has ligand-gated ion channel activity. The ligand-gated ion channel opens when a specific ligand has been bound by the channel complex or one of its constituent parts. GO:0015276 PRO:XQ ionotropic receptor PRO:XQ A protein that has channel activity. Channel proteins enable energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. channel-forming toxin protein channel/pore class transporter protein fam:chan nonselective channel protein pore class transporter protein pore protein protein PR:000044676 Category=family. channel protein A protein that has channel activity. Channel proteins enable energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. GO:0015267 PRO:XQ channel-forming toxin protein PRO:XQ channel/pore class transporter protein PRO:XQ fam:chan PRO:DAN nonselective channel protein PRO:XQ pore class transporter protein PRO:XQ pore protein PRO:XQ fam:LILR protein PR:000044780 Category=family. Requested by=HPO/MPO. leukocyte immunoglobulin-like receptor subfamily member fam:LILR PRO:DAN A tartrate-resistant acid phosphatase type 5 (human) that has had the signal peptide removed. UniProtKB:P13686, 22-325. Reactome:R-HSA-196938 PRO_0000023981 UniProtKB:P13686, 22-325 hACP5/SigPep- protein PR:000046244 Category=organism-modification. tartrate-resistant acid phosphatase type 5, signal peptide removed form (human) A tartrate-resistant acid phosphatase type 5 (human) that has had the signal peptide removed. UniProtKB:P13686, 22-325. PRO:DNx Reactome:R-HSA-196938 Reactome:R-HSA-196938 PR:000046244 located_in GO:0005829 PRO_0000023981 PRO:DNx UniProtKB:P13686, 22-325 PRO:DNx hACP5/SigPep- PRO:DNx A cholecystokinin (human) that has had the signal peptide removed. UniProtKB:P06307, 21-115. Reactome:R-HSA-388539 PRO_0000010536 UniProtKB:P06307, 21-115 hCCK/SigPep- protein PR:000046582 Category=organism-modification. cholecystokinin, signal peptide removed form (human) A cholecystokinin (human) that has had the signal peptide removed. UniProtKB:P06307, 21-115. PRO:DNx Reactome:R-HSA-388539 Reactome:R-HSA-388539 PR:000046582 located_in GO:0005576 PRO_0000010536 PRO:DNx UniProtKB:P06307, 21-115 PRO:DNx hCCK/SigPep- PRO:DNx A C-C chemokine receptor type 7 (human) that has had the signal peptide removed. UniProtKB:P32248, 25-378. Reactome:R-HSA-373125 PRO_0000012735 UniProtKB:P32248, 25-378 hCCR7/SigPep- protein PR:000046603 Category=organism-modification. C-C chemokine receptor type 7, signal peptide removed form (human) A C-C chemokine receptor type 7 (human) that has had the signal peptide removed. UniProtKB:P32248, 25-378. PRO:DNx Reactome:R-HSA-373125 Reactome:R-HSA-373125 PR:000046603 located_in GO:0005886 PRO_0000012735 PRO:DNx UniProtKB:P32248, 25-378 PRO:DNx hCCR7/SigPep- PRO:DNx A scavenger receptor cysteine-rich type 1 protein M130 (human) that has had the signal peptide removed. UniProtKB:Q86VB7, 42-1156. Reactome:R-HSA-2168868 Reactome:R-HSA-2230974 PRO_0000238938 UniProtKB:Q86VB7, 42-1156 hCD163/SigPep- protein PR:000046610 Category=organism-modification. scavenger receptor cysteine-rich type 1 protein M130, signal peptide removed form (human) A scavenger receptor cysteine-rich type 1 protein M130 (human) that has had the signal peptide removed. UniProtKB:Q86VB7, 42-1156. PRO:DNx Reactome:R-HSA-2168868 Reactome:R-HSA-2230974 Reactome:R-HSA-2168868 PR:000046610 located_in GO:0005886 Reactome:R-HSA-2230974 PR:000046610 located_in GO:0030666 PRO_0000238938 PRO:DNx UniProtKB:Q86VB7, 42-1156 PRO:DNx hCD163/SigPep- PRO:DNx A B-lymphocyte antigen CD19 (human) that has had the signal peptide removed. UniProtKB:P15391, 20-556. Reactome:R-HSA-197740 PRO_0000014648 UniProtKB:P15391, 20-556 hCD19/SigPep- protein PR:000046612 Category=organism-modification. B-lymphocyte antigen CD19, signal peptide removed form (human) A B-lymphocyte antigen CD19 (human) that has had the signal peptide removed. UniProtKB:P15391, 20-556. PRO:DNx Reactome:R-HSA-197740 Reactome:R-HSA-197740 PR:000046612 located_in GO:0005886 PRO_0000014648 PRO:DNx UniProtKB:P15391, 20-556 PRO:DNx hCD19/SigPep- PRO:DNx A T-cell surface glycoprotein CD1a (human) that has had the signal peptide removed. UniProtKB:P06126, 17-327. Reactome:R-HSA-197792 PRO_0000014578 UniProtKB:P06126, 17-327 hCD1A/SigPep- protein PR:000046614 Category=organism-modification. T-cell surface glycoprotein CD1a, signal peptide removed form (human) A T-cell surface glycoprotein CD1a (human) that has had the signal peptide removed. UniProtKB:P06126, 17-327. PRO:DNx Reactome:R-HSA-197792 Reactome:R-HSA-197792 PR:000046614 located_in GO:0005886 PRO_0000014578 PRO:DNx UniProtKB:P06126, 17-327 PRO:DNx hCD1A/SigPep- PRO:DNx A T-cell surface glycoprotein CD1c (human) that has had the signal peptide removed. UniProtKB:P29017, 18-333. Reactome:R-HSA-8850110 PRO_0000014580 UniProtKB:P29017, 18-333 hCD1C/SigPep- protein PR:000046616 Category=organism-modification. T-cell surface glycoprotein CD1c, signal peptide removed form (human) A T-cell surface glycoprotein CD1c (human) that has had the signal peptide removed. UniProtKB:P29017, 18-333. PRO:DNx Reactome:R-HSA-8850110 Reactome:R-HSA-8850110 PR:000046616 located_in GO:0005886 PRO_0000014580 PRO:DNx UniProtKB:P29017, 18-333 PRO:DNx hCD1C/SigPep- PRO:DNx An antigen-presenting glycoprotein CD1d (human) that has had the signal peptide removed. UniProtKB:P15813, 20-335. Reactome:R-HSA-197833 PRO_0000014581 UniProtKB:P15813, 20-335 hCD1D/SigPep- protein PR:000046617 Category=organism-modification. antigen-presenting glycoprotein CD1d, signal peptide removed form (human) An antigen-presenting glycoprotein CD1d (human) that has had the signal peptide removed. UniProtKB:P15813, 20-335. PRO:DNx Reactome:R-HSA-197833 Reactome:R-HSA-197833 PR:000046617 located_in GO:0005886 PRO_0000014581 PRO:DNx UniProtKB:P15813, 20-335 PRO:DNx hCD1D/SigPep- PRO:DNx A T-cell surface antigen CD2 (human) that has had the signal peptide removed. UniProtKB:P06729, 25-351. Reactome:R-HSA-197795 PRO_0000014600 UniProtKB:P06729, 25-351 hCD2/SigPep- protein PR:000046618 Category=organism-modification. T-cell surface antigen CD2, signal peptide removed form (human) A T-cell surface antigen CD2 (human) that has had the signal peptide removed. UniProtKB:P06729, 25-351. PRO:DNx Reactome:R-HSA-197795 Reactome:R-HSA-197795 PR:000046618 located_in GO:0005886 PRO_0000014600 PRO:DNx UniProtKB:P06729, 25-351 PRO:DNx hCD2/SigPep- PRO:DNx A B-cell receptor CD22 (human) that has had the signal peptide removed. UniProtKB:P20273, 20-847. Reactome:R-HSA-197703 PRO_0000014873 UniProtKB:P20273, 20-847 hCD22/SigPep- protein PR:000046621 Category=organism-modification. B-cell receptor CD22, signal peptide removed form (human) A B-cell receptor CD22 (human) that has had the signal peptide removed. UniProtKB:P20273, 20-847. PRO:DNx Reactome:R-HSA-197703 Reactome:R-HSA-197703 PR:000046621 located_in GO:0005886 PRO_0000014873 PRO:DNx UniProtKB:P20273, 20-847 PRO:DNx hCD22/SigPep- PRO:DNx A natural killer cell receptor 2B4 (human) that has had the signal peptide removed. UniProtKB:Q9BZW8, 22-370. Reactome:R-HSA-197846 PRO_0000014668 UniProtKB:Q9BZW8, 22-370 hCD244/SigPep- protein PR:000046624 Category=organism-modification. natural killer cell receptor 2B4, signal peptide removed form (human) A natural killer cell receptor 2B4 (human) that has had the signal peptide removed. UniProtKB:Q9BZW8, 22-370. PRO:DNx Reactome:R-HSA-197846 Reactome:R-HSA-197846 PR:000046624 located_in GO:0005886 PRO_0000014668 PRO:DNx UniProtKB:Q9BZW8, 22-370 PRO:DNx hCD244/SigPep- PRO:DNx A CD27 antigen (human) that has had the signal peptide removed. UniProtKB:P26842, 20-260. Reactome:R-HSA-5666994 PRO_0000034571 UniProtKB:P26842, 20-260 hCD27/SigPep- protein PR:000046625 Category=organism-modification. CD27 antigen, signal peptide removed form (human) A CD27 antigen (human) that has had the signal peptide removed. UniProtKB:P26842, 20-260. PRO:DNx Reactome:R-HSA-5666994 Reactome:R-HSA-5666994 PR:000046625 located_in GO:0005886 PRO_0000034571 PRO:DNx UniProtKB:P26842, 20-260 PRO:DNx hCD27/SigPep- PRO:DNx A myeloid cell surface antigen CD33 (human) that has had the signal peptide removed. UniProtKB:P20138, 18-364. Reactome:R-HSA-197719 Reactome:R-HSA-6799615 Reactome:R-HSA-6800959 PRO_0000014878 UniProtKB:P20138, 18-364 hCD33/SigPep- protein PR:000046634 Category=organism-modification. myeloid cell surface antigen CD33, signal peptide removed form (human) A myeloid cell surface antigen CD33 (human) that has had the signal peptide removed. UniProtKB:P20138, 18-364. PRO:DNx Reactome:R-HSA-197719 Reactome:R-HSA-197719 PR:000046634 located_in GO:0005886 Reactome:R-HSA-6799615 PR:000046634 located_in GO:0035579 Reactome:R-HSA-6800959 PR:000046634 located_in GO:0070821 PRO_0000014878 PRO:DNx UniProtKB:P20138, 18-364 PRO:DNx hCD33/SigPep- PRO:DNx A T-cell surface glycoprotein CD3 epsilon chain (human) that has had the signal peptide removed. UniProtKB:P07766, 23-207. Reactome:R-HSA-197906 PRO_0000014607 UniProtKB:P07766, 23-207 hCD3E/SigPep- protein PR:000046639 Category=organism-modification. T-cell surface glycoprotein CD3 epsilon chain, signal peptide removed form (human) A T-cell surface glycoprotein CD3 epsilon chain (human) that has had the signal peptide removed. UniProtKB:P07766, 23-207. PRO:DNx Reactome:R-HSA-197906 Reactome:R-HSA-197906 PR:000046639 located_in GO:0005886 PRO_0000014607 PRO:DNx UniProtKB:P07766, 23-207 PRO:DNx hCD3E/SigPep- PRO:DNx A CD44 antigen (human) that has had the signal peptide removed. UniProtKB:P16070, 21-742. Reactome:R-HSA-1031688 Reactome:R-HSA-6804776 PRO_0000026687 UniProtKB:P16070, 21-742 hCD44/SigPep- protein PR:000046641 Category=organism-modification. CD44 antigen, signal peptide removed form (human) A CD44 antigen (human) that has had the signal peptide removed. UniProtKB:P16070, 21-742. PRO:DNx Reactome:R-HSA-1031688 Reactome:R-HSA-1031688 PR:000046641 located_in GO:0005886 Reactome:R-HSA-6804776 PR:000046641 located_in GO:0030667 PRO_0000026687 PRO:DNx UniProtKB:P16070, 21-742 PRO:DNx hCD44/SigPep- PRO:DNx A T-lymphocyte activation antigen CD80 (human) that has had the signal peptide removed. UniProtKB:P33681, 35-288. Reactome:R-HSA-179789 PRO_0000014547 UniProtKB:P33681, 35-288 hCD80/SigPep- protein PR:000046650 Category=organism-modification. T-lymphocyte activation antigen CD80, signal peptide removed form (human) A T-lymphocyte activation antigen CD80 (human) that has had the signal peptide removed. UniProtKB:P33681, 35-288. PRO:DNx Reactome:R-HSA-179789 Reactome:R-HSA-179789 PR:000046650 located_in GO:0005886 PRO_0000014547 PRO:DNx UniProtKB:P33681, 35-288 PRO:DNx hCD80/SigPep- PRO:DNx A SLAM family member 5 (human) that has had the signal peptide removed. UniProtKB:Q9UIB8, 22-345. Reactome:R-HSA-3325587 PRO_0000252029 UniProtKB:Q9UIB8, 22-345 hCD84/SigPep- protein PR:000046651 Category=organism-modification. SLAM family member 5, signal peptide removed form (human) A SLAM family member 5 (human) that has had the signal peptide removed. UniProtKB:Q9UIB8, 22-345. PRO:DNx Reactome:R-HSA-3325587 Reactome:R-HSA-3325587 PR:000046651 located_in GO:0005886 PRO_0000252029 PRO:DNx UniProtKB:Q9UIB8, 22-345 PRO:DNx hCD84/SigPep- PRO:DNx A T-lymphocyte activation antigen CD86 (human) that has had the signal peptide removed. UniProtKB:P42081, 24-329. Reactome:R-HSA-179784 PRO_0000014550 UniProtKB:P42081, 24-329 hCD86/SigPep- protein PR:000046652 Category=organism-modification. T-lymphocyte activation antigen CD86, signal peptide removed form (human) A T-lymphocyte activation antigen CD86 (human) that has had the signal peptide removed. UniProtKB:P42081, 24-329. PRO:DNx Reactome:R-HSA-179784 Reactome:R-HSA-179784 PR:000046652 located_in GO:0005886 PRO_0000014550 PRO:DNx UniProtKB:P42081, 24-329 PRO:DNx hCD86/SigPep- PRO:DNx A T-cell surface glycoprotein CD8 alpha chain (human) that has had the signal peptide removed. UniProtKB:P01732, 22-235. Reactome:R-HSA-197601 PRO_0000014638 UniProtKB:P01732, 22-235 hCD8A/SigPep- protein PR:000046653 Category=organism-modification. T-cell surface glycoprotein CD8 alpha chain, signal peptide removed form (human) A T-cell surface glycoprotein CD8 alpha chain (human) that has had the signal peptide removed. UniProtKB:P01732, 22-235. PRO:DNx Reactome:R-HSA-197601 Reactome:R-HSA-197601 PR:000046653 located_in GO:0005886 PRO_0000014638 PRO:DNx UniProtKB:P01732, 22-235 PRO:DNx hCD8A/SigPep- PRO:DNx A T-cell surface glycoprotein CD8 beta chain (human) that has had the signal peptide removed. UniProtKB:P10966, 22-210. Reactome:R-HSA-2980537 Reactome:R-HSA-3149571 PRO_0000014643 UniProtKB:P10966, 22-210 hCD8B/SigPep- protein PR:000046654 Category=organism-modification. T-cell surface glycoprotein CD8 beta chain, signal peptide removed form (human) A T-cell surface glycoprotein CD8 beta chain (human) that has had the signal peptide removed. UniProtKB:P10966, 22-210. PRO:DNx Reactome:R-HSA-2980537 Reactome:R-HSA-3149571 Reactome:R-HSA-2980537 PR:000046654 located_in GO:0005886 Reactome:R-HSA-3149571 PR:000046654 located_in GO:0031901 PRO_0000014643 PRO:DNx UniProtKB:P10966, 22-210 PRO:DNx hCD8B/SigPep- PRO:DNx A collagen alpha-1(I) chain (human) that has had the signal peptide removed. UniProtKB:P02452, 23-1464. Reactome:R-HSA-1650777 Reactome:R-HSA-2268635 UniProtKB:P02452, 23-1464 hCOL1A1/SigPep- protein PR:000046823 Category=organism-modification. collagen alpha-1(I) chain, signal peptide removed form (human) A collagen alpha-1(I) chain (human) that has had the signal peptide removed. UniProtKB:P02452, 23-1464. PRO:DNx Reactome:R-HSA-1650777 Reactome:R-HSA-2268635 Reactome:R-HSA-1650777 PR:000046823 located_in GO:0005788 Reactome:R-HSA-2268635 PR:000046823 located_in GO:0005576 UniProtKB:P02452, 23-1464 PRO:DNx hCOL1A1/SigPep- PRO:DNx A complement receptor type 1 (human) that has had the signal peptide removed. UniProtKB:P17927, 42-2039. Reactome:R-HSA-6801286 Reactome:R-HSA-6801315 Reactome:R-HSA-977369 PRO_0000006009 UniProtKB:P17927, 42-2039 hCR1/SigPep- protein PR:000047062 Category=organism-modification. complement receptor type 1, signal peptide removed form (human) A complement receptor type 1 (human) that has had the signal peptide removed. UniProtKB:P17927, 42-2039. PRO:DNx Reactome:R-HSA-977369 Reactome:R-HSA-6801286 PR:000047062 located_in GO:0101003 Reactome:R-HSA-6801315 PR:000047062 located_in GO:0030667 Reactome:R-HSA-977369 PR:000047062 located_in GO:0005886 PRO_0000006009 PRO:DNx UniProtKB:P17927, 42-2039 PRO:DNx hCR1/SigPep- PRO:DNx A macrophage colony-stimulating factor 1 receptor (human) that has had the signal peptide removed. UniProtKB:P07333, 20-972. Reactome:R-HSA-197667 PRO_0000016765 UniProtKB:P07333, 20-972 hCSF1R/SigPep- protein PR:000047079 Category=organism-modification. macrophage colony-stimulating factor 1 receptor, signal peptide removed form (human) A macrophage colony-stimulating factor 1 receptor (human) that has had the signal peptide removed. UniProtKB:P07333, 20-972. PRO:DNx Reactome:R-HSA-197667 Reactome:R-HSA-197667 PR:000047079 located_in GO:0005886 PRO_0000016765 PRO:DNx UniProtKB:P07333, 20-972 PRO:DNx hCSF1R/SigPep- PRO:DNx A cytotoxic T-lymphocyte protein 4 (human) that has had the signal peptide removed. UniProtKB:P16410, 36-223. Reactome:R-HSA-179764 PRO_0000014734 UniProtKB:P16410, 36-223 hCTLA4/SigPep- protein PR:000047094 Category=organism-modification. cytotoxic T-lymphocyte protein 4, signal peptide removed form (human) A cytotoxic T-lymphocyte protein 4 (human) that has had the signal peptide removed. UniProtKB:P16410, 36-223. PRO:DNx Reactome:R-HSA-179764 Reactome:R-HSA-179764 PR:000047094 located_in GO:0005886 PRO_0000014734 PRO:DNx UniProtKB:P16410, 36-223 PRO:DNx hCTLA4/SigPep- PRO:DNx A high affinity immunoglobulin epsilon receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:P12319, 26-257. Reactome:R-HSA-197802 PRO_0000015161 UniProtKB:P12319, 26-257 hFCER1A/SigPep- protein PR:000047381 Category=organism-modification. high affinity immunoglobulin epsilon receptor subunit alpha, signal peptide removed form (human) A high affinity immunoglobulin epsilon receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:P12319, 26-257. PRO:DNx Reactome:R-HSA-197802 Reactome:R-HSA-197802 PR:000047381 located_in GO:0005886 PRO_0000015161 PRO:DNx UniProtKB:P12319, 26-257 PRO:DNx hFCER1A/SigPep- PRO:DNx A high affinity immunoglobulin gamma Fc receptor I (human) that has had the signal peptide removed. UniProtKB:P12314, 16-374. Reactome:R-HSA-1236781 Reactome:R-HSA-1236890 Reactome:R-HSA-197835 PRO_0000015139 UniProtKB:P12314, 16-374 hFCGR1A/SigPep- protein PR:000047384 Category=organism-modification. high affinity immunoglobulin gamma Fc receptor I, signal peptide removed form (human) A high affinity immunoglobulin gamma Fc receptor I (human) that has had the signal peptide removed. UniProtKB:P12314, 16-374. PRO:DNx Reactome:R-HSA-1236781 Reactome:R-HSA-1236890 Reactome:R-HSA-197835 Reactome:R-HSA-1236781 PR:000047384 located_in GO:0030669 Reactome:R-HSA-1236890 PR:000047384 located_in GO:0031901 Reactome:R-HSA-197835 PR:000047384 located_in GO:0005886 PRO_0000015139 PRO:DNx UniProtKB:P12314, 16-374 PRO:DNx hFCGR1A/SigPep- PRO:DNx A low affinity immunoglobulin gamma Fc region receptor II-b (human) that has had the signal peptide removed. UniProtKB:P31994, 43-310. Reactome:R-HSA-197854 PRO_0000015147 UniProtKB:P31994, 43-310 hFCGR2B/SigPep- protein PR:000047388 Category=organism-modification. low affinity immunoglobulin gamma Fc region receptor II-b, signal peptide removed form (human) A low affinity immunoglobulin gamma Fc region receptor II-b (human) that has had the signal peptide removed. UniProtKB:P31994, 43-310. PRO:DNx Reactome:R-HSA-197854 Reactome:R-HSA-197854 PR:000047388 located_in GO:0005886 PRO_0000015147 PRO:DNx UniProtKB:P31994, 43-310 PRO:DNx hFCGR2B/SigPep- PRO:DNx A receptor-type tyrosine-protein kinase FLT3 (human) that has had the signal peptide removed. UniProtKB:P36888, 27-993. Reactome:R-HSA-6786756 PRO_0000016778 UniProtKB:P36888, 27-993 hFLT3/SigPep- protein PR:000047430 Category=organism-modification. receptor-type tyrosine-protein kinase FLT3, signal peptide removed form (human) A receptor-type tyrosine-protein kinase FLT3 (human) that has had the signal peptide removed. UniProtKB:P36888, 27-993. PRO:DNx Reactome:R-HSA-6786756 Reactome:R-HSA-6786756 PR:000047430 located_in GO:0005886 PRO_0000016778 PRO:DNx UniProtKB:P36888, 27-993 PRO:DNx hFLT3/SigPep- PRO:DNx An interleukin-17 receptor B (human) that has had the signal peptide removed. UniProtKB:Q9NRM6, 18-502. Reactome:R-HSA-447257 PRO_0000011032 UniProtKB:Q9NRM6, 18-502 hIL17RB/SigPep- protein PR:000047991 Category=organism-modification. interleukin-17 receptor B, signal peptide removed form (human) An interleukin-17 receptor B (human) that has had the signal peptide removed. UniProtKB:Q9NRM6, 18-502. PRO:DNx Reactome:R-HSA-447257 Reactome:R-HSA-447257 PR:000047991 located_in GO:0005886 PRO_0000011032 PRO:DNx UniProtKB:Q9NRM6, 18-502 PRO:DNx hIL17RB/SigPep- PRO:DNx An interleukin-1 receptor-like 1 (human) that has had the signal peptide removed. UniProtKB:Q01638, 19-556. Reactome:R-HSA-197594 Reactome:R-HSA-8981971 PRO_0000015442 UniProtKB:Q01638, 19-556 hIL1RL1/SigPep- protein PR:000048001 Category=organism-modification. interleukin-1 receptor-like 1, signal peptide removed form (human) An interleukin-1 receptor-like 1 (human) that has had the signal peptide removed. UniProtKB:Q01638, 19-556. PRO:DNx Reactome:R-HSA-197594 Reactome:R-HSA-197594 PR:000048001 located_in GO:0005886 Reactome:R-HSA-8981971 PR:000048001 located_in GO:0005576 PRO_0000015442 PRO:DNx UniProtKB:Q01638, 19-556 PRO:DNx hIL1RL1/SigPep- PRO:DNx An interleukin-2 receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:P01589, 22-272. Reactome:R-HSA-450046 PRO_0000011024 UniProtKB:P01589, 22-272 hIL2RA/SigPep- protein PR:000048015 Category=organism-modification. interleukin-2 receptor subunit alpha, signal peptide removed form (human) An interleukin-2 receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:P01589, 22-272. PRO:DNx Reactome:R-HSA-450046 Reactome:R-HSA-450046 PR:000048015 located_in GO:0005886 PRO_0000011024 PRO:DNx UniProtKB:P01589, 22-272 PRO:DNx hIL2RA/SigPep- PRO:DNx An interleukin-2 receptor subunit beta (human) that has had the signal peptide removed. UniProtKB:P14784, 27-551. Reactome:R-HSA-197876 Reactome:R-HSA-8983172 PRO_0000010878 UniProtKB:P14784, 27-551 hIL2RB/SigPep- protein PR:000048016 Category=organism-modification. interleukin-2 receptor subunit beta, signal peptide removed form (human) An interleukin-2 receptor subunit beta (human) that has had the signal peptide removed. UniProtKB:P14784, 27-551. PRO:DNx Reactome:R-HSA-197876 Reactome:R-HSA-197876 PR:000048016 located_in GO:0005886 Reactome:R-HSA-8983172 PR:000048016 located_in GO:0005768 PRO_0000010878 PRO:DNx UniProtKB:P14784, 27-551 PRO:DNx hIL2RB/SigPep- PRO:DNx An interleukin-3 receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:P26951, 19-378. Reactome:R-HSA-879938 PRO_0000010883 UniProtKB:P26951, 19-378 hIL3RA/SigPep- protein PR:000048024 Category=organism-modification. interleukin-3 receptor subunit alpha, signal peptide removed form (human) An interleukin-3 receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:P26951, 19-378. PRO:DNx Reactome:R-HSA-879938 Reactome:R-HSA-879938 PR:000048024 located_in GO:0005886 PRO_0000010883 PRO:DNx UniProtKB:P26951, 19-378 PRO:DNx hIL3RA/SigPep- PRO:DNx An interleukin-5 receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:Q01344, 21-420. Reactome:R-HSA-450072 PRO_0000010893 UniProtKB:Q01344, 21-420 hIL5RA/SigPep- protein PR:000048027 Category=organism-modification. interleukin-5 receptor subunit alpha, signal peptide removed form (human) An interleukin-5 receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:Q01344, 21-420. PRO:DNx Reactome:R-HSA-450072 Reactome:R-HSA-450072 PR:000048027 located_in GO:0005886 PRO_0000010893 PRO:DNx UniProtKB:Q01344, 21-420 PRO:DNx hIL5RA/SigPep- PRO:DNx An interleukin-7 receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:P16871, 21-459. Reactome:R-HSA-449945 Reactome:R-HSA-9028500 PRO_0000010909 UniProtKB:P16871, 21-459 hIL7R/SigPep- protein PR:000048032 Category=organism-modification. interleukin-7 receptor subunit alpha, signal peptide removed form (human) An interleukin-7 receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:P16871, 21-459. PRO:DNx Reactome:R-HSA-449945 Reactome:R-HSA-449945 PR:000048032 located_in GO:0005886 Reactome:R-HSA-9028500 PR:000048032 located_in GO:0030669 PRO_0000010909 PRO:DNx UniProtKB:P16871, 21-459 PRO:DNx hIL7R/SigPep- PRO:DNx An integrin alpha-2 (human) that has had the signal peptide removed. UniProtKB:P17301, 30-1181. Reactome:R-HSA-57562 PRO_0000016233 UniProtKB:P17301, 30-1181 hITGA2/SigPep- protein PR:000048059 Category=organism-modification. integrin alpha-2, signal peptide removed form (human) An integrin alpha-2 (human) that has had the signal peptide removed. UniProtKB:P17301, 30-1181. PRO:DNx Reactome:R-HSA-57562 Reactome:R-HSA-57562 PR:000048059 located_in GO:0005886 PRO_0000016233 PRO:DNx UniProtKB:P17301, 30-1181 PRO:DNx hITGA2/SigPep- PRO:DNx An integrin alpha-4 (human) that has had the signal peptide removed. UniProtKB:P13612, 34-1032. Reactome:R-HSA-198007 PRO_0000016244 UniProtKB:P13612, 34-1032 hITGA4/SigPep- protein PR:000048061 Category=organism-modification. integrin alpha-4, signal peptide removed form (human) An integrin alpha-4 (human) that has had the signal peptide removed. UniProtKB:P13612, 34-1032. PRO:DNx Reactome:R-HSA-198007 Reactome:R-HSA-198007 PR:000048061 located_in GO:0005886 PRO_0000016244 PRO:DNx UniProtKB:P13612, 34-1032 PRO:DNx hITGA4/SigPep- PRO:DNx An integrin alpha-X (human) that has had the signal peptide removed. UniProtKB:P20702, 20-1163. Reactome:R-HSA-202764 Reactome:R-HSA-6801289 Reactome:R-HSA-6801305 Reactome:R-HSA-6801314 PRO_0000016294 UniProtKB:P20702, 20-1163 hITGAX/SigPep- protein PR:000048068 Category=organism-modification. integrin alpha-X, signal peptide removed form (human) An integrin alpha-X (human) that has had the signal peptide removed. UniProtKB:P20702, 20-1163. PRO:DNx Reactome:R-HSA-202764 Reactome:R-HSA-202764 PR:000048068 located_in GO:0005886 Reactome:R-HSA-6801289 PR:000048068 located_in GO:0030667 Reactome:R-HSA-6801305 PR:000048068 located_in GO:0101003 Reactome:R-HSA-6801314 PR:000048068 located_in GO:0070821 PRO_0000016294 PRO:DNx UniProtKB:P20702, 20-1163 PRO:DNx hITGAX/SigPep- PRO:DNx A vascular endothelial growth factor receptor 2 (human) that has had the signal peptide removed. UniProtKB:P35968, 20-1356. Reactome:R-HSA-195382 PRO_0000016771 UniProtKB:P35968, 20-1356 hKDR/SigPep- protein PR:000048096 Category=organism-modification. vascular endothelial growth factor receptor 2, signal peptide removed form (human) A vascular endothelial growth factor receptor 2 (human) that has had the signal peptide removed. UniProtKB:P35968, 20-1356. PRO:DNx Reactome:R-HSA-195382 Reactome:R-HSA-195382 PR:000048096 located_in GO:0005886 PRO_0000016771 PRO:DNx UniProtKB:P35968, 20-1356 PRO:DNx hKDR/SigPep- PRO:DNx A mast/stem cell growth factor receptor Kit (human) that has had the signal peptide removed. UniProtKB:P10721, 26-976. Reactome:R-HSA-197662 PRO_0000016754 UniProtKB:P10721, 26-976 hKIT/SigPep- protein PR:000048127 Category=organism-modification. mast/stem cell growth factor receptor Kit, signal peptide removed form (human) A mast/stem cell growth factor receptor Kit (human) that has had the signal peptide removed. UniProtKB:P10721, 26-976. PRO:DNx Reactome:R-HSA-197662 Reactome:R-HSA-197662 PR:000048127 located_in GO:0005886 PRO_0000016754 PRO:DNx UniProtKB:P10721, 26-976 PRO:DNx hKIT/SigPep- PRO:DNx A neutrophil gelatinase-associated lipocalin (human) that has had the signal peptide removed. UniProtKB:P80188, 21-198. Reactome:R-HSA-5215934 Reactome:R-HSA-6799614 PRO_0000017933 UniProtKB:P80188, 21-198 hLCN2/SigPep- protein PR:000048176 Category=organism-modification. neutrophil gelatinase-associated lipocalin, signal peptide removed form (human) A neutrophil gelatinase-associated lipocalin (human) that has had the signal peptide removed. UniProtKB:P80188, 21-198. PRO:DNx Reactome:R-HSA-5215934 Reactome:R-HSA-5215934 PR:000048176 located_in GO:0005576 Reactome:R-HSA-6799614 PR:000048176 located_in GO:0035580 PRO_0000017933 PRO:DNx UniProtKB:P80188, 21-198 PRO:DNx hLCN2/SigPep- PRO:DNx A leukocyte immunoglobulin-like receptor subfamily A member 4 (human) that has had the signal peptide removed. UniProtKB:P59901, 24-499. Reactome:R-HSA-6786744 PRO_0000014819 UniProtKB:P59901, 24-499 hLILRA4/SigPep- protein PR:000048202 Category=organism-modification. leukocyte immunoglobulin-like receptor subfamily A member 4, signal peptide removed form (human) A leukocyte immunoglobulin-like receptor subfamily A member 4 (human) that has had the signal peptide removed. UniProtKB:P59901, 24-499. PRO:DNx Reactome:R-HSA-6786744 Reactome:R-HSA-6786744 PR:000048202 located_in GO:0005886 PRO_0000014819 PRO:DNx UniProtKB:P59901, 24-499 PRO:DNx hLILRA4/SigPep- PRO:DNx A lactotransferrin (human) that has had the signal peptide removed. UniProtKB:P02788, 20-710. Reactome:R-HSA-1222567 Reactome:R-HSA-6799629 Reactome:R-HSA-6800962 Reactome:R-HSA-977171 PRO_0000035732 UniProtKB:P02788, 20-710 hLTF/SigPep- protein PR:000048272 Category=organism-modification. lactotransferrin, signal peptide removed form (human) A lactotransferrin (human) that has had the signal peptide removed. UniProtKB:P02788, 20-710. PRO:DNx Reactome:R-HSA-1222567 Reactome:R-HSA-977171 Reactome:R-HSA-1222567 PR:000048272 located_in GO:0097013 Reactome:R-HSA-6799629 PR:000048272 located_in GO:0035580 Reactome:R-HSA-6800962 PR:000048272 located_in GO:1904724 Reactome:R-HSA-977171 PR:000048272 located_in GO:0005576 PRO_0000035732 PRO:DNx UniProtKB:P02788, 20-710 PRO:DNx hLTF/SigPep- PRO:DNx A lumican (human) that has had the signal peptide removed. UniProtKB:P51884, 19-338. Reactome:R-HSA-2466189 PRO_0000032733 UniProtKB:P51884, 19-338 hLUM/SigPep- protein PR:000048273 Category=organism-modification. lumican, signal peptide removed form (human) A lumican (human) that has had the signal peptide removed. UniProtKB:P51884, 19-338. PRO:DNx Reactome:R-HSA-2466189 Reactome:R-HSA-2466189 PR:000048273 located_in GO:0005576 PRO_0000032733 PRO:DNx UniProtKB:P51884, 19-338 PRO:DNx hLUM/SigPep- PRO:DNx A tyrosine-protein kinase Mer (human) that has had the signal peptide removed. UniProtKB:Q12866, 21-999. Reactome:R-HSA-197593 PRO_0000024443 UniProtKB:Q12866, 21-999 hMERTK/SigPep- protein PR:000048369 Category=organism-modification. tyrosine-protein kinase Mer, signal peptide removed form (human) A tyrosine-protein kinase Mer (human) that has had the signal peptide removed. UniProtKB:Q12866, 21-999. PRO:DNx Reactome:R-HSA-197593 Reactome:R-HSA-197593 PR:000048369 located_in GO:0005886 PRO_0000024443 PRO:DNx UniProtKB:Q12866, 21-999 PRO:DNx hMERTK/SigPep- PRO:DNx A macrophage mannose receptor 1 (human) that has had the signal peptide removed. UniProtKB:P22897, 19-1456. Reactome:R-HSA-1216515 Reactome:R-HSA-1236785 Reactome:R-HSA-1236818 PRO_0000017548 UniProtKB:P22897, 19-1456 hMRC1/SigPep- protein PR:000048415 Category=organism-modification. macrophage mannose receptor 1, signal peptide removed form (human) A macrophage mannose receptor 1 (human) that has had the signal peptide removed. UniProtKB:P22897, 19-1456. PRO:DNx Reactome:R-HSA-1216515 Reactome:R-HSA-1236785 Reactome:R-HSA-1236818 Reactome:R-HSA-1216515 PR:000048415 located_in GO:0005886 Reactome:R-HSA-1236785 PR:000048415 located_in GO:0031901 Reactome:R-HSA-1236818 PR:000048415 located_in GO:0030669 PRO_0000017548 PRO:DNx UniProtKB:P22897, 19-1456 PRO:DNx hMRC1/SigPep- PRO:DNx A neural cell adhesion molecule 1 (human) that has had the signal peptide removed. UniProtKB:P13591, 20-858. Reactome:R-HSA-190987 PRO_0000015009 UniProtKB:P13591, 20-858 hNCAM1/SigPep- protein PR:000048517 Category=organism-modification. neural cell adhesion molecule 1, signal peptide removed form (human) A neural cell adhesion molecule 1 (human) that has had the signal peptide removed. UniProtKB:P13591, 20-858. PRO:DNx Reactome:R-HSA-190987 Reactome:R-HSA-190987 PR:000048517 located_in GO:0005886 PRO_0000015009 PRO:DNx UniProtKB:P13591, 20-858 PRO:DNx hNCAM1/SigPep- PRO:DNx A natural cytotoxicity triggering receptor 1 (human) that has had the signal peptide removed. UniProtKB:O76036, 22-304. Reactome:R-HSA-197739 PRO_0000015027 UniProtKB:O76036, 22-304 hNCR1/SigPep- protein PR:000048531 Category=organism-modification. natural cytotoxicity triggering receptor 1, signal peptide removed form (human) A natural cytotoxicity triggering receptor 1 (human) that has had the signal peptide removed. UniProtKB:O76036, 22-304. PRO:DNx Reactome:R-HSA-197739 Reactome:R-HSA-197739 PR:000048531 located_in GO:0005886 PRO_0000015027 PRO:DNx UniProtKB:O76036, 22-304 PRO:DNx hNCR1/SigPep- PRO:DNx A natural cytotoxicity triggering receptor 2 (human) that has had the signal peptide removed. UniProtKB:O95944, 22-276. Reactome:R-HSA-197652 PRO_0000015031 UniProtKB:O95944, 22-276 hNCR2/SigPep- protein PR:000048532 Category=organism-modification. natural cytotoxicity triggering receptor 2, signal peptide removed form (human) A natural cytotoxicity triggering receptor 2 (human) that has had the signal peptide removed. UniProtKB:O95944, 22-276. PRO:DNx Reactome:R-HSA-197652 Reactome:R-HSA-197652 PR:000048532 located_in GO:0005886 PRO_0000015031 PRO:DNx UniProtKB:O95944, 22-276 PRO:DNx hNCR2/SigPep- PRO:DNx A programmed cell death protein 1 (human) that has had the signal peptide removed. UniProtKB:Q15116, 21-288. Reactome:R-HSA-197604 PRO_0000014892 UniProtKB:Q15116, 21-288 hPDCD1/SigPep- protein PR:000048711 Category=organism-modification. programmed cell death protein 1, signal peptide removed form (human) A programmed cell death protein 1 (human) that has had the signal peptide removed. UniProtKB:Q15116, 21-288. PRO:DNx Reactome:R-HSA-197604 Reactome:R-HSA-197604 PR:000048711 located_in GO:0005886 PRO_0000014892 PRO:DNx UniProtKB:Q15116, 21-288 PRO:DNx hPDCD1/SigPep- PRO:DNx A platelet-derived growth factor receptor alpha (human) that has had the signal peptide removed. UniProtKB:P16234, 24-1089. Reactome:R-HSA-186794 PRO_0000016760 UniProtKB:P16234, 24-1089 hPDGFRA/SigPep- protein PR:000048723 Category=organism-modification. platelet-derived growth factor receptor alpha, signal peptide removed form (human) A platelet-derived growth factor receptor alpha (human) that has had the signal peptide removed. UniProtKB:P16234, 24-1089. PRO:DNx Reactome:R-HSA-186794 Reactome:R-HSA-186794 PR:000048723 located_in GO:0005886 PRO_0000016760 PRO:DNx UniProtKB:P16234, 24-1089 PRO:DNx hPDGFRA/SigPep- PRO:DNx A urokinase plasminogen activator surface receptor (human) that has had the signal peptide removed. UniProtKB:Q03405, 23-335. Reactome:R-HSA-162866 UniProtKB:Q03405, 23-335 hPLAUR/SigPep- protein PR:000048798 Category=organism-modification. urokinase plasminogen activator surface receptor, signal peptide removed form (human) A urokinase plasminogen activator surface receptor (human) that has had the signal peptide removed. UniProtKB:Q03405, 23-335. PRO:DNx Reactome:R-HSA-162866 Reactome:R-HSA-162866 PR:000048798 located_in GO:0005789 UniProtKB:Q03405, 23-335 PRO:DNx hPLAUR/SigPep- PRO:DNx A receptor-type tyrosine-protein phosphatase C (human) that has had the signal peptide removed. UniProtKB:P08575, 24-1304. Reactome:R-HSA-197931 Reactome:R-HSA-6806150 PRO_0000025470 UniProtKB:P08575, 24-1304 hPTPRC/SigPep- protein PR:000048962 Category=organism-modification. receptor-type tyrosine-protein phosphatase C, signal peptide removed form (human) A receptor-type tyrosine-protein phosphatase C (human) that has had the signal peptide removed. UniProtKB:P08575, 24-1304. PRO:DNx Reactome:R-HSA-197931 Reactome:R-HSA-197931 PR:000048962 located_in GO:0005886 Reactome:R-HSA-6806150 PR:000048962 located_in GO:0030667 PRO_0000025470 PRO:DNx UniProtKB:P08575, 24-1304 PRO:DNx hPTPRC/SigPep- PRO:DNx A syndecan-1 (human) that has had the signal peptide removed. UniProtKB:P18827, 23-310. Reactome:R-HSA-174758 Reactome:R-HSA-2054105 Reactome:R-HSA-2090025 PRO_0000033499 UniProtKB:P18827, 23-310 hSDC1/SigPep- protein PR:000049172 Category=organism-modification. syndecan-1, signal peptide removed form (human) A syndecan-1 (human) that has had the signal peptide removed. UniProtKB:P18827, 23-310. PRO:DNx Reactome:R-HSA-174758 Reactome:R-HSA-2054105 Reactome:R-HSA-2090025 Reactome:R-HSA-174758 PR:000049172 located_in GO:0005886 Reactome:R-HSA-2054105 PR:000049172 located_in GO:0005796 Reactome:R-HSA-2090025 PR:000049172 located_in GO:0043202 PRO_0000033499 PRO:DNx UniProtKB:P18827, 23-310 PRO:DNx hSDC1/SigPep- PRO:DNx A sialoadhesin (human) that has had the signal peptide removed. UniProtKB:Q9BZZ2, 20-1709. Reactome:R-HSA-197569 PRO_0000014968 UniProtKB:Q9BZZ2, 20-1709 hSIGLEC1/SigPep- protein PR:000049238 Category=organism-modification. sialoadhesin, signal peptide removed form (human) A sialoadhesin (human) that has had the signal peptide removed. UniProtKB:Q9BZZ2, 20-1709. PRO:DNx Reactome:R-HSA-197569 Reactome:R-HSA-197569 PR:000049238 located_in GO:0005886 PRO_0000014968 PRO:DNx UniProtKB:Q9BZZ2, 20-1709 PRO:DNx hSIGLEC1/SigPep- PRO:DNx A sialic acid-binding Ig-like lectin 5 (human) that has had the signal peptide removed. UniProtKB:O15389, 17-551. Reactome:R-HSA-197711 Reactome:R-HSA-6801283 Reactome:R-HSA-6801292 Reactome:R-HSA-6801320 PRO_0000014944 UniProtKB:O15389, 17-551 hSIGLEC5/SigPep- protein PR:000049245 Category=organism-modification. sialic acid-binding Ig-like lectin 5, signal peptide removed form (human) A sialic acid-binding Ig-like lectin 5 (human) that has had the signal peptide removed. UniProtKB:O15389, 17-551. PRO:DNx Reactome:R-HSA-197711 Reactome:R-HSA-197711 PR:000049245 located_in GO:0005886 Reactome:R-HSA-6801283 PR:000049245 located_in GO:0101003 Reactome:R-HSA-6801292 PR:000049245 located_in GO:0030667 Reactome:R-HSA-6801320 PR:000049245 located_in GO:0070821 PRO_0000014944 PRO:DNx UniProtKB:O15389, 17-551 PRO:DNx hSIGLEC5/SigPep- PRO:DNx A tyrosine-protein phosphatase non-receptor type substrate 1 (human) that has had the signal peptide removed. UniProtKB:P78324, 31-504. Reactome:R-HSA-3209922 Reactome:R-HSA-6803288 Reactome:R-HSA-6803321 PRO_0000014941 UniProtKB:P78324, 31-504 hSIRPA/SigPep- protein PR:000049250 Category=organism-modification. tyrosine-protein phosphatase non-receptor type substrate 1, signal peptide removed form (human) A tyrosine-protein phosphatase non-receptor type substrate 1 (human) that has had the signal peptide removed. UniProtKB:P78324, 31-504. PRO:DNx Reactome:R-HSA-3209922 Reactome:R-HSA-3209922 PR:000049250 located_in GO:0005886 Reactome:R-HSA-6803288 PR:000049250 located_in GO:0070821 Reactome:R-HSA-6803321 PR:000049250 located_in GO:0101003 PRO_0000014941 PRO:DNx UniProtKB:P78324, 31-504 PRO:DNx hSIRPA/SigPep- PRO:DNx A leukosialin (human) that has had the signal peptide removed. UniProtKB:P16150, 20-400. Reactome:R-HSA-204438 PRO_0000021588 UniProtKB:P16150, 20-400 hSPN/SigPep- protein PR:000049328 Category=organism-modification. leukosialin, signal peptide removed form (human) A leukosialin (human) that has had the signal peptide removed. UniProtKB:P16150, 20-400. PRO:DNx Reactome:R-HSA-204438 Reactome:R-HSA-204438 PR:000049328 located_in GO:0005886 PRO_0000021588 PRO:DNx UniProtKB:P16150, 20-400 PRO:DNx hSPN/SigPep- PRO:DNx A thrombomodulin (human) that has had the signal peptide removed. UniProtKB:P07204, 19-575. Reactome:R-HSA-141030 PRO_0000007771 UniProtKB:P07204, 19-575 hTHBD/SigPep- protein PR:000049437 Category=organism-modification. thrombomodulin, signal peptide removed form (human) A thrombomodulin (human) that has had the signal peptide removed. UniProtKB:P07204, 19-575. PRO:DNx Reactome:R-HSA-141030 Reactome:R-HSA-141030 PR:000049437 located_in GO:0005886 PRO_0000007771 PRO:DNx UniProtKB:P07204, 19-575 PRO:DNx hTHBD/SigPep- PRO:DNx A tumor necrosis factor receptor superfamily member 11A (human) that has had the signal peptide removed. UniProtKB:Q9Y6Q6, 30-616. Reactome:R-HSA-5668756 PRO_0000034585 UniProtKB:Q9Y6Q6, 30-616 hTNFRSF11A/SigPep- protein PR:000049488 Category=organism-modification. tumor necrosis factor receptor superfamily member 11A, signal peptide removed form (human) A tumor necrosis factor receptor superfamily member 11A (human) that has had the signal peptide removed. UniProtKB:Q9Y6Q6, 30-616. PRO:DNx Reactome:R-HSA-5668756 Reactome:R-HSA-5668756 PR:000049488 located_in GO:0005886 PRO_0000034585 PRO:DNx UniProtKB:Q9Y6Q6, 30-616 PRO:DNx hTNFRSF11A/SigPep- PRO:DNx A channel protein that has ion channel activity. An ion channel enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. IUPHARfam:689 fam:ion_chan protein PR:000049983 Category=family. ion channel protein A channel protein that has ion channel activity. An ion channel enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. IUPHARfam:689 PRO:XQ fam:ion_chan PRO:DAN An immunoglobulin complex whose components are encoded in the genome of human. hIg protein PR:000050032 Category=organism-complex. immunoglobulin complex (human) An immunoglobulin complex whose components are encoded in the genome of human. PRO:DAN hIg PRO:DAN 2 2 An IgD immunoglobulin complex whose components are encoded in the genome of human. IgD is composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds. An IgD 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. hIgD protein PR:000050170 Category=organism-complex. Requested by=HIPC. Requested by=CL. Note that an IgD immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgD immunoglobulin complex (human) An IgD immunoglobulin complex whose components are encoded in the genome of human. IgD is composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds. An IgD 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. GOC:add ISBN:0781765196 PMID:11282392 PRO:ADD hIgD PRO:DAN 2 2 An IgD immunoglobulin complex, circulating in human. Circulating IgD is composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. IgD antibody (human) hIgD/circulating protein PR:000050171 Category=organism-complex. Requested by=HIPC. Requested by=CL. IgD immunoglobulin complex, circulating (human) An IgD immunoglobulin complex, circulating in human. Circulating IgD is composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. GOC:add ISBN:0781765196 PMID:11282392 PRO:ADD IgD antibody (human) GOC:add PRO:ADD hIgD/circulating PRO:DAN A protein that is a translation product of some mRNA produced by a somatically recombined immunoglobulin heavy chain locus. IgH protein PR:000050174 Category=family. Requested by=IEDB. Note: In human, the IgH locus is described by https://www.genenames.org/cgi-bin/genefamilies/set/349. In mouse, the locus is described by MGI:96442. immunoglobulin heavy chain protein A protein that is a translation product of some mRNA produced by a somatically recombined immunoglobulin heavy chain locus. GOC:add PRO:ADD IgH PRO:DAN A protein that is a translation product of some mRNA produced by a somatically recombined immunoglobulin light chain locus. IgL protein PR:000050175 Category=family. Note: In human, the kappa light chain locus is described by https://www.genenames.org/cgi-bin/genefamilies/set/351, and the lambda light chain locus is described by https://www.genenames.org/cgi-bin/genefamilies/set/353. In mouse, the kappa locus is described by MGI:96494, and the lambda locus is described by MGI:96526. immunoglobulin light chain protein A protein that is a translation product of some mRNA produced by a somatically recombined immunoglobulin light chain locus. GOC:add PRO:ADD IgL PRO:DAN An immunoglobulin light chain protein that is produced from the immunoglobulin kappa locus. IgKappa protein PR:000050181 Category=gene. Note: In human, the kappa light chain locus is described by https://www.genenames.org/cgi-bin/genefamilies/set/351. In mouse, the kappa locus is described by MGI:96494. Ig kappa light chain protein An immunoglobulin light chain protein that is produced from the immunoglobulin kappa locus. PRO:DAN IgKappa PRO:DAN An immunoglobulin light chain protein that is produced from the immunoglobulin lambda locus. IgLambda protein PR:000050182 Category=gene. Note: In human, the lambda light chain locus is described by https://www.genenames.org/cgi-bin/genefamilies/set/353. In mouse, the lambda locus is described by MGI:96526. Ig lambda light chain protein An immunoglobulin light chain protein that is produced from the immunoglobulin lambda locus. PRO:DAN IgLambda PRO:DAN An immunoglobulin light chain protein that is encoded in the genome of human. hIgL protein PR:000050183 Category=organism-family. Note: The kappa light chain locus is described by https://www.genenames.org/cgi-bin/genefamilies/set/351, and the lambda light chain locus is described by https://www.genenames.org/cgi-bin/genefamilies/set/353. immunoglobulin light chain protein (human) An immunoglobulin light chain protein that is encoded in the genome of human. PRO:DAN hIgL PRO:DAN An Ig kappa light chain protein that is encoded in the genome of human. hIgKappa protein PR:000050184 Category=organism-gene. Note: The kappa light chain locus is described by https://www.genenames.org/cgi-bin/genefamilies/set/351. Ig kappa light chain protein (human) An Ig kappa light chain protein that is encoded in the genome of human. PRO:DAN hIgKappa PRO:DAN An Ig lambda light chain protein that is encoded in the genome of human. hIgLambda protein PR:000050185 Category=organism-gene. Note: The lambda light chain locus is described by https://www.genenames.org/cgi-bin/genefamilies/set/353. Ig lambda light chain protein (human) An Ig lambda light chain protein that is encoded in the genome of human. PRO:DAN hIgLambda PRO:DAN An immunoglobulin heavy chain protein in which the constant region is encoded by the IgD gene segment. IgHD immunoglobulin D heavy chain immunoglobulin delta heavy chain immunoglobulin heavy chain delta protein PR:000050186 Category=gene. Requested by=IEDB. IgD heavy chain protein An immunoglobulin heavy chain protein in which the constant region is encoded by the IgD gene segment. PRO:DAN IgHD PRO:DAN immunoglobulin D heavy chain PRO:DAN immunoglobulin delta heavy chain PRO:DAN immunoglobulin heavy chain delta PRO:DAN An IgD heavy chain protein that is encoded in the genome of human. hIgHD immunoglobulin D heavy chain (human) immunoglobulin delta heavy chain (human) immunoglobulin heavy chain delta (human) protein PR:000050187 Category=organism-gene. IgD heavy chain protein (human) An IgD heavy chain protein that is encoded in the genome of human. PRO:DAN hIgHD PRO:DAN immunoglobulin D heavy chain (human) PRO:DAN immunoglobulin delta heavy chain (human) PRO:DAN immunoglobulin heavy chain delta (human) PRO:DAN A receptor-type tyrosine-protein phosphatase C that is a translation product of a transcript that minimally includes the region encoded by the variable exon 4(A). CD45R PTPRC/iso:CD45R protein PR:000050216 Category=seqgroup. Requested by=CL. receptor-type tyrosine-protein phosphatase C isoform CD45R A receptor-type tyrosine-protein phosphatase C that is a translation product of a transcript that minimally includes the region encoded by the variable exon 4(A). GOC:add PRO:ADD PRO:DAN PTPRC/iso:CD45R PRO:DNx An MHC class II histocompatibility antigen alpha chain DRA that is encoded in the genome of mouse. mH2-Ea protein PR:000050370 Category=organism-gene. H-2 class II histocompatibility antigen, E alpha chain (mouse) An MHC class II histocompatibility antigen alpha chain DRA that is encoded in the genome of mouse. PRO:DAN mH2-Ea PRO:DAN A protein that is a translation product of the human HBA1, HBA2, HBB, HBD, HBE1, HBG1, HBG2, HBM, HBQ1, or HBZ genes, 1:1 orthologs thereof, or semi-orthologs thereof. fam:Hb protein PR:000050467 Category=family. hemoglobin subunit A protein that is a translation product of the human HBA1, HBA2, HBB, HBD, HBE1, HBG1, HBG2, HBM, HBQ1, or HBZ genes, 1:1 orthologs thereof, or semi-orthologs thereof. PRO:DAN fam:Hb PRO:DAN An endothelial transcription factor GATA-2 that is encoded in the genome of mouse. UniProtKB:O09100 GATA-binding protein 2 (mouse) mGATA2 protein Gata2 PR:O09100 Category=organism-gene. endothelial transcription factor GATA-2 (mouse) An endothelial transcription factor GATA-2 that is encoded in the genome of mouse. OMA:O09100 PRO:DNx GATA-binding protein 2 (mouse) UniProtKB:O09100 mGATA2 PRO:DNx Gata2 UniProtKB:O09100 An ectonucleotide pyrophosphatase/phosphodiesterase family member 3 that is encoded in the genome of human. Reactome:R-HSA-8939012 UniProtKB:O14638 CD203c (human) E-NPP 3 (human) NPP3 (human) PD-Ibeta (human) hENPP3 phosphodiesterase I beta (human) phosphodiesterase I/nucleotide pyrophosphatase 3 (human) protein ENPP3 PDNP3 PR:O14638 Category=organism-gene. ectonucleotide pyrophosphatase/phosphodiesterase family member 3 (human) An ectonucleotide pyrophosphatase/phosphodiesterase family member 3 that is encoded in the genome of human. PRO:WCB UniProtKB:O14638 Reactome:R-HSA-8939012 PR:O14638 located_in GO:0005886 CD203c (human) UniProtKB:O14638 E-NPP 3 (human) UniProtKB:O14638 NPP3 (human) UniProtKB:O14638 PD-Ibeta (human) UniProtKB:O14638 hENPP3 PRO:DNx phosphodiesterase I beta (human) UniProtKB:O14638 phosphodiesterase I/nucleotide pyrophosphatase 3 (human) UniProtKB:O14638 ENPP3 UniProtKB:O14638 PDNP3 UniProtKB:O14638 A homeobox protein Meis2 that is encoded in the genome of human. UniProtKB:O14770 Meis1-related protein 1 (human) hMEIS2 protein MEIS2 MRG1 PR:O14770 Category=organism-gene. homeobox protein Meis2 (human) A homeobox protein Meis2 that is encoded in the genome of human. PRO:DNx UniProtKB:O14770 Meis1-related protein 1 (human) UniProtKB:O14770 hMEIS2 PRO:DNx MEIS2 UniProtKB:O14770 MRG1 UniProtKB:O14770 A sialic acid-binding Ig-like lectin 5 that is encoded in the genome of human. UniProtKB:O15389 CD170 (human) CD33 antigen-like 2 (human) OB-BP2 (human) OB-binding protein 2 (human) hSIGLEC5 obesity-binding protein 2 (human) siglec-5 (human) protein CD33L2 OBBP2 SIGLEC5 PR:O15389 Category=organism-gene. sialic acid-binding Ig-like lectin 5 (human) A sialic acid-binding Ig-like lectin 5 that is encoded in the genome of human. PRO:WCB UniProtKB:O15389 CD170 (human) UniProtKB:O15389 CD33 antigen-like 2 (human) UniProtKB:O15389 OB-BP2 (human) UniProtKB:O15389 OB-binding protein 2 (human) UniProtKB:O15389 hSIGLEC5 PRO:DNx obesity-binding protein 2 (human) UniProtKB:O15389 siglec-5 (human) UniProtKB:O15389 CD33L2 UniProtKB:O15389 OBBP2 UniProtKB:O15389 SIGLEC5 UniProtKB:O15389 A tumor necrosis factor receptor superfamily member 11A that is encoded in the genome of mouse. UniProtKB:O35305 CD265 (mouse) ODFR (mouse) mTNFRSF11A osteoclast differentiation factor receptor (mouse) receptor activator of NF-KB (mouse) protein Rank Tnfrsf11a PR:O35305 Category=organism-gene. tumor necrosis factor receptor superfamily member 11A (mouse) A tumor necrosis factor receptor superfamily member 11A that is encoded in the genome of mouse. OMA:O35305 PRO:DNx CD265 (mouse) UniProtKB:O35305 ODFR (mouse) UniProtKB:O35305 mTNFRSF11A PRO:DNx osteoclast differentiation factor receptor (mouse) UniProtKB:O35305 receptor activator of NF-KB (mouse) UniProtKB:O35305 Rank UniProtKB:O35305 Tnfrsf11a UniProtKB:O35305 A platelet glycoprotein Ib alpha chain that is encoded in the genome of mouse. UniProtKB:O35930 CD42b (mouse) GP-Ib alpha (mouse) GPIb-alpha (mouse) GPIbA (mouse) glycoprotein Ibalpha (mouse) mGP1BA protein Gp1ba PR:O35930 Category=organism-gene. platelet glycoprotein Ib alpha chain (mouse) A platelet glycoprotein Ib alpha chain that is encoded in the genome of mouse. OMA:O35930 PRO:DNx CD42b (mouse) UniProtKB:O35930 GP-Ib alpha (mouse) UniProtKB:O35930 GPIb-alpha (mouse) UniProtKB:O35930 GPIbA (mouse) UniProtKB:O35930 glycoprotein Ibalpha (mouse) UniProtKB:O35930 mGP1BA PRO:DNx Gp1ba UniProtKB:O35930 A prominin-1 that is encoded in the genome of human. UniProtKB:O43490 CD133 (human) antigen AC133 (human) hPROM1 prominin-like protein 1 (human) protein MSTP061 PROM1 PROML1 PR:O43490 Category=organism-gene. prominin-1 (human) A prominin-1 that is encoded in the genome of human. PRO:CNA UniProtKB:O43490 CD133 (human) UniProtKB:O43490 antigen AC133 (human) UniProtKB:O43490 hPROM1 PRO:DNx prominin-like protein 1 (human) UniProtKB:O43490 MSTP061 UniProtKB:O43490 PROM1 UniProtKB:O43490 PROML1 UniProtKB:O43490 A C-C chemokine receptor type 6 that is encoded in the genome of mouse. UniProtKB:O54689 C-C CKR-6 (mouse) CC-CKR-6 (mouse) CCR-6 (mouse) CD196 (mouse) KY411 (mouse) mCCR6 protein Ccr6 Cmkbr6 PR:O54689 Category=organism-gene. C-C chemokine receptor type 6 (mouse) A C-C chemokine receptor type 6 that is encoded in the genome of mouse. OMA:O54689 PRO:DNx C-C CKR-6 (mouse) UniProtKB:O54689 CC-CKR-6 (mouse) UniProtKB:O54689 CCR-6 (mouse) UniProtKB:O54689 CD196 (mouse) UniProtKB:O54689 KY411 (mouse) UniProtKB:O54689 mCCR6 PRO:DNx Ccr6 UniProtKB:O54689 Cmkbr6 UniProtKB:O54689 A killer cell lectin-like receptor subfamily D member 1 that is encoded in the genome of mouse. UniProtKB:O54707 CD94 (mouse) killer cell lectin-like receptor subfamily D member 1 (mouse) mKLRD1 protein Cd94 Klrd1 PR:O54707 Category=organism-gene. natural killer cells antigen CD94 (mouse) A killer cell lectin-like receptor subfamily D member 1 that is encoded in the genome of mouse. OMA:O54707 PANTHER:PTHR22800:SF15 PRO:DNx CD94 (mouse) UniProtKB:O54707 killer cell lectin-like receptor subfamily D member 1 (mouse) UniProtKB:O54707 mKLRD1 PRO:DNx Cd94 UniProtKB:O54707 Klrd1 UniProtKB:O54707 An eomesodermin that is encoded in the genome of mouse. UniProtKB:O54839 T-box brain protein 2 (mouse) T-brain-2 (mouse) TBR-2 (mouse) mEOMES protein Eomes Tbr2 PR:O54839 Category=organism-gene. eomesodermin homolog (mouse) An eomesodermin that is encoded in the genome of mouse. OMA:O54839 PRO:DNx T-box brain protein 2 (mouse) UniProtKB:O54839 T-brain-2 (mouse) UniProtKB:O54839 TBR-2 (mouse) UniProtKB:O54839 mEOMES PRO:DNx Eomes UniProtKB:O54839 Tbr2 UniProtKB:O54839 A prominin-1 that is encoded in the genome of mouse. UniProtKB:O54990 CD133 (mouse) antigen AC133 homolog (mouse) mPROM1 prominin-like protein 1 (mouse) protein Prom Prom1 Proml1 PR:O54990 Category=organism-gene. prominin-1 (mouse) A prominin-1 that is encoded in the genome of mouse. OMA:O54990 PRO:DNx CD133 (mouse) UniProtKB:O54990 antigen AC133 homolog (mouse) UniProtKB:O54990 mPROM1 PRO:DNx prominin-like protein 1 (mouse) UniProtKB:O54990 Prom UniProtKB:O54990 Prom1 UniProtKB:O54990 Proml1 UniProtKB:O54990 A natural cytotoxicity triggering receptor 1 that is encoded in the genome of human. NK cell-activating receptor (human) UniProtKB:O76036 CD335 (human) NK-p46 (human) NKp46 (human) hNCR1 hNKp46 lymphocyte antigen 94 homolog (human) natural killer cell p46-related protein (human) protein LY94 NCR1 PR:O76036 Category=organism-gene. natural cytotoxicity triggering receptor 1 (human) A natural cytotoxicity triggering receptor 1 that is encoded in the genome of human. PRO:WCB UniProtKB:O76036 NK cell-activating receptor (human) UniProtKB:O76036 CD335 (human) UniProtKB:O76036 NK-p46 (human) UniProtKB:O76036 NKp46 (human) UniProtKB:O76036 hNCR1 PRO:DNx hNKp46 UniProtKB:O76036 lymphocyte antigen 94 homolog (human) UniProtKB:O76036 natural killer cell p46-related protein (human) UniProtKB:O76036 LY94 UniProtKB:O76036 NCR1 UniProtKB:O76036 A gamma-synuclein that is encoded in the genome of human. UniProtKB:O76070 SR (human) breast cancer-specific gene 1 protein (human) hSNCG synoretin (human) protein BCSG1 PERSYN PRSN SNCG PR:O76070 Category=organism-gene. gamma-synuclein (human) A gamma-synuclein that is encoded in the genome of human. PRO:DNx UniProtKB:O76070 SR (human) UniProtKB:O76070 breast cancer-specific gene 1 protein (human) UniProtKB:O76070 hSNCG PRO:DNx synoretin (human) UniProtKB:O76070 BCSG1 UniProtKB:O76070 PERSYN UniProtKB:O76070 PRSN UniProtKB:O76070 SNCG UniProtKB:O76070 A CD83 molecule that is encoded in the genome of mouse. UniProtKB:O88324 CD83 (mouse) mCD83 protein Cd83 PR:O88324 Category=organism-gene. CD83 antigen (mouse) A CD83 molecule that is encoded in the genome of mouse. OMA:O88324 PANTHER:PTHR15193:SF0 PRO:DNx CD83 (mouse) UniProtKB:O88324 mCD83 PRO:DNx Cd83 UniProtKB:O88324 A C-X-C chemokine receptor type 3 that is encoded in the genome of mouse. UniProtKB:O88410 CD183 (mouse) CXC-R3 (mouse) CXCR-3 (mouse) IP-10 receptor (mouse) interferon-inducible protein 10 receptor (mouse) mCXCR3 protein Cmkar3 Cxcr3 PR:O88410 Category=organism-gene. C-X-C chemokine receptor type 3 (mouse) A C-X-C chemokine receptor type 3 that is encoded in the genome of mouse. OMA:O88410 PRO:DNx CD183 (mouse) UniProtKB:O88410 CXC-R3 (mouse) UniProtKB:O88410 CXCR-3 (mouse) UniProtKB:O88410 IP-10 receptor (mouse) UniProtKB:O88410 interferon-inducible protein 10 receptor (mouse) UniProtKB:O88410 mCXCR3 PRO:DNx Cmkar3 UniProtKB:O88410 Cxcr3 UniProtKB:O88410 A killer cell lectin-like receptor subfamily G member 1 that is encoded in the genome of mouse. UniProtKB:O88713 mKLRG1 mast cell function-associated antigen 2F1 (mouse) protein Klrg1 Mafa PR:O88713 Category=organism-gene. killer cell lectin-like receptor subfamily G member 1 (mouse) A killer cell lectin-like receptor subfamily G member 1 that is encoded in the genome of mouse. OMA:O88713 PRO:DNx mKLRG1 PRO:DNx mast cell function-associated antigen 2F1 (mouse) UniProtKB:O88713 Klrg1 UniProtKB:O88713 Mafa UniProtKB:O88713 A complement component C1q receptor that is encoded in the genome of mouse. UniProtKB:O89103 C1q/MBL/SPA receptor (mouse) C1qR(p) (mouse) C1qRp (mouse) CD93 (mouse) Ly-68 (mouse) cell surface antigen AA4 (mouse) complement component 1 q subcomponent receptor 1 (mouse) lymphocyte antigen 68 (mouse) mCD93 protein Aa4 C1qr1 C1qrp Cd93 Ly68 PR:O89103 Category=organism-gene. complement component C1q receptor (mouse) A complement component C1q receptor that is encoded in the genome of mouse. OMA:O89103 PRO:DNx C1q/MBL/SPA receptor (mouse) UniProtKB:O89103 C1qR(p) (mouse) UniProtKB:O89103 C1qRp (mouse) UniProtKB:O89103 CD93 (mouse) UniProtKB:O89103 Ly-68 (mouse) UniProtKB:O89103 cell surface antigen AA4 (mouse) UniProtKB:O89103 complement component 1 q subcomponent receptor 1 (mouse) UniProtKB:O89103 lymphocyte antigen 68 (mouse) UniProtKB:O89103 mCD93 PRO:DNx Aa4 UniProtKB:O89103 C1qr1 UniProtKB:O89103 C1qrp UniProtKB:O89103 Cd93 UniProtKB:O89103 Ly68 UniProtKB:O89103 An eomesodermin that is encoded in the genome of human. UniProtKB:O95936 T-box brain protein 2 (human) T-brain-2 (human) TBR-2 (human) hEOMES protein EOMES TBR2 PR:O95936 Category=organism-gene. eomesodermin homolog (human) An eomesodermin that is encoded in the genome of human. PRO:CNA UniProtKB:O95936 T-box brain protein 2 (human) UniProtKB:O95936 T-brain-2 (human) UniProtKB:O95936 TBR-2 (human) UniProtKB:O95936 hEOMES PRO:DNx EOMES UniProtKB:O95936 TBR2 UniProtKB:O95936 A natural cytotoxicity triggering receptor 2 that is encoded in the genome of human. NK cell-activating receptor (human) UniProtKB:O95944 CD336 (human) NK-p44 (human) NKp44 (human) hNCR2 lymphocyte antigen 95 homolog (human) natural killer cell p44-related protein (human) protein LY95 NCR2 PR:O95944 Category=organism-gene. natural cytotoxicity triggering receptor 2 (human) A natural cytotoxicity triggering receptor 2 that is encoded in the genome of human. PRO:WCB UniProtKB:O95944 NK cell-activating receptor (human) UniProtKB:O95944 CD336 (human) UniProtKB:O95944 NK-p44 (human) UniProtKB:O95944 NKp44 (human) UniProtKB:O95944 hNCR2 PRO:DNx lymphocyte antigen 95 homolog (human) UniProtKB:O95944 natural killer cell p44-related protein (human) UniProtKB:O95944 LY95 UniProtKB:O95944 NCR2 UniProtKB:O95944 A proto-oncogene c-Fos that is encoded in the genome of human. Reactome:R-HSA-450216 UniProtKB:P01100 G0/G1 switch regulatory protein 7 (human) cellular oncogene fos (human) hFOS protein FOS G0S7 PR:P01100 Category=organism-gene. proto-oncogene c-Fos (human) A proto-oncogene c-Fos that is encoded in the genome of human. PRO:DNx UniProtKB:P01100 Reactome:R-HSA-450216 PR:P01100 located_in GO:0005654 G0/G1 switch regulatory protein 7 (human) UniProtKB:P01100 cellular oncogene fos (human) UniProtKB:P01100 hFOS PRO:DNx FOS UniProtKB:P01100 G0S7 UniProtKB:P01100 A proto-oncogene c-Fos that is encoded in the genome of mouse. UniProtKB:P01101 cellular oncogene fos (mouse) mFOS protein Fos PR:P01101 Category=organism-gene. proto-oncogene c-Fos (mouse) A proto-oncogene c-Fos that is encoded in the genome of mouse. OMA:P01101 PRO:DNx cellular oncogene fos (mouse) UniProtKB:P01101 mFOS PRO:DNx Fos UniProtKB:P01101 A VIP peptides that is encoded in the genome of human. UniProtKB:P01282 hVIP vasoactive intestinal peptides (human) vasoactive intestinal polypeptides (human) protein VIP PR:P01282 Category=organism-gene. VIP peptides (human) A VIP peptides that is encoded in the genome of human. PRO:DNx UniProtKB:P01282 hVIP PRO:DNx vasoactive intestinal peptides (human) PRO:DAN vasoactive intestinal polypeptides (human) PRO:DAN VIP UniProtKB:P01282 An interleukin-2 receptor subunit alpha that is encoded in the genome of human. p55 (human) UniProtKB:P01589 CD25 (human) IL-2 receptor subunit alpha (human) IL-2-RA (human) IL-2R subunit alpha (human) IL2-RA (human) TAC antigen (human) hIL2RA protein IL2RA PR:P01589 Category=organism-gene. interleukin-2 receptor subunit alpha (human) An interleukin-2 receptor subunit alpha that is encoded in the genome of human. PRO:CNA UniProtKB:P01589 p55 (human) UniProtKB:P01589 CD25 (human) UniProtKB:P01589 IL-2 receptor subunit alpha (human) UniProtKB:P01589 IL-2-RA (human) UniProtKB:P01589 IL-2R subunit alpha (human) UniProtKB:P01589 IL2-RA (human) UniProtKB:P01589 TAC antigen (human) UniProtKB:P01589 hIL2RA PRO:DNx IL2RA UniProtKB:P01589 An interleukin-2 receptor subunit alpha that is encoded in the genome of mouse. p55 (mouse) UniProtKB:P01590 CD25 (mouse) IL-2 receptor subunit alpha (mouse) IL-2-RA (mouse) IL-2R subunit alpha (mouse) IL2-RA (mouse) mIL2RA protein Il2r Il2ra PR:P01590 Category=organism-gene. interleukin-2 receptor subunit alpha (mouse) An interleukin-2 receptor subunit alpha that is encoded in the genome of mouse. OMA:P01590 PRO:DNx p55 (mouse) UniProtKB:P01590 CD25 (mouse) UniProtKB:P01590 IL-2 receptor subunit alpha (mouse) UniProtKB:P01590 IL-2-RA (mouse) UniProtKB:P01590 IL-2R subunit alpha (mouse) UniProtKB:P01590 IL2-RA (mouse) UniProtKB:P01590 mIL2RA PRO:DNx Il2r UniProtKB:P01590 Il2ra UniProtKB:P01590 A CD4 molecule that is encoded in the genome of human. UniProtKB:P01730 T-cell surface antigen T4/Leu-3 (human) hCD4 protein CD4 PR:P01730 Category=organism-gene. T-cell surface glycoprotein CD4 (human) A CD4 molecule that is encoded in the genome of human. PRO:DNx UniProtKB:P01730 T-cell surface antigen T4/Leu-3 (human) UniProtKB:P01730 hCD4 PRO:DNx CD4 UniProtKB:P01730 A T-cell surface glycoprotein CD8 alpha chain that is encoded in the genome of mouse. UniProtKB:P01731 CD8a (mouse) T-cell surface glycoprotein Lyt-2 (mouse) mCD8A protein Cd8a Lyt-2 Lyt2 PR:P01731 Category=organism-gene. T-cell surface glycoprotein CD8 alpha chain (mouse) A T-cell surface glycoprotein CD8 alpha chain that is encoded in the genome of mouse. OMA:P01731 PRO:DNx CD8a (mouse) UniProtKB:P01731 T-cell surface glycoprotein Lyt-2 (mouse) UniProtKB:P01731 mCD8A PRO:DNx Cd8a UniProtKB:P01731 Lyt-2 UniProtKB:P01731 Lyt2 UniProtKB:P01731 A T-cell surface glycoprotein CD8 alpha chain that is encoded in the genome of human. UniProtKB:P01732 CD8a (human) T-lymphocyte differentiation antigen T8/Leu-2 (human) hCD8A protein CD8A MAL PR:P01732 Category=organism-gene. T-cell surface glycoprotein CD8 alpha chain (human) A T-cell surface glycoprotein CD8 alpha chain that is encoded in the genome of human. PRO:CNA UniProtKB:P01732 CD8a (human) UniProtKB:P01732 T-lymphocyte differentiation antigen T8/Leu-2 (human) UniProtKB:P01732 hCD8A PRO:DNx CD8A UniProtKB:P01732 MAL UniProtKB:P01732 A T-cell surface glycoprotein CD8 alpha chain isoform 1 that is encoded in the genome of human. UniProtKB:P01732-1 T-cell surface glycoprotein CD8 alpha chain isoform mCD8alpha (human) T-cell surface glycoprotein CD8 alpha chain isoform membrane (human) hCD8A/iso:1 protein PR:P01732-1 Category=organism-sequence. T-cell surface glycoprotein CD8 alpha chain isoform 1 (human) A T-cell surface glycoprotein CD8 alpha chain isoform 1 that is encoded in the genome of human. PRO:DAN T-cell surface glycoprotein CD8 alpha chain isoform mCD8alpha (human) UniProtKB:P01732 T-cell surface glycoprotein CD8 alpha chain isoform membrane (human) UniProtKB:P01732 hCD8A/iso:1 PRO:DNx A Thy-1 membrane glycoprotein that is encoded in the genome of mouse. UniProtKB:P01831 CD90 (mouse) Thy-1 antigen (mouse) mTHY1 protein Thy-1 Thy1 PR:P01831 Category=organism-gene. Thy-1 membrane glycoprotein (mouse) A Thy-1 membrane glycoprotein that is encoded in the genome of mouse. OMA:P01831 PRO:DNx CD90 (mouse) UniProtKB:P01831 Thy-1 antigen (mouse) UniProtKB:P01831 mTHY1 PRO:DNx Thy-1 UniProtKB:P01831 Thy1 UniProtKB:P01831 An MHC class II histocompatibility antigen alpha chain DRA that is encoded in the genome of human. MRO:0000693 UniProtKB:P01903 HLA-DRA chain MHC class II antigen DRA (human) hHLA-DRA protein HLA-DRA HLA-DRA1 PR:P01903 Category=organism-gene. Requested by=IEDB. HLA class II histocompatibility antigen, DR alpha chain (human) An MHC class II histocompatibility antigen alpha chain DRA that is encoded in the genome of human. PRO:WCB UniProtKB:P01903 HLA-DRA chain MRO:0000693 MHC class II antigen DRA (human) UniProtKB:P01903 hHLA-DRA PRO:DNx HLA-DRA UniProtKB:P01903 HLA-DRA1 UniProtKB:P01903 A hemoglobin subunit zeta that is encoded in the genome of human. UniProtKB:P02008 HBAZ (human) hHBZ hemoglobin zeta chain (human) zeta-globin (human) protein HBZ HBZ2 PR:P02008 Category=organism-gene. hemoglobin subunit zeta (human) A hemoglobin subunit zeta that is encoded in the genome of human. PRO:DNx UniProtKB:P02008 HBAZ (human) UniProtKB:P02008 hHBZ PRO:DNx hemoglobin zeta chain (human) UniProtKB:P02008 zeta-globin (human) UniProtKB:P02008 HBZ UniProtKB:P02008 HBZ2 UniProtKB:P02008 A hemoglobin subunit beta-1 that is encoded in the genome of mouse. UniProtKB:P02088 beta-1-globin (mouse) hemoglobin beta-1 chain (mouse) hemoglobin beta-major chain (mouse) mHbb-b1 protein Hbb-b1 PR:P02088 Category=organism-gene. hemoglobin subunit beta-1 (mouse) A hemoglobin subunit beta-1 that is encoded in the genome of mouse. PRO:DNx UniProtKB:P02088 beta-1-globin (mouse) UniProtKB:P02088 hemoglobin beta-1 chain (mouse) UniProtKB:P02088 hemoglobin beta-major chain (mouse) UniProtKB:P02088 mHbb-b1 PRO:DNx Hbb-b1 UniProtKB:P02088 A collagen alpha-1(I) chain that is encoded in the genome of human. UniProtKB:P02452 alpha-1 type I collagen (human) hCOL1A1 protein COL1A1 PR:P02452 Category=organism-gene. collagen alpha-1(I) chain (human) A collagen alpha-1(I) chain that is encoded in the genome of human. PRO:CNA UniProtKB:P02452 alpha-1 type I collagen (human) UniProtKB:P02452 hCOL1A1 PRO:DNx COL1A1 UniProtKB:P02452 A glycophorin-A that is encoded in the genome of human. UniProtKB:P02724 CD235a (human) MN sialoglycoprotein (human) PAS-2 (human) hGYPA sialoglycoprotein alpha (human) protein GPA GYPA PR:P02724 Category=organism-gene. glycophorin-A (human) A glycophorin-A that is encoded in the genome of human. PRO:CNA UniProtKB:P02724 CD235a (human) UniProtKB:P02724 MN sialoglycoprotein (human) UniProtKB:P02724 PAS-2 (human) UniProtKB:P02724 hGYPA PRO:DNx sialoglycoprotein alpha (human) UniProtKB:P02724 GPA UniProtKB:P02724 GYPA UniProtKB:P02724 A transferrin receptor protein 1 that is encoded in the genome of human. TR (human) p90 (human) Reactome:R-HSA-434196 Reactome:R-HSA-434330 Reactome:R-HSA-8869124 Reactome:R-HSA-8961829 Reactome:R-HSA-917983 UniProtKB:P02786 CD71 (human) T9 (human) TfR (human) TfR1 (human) Trfr (human) hTFRC protein TFRC PR:P02786 Category=organism-gene. transferrin receptor protein 1 (human) A transferrin receptor protein 1 that is encoded in the genome of human. PRO:WCB UniProtKB:P02786 TR (human) UniProtKB:P02786 p90 (human) UniProtKB:P02786 Reactome:R-HSA-434196 PR:P02786 located_in GO:0030659 Reactome:R-HSA-434330 PR:P02786 located_in GO:0000139 Reactome:R-HSA-8869124 PR:P02786 located_in GO:0030665 Reactome:R-HSA-8961829 PR:P02786 located_in GO:0010008 Reactome:R-HSA-917983 PR:P02786 located_in GO:0005886 CD71 (human) UniProtKB:P02786 T9 (human) UniProtKB:P02786 TfR (human) UniProtKB:P02786 TfR1 (human) UniProtKB:P02786 Trfr (human) UniProtKB:P02786 hTFRC PRO:DNx TFRC UniProtKB:P02786 A lactotransferrin that is encoded in the genome of human. UniProtKB:P02788 growth-inhibiting protein 12 (human) hLTF lactoferrin (human) talalactoferrin (human) protein GIG12 LF LTF PR:P02788 Category=organism-gene. lactotransferrin (human) A lactotransferrin that is encoded in the genome of human. PRO:DNx UniProtKB:P02788 growth-inhibiting protein 12 (human) UniProtKB:P02788 hLTF PRO:DNx lactoferrin (human) UniProtKB:P02788 talalactoferrin (human) UniProtKB:P02788 GIG12 UniProtKB:P02788 LF UniProtKB:P02788 LTF UniProtKB:P02788 A glial fibrillary acidic protein that is encoded in the genome of mouse. UniProtKB:P03995 GFAP (mouse) mGFAP protein Gfap PR:P03995 Category=organism-gene. glial fibrillary acidic protein (mouse) A glial fibrillary acidic protein that is encoded in the genome of mouse. OMA:P03995 PRO:DNx GFAP (mouse) UniProtKB:P03995 mGFAP PRO:DNx Gfap UniProtKB:P03995 A DNA nucleotidylexotransferase that is encoded in the genome of human. terminal transferase (human) UniProtKB:P04053 hDNTT terminal addition enzyme (human) terminal deoxynucleotidyltransferase (human) protein DNTT TDT PR:P04053 Category=organism-gene. DNA nucleotidylexotransferase (human) A DNA nucleotidylexotransferase that is encoded in the genome of human. PRO:DNx UniProtKB:P04053 terminal transferase (human) UniProtKB:P04053 hDNTT PRO:DNx terminal addition enzyme (human) UniProtKB:P04053 terminal deoxynucleotidyltransferase (human) UniProtKB:P04053 DNTT UniProtKB:P04053 TDT UniProtKB:P04053 A Thy-1 membrane glycoprotein that is encoded in the genome of human. UniProtKB:P04216 CD90 (human) CDw90 (human) Thy-1 antigen (human) hTHY1 protein THY1 PR:P04216 Category=organism-gene. Thy-1 membrane glycoprotein (human) A Thy-1 membrane glycoprotein that is encoded in the genome of human. PRO:WCB UniProtKB:P04216 CD90 (human) UniProtKB:P04216 CDw90 (human) UniProtKB:P04216 Thy-1 antigen (human) UniProtKB:P04216 hTHY1 PRO:DNx THY1 UniProtKB:P04216 An arginase-1 that is encoded in the genome of human. Reactome:R-HSA-6798764 Reactome:R-HSA-6801011 Reactome:R-HSA-6806221 Reactome:R-HSA-70561 UniProtKB:P05089 hARG1 liver-type arginase (human) type I arginase (human) protein ARG1 PR:P05089 Category=organism-gene. arginase-1 (human) An arginase-1 that is encoded in the genome of human. PRO:WCB UniProtKB:P05089 Reactome:R-HSA-6798764 PR:P05089 located_in GO:0035578 Reactome:R-HSA-6801011 PR:P05089 located_in GO:0035580 Reactome:R-HSA-6806221 PR:P05089 located_in GO:0005576 Reactome:R-HSA-70561 PR:P05089 located_in GO:0005829 hARG1 PRO:DNx liver-type arginase (human) UniProtKB:P05089 type I arginase (human) UniProtKB:P05089 ARG1 UniProtKB:P05089 A myeloperoxidase that is encoded in the genome of human. UniProtKB:P05164 hMPO protein MPO PR:P05164 Category=organism-gene. myeloperoxidase (human) A myeloperoxidase that is encoded in the genome of human. PRO:DNx UniProtKB:P05164 hMPO PRO:DNx MPO UniProtKB:P05164 A mast/stem cell growth factor receptor that is encoded in the genome of mouse. UniProtKB:P05532 CD117 (mouse) SCFR (mouse) mKIT proto-oncogene c-Kit (mouse) tyrosine-protein kinase Kit (mouse) protein Kit Sl PR:P05532 Category=organism-gene. mast/stem cell growth factor receptor Kit (mouse) A mast/stem cell growth factor receptor that is encoded in the genome of mouse. OMA:MOUSE17014 PRO:DNx CD117 (mouse) UniProtKB:P05532 SCFR (mouse) UniProtKB:P05532 mKIT PRO:DNx proto-oncogene c-Kit (mouse) UniProtKB:P05532 tyrosine-protein kinase Kit (mouse) UniProtKB:P05532 Kit UniProtKB:P05532 Sl UniProtKB:P05532 A lymphocyte antigen 6A-2/6E-1 that is encoded in the genome of mouse. TAP (mouse) UniProtKB:P05533 Ly-6A.2/Ly-6E.1 (mouse) SCA-1 (mouse) Stem cell antigen 1 (mouse) T-cell-activating protein (mouse) mLy6a protein Ly6 Ly6a PR:P05533 Category=organism-gene. lymphocyte antigen 6A-2/6E-1 (mouse) A lymphocyte antigen 6A-2/6E-1 that is encoded in the genome of mouse. PRO:CNA UniProtKB:P05533 TAP (mouse) UniProtKB:P05533 Ly-6A.2/Ly-6E.1 (mouse) UniProtKB:P05533 SCA-1 (mouse) UniProtKB:P05533 Stem cell antigen 1 (mouse) UniProtKB:P05533 T-cell-activating protein (mouse) UniProtKB:P05533 mLy6a PRO:DNx Ly6 UniProtKB:P05533 Ly6a UniProtKB:P05533 An integrin alpha-M that is encoded in the genome of mouse. UniProtKB:P05555 CD11 antigen-like family member B (mouse) CD11b (mouse) CR-3 alpha chain (mouse) cell surface glycoprotein MAC-1 subunit alpha (mouse) leukocyte adhesion receptor MO1 (mouse) mITGAM protein Itgam PR:P05555 Category=organism-gene. integrin alpha-M (mouse) An integrin alpha-M that is encoded in the genome of mouse. OMA:P05555 PRO:DNx CD11 antigen-like family member B (mouse) UniProtKB:P05555 CD11b (mouse) UniProtKB:P05555 CR-3 alpha chain (mouse) UniProtKB:P05555 cell surface glycoprotein MAC-1 subunit alpha (mouse) UniProtKB:P05555 leukocyte adhesion receptor MO1 (mouse) UniProtKB:P05555 mITGAM PRO:DNx Itgam UniProtKB:P05555 A T-cell surface glycoprotein CD1a that is encoded in the genome of human. MRO:0000888 UniProtKB:P06126 CD1a (human) T-cell surface antigen T6/Leu-6 (human) hCD1A hTa1 thymocyte antigen human CD1a chain protein CD1A PR:P06126 Category=organism-gene. T-cell surface glycoprotein CD1a (human) A T-cell surface glycoprotein CD1a that is encoded in the genome of human. PRO:WCB UniProtKB:P06126 CD1a (human) UniProtKB:P06126 T-cell surface antigen T6/Leu-6 (human) UniProtKB:P06126 hCD1A PRO:DNx hTa1 thymocyte antigen UniProtKB:P06126 human CD1a chain MRO:0000888 CD1A UniProtKB:P06126 A T-cell surface glycoprotein CD5 that is encoded in the genome of human. UniProtKB:P06127 hCD5 lymphocyte antigen T1/Leu-1 (human) protein CD5 LEU1 PR:P06127 Category=organism-gene. T-cell surface glycoprotein CD5 (human) A T-cell surface glycoprotein CD5 that is encoded in the genome of human. PRO:WCB UniProtKB:P06127 hCD5 PRO:DNx lymphocyte antigen T1/Leu-1 (human) UniProtKB:P06127 CD5 UniProtKB:P06127 LEU1 UniProtKB:P06127 A cholecystokinin that is encoded in the genome of human. UniProtKB:P06307 hCCK protein CCK PR:P06307 Category=organism-gene. cholecystokinin (human) A cholecystokinin that is encoded in the genome of human. PRO:DNx UniProtKB:P06307 hCCK PRO:DNx CCK UniProtKB:P06307 A CD4 molecule that is encoded in the genome of mouse. UniProtKB:P06332 CD4 (mouse) T-cell differentiation antigen L3T4 (mouse) T-cell surface antigen T4/Leu-3 (mouse) mCD4 protein Cd4 PR:P06332 Category=organism-gene. T-cell surface glycoprotein CD4 (mouse) A CD4 molecule that is encoded in the genome of mouse. OMA:P06332 PRO:DNx CD4 (mouse) UniProtKB:P06332 T-cell differentiation antigen L3T4 (mouse) UniProtKB:P06332 T-cell surface antigen T4/Leu-3 (mouse) UniProtKB:P06332 mCD4 PRO:DNx Cd4 UniProtKB:P06332 A hemoglobin subunit zeta that is encoded in the genome of mouse. UniProtKB:P06467 alpha-like embryonic globin chain x (mouse) hemoglobin zeta chain (mouse) mHBZ zeta-globin (mouse) protein Hba-x Hbz Hbz1 PR:P06467 Category=organism-gene. hemoglobin subunit zeta (mouse) A hemoglobin subunit zeta that is encoded in the genome of mouse. OMA:P06467 PRO:DNx alpha-like embryonic globin chain x (mouse) UniProtKB:P06467 hemoglobin zeta chain (mouse) UniProtKB:P06467 mHBZ PRO:DNx zeta-globin (mouse) UniProtKB:P06467 Hba-x UniProtKB:P06467 Hbz UniProtKB:P06467 Hbz1 UniProtKB:P06467 A CD2 molecule that is encoded in the genome of human. UniProtKB:P06729 LFA-2 (human) LFA-3 receptor (human) T-cell surface antigen T11/Leu-5 (human) erythrocyte receptor (human) hCD2 rosette receptor (human) protein CD2 SRBC PR:P06729 Category=organism-gene. T-cell surface antigen CD2 (human) A CD2 molecule that is encoded in the genome of human. PRO:CNA UniProtKB:P06729 LFA-2 (human) UniProtKB:P06729 LFA-3 receptor (human) UniProtKB:P06729 T-cell surface antigen T11/Leu-5 (human) UniProtKB:P06729 erythrocyte receptor (human) UniProtKB:P06729 hCD2 PRO:DNx rosette receptor (human) UniProtKB:P06729 CD2 UniProtKB:P06729 SRBC UniProtKB:P06729 A low affinity immunoglobulin epsilon Fc receptor that is encoded in the genome of human. Reactome:R-HSA-2127280 UniProtKB:P06734 BLAST-2 (human) C-type lectin domain family 4 member J (human) CD23 (human) Fc-epsilon-RII (human) hFCER2 immunoglobulin E-binding factor (human) lymphocyte IgE receptor (human) protein CD23A CLEC4J FCE2 FCER2 IGEBF PR:P06734 Category=organism-gene. low affinity immunoglobulin epsilon Fc receptor (human) A low affinity immunoglobulin epsilon Fc receptor that is encoded in the genome of human. PRO:WCB UniProtKB:P06734 Reactome:R-HSA-2127280 PR:P06734 located_in GO:0005886 BLAST-2 (human) UniProtKB:P06734 C-type lectin domain family 4 member J (human) UniProtKB:P06734 CD23 (human) UniProtKB:P06734 Fc-epsilon-RII (human) UniProtKB:P06734 hFCER2 PRO:DNx immunoglobulin E-binding factor (human) UniProtKB:P06734 lymphocyte IgE receptor (human) UniProtKB:P06734 CD23A UniProtKB:P06734 CLEC4J UniProtKB:P06734 FCE2 UniProtKB:P06734 FCER2 UniProtKB:P06734 IGEBF UniProtKB:P06734 A myb proto-oncogene protein that is encoded in the genome of mouse. UniProtKB:P06876 mMYB proto-oncogene c-Myb (mouse) protein Myb PR:P06876 Category=organism-gene. transcriptional activator Myb (mouse) A myb proto-oncogene protein that is encoded in the genome of mouse. OMA:P06876 PRO:DNx mMYB PRO:DNx proto-oncogene c-Myb (mouse) UniProtKB:P06876 Myb UniProtKB:P06876 A thrombomodulin that is encoded in the genome of human. UniProtKB:P07204 CD141 (human) TM (human) fetomodulin (human) hTHBD protein THBD THRM PR:P07204 Category=organism-gene. thrombomodulin (human) A thrombomodulin that is encoded in the genome of human. PRO:WCB UniProtKB:P07204 CD141 (human) UniProtKB:P07204 TM (human) UniProtKB:P07204 fetomodulin (human) UniProtKB:P07204 hTHBD PRO:DNx THBD UniProtKB:P07204 THRM UniProtKB:P07204 A macrophage colony-stimulating factor 1 receptor that is encoded in the genome of human. DTO:03100090 UniProtKB:P07333 CD115 (human) CSF-1 receptor (human) CSF-1-R (human) CSF-1R (human) M-CSF-R (human) hCSF1R proto-oncogene c-Fms (human) protein CSF1R FMS PR:P07333 Category=organism-gene. macrophage colony-stimulating factor 1 receptor (human) A macrophage colony-stimulating factor 1 receptor that is encoded in the genome of human. PRO:WCB UniProtKB:P07333 CD115 (human) UniProtKB:P07333 CSF-1 receptor (human) UniProtKB:P07333 CSF-1-R (human) UniProtKB:P07333 CSF-1R (human) UniProtKB:P07333 M-CSF-R (human) UniProtKB:P07333 hCSF1R PRO:DNx proto-oncogene c-Fms (human) UniProtKB:P07333 CSF1R UniProtKB:P07333 FMS UniProtKB:P07333 A platelet glycoprotein Ib alpha chain that is encoded in the genome of human. UniProtKB:P07359 CD42b (human) GP-Ib alpha (human) GPIb-alpha (human) GPIbA (human) antigen CD42b-alpha (human) glycoprotein Ibalpha (human) hGP1BA protein GP1BA PR:P07359 Category=organism-gene. platelet glycoprotein Ib alpha chain (human) A platelet glycoprotein Ib alpha chain that is encoded in the genome of human. PRO:WCB UniProtKB:P07359 CD42b (human) UniProtKB:P07359 GP-Ib alpha (human) UniProtKB:P07359 GPIb-alpha (human) UniProtKB:P07359 GPIbA (human) UniProtKB:P07359 antigen CD42b-alpha (human) UniProtKB:P07359 glycoprotein Ibalpha (human) UniProtKB:P07359 hGP1BA PRO:DNx GP1BA UniProtKB:P07359 A CD3 epsilon that is encoded in the genome of human. UniProtKB:P07766 CD3e (human) T-cell surface antigen T3/Leu-4 epsilon chain (human) hCD3E protein CD3E T3E PR:P07766 Category=organism-gene. T-cell surface glycoprotein CD3 epsilon chain (human) A CD3 epsilon that is encoded in the genome of human. PRO:CNA UniProtKB:P07766 CD3e (human) UniProtKB:P07766 T-cell surface antigen T3/Leu-4 epsilon chain (human) UniProtKB:P07766 hCD3E PRO:DNx CD3E UniProtKB:P07766 T3E UniProtKB:P07766 A lactotransferrin that is encoded in the genome of mouse. UniProtKB:P08071 lactoferrin (mouse) mLTF protein Ltf PR:P08071 Category=organism-gene. lactotransferrin (mouse) A lactotransferrin that is encoded in the genome of mouse. OMA:P08071 PRO:DNx lactoferrin (mouse) UniProtKB:P08071 mLTF PRO:DNx Ltf UniProtKB:P08071 A low affinity immunoglobulin gamma Fc region receptor II that is encoded in the genome of mouse. UniProtKB:P08101 CD32 (mouse) Fc gamma receptor IIB (mouse) Fc-gamma RII (mouse) Fc-gamma-RIIB (mouse) FcRII (mouse) IgG Fc receptor II beta (mouse) lymphocyte antigen 17 (mouse) mFcgr2 protein Fcgr2 Fcgr2b Ly-17 PR:P08101 Category=organism-gene. low affinity immunoglobulin gamma Fc region receptor II (mouse) A low affinity immunoglobulin gamma Fc region receptor II that is encoded in the genome of mouse. PRO:CNA UniProtKB:P08101 CD32 (mouse) UniProtKB:P08101 Fc gamma receptor IIB (mouse) UniProtKB:P08101 Fc-gamma RII (mouse) UniProtKB:P08101 Fc-gamma-RIIB (mouse) UniProtKB:P08101 FcRII (mouse) UniProtKB:P08101 IgG Fc receptor II beta (mouse) UniProtKB:P08101 lymphocyte antigen 17 (mouse) UniProtKB:P08101 mFcgr2 PRO:DNx Fcgr2 UniProtKB:P08101 Fcgr2b UniProtKB:P08101 Ly-17 UniProtKB:P08101 An early growth response protein 2 that is encoded in the genome of mouse. UniProtKB:P08152 E3 SUMO-protein transferase ERG2 (mouse) EGR-2 (mouse) early growth response protein 2 (mouse) mEGR2 zinc finger protein Krox-20 (mouse) protein Egr-2 Egr2 Krox-20 Zfp-25 PR:P08152 Category=organism-gene. E3 SUMO-protein ligase EGR2 (mouse) An early growth response protein 2 that is encoded in the genome of mouse. OMA:P08152 PRO:DNx E3 SUMO-protein transferase ERG2 (mouse) UniProtKB:P08152 EGR-2 (mouse) UniProtKB:P08152 early growth response protein 2 (mouse) UniProtKB:P08152 mEGR2 PRO:DNx zinc finger protein Krox-20 (mouse) UniProtKB:P08152 Egr-2 UniProtKB:P08152 Egr2 UniProtKB:P08152 Krox-20 UniProtKB:P08152 Zfp-25 UniProtKB:P08152 A neprilysin that is encoded in the genome of human. UniProtKB:P08473 CALLA (human) CD10 (human) NEP (human) SFE (human) atriopeptidase (human) common acute lymphocytic leukemia antigen (human) enkephalinase (human) hMME neutral endopeptidase (human) neutral endopeptidase 24.11 (human) skin fibroblast elastase (human) protein EPN MME PR:P08473 Category=organism-gene. neprilysin (human) A neprilysin that is encoded in the genome of human. PRO:WCB UniProtKB:P08473 CALLA (human) UniProtKB:P08473 CD10 (human) UniProtKB:P08473 NEP (human) UniProtKB:P08473 SFE (human) UniProtKB:P08473 atriopeptidase (human) UniProtKB:P08473 common acute lymphocytic leukemia antigen (human) UniProtKB:P08473 enkephalinase (human) UniProtKB:P08473 hMME PRO:DNx neutral endopeptidase (human) UniProtKB:P08473 neutral endopeptidase 24.11 (human) UniProtKB:P08473 skin fibroblast elastase (human) UniProtKB:P08473 EPN UniProtKB:P08473 MME UniProtKB:P08473 A low affinity immunoglobulin gamma Fc region receptor III that is encoded in the genome of mouse. UniProtKB:P08508 CD16 (mouse) Fc-gamma RIII (mouse) FcRIII (mouse) IgG Fc receptor III (mouse) mFcgr3 protein Fcgr3 PR:P08508 Category=organism-gene. low affinity immunoglobulin gamma Fc region receptor III (mouse) A low affinity immunoglobulin gamma Fc region receptor III that is encoded in the genome of mouse. PRO:CNA UniProtKB:P08508 CD16 (mouse) UniProtKB:P08508 Fc-gamma RIII (mouse) UniProtKB:P08508 FcRIII (mouse) UniProtKB:P08508 IgG Fc receptor III (mouse) UniProtKB:P08508 mFcgr3 PRO:DNx Fcgr3 UniProtKB:P08508 An integrin alpha-IIb that is encoded in the genome of human. UniProtKB:P08514 CD41 (human) GPIIb (human) GPalpha IIb (human) hITGA2B platelet membrane glycoprotein IIb (human) protein GP2B ITGA2B ITGAB PR:P08514 Category=organism-gene. integrin alpha-IIb (human) An integrin alpha-IIb that is encoded in the genome of human. PRO:DNx UniProtKB:P08514 CD41 (human) UniProtKB:P08514 GPIIb (human) UniProtKB:P08514 GPalpha IIb (human) UniProtKB:P08514 hITGA2B PRO:DNx platelet membrane glycoprotein IIb (human) UniProtKB:P08514 GP2B UniProtKB:P08514 ITGA2B UniProtKB:P08514 ITGAB UniProtKB:P08514 A CD14 molecule that is encoded in the genome of human. UniProtKB:P08571 hCD14 myeloid cell-specific leucine-rich glycoprotein (human) protein CD14 PR:P08571 Category=organism-gene. monocyte differentiation antigen CD14 (human) A CD14 molecule that is encoded in the genome of human. PRO:WCB UniProtKB:P08571 hCD14 PRO:DNx myeloid cell-specific leucine-rich glycoprotein (human) UniProtKB:P08571 CD14 UniProtKB:P08571 A receptor-type tyrosine-protein phosphatase C that is encoded in the genome of human. UniProtKB:P08575 L-CA (human) T200 (human) hPTPRC leukocyte common antigen (human) protein CD45 PTPRC PR:P08575 Category=organism-gene. receptor-type tyrosine-protein phosphatase C (human) A receptor-type tyrosine-protein phosphatase C that is encoded in the genome of human. PRO:CNA UniProtKB:P08575 L-CA (human) UniProtKB:P08575 T200 (human) UniProtKB:P08575 hPTPRC PRO:DNx leukocyte common antigen (human) UniProtKB:P08575 CD45 UniProtKB:P08575 PTPRC UniProtKB:P08575 A receptor-type tyrosine-protein phosphatase C isoform CD45RABC that is encoded in the genome of human. UniProtKB:P08575-3 hPTPRC/iso:CD45RABC protein PR:P08575-3 Category=organism-sequence. receptor-type tyrosine-protein phosphatase C isoform CD45RABC (human) A receptor-type tyrosine-protein phosphatase C isoform CD45RABC that is encoded in the genome of human. PRO:DAN hPTPRC/iso:CD45RABC PRO:DNx A receptor-type tyrosine-protein phosphatase C isoform CD45RO that is encoded in the genome of human. UniProtKB:P08575-4 CD45RO (human) hPTPRC/iso:CD45RO protein PR:P08575-4 Category=organism-sequence. receptor-type tyrosine-protein phosphatase C isoform CD45RO (human) A receptor-type tyrosine-protein phosphatase C isoform CD45RO that is encoded in the genome of human. GOC:add PRO:ADD PRO:DAN CD45RO (human) GOC:add PRO:ADD hPTPRC/iso:CD45RO PRO:DNx A receptor-type tyrosine-protein phosphatase C isoform CD45RA that is encoded in the genome of human. UniProtKB:P08575-8 CD45RA (human) hPTPRC/iso:CD45RA protein PR:P08575-8 Category=organism-sequence. Requested by=CL. receptor-type tyrosine-protein phosphatase C isoform CD45RA (human) A receptor-type tyrosine-protein phosphatase C isoform CD45RA that is encoded in the genome of human. GOC:add PRO:ADD PRO:DAN hPTPRC/iso:CD45RA PRO:DNx A CD2 molecule that is encoded in the genome of mouse. UniProtKB:P08920 CD2 (mouse) LFA-2 (mouse) LFA-3 receptor (mouse) T-cell surface antigen T11/Leu-5 (mouse) lymphocyte antigen 37 (mouse) mCD2 protein Cd2 Ly-37 PR:P08920 Category=organism-gene. T-cell surface antigen CD2 (mouse) A CD2 molecule that is encoded in the genome of mouse. OMA:P08920 PRO:DNx CD2 (mouse) UniProtKB:P08920 LFA-2 (mouse) UniProtKB:P08920 LFA-3 receptor (mouse) UniProtKB:P08920 T-cell surface antigen T11/Leu-5 (mouse) UniProtKB:P08920 lymphocyte antigen 37 (mouse) UniProtKB:P08920 mCD2 PRO:DNx Cd2 UniProtKB:P08920 Ly-37 UniProtKB:P08920 A cholecystokinin that is encoded in the genome of mouse. UniProtKB:P09240 CCK (mouse) mCCK protein Cck PR:P09240 Category=organism-gene. cholecystokinin (mouse) A cholecystokinin that is encoded in the genome of mouse. OMA:P09240 PRO:DNx CCK (mouse) UniProtKB:P09240 mCCK PRO:DNx Cck UniProtKB:P09240 A CD48 molecule that is encoded in the genome of human. UniProtKB:P09326 B-lymphocyte activation marker BLAST-1 (human) BCM1 surface antigen (human) SLAM family member 2 (human) SLAMF2 (human) TCT.1 (human) hCD48 leukocyte antigen MEM-102 (human) signaling lymphocytic activation molecule 2 (human) protein BCM1 BLAST1 CD48 PR:P09326 Category=organism-gene. CD48 antigen (human) A CD48 molecule that is encoded in the genome of human. PRO:WCB UniProtKB:P09326 B-lymphocyte activation marker BLAST-1 (human) UniProtKB:P09326 BCM1 surface antigen (human) UniProtKB:P09326 SLAM family member 2 (human) UniProtKB:P09326 SLAMF2 (human) UniProtKB:P09326 TCT.1 (human) UniProtKB:P09326 hCD48 PRO:DNx leukocyte antigen MEM-102 (human) UniProtKB:P09326 signaling lymphocytic activation molecule 2 (human) UniProtKB:P09326 BCM1 UniProtKB:P09326 BLAST1 UniProtKB:P09326 CD48 UniProtKB:P09326 A galectin-1 that is encoded in the genome of human. UniProtKB:P09382 14 kDa laminin-binding protein (human) 14 kDa lectin (human) HBL (human) HLBP14 (human) HPL (human) S-Lac lectin 1 (human) beta-galactoside-binding lectin L-14-I (human) gal-1 (human) galaptin (human) hLGALS1 lactose-binding lectin 1 (human) lectin galactoside-binding soluble 1 (human) putative MAPK-activating protein PM12 (human) protein LGALS1 PR:P09382 Category=organism-gene. galectin-1 (human) A galectin-1 that is encoded in the genome of human. PRO:DNx UniProtKB:P09382 14 kDa laminin-binding protein (human) UniProtKB:P09382 14 kDa lectin (human) UniProtKB:P09382 HBL (human) UniProtKB:P09382 HLBP14 (human) UniProtKB:P09382 HPL (human) UniProtKB:P09382 S-Lac lectin 1 (human) UniProtKB:P09382 beta-galactoside-binding lectin L-14-I (human) UniProtKB:P09382 gal-1 (human) UniProtKB:P09382 galaptin (human) UniProtKB:P09382 hLGALS1 PRO:DNx lactose-binding lectin 1 (human) UniProtKB:P09382 lectin galactoside-binding soluble 1 (human) UniProtKB:P09382 putative MAPK-activating protein PM12 (human) UniProtKB:P09382 LGALS1 UniProtKB:P09382 A CD7 molecule that is encoded in the genome of human. UniProtKB:P09564 GP40 (human) T-cell leukemia antigen (human) T-cell surface antigen Leu-9 (human) TP41 (human) hCD7 protein CD7 PR:P09564 Category=organism-gene. T-cell antigen CD7 (human) A CD7 molecule that is encoded in the genome of human. PRO:WCB UniProtKB:P09564 GP40 (human) UniProtKB:P09564 T-cell leukemia antigen (human) UniProtKB:P09564 T-cell surface antigen Leu-9 (human) UniProtKB:P09564 TP41 (human) UniProtKB:P09564 hCD7 PRO:DNx CD7 UniProtKB:P09564 A macrophage colony-stimulating factor 1 receptor that is encoded in the genome of mouse. UniProtKB:P09581 CD115 (mouse) CSF-1 receptor (mouse) CSF-1-R (mouse) CSF-1R (mouse) M-CSF-R (mouse) mCSF1R proto-oncogene c-Fms (mouse) protein Csf1r Csfmr Fms PR:P09581 Category=organism-gene. macrophage colony-stimulating factor 1 receptor (mouse) A macrophage colony-stimulating factor 1 receptor that is encoded in the genome of mouse. OMA:P09581 PRO:DNx CD115 (mouse) UniProtKB:P09581 CSF-1 receptor (mouse) UniProtKB:P09581 CSF-1-R (mouse) UniProtKB:P09581 CSF-1R (mouse) UniProtKB:P09581 M-CSF-R (mouse) UniProtKB:P09581 mCSF1R PRO:DNx proto-oncogene c-Fms (mouse) UniProtKB:P09581 Csf1r UniProtKB:P09581 Csfmr UniProtKB:P09581 Fms UniProtKB:P09581 A cytotoxic T-lymphocyte protein 4 that is encoded in the genome of mouse. UniProtKB:P09793 CD152 (mouse) CTLA-4 (mouse) cytotoxic T-lymphocyte-associated antigen 4 (mouse) mCTLA4 protein Cd152 Ctla4 PR:P09793 Category=organism-gene. cytotoxic T-lymphocyte protein 4 (mouse) A cytotoxic T-lymphocyte protein 4 that is encoded in the genome of mouse. OMA:P09793 PRO:DNx CD152 (mouse) UniProtKB:P09793 CTLA-4 (mouse) UniProtKB:P09793 cytotoxic T-lymphocyte-associated antigen 4 (mouse) UniProtKB:P09793 mCTLA4 PRO:DNx Cd152 UniProtKB:P09793 Ctla4 UniProtKB:P09793 A cadherin-1 that is encoded in the genome of mouse. UniProtKB:P09803 ARC-1 (mouse) CD324 (mouse) E-cadherin (mouse) epithelial cadherin (mouse) mCDH1 uvomorulin (mouse) protein Cdh1 PR:P09803 Category=organism-gene. cadherin-1 (mouse) A cadherin-1 that is encoded in the genome of mouse. OMA:P09803 PRO:DNx ARC-1 (mouse) UniProtKB:P09803 CD324 (mouse) UniProtKB:P09803 E-cadherin (mouse) UniProtKB:P09803 epithelial cadherin (mouse) UniProtKB:P09803 mCDH1 PRO:DNx uvomorulin (mouse) UniProtKB:P09803 Cdh1 UniProtKB:P09803 A DNA nucleotidylexotransferase that is encoded in the genome of mouse. UniProtKB:P09838 TDT (mouse) mDNTT terminal addition enzyme (mouse) terminal deoxynucleotidyltransferase (mouse) protein Dntt Tdt terminal transferase (mouse) PR:P09838 Category=organism-gene. DNA nucleotidylexotransferase (mouse) A DNA nucleotidylexotransferase that is encoded in the genome of mouse. OMA:P09838 PRO:DNx TDT (mouse) UniProtKB:P09838 mDNTT PRO:DNx terminal addition enzyme (mouse) UniProtKB:P09838 terminal deoxynucleotidyltransferase (mouse) UniProtKB:P09838 Dntt UniProtKB:P09838 Tdt UniProtKB:P09838 terminal transferase (mouse) UniProtKB:P09838 A lymphocyte antigen 6C2 that is encoded in the genome of mouse. UniProtKB:P0CW03 Ly-6C2 (mouse) mLy6c2 protein Ly6c Ly6c2 PR:P0CW03 Category=organism-gene. lymphocyte antigen 6C2 (mouse) A lymphocyte antigen 6C2 that is encoded in the genome of mouse. PRO:CNA UniProtKB:P0CW03 Ly-6C2 (mouse) UniProtKB:P0CW03 mLy6c2 PRO:DNx Ly6c UniProtKB:P0CW03 Ly6c2 UniProtKB:P0CW03 A granzyme B that is encoded in the genome of human. HLP (human) UniProtKB:P10144 C11 (human) CTLA-1 (human) CTSGL1 (human) SECT (human) T-cell serine protease 1-3E (human) cathepsin G-like 1 (human) cytotoxic T-lymphocyte proteinase 2 (human) fragmentin-2 (human) granzyme-2 (human) hGZMB human lymphocyte protein lymphocyte protease (human) protein CGL1 CSPB CTLA1 GRB GZMB PR:P10144 Category=organism-gene. granzyme B (human) A granzyme B that is encoded in the genome of human. PRO:CNA UniProtKB:P10144 HLP (human) UniProtKB:P10144 C11 (human) UniProtKB:P10144 CTLA-1 (human) UniProtKB:P10144 CTSGL1 (human) UniProtKB:P10144 SECT (human) UniProtKB:P10144 T-cell serine protease 1-3E (human) UniProtKB:P10144 cathepsin G-like 1 (human) UniProtKB:P10144 cytotoxic T-lymphocyte proteinase 2 (human) UniProtKB:P10144 fragmentin-2 (human) UniProtKB:P10144 granzyme-2 (human) UniProtKB:P10144 hGZMB PRO:DNx human lymphocyte protein UniProtKB:P10144 lymphocyte protease (human) UniProtKB:P10144 CGL1 UniProtKB:P10144 CSPB UniProtKB:P10144 CTLA1 UniProtKB:P10144 GRB UniProtKB:P10144 GZMB UniProtKB:P10144 A non-secretory ribonuclease that is encoded in the genome of human. UniProtKB:P10153 RNase 2 (human) RNase UpI-2 (human) eosinophil-derived neurotoxin (human) hRNASE2 ribonuclease 2 (human) ribonuclease US (human) protein EDN RNASE2 RNS2 PR:P10153 Category=organism-gene. non-secretory ribonuclease (human) A non-secretory ribonuclease that is encoded in the genome of human. PRO:DNx UniProtKB:P10153 RNase 2 (human) UniProtKB:P10153 RNase UpI-2 (human) UniProtKB:P10153 eosinophil-derived neurotoxin (human) UniProtKB:P10153 hRNASE2 PRO:DNx ribonuclease 2 (human) UniProtKB:P10153 ribonuclease US (human) UniProtKB:P10153 EDN UniProtKB:P10153 RNASE2 UniProtKB:P10153 RNS2 UniProtKB:P10153 A myb proto-oncogene protein that is encoded in the genome of human. Reactome:R-HSA-992697 UniProtKB:P10242 hMYB proto-oncogene c-Myb (human) protein MYB PR:P10242 Category=organism-gene. transcriptional activator Myb (human) A myb proto-oncogene protein that is encoded in the genome of human. PRO:DNx UniProtKB:P10242 Reactome:R-HSA-992697 PR:P10242 located_in GO:0005654 hMYB PRO:DNx proto-oncogene c-Myb (human) UniProtKB:P10242 MYB UniProtKB:P10242 A T-cell surface glycoprotein CD8 beta chain that is encoded in the genome of mouse. UniProtKB:P10300 CD8b (mouse) T-cell membrane glycoprotein Ly-3 (mouse) T-cell surface glycoprotein Lyt-3 (mouse) lymphocyte antigen 3 (mouse) mCD8B protein Cd8b Cd8b1 Ly-3 Lyt-3 Lyt3 PR:P10300 Category=organism-gene. T-cell surface glycoprotein CD8 beta chain (mouse) A T-cell surface glycoprotein CD8 beta chain that is encoded in the genome of mouse. OMA:P10300 PRO:DNx CD8b (mouse) UniProtKB:P10300 T-cell membrane glycoprotein Ly-3 (mouse) UniProtKB:P10300 T-cell surface glycoprotein Lyt-3 (mouse) UniProtKB:P10300 lymphocyte antigen 3 (mouse) UniProtKB:P10300 mCD8B PRO:DNx Cd8b UniProtKB:P10300 Cd8b1 UniProtKB:P10300 Ly-3 UniProtKB:P10300 Lyt-3 UniProtKB:P10300 Lyt3 UniProtKB:P10300 A mast/stem cell growth factor receptor that is encoded in the genome of human. DTO:03100231 UniProtKB:P10721 CD117 (human) PBT (human) hKIT p145 c-kit (human) piebald trait protein (human) proto-oncogene c-Kit (human) tyrosine-protein kinase Kit (human) v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (human) protein KIT SCFR PR:P10721 Category=organism-gene. mast/stem cell growth factor receptor Kit (human) A mast/stem cell growth factor receptor that is encoded in the genome of human. PRO:WCB UniProtKB:P10721 CD117 (human) UniProtKB:P10721 PBT (human) UniProtKB:P10721 hKIT PRO:DNx p145 c-kit (human) UniProtKB:P10721 piebald trait protein (human) UniProtKB:P10721 proto-oncogene c-Kit (human) UniProtKB:P10721 tyrosine-protein kinase Kit (human) UniProtKB:P10721 v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (human) UniProtKB:P10721 KIT UniProtKB:P10721 SCFR UniProtKB:P10721 A T-cell-specific surface glycoprotein CD28 that is encoded in the genome of human. UniProtKB:P10747 TP44 (human) hCD28 protein CD28 PR:P10747 Category=organism-gene. T-cell-specific surface glycoprotein CD28 (human) A T-cell-specific surface glycoprotein CD28 that is encoded in the genome of human. PRO:WCB UniProtKB:P10747 TP44 (human) UniProtKB:P10747 hCD28 PRO:DNx CD28 UniProtKB:P10747 A CD14 molecule that is encoded in the genome of mouse. UniProtKB:P10810 CD14 (mouse) mCD14 myeloid cell-specific leucine-rich glycoprotein (mouse) protein Cd14 PR:P10810 Category=organism-gene. monocyte differentiation antigen CD14 (mouse) A CD14 molecule that is encoded in the genome of mouse. OMA:P10810 PRO:WCB CD14 (mouse) UniProtKB:P10810 mCD14 PRO:DNx myeloid cell-specific leucine-rich glycoprotein (mouse) UniProtKB:P10810 Cd14 UniProtKB:P10810 A perforin-1 that is encoded in the genome of mouse. UniProtKB:P10820 P1 (mouse) cytolysin (mouse) lymphocyte pore-forming protein (mouse) mPRF1 protein Pfp Prf1 PR:P10820 Category=organism-gene. perforin-1 (mouse) A perforin-1 that is encoded in the genome of mouse. OMA:P10820 PRO:DNx P1 (mouse) UniProtKB:P10820 cytolysin (mouse) UniProtKB:P10820 lymphocyte pore-forming protein (mouse) UniProtKB:P10820 mPRF1 PRO:DNx Pfp UniProtKB:P10820 Prf1 UniProtKB:P10820 A T-cell surface glycoprotein CD8 beta chain that is encoded in the genome of human. UniProtKB:P10966 CD8b (human) hCD8B protein CD8B CD8B1 PR:P10966 Category=organism-gene. T-cell surface glycoprotein CD8 beta chain (human) A T-cell surface glycoprotein CD8 beta chain that is encoded in the genome of human. PRO:CNA UniProtKB:P10966 CD8b (human) UniProtKB:P10966 hCD8B PRO:DNx CD8B UniProtKB:P10966 CD8B1 UniProtKB:P10966 A T-cell surface glycoprotein CD8 beta chain isoform 1 that is encoded in the genome of human. UniProtKB:P10966-1 T-cell surface glycoprotein CD8 beta chain isoform M-1 (human) T-cell surface glycoprotein CD8 beta chain isoform Mbeta1 (human) hCD8B/iso:1 protein PR:P10966-1 Category=organism-sequence. T-cell surface glycoprotein CD8 beta chain isoform 1 (human) A T-cell surface glycoprotein CD8 beta chain isoform 1 that is encoded in the genome of human. PRO:DAN T-cell surface glycoprotein CD8 beta chain isoform M-1 (human) UniProtKB:P10966 T-cell surface glycoprotein CD8 beta chain isoform Mbeta1 (human) UniProtKB:P10966 hCD8B/iso:1 PRO:DNx A collagen alpha-1(I) chain that is encoded in the genome of mouse. UniProtKB:P11087 alpha-1 type I collagen (mouse) mCOL1A1 protein Col1a1 Cola1 PR:P11087 Category=organism-gene. collagen alpha-1(I) chain (mouse) A collagen alpha-1(I) chain that is encoded in the genome of mouse. OMA:P11087 PRO:DNx alpha-1 type I collagen (mouse) UniProtKB:P11087 mCOL1A1 PRO:DNx Col1a1 UniProtKB:P11087 Cola1 UniProtKB:P11087 An early growth response protein 2 that is encoded in the genome of human. Reactome:R-HSA-977385 UniProtKB:P11161 AT591 (human) E3 SUMO-protein transferase ERG2 (human) EGR-2 (human) early growth response protein 2 (human) hEGR2 zinc finger protein Krox-20 (human) protein EGR2 KROX20 PR:P11161 Category=organism-gene. E3 SUMO-protein ligase EGR2 (human) An early growth response protein 2 that is encoded in the genome of human. PRO:CNA UniProtKB:P11161 Reactome:R-HSA-977385 PR:P11161 located_in GO:0005654 AT591 (human) UniProtKB:P11161 E3 SUMO-protein transferase ERG2 (human) UniProtKB:P11161 EGR-2 (human) UniProtKB:P11161 early growth response protein 2 (human) UniProtKB:P11161 hEGR2 PRO:DNx zinc finger protein Krox-20 (human) UniProtKB:P11161 EGR2 UniProtKB:P11161 KROX20 UniProtKB:P11161 An integrin alpha-M that is encoded in the genome of human. UniProtKB:P11215 CD11 antigen-like family member B (human) CR-3 alpha chain (human) cell surface glycoprotein MAC-1 subunit alpha (human) hITGAM leukocyte adhesion receptor MO1 (human) neutrophil adherence receptor (human) protein CD11B CR3A ITGAM PR:P11215 Category=organism-gene. integrin alpha-M (human) An integrin alpha-M that is encoded in the genome of human. PRO:DNx UniProtKB:P11215 CD11 antigen-like family member B (human) UniProtKB:P11215 CR-3 alpha chain (human) UniProtKB:P11215 cell surface glycoprotein MAC-1 subunit alpha (human) UniProtKB:P11215 hITGAM PRO:DNx leukocyte adhesion receptor MO1 (human) UniProtKB:P11215 neutrophil adherence receptor (human) UniProtKB:P11215 CD11B UniProtKB:P11215 CR3A UniProtKB:P11215 ITGAM UniProtKB:P11215 A myeloperoxidase that is encoded in the genome of mouse. UniProtKB:P11247 MPO (mouse) mMPO protein Mpo PR:P11247 Category=organism-gene. myeloperoxidase (mouse) A myeloperoxidase that is encoded in the genome of mouse. OMA:P11247 PRO:DNx MPO (mouse) UniProtKB:P11247 mMPO PRO:DNx Mpo UniProtKB:P11247 An antigen-presenting glycoprotein CD1d that is encoded in the genome of mouse. UniProtKB:P11609 CD1d.1 (mouse) mCD1D protein Cd1.1 Cd1d1 PR:P11609 Category=organism-gene. antigen-presenting glycoprotein CD1d1 (mouse) An antigen-presenting glycoprotein CD1d that is encoded in the genome of mouse. PRO:WCB CD1d.1 (mouse) UniProtKB:P11609 mCD1D PRO:DNx Cd1.1 UniProtKB:P11609 Cd1d1 UniProtKB:P11609 A neutrophil gelatinase-associated lipocalin that is encoded in the genome of mouse. p25 (mouse) UniProtKB:P11672 24p3 (mouse) NGAL (mouse) SV-40-induced 24p3 protein (mouse) lipocalin-2 (mouse) mLCN2 oncogene 24p3 (mouse) siderocalin LCN2 (mouse) protein Lcn2 PR:P11672 Category=organism-gene. neutrophil gelatinase-associated lipocalin (mouse) A neutrophil gelatinase-associated lipocalin that is encoded in the genome of mouse. OMA:P11672 PRO:DNx p25 (mouse) UniProtKB:P11672 24p3 (mouse) UniProtKB:P11672 NGAL (mouse) UniProtKB:P11672 SV-40-induced 24p3 protein (mouse) UniProtKB:P11672 lipocalin-2 (mouse) UniProtKB:P11672 mLCN2 PRO:DNx oncogene 24p3 (mouse) UniProtKB:P11672 siderocalin LCN2 (mouse) UniProtKB:P11672 Lcn2 UniProtKB:P11672 An eosinophil peroxidase that is encoded in the genome of human. UniProtKB:P11678 hEPX protein EPER EPO EPP EPX PR:P11678 Category=organism-gene. eosinophil peroxidase (human) An eosinophil peroxidase that is encoded in the genome of human. PRO:DNx UniProtKB:P11678 hEPX PRO:DNx EPER UniProtKB:P11678 EPO UniProtKB:P11678 EPP UniProtKB:P11678 EPX UniProtKB:P11678 A membrane-spanning 4-domains subfamily A member 1 that is encoded in the genome of human. UniProtKB:P11836 B-lymphocyte surface antigen B1 (human) Bp35 (human) hMS4A1 leukocyte surface antigen Leu-16 (human) membrane-spanning 4-domains subfamily A member 1 (human) protein CD20 MS4A1 PR:P11836 Category=organism-gene. B-lymphocyte antigen CD20 (human) A membrane-spanning 4-domains subfamily A member 1 that is encoded in the genome of human. PRO:WCB UniProtKB:P11836 B-lymphocyte surface antigen B1 (human) UniProtKB:P11836 Bp35 (human) UniProtKB:P11836 hMS4A1 PRO:DNx leukocyte surface antigen Leu-16 (human) UniProtKB:P11836 membrane-spanning 4-domains subfamily A member 1 (human) UniProtKB:P11836 CD20 UniProtKB:P11836 MS4A1 UniProtKB:P11836 An immunoglobulin iota chain that is encoded in the genome of human. UniProtKB:P12018 CD179 antigen-like family member A (human) CD179a (human) V(pre)B protein (human) VpreB protein (human) hVPREB1 protein VPreB1 (human) protein VPREB VPREB1 PR:P12018 Category=organism-gene. immunoglobulin iota chain (human) An immunoglobulin iota chain that is encoded in the genome of human. PRO:WCB UniProtKB:P12018 CD179 antigen-like family member A (human) UniProtKB:P12018 CD179a (human) UniProtKB:P12018 V(pre)B protein (human) UniProtKB:P12018 VpreB protein (human) UniProtKB:P12018 hVPREB1 PRO:DNx protein VPreB1 (human) UniProtKB:P12018 VPREB UniProtKB:P12018 VPREB1 UniProtKB:P12018 A high affinity immunoglobulin gamma Fc receptor I that is encoded in the genome of human. UniProtKB:P12314 CD64 (human) Fc-gamma RI (human) Fc-gamma RIA (human) FcRI (human) FcgammaRIa (human) IgG Fc receptor I (human) hFCGR1A protein FCG1 FCGR1 FCGR1A IGFR1 PR:P12314 Category=organism-gene. high affinity immunoglobulin gamma Fc receptor I (human) A high affinity immunoglobulin gamma Fc receptor I that is encoded in the genome of human. PRO:CNA UniProtKB:P12314 CD64 (human) UniProtKB:P12314 Fc-gamma RI (human) UniProtKB:P12314 Fc-gamma RIA (human) UniProtKB:P12314 FcRI (human) UniProtKB:P12314 FcgammaRIa (human) UniProtKB:P12314 IgG Fc receptor I (human) UniProtKB:P12314 hFCGR1A PRO:DNx FCG1 UniProtKB:P12314 FCGR1 UniProtKB:P12314 FCGR1A UniProtKB:P12314 IGFR1 UniProtKB:P12314 A high affinity immunoglobulin epsilon receptor subunit alpha that is encoded in the genome of human. FcERI (human) UniProtKB:P12319 Fc-epsilon RI-alpha (human) IgE Fc receptor subunit alpha (human) hFCER1A protein FCE1A FCER1A PR:P12319 Category=organism-gene. high affinity immunoglobulin epsilon receptor subunit alpha (human) A high affinity immunoglobulin epsilon receptor subunit alpha that is encoded in the genome of human. PRO:DNx UniProtKB:P12319 FcERI (human) UniProtKB:P12319 Fc-epsilon RI-alpha (human) UniProtKB:P12319 IgE Fc receptor subunit alpha (human) UniProtKB:P12319 hFCER1A PRO:DNx FCE1A UniProtKB:P12319 FCER1A UniProtKB:P12319 An eosinophil cationic protein that is encoded in the genome of human. UniProtKB:P12724 RNase 3 (human) hRNASE3 protein ECP RNASE3 RNS3 ribonuclease 3 (human) PR:P12724 Category=organism-gene. eosinophil cationic protein (human) An eosinophil cationic protein that is encoded in the genome of human. PRO:DNx UniProtKB:P12724 RNase 3 (human) UniProtKB:P12724 hRNASE3 PRO:DNx ECP UniProtKB:P12724 RNASE3 UniProtKB:P12724 RNS3 UniProtKB:P12724 ribonuclease 3 (human) UniProtKB:P12724 A cadherin-1 that is encoded in the genome of human. UniProtKB:P12830 CAM 120/80 (human) CD324 (human) E-cadherin (human) epithelial cadherin (human) hCDH1 uvomorulin (human) protein CDH1 CDHE UVO PR:P12830 Category=organism-gene. cadherin-1 (human) A cadherin-1 that is encoded in the genome of human. PRO:WCB UniProtKB:P12830 CAM 120/80 (human) UniProtKB:P12830 CD324 (human) UniProtKB:P12830 E-cadherin (human) UniProtKB:P12830 epithelial cadherin (human) UniProtKB:P12830 hCDH1 PRO:DNx uvomorulin (human) UniProtKB:P12830 CDH1 UniProtKB:P12830 CDHE UniProtKB:P12830 UVO UniProtKB:P12830 A T-cell surface glycoprotein CD5 that is encoded in the genome of mouse. UniProtKB:P13379 CD5 (mouse) Lyt-1 (mouse) lymphocyte antigen 1 (mouse) mCD5 protein Cd5 Ly-1 PR:P13379 Category=organism-gene. T-cell surface glycoprotein CD5 (mouse) A T-cell surface glycoprotein CD5 that is encoded in the genome of mouse. OMA:P13379 PRO:DNx CD5 (mouse) UniProtKB:P13379 Lyt-1 (mouse) UniProtKB:P13379 lymphocyte antigen 1 (mouse) UniProtKB:P13379 mCD5 PRO:DNx Cd5 UniProtKB:P13379 Ly-1 UniProtKB:P13379 A neural cell adhesion molecule 1 that is encoded in the genome of human. UniProtKB:P13591 CD56 (human) N-CAM-1 (human) NCAM-1 (human) hNCAM1 protein NCAM NCAM1 PR:P13591 Category=organism-gene. neural cell adhesion molecule 1 (human) A neural cell adhesion molecule 1 that is encoded in the genome of human. PRO:CNA UniProtKB:P13591 CD56 (human) UniProtKB:P13591 N-CAM-1 (human) UniProtKB:P13591 NCAM-1 (human) UniProtKB:P13591 hNCAM1 PRO:DNx NCAM UniProtKB:P13591 NCAM1 UniProtKB:P13591 A neural cell adhesion molecule 1 that is encoded in the genome of mouse. UniProtKB:P13595 CD56 (mouse) N-CAM-1 (mouse) NCAM-1 (mouse) mNCAM1 protein Ncam Ncam1 PR:P13595 Category=organism-gene. neural cell adhesion molecule 1 (mouse) A neural cell adhesion molecule 1 that is encoded in the genome of mouse. OMA:P13595 PRO:DNx CD56 (mouse) UniProtKB:P13595 N-CAM-1 (mouse) UniProtKB:P13595 NCAM-1 (mouse) UniProtKB:P13595 mNCAM1 PRO:DNx Ncam UniProtKB:P13595 Ncam1 UniProtKB:P13595 An integrin alpha-4 that is encoded in the genome of human. UniProtKB:P13612 CD49 antigen-like family member D (human) VLA-4 subunit alpha (human) hITGA4 integrin alpha-IV (human) protein CD49D ITGA4 PR:P13612 Category=organism-gene. integrin alpha-4 (human) An integrin alpha-4 that is encoded in the genome of human. PRO:DNx UniProtKB:P13612 CD49 antigen-like family member D (human) UniProtKB:P13612 VLA-4 subunit alpha (human) UniProtKB:P13612 hITGA4 PRO:DNx integrin alpha-IV (human) UniProtKB:P13612 CD49D UniProtKB:P13612 ITGA4 UniProtKB:P13612 A tartrate-resistant acid phosphatase type 5 that is encoded in the genome of human. UniProtKB:P13686 TR-AP (human) TrATPase (human) hACP5 tartrate-resistant acid ATPase (human) type 5 acid phosphatase (human) protein ACP5 PR:P13686 Category=organism-gene. tartrate-resistant acid phosphatase type 5 (human) A tartrate-resistant acid phosphatase type 5 that is encoded in the genome of human. PRO:WCB UniProtKB:P13686 TR-AP (human) UniProtKB:P13686 TrATPase (human) UniProtKB:P13686 hACP5 PRO:DNx tartrate-resistant acid ATPase (human) UniProtKB:P13686 type 5 acid phosphatase (human) UniProtKB:P13686 ACP5 UniProtKB:P13686 A bone marrow proteoglycan that is encoded in the genome of human. UniProtKB:P13727 BMPG (human) hPRG2 proteoglycan 2 (human) protein MBP PRG2 PR:P13727 Category=organism-gene. bone marrow proteoglycan (human) A bone marrow proteoglycan that is encoded in the genome of human. PRO:DNx UniProtKB:P13727 BMPG (human) UniProtKB:P13727 hPRG2 PRO:DNx proteoglycan 2 (human) UniProtKB:P13727 MBP UniProtKB:P13727 PRG2 UniProtKB:P13727 A bone marrow proteoglycan isoform 1 that is encoded in the genome of human. UniProtKB:P13727-1 hPRG2/iso:1 protein PR:P13727-1 Category=organism-sequence. bone marrow proteoglycan isoform 1 (human) A bone marrow proteoglycan isoform 1 that is encoded in the genome of human. PRO:CNA hPRG2/iso:1 PRO:DNx A glial fibrillary acidic protein that is encoded in the genome of human. Reactome:R-HSA-1253311 Reactome:R-HSA-9625195 UniProtKB:P14136 hGFAP protein GFAP PR:P14136 Category=organism-gene. glial fibrillary acidic protein (human) A glial fibrillary acidic protein that is encoded in the genome of human. PRO:DNx UniProtKB:P14136 Reactome:R-HSA-1253311 PR:P14136 located_in GO:0005829 Reactome:R-HSA-9625195 PR:P14136 located_in GO:0005765 hGFAP PRO:DNx GFAP UniProtKB:P14136 An L-selectin that is encoded in the genome of human. UniProtKB:P14151 CD62 antigen-like family member L (human) CD62L (human) LAM-1 (human) LECAM1 (human) TQ1 (human) gp90-MEL (human) hSELL leukocyte adhesion molecule 1 (human) leukocyte surface antigen Leu-8 (human) leukocyte-endothelial cell adhesion molecule 1 (human) lymph node homing receptor (human) protein LNHR LYAM1 SELL PR:P14151 Category=organism-gene. L-selectin (human) An L-selectin that is encoded in the genome of human. PRO:JAN UniProtKB:P14151 CD62 antigen-like family member L (human) UniProtKB:P14151 CD62L (human) UniProtKB:P14151 LAM-1 (human) UniProtKB:P14151 LECAM1 (human) UniProtKB:P14151 TQ1 (human) UniProtKB:P14151 gp90-MEL (human) UniProtKB:P14151 hSELL PRO:DNx leukocyte adhesion molecule 1 (human) UniProtKB:P14151 leukocyte surface antigen Leu-8 (human) UniProtKB:P14151 leukocyte-endothelial cell adhesion molecule 1 (human) UniProtKB:P14151 lymph node homing receptor (human) UniProtKB:P14151 LNHR UniProtKB:P14151 LYAM1 UniProtKB:P14151 SELL UniProtKB:P14151 A perforin-1 that is encoded in the genome of human. P1 (human) UniProtKB:P14222 cytolysin (human) hPRF1 lymphocyte pore-forming protein (human) protein PFP PRF1 PR:P14222 Category=organism-gene. perforin-1 (human) A perforin-1 that is encoded in the genome of human. PRO:CNA UniProtKB:P14222 P1 (human) UniProtKB:P14222 cytolysin (human) UniProtKB:P14222 hPRF1 PRO:DNx lymphocyte pore-forming protein (human) UniProtKB:P14222 PFP UniProtKB:P14222 PRF1 UniProtKB:P14222 An interleukin-1 receptor-like 1 that is encoded in the genome of mouse. UniProtKB:P14719 interleukin-33 receptor alpha chain (mouse) lymphocyte antigen 84 (mouse) mIL1RL1 protein ST2 (mouse) protein T1 (mouse) protein Il1rl1 Ly84 St2 Ste2 PR:P14719 Category=organism-gene. interleukin-1 receptor-like 1 (mouse) An interleukin-1 receptor-like 1 that is encoded in the genome of mouse. OMA:P14719 PRO:DNx interleukin-33 receptor alpha chain (mouse) UniProtKB:P14719 lymphocyte antigen 84 (mouse) UniProtKB:P14719 mIL1RL1 PRO:DNx protein ST2 (mouse) UniProtKB:P14719 protein T1 (mouse) UniProtKB:P14719 Il1rl1 UniProtKB:P14719 Ly84 UniProtKB:P14719 St2 UniProtKB:P14719 Ste2 UniProtKB:P14719 An interleukin-2 receptor subunit beta that is encoded in the genome of human. p75 (human) UniProtKB:P14784 CD122 (human) IL-2 receptor subunit beta (human) IL-2R subunit beta (human) IL-2RB (human) hIL2RB high affinity IL-2 receptor subunit beta (human) interleukin-15 receptor subunit beta (human) p70-75 (human) protein IL15RB IL2RB PR:P14784 Category=organism-gene. interleukin-2 receptor subunit beta (human) An interleukin-2 receptor subunit beta that is encoded in the genome of human. PRO:CNA UniProtKB:P14784 p75 (human) UniProtKB:P14784 CD122 (human) UniProtKB:P14784 IL-2 receptor subunit beta (human) UniProtKB:P14784 IL-2R subunit beta (human) UniProtKB:P14784 IL-2RB (human) UniProtKB:P14784 hIL2RB PRO:DNx high affinity IL-2 receptor subunit beta (human) UniProtKB:P14784 interleukin-15 receptor subunit beta (human) UniProtKB:P14784 p70-75 (human) UniProtKB:P14784 IL15RB UniProtKB:P14784 IL2RB UniProtKB:P14784 An aminopeptidase N that is encoded in the genome of human. UniProtKB:P15144 AP-M (human) AP-N (human) alanyl aminopeptidase (human) aminopeptidase M (human) gp150 (human) hANPEP hAPN microsomal aminopeptidase (human) myeloid plasma membrane glycoprotein CD13 (human) protein ANPEP APN CD13 PEPN PR:P15144 Category=organism-gene. aminopeptidase N (human) An aminopeptidase N that is encoded in the genome of human. PRO:WCB UniProtKB:P15144 AP-M (human) UniProtKB:P15144 AP-N (human) UniProtKB:P15144 alanyl aminopeptidase (human) UniProtKB:P15144 aminopeptidase M (human) UniProtKB:P15144 gp150 (human) UniProtKB:P15144 hANPEP PRO:DNx hAPN UniProtKB:P15144 microsomal aminopeptidase (human) UniProtKB:P15144 myeloid plasma membrane glycoprotein CD13 (human) UniProtKB:P15144 ANPEP UniProtKB:P15144 APN UniProtKB:P15144 CD13 UniProtKB:P15144 PEPN UniProtKB:P15144 A thrombomodulin that is encoded in the genome of mouse. UniProtKB:P15306 CD141 (mouse) TM (mouse) fetomodulin (mouse) mTHBD protein Thbd PR:P15306 Category=organism-gene. thrombomodulin (mouse) A thrombomodulin that is encoded in the genome of mouse. OMA:P15306 PRO:DNx CD141 (mouse) UniProtKB:P15306 TM (mouse) UniProtKB:P15306 fetomodulin (mouse) UniProtKB:P15306 mTHBD PRO:DNx Thbd UniProtKB:P15306 A CD44 molecule that is encoded in the genome of mouse. UniProtKB:P15379 CD44 (mouse) ECMR-III (mouse) GP90 lymphocyte homing/adhesion receptor (mouse) HUTCH-I (mouse) PGP-1 (mouse) PGP-I (mouse) extracellular matrix receptor III (mouse) hermes antigen (mouse) hyaluronate receptor (mouse) lymphocyte antigen 24 (mouse) mCD44 phagocytic glycoprotein 1 (mouse) phagocytic glycoprotein I (mouse) protein Cd44 Ly-24 PR:P15379 Category=organism-gene. CD44 antigen (mouse) A CD44 molecule that is encoded in the genome of mouse. OMA:P15379 PRO:WCB CD44 (mouse) UniProtKB:P15379 ECMR-III (mouse) UniProtKB:P15379 GP90 lymphocyte homing/adhesion receptor (mouse) UniProtKB:P15379 HUTCH-I (mouse) UniProtKB:P15379 PGP-1 (mouse) UniProtKB:P15379 PGP-I (mouse) UniProtKB:P15379 extracellular matrix receptor III (mouse) UniProtKB:P15379 hermes antigen (mouse) UniProtKB:P15379 hyaluronate receptor (mouse) UniProtKB:P15379 lymphocyte antigen 24 (mouse) UniProtKB:P15379 mCD44 PRO:DNx phagocytic glycoprotein 1 (mouse) UniProtKB:P15379 phagocytic glycoprotein I (mouse) UniProtKB:P15379 Cd44 UniProtKB:P15379 Ly-24 UniProtKB:P15379 A CD19 molecule that is encoded in the genome of human. UniProtKB:P15391 B-lymphocyte surface antigen B4 (human) T-cell surface antigen Leu-12 (human) differentiation antigen CD19 (human) hCD19 protein CD19 PR:P15391 Category=organism-gene. B-lymphocyte antigen CD19 (human) B-lymphocyte surface antigen B4 (human) UniProtKB:P15391 T-cell surface antigen Leu-12 (human) UniProtKB:P15391 differentiation antigen CD19 (human) UniProtKB:P15391 hCD19 PRO:DNx CD19 UniProtKB:P15391 A leukosialin that is encoded in the genome of mouse. UniProtKB:P15702 B-cell differentiation antigen LP-3 (mouse) CD43 (mouse) Ly-48 (mouse) leukocyte sialoglycoprotein (mouse) lymphocyte antigen 48 (mouse) mSPN sialophorin (mouse) protein Spn PR:P15702 Category=organism-gene. leukosialin (mouse) A leukosialin that is encoded in the genome of mouse. OMA:P15702 PRO:DNx B-cell differentiation antigen LP-3 (mouse) UniProtKB:P15702 CD43 (mouse) UniProtKB:P15702 Ly-48 (mouse) UniProtKB:P15702 leukocyte sialoglycoprotein (mouse) UniProtKB:P15702 lymphocyte antigen 48 (mouse) UniProtKB:P15702 mSPN PRO:DNx sialophorin (mouse) UniProtKB:P15702 Spn UniProtKB:P15702 An antigen-presenting glycoprotein CD1d that is encoded in the genome of human. MRO:0000891 UniProtKB:P15813 CD1d (human) R3G1 (human) hCD1D human CD1d chain protein CD1D PR:P15813 Category=organism-gene. antigen-presenting glycoprotein CD1d (human) An antigen-presenting glycoprotein CD1d that is encoded in the genome of human. PRO:WCB UniProtKB:P15813 CD1d (human) UniProtKB:P15813 R3G1 (human) UniProtKB:P15813 hCD1D PRO:DNx human CD1d chain MRO:0000891 CD1D UniProtKB:P15813 An immunoglobulin lambda-like polypeptide 1 that is encoded in the genome of human. UniProtKB:P15814 CD179 antigen-like family member B (human) CD179b (human) Ig lambda-5 (human) hIGLL1 immunoglobulin omega polypeptide (human) immunoglobulin-related protein 14.1 (human) protein IGL1 IGLL1 PR:P15814 Category=organism-gene. immunoglobulin lambda-like polypeptide 1 (human) An immunoglobulin lambda-like polypeptide 1 that is encoded in the genome of human. PRO:WCB UniProtKB:P15814 CD179 antigen-like family member B (human) UniProtKB:P15814 CD179b (human) UniProtKB:P15814 Ig lambda-5 (human) UniProtKB:P15814 hIGLL1 PRO:DNx immunoglobulin omega polypeptide (human) UniProtKB:P15814 immunoglobulin-related protein 14.1 (human) UniProtKB:P15814 IGL1 UniProtKB:P15814 IGLL1 UniProtKB:P15814 A V(D)J recombination-activating protein 1 that is encoded in the genome of human. Reactome:R-HSA-5692681 UniProtKB:P15918 RAG-1 (human) RING finger protein 74 (human) hRAG1 protein RAG1 RNF74 PR:P15918 Category=organism-gene. V(D)J recombination-activating protein 1 (human) A V(D)J recombination-activating protein 1 that is encoded in the genome of human. PRO:CNA UniProtKB:P15918 Reactome:R-HSA-5692681 PR:P15918 located_in GO:0005654 RAG-1 (human) UniProtKB:P15918 RING finger protein 74 (human) UniProtKB:P15918 hRAG1 PRO:DNx RAG1 UniProtKB:P15918 RNF74 UniProtKB:P15918 A V(D)J recombination-activating protein 1 that is encoded in the genome of mouse. UniProtKB:P15919 RAG-1 (mouse) mRAG1 protein Rag1 PR:P15919 Category=organism-gene. V(D)J recombination-activating protein 1 (mouse) A V(D)J recombination-activating protein 1 that is encoded in the genome of mouse. OMA:P15919 PRO:DNx RAG-1 (mouse) UniProtKB:P15919 mRAG1 PRO:DNx Rag1 UniProtKB:P15919 An erythroid transcription factor that is encoded in the genome of human. GF-1 (human) Reactome:R-HSA-996772 UniProtKB:P15976 GATA-1 (human) GATA-binding factor 1 (human) NF-E1 DNA-binding protein (human) hGATA1 protein ERYF1 GATA1 GF1 PR:P15976 Category=organism-gene. erythroid transcription factor (human) An erythroid transcription factor that is encoded in the genome of human. PRO:DNx UniProtKB:P15976 GF-1 (human) UniProtKB:P15976 Reactome:R-HSA-996772 PR:P15976 located_in GO:0005654 GATA-1 (human) UniProtKB:P15976 GATA-binding factor 1 (human) UniProtKB:P15976 NF-E1 DNA-binding protein (human) UniProtKB:P15976 hGATA1 PRO:DNx ERYF1 UniProtKB:P15976 GATA1 UniProtKB:P15976 GF1 UniProtKB:P15976 A galectin-1 that is encoded in the genome of mouse. UniProtKB:P16045 14 kDa lectin (mouse) S-Lac lectin 1 (mouse) beta-galactoside-binding lectin L-14-I (mouse) gal-1 (mouse) galaptin (mouse) lactose-binding lectin 1 (mouse) lectin galactoside-binding soluble 1 (mouse) mLGALS1 protein Gbp Lgals1 PR:P16045 Category=organism-gene. galectin-1 (mouse) A galectin-1 that is encoded in the genome of mouse. OMA:P16045 PRO:DNx 14 kDa lectin (mouse) UniProtKB:P16045 S-Lac lectin 1 (mouse) UniProtKB:P16045 beta-galactoside-binding lectin L-14-I (mouse) UniProtKB:P16045 gal-1 (mouse) UniProtKB:P16045 galaptin (mouse) UniProtKB:P16045 lactose-binding lectin 1 (mouse) UniProtKB:P16045 lectin galactoside-binding soluble 1 (mouse) UniProtKB:P16045 mLGALS1 PRO:DNx Gbp UniProtKB:P16045 Lgals1 UniProtKB:P16045 A CD44 molecule that is encoded in the genome of human. PGP-I (human) UniProtKB:P16070 CDw44 (human) ECMR-III (human) GP90 lymphocyte homing/adhesion receptor (human) HUTCH-I (human) PGP-1 (human) epican (human) extracellular matrix receptor III (human) hCD44 heparan sulfate proteoglycan (human) hermes antigen (human) hyaluronate receptor (human) phagocytic glycoprotein 1 (human) phagocytic glycoprotein I (human) protein CD44 LHR MDU2 MDU3 MIC4 PR:P16070 Category=organism-gene. CD44 antigen (human) A CD44 molecule that is encoded in the genome of human. PRO:WCB UniProtKB:P16070 PGP-I (human) UniProtKB:P16070 CDw44 (human) UniProtKB:P16070 ECMR-III (human) UniProtKB:P16070 GP90 lymphocyte homing/adhesion receptor (human) UniProtKB:P16070 HUTCH-I (human) UniProtKB:P16070 PGP-1 (human) UniProtKB:P16070 epican (human) UniProtKB:P16070 extracellular matrix receptor III (human) UniProtKB:P16070 hCD44 PRO:DNx heparan sulfate proteoglycan (human) UniProtKB:P16070 hermes antigen (human) UniProtKB:P16070 hyaluronate receptor (human) UniProtKB:P16070 phagocytic glycoprotein 1 (human) UniProtKB:P16070 phagocytic glycoprotein I (human) UniProtKB:P16070 CD44 UniProtKB:P16070 LHR UniProtKB:P16070 MDU2 UniProtKB:P16070 MDU3 UniProtKB:P16070 MIC4 UniProtKB:P16070 A leukosialin that is encoded in the genome of human. UniProtKB:P16150 GALGP (human) GPL115 (human) galactoglycoprotein (human) hSPN leukocyte sialoglycoprotein (human) sialophorin (human) protein CD43 SPN PR:P16150 Category=organism-gene. leukosialin (human) A leukosialin that is encoded in the genome of human. PRO:WCB UniProtKB:P16150 GALGP (human) UniProtKB:P16150 GPL115 (human) UniProtKB:P16150 galactoglycoprotein (human) UniProtKB:P16150 hSPN PRO:DNx leukocyte sialoglycoprotein (human) UniProtKB:P16150 sialophorin (human) UniProtKB:P16150 CD43 UniProtKB:P16150 SPN UniProtKB:P16150 An alpha-type platelet-derived growth factor receptor that is encoded in the genome of human. DTO:03100403 UniProtKB:P16234 CD140 antigen-like family member A (human) CD140a (human) CD140a antigen (human) PDGF-R-alpha (human) PDGFR-2 (human) PDGFR-alpha (human) alpha platelet-derived growth factor receptor (human) alpha-type platelet-derived growth factor receptor (human) hPDGFRA platelet-derived growth factor alpha receptor (human) platelet-derived growth factor receptor 2 (human) protein PDGFR2 PDGFRA RHEPDGFRA PR:P16234 Category=organism-gene. platelet-derived growth factor receptor alpha (human) An alpha-type platelet-derived growth factor receptor that is encoded in the genome of human. PRO:WCB UniProtKB:P16234 CD140 antigen-like family member A (human) UniProtKB:P16234 CD140a (human) UniProtKB:P16234 CD140a antigen (human) UniProtKB:P16234 PDGF-R-alpha (human) UniProtKB:P16234 PDGFR-2 (human) UniProtKB:P16234 PDGFR-alpha (human) UniProtKB:P16234 alpha platelet-derived growth factor receptor (human) UniProtKB:P16234 alpha-type platelet-derived growth factor receptor (human) UniProtKB:P16234 hPDGFRA PRO:DNx platelet-derived growth factor alpha receptor (human) UniProtKB:P16234 platelet-derived growth factor receptor 2 (human) UniProtKB:P16234 PDGFR2 UniProtKB:P16234 PDGFRA UniProtKB:P16234 RHEPDGFRA UniProtKB:P16234 An interleukin-2 receptor subunit beta that is encoded in the genome of mouse. UniProtKB:P16297 CD122 (mouse) IL-2 receptor subunit beta (mouse) IL-2R subunit beta (mouse) IL-2RB (mouse) high affinity IL-2 receptor subunit beta (mouse) mIL2RB p70-75 (mouse) protein Il2rb PR:P16297 Category=organism-gene. interleukin-2 receptor subunit beta (mouse) An interleukin-2 receptor subunit beta that is encoded in the genome of mouse. OMA:P16297 PRO:DNx CD122 (mouse) UniProtKB:P16297 IL-2 receptor subunit beta (mouse) UniProtKB:P16297 IL-2R subunit beta (mouse) UniProtKB:P16297 IL-2RB (mouse) UniProtKB:P16297 high affinity IL-2 receptor subunit beta (mouse) UniProtKB:P16297 mIL2RB PRO:DNx p70-75 (mouse) UniProtKB:P16297 Il2rb UniProtKB:P16297 A glutamyl aminopeptidase that is encoded in the genome of mouse. EAP (mouse) UniProtKB:P16406 AP-A (mouse) BP-1/6C3 antigen (mouse) CD249 (mouse) aminopeptidase A (mouse) mENPEP protein Enpep PR:P16406 Category=organism-gene. glutamyl aminopeptidase (mouse) A glutamyl aminopeptidase that is encoded in the genome of mouse. OMA:P16406 PRO:DNx EAP (mouse) UniProtKB:P16406 AP-A (mouse) UniProtKB:P16406 BP-1/6C3 antigen (mouse) UniProtKB:P16406 CD249 (mouse) UniProtKB:P16406 aminopeptidase A (mouse) UniProtKB:P16406 mENPEP PRO:DNx Enpep UniProtKB:P16406 A cytotoxic T-lymphocyte protein 4 that is encoded in the genome of human. UniProtKB:P16410 CTLA-4 (human) cytotoxic T-lymphocyte-associated antigen 4 (human) hCTLA4 protein CD152 CTLA4 PR:P16410 Category=organism-gene. cytotoxic T-lymphocyte protein 4 (human) A cytotoxic T-lymphocyte protein 4 that is encoded in the genome of human. PRO:WCB UniProtKB:P16410 CTLA-4 (human) UniProtKB:P16410 cytotoxic T-lymphocyte-associated antigen 4 (human) UniProtKB:P16410 hCTLA4 PRO:DNx CD152 UniProtKB:P16410 CTLA4 UniProtKB:P16410 A platelet glycoprotein 4 that is encoded in the genome of human. UniProtKB:P16671 FAT (human) GPIIIB (human) GPIV (human) PAS IV (human) PAS-4 (human) fatty acid translocase (human) glycoprotein IIIb (human) hCD36 leukocyte differentiation antigen CD36 (human) platelet collagen receptor (human) platelet glycoprotein IV (human) thrombospondin receptor (human) protein CD36 GP3B GP4 PR:P16671 Category=organism-gene. platelet glycoprotein 4 (human) A platelet glycoprotein 4 that is encoded in the genome of human. PRO:WCB UniProtKB:P16671 FAT (human) UniProtKB:P16671 GPIIIB (human) UniProtKB:P16671 GPIV (human) UniProtKB:P16671 PAS IV (human) UniProtKB:P16671 PAS-4 (human) UniProtKB:P16671 fatty acid translocase (human) UniProtKB:P16671 glycoprotein IIIb (human) UniProtKB:P16671 hCD36 PRO:DNx leukocyte differentiation antigen CD36 (human) UniProtKB:P16671 platelet collagen receptor (human) UniProtKB:P16671 platelet glycoprotein IV (human) UniProtKB:P16671 thrombospondin receptor (human) UniProtKB:P16671 CD36 UniProtKB:P16671 GP3B UniProtKB:P16671 GP4 UniProtKB:P16671 An interleukin-7 receptor subunit alpha that is encoded in the genome of human. UniProtKB:P16871 CD127 (human) CDw127 (human) IL-7 receptor subunit alpha (human) IL-7R subunit alpha (human) IL-7R-alpha (human) IL-7RA (human) hIL7R protein IL7R PR:P16871 Category=organism-gene. interleukin-7 receptor subunit alpha (human) An interleukin-7 receptor subunit alpha that is encoded in the genome of human. PRO:WCB UniProtKB:P16871 CD127 (human) UniProtKB:P16871 CDw127 (human) UniProtKB:P16871 IL-7 receptor subunit alpha (human) UniProtKB:P16871 IL-7R subunit alpha (human) UniProtKB:P16871 IL-7R-alpha (human) UniProtKB:P16871 IL-7RA (human) UniProtKB:P16871 hIL7R PRO:DNx IL7R UniProtKB:P16871 An interleukin-7 receptor subunit alpha that is encoded in the genome of mouse. UniProtKB:P16872 CD127 (mouse) IL-7 receptor subunit alpha (mouse) IL-7R subunit alpha (mouse) IL-7R-alpha (mouse) IL-7RA (mouse) mIL7R protein Il7r PR:P16872 Category=organism-gene. interleukin-7 receptor subunit alpha (mouse) An interleukin-7 receptor subunit alpha that is encoded in the genome of mouse. OMA:P16872 PRO:DNx CD127 (mouse) UniProtKB:P16872 IL-7 receptor subunit alpha (mouse) UniProtKB:P16872 IL-7R subunit alpha (mouse) UniProtKB:P16872 IL-7R-alpha (mouse) UniProtKB:P16872 IL-7RA (mouse) UniProtKB:P16872 mIL7R PRO:DNx Il7r UniProtKB:P16872 An integrin alpha-2 that is encoded in the genome of human. UniProtKB:P17301 CD49 antigen-like family member B (human) GPIa (human) VLA-2 subunit alpha (human) collagen receptor (human) hITGA2 platelet membrane glycoprotein Ia (human) protein CD49B ITGA2 PR:P17301 Category=organism-gene. integrin alpha-2 (human) An integrin alpha-2 that is encoded in the genome of human. PRO:CNA UniProtKB:P17301 CD49 antigen-like family member B (human) UniProtKB:P17301 GPIa (human) UniProtKB:P17301 VLA-2 subunit alpha (human) UniProtKB:P17301 collagen receptor (human) UniProtKB:P17301 hITGA2 PRO:DNx platelet membrane glycoprotein Ia (human) UniProtKB:P17301 CD49B UniProtKB:P17301 ITGA2 UniProtKB:P17301 A transcription factor PU.1 that is encoded in the genome of mouse. UniProtKB:P17433 31 kDa-transforming protein (mouse) SFFV proviral integration 1 protein (mouse) mSPI1 protein Sfpi-1 Sfpi1 Spi1 PR:P17433 Category=organism-gene. transcription factor PU.1 (mouse) A transcription factor PU.1 that is encoded in the genome of mouse. OMA:P17433 PRO:DNx 31 kDa-transforming protein (mouse) UniProtKB:P17433 SFFV proviral integration 1 protein (mouse) UniProtKB:P17433 mSPI1 PRO:DNx Sfpi-1 UniProtKB:P17433 Sfpi1 UniProtKB:P17433 Spi1 UniProtKB:P17433 A T-cell acute lymphocytic leukemia protein 1 that is encoded in the genome of human. Reactome:R-HSA-8956511 UniProtKB:P17542 Stem cell protein (human) T-cell leukemia/lymphoma protein 5 (human) TAL-1 (human) class A basic helix-loop-helix protein 17 (human) hTAL1 protein BHLHA17 SCL TAL1 TCL5 PR:P17542 Category=organism-gene. T-cell acute lymphocytic leukemia protein 1 (human) A T-cell acute lymphocytic leukemia protein 1 that is encoded in the genome of human. PRO:DNx UniProtKB:P17542 Reactome:R-HSA-8956511 PR:P17542 located_in GO:0005654 Stem cell protein (human) UniProtKB:P17542 T-cell leukemia/lymphoma protein 5 (human) UniProtKB:P17542 TAL-1 (human) UniProtKB:P17542 class A basic helix-loop-helix protein 17 (human) UniProtKB:P17542 hTAL1 PRO:DNx BHLHA17 UniProtKB:P17542 SCL UniProtKB:P17542 TAL1 UniProtKB:P17542 TCL5 UniProtKB:P17542 An erythroid transcription factor that is encoded in the genome of mouse. UniProtKB:P17679 Eryf1 (mouse) GATA-1 (mouse) GATA-binding factor 1 (mouse) GF-1 (mouse) NF-E1 DNA-binding protein (mouse) mGATA1 protein Gata1 Gf-1 PR:P17679 Category=organism-gene. erythroid transcription factor (mouse) An erythroid transcription factor that is encoded in the genome of mouse. OMA:P17679 PRO:DNx Eryf1 (mouse) UniProtKB:P17679 GATA-1 (mouse) UniProtKB:P17679 GATA-binding factor 1 (mouse) UniProtKB:P17679 GF-1 (mouse) UniProtKB:P17679 NF-E1 DNA-binding protein (mouse) UniProtKB:P17679 mGATA1 PRO:DNx Gata1 UniProtKB:P17679 Gf-1 UniProtKB:P17679 An endoglin that is encoded in the genome of human. UniProtKB:P17813 CD105 (human) hENG protein END ENG PR:P17813 Category=organism-gene. endoglin (human) An endoglin that is encoded in the genome of human. PRO:CNA UniProtKB:P17813 CD105 (human) UniProtKB:P17813 hENG PRO:DNx END UniProtKB:P17813 ENG UniProtKB:P17813 A complement receptor type 1 that is encoded in the genome of human. UniProtKB:P17927 C3b/C4b receptor (human) CD35 (human) hCR1 protein C3BR CR1 PR:P17927 Category=organism-gene. complement receptor type 1 (human) A complement receptor type 1 that is encoded in the genome of human. PRO:WCB UniProtKB:P17927 C3b/C4b receptor (human) UniProtKB:P17927 CD35 (human) UniProtKB:P17927 hCR1 PRO:DNx C3BR UniProtKB:P17927 CR1 UniProtKB:P17927 A transcription factor PU.1 that is encoded in the genome of human. Reactome:R-HSA-8865503 UniProtKB:P17947 31 kDa-transforming protein (human) hSPI1 protein SPI1 PR:P17947 Category=organism-gene. transcription factor PU.1 (human) A transcription factor PU.1 that is encoded in the genome of human. PRO:WCB UniProtKB:P17947 Reactome:R-HSA-8865503 PR:P17947 located_in GO:0005654 31 kDa-transforming protein (human) UniProtKB:P17947 hSPI1 PRO:DNx SPI1 UniProtKB:P17947 A CD48 molecule that is encoded in the genome of mouse. UniProtKB:P18181 BCM1 surface antigen (mouse) BLAST-1 (mouse) CD48 (mouse) HM48-1 (mouse) MRC OX-45 surface antigen (mouse) SLAM family member 2 (mouse) SLAMF2 (mouse) mCD48 sgp-60 (mouse) signaling lymphocytic activation molecule 2 (mouse) protein Bcm-1 Cd48 PR:P18181 Category=organism-gene. CD48 antigen (mouse) A CD48 molecule that is encoded in the genome of mouse. OMA:P18181 PRO:DNx BCM1 surface antigen (mouse) UniProtKB:P18181 BLAST-1 (mouse) UniProtKB:P18181 CD48 (mouse) UniProtKB:P18181 HM48-1 (mouse) UniProtKB:P18181 MRC OX-45 surface antigen (mouse) UniProtKB:P18181 SLAM family member 2 (mouse) UniProtKB:P18181 SLAMF2 (mouse) UniProtKB:P18181 mCD48 PRO:DNx sgp-60 (mouse) UniProtKB:P18181 signaling lymphocytic activation molecule 2 (mouse) UniProtKB:P18181 Bcm-1 UniProtKB:P18181 Cd48 UniProtKB:P18181 An L-selectin that is encoded in the genome of mouse. UniProtKB:P18337 CD62 antigen-like family member L (mouse) CD62L (mouse) LAM-1 (mouse) LECAM1 (mouse) leukocyte adhesion molecule 1 (mouse) leukocyte-endothelial cell adhesion molecule 1 (mouse) lymph node homing receptor (mouse) lymphocyte antigen 22 (mouse) lymphocyte surface MEL-14 antigen (mouse) mSELL protein Lnhr Ly-22 Ly22 Sell PR:P18337 Category=organism-gene. L-selectin (mouse) An L-selectin that is encoded in the genome of mouse. OMA:P18337 PRO:DNx CD62 antigen-like family member L (mouse) UniProtKB:P18337 CD62L (mouse) UniProtKB:P18337 LAM-1 (mouse) UniProtKB:P18337 LECAM1 (mouse) UniProtKB:P18337 leukocyte adhesion molecule 1 (mouse) UniProtKB:P18337 leukocyte-endothelial cell adhesion molecule 1 (mouse) UniProtKB:P18337 lymph node homing receptor (mouse) UniProtKB:P18337 lymphocyte antigen 22 (mouse) UniProtKB:P18337 lymphocyte surface MEL-14 antigen (mouse) UniProtKB:P18337 mSELL PRO:DNx Lnhr UniProtKB:P18337 Ly-22 UniProtKB:P18337 Ly22 UniProtKB:P18337 Sell UniProtKB:P18337 A syndecan-1 that is encoded in the genome of human. UniProtKB:P18827 CD138 (human) SYND1 (human) hSDC1 protein SDC SDC1 PR:P18827 Category=organism-gene. syndecan-1 (human) A syndecan-1 that is encoded in the genome of human. PRO:WCB UniProtKB:P18827 CD138 (human) UniProtKB:P18827 SYND1 (human) UniProtKB:P18827 hSDC1 PRO:DNx SDC UniProtKB:P18827 SDC1 UniProtKB:P18827 A syndecan-1 that is encoded in the genome of mouse. UniProtKB:P18828 CD138 (mouse) SYND1 (mouse) mSDC1 protein Sdc1 Synd-1 Synd1 PR:P18828 Category=organism-gene. syndecan-1 (mouse) A syndecan-1 that is encoded in the genome of mouse. OMA:P18828 PRO:DNx CD138 (mouse) UniProtKB:P18828 SYND1 (mouse) UniProtKB:P18828 mSDC1 PRO:DNx Sdc1 UniProtKB:P18828 Synd-1 UniProtKB:P18828 Synd1 UniProtKB:P18828 A complement receptor type 2 that is encoded in the genome of mouse. UniProtKB:P19070 CD21 (mouse) complement C3d receptor (mouse) mCR2 protein Cr2 PR:P19070 Category=organism-gene. complement receptor type 2 (mouse) A complement receptor type 2 that is encoded in the genome of mouse. PRO:WCB CD21 (mouse) UniProtKB:P19070 complement C3d receptor (mouse) UniProtKB:P19070 mCR2 PRO:DNx Cr2 UniProtKB:P19070 A membrane-spanning 4-domains subfamily A member 1 that is encoded in the genome of mouse. UniProtKB:P19437 B-cell differentiation antigen Ly-44 (mouse) CD20 (mouse) lymphocyte antigen 44 (mouse) mMS4A1 membrane-spanning 4-domains subfamily A member 1 (mouse) protein Cd20 Ly-44 Ms4a1 Ms4a2 PR:P19437 Category=organism-gene. B-lymphocyte antigen CD20 (mouse) A membrane-spanning 4-domains subfamily A member 1 that is encoded in the genome of mouse. OMA:P19437 PRO:DNx B-cell differentiation antigen Ly-44 (mouse) UniProtKB:P19437 CD20 (mouse) UniProtKB:P19437 lymphocyte antigen 44 (mouse) UniProtKB:P19437 mMS4A1 PRO:DNx membrane-spanning 4-domains subfamily A member 1 (mouse) UniProtKB:P19437 Cd20 UniProtKB:P19437 Ly-44 UniProtKB:P19437 Ms4a1 UniProtKB:P19437 Ms4a2 UniProtKB:P19437 A complement receptor type 2 that is encoded in the genome of human. UniProtKB:P20023 CD21 (human) Cr2 (human) EBV receptor (human) complement C3d receptor (human) epstein-Barr virus receptor (human) hCR2 protein C3DR CR2 PR:P20023 Category=organism-gene. complement receptor type 2 (human) A complement receptor type 2 that is encoded in the genome of human. PRO:WCB UniProtKB:P20023 CD21 (human) UniProtKB:P20023 Cr2 (human) UniProtKB:P20023 EBV receptor (human) UniProtKB:P20023 complement C3d receptor (human) UniProtKB:P20023 epstein-Barr virus receptor (human) UniProtKB:P20023 hCR2 PRO:DNx C3DR UniProtKB:P20023 CR2 UniProtKB:P20023 A CD33 molecule that is encoded in the genome of human. UniProtKB:P20138 gp67 (human) hCD33 sialic acid-binding Ig-like lectin 3 (human) siglec-3 (human) protein CD33 SIGLEC3 PR:P20138 Category=organism-gene. myeloid cell surface antigen CD33 (human) A CD33 molecule that is encoded in the genome of human. PRO:WCB UniProtKB:P20138 gp67 (human) UniProtKB:P20138 hCD33 PRO:DNx sialic acid-binding Ig-like lectin 3 (human) UniProtKB:P20138 siglec-3 (human) UniProtKB:P20138 CD33 UniProtKB:P20138 SIGLEC3 UniProtKB:P20138 A B-cell receptor CD22 that is encoded in the genome of human. UniProtKB:P20273 B-lymphocyte cell adhesion molecule (human) BL-CAM (human) T-cell surface antigen Leu-14 (human) hCD22 sialic acid-binding Ig-like lectin 2 (human) siglec-2 (human) protein CD22 SIGLEC2 PR:P20273 Category=organism-gene. B-cell receptor CD22 (human) A B-cell receptor CD22 that is encoded in the genome of human. PRO:WCB UniProtKB:P20273 B-lymphocyte cell adhesion molecule (human) UniProtKB:P20273 BL-CAM (human) UniProtKB:P20273 T-cell surface antigen Leu-14 (human) UniProtKB:P20273 hCD22 PRO:DNx sialic acid-binding Ig-like lectin 2 (human) UniProtKB:P20273 siglec-2 (human) UniProtKB:P20273 CD22 UniProtKB:P20273 SIGLEC2 UniProtKB:P20273 A parvalbumin alpha that is encoded in the genome of human. UniProtKB:P20472 hPVALB protein PVALB PR:P20472 Category=organism-gene. parvalbumin alpha (human) A parvalbumin alpha that is encoded in the genome of human. PRO:DNx UniProtKB:P20472 hPVALB PRO:DNx PVALB UniProtKB:P20472 A high affinity immunoglobulin epsilon receptor subunit alpha that is encoded in the genome of mouse. UniProtKB:P20489 Fc-epsilon RI-alpha (mouse) IgE Fc receptor subunit alpha (mouse) mFCER1A protein FcERI (mouse) Fce1a Fcer1a PR:P20489 Category=organism-gene. high affinity immunoglobulin epsilon receptor subunit alpha (mouse) A high affinity immunoglobulin epsilon receptor subunit alpha that is encoded in the genome of mouse. OMA:P20489 PRO:DNx Fc-epsilon RI-alpha (mouse) UniProtKB:P20489 IgE Fc receptor subunit alpha (mouse) UniProtKB:P20489 mFCER1A PRO:DNx FcERI (mouse) UniProtKB:P20489 Fce1a UniProtKB:P20489 Fcer1a UniProtKB:P20489 A low affinity immunoglobulin epsilon Fc receptor that is encoded in the genome of mouse. UniProtKB:P20693 CD23 (mouse) Fc-epsilon-RII (mouse) lymphocyte IgE receptor (mouse) mFCER2 protein Fcer2 Fcer2a PR:P20693 Category=organism-gene. low affinity immunoglobulin epsilon Fc receptor (mouse) A low affinity immunoglobulin epsilon Fc receptor that is encoded in the genome of mouse. OMA:P20693 PRO:DNx CD23 (mouse) UniProtKB:P20693 Fc-epsilon-RII (mouse) UniProtKB:P20693 lymphocyte IgE receptor (mouse) UniProtKB:P20693 mFCER2 PRO:DNx Fcer2 UniProtKB:P20693 Fcer2a UniProtKB:P20693 An integrin alpha-X that is encoded in the genome of human. UniProtKB:P20702 CD11 antigen-like family member C (human) Leu M5 (human) hITGAX leukocyte adhesion glycoprotein p150,95 alpha chain (human) leukocyte adhesion receptor p150,95 (human) protein CD11C ITGAX PR:P20702 Category=organism-gene. integrin alpha-X (human) CD11 antigen-like family member C (human) UniProtKB:P20702 Leu M5 (human) UniProtKB:P20702 hITGAX PRO:DNx leukocyte adhesion glycoprotein p150,95 alpha chain (human) UniProtKB:P20702 leukocyte adhesion receptor p150,95 (human) UniProtKB:P20702 CD11C UniProtKB:P20702 ITGAX UniProtKB:P20702 A T-cell surface glycoprotein YE1/48 that is encoded in the genome of mouse. UniProtKB:P20937 T lymphocyte antigen A1 (mouse) lymphocyte antigen 49a (mouse) mKlra1 protein Klra1 Ly-49 Ly-49a Ly49 Ly49A PR:P20937 Category=organism-gene. T-cell surface glycoprotein YE1/48 (mouse) A T-cell surface glycoprotein YE1/48 that is encoded in the genome of mouse. PRO:DNx UniProtKB:P20937 T lymphocyte antigen A1 (mouse) UniProtKB:P20937 lymphocyte antigen 49a (mouse) UniProtKB:P20937 mKlra1 PRO:DNx Klra1 UniProtKB:P20937 Ly-49 UniProtKB:P20937 Ly-49a UniProtKB:P20937 Ly49 UniProtKB:P20937 Ly49A UniProtKB:P20937 An interleukin-5 receptor subunit alpha that is encoded in the genome of mouse. UniProtKB:P21183 CD125 (mouse) IL-5 receptor subunit alpha (mouse) IL-5R subunit alpha (mouse) IL-5R-alpha (mouse) IL-5RA (mouse) mIL5RA protein Il5r Il5ra PR:P21183 Category=organism-gene. interleukin-5 receptor subunit alpha (mouse) An interleukin-5 receptor subunit alpha that is encoded in the genome of mouse. OMA:P21183 PRO:DNx CD125 (mouse) UniProtKB:P21183 IL-5 receptor subunit alpha (mouse) UniProtKB:P21183 IL-5R subunit alpha (mouse) UniProtKB:P21183 IL-5R-alpha (mouse) UniProtKB:P21183 IL-5RA (mouse) UniProtKB:P21183 mIL5RA PRO:DNx Il5r UniProtKB:P21183 Il5ra UniProtKB:P21183 An fMet-Leu-Phe receptor that is encoded in the genome of human. DTO:02100098 Reactome:R-HSA-375450 Reactome:R-HSA-6799143 Reactome:R-HSA-6800878 Reactome:R-HSA-6800929 UniProtKB:P21462 FPR (human) N-formyl peptide receptor (human) N-formylpeptide chemoattractant receptor (human) fMLP receptor (human) hFPR1 protein FPR1 PR:P21462 Category=organism-gene. fMet-Leu-Phe receptor (human) An fMet-Leu-Phe receptor that is encoded in the genome of human. PRO:WCB UniProtKB:P21462 Reactome:R-HSA-375450 PR:P21462 located_in GO:0005886 Reactome:R-HSA-6799143 PR:P21462 located_in GO:0035577 Reactome:R-HSA-6800878 PR:P21462 located_in GO:0101003 Reactome:R-HSA-6800929 PR:P21462 located_in GO:0030667 FPR (human) UniProtKB:P21462 N-formyl peptide receptor (human) UniProtKB:P21462 N-formylpeptide chemoattractant receptor (human) UniProtKB:P21462 fMLP receptor (human) UniProtKB:P21462 hFPR1 PRO:DNx FPR1 UniProtKB:P21462 A macrophage scavenger receptor types I and II that is encoded in the genome of human. UniProtKB:P21757 CD204 (human) hMSR1 macrophage acetylated LDL receptor I and II (human) scavenger receptor class A member 1 (human) protein MSR1 SCARA1 PR:P21757 Category=organism-gene. macrophage scavenger receptor types I and II (human) A macrophage scavenger receptor types I and II that is encoded in the genome of human. PRO:WCB UniProtKB:P21757 CD204 (human) UniProtKB:P21757 hMSR1 PRO:DNx macrophage acetylated LDL receptor I and II (human) UniProtKB:P21757 scavenger receptor class A member 1 (human) UniProtKB:P21757 MSR1 UniProtKB:P21757 SCARA1 UniProtKB:P21757 A V(D)J recombination-activating protein 2 that is encoded in the genome of mouse. UniProtKB:P21784 RAG-2 (mouse) mRAG2 protein Rag-2 Rag2 PR:P21784 Category=organism-gene. V(D)J recombination-activating protein 2 (mouse) A V(D)J recombination-activating protein 2 that is encoded in the genome of mouse. OMA:P21784 PRO:DNx RAG-2 (mouse) UniProtKB:P21784 mRAG2 PRO:DNx Rag-2 UniProtKB:P21784 Rag2 UniProtKB:P21784 A CD9 molecule that is encoded in the genome of human. p24 (human) UniProtKB:P21926 5H9 antigen (human) MRP-1 (human) cell growth-inhibiting gene 2 protein (human) hCD9 leukocyte antigen MIC3 (human) motility-related protein (human) tetraspanin-29 (human) tspan-29 (human) protein CD9 GIG2 MIC3 TSPAN29 PR:P21926 Category=organism-gene. CD9 antigen (human) A CD9 molecule that is encoded in the genome of human. PRO:DNx UniProtKB:P21926 p24 (human) UniProtKB:P21926 5H9 antigen (human) UniProtKB:P21926 MRP-1 (human) UniProtKB:P21926 cell growth-inhibiting gene 2 protein (human) UniProtKB:P21926 hCD9 PRO:DNx leukocyte antigen MIC3 (human) UniProtKB:P21926 motility-related protein (human) UniProtKB:P21926 tetraspanin-29 (human) UniProtKB:P21926 tspan-29 (human) UniProtKB:P21926 CD9 UniProtKB:P21926 GIG2 UniProtKB:P21926 MIC3 UniProtKB:P21926 TSPAN29 UniProtKB:P21926 An alpha-(1,3)-fucosyltransferase 4 that is encoded in the genome of human. galactoside 3-L-fucosyltransferase (human) Reactome:R-HSA-9034106 UniProtKB:P22083 ELAM-1 ligand fucosyltransferase (human) Fuc-TIV (human) FucT-IV (human) fucosyltransferase 4 (human) fucosyltransferase IV (human) hFUT4 protein ELFT FCT3A FUT4 PR:P22083 Category=organism-gene. alpha-(1,3)-fucosyltransferase 4 (human) An alpha-(1,3)-fucosyltransferase 4 that is encoded in the genome of human. PRO:CNA UniProtKB:P22083 galactoside 3-L-fucosyltransferase (human) UniProtKB:P22083 Reactome:R-HSA-9034106 PR:P22083 located_in GO:0000139 ELAM-1 ligand fucosyltransferase (human) UniProtKB:P22083 Fuc-TIV (human) UniProtKB:P22083 FucT-IV (human) UniProtKB:P22083 fucosyltransferase 4 (human) UniProtKB:P22083 fucosyltransferase IV (human) UniProtKB:P22083 hFUT4 PRO:DNx ELFT UniProtKB:P22083 FCT3A UniProtKB:P22083 FUT4 UniProtKB:P22083 A T-cell acute lymphocytic leukemia protein 1 that is encoded in the genome of mouse. UniProtKB:P22091 Stem cell protein (mouse) TAL-1 (mouse) mTAL1 protein Scl Tal-1 Tal1 PR:P22091 Category=organism-gene. T-cell acute lymphocytic leukemia protein 1 homolog (mouse) A T-cell acute lymphocytic leukemia protein 1 that is encoded in the genome of mouse. OMA:P22091 PRO:DNx Stem cell protein (mouse) UniProtKB:P22091 TAL-1 (mouse) UniProtKB:P22091 mTAL1 PRO:DNx Scl UniProtKB:P22091 Tal-1 UniProtKB:P22091 Tal1 UniProtKB:P22091 A CD3 epsilon that is encoded in the genome of mouse. UniProtKB:P22646 CD3e (mouse) T-cell surface antigen T3/Leu-4 epsilon chain (mouse) mCD3E protein Cd3e PR:P22646 Category=organism-gene. T-cell surface glycoprotein CD3 epsilon chain (mouse) A CD3 epsilon that is encoded in the genome of mouse. OMA:P22646 PRO:DNx CD3e (mouse) UniProtKB:P22646 T-cell surface antigen T3/Leu-4 epsilon chain (mouse) UniProtKB:P22646 mCD3E PRO:DNx Cd3e UniProtKB:P22646 A macrophage mannose receptor 1 that is encoded in the genome of human. UniProtKB:P22897 C-type lectin domain family 13 member D (human) C-type lectin domain family 13 member D-like (human) CD206 (human) MMR (human) hMR hMRC1 human mannose receptor macrophage mannose receptor 1-like protein 1 (human) protein CLEC13D CLEC13DL MRC1 MRC1L1 PR:P22897 Category=organism-gene. macrophage mannose receptor 1 (human) A macrophage mannose receptor 1 that is encoded in the genome of human. PRO:CNA UniProtKB:P22897 C-type lectin domain family 13 member D (human) UniProtKB:P22897 C-type lectin domain family 13 member D-like (human) UniProtKB:P22897 CD206 (human) UniProtKB:P22897 MMR (human) UniProtKB:P22897 hMR UniProtKB:P22897 hMRC1 PRO:DNx human mannose receptor UniProtKB:P22897 macrophage mannose receptor 1-like protein 1 (human) UniProtKB:P22897 CLEC13D UniProtKB:P22897 CLEC13DL UniProtKB:P22897 MRC1 UniProtKB:P22897 MRC1L1 UniProtKB:P22897 An endothelial transcription factor GATA-2 that is encoded in the genome of human. Reactome:R-HSA-996735 UniProtKB:P23769 GATA-binding protein 2 (human) hGATA2 protein GATA2 PR:P23769 Category=organism-gene. endothelial transcription factor GATA-2 (human) An endothelial transcription factor GATA-2 that is encoded in the genome of human. PRO:DNx UniProtKB:P23769 Reactome:R-HSA-996735 PR:P23769 located_in GO:0005654 GATA-binding protein 2 (human) UniProtKB:P23769 hGATA2 PRO:DNx GATA2 UniProtKB:P23769 A trans-acting T-cell-specific transcription factor GATA-3 that is encoded in the genome of human. Reactome:R-HSA-996768 UniProtKB:P23771 GATA-binding factor 3 (human) hGATA3 protein GATA3 PR:P23771 Category=organism-gene. trans-acting T-cell-specific transcription factor GATA-3 (human) A trans-acting T-cell-specific transcription factor GATA-3 that is encoded in the genome of human. PRO:WCB UniProtKB:P23771 Reactome:R-HSA-996768 PR:P23771 located_in GO:0005654 GATA-binding factor 3 (human) UniProtKB:P23771 hGATA3 PRO:DNx GATA3 UniProtKB:P23771 A trans-acting T-cell-specific transcription factor GATA-3 that is encoded in the genome of mouse. UniProtKB:P23772 GATA-binding factor 3 (mouse) mGATA3 protein Gata-3 Gata3 PR:P23772 Category=organism-gene. trans-acting T-cell-specific transcription factor GATA-3 (mouse) A trans-acting T-cell-specific transcription factor GATA-3 that is encoded in the genome of mouse. OMA:P23772 PRO:DNx GATA-binding factor 3 (mouse) UniProtKB:P23772 mGATA3 PRO:DNx Gata-3 UniProtKB:P23772 Gata3 UniProtKB:P23772 A signal transducer CD24 that is encoded in the genome of mouse. UniProtKB:P24807 CD24 (mouse) HSA (mouse) M1/69-J11D heat stable antigen (mouse) R13-Ag (mouse) X62 heat stable antigen (mouse) lymphocyte antigen 52 (mouse) mCD24 nectadrin (mouse) protein Cd24 Cd24a Ly-52 PR:P24807 Category=organism-gene. signal transducer CD24 (mouse) A signal transducer CD24 that is encoded in the genome of mouse. OMA:P24807 PRO:WCB CD24 (mouse) UniProtKB:P24807 HSA (mouse) UniProtKB:P24807 M1/69-J11D heat stable antigen (mouse) UniProtKB:P24807 R13-Ag (mouse) UniProtKB:P24807 X62 heat stable antigen (mouse) UniProtKB:P24807 lymphocyte antigen 52 (mouse) UniProtKB:P24807 mCD24 PRO:DNx nectadrin (mouse) UniProtKB:P24807 Cd24 UniProtKB:P24807 Cd24a UniProtKB:P24807 Ly-52 UniProtKB:P24807 A C-X-C chemokine receptor type 1 that is encoded in the genome of human. DTO:02100075 Reactome:R-HSA-373805 Reactome:R-HSA-6804780 UniProtKB:P25024 CD181 (human) CDw128a (human) CXC-R1 (human) CXCR-1 (human) IL-8 receptor type 1 (human) IL-8R A (human) hCXCR1 high affinity interleukin-8 receptor A (human) protein CMKAR1 CXCR1 IL8RA PR:P25024 Category=organism-gene. C-X-C chemokine receptor type 1 (human) A C-X-C chemokine receptor type 1 that is encoded in the genome of human. PRO:WCB UniProtKB:P25024 Reactome:R-HSA-373805 PR:P25024 located_in GO:0005886 Reactome:R-HSA-6804780 PR:P25024 located_in GO:0030667 CD181 (human) UniProtKB:P25024 CDw128a (human) UniProtKB:P25024 CXC-R1 (human) UniProtKB:P25024 CXCR-1 (human) UniProtKB:P25024 IL-8 receptor type 1 (human) UniProtKB:P25024 IL-8R A (human) UniProtKB:P25024 hCXCR1 PRO:DNx high affinity interleukin-8 receptor A (human) UniProtKB:P25024 CMKAR1 UniProtKB:P25024 CXCR1 UniProtKB:P25024 IL8RA UniProtKB:P25024 A C-X-C chemokine receptor type 2 that is encoded in the genome of human. DTO:02100076 Reactome:R-HSA-373796 Reactome:R-HSA-6804771 UniProtKB:P25025 CD182 (human) CDw128b (human) CXC-R2 (human) CXCR-2 (human) GRO/MGSA receptor (human) IL-8 receptor type 2 (human) IL-8R B (human) hCXCR2 high affinity interleukin-8 receptor B (human) protein CXCR2 IL8RB PR:P25025 Category=organism-gene. Requested by=PubChem. C-X-C chemokine receptor type 2 (human) A C-X-C chemokine receptor type 2 that is encoded in the genome of human. PRO:WCB UniProtKB:P25025 Reactome:R-HSA-373796 PR:P25025 located_in GO:0005886 Reactome:R-HSA-6804771 PR:P25025 located_in GO:0030667 CD182 (human) UniProtKB:P25025 CDw128b (human) UniProtKB:P25025 CXC-R2 (human) UniProtKB:P25025 CXCR-2 (human) UniProtKB:P25025 GRO/MGSA receptor (human) UniProtKB:P25025 IL-8 receptor type 2 (human) UniProtKB:P25025 IL-8R B (human) UniProtKB:P25025 hCXCR2 PRO:DNx high affinity interleukin-8 receptor B (human) UniProtKB:P25025 CXCR2 UniProtKB:P25025 IL8RB UniProtKB:P25025 A signal transducer CD24 that is encoded in the genome of human. UniProtKB:P25063 hCD24 small cell lung carcinoma cluster 4 antigen (human) protein CD24 CD24A PR:P25063 Category=organism-gene. signal transducer CD24 (human) A signal transducer CD24 that is encoded in the genome of human. PRO:WCB UniProtKB:P25063 hCD24 PRO:DNx small cell lung carcinoma cluster 4 antigen (human) UniProtKB:P25063 CD24 UniProtKB:P25063 CD24A UniProtKB:P25063 A CD19 molecule that is encoded in the genome of mouse. UniProtKB:P25918 CD19 (mouse) differentiation antigen CD19 (mouse) mCD19 protein Cd19 PR:P25918 Category=organism-gene. B-lymphocyte antigen CD19 (mouse) A CD19 molecule that is encoded in the genome of mouse. OMA:P25918 PRO:DNx CD19 (mouse) UniProtKB:P25918 differentiation antigen CD19 (mouse) UniProtKB:P25918 mCD19 PRO:DNx Cd19 UniProtKB:P25918 An integrin beta-7 that is encoded in the genome of human. UniProtKB:P26010 Gut homing receptor beta subunit (human) hITGB7 protein ITGB7 PR:P26010 Category=organism-gene. integrin beta-7 (human) An integrin beta-7 that is encoded in the genome of human. PRO:DNx UniProtKB:P26010 Gut homing receptor beta subunit (human) UniProtKB:P26010 hITGB7 PRO:DNx ITGB7 UniProtKB:P26010 An integrin beta-7 that is encoded in the genome of mouse. UniProtKB:P26011 M290 IEL antigen (mouse) integrin beta-P (mouse) mITGB7 protein Itgb7 PR:P26011 Category=organism-gene. integrin beta-7 (mouse) An integrin beta-7 that is encoded in the genome of mouse. OMA:P26011 PRO:DNx M290 IEL antigen (mouse) UniProtKB:P26011 integrin beta-P (mouse) UniProtKB:P26011 mITGB7 PRO:DNx Itgb7 UniProtKB:P26011 A high affinity immunoglobulin gamma Fc receptor I that is encoded in the genome of mouse. UniProtKB:P26151 CD64 (mouse) Fc-gamma RI (mouse) FcRI (mouse) IgG Fc receptor I (mouse) mFCGR1A protein Fcg1 Fcgr1 PR:P26151 Category=organism-gene. high affinity immunoglobulin gamma Fc receptor I (mouse) A high affinity immunoglobulin gamma Fc receptor I that is encoded in the genome of mouse. OMA:P26151 PRO:DNx CD64 (mouse) UniProtKB:P26151 Fc-gamma RI (mouse) UniProtKB:P26151 FcRI (mouse) UniProtKB:P26151 IgG Fc receptor I (mouse) UniProtKB:P26151 mFCGR1A PRO:DNx Fcg1 UniProtKB:P26151 Fcgr1 UniProtKB:P26151 An alpha-type platelet-derived growth factor receptor that is encoded in the genome of mouse. UniProtKB:P26618 CD140 antigen-like family member A (mouse) CD140a (mouse) PDGF-R-alpha (mouse) PDGFR-alpha (mouse) alpha platelet-derived growth factor receptor (mouse) alpha-type platelet-derived growth factor receptor (mouse) mPDGFRA platelet-derived growth factor alpha receptor (mouse) protein Pdgfra PR:P26618 Category=organism-gene. platelet-derived growth factor receptor alpha (mouse) An alpha-type platelet-derived growth factor receptor that is encoded in the genome of mouse. OMA:P26618 PRO:DNx CD140 antigen-like family member A (mouse) UniProtKB:P26618 CD140a (mouse) UniProtKB:P26618 PDGF-R-alpha (mouse) UniProtKB:P26618 PDGFR-alpha (mouse) UniProtKB:P26618 alpha platelet-derived growth factor receptor (mouse) UniProtKB:P26618 alpha-type platelet-derived growth factor receptor (mouse) UniProtKB:P26618 mPDGFRA PRO:DNx platelet-derived growth factor alpha receptor (mouse) UniProtKB:P26618 Pdgfra UniProtKB:P26618 An NKG2-A/NKG2-B type II integral membrane protein that is encoded in the genome of human. Reactome:R-HSA-3006545 UniProtKB:P26715 CD159 antigen-like family member A (human) CD159a (human) NK cell receptor A (human) NKG2-A/B-activating NK receptor (human) hKLRC1 protein KLRC1 NKG2A PR:P26715 Category=organism-gene. NKG2-A/NKG2-B type II integral membrane protein (human) An NKG2-A/NKG2-B type II integral membrane protein that is encoded in the genome of human. PRO:WCB UniProtKB:P26715 Reactome:R-HSA-3006545 PR:P26715 located_in GO:0005886 CD159 antigen-like family member A (human) UniProtKB:P26715 CD159a (human) UniProtKB:P26715 NK cell receptor A (human) UniProtKB:P26715 NKG2-A/B-activating NK receptor (human) UniProtKB:P26715 hKLRC1 PRO:DNx KLRC1 UniProtKB:P26715 NKG2A UniProtKB:P26715 A CD27 molecule that is encoded in the genome of human. UniProtKB:P26842 CD27L receptor (human) T-cell activation antigen CD27 (human) T14 (human) hCD27 tumor necrosis factor receptor superfamily member 7 (human) protein CD27 TNFRSF7 PR:P26842 Category=organism-gene. CD27 antigen (human) A CD27 molecule that is encoded in the genome of human. PRO:WCB UniProtKB:P26842 CD27L receptor (human) UniProtKB:P26842 T-cell activation antigen CD27 (human) UniProtKB:P26842 T14 (human) UniProtKB:P26842 hCD27 PRO:DNx tumor necrosis factor receptor superfamily member 7 (human) UniProtKB:P26842 CD27 UniProtKB:P26842 TNFRSF7 UniProtKB:P26842 An interleukin-3 receptor class 2 alpha chain that is encoded in the genome of human. UniProtKB:P26951 CD123 (human) IL-3 receptor subunit alpha (human) IL-3R subunit alpha (human) IL-3R-alpha (human) IL-3RA (human) hIL3RA protein IL3R IL3RA PR:P26951 Category=organism-gene. interleukin-3 receptor subunit alpha (human) An interleukin-3 receptor class 2 alpha chain that is encoded in the genome of human. PRO:WCB UniProtKB:P26951 CD123 (human) UniProtKB:P26951 IL-3 receptor subunit alpha (human) UniProtKB:P26951 IL-3R subunit alpha (human) UniProtKB:P26951 IL-3R-alpha (human) UniProtKB:P26951 IL-3RA (human) UniProtKB:P26951 hIL3RA PRO:DNx IL3R UniProtKB:P26951 IL3RA UniProtKB:P26951 An interleukin-3 receptor class 2 alpha chain that is encoded in the genome of mouse. UniProtKB:P26952 CD123 (mouse) IL-3 receptor subunit alpha (mouse) IL-3R subunit alpha (mouse) IL-3R-alpha (mouse) IL-3RA (mouse) interleukin-3 receptor class II alpha chain (mouse) mIL3RA protein Il3ra Sut-1 PR:P26952 Category=organism-gene. interleukin-3 receptor subunit alpha (mouse) An interleukin-3 receptor class 2 alpha chain that is encoded in the genome of mouse. OMA:P26952 PRO:DNx CD123 (mouse) UniProtKB:P26952 IL-3 receptor subunit alpha (mouse) UniProtKB:P26952 IL-3R subunit alpha (mouse) UniProtKB:P26952 IL-3R-alpha (mouse) UniProtKB:P26952 IL-3RA (mouse) UniProtKB:P26952 interleukin-3 receptor class II alpha chain (mouse) UniProtKB:P26952 mIL3RA PRO:DNx Il3ra UniProtKB:P26952 Sut-1 UniProtKB:P26952 A tumor necrosis factor ligand superfamily member 5 that is encoded in the genome of mouse. UniProtKB:P27548 CD154 (mouse) CD40-L (mouse) T-cell antigen Gp39 (mouse) TNF-related activation protein (mouse) TRAP (mouse) mCD40LG tumor necrosis factor ligand superfamily member 5 (mouse) protein Cd40l Cd40lg Tnfsf5 PR:P27548 Category=organism-gene. CD40 ligand (mouse) A tumor necrosis factor ligand superfamily member 5 that is encoded in the genome of mouse. OMA:P27548 PRO:DNx CD154 (mouse) UniProtKB:P27548 CD40-L (mouse) UniProtKB:P27548 T-cell antigen Gp39 (mouse) UniProtKB:P27548 TNF-related activation protein (mouse) UniProtKB:P27548 TRAP (mouse) UniProtKB:P27548 mCD40LG PRO:DNx tumor necrosis factor ligand superfamily member 5 (mouse) UniProtKB:P27548 Cd40l UniProtKB:P27548 Cd40lg UniProtKB:P27548 Tnfsf5 UniProtKB:P27548 A killer cell lectin-like receptor subfamily B member 1C that is encoded in the genome of mouse. UniProtKB:P27814 CD161 antigen-like family member C (mouse) CD161c (mouse) Ly-55c (mouse) NK1.1 (mouse) NKR-P1 40 (mouse) NKR-P1.9 (mouse) NKR-P1C (mouse) lymphocyte antigen 55c (mouse) mKlrb1c natural killer cell surface protein P1-40 (mouse) protein Klrb1c Ly55c Nkrp1c PR:P27814 Category=organism-gene. killer cell lectin-like receptor subfamily B member 1C (mouse) A killer cell lectin-like receptor subfamily B member 1C that is encoded in the genome of mouse. PRO:CNA UniProtKB:P27814 CD161 antigen-like family member C (mouse) UniProtKB:P27814 CD161c (mouse) UniProtKB:P27814 Ly-55c (mouse) UniProtKB:P27814 NK1.1 (mouse) UniProtKB:P27814 NKR-P1 40 (mouse) UniProtKB:P27814 NKR-P1.9 (mouse) UniProtKB:P27814 NKR-P1C (mouse) UniProtKB:P27814 lymphocyte antigen 55c (mouse) UniProtKB:P27814 mKlrb1c PRO:DNx natural killer cell surface protein P1-40 (mouse) UniProtKB:P27814 Klrb1c UniProtKB:P27814 Ly55c UniProtKB:P27814 Nkrp1c UniProtKB:P27814 A CD34 molecule that is encoded in the genome of human. UniProtKB:P28906 hCD34 protein CD34 PR:P28906 Category=organism-gene. hematopoietic progenitor cell antigen CD34 (human) hCD34 PRO:DNx CD34 UniProtKB:P28906 An ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 that is encoded in the genome of human. Reactome:R-HSA-8938080 UniProtKB:P28907 2'-phospho-ADP-ribosyl cyclase (human) 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase (human) 2'-phospho-cyclic-ADP-ribose transferase (human) ADP-ribosyl cyclase 1 (human) ADPRC 1 (human) T10 (human) cADPr hydrolase 1 (human) cyclic ADP-ribose hydrolase 1 (human) hCD38 protein CD38 PR:P28907 Category=organism-gene. ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 (human) An ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 that is encoded in the genome of human. PRO:WCB UniProtKB:P28907 Reactome:R-HSA-8938080 PR:P28907 located_in GO:0005886 2'-phospho-ADP-ribosyl cyclase (human) UniProtKB:P28907 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase (human) UniProtKB:P28907 2'-phospho-cyclic-ADP-ribose transferase (human) UniProtKB:P28907 ADPRC 1 (human) UniProtKB:P28907 T10 (human) UniProtKB:P28907 cADPr hydrolase 1 (human) UniProtKB:P28907 cyclic ADP-ribose hydrolase 1 (human) UniProtKB:P28907 hCD38 PRO:DNx CD38 UniProtKB:P28907 A T-cell surface glycoprotein CD1c that is encoded in the genome of human. MRO:0000890 UniProtKB:P29017 CD1c (human) hCD1C human CD1c chain protein CD1C PR:P29017 Category=organism-gene. T-cell surface glycoprotein CD1c (human) A T-cell surface glycoprotein CD1c that is encoded in the genome of human. PRO:WCB UniProtKB:P29017 CD1c (human) UniProtKB:P29017 hCD1C PRO:DNx human CD1c chain MRO:0000890 CD1C UniProtKB:P29017 A tumor necrosis factor ligand superfamily member 5 that is encoded in the genome of human. Reactome:R-HSA-198113 UniProtKB:P29965 CD154 (human) CD40-L (human) T-cell antigen Gp39 (human) TNF-related activation protein (human) hCD40LG tumor necrosis factor ligand superfamily member 5 (human) protein CD40L CD40LG TNFSF5 TRAP PR:P29965 Category=organism-gene. CD40 ligand (human) A tumor necrosis factor ligand superfamily member 5 that is encoded in the genome of human. PRO:WCB UniProtKB:P29965 Reactome:R-HSA-198113 PR:P29965 located_in GO:0005886 CD154 (human) UniProtKB:P29965 CD40-L (human) UniProtKB:P29965 T-cell antigen Gp39 (human) UniProtKB:P29965 TNF-related activation protein (human) UniProtKB:P29965 hCD40LG PRO:DNx tumor necrosis factor ligand superfamily member 5 (human) UniProtKB:P29965 CD40L UniProtKB:P29965 CD40LG UniProtKB:P29965 TNFSF5 UniProtKB:P29965 TRAP UniProtKB:P29965 A macrophage scavenger receptor types I and II that is encoded in the genome of mouse. UniProtKB:P30204 CD204 (mouse) SR-A (mouse) mMSR1 macrophage acetylated LDL receptor I and II (mouse) scavenger receptor type A (mouse) protein Msr1 Scvr PR:P30204 Category=organism-gene. macrophage scavenger receptor types I and II (mouse) A macrophage scavenger receptor types I and II that is encoded in the genome of mouse. OMA:P30204 PRO:DNx CD204 (mouse) UniProtKB:P30204 SR-A (mouse) UniProtKB:P30204 mMSR1 PRO:DNx macrophage acetylated LDL receptor I and II (mouse) UniProtKB:P30204 scavenger receptor type A (mouse) UniProtKB:P30204 Msr1 UniProtKB:P30204 Scvr UniProtKB:P30204 A T-cell-specific surface glycoprotein CD28 that is encoded in the genome of mouse. UniProtKB:P31041 CD28 (mouse) mCD28 protein Cd28 PR:P31041 Category=organism-gene. T-cell-specific surface glycoprotein CD28 (mouse) A T-cell-specific surface glycoprotein CD28 that is encoded in the genome of mouse. OMA:P31041 PRO:DNx CD28 (mouse) UniProtKB:P31041 mCD28 PRO:DNx Cd28 UniProtKB:P31041 A low affinity immunoglobulin gamma Fc region receptor II-b that is encoded in the genome of human. CD32 (human) CDw32 (human) UniProtKB:P31994 Fc-gamma RII-b (human) Fc-gamma-RIIb (human) FcRII-b (human) IgG Fc receptor II-b (human) hFCGR2B protein CD32 FCG2 FCGR2B IGFR2 PR:P31994 Category=organism-gene. low affinity immunoglobulin gamma Fc region receptor II-b (human) A low affinity immunoglobulin gamma Fc region receptor II-b that is encoded in the genome of human. PRO:CNA UniProtKB:P31994 CD32 (human) UniProtKB:P31994 CDw32 (human) UniProtKB:P31994 Fc-gamma RII-b (human) UniProtKB:P31994 Fc-gamma-RIIb (human) UniProtKB:P31994 FcRII-b (human) UniProtKB:P31994 IgG Fc receptor II-b (human) UniProtKB:P31994 hFCGR2B PRO:DNx CD32 UniProtKB:P31994 FCG2 UniProtKB:P31994 FCGR2B UniProtKB:P31994 IGFR2 UniProtKB:P31994 A macrosialin that is encoded in the genome of mouse. UniProtKB:P31996 CD68 (mouse) mCD68 protein Cd68 PR:P31996 Category=organism-gene. macrosialin (mouse) A macrosialin that is encoded in the genome of mouse. OMA:P31996 PRO:DNx CD68 (mouse) UniProtKB:P31996 mCD68 PRO:DNx Cd68 UniProtKB:P31996 A carcinoembryonic antigen-related cell adhesion molecule 8 that is encoded in the genome of human. UniProtKB:P31997 CD66b (human) CD67 antigen (human) carcinoembryonic antigen CGM6 (human) hCEACAM8 non-specific cross-reacting antigen NCA-95 (human) protein CEACAM8 CGM6 PR:P31997 Category=organism-gene. carcinoembryonic antigen-related cell adhesion molecule 8 (human) A carcinoembryonic antigen-related cell adhesion molecule 8 that is encoded in the genome of human. PRO:CNA UniProtKB:P31997 CD66b (human) UniProtKB:P31997 CD67 antigen (human) UniProtKB:P31997 carcinoembryonic antigen CGM6 (human) UniProtKB:P31997 hCEACAM8 PRO:DNx non-specific cross-reacting antigen NCA-95 (human) UniProtKB:P31997 CEACAM8 UniProtKB:P31997 CGM6 UniProtKB:P31997 A C-C chemokine receptor type 1 that is encoded in the genome of human. DTO:02100053 Reactome:R-HSA-373107 UniProtKB:P32246 C-C CKR-1 (human) CC-CKR-1 (human) CCR-1 (human) CD191 (human) HM145 (human) LD78 receptor (human) MIP-1alpha-R (human) RANTES-R (human) hCCR1 macrophage inflammatory protein 1-alpha receptor (human) protein CCR1 CMKBR1 CMKR1 SCYAR1 PR:P32246 Category=organism-gene. C-C chemokine receptor type 1 (human) A C-C chemokine receptor type 1 that is encoded in the genome of human. PRO:WCB UniProtKB:P32246 Reactome:R-HSA-373107 PR:P32246 located_in GO:0005886 C-C CKR-1 (human) UniProtKB:P32246 CC-CKR-1 (human) UniProtKB:P32246 CCR-1 (human) UniProtKB:P32246 CD191 (human) UniProtKB:P32246 HM145 (human) UniProtKB:P32246 LD78 receptor (human) UniProtKB:P32246 MIP-1alpha-R (human) UniProtKB:P32246 RANTES-R (human) UniProtKB:P32246 hCCR1 PRO:DNx macrophage inflammatory protein 1-alpha receptor (human) UniProtKB:P32246 CCR1 UniProtKB:P32246 CMKBR1 UniProtKB:P32246 CMKR1 UniProtKB:P32246 SCYAR1 UniProtKB:P32246 A C-C chemokine receptor type 7 that is encoded in the genome of human. DTO:02100059 UniProtKB:P32248 BLR2 (human) C-C CKR-7 (human) CC-CKR-7 (human) CCR-7 (human) CD197 (human) CDw197 (human) EBV-induced G-protein coupled receptor 1 (human) MIP-3 beta receptor (human) epstein-Barr virus-induced G-protein coupled receptor 1 (human) hCCR7 protein CCR7 CMKBR7 EBI1 EVI1 PR:P32248 Category=organism-gene. C-C chemokine receptor type 7 (human) A C-C chemokine receptor type 7 that is encoded in the genome of human. PRO:WCB UniProtKB:P32248 BLR2 (human) UniProtKB:P32248 C-C CKR-7 (human) UniProtKB:P32248 CC-CKR-7 (human) UniProtKB:P32248 CCR-7 (human) UniProtKB:P32248 CD197 (human) UniProtKB:P32248 CDw197 (human) UniProtKB:P32248 EBV-induced G-protein coupled receptor 1 (human) UniProtKB:P32248 MIP-3 beta receptor (human) UniProtKB:P32248 epstein-Barr virus-induced G-protein coupled receptor 1 (human) UniProtKB:P32248 hCCR7 PRO:DNx CCR7 UniProtKB:P32248 CMKBR7 UniProtKB:P32248 EBI1 UniProtKB:P32248 EVI1 UniProtKB:P32248 A C-X-C chemokine receptor type 5 that is encoded in the genome of human. DTO:02100079 Reactome:R-HSA-444505 UniProtKB:P32302 CD185 (human) CXC-R5 (human) CXCR-5 (human) MDR-15 (human) burkitt lymphoma receptor 1 (human) hCXCR5 monocyte-derived receptor 15 (human) protein BLR1 CXCR5 MDR15 PR:P32302 Category=organism-gene. C-X-C chemokine receptor type 5 (human) A C-X-C chemokine receptor type 5 that is encoded in the genome of human. PRO:WCB UniProtKB:P32302 Reactome:R-HSA-444505 PR:P32302 located_in GO:0005886 CD185 (human) UniProtKB:P32302 CXC-R5 (human) UniProtKB:P32302 CXCR-5 (human) UniProtKB:P32302 MDR-15 (human) UniProtKB:P32302 burkitt lymphoma receptor 1 (human) UniProtKB:P32302 hCXCR5 PRO:DNx monocyte-derived receptor 15 (human) UniProtKB:P32302 BLR1 UniProtKB:P32302 CXCR5 UniProtKB:P32302 MDR15 UniProtKB:P32302 A VIP peptides that is encoded in the genome of mouse. UniProtKB:P32648 mVIP protein Vip PR:P32648 Category=organism-gene. VIP peptides (mouse) A VIP peptides that is encoded in the genome of mouse. OMA:P32648 PRO:DNx mVIP PRO:DNx Vip UniProtKB:P32648 A parvalbumin alpha that is encoded in the genome of mouse. UniProtKB:P32848 mPVALB protein Pva Pvalb PR:P32848 Category=organism-gene. parvalbumin alpha (mouse) A parvalbumin alpha that is encoded in the genome of mouse. OMA:P32848 PRO:DNx mPVALB PRO:DNx Pva UniProtKB:P32848 Pvalb UniProtKB:P32848 A cadherin-5 that is encoded in the genome of human. UniProtKB:P33151 7B4 antigen (human) CD144 (human) VE-cadherin (human) hCDH5 vascular endothelial cadherin (human) protein CDH5 PR:P33151 Category=organism-gene. cadherin-5 (human) A cadherin-5 that is encoded in the genome of human. PRO:WCB UniProtKB:P33151 7B4 antigen (human) UniProtKB:P33151 CD144 (human) UniProtKB:P33151 VE-cadherin (human) UniProtKB:P33151 hCDH5 PRO:DNx vascular endothelial cadherin (human) UniProtKB:P33151 CDH5 UniProtKB:P33151 A CD80 molecule that is encoded in the genome of human. UniProtKB:P33681 B7 (human) BB1 (human) CTLA-4 counter-receptor B7.1 (human) activation B7-1 antigen (human) hCD80 protein CD28LG CD28LG1 CD80 LAB7 PR:P33681 Category=organism-gene. T-lymphocyte activation antigen CD80 (human) A CD80 molecule that is encoded in the genome of human. PRO:WCB UniProtKB:P33681 B7 (human) UniProtKB:P33681 BB1 (human) UniProtKB:P33681 CTLA-4 counter-receptor B7.1 (human) UniProtKB:P33681 activation B7-1 antigen (human) UniProtKB:P33681 hCD80 PRO:DNx CD28LG UniProtKB:P33681 CD28LG1 UniProtKB:P33681 CD80 UniProtKB:P33681 LAB7 UniProtKB:P33681 An fMet-Leu-Phe receptor that is encoded in the genome of mouse. UniProtKB:P33766 FPR (mouse) N-formyl peptide receptor (mouse) N-formylpeptide chemoattractant receptor (mouse) fMLP receptor (mouse) mFPR1 protein Fpr1 PR:P33766 Category=organism-gene. fMet-Leu-Phe receptor (mouse) An fMet-Leu-Phe receptor that is encoded in the genome of mouse. OMA:P33766 PRO:DNx FPR (mouse) UniProtKB:P33766 N-formyl peptide receptor (mouse) UniProtKB:P33766 N-formylpeptide chemoattractant receptor (mouse) UniProtKB:P33766 fMLP receptor (mouse) UniProtKB:P33766 mFPR1 PRO:DNx Fpr1 UniProtKB:P33766 A macrosialin that is encoded in the genome of human. gp110 (human) UniProtKB:P34810 hCD68 protein CD68 PR:P34810 Category=organism-gene. macrosialin (human) A macrosialin that is encoded in the genome of human. PRO:WCB UniProtKB:P34810 gp110 (human) UniProtKB:P34810 hCD68 PRO:DNx CD68 UniProtKB:P34810 A B-cell receptor CD22 that is encoded in the genome of mouse. UniProtKB:P35329 B-lymphocyte cell adhesion molecule (mouse) BL-CAM (mouse) CD22 (mouse) T-cell surface antigen Leu-14 (mouse) mCD22 sialic acid-binding Ig-like lectin 2 (mouse) siglec-2 (mouse) protein Cd22 Lyb-8 Siglec2 PR:P35329 Category=organism-gene. B-cell receptor CD22 (mouse) A B-cell receptor CD22 that is encoded in the genome of mouse. PRO:WCB B-lymphocyte cell adhesion molecule (mouse) UniProtKB:P35329 BL-CAM (mouse) UniProtKB:P35329 CD22 (mouse) UniProtKB:P35329 T-cell surface antigen Leu-14 (mouse) UniProtKB:P35329 mCD22 PRO:DNx sialic acid-binding Ig-like lectin 2 (mouse) UniProtKB:P35329 siglec-2 (mouse) UniProtKB:P35329 Cd22 UniProtKB:P35329 Lyb-8 UniProtKB:P35329 Siglec2 UniProtKB:P35329 A C-X-C chemokine receptor type 2 that is encoded in the genome of mouse. UniProtKB:P35343 CD182 (mouse) CXC-R2 (mouse) CXCR-2 (mouse) GRO/MGSA receptor (mouse) IL-8R B (mouse) high affinity interleukin-8 receptor B (mouse) mCXCR2 protein Cmkar2 Cxcr2 Gpcr16 Il8rb PR:P35343 Category=organism-gene. C-X-C chemokine receptor type 2 (mouse) A C-X-C chemokine receptor type 2 that is encoded in the genome of mouse. PRO:WCB CD182 (mouse) UniProtKB:P35343 CXC-R2 (mouse) UniProtKB:P35343 CXCR-2 (mouse) UniProtKB:P35343 GRO/MGSA receptor (mouse) UniProtKB:P35343 IL-8R B (mouse) UniProtKB:P35343 high affinity interleukin-8 receptor B (mouse) UniProtKB:P35343 mCXCR2 PRO:DNx Cmkar2 UniProtKB:P35343 Cxcr2 UniProtKB:P35343 Gpcr16 UniProtKB:P35343 Il8rb UniProtKB:P35343 A urokinase plasminogen activator surface receptor that is encoded in the genome of mouse. UniProtKB:P35456 CD87 (mouse) U-PAR (mouse) mPLAUR uPAR (mouse) protein Plaur PR:P35456 Category=organism-gene. urokinase plasminogen activator surface receptor (mouse) A urokinase plasminogen activator surface receptor that is encoded in the genome of mouse. OMA:P35456 PRO:DNx CD87 (mouse) UniProtKB:P35456 U-PAR (mouse) UniProtKB:P35456 mPLAUR PRO:DNx uPAR (mouse) UniProtKB:P35456 Plaur UniProtKB:P35456 A lymphocyte antigen 6G that is encoded in the genome of mouse. UniProtKB:P35461 Ly-6G (mouse) Ly-6G.1 (mouse) mLy6g protein Ly6g PR:P35461 Category=organism-gene. lymphocyte antigen 6G (mouse) A lymphocyte antigen 6G that is encoded in the genome of mouse. PRO:CNA UniProtKB:P35461 Ly-6G (mouse) UniProtKB:P35461 Ly-6G.1 (mouse) UniProtKB:P35461 mLy6g PRO:DNx Ly6g UniProtKB:P35461 A vascular endothelial growth factor receptor 2 that is encoded in the genome of mouse. UniProtKB:P35918 CD309 (mouse) FLK-1 (mouse) VEGFR-2 (mouse) fetal liver kinase 1 (mouse) kinase NYK (mouse) mKDR protein-tyrosine kinase receptor flk-1 (mouse) protein Flk-1 Flk1 Kdr PR:P35918 Category=organism-gene. vascular endothelial growth factor receptor 2 (mouse) A vascular endothelial growth factor receptor 2 that is encoded in the genome of mouse. OMA:P35918 PRO:DNx CD309 (mouse) UniProtKB:P35918 FLK-1 (mouse) UniProtKB:P35918 VEGFR-2 (mouse) UniProtKB:P35918 fetal liver kinase 1 (mouse) UniProtKB:P35918 kinase NYK (mouse) UniProtKB:P35918 mKDR PRO:DNx protein-tyrosine kinase receptor flk-1 (mouse) UniProtKB:P35918 Flk-1 UniProtKB:P35918 Flk1 UniProtKB:P35918 Kdr UniProtKB:P35918 A vascular endothelial growth factor receptor 2 that is encoded in the genome of human. DTO:03100560 UniProtKB:P35968 CD309 (human) FLK-1 (human) VEGFR-2 (human) fetal liver kinase 1 (human) hKDR kinase insert domain receptor (human) protein-tyrosine kinase receptor flk-1 (human) protein FLK1 KDR VEGFR2 PR:P35968 Category=organism-gene. vascular endothelial growth factor receptor 2 (human) A vascular endothelial growth factor receptor 2 that is encoded in the genome of human. PRO:WCB UniProtKB:P35968 CD309 (human) UniProtKB:P35968 FLK-1 (human) UniProtKB:P35968 VEGFR-2 (human) UniProtKB:P35968 fetal liver kinase 1 (human) UniProtKB:P35968 hKDR PRO:DNx kinase insert domain receptor (human) UniProtKB:P35968 protein-tyrosine kinase receptor flk-1 (human) UniProtKB:P35968 FLK1 UniProtKB:P35968 KDR UniProtKB:P35968 VEGFR2 UniProtKB:P35968 A neuronal acetylcholine receptor subunit alpha-7 that is encoded in the genome of human. DTO:01100012 UniProtKB:P36544 hCHRNA7 protein CHRNA7 NACHRA7 PR:P36544 Category=organism-gene. neuronal acetylcholine receptor subunit alpha-7 (human) A neuronal acetylcholine receptor subunit alpha-7 that is encoded in the genome of human. PRO:DNx UniProtKB:P36544 hCHRNA7 PRO:DNx CHRNA7 UniProtKB:P36544 NACHRA7 UniProtKB:P36544 A receptor-type tyrosine-protein kinase FLT3 that is encoded in the genome of human. STK-1 (human) DTO:03100154 UniProtKB:P36888 FL cytokine receptor (human) FLK-2 (human) FLT-3 (human) Stem cell tyrosine kinase 1 (human) fetal liver kinase-2 (human) fms-like tyrosine kinase 3 (human) hFLT3 protein CD135 FLK2 FLT3 STK1 PR:P36888 Category=organism-gene. receptor-type tyrosine-protein kinase FLT3 (human) A receptor-type tyrosine-protein kinase FLT3 that is encoded in the genome of human. PRO:WCB UniProtKB:P36888 STK-1 (human) UniProtKB:P36888 FL cytokine receptor (human) UniProtKB:P36888 FLK-2 (human) UniProtKB:P36888 FLT-3 (human) UniProtKB:P36888 Stem cell tyrosine kinase 1 (human) UniProtKB:P36888 fetal liver kinase-2 (human) UniProtKB:P36888 fms-like tyrosine kinase 3 (human) UniProtKB:P36888 hFLT3 PRO:DNx CD135 UniProtKB:P36888 FLK2 UniProtKB:P36888 FLT3 UniProtKB:P36888 STK1 UniProtKB:P36888 A CD69 molecule that is encoded in the genome of mouse. UniProtKB:P37217 CD69 (mouse) mCD69 protein Cd69 PR:P37217 Category=organism-gene. early activation antigen CD69 (mouse) A CD69 molecule that is encoded in the genome of mouse. OMA:P37217 PRO:DNx CD69 (mouse) UniProtKB:P37217 mCD69 PRO:DNx Cd69 UniProtKB:P37217 An integrin alpha-E that is encoded in the genome of human. UniProtKB:P38570 CD103 (human) HML-1 antigen (human) hITGAE integrin alpha-IEL (human) mucosal lymphocyte 1 antigen (human) protein ITGAE PR:P38570 Category=organism-gene. integrin alpha-E (human) An integrin alpha-E that is encoded in the genome of human. PRO:CNA UniProtKB:P38570 CD103 (human) UniProtKB:P38570 HML-1 antigen (human) UniProtKB:P38570 hITGAE PRO:DNx integrin alpha-IEL (human) UniProtKB:P38570 mucosal lymphocyte 1 antigen (human) UniProtKB:P38570 ITGAE UniProtKB:P38570 A CD9 molecule that is encoded in the genome of mouse. UniProtKB:P40240 CD9 (mouse) mCD9 protein Cd9 PR:P40240 Category=organism-gene. CD9 antigen (mouse) A CD9 molecule that is encoded in the genome of mouse. OMA:P40240 PRO:DNx CD9 (mouse) UniProtKB:P40240 mCD9 PRO:DNx Cd9 UniProtKB:P40240 A B-cell lymphoma 6 protein that is encoded in the genome of human. Reactome:R-HSA-5223066 UniProtKB:P41182 B-cell lymphoma 5 protein (human) BCL-5 (human) BCL-6 (human) hBCL6 protein LAZ-3 (human) zinc finger and BTB domain-containing protein 27 (human) zinc finger protein 51 (human) protein BCL5 BCL6 LAZ3 ZBTB27 ZNF51 PR:P41182 Category=organism-gene. B-cell lymphoma 6 protein (human) A B-cell lymphoma 6 protein that is encoded in the genome of human. PRO:CNA UniProtKB:P41182 Reactome:R-HSA-5223066 PR:P41182 located_in GO:0005654 B-cell lymphoma 5 protein (human) UniProtKB:P41182 BCL-5 (human) UniProtKB:P41182 BCL-6 (human) UniProtKB:P41182 hBCL6 PRO:DNx protein LAZ-3 (human) UniProtKB:P41182 zinc finger and BTB domain-containing protein 27 (human) UniProtKB:P41182 zinc finger protein 51 (human) UniProtKB:P41182 BCL5 UniProtKB:P41182 BCL6 UniProtKB:P41182 LAZ3 UniProtKB:P41182 ZBTB27 UniProtKB:P41182 ZNF51 UniProtKB:P41182 A B-cell lymphoma 6 protein that is encoded in the genome of mouse. UniProtKB:P41183 mBCL6 protein Bcl-6 Bcl6 PR:P41183 Category=organism-gene. B-cell lymphoma 6 protein homolog (mouse) A B-cell lymphoma 6 protein that is encoded in the genome of mouse. OMA:P41183 PRO:DNx mBCL6 PRO:DNx Bcl-6 UniProtKB:P41183 Bcl6 UniProtKB:P41183 A CD27 molecule that is encoded in the genome of mouse. UniProtKB:P41272 CD27 (mouse) CD27L receptor (mouse) T-cell activation antigen CD27 (mouse) mCD27 tumor necrosis factor receptor superfamily member 7 (mouse) protein Cd27 Tnfrsf7 PR:P41272 Category=organism-gene. CD27 antigen (mouse) A CD27 molecule that is encoded in the genome of mouse. OMA:P41272 PRO:DNx CD27 (mouse) UniProtKB:P41272 CD27L receptor (mouse) UniProtKB:P41272 T-cell activation antigen CD27 (mouse) UniProtKB:P41272 mCD27 PRO:DNx tumor necrosis factor receptor superfamily member 7 (mouse) UniProtKB:P41272 Cd27 UniProtKB:P41272 Tnfrsf7 UniProtKB:P41272 A C-C chemokine receptor type 2 that is encoded in the genome of human. DTO:02100054 Reactome:R-HSA-2976755 UniProtKB:P41597 C-C CKR-2 (human) CC-CKR-2 (human) CCR-2 (human) CD192 (human) MCP-1-R (human) hCCR2 monocyte chemoattractant protein 1 receptor (human) protein CCR2 CMKBR2 PR:P41597 Category=organism-gene. C-C chemokine receptor type 2 (human) A C-C chemokine receptor type 2 that is encoded in the genome of human. PRO:WCB UniProtKB:P41597 Reactome:R-HSA-2976755 PR:P41597 located_in GO:0005886 C-C CKR-2 (human) UniProtKB:P41597 CC-CKR-2 (human) UniProtKB:P41597 CCR-2 (human) UniProtKB:P41597 CD192 (human) UniProtKB:P41597 MCP-1-R (human) UniProtKB:P41597 hCCR2 PRO:DNx monocyte chemoattractant protein 1 receptor (human) UniProtKB:P41597 CCR2 UniProtKB:P41597 CMKBR2 UniProtKB:P41597 A CD86 molecule that is encoded in the genome of human. UniProtKB:P42081 B70 (human) BU63 (human) CTLA-4 counter-receptor B7.2 (human) FUN-1 (human) activation B7-2 antigen (human) hCD86 protein CD28LG2 CD86 PR:P42081 Category=organism-gene. T-lymphocyte activation antigen CD86 (human) A CD86 molecule that is encoded in the genome of human. PRO:WCB UniProtKB:P42081 B70 (human) UniProtKB:P42081 BU63 (human) UniProtKB:P42081 CTLA-4 counter-receptor B7.2 (human) UniProtKB:P42081 FUN-1 (human) UniProtKB:P42081 activation B7-2 antigen (human) UniProtKB:P42081 hCD86 PRO:DNx CD28LG2 UniProtKB:P42081 CD86 UniProtKB:P42081 A CD86 molecule that is encoded in the genome of mouse. UniProtKB:P42082 CD86 (mouse) ETC-1 (mouse) activation B7-2 antigen (mouse) early T-cell costimulatory molecule 1 (mouse) mCD86 protein Cd86 PR:P42082 Category=organism-gene. T-lymphocyte activation antigen CD86 (mouse) A CD86 molecule that is encoded in the genome of mouse. OMA:P42082 PRO:DNx CD86 (mouse) UniProtKB:P42082 ETC-1 (mouse) UniProtKB:P42082 activation B7-2 antigen (mouse) UniProtKB:P42082 early T-cell costimulatory molecule 1 (mouse) UniProtKB:P42082 mCD86 PRO:DNx Cd86 UniProtKB:P42082 A cathepsin K that is encoded in the genome of human. cathepsin X (human) UniProtKB:P43235 cathepsin O2 (human) hCTSK protein CTSK CTSO CTSO2 cathepsin O (human) PR:P43235 Category=organism-gene. cathepsin K (human) A cathepsin K that is encoded in the genome of human. PRO:WCB UniProtKB:P43235 cathepsin X (human) UniProtKB:P43235 cathepsin O2 (human) UniProtKB:P43235 hCTSK PRO:DNx CTSK UniProtKB:P43235 CTSO UniProtKB:P43235 CTSO2 UniProtKB:P43235 cathepsin O (human) UniProtKB:P43235 A C-C chemokine receptor type 7 that is encoded in the genome of mouse. UniProtKB:P47774 C-C CKR-7 (mouse) CC-CKR-7 (mouse) CCR-7 (mouse) CD197 (mouse) EBI1 (mouse) EBV-induced G-protein coupled receptor 1 (mouse) MIP-3 beta receptor (mouse) epstein-Barr virus-induced G-protein coupled receptor 1 (mouse) mCCR7 protein Ccr7 Cmkbr7 Ebi1 Ebi1h PR:P47774 Category=organism-gene. C-C chemokine receptor type 7 (mouse) A C-C chemokine receptor type 7 that is encoded in the genome of mouse. OMA:P47774 PRO:DNx C-C CKR-7 (mouse) UniProtKB:P47774 CC-CKR-7 (mouse) UniProtKB:P47774 CCR-7 (mouse) UniProtKB:P47774 CD197 (mouse) UniProtKB:P47774 EBI1 (mouse) UniProtKB:P47774 EBV-induced G-protein coupled receptor 1 (mouse) UniProtKB:P47774 MIP-3 beta receptor (mouse) UniProtKB:P47774 epstein-Barr virus-induced G-protein coupled receptor 1 (mouse) UniProtKB:P47774 mCCR7 PRO:DNx Ccr7 UniProtKB:P47774 Cmkbr7 UniProtKB:P47774 Ebi1 UniProtKB:P47774 Ebi1h UniProtKB:P47774 A CX3C chemokine receptor 1 that is encoded in the genome of human. DTO:02100074 Reactome:R-HSA-2980688 UniProtKB:P49238 C-X3-C CKR-1 (human) CMK-BRL-1 (human) CMK-BRL1 (human) G-protein coupled receptor 13 (human) V28 (human) beta chemokine receptor-like 1 (human) fractalkine receptor (human) hCX3CR1 protein CMKBRL1 CX3CR1 GPR13 PR:P49238 Category=organism-gene. CX3C chemokine receptor 1 (human) A CX3C chemokine receptor 1 that is encoded in the genome of human. PRO:WCB UniProtKB:P49238 Reactome:R-HSA-2980688 PR:P49238 located_in GO:0005886 C-X3-C CKR-1 (human) UniProtKB:P49238 CMK-BRL-1 (human) UniProtKB:P49238 CMK-BRL1 (human) UniProtKB:P49238 G-protein coupled receptor 13 (human) UniProtKB:P49238 V28 (human) UniProtKB:P49238 beta chemokine receptor-like 1 (human) UniProtKB:P49238 fractalkine receptor (human) UniProtKB:P49238 hCX3CR1 PRO:DNx CMKBRL1 UniProtKB:P49238 CX3CR1 UniProtKB:P49238 GPR13 UniProtKB:P49238 An eosinophil peroxidase that is encoded in the genome of mouse. UniProtKB:P49290 EPO (mouse) mEPX protein Eper Epx PR:P49290 Category=organism-gene. eosinophil peroxidase (mouse) An eosinophil peroxidase that is encoded in the genome of mouse. OMA:P49290 PRO:DNx EPO (mouse) UniProtKB:P49290 mEPX PRO:DNx Eper UniProtKB:P49290 Epx UniProtKB:P49290 A neuronal acetylcholine receptor subunit alpha-7 that is encoded in the genome of mouse. UniProtKB:P49582 mChrna7 protein Acra7 Chrna7 PR:P49582 Category=organism-gene. neuronal acetylcholine receptor subunit alpha-7 (mouse) A neuronal acetylcholine receptor subunit alpha-7 that is encoded in the genome of mouse. PRO:DAN mChrna7 PRO:DNx Acra7 UniProtKB:P49582 Chrna7 UniProtKB:P49582 A C-X-C chemokine receptor type 3 that is encoded in the genome of human. DTO:02100077 Reactome:R-HSA-2980699 UniProtKB:P49682 CD183 (human) CKR-L2 (human) CXC-R3 (human) CXCR-3 (human) G protein-coupled receptor 9 (human) IP-10 receptor (human) hCXCR3 interferon-inducible protein 10 receptor (human) protein CXCR3 GPR9 PR:P49682 Category=organism-gene. C-X-C chemokine receptor type 3 (human) A C-X-C chemokine receptor type 3 that is encoded in the genome of human. PRO:WCB UniProtKB:P49682 Reactome:R-HSA-2980699 PR:P49682 located_in GO:0005886 CD183 (human) UniProtKB:P49682 CKR-L2 (human) UniProtKB:P49682 CXC-R3 (human) UniProtKB:P49682 CXCR-3 (human) UniProtKB:P49682 G protein-coupled receptor 9 (human) UniProtKB:P49682 IP-10 receptor (human) UniProtKB:P49682 hCXCR3 PRO:DNx interferon-inducible protein 10 receptor (human) UniProtKB:P49682 CXCR3 UniProtKB:P49682 GPR9 UniProtKB:P49682 A CCAAT/enhancer-binding protein alpha that is encoded in the genome of human. Reactome:R-HSA-381289 UniProtKB:P49715 C/EBP alpha (human) hCEBPA protein CEBP CEBPA PR:P49715 Category=organism-gene. CCAAT/enhancer-binding protein alpha (human) A CCAAT/enhancer-binding protein alpha that is encoded in the genome of human. PRO:DNx UniProtKB:P49715 Reactome:R-HSA-381289 PR:P49715 located_in GO:0005654 C/EBP alpha (human) UniProtKB:P49715 hCEBPA PRO:DNx CEBP UniProtKB:P49715 CEBPA UniProtKB:P49715 A CD7 molecule that is encoded in the genome of mouse. UniProtKB:P50283 CD7 (mouse) mCD7 protein Cd7 PR:P50283 Category=organism-gene. T-cell antigen CD7 (mouse) A CD7 molecule that is encoded in the genome of mouse. OMA:P50283 PRO:DNx CD7 (mouse) UniProtKB:P50283 mCD7 PRO:DNx Cd7 UniProtKB:P50283 A LIM/homeobox protein Lhx3 that is encoded in the genome of mouse. UniProtKB:P50481 LIM homeobox protein 3 (mouse) homeobox protein LIM-3 (mouse) homeobox protein P-LIM (mouse) mLHX3 protein Lhx3 Lim-3 Lim3 Plim PR:P50481 Category=organism-gene. LIM/homeobox protein Lhx3 (mouse) A LIM/homeobox protein Lhx3 that is encoded in the genome of mouse. OMA:P50481 PRO:DNx LIM homeobox protein 3 (mouse) UniProtKB:P50481 homeobox protein LIM-3 (mouse) UniProtKB:P50481 homeobox protein P-LIM (mouse) UniProtKB:P50481 mLHX3 PRO:DNx Lhx3 UniProtKB:P50481 Lim-3 UniProtKB:P50481 Lim3 UniProtKB:P50481 Plim UniProtKB:P50481 A nuclear receptor ROR-gamma that is encoded in the genome of human. DTO:00117492 Reactome:R-HSA-446177 UniProtKB:P51449 RAR-related orphan receptor C (human) hRORC nuclear receptor RZR-gamma (human) nuclear receptor subfamily 1 group F member 3 (human) retinoid-related orphan receptor-gamma (human) protein NR1F3 RORC RORG RZRG PR:P51449 Category=organism-gene. nuclear receptor ROR-gamma (human) A nuclear receptor ROR-gamma that is encoded in the genome of human. PRO:WCB UniProtKB:P51449 Reactome:R-HSA-446177 PR:P51449 located_in GO:0005654 RAR-related orphan receptor C (human) UniProtKB:P51449 hRORC PRO:DNx nuclear receptor RZR-gamma (human) UniProtKB:P51449 nuclear receptor subfamily 1 group F member 3 (human) UniProtKB:P51449 retinoid-related orphan receptor-gamma (human) UniProtKB:P51449 NR1F3 UniProtKB:P51449 RORC UniProtKB:P51449 RORG UniProtKB:P51449 RZRG UniProtKB:P51449 A nuclear receptor ROR-gamma that is encoded in the genome of mouse. UniProtKB:P51450 RAR-related orphan receptor C (mouse) TOR (mouse) mRORC nuclear receptor RZR-gamma (mouse) nuclear receptor subfamily 1 group F member 3 (mouse) retinoid-related orphan receptor-gamma (mouse) thymus orphan receptor (mouse) protein Nr1f3 Rorc Rorg Thor PR:P51450 Category=organism-gene. nuclear receptor ROR-gamma (mouse) A nuclear receptor ROR-gamma that is encoded in the genome of mouse. OMA:P51450 PRO:DNx RAR-related orphan receptor C (mouse) UniProtKB:P51450 TOR (mouse) UniProtKB:P51450 mRORC PRO:DNx nuclear receptor RZR-gamma (mouse) UniProtKB:P51450 nuclear receptor subfamily 1 group F member 3 (mouse) UniProtKB:P51450 retinoid-related orphan receptor-gamma (mouse) UniProtKB:P51450 thymus orphan receptor (mouse) UniProtKB:P51450 Nr1f3 UniProtKB:P51450 Rorc UniProtKB:P51450 Rorg UniProtKB:P51450 Thor UniProtKB:P51450 A nuclear receptor ROR-gamma isoform 2 that is encoded in the genome of mouse. UniProtKB:P51450-2 mRORC/iso:2 nuclear receptor ROR-gamma isoform RORgT (mouse) protein PR:P51450-2 Category=organism-sequence. nuclear receptor ROR-gamma isoform 2 (mouse) A nuclear receptor ROR-gamma isoform 2 that is encoded in the genome of mouse. PRO:CNA mRORC/iso:2 PRO:DNx nuclear receptor ROR-gamma isoform RORgT (mouse) UniProtKB:P51450 A C-C chemokine receptor type 1 that is encoded in the genome of mouse. UniProtKB:P51675 C-C CKR-1 (mouse) CC-CKR-1 (mouse) CCR-1 (mouse) CCR1 (mouse) CD191 (mouse) MIP-1alpha-R (mouse) RANTES-R (mouse) mCCR1 macrophage inflammatory protein 1-alpha receptor (mouse) protein Ccr1 Cmkbr1 PR:P51675 Category=organism-gene. C-C chemokine receptor type 1 (mouse) A C-C chemokine receptor type 1 that is encoded in the genome of mouse. OMA:P51675 PRO:DNx C-C CKR-1 (mouse) UniProtKB:P51675 CC-CKR-1 (mouse) UniProtKB:P51675 CCR-1 (mouse) UniProtKB:P51675 CCR1 (mouse) UniProtKB:P51675 CD191 (mouse) UniProtKB:P51675 MIP-1alpha-R (mouse) UniProtKB:P51675 RANTES-R (mouse) UniProtKB:P51675 mCCR1 PRO:DNx macrophage inflammatory protein 1-alpha receptor (mouse) UniProtKB:P51675 Ccr1 UniProtKB:P51675 Cmkbr1 UniProtKB:P51675 A C-C chemokine receptor type 3 that is encoded in the genome of human. DTO:02100055 Reactome:R-HSA-373106 UniProtKB:P51677 C C CKR3 (human) C-C CKR-3 (human) CC-CKR-3 (human) CCR-3 (human) CD193 (human) CKR 3 (human) CKR3 (human) eosinophil eotaxin receptor (human) hCCR3 protein CCR3 CMKBR3 PR:P51677 Category=organism-gene. C-C chemokine receptor type 3 (human) A C-C chemokine receptor type 3 that is encoded in the genome of human. PRO:WCB UniProtKB:P51677 Reactome:R-HSA-373106 PR:P51677 located_in GO:0005886 C C CKR3 (human) UniProtKB:P51677 C-C CKR-3 (human) UniProtKB:P51677 CC-CKR-3 (human) UniProtKB:P51677 CCR-3 (human) UniProtKB:P51677 CD193 (human) UniProtKB:P51677 CKR 3 (human) UniProtKB:P51677 CKR3 (human) UniProtKB:P51677 eosinophil eotaxin receptor (human) UniProtKB:P51677 hCCR3 PRO:DNx CCR3 UniProtKB:P51677 CMKBR3 UniProtKB:P51677 A C-C chemokine receptor type 3 that is encoded in the genome of mouse. UniProtKB:P51678 C-C CKR-3 (mouse) CC-CKR-3 (mouse) CCR-3 (mouse) CCR3 (mouse) CD193 (mouse) CKR3 (mouse) MIP-1 alpha RL2 (mouse) mCCR3 macrophage inflammatory protein 1-alpha receptor-like 2 (mouse) protein Ccr3 Cmkbr1l2 Cmkbr3 PR:P51678 Category=organism-gene. probable C-C chemokine receptor type 3 (mouse) A C-C chemokine receptor type 3 that is encoded in the genome of mouse. OMA:P51678 PRO:DNx C-C CKR-3 (mouse) UniProtKB:P51678 CC-CKR-3 (mouse) UniProtKB:P51678 CCR-3 (mouse) UniProtKB:P51678 CCR3 (mouse) UniProtKB:P51678 CD193 (mouse) UniProtKB:P51678 CKR3 (mouse) UniProtKB:P51678 MIP-1 alpha RL2 (mouse) UniProtKB:P51678 mCCR3 PRO:DNx macrophage inflammatory protein 1-alpha receptor-like 2 (mouse) UniProtKB:P51678 Ccr3 UniProtKB:P51678 Cmkbr1l2 UniProtKB:P51678 Cmkbr3 UniProtKB:P51678 A C-C chemokine receptor type 4 that is encoded in the genome of human. DTO:02100056 Reactome:R-HSA-373090 UniProtKB:P51679 C-C CKR-4 (human) CC-CKR-4 (human) CCR-4 (human) CD194 (human) K5-5 (human) hCCR4 protein CCR4 CMKBR4 PR:P51679 Category=organism-gene. C-C chemokine receptor type 4 (human) A C-C chemokine receptor type 4 that is encoded in the genome of human. PRO:WCB UniProtKB:P51679 Reactome:R-HSA-373090 PR:P51679 located_in GO:0005886 C-C CKR-4 (human) UniProtKB:P51679 CC-CKR-4 (human) UniProtKB:P51679 CCR-4 (human) UniProtKB:P51679 CD194 (human) UniProtKB:P51679 K5-5 (human) UniProtKB:P51679 hCCR4 PRO:DNx CCR4 UniProtKB:P51679 CMKBR4 UniProtKB:P51679 A C-C chemokine receptor type 4 that is encoded in the genome of mouse. UniProtKB:P51680 C-C CKR-4 (mouse) CC-CKR-4 (mouse) CCR-4 (mouse) CCR4 (mouse) CD194 (mouse) mCCR4 protein Ccr4 Cmkbr4 PR:P51680 Category=organism-gene. C-C chemokine receptor type 4 (mouse) A C-C chemokine receptor type 4 that is encoded in the genome of mouse. OMA:P51680 PRO:DNx C-C CKR-4 (mouse) UniProtKB:P51680 CC-CKR-4 (mouse) UniProtKB:P51680 CCR-4 (mouse) UniProtKB:P51680 CCR4 (mouse) UniProtKB:P51680 CD194 (mouse) UniProtKB:P51680 mCCR4 PRO:DNx Ccr4 UniProtKB:P51680 Cmkbr4 UniProtKB:P51680 A C-C chemokine receptor type 5 that is encoded in the genome of human. DTO:02100057 Reactome:R-HSA-171279 UniProtKB:P51681 C-C CKR-5 (human) CC-CKR-5 (human) CCR-5 (human) CD195 (human) CHEMR13 (human) HIV-1 fusion coreceptor (human) hCCR5 protein CCR5 CMKBR5 PR:P51681 Category=organism-gene. C-C chemokine receptor type 5 (human) A C-C chemokine receptor type 5 that is encoded in the genome of human. PRO:WCB UniProtKB:P51681 Reactome:R-HSA-171279 PR:P51681 located_in GO:0005886 C-C CKR-5 (human) UniProtKB:P51681 CC-CKR-5 (human) UniProtKB:P51681 CCR-5 (human) UniProtKB:P51681 CD195 (human) UniProtKB:P51681 CHEMR13 (human) UniProtKB:P51681 HIV-1 fusion coreceptor (human) UniProtKB:P51681 hCCR5 PRO:DNx CCR5 UniProtKB:P51681 CMKBR5 UniProtKB:P51681 A C-C chemokine receptor type 5 that is encoded in the genome of mouse. UniProtKB:P51682 C-C CKR-5 (mouse) CC-CKR-5 (mouse) CCR-5 (mouse) CD195 (mouse) MIP-1 alpha receptor (mouse) mCCR5 protein Ccr5 Cmkbr5 PR:P51682 Category=organism-gene. C-C chemokine receptor type 5 (mouse) A C-C chemokine receptor type 5 that is encoded in the genome of mouse. OMA:P51682 PRO:DNx C-C CKR-5 (mouse) UniProtKB:P51682 CC-CKR-5 (mouse) UniProtKB:P51682 CCR-5 (mouse) UniProtKB:P51682 CD195 (mouse) UniProtKB:P51682 MIP-1 alpha receptor (mouse) UniProtKB:P51682 mCCR5 PRO:DNx Ccr5 UniProtKB:P51682 Cmkbr5 UniProtKB:P51682 A C-C chemokine receptor type 2 that is encoded in the genome of mouse. UniProtKB:P51683 C-C CKR-2 (mouse) CC-CKR-2 (mouse) CCR-2 (mouse) CCR2 (mouse) CD192 (mouse) JE/FIC receptor (mouse) MCP-1 receptor (mouse) mCCR2 protein Ccr2 Cmkbr2 PR:P51683 Category=organism-gene. C-C chemokine receptor type 2 (mouse) A C-C chemokine receptor type 2 that is encoded in the genome of mouse. OMA:P51683 PRO:DNx C-C CKR-2 (mouse) UniProtKB:P51683 CC-CKR-2 (mouse) UniProtKB:P51683 CCR-2 (mouse) UniProtKB:P51683 CCR2 (mouse) UniProtKB:P51683 CD192 (mouse) UniProtKB:P51683 JE/FIC receptor (mouse) UniProtKB:P51683 MCP-1 receptor (mouse) UniProtKB:P51683 mCCR2 PRO:DNx Ccr2 UniProtKB:P51683 Cmkbr2 UniProtKB:P51683 A C-C chemokine receptor type 6 that is encoded in the genome of human. DTO:02100058 Reactome:R-HSA-373089 UniProtKB:P51684 C-C CKR-6 (human) CC-CKR-6 (human) CCR-6 (human) CD196 (human) CKR-L3 (human) DRY6 (human) G-protein coupled receptor 29 (human) GPR-CY4 (human) GPRCY4 (human) LARC receptor (human) chemokine receptor-like 3 (human) hCCR6 protein CCR6 CKRL3 CMKBR6 GPR29 STRL22 PR:P51684 Category=organism-gene. C-C chemokine receptor type 6 (human) A C-C chemokine receptor type 6 that is encoded in the genome of human. PRO:WCB UniProtKB:P51684 Reactome:R-HSA-373089 PR:P51684 located_in GO:0005886 C-C CKR-6 (human) UniProtKB:P51684 CC-CKR-6 (human) UniProtKB:P51684 CCR-6 (human) UniProtKB:P51684 CD196 (human) UniProtKB:P51684 CKR-L3 (human) UniProtKB:P51684 DRY6 (human) UniProtKB:P51684 G-protein coupled receptor 29 (human) UniProtKB:P51684 GPR-CY4 (human) UniProtKB:P51684 GPRCY4 (human) UniProtKB:P51684 LARC receptor (human) UniProtKB:P51684 chemokine receptor-like 3 (human) UniProtKB:P51684 hCCR6 PRO:DNx CCR6 UniProtKB:P51684 CKRL3 UniProtKB:P51684 CMKBR6 UniProtKB:P51684 GPR29 UniProtKB:P51684 STRL22 UniProtKB:P51684 A lumican that is encoded in the genome of human. UniProtKB:P51884 KSPG lumican (human) hLUM keratan sulfate proteoglycan lumican (human) protein LDC LUM SLRR2D PR:P51884 Category=organism-gene. lumican (human) A lumican that is encoded in the genome of human. PRO:DNx UniProtKB:P51884 KSPG lumican (human) UniProtKB:P51884 hLUM PRO:DNx keratan sulfate proteoglycan lumican (human) UniProtKB:P51884 LDC UniProtKB:P51884 LUM UniProtKB:P51884 SLRR2D UniProtKB:P51884 A lumican that is encoded in the genome of mouse. UniProtKB:P51885 KSPG lumican (mouse) keratan sulfate proteoglycan lumican (mouse) mLUM protein Lcn Ldc Lum PR:P51885 Category=organism-gene. lumican (mouse) A lumican that is encoded in the genome of mouse. OMA:P51885 PRO:DNx KSPG lumican (mouse) UniProtKB:P51885 keratan sulfate proteoglycan lumican (mouse) UniProtKB:P51885 mLUM PRO:DNx Lcn UniProtKB:P51885 Ldc UniProtKB:P51885 Lum UniProtKB:P51885 A CCAAT/enhancer-binding protein alpha that is encoded in the genome of mouse. UniProtKB:P53566 C/EBP alpha (mouse) mCEBPA protein Cebp Cebpa PR:P53566 Category=organism-gene. CCAAT/enhancer-binding protein alpha (mouse) A CCAAT/enhancer-binding protein alpha that is encoded in the genome of mouse. OMA:P53566 PRO:DNx C/EBP alpha (mouse) UniProtKB:P53566 mCEBPA PRO:DNx Cebp UniProtKB:P53566 Cebpa UniProtKB:P53566 A cathepsin K that is encoded in the genome of mouse. UniProtKB:P55097 mCTSK protein Ctsk PR:P55097 Category=organism-gene. cathepsin K (mouse) A cathepsin K that is encoded in the genome of mouse. OMA:P55097 PRO:DNx mCTSK PRO:DNx Ctsk UniProtKB:P55097 A cadherin-5 that is encoded in the genome of mouse. UniProtKB:P55284 CD144 (mouse) VE-cadherin (mouse) mCDH5 vascular endothelial cadherin (mouse) protein Cdh5 PR:P55284 Category=organism-gene. cadherin-5 (mouse) A cadherin-5 that is encoded in the genome of mouse. OMA:P55284 PRO:DNx CD144 (mouse) UniProtKB:P55284 VE-cadherin (mouse) UniProtKB:P55284 mCDH5 PRO:DNx vascular endothelial cadherin (mouse) UniProtKB:P55284 Cdh5 UniProtKB:P55284 A V(D)J recombination-activating protein 2 that is encoded in the genome of human. Reactome:R-HSA-5692675 UniProtKB:P55895 RAG-2 (human) hRAG2 protein RAG2 PR:P55895 Category=organism-gene. V(D)J recombination-activating protein 2 (human) A V(D)J recombination-activating protein 2 that is encoded in the genome of human. PRO:CNA UniProtKB:P55895 Reactome:R-HSA-5692675 PR:P55895 located_in GO:0005654 RAG-2 (human) UniProtKB:P55895 hRAG2 PRO:DNx RAG2 UniProtKB:P55895 An ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 that is encoded in the genome of mouse. UniProtKB:P56528 2'-phospho-ADP-ribosyl cyclase (mouse) 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase (mouse) 2'-phospho-cyclic-ADP-ribose transferase (mouse) ADP-ribosyl cyclase 1 (mouse) ADPRC 1 (mouse) CD38 (mouse) I-19 (mouse) NIM-R5 antigen (mouse) cADPr hydrolase 1 (mouse) cyclic ADP-ribose hydrolase 1 (mouse) mCD38 protein Cd38 PR:P56528 Category=organism-gene. ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 (mouse) An ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 that is encoded in the genome of mouse. OMA:P56528 PRO:DNx 2'-phospho-ADP-ribosyl cyclase (mouse) UniProtKB:P56528 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase (mouse) UniProtKB:P56528 2'-phospho-cyclic-ADP-ribose transferase (mouse) UniProtKB:P56528 ADP-ribosyl cyclase 1 (mouse) UniProtKB:P56528 ADPRC 1 (mouse) UniProtKB:P56528 CD38 (mouse) UniProtKB:P56528 I-19 (mouse) UniProtKB:P56528 NIM-R5 antigen (mouse) UniProtKB:P56528 cADPr hydrolase 1 (mouse) UniProtKB:P56528 cyclic ADP-ribose hydrolase 1 (mouse) UniProtKB:P56528 mCD38 PRO:DNx Cd38 UniProtKB:P56528 A leukocyte immunoglobulin-like receptor subfamily A member 4 that is encoded in the genome of human. UniProtKB:P59901 CD85 antigen-like family member G (human) CD85g (human) ILT-7 (human) hLILRA4 immunoglobulin-like transcript 7 (human) protein ILT7 LILRA4 PR:P59901 Category=organism-gene. leukocyte immunoglobulin-like receptor subfamily A member 4 (human) A leukocyte immunoglobulin-like receptor subfamily A member 4 that is encoded in the genome of human. PRO:WCB UniProtKB:P59901 CD85 antigen-like family member G (human) UniProtKB:P59901 CD85g (human) UniProtKB:P59901 ILT-7 (human) UniProtKB:P59901 hLILRA4 PRO:DNx immunoglobulin-like transcript 7 (human) UniProtKB:P59901 ILT7 UniProtKB:P59901 LILRA4 UniProtKB:P59901 A somatostatin that is encoded in the genome of mouse. UniProtKB:P60041 mSST protein Smst Sst PR:P60041 Category=organism-gene. somatostatin (mouse) A somatostatin that is encoded in the genome of mouse. OMA:P60041 PRO:DNx mSST PRO:DNx Smst UniProtKB:P60041 Sst UniProtKB:P60041 A C-X-C chemokine receptor type 4 that is encoded in the genome of human. LAP-3 (human) DTO:02100078 Reactome:R-HSA-2980772 UniProtKB:P61073 CD184 (human) CXC-R4 (human) CXCR-4 (human) FB22 (human) HM89 (human) LCR1 (human) LESTR (human) LPS-associated protein 3 (human) NPYRL (human) SDF-1 receptor (human) fusin (human) hCXCR4 leukocyte-derived seven transmembrane domain receptor (human) lipopolysaccharide-associated protein 3 (human) stromal cell-derived factor 1 receptor (human) protein CXCR4 PR:P61073 Category=organism-gene. C-X-C chemokine receptor type 4 (human) A C-X-C chemokine receptor type 4 that is encoded in the genome of human. PRO:WCB UniProtKB:P61073 LAP-3 (human) UniProtKB:P61073 Reactome:R-HSA-2980772 PR:P61073 located_in GO:0005886 CD184 (human) UniProtKB:P61073 CXC-R4 (human) UniProtKB:P61073 CXCR-4 (human) UniProtKB:P61073 FB22 (human) UniProtKB:P61073 HM89 (human) UniProtKB:P61073 LCR1 (human) UniProtKB:P61073 LESTR (human) UniProtKB:P61073 LPS-associated protein 3 (human) UniProtKB:P61073 NPYRL (human) UniProtKB:P61073 SDF-1 receptor (human) UniProtKB:P61073 fusin (human) UniProtKB:P61073 hCXCR4 PRO:DNx leukocyte-derived seven transmembrane domain receptor (human) UniProtKB:P61073 lipopolysaccharide-associated protein 3 (human) UniProtKB:P61073 stromal cell-derived factor 1 receptor (human) UniProtKB:P61073 CXCR4 UniProtKB:P61073 A somatostatin that is encoded in the genome of human. UniProtKB:P61278 growth hormone release-inhibiting factor (human) hSST protein SST PR:P61278 Category=organism-gene. somatostatin (human) A somatostatin that is encoded in the genome of human. PRO:DNx UniProtKB:P61278 growth hormone release-inhibiting factor (human) UniProtKB:P61278 hSST PRO:DNx SST UniProtKB:P61278 A C-X-C chemokine receptor type 4 that is encoded in the genome of mouse. UniProtKB:P70658 CD184 (mouse) CXC-R4 (mouse) CXCR-4 (mouse) LESTR (mouse) PB-CKR (mouse) SDF-1 receptor (mouse) fusin (mouse) leukocyte-derived seven transmembrane domain receptor (mouse) mCXCR4 pre-B-cell-derived chemokine receptor (mouse) stromal cell-derived factor 1 receptor (mouse) protein Cmkar4 Cxcr4 Lestr Sdf1r PR:P70658 Category=organism-gene. C-X-C chemokine receptor type 4 (mouse) A C-X-C chemokine receptor type 4 that is encoded in the genome of mouse. OMA:P70658 PRO:DNx CD184 (mouse) UniProtKB:P70658 CXC-R4 (mouse) UniProtKB:P70658 CXCR-4 (mouse) UniProtKB:P70658 LESTR (mouse) UniProtKB:P70658 PB-CKR (mouse) UniProtKB:P70658 SDF-1 receptor (mouse) UniProtKB:P70658 fusin (mouse) UniProtKB:P70658 leukocyte-derived seven transmembrane domain receptor (mouse) UniProtKB:P70658 mCXCR4 PRO:DNx pre-B-cell-derived chemokine receptor (mouse) UniProtKB:P70658 stromal cell-derived factor 1 receptor (mouse) UniProtKB:P70658 Cmkar4 UniProtKB:P70658 Cxcr4 UniProtKB:P70658 Lestr UniProtKB:P70658 Sdf1r UniProtKB:P70658 A tyrosine-protein phosphatase non-receptor type substrate 1 that is encoded in the genome of human. p84 (human) UniProtKB:P78324 CD172 antigen-like family member A (human) CD172a (human) MyD-1 antigen (human) SHP substrate 1 (human) SHPS-1 (human) Sirp-alpha-1 (human) Sirp-alpha-2 (human) Sirp-alpha-3 (human) brain Ig-like molecule with tyrosine-based activation motifs (human) hSIRPA inhibitory receptor SHPS-1 (human) macrophage fusion receptor (human) signal-regulatory protein alpha-1 (human) signal-regulatory protein alpha-2 (human) signal-regulatory protein alpha-3 (human) protein BIT MFR MYD1 PTPNS1 SHPS1 SIRP SIRPA PR:P78324 Category=organism-gene. tyrosine-protein phosphatase non-receptor type substrate 1 (human) A tyrosine-protein phosphatase non-receptor type substrate 1 that is encoded in the genome of human. PRO:WCB UniProtKB:P78324 p84 (human) UniProtKB:P78324 CD172 antigen-like family member A (human) UniProtKB:P78324 CD172a (human) UniProtKB:P78324 MyD-1 antigen (human) UniProtKB:P78324 SHP substrate 1 (human) UniProtKB:P78324 SHPS-1 (human) UniProtKB:P78324 Sirp-alpha-1 (human) UniProtKB:P78324 Sirp-alpha-2 (human) UniProtKB:P78324 Sirp-alpha-3 (human) UniProtKB:P78324 brain Ig-like molecule with tyrosine-based activation motifs (human) UniProtKB:P78324 hSIRPA PRO:DNx inhibitory receptor SHPS-1 (human) UniProtKB:P78324 macrophage fusion receptor (human) UniProtKB:P78324 signal-regulatory protein alpha-1 (human) UniProtKB:P78324 signal-regulatory protein alpha-2 (human) UniProtKB:P78324 signal-regulatory protein alpha-3 (human) UniProtKB:P78324 BIT UniProtKB:P78324 MFR UniProtKB:P78324 MYD1 UniProtKB:P78324 PTPNS1 UniProtKB:P78324 SHPS1 UniProtKB:P78324 SIRP UniProtKB:P78324 SIRPA UniProtKB:P78324 An iroquois-class homeodomain protein IRX-6 that is encoded in the genome of human. UniProtKB:P78412 hIRX6 homeodomain protein IRXB3 (human) iroquois homeobox protein 6 (human) protein IRX6 IRX7 IRXB3 PR:P78412 Category=organism-gene. iroquois-class homeodomain protein IRX-6 (human) An iroquois-class homeodomain protein IRX-6 that is encoded in the genome of human. PRO:DNx UniProtKB:P78412 hIRX6 PRO:DNx homeodomain protein IRXB3 (human) UniProtKB:P78412 iroquois homeobox protein 6 (human) UniProtKB:P78412 IRX6 UniProtKB:P78412 IRX7 UniProtKB:P78412 IRXB3 UniProtKB:P78412 A neutrophil gelatinase-associated lipocalin that is encoded in the genome of human. p25 (human) UniProtKB:P80188 25 kDa alpha-2-microglobulin-related subunit of MMP-9 (human) hLCN2 lipocalin-2 (human) oncogene 24p3 (human) siderocalin (human) protein HNL LCN2 NGAL PR:P80188 Category=organism-gene. neutrophil gelatinase-associated lipocalin (human) A neutrophil gelatinase-associated lipocalin that is encoded in the genome of human. PRO:DNx UniProtKB:P80188 p25 (human) UniProtKB:P80188 25 kDa alpha-2-microglobulin-related subunit of MMP-9 (human) UniProtKB:P80188 hLCN2 PRO:DNx lipocalin-2 (human) UniProtKB:P80188 oncogene 24p3 (human) UniProtKB:P80188 siderocalin (human) UniProtKB:P80188 HNL UniProtKB:P80188 LCN2 UniProtKB:P80188 NGAL UniProtKB:P80188 A homeobox protein Meis2 that is encoded in the genome of mouse. UniProtKB:P97367 Meis1-related protein 1 (mouse) mMEIS2 protein Meis2 Mrg1 Stra10 PR:P97367 Category=organism-gene. homeobox protein Meis2 (mouse) A homeobox protein Meis2 that is encoded in the genome of mouse. OMA:P97367 PRO:DNx Meis1-related protein 1 (mouse) UniProtKB:P97367 mMEIS2 PRO:DNx Meis2 UniProtKB:P97367 Mrg1 UniProtKB:P97367 Stra10 UniProtKB:P97367 An aminopeptidase N that is encoded in the genome of mouse. UniProtKB:P97449 AP-M (mouse) AP-N (mouse) CD13 (mouse) alanyl aminopeptidase (mouse) aminopeptidase M (mouse) mANPEP mAPN membrane protein p161 (mouse) microsomal aminopeptidase (mouse) protein Anpep Lap-1 Lap1 PR:P97449 Category=organism-gene. aminopeptidase N (mouse) An aminopeptidase N that is encoded in the genome of mouse. OMA:P97449 PRO:DNx AP-M (mouse) UniProtKB:P97449 AP-N (mouse) UniProtKB:P97449 CD13 (mouse) UniProtKB:P97449 alanyl aminopeptidase (mouse) UniProtKB:P97449 aminopeptidase M (mouse) UniProtKB:P97449 mANPEP PRO:DNx mAPN UniProtKB:P97449 membrane protein p161 (mouse) UniProtKB:P97449 microsomal aminopeptidase (mouse) UniProtKB:P97449 Anpep UniProtKB:P97449 Lap-1 UniProtKB:P97449 Lap1 UniProtKB:P97449 A tyrosine-protein phosphatase non-receptor type substrate 1 that is encoded in the genome of mouse. p84 (mouse) UniProtKB:P97797 CD172 antigen-like family member A (mouse) CD172a (mouse) MyD-1 antigen (mouse) SHP substrate 1 (mouse) SHPS-1 (mouse) Sirp-alpha-1 (mouse) brain Ig-like molecule with tyrosine-based activation motifs (mouse) inhibitory receptor SHPS-1 (mouse) mSIRP-alpha1 mSIRPA signal-regulatory protein alpha-1 (mouse) protein Bit Myd1 Ptpns1 Shps1 Sirp Sirpa PR:P97797 Category=organism-gene. tyrosine-protein phosphatase non-receptor type substrate 1 (mouse) A tyrosine-protein phosphatase non-receptor type substrate 1 that is encoded in the genome of mouse. PRO:DAN p84 (mouse) UniProtKB:P97797 CD172 antigen-like family member A (mouse) UniProtKB:P97797 CD172a (mouse) UniProtKB:P97797 MyD-1 antigen (mouse) UniProtKB:P97797 SHP substrate 1 (mouse) UniProtKB:P97797 SHPS-1 (mouse) UniProtKB:P97797 Sirp-alpha-1 (mouse) UniProtKB:P97797 brain Ig-like molecule with tyrosine-based activation motifs (mouse) UniProtKB:P97797 inhibitory receptor SHPS-1 (mouse) UniProtKB:P97797 mSIRP-alpha1 UniProtKB:P97797 mSIRPA PRO:DNx signal-regulatory protein alpha-1 (mouse) UniProtKB:P97797 Bit UniProtKB:P97797 Myd1 UniProtKB:P97797 Ptpns1 UniProtKB:P97797 Shps1 UniProtKB:P97797 Sirp UniProtKB:P97797 Sirpa UniProtKB:P97797 A receptor-type tyrosine-protein kinase FLT3 that is encoded in the genome of mouse. UniProtKB:Q00342 CD135 (mouse) FL cytokine receptor (mouse) FLK-2 (mouse) FLT-3 (mouse) fetal liver kinase 2 (mouse) fms-like tyrosine kinase 3 (mouse) mFLT3 tyrosine-protein kinase receptor flk-2 (mouse) protein Flk-2 Flt-3 Flt3 PR:Q00342 Category=organism-gene. receptor-type tyrosine-protein kinase FLT3 (mouse) A receptor-type tyrosine-protein kinase FLT3 that is encoded in the genome of mouse. OMA:Q00342 PRO:DNx CD135 (mouse) UniProtKB:Q00342 FL cytokine receptor (mouse) UniProtKB:Q00342 FLK-2 (mouse) UniProtKB:Q00342 FLT-3 (mouse) UniProtKB:Q00342 fetal liver kinase 2 (mouse) UniProtKB:Q00342 fms-like tyrosine kinase 3 (mouse) UniProtKB:Q00342 mFLT3 PRO:DNx tyrosine-protein kinase receptor flk-2 (mouse) UniProtKB:Q00342 Flk-2 UniProtKB:Q00342 Flt-3 UniProtKB:Q00342 Flt3 UniProtKB:Q00342 A CD80 molecule that is encoded in the genome of mouse. UniProtKB:Q00609 CD80 (mouse) activation B7-1 antigen (mouse) mCD80 protein B7 Cd80 PR:Q00609 Category=organism-gene. T-lymphocyte activation antigen CD80 (mouse) A CD80 molecule that is encoded in the genome of mouse. OMA:Q00609 PRO:DNx CD80 (mouse) UniProtKB:Q00609 activation B7-1 antigen (mouse) UniProtKB:Q00609 mCD80 PRO:DNx B7 UniProtKB:Q00609 Cd80 UniProtKB:Q00609 An integrin alpha-4 that is encoded in the genome of mouse. UniProtKB:Q00651 CD49 antigen-like family member D (mouse) CD49d (mouse) LPAM subunit alpha (mouse) VLA-4 subunit alpha (mouse) integrin alpha-IV (mouse) lymphocyte Peyer patch adhesion molecules subunit alpha (mouse) mITGA4 protein Itga4 PR:Q00651 Category=organism-gene. integrin alpha-4 (mouse) An integrin alpha-4 that is encoded in the genome of mouse. OMA:Q00651 PRO:DNx CD49 antigen-like family member D (mouse) UniProtKB:Q00651 CD49d (mouse) UniProtKB:Q00651 LPAM subunit alpha (mouse) UniProtKB:Q00651 VLA-4 subunit alpha (mouse) UniProtKB:Q00651 integrin alpha-IV (mouse) UniProtKB:Q00651 lymphocyte Peyer patch adhesion molecules subunit alpha (mouse) UniProtKB:Q00651 mITGA4 PRO:DNx Itga4 UniProtKB:Q00651 A nuclear factor NF-kappa-B p100 subunit that is encoded in the genome of human. Reactome:R-HSA-2677931 UniProtKB:Q00653 DNA-binding factor KBF2 (human) H2TF1 (human) hNFKB2 lymphocyte translocation chromosome 10 protein (human) nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (human) oncogene Lyt-10 (human) protein LYT10 NFKB2 PR:Q00653 Category=organism-gene. nuclear factor NF-kappa-B p100 subunit (human) A nuclear factor NF-kappa-B p100 subunit that is encoded in the genome of human. PRO:DNx UniProtKB:Q00653 Reactome:R-HSA-2677931 PR:Q00653 located_in GO:0005829 DNA-binding factor KBF2 (human) UniProtKB:Q00653 H2TF1 (human) UniProtKB:Q00653 hNFKB2 PRO:DNx lymphocyte translocation chromosome 10 protein (human) UniProtKB:Q00653 nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (human) UniProtKB:Q00653 oncogene Lyt-10 (human) UniProtKB:Q00653 LYT10 UniProtKB:Q00653 NFKB2 UniProtKB:Q00653 A CD83 molecule that is encoded in the genome of human. UniProtKB:Q01151 B-cell activation protein (human) cell surface protein HB15 (human) hCD83 protein CD83 PR:Q01151 Category=organism-gene. CD83 antigen (human) A CD83 molecule that is encoded in the genome of human. PRO:WCB UniProtKB:Q01151 B-cell activation protein (human) UniProtKB:Q01151 cell surface protein HB15 (human) UniProtKB:Q01151 hCD83 PRO:DNx CD83 UniProtKB:Q01151 A runt-related transcription factor 1 that is encoded in the genome of human. Reactome:R-HSA-5667138 Reactome:R-HSA-8865295 UniProtKB:Q01196 CBF-alpha-2 (human) PEA2-alpha B (human) PEBP2-alpha B (human) SL3-3 enhancer factor 1 alpha B subunit (human) SL3/AKV core-binding factor alpha B subunit (human) acute myeloid leukemia 1 protein (human) core-binding factor subunit alpha-2 (human) hRUNX1 oncogene AML-1 (human) polyomavirus enhancer-binding protein 2 alpha B subunit (human) protein AML1 CBFA2 RUNX1 PR:Q01196 Category=organism-gene. runt-related transcription factor 1 (human) A runt-related transcription factor 1 that is encoded in the genome of human. PRO:PD Reactome:R-HSA-5667138 PR:Q01196 located_in GO:0005886 Reactome:R-HSA-8865295 PR:Q01196 located_in GO:0005654 CBF-alpha-2 (human) UniProtKB:Q01196 PEA2-alpha B (human) UniProtKB:Q01196 PEBP2-alpha B (human) UniProtKB:Q01196 SL3-3 enhancer factor 1 alpha B subunit (human) UniProtKB:Q01196 SL3/AKV core-binding factor alpha B subunit (human) UniProtKB:Q01196 acute myeloid leukemia 1 protein (human) UniProtKB:Q01196 core-binding factor subunit alpha-2 (human) UniProtKB:Q01196 hRUNX1 PRO:DNx oncogene AML-1 (human) UniProtKB:Q01196 polyomavirus enhancer-binding protein 2 alpha B subunit (human) UniProtKB:Q01196 AML1 UniProtKB:Q01196 CBFA2 UniProtKB:Q01196 RUNX1 UniProtKB:Q01196 An interleukin-5 receptor subunit alpha that is encoded in the genome of human. UniProtKB:Q01344 CD125 (human) CDw125 (human) IL-5 receptor subunit alpha (human) IL-5R subunit alpha (human) IL-5R-alpha (human) IL-5RA (human) hIL5RA protein IL5R IL5RA PR:Q01344 Category=organism-gene. interleukin-5 receptor subunit alpha (human) An interleukin-5 receptor subunit alpha that is encoded in the genome of human. PRO:WCB UniProtKB:Q01344 CD125 (human) UniProtKB:Q01344 CDw125 (human) UniProtKB:Q01344 IL-5 receptor subunit alpha (human) UniProtKB:Q01344 IL-5R subunit alpha (human) UniProtKB:Q01344 IL-5R-alpha (human) UniProtKB:Q01344 IL-5RA (human) UniProtKB:Q01344 hIL5RA PRO:DNx IL5R UniProtKB:Q01344 IL5RA UniProtKB:Q01344 An interleukin-1 receptor-like 1 that is encoded in the genome of human. UniProtKB:Q01638 hIL1RL1 protein ST2 (human) protein DER4 IL1RL1 ST2 T1 PR:Q01638 Category=organism-gene. interleukin-1 receptor-like 1 (human) An interleukin-1 receptor-like 1 that is encoded in the genome of human. PRO:DNx UniProtKB:Q01638 hIL1RL1 PRO:DNx protein ST2 (human) UniProtKB:Q01638 DER4 UniProtKB:Q01638 IL1RL1 UniProtKB:Q01638 ST2 UniProtKB:Q01638 T1 UniProtKB:Q01638 A programmed cell death protein 1 that is encoded in the genome of mouse. UniProtKB:Q02242 CD279 (mouse) mPD-1 mPDCD1 protein PD-1 (mouse) protein Pd1 Pdcd1 PR:Q02242 Category=organism-gene. programmed cell death protein 1 (mouse) A programmed cell death protein 1 that is encoded in the genome of mouse. OMA:Q02242 PRO:DNx CD279 (mouse) UniProtKB:Q02242 mPD-1 UniProtKB:Q02242 mPDCD1 PRO:DNx protein PD-1 (mouse) UniProtKB:Q02242 Pd1 UniProtKB:Q02242 Pdcd1 UniProtKB:Q02242 A paired box protein PAX-5 that is encoded in the genome of human. Reactome:R-HSA-158583 UniProtKB:Q02548 B-cell-specific transcription factor (human) BSAP (human) hPAX5 protein PAX5 PR:Q02548 Category=organism-gene. paired box protein Pax-5 (human) A paired box protein PAX-5 that is encoded in the genome of human. PRO:WCB UniProtKB:Q02548 Reactome:R-HSA-158583 PR:Q02548 located_in GO:0005654 B-cell-specific transcription factor (human) UniProtKB:Q02548 BSAP (human) UniProtKB:Q02548 hPAX5 PRO:DNx PAX5 UniProtKB:Q02548 A paired box protein PAX-5 that is encoded in the genome of mouse. UniProtKB:Q02650 B-cell-specific transcription factor (mouse) BSAP (mouse) mPAX5 protein Pax-5 Pax5 PR:Q02650 Category=organism-gene. paired box protein Pax-5 (mouse) A paired box protein PAX-5 that is encoded in the genome of mouse. OMA:Q02650 PRO:DNx B-cell-specific transcription factor (mouse) UniProtKB:Q02650 BSAP (mouse) UniProtKB:Q02650 mPAX5 PRO:DNx Pax-5 UniProtKB:Q02650 Pax5 UniProtKB:Q02650 A runt-related transcription factor 1 that is encoded in the genome of mouse. UniProtKB:Q03347 CBF-alpha-2 (mouse) PEA2-alpha B (mouse) PEBP2-alpha B (mouse) SL3-3 enhancer factor 1 alpha B subunit (mouse) SL3/AKV core-binding factor alpha B subunit (mouse) acute myeloid leukemia 1 protein (mouse) core-binding factor subunit alpha-2 (mouse) mRUNX1 oncogene AML-1 (mouse) polyomavirus enhancer-binding protein 2 alpha B subunit (mouse) protein Aml1 Cbfa2 Pebp2ab Runx1 PR:Q03347 Category=organism-gene. runt-related transcription factor 1 (mouse) A runt-related transcription factor 1 that is encoded in the genome of mouse. OMA:Q03347 PRO:DNx CBF-alpha-2 (mouse) UniProtKB:Q03347 PEA2-alpha B (mouse) UniProtKB:Q03347 PEBP2-alpha B (mouse) UniProtKB:Q03347 SL3-3 enhancer factor 1 alpha B subunit (mouse) UniProtKB:Q03347 SL3/AKV core-binding factor alpha B subunit (mouse) UniProtKB:Q03347 acute myeloid leukemia 1 protein (mouse) UniProtKB:Q03347 core-binding factor subunit alpha-2 (mouse) UniProtKB:Q03347 mRUNX1 PRO:DNx oncogene AML-1 (mouse) UniProtKB:Q03347 polyomavirus enhancer-binding protein 2 alpha B subunit (mouse) UniProtKB:Q03347 Aml1 UniProtKB:Q03347 Cbfa2 UniProtKB:Q03347 Pebp2ab UniProtKB:Q03347 Runx1 UniProtKB:Q03347 A urokinase plasminogen activator surface receptor that is encoded in the genome of human. UniProtKB:Q03405 CD87 (human) U-PAR (human) hPLAUR monocyte activation antigen Mo3 (human) protein MO3 PLAUR UPAR PR:Q03405 Category=organism-gene. urokinase plasminogen activator surface receptor (human) A urokinase plasminogen activator surface receptor that is encoded in the genome of human. PRO:WCB UniProtKB:Q03405 CD87 (human) UniProtKB:Q03405 U-PAR (human) UniProtKB:Q03405 hPLAUR PRO:DNx monocyte activation antigen Mo3 (human) UniProtKB:Q03405 MO3 UniProtKB:Q03405 PLAUR UniProtKB:Q03405 UPAR UniProtKB:Q03405 A C-X-C chemokine receptor type 5 that is encoded in the genome of mouse. UniProtKB:Q04683 CD185 (mouse) CXC-R5 (mouse) CXCR-5 (mouse) burkitt lymphoma receptor 1 homolog (mouse) mCXCR5 protein Blr1 Cxcr5 Gpcr6 PR:Q04683 Category=organism-gene. C-X-C chemokine receptor type 5 (mouse) A C-X-C chemokine receptor type 5 that is encoded in the genome of mouse. OMA:Q04683 PRO:DNx CD185 (mouse) UniProtKB:Q04683 CXC-R5 (mouse) UniProtKB:Q04683 CXCR-5 (mouse) UniProtKB:Q04683 burkitt lymphoma receptor 1 homolog (mouse) UniProtKB:Q04683 mCXCR5 PRO:DNx Blr1 UniProtKB:Q04683 Cxcr5 UniProtKB:Q04683 Gpcr6 UniProtKB:Q04683 A tartrate-resistant acid phosphatase type 5 that is encoded in the genome of mouse. UniProtKB:Q05117 TR-AP (mouse) TrATPase (mouse) mACP5 tartrate-resistant acid ATPase (mouse) type 5 acid phosphatase (mouse) protein Acp5 T5ap Trap PR:Q05117 Category=organism-gene. tartrate-resistant acid phosphatase type 5 (mouse) A tartrate-resistant acid phosphatase type 5 that is encoded in the genome of mouse. OMA:Q05117 PRO:DNx TR-AP (mouse) UniProtKB:Q05117 TrATPase (mouse) UniProtKB:Q05117 mACP5 PRO:DNx tartrate-resistant acid ATPase (mouse) UniProtKB:Q05117 type 5 acid phosphatase (mouse) UniProtKB:Q05117 Acp5 UniProtKB:Q05117 T5ap UniProtKB:Q05117 Trap UniProtKB:Q05117 A glutamyl aminopeptidase that is encoded in the genome of human. EAP (human) Reactome:R-HSA-2022341 UniProtKB:Q07075 AP-A (human) CD249 (human) aminopeptidase A (human) differentiation antigen gp160 (human) hENPEP protein ENPEP PR:Q07075 Category=organism-gene. glutamyl aminopeptidase (human) A glutamyl aminopeptidase that is encoded in the genome of human. PRO:WCB UniProtKB:Q07075 EAP (human) UniProtKB:Q07075 Reactome:R-HSA-2022341 PR:Q07075 located_in GO:0005886 AP-A (human) UniProtKB:Q07075 CD249 (human) UniProtKB:Q07075 aminopeptidase A (human) UniProtKB:Q07075 differentiation antigen gp160 (human) UniProtKB:Q07075 hENPEP PRO:DNx ENPEP UniProtKB:Q07075 A CD69 molecule that is encoded in the genome of human. UniProtKB:Q07108 AIM (human) BL-AC/P26 (human) C-type lectin domain family 2 member C (human) EA1 (human) GP32/28 (human) MLR-3 (human) activation inducer molecule (human) early T-cell activation antigen p60 (human) hCD69 leukocyte surface antigen Leu-23 (human) protein CD69 CLEC2C PR:Q07108 Category=organism-gene. early activation antigen CD69 (human) A CD69 molecule that is encoded in the genome of human. PRO:CNA UniProtKB:Q07108 AIM (human) UniProtKB:Q07108 BL-AC/P26 (human) UniProtKB:Q07108 C-type lectin domain family 2 member C (human) UniProtKB:Q07108 EA1 (human) UniProtKB:Q07108 GP32/28 (human) UniProtKB:Q07108 MLR-3 (human) UniProtKB:Q07108 activation inducer molecule (human) UniProtKB:Q07108 early T-cell activation antigen p60 (human) UniProtKB:Q07108 hCD69 PRO:DNx leukocyte surface antigen Leu-23 (human) UniProtKB:Q07108 CD69 UniProtKB:Q07108 CLEC2C UniProtKB:Q07108 A natural killer cell receptor 2B4 that is encoded in the genome of mouse. UniProtKB:Q07763 CD244 (mouse) NK cell type I receptor protein 2B4 (mouse) NKR2B4 (mouse) SLAM family member 4 (mouse) SLAMF4 (mouse) mCD244 non-MHC restricted killing associated (mouse) signaling lymphocytic activation molecule 4 (mouse) protein 2b4 Cd244 Nmrk PR:Q07763 Category=organism-gene. natural killer cell receptor 2B4 (mouse) A natural killer cell receptor 2B4 that is encoded in the genome of mouse. OMA:Q07763 PRO:DNx CD244 (mouse) UniProtKB:Q07763 NK cell type I receptor protein 2B4 (mouse) UniProtKB:Q07763 NKR2B4 (mouse) UniProtKB:Q07763 SLAM family member 4 (mouse) UniProtKB:Q07763 SLAMF4 (mouse) UniProtKB:Q07763 mCD244 PRO:DNx non-MHC restricted killing associated (mouse) UniProtKB:Q07763 signaling lymphocytic activation molecule 4 (mouse) UniProtKB:Q07763 2b4 UniProtKB:Q07763 Cd244 UniProtKB:Q07763 Nmrk UniProtKB:Q07763 A platelet glycoprotein 4 that is encoded in the genome of mouse. UniProtKB:Q08857 CD36 (mouse) GPIIIB (mouse) GPIV (mouse) PAS IV (mouse) PAS-4 (mouse) glycoprotein IIIb (mouse) mCD36 platelet glycoprotein IV (mouse) protein Cd36 PR:Q08857 Category=organism-gene. platelet glycoprotein 4 (mouse) A platelet glycoprotein 4 that is encoded in the genome of mouse. OMA:Q08857 PRO:DNx CD36 (mouse) UniProtKB:Q08857 GPIIIB (mouse) UniProtKB:Q08857 GPIV (mouse) UniProtKB:Q08857 PAS IV (mouse) UniProtKB:Q08857 PAS-4 (mouse) UniProtKB:Q08857 glycoprotein IIIb (mouse) UniProtKB:Q08857 mCD36 PRO:DNx platelet glycoprotein IV (mouse) UniProtKB:Q08857 Cd36 UniProtKB:Q08857 A bone marrow stromal antigen 2 that is encoded in the genome of human. UniProtKB:Q10589 BST-2 (human) CD317 (human) HM1.24 antigen (human) hBST2 tetherin (human) protein BST2 PR:Q10589 Category=organism-gene. bone marrow stromal antigen 2 (human) A bone marrow stromal antigen 2 that is encoded in the genome of human. PRO:WCB UniProtKB:Q10589 BST-2 (human) UniProtKB:Q10589 CD317 (human) UniProtKB:Q10589 HM1.24 antigen (human) UniProtKB:Q10589 hBST2 PRO:DNx tetherin (human) UniProtKB:Q10589 BST2 UniProtKB:Q10589 An alpha-(1,3)-fucosyltransferase 4 that is encoded in the genome of mouse. UniProtKB:Q11127 Fuc-TIV (mouse) FucT-IV (mouse) fucosyltransferase 4 (mouse) fucosyltransferase IV (mouse) galactoside 3-L-fucosyltransferase (mouse) mFUT4 protein Elft Fut4 PR:Q11127 Category=organism-gene. alpha-(1,3)-fucosyltransferase 4 (mouse) An alpha-(1,3)-fucosyltransferase 4 that is encoded in the genome of mouse. OMA:Q11127 PRO:DNx Fuc-TIV (mouse) UniProtKB:Q11127 FucT-IV (mouse) UniProtKB:Q11127 fucosyltransferase 4 (mouse) UniProtKB:Q11127 fucosyltransferase IV (mouse) UniProtKB:Q11127 galactoside 3-L-fucosyltransferase (mouse) UniProtKB:Q11127 mFUT4 PRO:DNx Elft UniProtKB:Q11127 Fut4 UniProtKB:Q11127 A tyrosine-protein kinase Mer that is encoded in the genome of human. DTO:03100312 UniProtKB:Q12866 hMERTK proto-oncogene c-Mer (human) receptor tyrosine kinase MerTK (human) protein MER MERTK PR:Q12866 Category=organism-gene. tyrosine-protein kinase Mer (human) A tyrosine-protein kinase Mer that is encoded in the genome of human. PRO:DNx UniProtKB:Q12866 hMERTK PRO:DNx proto-oncogene c-Mer (human) UniProtKB:Q12866 receptor tyrosine kinase MerTK (human) UniProtKB:Q12866 MER UniProtKB:Q12866 MERTK UniProtKB:Q12866 A killer cell lectin-like receptor subfamily B member 1 that is encoded in the genome of human. Reactome:R-HSA-2132225 UniProtKB:Q12918 C-type lectin domain family 5 member B (human) CD161 (human) HNKR-P1a (human) NKR-P1A (human) hKLRB1 natural killer cell surface protein P1A (human) protein CLEC5B KLRB1 NKRP1A PR:Q12918 Category=organism-gene. killer cell lectin-like receptor subfamily B member 1 (human) A killer cell lectin-like receptor subfamily B member 1 that is encoded in the genome of human. PRO:DAN Reactome:R-HSA-2132225 PR:Q12918 located_in GO:0005886 C-type lectin domain family 5 member B (human) UniProtKB:Q12918 CD161 (human) UniProtKB:Q12918 HNKR-P1a (human) UniProtKB:Q12918 NKR-P1A (human) UniProtKB:Q12918 hKLRB1 PRO:DNx natural killer cell surface protein P1A (human) UniProtKB:Q12918 CLEC5B UniProtKB:Q12918 KLRB1 UniProtKB:Q12918 NKRP1A UniProtKB:Q12918 A killer cell lectin-like receptor subfamily D member 1 that is encoded in the genome of human. Reactome:R-HSA-2326854 UniProtKB:Q13241 KP43 (human) NK cell receptor (human) hKLRD1 killer cell lectin-like receptor subfamily D member 1 (human) protein CD94 KLRD1 PR:Q13241 Category=organism-gene. natural killer cells antigen CD94 (human) A killer cell lectin-like receptor subfamily D member 1 that is encoded in the genome of human. PRO:WCB UniProtKB:Q13241 Reactome:R-HSA-2326854 PR:Q13241 located_in GO:0005886 KP43 (human) UniProtKB:Q13241 NK cell receptor (human) UniProtKB:Q13241 hKLRD1 PRO:DNx killer cell lectin-like receptor subfamily D member 1 (human) UniProtKB:Q13241 CD94 UniProtKB:Q13241 KLRD1 UniProtKB:Q13241 A SLAM family member 1 that is encoded in the genome of human. UniProtKB:Q13291 CD150 (human) CDw150 (human) IPO-3 (human) SLAM family member 1 (human) hSLAMF1 protein SLAM SLAMF1 PR:Q13291 Category=organism-gene. signaling lymphocytic activation molecule (human) A SLAM family member 1 that is encoded in the genome of human. PRO:WCB UniProtKB:Q13291 CD150 (human) UniProtKB:Q13291 CDw150 (human) UniProtKB:Q13291 IPO-3 (human) UniProtKB:Q13291 SLAM family member 1 (human) UniProtKB:Q13291 hSLAMF1 PRO:DNx SLAM UniProtKB:Q13291 SLAMF1 UniProtKB:Q13291 A transmembrane emp24 domain-containing protein 1 that is encoded in the genome of human. UniProtKB:Q13445 Tp24 (human) hTMED1 interleukin-1 receptor-like 1 ligand (human) p24 family protein gamma-1 (human) p24gamma1 (human) putative T1/ST2 receptor-binding protein (human) protein IL1RL1L IL1RL1LG TMED1 PR:Q13445 Category=organism-gene. transmembrane emp24 domain-containing protein 1 (human) A transmembrane emp24 domain-containing protein 1 that is encoded in the genome of human. PRO:DNx UniProtKB:Q13445 Tp24 (human) UniProtKB:Q13445 hTMED1 PRO:DNx interleukin-1 receptor-like 1 ligand (human) UniProtKB:Q13445 p24 family protein gamma-1 (human) UniProtKB:Q13445 p24gamma1 (human) UniProtKB:Q13445 putative T1/ST2 receptor-binding protein (human) UniProtKB:Q13445 IL1RL1L UniProtKB:Q13445 IL1RL1LG UniProtKB:Q13445 TMED1 UniProtKB:Q13445 A short transient receptor potential cation channel TRPC3 that is encoded in the genome of human. DTO:01100321 Reactome:R-HSA-426172 UniProtKB:Q13507 TRP-3 (human) TrpC3 (human) hTRPC3 hTrp-3 hTrp3 transient receptor protein 3 (human) protein TRP3 TRPC3 PR:Q13507 Category=organism-gene. short transient receptor potential channel 3 (human) A short transient receptor potential cation channel TRPC3 that is encoded in the genome of human. PRO:CNA UniProtKB:Q13507 Reactome:R-HSA-426172 PR:Q13507 located_in GO:0005886 TRP-3 (human) UniProtKB:Q13507 TrpC3 (human) UniProtKB:Q13507 hTRPC3 PRO:DNx hTrp-3 UniProtKB:Q13507 hTrp3 UniProtKB:Q13507 transient receptor protein 3 (human) UniProtKB:Q13507 TRP3 UniProtKB:Q13507 TRPC3 UniProtKB:Q13507 An adhesion G protein-coupled receptor E1 that is encoded in the genome of human. DTO:02100089 UniProtKB:Q14246 EGF-like module receptor 1 (human) EGF-like module-containing mucin-like hormone receptor-like 1 (human) EMR1 hormone receptor (human) hADGRE1 protein ADGRE1 EMR1 TM7LN3 PR:Q14246 Category=organism-gene. adhesion G protein-coupled receptor E1 (human) An adhesion G protein-coupled receptor E1 that is encoded in the genome of human. PRO:WCB UniProtKB:Q14246 EGF-like module receptor 1 (human) UniProtKB:Q14246 EMR1 hormone receptor (human) UniProtKB:Q14246 hADGRE1 PRO:DNx ADGRE1 UniProtKB:Q14246 EMR1 UniProtKB:Q14246 TM7LN3 UniProtKB:Q14246 A programmed cell death protein 1 that is encoded in the genome of human. UniProtKB:Q15116 CD279 (human) hPD-1 hPDCD1 protein PD-1 (human) protein PD1 PDCD1 PR:Q15116 Category=organism-gene. programmed cell death protein 1 (human) A programmed cell death protein 1 that is encoded in the genome of human. PRO:WCB UniProtKB:Q15116 CD279 (human) UniProtKB:Q15116 hPD-1 UniProtKB:Q15116 hPDCD1 PRO:DNx protein PD-1 (human) UniProtKB:Q15116 PD1 UniProtKB:Q15116 PDCD1 UniProtKB:Q15116 A CCAAT/enhancer-binding protein epsilon that is encoded in the genome of human. Reactome:R-HSA-3234072 UniProtKB:Q15744 C/EBP epsilon (human) hCEBPE protein CEBPE PR:Q15744 Category=organism-gene. CCAAT/enhancer-binding protein epsilon (human) A CCAAT/enhancer-binding protein epsilon that is encoded in the genome of human. PRO:DNx UniProtKB:Q15744 Reactome:R-HSA-3234072 PR:Q15744 located_in GO:0005654 C/EBP epsilon (human) UniProtKB:Q15744 hCEBPE PRO:DNx CEBPE UniProtKB:Q15744 A SLAM family member 5 that is encoded in the genome of mouse. UniProtKB:Q18PI6 CD84 (mouse) leukocyte differentiation antigen CD84 (mouse) mCD84 signaling lymphocytic activation molecule 5 (mouse) protein Cd84 Slamf5 PR:Q18PI6 Category=organism-gene. SLAM family member 5 (mouse) A SLAM family member 5 that is encoded in the genome of mouse. OMA:Q18PI6 PRO:DNx CD84 (mouse) UniProtKB:Q18PI6 leukocyte differentiation antigen CD84 (mouse) UniProtKB:Q18PI6 mCD84 PRO:DNx signaling lymphocytic activation molecule 5 (mouse) UniProtKB:Q18PI6 Cd84 UniProtKB:Q18PI6 Slamf5 UniProtKB:Q18PI6 A scavenger receptor cysteine-rich type 1 protein M130 that is encoded in the genome of mouse. UniProtKB:Q2VLH6 CD163 (mouse) mCD163 protein Cd163 M130 PR:Q2VLH6 Category=organism-gene. scavenger receptor cysteine-rich type 1 protein M130 (mouse) A scavenger receptor cysteine-rich type 1 protein M130 that is encoded in the genome of mouse. OMA:Q2VLH6 PRO:DNx CD163 (mouse) UniProtKB:Q2VLH6 mCD163 PRO:DNx Cd163 UniProtKB:Q2VLH6 M130 UniProtKB:Q2VLH6 A transmembrane emp24 domain-containing protein 1 that is encoded in the genome of mouse. UniProtKB:Q3V009 interleukin-1 receptor-like 1 ligand (mouse) mTMED1 p24 family protein gamma-1 (mouse) p24gamma1 (mouse) putative T1/ST2 receptor-binding protein (mouse) protein Il1rl1l Tmed1 PR:Q3V009 Category=organism-gene. transmembrane emp24 domain-containing protein 1 (mouse) A transmembrane emp24 domain-containing protein 1 that is encoded in the genome of mouse. OMA:Q3V009 PRO:DNx interleukin-1 receptor-like 1 ligand (mouse) UniProtKB:Q3V009 mTMED1 PRO:DNx p24 family protein gamma-1 (mouse) UniProtKB:Q3V009 p24gamma1 (mouse) UniProtKB:Q3V009 putative T1/ST2 receptor-binding protein (mouse) UniProtKB:Q3V009 Il1rl1l UniProtKB:Q3V009 Tmed1 UniProtKB:Q3V009 A cell surface glycoprotein CD200 receptor 3 that is encoded in the genome of mouse. UniProtKB:Q5UKY4 CD200 cell surface glycoprotein receptor-like 3 (mouse) CD200 cell surface glycoprotein receptor-like b (mouse) CD200 receptor-like 3 (mouse) cell surface glycoprotein OX2 receptor 3 (mouse) mCd200r3 protein Cd200r3 Cd200rlb PR:Q5UKY4 Category=organism-gene. cell surface glycoprotein CD200 receptor 3 (mouse) A cell surface glycoprotein CD200 receptor 3 that is encoded in the genome of mouse. PRO:DNx UniProtKB:Q5UKY4 CD200 cell surface glycoprotein receptor-like 3 (mouse) UniProtKB:Q5UKY4 CD200 cell surface glycoprotein receptor-like b (mouse) UniProtKB:Q5UKY4 CD200 receptor-like 3 (mouse) UniProtKB:Q5UKY4 cell surface glycoprotein OX2 receptor 3 (mouse) UniProtKB:Q5UKY4 mCd200r3 PRO:DNx Cd200r3 UniProtKB:Q5UKY4 Cd200rlb UniProtKB:Q5UKY4 A killer cell lectin-like receptor 4 that is encoded in the genome of mouse. UniProtKB:Q60651 T-cell surface glycoprotein Ly-49D (mouse) lymphocyte antigen 49d (mouse) mKlra4 protein Klra4 Ly-49d Ly49-d Ly49d PR:Q60651 Category=organism-gene. killer cell lectin-like receptor 4 (mouse) A killer cell lectin-like receptor 4 that is encoded in the genome of mouse. PRO:DNx UniProtKB:Q60651 T-cell surface glycoprotein Ly-49D (mouse) UniProtKB:Q60651 lymphocyte antigen 49d (mouse) UniProtKB:Q60651 mKlra4 PRO:DNx Klra4 UniProtKB:Q60651 Ly-49d UniProtKB:Q60651 Ly49-d UniProtKB:Q60651 Ly49d UniProtKB:Q60651 An integrin alpha-E that is encoded in the genome of mouse. UniProtKB:Q60677 CD103 (mouse) integrin alpha M290 (mouse) mITGAE protein Itgae PR:Q60677 Category=organism-gene. integrin alpha-E (mouse) An integrin alpha-E that is encoded in the genome of mouse. OMA:Q60677 PRO:DNx CD103 (mouse) UniProtKB:Q60677 integrin alpha M290 (mouse) UniProtKB:Q60677 mITGAE PRO:DNx Itgae UniProtKB:Q60677 A killer cell lectin-like receptor 8 that is encoded in the genome of mouse. UniProtKB:Q60682 T-cell surface glycoprotein Ly-49H (mouse) lymphocyte antigen 49h (mouse) mKlra8 protein Klra8 Ly-49h Ly49-h Ly49H PR:Q60682 Category=organism-gene. killer cell lectin-like receptor 8 (mouse) A killer cell lectin-like receptor 8 that is encoded in the genome of mouse. PRO:DNx UniProtKB:Q60682 T-cell surface glycoprotein Ly-49H (mouse) UniProtKB:Q60682 lymphocyte antigen 49h (mouse) UniProtKB:Q60682 mKlra8 PRO:DNx Klra8 UniProtKB:Q60682 Ly-49h UniProtKB:Q60682 Ly49-h UniProtKB:Q60682 Ly49H UniProtKB:Q60682 A macrophage receptor MARCO that is encoded in the genome of mouse. UniProtKB:Q60754 mMARCO macrophage receptor with collagenous structure (mouse) protein Marco PR:Q60754 Category=organism-gene. macrophage receptor MARCO (mouse) A macrophage receptor MARCO that is encoded in the genome of mouse. OMA:Q60754 PRO:DNx mMARCO PRO:DNx macrophage receptor with collagenous structure (mouse) UniProtKB:Q60754 Marco UniProtKB:Q60754 A lymphocyte antigen 75 that is encoded in the genome of mouse. UniProtKB:Q60767 CD205 (mouse) DEC-205 (mouse) Ly-75 (mouse) mLY75 protein Cd205 Ly75 PR:Q60767 Category=organism-gene. lymphocyte antigen 75 (mouse) A lymphocyte antigen 75 that is encoded in the genome of mouse. PRO:DAN CD205 (mouse) UniProtKB:Q60767 DEC-205 (mouse) UniProtKB:Q60767 Ly-75 (mouse) UniProtKB:Q60767 mLY75 PRO:DNx Cd205 UniProtKB:Q60767 Ly75 UniProtKB:Q60767 A tyrosine-protein kinase Mer that is encoded in the genome of mouse. UniProtKB:Q60805 mMERTK proto-oncogene c-Mer (mouse) receptor tyrosine kinase MerTK (mouse) protein Mer Mertk PR:Q60805 Category=organism-gene. tyrosine-protein kinase Mer (mouse) A tyrosine-protein kinase Mer that is encoded in the genome of mouse. OMA:Q60805 PRO:DNx mMERTK PRO:DNx proto-oncogene c-Mer (mouse) UniProtKB:Q60805 receptor tyrosine kinase MerTK (mouse) UniProtKB:Q60805 Mer UniProtKB:Q60805 Mertk UniProtKB:Q60805 An arginase-1 that is encoded in the genome of mouse. UniProtKB:Q61176 liver-type arginase (mouse) mARG1 type I arginase (mouse) protein Arg1 PR:Q61176 Category=organism-gene. arginase-1 (mouse) An arginase-1 that is encoded in the genome of mouse. OMA:Q61176 PRO:DNx liver-type arginase (mouse) UniProtKB:Q61176 mARG1 PRO:DNx type I arginase (mouse) UniProtKB:Q61176 Arg1 UniProtKB:Q61176 A neprilysin that is encoded in the genome of mouse. UniProtKB:Q61391 CD10 (mouse) NEP (mouse) SFE (mouse) atriopeptidase (mouse) enkephalinase (mouse) mMME neutral endopeptidase (mouse) neutral endopeptidase 24.11 (mouse) skin fibroblast elastase (mouse) protein Mme PR:Q61391 Category=organism-gene. neprilysin (mouse) A neprilysin that is encoded in the genome of mouse. OMA:Q61391 PRO:DNx CD10 (mouse) UniProtKB:Q61391 NEP (mouse) UniProtKB:Q61391 SFE (mouse) UniProtKB:Q61391 atriopeptidase (mouse) UniProtKB:Q61391 enkephalinase (mouse) UniProtKB:Q61391 mMME PRO:DNx neutral endopeptidase (mouse) UniProtKB:Q61391 neutral endopeptidase 24.11 (mouse) UniProtKB:Q61391 skin fibroblast elastase (mouse) UniProtKB:Q61391 Mme UniProtKB:Q61391 An adhesion G protein-coupled receptor E1 that is encoded in the genome of mouse. UniProtKB:Q61549 EGF-like module receptor 1 (mouse) EGF-like module-containing mucin-like hormone receptor-like 1 (mouse) EMR1 hormone receptor (mouse) cell surface glycoprotein F4/80 (mouse) mADGRE1 protein Adgre1 Emr1 Gpf480 PR:Q61549 Category=organism-gene. adhesion G protein-coupled receptor E1 (mouse) An adhesion G protein-coupled receptor E1 that is encoded in the genome of mouse. OMA:Q61549 PRO:DNx EGF-like module receptor 1 (mouse) UniProtKB:Q61549 EGF-like module-containing mucin-like hormone receptor-like 1 (mouse) UniProtKB:Q61549 EMR1 hormone receptor (mouse) UniProtKB:Q61549 cell surface glycoprotein F4/80 (mouse) UniProtKB:Q61549 mADGRE1 PRO:DNx Adgre1 UniProtKB:Q61549 Emr1 UniProtKB:Q61549 Gpf480 UniProtKB:Q61549 A macrophage mannose receptor 1 that is encoded in the genome of mouse. UniProtKB:Q61830 CD206 (mouse) MMR (mouse) mMRC1 protein Mrc1 PR:Q61830 Category=organism-gene. macrophage mannose receptor 1 (mouse) A macrophage mannose receptor 1 that is encoded in the genome of mouse. OMA:Q61830 PRO:DNx CD206 (mouse) UniProtKB:Q61830 MMR (mouse) UniProtKB:Q61830 mMRC1 PRO:DNx Mrc1 UniProtKB:Q61830 A bone marrow proteoglycan that is encoded in the genome of mouse. UniProtKB:Q61878 BMPG (mouse) mPRG2 proteoglycan 2 (mouse) protein Mbp-1 Prg2 PR:Q61878 Category=organism-gene. bone marrow proteoglycan (mouse) A bone marrow proteoglycan that is encoded in the genome of mouse. OMA:Q61878 PRO:DNx BMPG (mouse) UniProtKB:Q61878 mPRG2 PRO:DNx proteoglycan 2 (mouse) UniProtKB:Q61878 Mbp-1 UniProtKB:Q61878 Prg2 UniProtKB:Q61878 A bone marrow proteoglycan isoform 1 that is encoded in the genome of mouse. UniProtKB:Q61878-1 mPRG2/iso:1 protein PR:Q61878-1 Category=organism-sequence. bone marrow proteoglycan isoform 1 (mouse) A bone marrow proteoglycan isoform 1 that is encoded in the genome of mouse. PRO:CNA mPRG2/iso:1 PRO:DNx A sialoadhesin that is encoded in the genome of mouse. UniProtKB:Q62230 CD169 (mouse) SER (mouse) mSIGLEC1 sheep erythrocyte receptor (mouse) sialic acid-binding Ig-like lectin 1 (mouse) siglec-1 (mouse) protein Sa Siglec1 Sn PR:Q62230 Category=organism-gene. sialoadhesin (mouse) A sialoadhesin that is encoded in the genome of mouse. PRO:WCB CD169 (mouse) UniProtKB:Q62230 SER (mouse) UniProtKB:Q62230 mSIGLEC1 PRO:DNx sheep erythrocyte receptor (mouse) UniProtKB:Q62230 sialic acid-binding Ig-like lectin 1 (mouse) UniProtKB:Q62230 siglec-1 (mouse) UniProtKB:Q62230 Sa UniProtKB:Q62230 Siglec1 UniProtKB:Q62230 Sn UniProtKB:Q62230 A transferrin receptor protein 1 that is encoded in the genome of mouse. UniProtKB:Q62351 CD71 (mouse) TfR (mouse) TfR1 (mouse) mTFRC protein TR (mouse) Tfrc Trfr PR:Q62351 Category=organism-gene. transferrin receptor protein 1 (mouse) A transferrin receptor protein 1 that is encoded in the genome of mouse. OMA:Q62351 PRO:DNx CD71 (mouse) UniProtKB:Q62351 TfR (mouse) UniProtKB:Q62351 TfR1 (mouse) UniProtKB:Q62351 mTFRC PRO:DNx TR (mouse) UniProtKB:Q62351 Tfrc UniProtKB:Q62351 Trfr UniProtKB:Q62351 An integrin alpha-2 that is encoded in the genome of mouse. UniProtKB:Q62469 CD49 antigen-like family member B (mouse) CD49b (mouse) GPIa (mouse) VLA-2 subunit alpha (mouse) collagen receptor (mouse) mITGA2 platelet membrane glycoprotein Ia (mouse) protein Itga2 PR:Q62469 Category=organism-gene. integrin alpha-2 (mouse) An integrin alpha-2 that is encoded in the genome of mouse. OMA:Q62469 PRO:DNx CD49 antigen-like family member B (mouse) UniProtKB:Q62469 CD49b (mouse) UniProtKB:Q62469 GPIa (mouse) UniProtKB:Q62469 VLA-2 subunit alpha (mouse) UniProtKB:Q62469 collagen receptor (mouse) UniProtKB:Q62469 mITGA2 PRO:DNx platelet membrane glycoprotein Ia (mouse) UniProtKB:Q62469 Itga2 UniProtKB:Q62469 An endoglin that is encoded in the genome of mouse. UniProtKB:Q63961 CD105 (mouse) cell surface MJ7/18 antigen (mouse) mENG protein Edg Eng PR:Q63961 Category=organism-gene. endoglin (mouse) An endoglin that is encoded in the genome of mouse. OMA:Q63961 PRO:DNx CD105 (mouse) UniProtKB:Q63961 cell surface MJ7/18 antigen (mouse) UniProtKB:Q63961 mENG PRO:DNx Edg UniProtKB:Q63961 Eng UniProtKB:Q63961 A CD33 molecule that is encoded in the genome of mouse. UniProtKB:Q63994 CD33 (mouse) mCD33 sialic acid-binding Ig-like lectin 3 (mouse) siglec-3 (mouse) protein Cd33 Siglec3 PR:Q63994 Category=organism-gene. myeloid cell surface antigen CD33 (mouse) A CD33 molecule that is encoded in the genome of mouse. OMA:Q63994 PRO:DNx CD33 (mouse) UniProtKB:Q63994 mCD33 PRO:DNx sialic acid-binding Ig-like lectin 3 (mouse) UniProtKB:Q63994 siglec-3 (mouse) UniProtKB:Q63994 Cd33 UniProtKB:Q63994 Siglec3 UniProtKB:Q63994 A CD34 molecule that is encoded in the genome of mouse. UniProtKB:Q64314 CD34 (mouse) mCD34 protein Cd34 PR:Q64314 Category=organism-gene. hematopoietic progenitor cell antigen CD34 (mouse) A CD34 molecule that is encoded in the genome of mouse. OMA:Q64314 PRO:DNx CD34 (mouse) UniProtKB:Q64314 mCD34 PRO:DNx Cd34 UniProtKB:Q64314 A killer cell lectin-like receptor 3 that is encoded in the genome of mouse. UniProtKB:Q64329 5E6 (mouse) Nk2.1 (mouse) T-cell surface glycoprotein Ly-49C (mouse) lymphocyte antigen 49c (mouse) mKlra3 protein Klra3 Ly-49c Ly49C PR:Q64329 Category=organism-gene. killer cell lectin-like receptor 3 (mouse) A killer cell lectin-like receptor 3 that is encoded in the genome of mouse. PRO:DNx UniProtKB:Q64329 5E6 (mouse) UniProtKB:Q64329 Nk2.1 (mouse) UniProtKB:Q64329 T-cell surface glycoprotein Ly-49C (mouse) UniProtKB:Q64329 lymphocyte antigen 49c (mouse) UniProtKB:Q64329 mKlra3 PRO:DNx Klra3 UniProtKB:Q64329 Ly-49c UniProtKB:Q64329 Ly49C UniProtKB:Q64329 A lactosylceramide 4-alpha-galactosyltransferase that is encoded in the genome of mouse. UniProtKB:Q67BJ4 Gb3 synthase (mouse) UDP-galactose:beta-D-galactosyl-beta1-R 4-alpha-D-galactosyltransferase (mouse) alpha-1,4-galactosyltransferase (mouse) alpha4Gal-T1 (mouse) globotriaosylceramide synthase (mouse) mA4GALT protein A4galt alpha-1,4-N-acetylglucosaminyltransferase (mouse) PR:Q67BJ4 Category=organism-gene. lactosylceramide 4-alpha-galactosyltransferase (mouse) A lactosylceramide 4-alpha-galactosyltransferase that is encoded in the genome of mouse. OMA:Q67BJ4 PRO:DNx Gb3 synthase (mouse) UniProtKB:Q67BJ4 UDP-galactose:beta-D-galactosyl-beta1-R 4-alpha-D-galactosyltransferase (mouse) UniProtKB:Q67BJ4 alpha-1,4-galactosyltransferase (mouse) UniProtKB:Q67BJ4 alpha4Gal-T1 (mouse) UniProtKB:Q67BJ4 globotriaosylceramide synthase (mouse) UniProtKB:Q67BJ4 mA4GALT PRO:DNx A4galt UniProtKB:Q67BJ4 alpha-1,4-N-acetylglucosaminyltransferase (mouse) PRO:DNx UniProtKB:Q67BJ4 An ectonucleotide pyrophosphatase/phosphodiesterase family member 3 that is encoded in the genome of mouse. UniProtKB:Q6DYE8 CD203c (mouse) E-NPP 3 (mouse) PD-Ibeta (mouse) mENPP3 phosphodiesterase I beta (mouse) phosphodiesterase I/nucleotide pyrophosphatase 3 (mouse) protein Enpp3 PR:Q6DYE8 Category=organism-gene. ectonucleotide pyrophosphatase/phosphodiesterase family member 3 (mouse) An ectonucleotide pyrophosphatase/phosphodiesterase family member 3 that is encoded in the genome of mouse. OMA:Q6DYE8 PRO:DNx CD203c (mouse) UniProtKB:Q6DYE8 E-NPP 3 (mouse) UniProtKB:Q6DYE8 PD-Ibeta (mouse) UniProtKB:Q6DYE8 mENPP3 PRO:DNx phosphodiesterase I beta (mouse) UniProtKB:Q6DYE8 phosphodiesterase I/nucleotide pyrophosphatase 3 (mouse) UniProtKB:Q6DYE8 Enpp3 UniProtKB:Q6DYE8 A C-type lectin domain family 6 member A that is encoded in the genome of human. Reactome:R-HSA-1472857 UniProtKB:Q6EIG7 C-type lectin superfamily member 10 (human) DC-associated C-type lectin 2 (human) dectin-2 (human) dendritic cell-associated C-type lectin 2 (human) hCLEC6A protein CLEC6A CLECSF10 DECTIN2 PR:Q6EIG7 Category=organism-gene. C-type lectin domain family 6 member A (human) A C-type lectin domain family 6 member A that is encoded in the genome of human. PRO:WCB UniProtKB:Q6EIG7 Reactome:R-HSA-1472857 PR:Q6EIG7 located_in GO:0005886 C-type lectin superfamily member 10 (human) UniProtKB:Q6EIG7 DC-associated C-type lectin 2 (human) UniProtKB:Q6EIG7 dectin-2 (human) UniProtKB:Q6EIG7 dendritic cell-associated C-type lectin 2 (human) UniProtKB:Q6EIG7 hCLEC6A PRO:DNx CLEC6A UniProtKB:Q6EIG7 CLECSF10 UniProtKB:Q6EIG7 DECTIN2 UniProtKB:Q6EIG7 A CCAAT/enhancer-binding protein epsilon that is encoded in the genome of mouse. UniProtKB:Q6PZD9 C/EBP epsilon (mouse) mCEBPE protein Cebpe Gm294 PR:Q6PZD9 Category=organism-gene. CCAAT/enhancer-binding protein epsilon (mouse) A CCAAT/enhancer-binding protein epsilon that is encoded in the genome of mouse. OMA:Q6PZD9 PRO:DNx C/EBP epsilon (mouse) UniProtKB:Q6PZD9 mCEBPE PRO:DNx Cebpe UniProtKB:Q6PZD9 Gm294 UniProtKB:Q6PZD9 A C-type lectin domain family 7 member A that is encoded in the genome of mouse. UniProtKB:Q6QLQ4 C-type lectin superfamily member 12 (mouse) CD369 (mouse) DC-associated C-type lectin 1 (mouse) beta-glucan receptor (mouse) dectin-1 (mouse) dendritic cell-associated C-type lectin 1 (mouse) mCLEC7A protein Bgr Clec7a Clecsf12 Dectin1 PR:Q6QLQ4 Category=organism-gene. C-type lectin domain family 7 member A (mouse) A C-type lectin domain family 7 member A that is encoded in the genome of mouse. OMA:Q6QLQ4 PRO:DNx C-type lectin superfamily member 12 (mouse) UniProtKB:Q6QLQ4 CD369 (mouse) UniProtKB:Q6QLQ4 DC-associated C-type lectin 1 (mouse) UniProtKB:Q6QLQ4 beta-glucan receptor (mouse) UniProtKB:Q6QLQ4 dectin-1 (mouse) UniProtKB:Q6QLQ4 dendritic cell-associated C-type lectin 1 (mouse) UniProtKB:Q6QLQ4 mCLEC7A PRO:DNx Bgr UniProtKB:Q6QLQ4 Clec7a UniProtKB:Q6QLQ4 Clecsf12 UniProtKB:Q6QLQ4 Dectin1 UniProtKB:Q6QLQ4 A scavenger receptor cysteine-rich type 1 protein M130 that is encoded in the genome of human. UniProtKB:Q86VB7 hCD163 hemoglobin scavenger receptor (human) protein CD163 M130 PR:Q86VB7 Category=organism-gene. scavenger receptor cysteine-rich type 1 protein M130 (human) A scavenger receptor cysteine-rich type 1 protein M130 that is encoded in the genome of human. PRO:WCB UniProtKB:Q86VB7 hCD163 PRO:DNx hemoglobin scavenger receptor (human) UniProtKB:Q86VB7 CD163 UniProtKB:Q86VB7 M130 UniProtKB:Q86VB7 A natural cytotoxicity triggering receptor 1 that is encoded in the genome of mouse. UniProtKB:Q8C567 CD335 (mouse) NK-p46 (mouse) NKp46 (mouse) activating receptor 1 (mouse) lymphocyte antigen 94 (mouse) mAR-1 mNCR1 mNKp46 natural killer cell p46-related protein (mouse) protein Ly94 Ncr1 PR:Q8C567 Category=organism-gene. natural cytotoxicity triggering receptor 1 (mouse) A natural cytotoxicity triggering receptor 1 that is encoded in the genome of mouse. PRO:WCB CD335 (mouse) UniProtKB:Q8C567 NK-p46 (mouse) UniProtKB:Q8C567 NKp46 (mouse) UniProtKB:Q8C567 activating receptor 1 (mouse) UniProtKB:Q8C567 lymphocyte antigen 94 (mouse) UniProtKB:Q8C567 mAR-1 UniProtKB:Q8C567 mNCR1 PRO:DNx mNKp46 UniProtKB:Q8C567 natural killer cell p46-related protein (mouse) UniProtKB:Q8C567 Ly94 UniProtKB:Q8C567 Ncr1 UniProtKB:Q8C567 A CD209 molecule-like protein B that is encoded in the genome of mouse. CD209 (mouse) UniProtKB:Q8CJ91 DC-SIGN-related protein 1 (mouse) DC-SIGNR1 (mouse) OtB7 (mouse) mCd209b protein Cd209b PR:Q8CJ91 Category=organism-gene. CD209 antigen-like protein B (mouse) A CD209 molecule-like protein B that is encoded in the genome of mouse. PRO:DNx UniProtKB:Q8CJ91 CD209 (mouse) UniProtKB:Q8CJ91 DC-SIGN-related protein 1 (mouse) UniProtKB:Q8CJ91 DC-SIGNR1 (mouse) UniProtKB:Q8CJ91 OtB7 (mouse) UniProtKB:Q8CJ91 mCd209b PRO:DNx Cd209b UniProtKB:Q8CJ91 A bone marrow stromal antigen 2 that is encoded in the genome of mouse. UniProtKB:Q8R2Q8 BST-2 (mouse) CD317 (mouse) HM1.24 antigen (mouse) mBST2 protein Bst2 PR:Q8R2Q8 Category=organism-gene. bone marrow stromal antigen 2 (mouse) A bone marrow stromal antigen 2 that is encoded in the genome of mouse. OMA:Q8R2Q8 PRO:DNx BST-2 (mouse) UniProtKB:Q8R2Q8 CD317 (mouse) UniProtKB:Q8R2Q8 HM1.24 antigen (mouse) UniProtKB:Q8R2Q8 mBST2 PRO:DNx Bst2 UniProtKB:Q8R2Q8 A netrin-G1 that is encoded in the genome of mouse. UniProtKB:Q8R4G0 laminet-1 (mouse) mNTNG1 protein Kiaa0976 Lmnt1 Ntng1 PR:Q8R4G0 Category=organism-gene. netrin-G1 (mouse) A netrin-G1 that is encoded in the genome of mouse. OMA:Q8R4G0 PRO:DNx laminet-1 (mouse) UniProtKB:Q8R4G0 mNTNG1 PRO:DNx Kiaa0976 UniProtKB:Q8R4G0 Lmnt1 UniProtKB:Q8R4G0 Ntng1 UniProtKB:Q8R4G0 A neuropilin and tolloid-like protein 1 that is encoded in the genome of mouse. UniProtKB:Q8R4I7 brain-specific transmembrane protein containing 2 CUB and 1 LDL-receptor class A domains protein 1 (mouse) mNETO1 protein Btcl1 Neto1 PR:Q8R4I7 Category=organism-gene. neuropilin and tolloid-like protein 1 (mouse) A neuropilin and tolloid-like protein 1 that is encoded in the genome of mouse. OMA:Q8R4I7 PRO:DNx brain-specific transmembrane protein containing 2 CUB and 1 LDL-receptor class A domains protein 1 (mouse) UniProtKB:Q8R4I7 mNETO1 PRO:DNx Btcl1 UniProtKB:Q8R4I7 Neto1 UniProtKB:Q8R4I7 A neuropilin and tolloid-like protein 1 that is encoded in the genome of human. UniProtKB:Q8TDF5 brain-specific transmembrane protein containing 2 CUB and 1 LDL-receptor class A domains protein 1 (human) hNETO1 protein BTCL1 NETO1 PR:Q8TDF5 Category=organism-gene. neuropilin and tolloid-like protein 1 (human) A neuropilin and tolloid-like protein 1 that is encoded in the genome of human. PRO:DNx UniProtKB:Q8TDF5 brain-specific transmembrane protein containing 2 CUB and 1 LDL-receptor class A domains protein 1 (human) UniProtKB:Q8TDF5 hNETO1 PRO:DNx BTCL1 UniProtKB:Q8TDF5 NETO1 UniProtKB:Q8TDF5 A C-type lectin domain family 4 member K that is encoded in the genome of mouse. UniProtKB:Q8VBX4 CD207 (mouse) langerin (mouse) mCD207 protein Cd207 Clec4k PR:Q8VBX4 Category=organism-gene. C-type lectin domain family 4 member K (mouse) A C-type lectin domain family 4 member K that is encoded in the genome of mouse. OMA:Q8VBX4 PRO:DNx CD207 (mouse) UniProtKB:Q8VBX4 langerin (mouse) UniProtKB:Q8VBX4 mCD207 PRO:DNx Cd207 UniProtKB:Q8VBX4 Clec4k UniProtKB:Q8VBX4 A C-type lectin domain family 4 member C that is encoded in the genome of human. Reactome:R-HSA-2130705 Reactome:R-HSA-6800186 Reactome:R-HSA-6800915 Reactome:R-HSA-6801022 UniProtKB:Q8WTT0 BDCA-2 (human) C-type lectin superfamily member 7 (human) CD303 (human) blood dendritic cell antigen 2 (human) dendritic lectin (human) hCLEC4C protein BDCA2 CLEC4C CLECSF11 CLECSF7 DLEC HECL UNQ9361/PRO34150 PR:Q8WTT0 Category=organism-gene. C-type lectin domain family 4 member C (human) A C-type lectin domain family 4 member C that is encoded in the genome of human. PRO:WCB UniProtKB:Q8WTT0 Reactome:R-HSA-2130705 PR:Q8WTT0 located_in GO:0005886 Reactome:R-HSA-6800186 PR:Q8WTT0 located_in GO:0070821 Reactome:R-HSA-6800915 PR:Q8WTT0 located_in GO:0101003 Reactome:R-HSA-6801022 PR:Q8WTT0 located_in GO:0030667 BDCA-2 (human) UniProtKB:Q8WTT0 C-type lectin superfamily member 7 (human) UniProtKB:Q8WTT0 CD303 (human) UniProtKB:Q8WTT0 blood dendritic cell antigen 2 (human) UniProtKB:Q8WTT0 dendritic lectin (human) UniProtKB:Q8WTT0 hCLEC4C PRO:DNx BDCA2 UniProtKB:Q8WTT0 CLEC4C UniProtKB:Q8WTT0 CLECSF11 UniProtKB:Q8WTT0 CLECSF7 UniProtKB:Q8WTT0 DLEC UniProtKB:Q8WTT0 HECL UniProtKB:Q8WTT0 UNQ9361/PRO34150 UniProtKB:Q8WTT0 A killer cell lectin-like receptor subfamily G member 1 that is encoded in the genome of human. Reactome:R-HSA-198006 UniProtKB:Q96E93 C-type lectin domain family 15 member A (human) ITIM-containing receptor MAFA-L (human) MAFA-like receptor (human) hKLRG1 mast cell function-associated antigen (human) protein CLEC15A KLRG1 MAFA MAFAL PR:Q96E93 Category=organism-gene. killer cell lectin-like receptor subfamily G member 1 (human) A killer cell lectin-like receptor subfamily G member 1 that is encoded in the genome of human. PRO:DNx UniProtKB:Q96E93 Reactome:R-HSA-198006 PR:Q96E93 located_in GO:0005886 C-type lectin domain family 15 member A (human) UniProtKB:Q96E93 ITIM-containing receptor MAFA-L (human) UniProtKB:Q96E93 MAFA-like receptor (human) UniProtKB:Q96E93 hKLRG1 PRO:DNx mast cell function-associated antigen (human) UniProtKB:Q96E93 CLEC15A UniProtKB:Q96E93 KLRG1 UniProtKB:Q96E93 MAFA UniProtKB:Q96E93 MAFAL UniProtKB:Q96E93 A forkhead box protein P3 that is encoded in the genome of mouse. UniProtKB:Q99JB6 mFOXP3 scurfin (mouse) protein Foxp3 PR:Q99JB6 Category=organism-gene. forkhead box protein P3 (mouse) A forkhead box protein P3 that is encoded in the genome of mouse. OMA:Q99JB6 PRO:DNx mFOXP3 PRO:DNx scurfin (mouse) UniProtKB:Q99JB6 Foxp3 UniProtKB:Q99JB6 A C-type lectin domain family 7 member A that is encoded in the genome of human. Reactome:R-HSA-2130683 UniProtKB:Q9BXN2 C-type lectin superfamily member 12 (human) CD369 (human) DC-associated C-type lectin 1 (human) beta-glucan receptor (human) dectin-1 (human) dendritic cell-associated C-type lectin 1 (human) hCLEC7A protein BGR CLEC7A CLECSF12 DECTIN1 UNQ539/PRO1082 PR:Q9BXN2 Category=organism-gene. C-type lectin domain family 7 member A (human) A C-type lectin domain family 7 member A that is encoded in the genome of human. PRO:WCB UniProtKB:Q9BXN2 Reactome:R-HSA-2130683 PR:Q9BXN2 located_in GO:0005886 C-type lectin superfamily member 12 (human) UniProtKB:Q9BXN2 CD369 (human) UniProtKB:Q9BXN2 DC-associated C-type lectin 1 (human) UniProtKB:Q9BXN2 beta-glucan receptor (human) UniProtKB:Q9BXN2 dectin-1 (human) UniProtKB:Q9BXN2 dendritic cell-associated C-type lectin 1 (human) UniProtKB:Q9BXN2 hCLEC7A PRO:DNx BGR UniProtKB:Q9BXN2 CLEC7A UniProtKB:Q9BXN2 CLECSF12 UniProtKB:Q9BXN2 DECTIN1 UniProtKB:Q9BXN2 UNQ539/PRO1082 UniProtKB:Q9BXN2 A forkhead box protein P3 that is encoded in the genome of human. Reactome:R-HSA-8865539 UniProtKB:Q9BZS1 hFOXP3 scurfin (human) protein FOXP3 IPEX JM2 PR:Q9BZS1 Category=organism-gene. forkhead box protein P3 (human) A forkhead box protein P3 that is encoded in the genome of human. PRO:CNA UniProtKB:Q9BZS1 Reactome:R-HSA-8865539 PR:Q9BZS1 located_in GO:0005654 hFOXP3 PRO:DNx scurfin (human) UniProtKB:Q9BZS1 FOXP3 UniProtKB:Q9BZS1 IPEX UniProtKB:Q9BZS1 JM2 UniProtKB:Q9BZS1 A natural killer cell receptor 2B4 that is encoded in the genome of human. UniProtKB:Q9BZW8 NAIL (human) NK cell activation-inducing ligand (human) NK cell type I receptor protein 2B4 (human) NKR2B4 (human) SLAM family member 4 (human) SLAMF4 (human) h2B4 (human) hCD244 signaling lymphocytic activation molecule 4 (human) protein 2B4 CD244 PR:Q9BZW8 Category=organism-gene. natural killer cell receptor 2B4 (human) A natural killer cell receptor 2B4 that is encoded in the genome of human. PRO:WCB UniProtKB:Q9BZW8 NAIL (human) UniProtKB:Q9BZW8 NK cell activation-inducing ligand (human) UniProtKB:Q9BZW8 NK cell type I receptor protein 2B4 (human) UniProtKB:Q9BZW8 NKR2B4 (human) UniProtKB:Q9BZW8 SLAM family member 4 (human) UniProtKB:Q9BZW8 SLAMF4 (human) UniProtKB:Q9BZW8 h2B4 (human) UniProtKB:Q9BZW8 hCD244 PRO:DNx signaling lymphocytic activation molecule 4 (human) UniProtKB:Q9BZW8 2B4 UniProtKB:Q9BZW8 CD244 UniProtKB:Q9BZW8 A sialoadhesin that is encoded in the genome of human. UniProtKB:Q9BZZ2 CD169 (human) hSIGLEC1 sialic acid-binding Ig-like lectin 1 (human) siglec-1 (human) protein SIGLEC1 SN PR:Q9BZZ2 Category=organism-gene. sialoadhesin (human) A sialoadhesin that is encoded in the genome of human. PRO:WCB UniProtKB:Q9BZZ2 CD169 (human) UniProtKB:Q9BZZ2 hSIGLEC1 PRO:DNx sialic acid-binding Ig-like lectin 1 (human) UniProtKB:Q9BZZ2 siglec-1 (human) UniProtKB:Q9BZZ2 SIGLEC1 UniProtKB:Q9BZZ2 SN UniProtKB:Q9BZZ2 A lysosome-associated membrane glycoprotein 5 that is encoded in the genome of mouse. UniProtKB:Q9D387 BAD-LAMP (mouse) LAMP-5 (mouse) brain and dendritic cell-associated LAMP (mouse) brain-associated LAMP-like protein (mouse) lysosome-associated membrane protein 5 (mouse) mLAMP5 protein Lamp5 PR:Q9D387 Category=organism-gene. lysosome-associated membrane glycoprotein 5 (mouse) A lysosome-associated membrane glycoprotein 5 that is encoded in the genome of mouse. OMA:Q9D387 PRO:DNx BAD-LAMP (mouse) UniProtKB:Q9D387 LAMP-5 (mouse) UniProtKB:Q9D387 brain and dendritic cell-associated LAMP (mouse) UniProtKB:Q9D387 brain-associated LAMP-like protein (mouse) UniProtKB:Q9D387 lysosome-associated membrane protein 5 (mouse) UniProtKB:Q9D387 mLAMP5 PRO:DNx Lamp5 UniProtKB:Q9D387 An iroquois-class homeodomain protein IRX-6 that is encoded in the genome of mouse. UniProtKB:Q9ER75 homeodomain protein IRXB3 (mouse) iroquois homeobox protein 6 (mouse) mIRX6 protein Irx6 Irxb3 PR:Q9ER75 Category=organism-gene. iroquois-class homeodomain protein IRX-6 (mouse) An iroquois-class homeodomain protein IRX-6 that is encoded in the genome of mouse. OMA:Q9ER75 PRO:DNx homeodomain protein IRXB3 (mouse) UniProtKB:Q9ER75 iroquois homeobox protein 6 (mouse) UniProtKB:Q9ER75 mIRX6 PRO:DNx Irx6 UniProtKB:Q9ER75 Irxb3 UniProtKB:Q9ER75 An interleukin-17 receptor B that is encoded in the genome of mouse. UniProtKB:Q9JIP3 IL-17 receptor B (mouse) IL-17 receptor homolog 1 (mouse) IL-17B receptor (mouse) IL-17ER (mouse) IL-17RB (mouse) IL-17Rh1 (mouse) IL17Rh1 (mouse) interleukin-17B receptor (mouse) mIL17RB protein Evi27 Il17br Il17rb PR:Q9JIP3 Category=organism-gene. interleukin-17 receptor B (mouse) An interleukin-17 receptor B that is encoded in the genome of mouse. OMA:Q9JIP3 PRO:DNx IL-17 receptor B (mouse) UniProtKB:Q9JIP3 IL-17 receptor homolog 1 (mouse) UniProtKB:Q9JIP3 IL-17B receptor (mouse) UniProtKB:Q9JIP3 IL-17ER (mouse) UniProtKB:Q9JIP3 IL-17RB (mouse) UniProtKB:Q9JIP3 IL-17Rh1 (mouse) UniProtKB:Q9JIP3 IL17Rh1 (mouse) UniProtKB:Q9JIP3 interleukin-17B receptor (mouse) UniProtKB:Q9JIP3 mIL17RB PRO:DNx Evi27 UniProtKB:Q9JIP3 Il17br UniProtKB:Q9JIP3 Il17rb UniProtKB:Q9JIP3 A T-box transcription factor TBX21 that is encoded in the genome of mouse. UniProtKB:Q9JKD8 T-box protein 21 (mouse) T-cell-specific T-box transcription factor T-bet (mouse) mTBX21 transcription factor TBLYM (mouse) protein Tbet Tblym Tbx21 PR:Q9JKD8 Category=organism-gene. T-box transcription factor TBX21 (mouse) A T-box transcription factor TBX21 that is encoded in the genome of mouse. OMA:Q9JKD8 PRO:DNx T-box protein 21 (mouse) UniProtKB:Q9JKD8 T-cell-specific T-box transcription factor T-bet (mouse) UniProtKB:Q9JKD8 mTBX21 PRO:DNx transcription factor TBLYM (mouse) UniProtKB:Q9JKD8 Tbet UniProtKB:Q9JKD8 Tblym UniProtKB:Q9JKD8 Tbx21 UniProtKB:Q9JKD8 A C-type lectin domain family 6 member A that is encoded in the genome of mouse. UniProtKB:Q9JKF4 C-type lectin superfamily member 10 (mouse) DC-associated C-type lectin 2 (mouse) dectin-2 (mouse) dendritic cell-associated C-type lectin 2 (mouse) mCLEC6A protein Clec4n Clec6a Clecsf10 Dectin2 PR:Q9JKF4 Category=organism-gene. C-type lectin domain family 6 member A (mouse) A C-type lectin domain family 6 member A that is encoded in the genome of mouse. OMA:Q9JKF4 PRO:DNx C-type lectin superfamily member 10 (mouse) UniProtKB:Q9JKF4 DC-associated C-type lectin 2 (mouse) UniProtKB:Q9JKF4 dectin-2 (mouse) UniProtKB:Q9JKF4 dendritic cell-associated C-type lectin 2 (mouse) UniProtKB:Q9JKF4 mCLEC6A PRO:DNx Clec4n UniProtKB:Q9JKF4 Clec6a UniProtKB:Q9JKF4 Clecsf10 UniProtKB:Q9JKF4 Dectin2 UniProtKB:Q9JKF4 A CD209 molecule that is encoded in the genome of human. Reactome:R-HSA-2079928 UniProtKB:Q9NNX6 C-type lectin domain family 4 member L (human) DC-SIGN (human) DC-SIGN1 (human) dendritic cell-specific ICAM-3-grabbing non-integrin 1 (human) hCD209 protein CD209 CLEC4L PR:Q9NNX6 Category=organism-gene. CD209 antigen (human) A CD209 molecule that is encoded in the genome of human. PRO:WCB UniProtKB:Q9NNX6 Reactome:R-HSA-2079928 PR:Q9NNX6 located_in GO:0005886 C-type lectin domain family 4 member L (human) UniProtKB:Q9NNX6 DC-SIGN (human) UniProtKB:Q9NNX6 DC-SIGN1 (human) UniProtKB:Q9NNX6 dendritic cell-specific ICAM-3-grabbing non-integrin 1 (human) UniProtKB:Q9NNX6 hCD209 PRO:DNx CD209 UniProtKB:Q9NNX6 CLEC4L UniProtKB:Q9NNX6 A lactosylceramide 4-alpha-galactosyltransferase that is encoded in the genome of human. UniProtKB:Q9NPC4 CD77 synthase (human) Gb3 synthase (human) P1/Pk synthase (human) UDP-galactose:beta-D-galactosyl-beta1-R 4-alpha-D-galactosyltransferase (human) alpha-1,4-galactosyltransferase (human) alpha4Gal-T1 (human) globotriaosylceramide synthase (human) hA4GALT protein A14GALT A4GALT A4GALT1 alpha-1,4-N-acetylglucosaminyltransferase (human) PR:Q9NPC4 Category=organism-gene. lactosylceramide 4-alpha-galactosyltransferase (human) A lactosylceramide 4-alpha-galactosyltransferase that is encoded in the genome of human. PRO:DNx UniProtKB:Q9NPC4 CD77 synthase (human) UniProtKB:Q9NPC4 Gb3 synthase (human) UniProtKB:Q9NPC4 P1/Pk synthase (human) UniProtKB:Q9NPC4 UDP-galactose:beta-D-galactosyl-beta1-R 4-alpha-D-galactosyltransferase (human) UniProtKB:Q9NPC4 alpha-1,4-galactosyltransferase (human) UniProtKB:Q9NPC4 alpha4Gal-T1 (human) UniProtKB:Q9NPC4 globotriaosylceramide synthase (human) UniProtKB:Q9NPC4 hA4GALT PRO:DNx A14GALT UniProtKB:Q9NPC4 A4GALT UniProtKB:Q9NPC4 A4GALT1 UniProtKB:Q9NPC4 alpha-1,4-N-acetylglucosaminyltransferase (human) UniProtKB:Q9NPC4 A complement component C1q receptor that is encoded in the genome of human. UniProtKB:Q9NPY3 C1q/MBL/SPA receptor (human) C1qR (human) C1qR(p) (human) C1qRp (human) CDw93 (human) complement component 1 q subcomponent receptor 1 (human) hCD93 matrix-remodeling-associated protein 4 (human) protein C1QR1 CD93 MXRA4 PR:Q9NPY3 Category=organism-gene. complement component C1q receptor (human) A complement component C1q receptor that is encoded in the genome of human. PRO:WCB UniProtKB:Q9NPY3 C1q/MBL/SPA receptor (human) UniProtKB:Q9NPY3 C1qR (human) UniProtKB:Q9NPY3 C1qR(p) (human) UniProtKB:Q9NPY3 C1qRp (human) UniProtKB:Q9NPY3 CDw93 (human) UniProtKB:Q9NPY3 complement component 1 q subcomponent receptor 1 (human) UniProtKB:Q9NPY3 hCD93 PRO:DNx matrix-remodeling-associated protein 4 (human) UniProtKB:Q9NPY3 C1QR1 UniProtKB:Q9NPY3 CD93 UniProtKB:Q9NPY3 MXRA4 UniProtKB:Q9NPY3 An interleukin-17 receptor B that is encoded in the genome of human. UniProtKB:Q9NRM6 IL-17 receptor B (human) IL-17 receptor homolog 1 (human) IL-17B receptor (human) IL-17RB (human) IL-17Rh1 (human) IL17Rh1 (human) cytokine receptor-like 4 (human) hIL17RB interleukin-17B receptor (human) protein CRL4 EVI27 IL17BR IL17RB UNQ2501/PRO19612 PR:Q9NRM6 Category=organism-gene. interleukin-17 receptor B (human) An interleukin-17 receptor B that is encoded in the genome of human. PRO:DNx UniProtKB:Q9NRM6 IL-17 receptor B (human) UniProtKB:Q9NRM6 IL-17 receptor homolog 1 (human) UniProtKB:Q9NRM6 IL-17B receptor (human) UniProtKB:Q9NRM6 IL-17RB (human) UniProtKB:Q9NRM6 IL-17Rh1 (human) UniProtKB:Q9NRM6 IL17Rh1 (human) UniProtKB:Q9NRM6 cytokine receptor-like 4 (human) UniProtKB:Q9NRM6 hIL17RB PRO:DNx interleukin-17B receptor (human) UniProtKB:Q9NRM6 CRL4 UniProtKB:Q9NRM6 EVI27 UniProtKB:Q9NRM6 IL17BR UniProtKB:Q9NRM6 IL17RB UniProtKB:Q9NRM6 UNQ2501/PRO19612 UniProtKB:Q9NRM6 An integrin alpha-IIb that is encoded in the genome of mouse. UniProtKB:Q9QUM0 CD41 (mouse) GPIIb (mouse) GPalpha IIb (mouse) mITGA2B platelet membrane glycoprotein IIb (mouse) protein Itga2b PR:Q9QUM0 Category=organism-gene. integrin alpha-IIb (mouse) An integrin alpha-IIb that is encoded in the genome of mouse. OMA:Q9QUM0 PRO:DNx CD41 (mouse) UniProtKB:Q9QUM0 GPIIb (mouse) UniProtKB:Q9QUM0 GPalpha IIb (mouse) UniProtKB:Q9QUM0 mITGA2B PRO:DNx platelet membrane glycoprotein IIb (mouse) UniProtKB:Q9QUM0 Itga2b UniProtKB:Q9QUM0 A SLAM family member 1 that is encoded in the genome of mouse. UniProtKB:Q9QUM4 CD150 (mouse) SLAM family member 1 (mouse) mSLAMF1 protein Slam Slamf1 PR:Q9QUM4 Category=organism-gene. signaling lymphocytic activation molecule (mouse) A SLAM family member 1 that is encoded in the genome of mouse. OMA:Q9QUM4 PRO:DNx CD150 (mouse) UniProtKB:Q9QUM4 SLAM family member 1 (mouse) UniProtKB:Q9QUM4 mSLAMF1 PRO:DNx Slam UniProtKB:Q9QUM4 Slamf1 UniProtKB:Q9QUM4 An integrin alpha-X that is encoded in the genome of mouse. UniProtKB:Q9QXH4 CD11 antigen-like family member C (mouse) CD11c (mouse) leukocyte adhesion glycoprotein p150,95 alpha chain (mouse) leukocyte adhesion receptor p150,95 (mouse) mITGAX protein Itgax PR:Q9QXH4 Category=organism-gene. integrin alpha-X (mouse) An integrin alpha-X that is encoded in the genome of mouse. OMA:Q9QXH4 PRO:DNx CD11 antigen-like family member C (mouse) UniProtKB:Q9QXH4 CD11c (mouse) UniProtKB:Q9QXH4 leukocyte adhesion glycoprotein p150,95 alpha chain (mouse) UniProtKB:Q9QXH4 leukocyte adhesion receptor p150,95 (mouse) UniProtKB:Q9QXH4 mITGAX PRO:DNx Itgax UniProtKB:Q9QXH4 A short transient receptor potential cation channel TRPC3 that is encoded in the genome of mouse. UniProtKB:Q9QZC1 TRP-3 (mouse) Trp-related protein 3 (mouse) TrpC3 (mouse) mTRPC3 mTrp3 receptor-activated cation channel TRP3 (mouse) transient receptor protein 3 (mouse) protein Trp3 Trpc3 Trrp3 PR:Q9QZC1 Category=organism-gene. short transient receptor potential channel 3 (mouse) A short transient receptor potential cation channel TRPC3 that is encoded in the genome of mouse. OMA:Q9QZC1 PRO:DNx TRP-3 (mouse) UniProtKB:Q9QZC1 Trp-related protein 3 (mouse) UniProtKB:Q9QZC1 TrpC3 (mouse) UniProtKB:Q9QZC1 mTRPC3 PRO:DNx mTrp3 UniProtKB:Q9QZC1 receptor-activated cation channel TRP3 (mouse) UniProtKB:Q9QZC1 transient receptor protein 3 (mouse) UniProtKB:Q9QZC1 Trp3 UniProtKB:Q9QZC1 Trpc3 UniProtKB:Q9QZC1 Trrp3 UniProtKB:Q9QZC1 A LIM/homeobox protein Lhx3 that is encoded in the genome of human. Reactome:R-HSA-9010582 UniProtKB:Q9UBR4 LIM homeobox protein 3 (human) hLHX3 protein LHX3 PR:Q9UBR4 Category=organism-gene. LIM/homeobox protein Lhx3 (human) A LIM/homeobox protein Lhx3 that is encoded in the genome of human. PRO:DNx UniProtKB:Q9UBR4 Reactome:R-HSA-9010582 PR:Q9UBR4 located_in GO:0005654 LIM homeobox protein 3 (human) UniProtKB:Q9UBR4 hLHX3 PRO:DNx LHX3 UniProtKB:Q9UBR4 A macrophage receptor MARCO that is encoded in the genome of human. UniProtKB:Q9UEW3 hMARCO macrophage receptor with collagenous structure (human) scavenger receptor class A member 2 (human) protein MARCO SCARA2 PR:Q9UEW3 Category=organism-gene. macrophage receptor MARCO (human) A macrophage receptor MARCO that is encoded in the genome of human. PRO:WCB UniProtKB:Q9UEW3 hMARCO PRO:DNx macrophage receptor with collagenous structure (human) UniProtKB:Q9UEW3 scavenger receptor class A member 2 (human) UniProtKB:Q9UEW3 MARCO UniProtKB:Q9UEW3 SCARA2 UniProtKB:Q9UEW3 A SLAM family member 5 that is encoded in the genome of human. UniProtKB:Q9UIB8 Hly9-beta (human) cell surface antigen MAX.3 (human) hCD84 leukocyte differentiation antigen CD84 (human) signaling lymphocytic activation molecule 5 (human) protein CD84 SLAMF5 PR:Q9UIB8 Category=organism-gene. SLAM family member 5 (human) A SLAM family member 5 that is encoded in the genome of human. PRO:WCB UniProtKB:Q9UIB8 Hly9-beta (human) UniProtKB:Q9UIB8 cell surface antigen MAX.3 (human) UniProtKB:Q9UIB8 hCD84 PRO:DNx leukocyte differentiation antigen CD84 (human) UniProtKB:Q9UIB8 signaling lymphocytic activation molecule 5 (human) UniProtKB:Q9UIB8 CD84 UniProtKB:Q9UIB8 SLAMF5 UniProtKB:Q9UIB8 A C-type lectin domain family 4 member K that is encoded in the genome of human. Reactome:R-HSA-1216519 Reactome:R-HSA-1236762 Reactome:R-HSA-1236852 UniProtKB:Q9UJ71 hCD207 langerin (human) protein CD207 CLEC4K PR:Q9UJ71 Category=organism-gene. C-type lectin domain family 4 member K (human) A C-type lectin domain family 4 member K that is encoded in the genome of human. PRO:WCB UniProtKB:Q9UJ71 Reactome:R-HSA-1216519 PR:Q9UJ71 located_in GO:0005886 Reactome:R-HSA-1236762 PR:Q9UJ71 located_in GO:0030669 Reactome:R-HSA-1236852 PR:Q9UJ71 located_in GO:0031901 hCD207 PRO:DNx langerin (human) UniProtKB:Q9UJ71 CD207 UniProtKB:Q9UJ71 CLEC4K UniProtKB:Q9UJ71 A lysosome-associated membrane glycoprotein 5 that is encoded in the genome of human. UniProtKB:Q9UJQ1 BAD-LAMP (human) LAMP-5 (human) brain and dendritic cell-associated LAMP (human) brain-associated LAMP-like protein (human) hLAMP5 lysosome-associated membrane protein 5 (human) protein C20orf103 LAMP5 PR:Q9UJQ1 Category=organism-gene. lysosome-associated membrane glycoprotein 5 (human) A lysosome-associated membrane glycoprotein 5 that is encoded in the genome of human. PRO:DNx UniProtKB:Q9UJQ1 BAD-LAMP (human) UniProtKB:Q9UJQ1 LAMP-5 (human) UniProtKB:Q9UJQ1 brain and dendritic cell-associated LAMP (human) UniProtKB:Q9UJQ1 brain-associated LAMP-like protein (human) UniProtKB:Q9UJQ1 hLAMP5 PRO:DNx lysosome-associated membrane protein 5 (human) UniProtKB:Q9UJQ1 C20orf103 UniProtKB:Q9UJQ1 LAMP5 UniProtKB:Q9UJQ1 A T-box transcription factor TBX21 that is encoded in the genome of human. UniProtKB:Q9UL17 T-box protein 21 (human) T-cell-specific T-box transcription factor T-bet (human) hTBX21 transcription factor TBLYM (human) protein TBET TBLYM TBX21 PR:Q9UL17 Category=organism-gene. T-box transcription factor TBX21 (human) A T-box transcription factor TBX21 that is encoded in the genome of human. PRO:WCB UniProtKB:Q9UL17 T-box protein 21 (human) UniProtKB:Q9UL17 T-cell-specific T-box transcription factor T-bet (human) UniProtKB:Q9UL17 hTBX21 PRO:DNx transcription factor TBLYM (human) UniProtKB:Q9UL17 TBET UniProtKB:Q9UL17 TBLYM UniProtKB:Q9UL17 TBX21 UniProtKB:Q9UL17 A nuclear factor NF-kappa-B p100 subunit that is encoded in the genome of mouse. UniProtKB:Q9WTK5 DNA-binding factor KBF2 (mouse) mNFKB2 nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (mouse) protein Nfkb2 PR:Q9WTK5 Category=organism-gene. nuclear factor NF-kappa-B p100 subunit (mouse) A nuclear factor NF-kappa-B p100 subunit that is encoded in the genome of mouse. OMA:Q9WTK5 PRO:DNx DNA-binding factor KBF2 (mouse) UniProtKB:Q9WTK5 mNFKB2 PRO:DNx nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (mouse) UniProtKB:Q9WTK5 Nfkb2 UniProtKB:Q9WTK5 An inducible T-cell costimulator that is encoded in the genome of mouse. UniProtKB:Q9WVS0 CCLP (mouse) CD278 (mouse) CD28 and CTLA-4-like protein (mouse) CD28-related protein 1 (mouse) activation-inducible lymphocyte immunomediatory molecule (mouse) mICOS protein Ailim CRP-1 (mouse) Icos PR:Q9WVS0 Category=organism-gene. inducible T-cell costimulator (mouse) An inducible T-cell costimulator that is encoded in the genome of mouse. OMA:Q9WVS0 PRO:DNx CCLP (mouse) UniProtKB:Q9WVS0 CD278 (mouse) UniProtKB:Q9WVS0 CD28 and CTLA-4-like protein (mouse) UniProtKB:Q9WVS0 CD28-related protein 1 (mouse) UniProtKB:Q9WVS0 activation-inducible lymphocyte immunomediatory molecule (mouse) UniProtKB:Q9WVS0 mICOS PRO:DNx Ailim UniProtKB:Q9WVS0 CRP-1 (mouse) UniProtKB:Q9WVS0 Icos UniProtKB:Q9WVS0 A netrin-G1 that is encoded in the genome of human. UniProtKB:Q9Y2I2 hNTNG1 laminet-1 (human) protein KIAA0976 LMNT1 NTNG1 UNQ571/PRO1133 PR:Q9Y2I2 Category=organism-gene. netrin-G1 (human) A netrin-G1 that is encoded in the genome of human. PRO:DNx UniProtKB:Q9Y2I2 hNTNG1 PRO:DNx laminet-1 (human) UniProtKB:Q9Y2I2 KIAA0976 UniProtKB:Q9Y2I2 LMNT1 UniProtKB:Q9Y2I2 NTNG1 UniProtKB:Q9Y2I2 UNQ571/PRO1133 UniProtKB:Q9Y2I2 A prostaglandin D2 receptor DP2 that is encoded in the genome of human. DTO:02100741 Reactome:R-HSA-416895 UniProtKB:Q9Y5Y4 CD294 (human) G-protein coupled receptor 44 (human) chemoattractant receptor-homologous molecule expressed on Th2 cells (human) hPTGDR2 protein CRTH2 DL1R GPR44 PTGDR2 PR:Q9Y5Y4 Category=organism-gene. prostaglandin D2 receptor 2 (human) A prostaglandin D2 receptor DP2 that is encoded in the genome of human. PRO:WCB UniProtKB:Q9Y5Y4 Reactome:R-HSA-416895 PR:Q9Y5Y4 located_in GO:0005886 CD294 (human) UniProtKB:Q9Y5Y4 G-protein coupled receptor 44 (human) UniProtKB:Q9Y5Y4 chemoattractant receptor-homologous molecule expressed on Th2 cells (human) UniProtKB:Q9Y5Y4 hPTGDR2 PRO:DNx CRTH2 UniProtKB:Q9Y5Y4 DL1R UniProtKB:Q9Y5Y4 GPR44 UniProtKB:Q9Y5Y4 PTGDR2 UniProtKB:Q9Y5Y4 A tumor necrosis factor receptor superfamily member 11A that is encoded in the genome of human. UniProtKB:Q9Y6Q6 CD265 (human) ODFR (human) hTNFRSF11A osteoclast differentiation factor receptor (human) receptor activator of NF-KB (human) protein RANK TNFRSF11A PR:Q9Y6Q6 Category=organism-gene. tumor necrosis factor receptor superfamily member 11A (human) A tumor necrosis factor receptor superfamily member 11A that is encoded in the genome of human. PRO:WCB UniProtKB:Q9Y6Q6 CD265 (human) UniProtKB:Q9Y6Q6 ODFR (human) UniProtKB:Q9Y6Q6 hTNFRSF11A PRO:DNx osteoclast differentiation factor receptor (human) UniProtKB:Q9Y6Q6 receptor activator of NF-KB (human) UniProtKB:Q9Y6Q6 RANK UniProtKB:Q9Y6Q6 TNFRSF11A UniProtKB:Q9Y6Q6 An inducible T-cell costimulator that is encoded in the genome of human. UniProtKB:Q9Y6W8 CD278 (human) activation-inducible lymphocyte immunomediatory molecule (human) hICOS protein AILIM ICOS PR:Q9Y6W8 Category=organism-gene. inducible T-cell costimulator (human) An inducible T-cell costimulator that is encoded in the genome of human. PRO:WCB UniProtKB:Q9Y6W8 CD278 (human) UniProtKB:Q9Y6W8 activation-inducible lymphocyte immunomediatory molecule (human) UniProtKB:Q9Y6W8 hICOS PRO:DNx AILIM UniProtKB:Q9Y6W8 ICOS UniProtKB:Q9Y6W8 A CX3C chemokine receptor 1 that is encoded in the genome of mouse. UniProtKB:Q9Z0D9 C-X3-C CKR-1 (mouse) CX3CR1 (mouse) fractalkine receptor (mouse) mCX3CR1 protein Cx3cr1 PR:Q9Z0D9 Category=organism-gene. CX3C chemokine receptor 1 (mouse) A CX3C chemokine receptor 1 that is encoded in the genome of mouse. OMA:Q9Z0D9 PRO:DNx C-X3-C CKR-1 (mouse) UniProtKB:Q9Z0D9 CX3CR1 (mouse) UniProtKB:Q9Z0D9 fractalkine receptor (mouse) UniProtKB:Q9Z0D9 mCX3CR1 PRO:DNx Cx3cr1 UniProtKB:Q9Z0D9 A gamma-synuclein that is encoded in the genome of mouse. UniProtKB:Q9Z0F7 mSNCG persyn (mouse) protein Persyn Sncg PR:Q9Z0F7 Category=organism-gene. gamma-synuclein (mouse) A gamma-synuclein that is encoded in the genome of mouse. OMA:Q9Z0F7 PRO:DNx mSNCG PRO:DNx persyn (mouse) UniProtKB:Q9Z0F7 Persyn UniProtKB:Q9Z0F7 Sncg UniProtKB:Q9Z0F7 A prostaglandin D2 receptor DP2 that is encoded in the genome of mouse. UniProtKB:Q9Z2J6 CD294 (mouse) G-protein coupled receptor 44 (mouse) chemoattractant receptor-homologous molecule expressed on Th2 cells (mouse) mPTGDR2 protein Crth2 Gpr44 Ptgdr2 PR:Q9Z2J6 Category=organism-gene. prostaglandin D2 receptor 2 (mouse) A prostaglandin D2 receptor DP2 that is encoded in the genome of mouse. OMA:Q9Z2J6 PRO:DNx CD294 (mouse) UniProtKB:Q9Z2J6 G-protein coupled receptor 44 (mouse) UniProtKB:Q9Z2J6 chemoattractant receptor-homologous molecule expressed on Th2 cells (mouse) UniProtKB:Q9Z2J6 mPTGDR2 PRO:DNx Crth2 UniProtKB:Q9Z2J6 Gpr44 UniProtKB:Q9Z2J6 Ptgdr2 UniProtKB:Q9Z2J6 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 protein-coding sequence SO:0000010 Category=external. protein_coding An extent of biological sequence. located_sequence_feature sequence feature sequence located sequence feature SO:0000110 sequence_feature An extent of biological sequence. SO:ke signal peptide sequence signal SO:0000418 The signal peptide can be cleaved either co- or post-translationally. For this reason, we do not use the derives_from relation when defining protein forms lacking the signal peptide (because the precursor form might not yet exist at the time of removal). signal_peptide signal uniprot:feature_type A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. sequence SO:0000704 gene A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. SO:immuno_workshop sequence SO:0001062 propeptide protein coding gene sequence SO:0001217 protein_coding_gene 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 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 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 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 A light sensing organ composed of ommatidia The term compound eye is sometimes used for the multi-unit eyes of annelids, bivalves, echinoderms. We follow Richter et al and restrict this class to the arthropod structure for these structures BTO:0001921 FBbt:00004508 HAO:0000217 TGMA:0000024 uberon Facettenauge Komplexauge adult compound eye faceted eye insect eye zusammengesetztes Auge UBERON:0000018 compound eye https://github.com/obophenotype/uberon/issues/457 A light sensing organ composed of ommatidia FB:gg The term compound eye is sometimes used for the multi-unit eyes of annelids, bivalves, echinoderms. We follow Richter et al and restrict this class to the arthropod structure for these structures Facettenauge BTO:0001921 Komplexauge BTO:0001921 zusammengesetztes Auge BTO:0001921 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 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 The fluid surrounding the ovum and granulosa cells in the ovarian follicle. Generally, larger species such as ovine, equine, porcine, human, and bovine have larger follicles, with the fluid comprising a substantial proportion of the volume of the follicles at ovulation (estimated at >95% in bovine [3]). Smaller species such as rats and mice have smaller follicles with fractionally less follicular fluid[20164441] The follicular fluid contains sex steroids, glycoprotein hormones, plasma proteins, mucopolysaccharides, and enzymes and is rich in hyaluronic acid. BTO:0004383 CALOHA:TS-0728 FMA:18665 GAID:372 MA:0002511 MESH:D015571 NCIT:C52556 UMLS:C1709369 liquor follicularis liquor folliculi ovary follicle fluid uberon antral fluid, ovarian follicle liquor folliculi ovarian follicular fluid ovary follicular fluid UBERON:0000038 follicular fluid http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png The fluid surrounding the ovum and granulosa cells in the ovarian follicle. ISBN:145114847X MESH:D015571 UMLS:C1709369 ncithesaurus:Ovarian_Follicle_Fluid liquor follicularis FMA:18665 liquor folliculi ovary follicle fluid MA:0002511 liquor folliculi ovarian follicular fluid BTO:0004383 ovary follicular fluid BTO:0004383 Region of ovarian follicle filled with follicular fluid. EMAPA:37867 FMA:18675 antral cavity antrum folliculare ovarian follicle antrum uberon antrum follicularum UBERON:0000039 follicular antrum Region of ovarian follicle filled with follicular fluid. EMAPA:37867 MA:th antral cavity FMA:18675 antrum folliculare FMA:18675 ovarian follicle antrum GO:0001548 antrum follicularum 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 Sensory ganglia located on the dorsal spinal roots within the vertebral column. The spinal ganglion cells are pseudounipolar. The single primary branch bifurcates sending a peripheral process to carry sensory information from the periphery and a central branch which relays that information to the spinal cord or brain. (MSH) * ganglion found on the posterior root of each spinal nerve, composed of the unipolar nerve cell bodies of the sensory neurons of the nerve. (CSP) Trunk ganglion which is located adjacent to the spine on a dorsal root and contains the cell bodies of afferent sensory nerves.[TAO] 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] The sensory ganglia of spinal nerves arise only from the neural crest, whereas many sensory ganglia of the 'dorsal' cranial nerves arise from epibranchial placodes as well as the neural crest[DOI:10.1093/icb/icn065] MA and EMAPA introduce distinct classes for what appears to be the same thing UBERON:0026602 AAO:0011032 BIRNLEX:2596 BIRNLEX:2598 BTO:0001264 CALOHA:TS-0954 EFO:0000900 EHDAA2:0000418 EHDAA2:0001897 EHDAA:2899 EMAPA:16667 EMAPA:16668 EMAPA:18372 EV:0100373 FMA:5888 MA:0000231 MA:0000232 MAT:0000162 MIAA:0000162 NCIT:C12462 TAO:0000200 UMLS:C0017070 VHOG:0000222 XAO:0000210 ZFA:0000200 dorsal root ganglion ganglion of dorsal root ganglion spinalis spinal ganglion spinal ganglion part of peripheral nervous system uberon DRG dorsal root ganglia ganglion sensorium nervi spinalis ganglion spinale posterior root ganglion UBERON:0000044 dorsal root ganglion http://upload.wikimedia.org/wikipedia/commons/7/71/DRG_Chicken_e7.jpg MA ZFA Sensory ganglia located on the dorsal spinal roots within the vertebral column. The spinal ganglion cells are pseudounipolar. The single primary branch bifurcates sending a peripheral process to carry sensory information from the periphery and a central branch which relays that information to the spinal cord or brain. (MSH) * ganglion found on the posterior root of each spinal nerve, composed of the unipolar nerve cell bodies of the sensory neurons of the nerve. (CSP) BIRNLEX:2596 Trunk ganglion which is located adjacent to the spine on a dorsal root and contains the cell bodies of afferent sensory nerves.[TAO] 2012-08-14 TAO:0000200 TAO ZFIN:curator 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:0000222 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) MA and EMAPA introduce distinct classes for what appears to be the same thing FMA UMLS:C0017070 BIRNLEX:2596 UMLS:C0017070 ncithesaurus:Dorsal_Root_Ganglion dorsal root ganglion BTO:0001264 ganglion of dorsal root OBOL:automatic ganglion spinalis FMA:5888 spinal ganglion FMA:5888 spinal ganglion part of peripheral nervous system BIRNLEX:2598 DRG dorsal root ganglia ganglion sensorium nervi spinalis ganglion sensorium nervi spinalis BTO:0001264 ganglion spinale BTO:0001264 posterior root ganglion EMAPA:16668 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 BTO 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 C-shaped bundle of fibres (axons) in the brain, and carries signals from the hippocampus to the mammillary bodies and septal nuclei. It is typically divided into the columns (crus), body, commissure and the pre-commissural and post-commissural fornix (MM). fornix BAMS:f BIRNLEX:705 DHBA:10576 DMBA:17767 EMAPA:35352 FMA:61965 FMA:83865 HBA:9249 MA:0002747 NCIT:C32289 UMLS:C0152334 UMLS:C0458370 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=268 brain fornix cerebral fornix forebrain fornix fornix of neuraxis neuraxis fornix uberon fornix (column and body of fornix) fornix cerebri fornix hippocampus hippocampus fornix UBERON:0000052 fornix of brain http://upload.wikimedia.org/wikipedia/commons/2/21/Gray747.png NIFSTD A C-shaped bundle of fibres (axons) in the brain, and carries signals from the hippocampus to the mammillary bodies and septal nuclei. It is typically divided into the columns (crus), body, commissure and the pre-commissural and post-commissural fornix (MM). BIRNLEX:705 FMA:61965 inferred UMLS:C0152334 BIRNLEX:705 UMLS:C0458370 ncithesaurus:Cerebral_Fornix http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=268 BIRNLEX:705 forebrain fornix FMA:61965 fornix of neuraxis FMA:83865 neuraxis fornix FMA:83865 fornix (column and body of fornix) FMA:61965 fornix cerebri NeuroNames:268 Thickened areas of the saccule or utricle where the termination of the vestibular nerve occurs[MESH,modified]. this refers to the inner ear structure, not the macula of the retina. We follow ZFA in including a grouping class for the macula of utricle and sacule Patches of thickened, pseudostratified epithelium of the inner ear, consisting of regular arrays of sensory hair cells interspersed with supporting cells. Each patch has its own charcteristic shape and polarity pattern. (See Anatomical Atlas entry for sensory patches of the ear by T. Whitfield.)[TAO] macular GAID:777 MESH:D008267 TAO:0000386 ZFA:0000386 macula maculae sensory macula sensory patch uberon acoustic macula acoustic maculae UBERON:0000054 macula Thickened areas of the saccule or utricle where the termination of the vestibular nerve occurs[MESH,modified]. MESH:A09.246.631.909.625.125 Patches of thickened, pseudostratified epithelium of the inner ear, consisting of regular arrays of sensory hair cells interspersed with supporting cells. Each patch has its own charcteristic shape and polarity pattern. (See Anatomical Atlas entry for sensory patches of the ear by T. Whitfield.)[TAO] 2012-08-14 TAO:0000386 TAO ZFIN:curator maculae sensory macula ZFA:0000386 sensory patch ZFA:0000386 acoustic macula MESH:A09.246.631.909.625.125 acoustic maculae MESH:A09.246.631.909.625.125 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 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 A capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney[GO]. ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule? Melissa Haendel 2009-06-18T09:26:37Z glomerulus BTO:0000530 CALOHA:TS-0862 EFO:0003667 EMAPA:28329 EV:0100386 FMA:15624 MA:0001657 MESH:D007678 NCIT:C13250 TAO:0001288 UMLS:C0022663 ZFA:0001288 renal glomeruli uberon Malphigian glomerulus Malpighian glomerulus Malpighian tuft glomerular capillary tuft glomerular tuft glomerulus renis renal corpuscle UBERON:0000074 renal glomerulus Renal:corpuscle.svg http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg FMA MA A capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney[GO]. MP:0005325 ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule? ZFA UMLS:C0022663 ncithesaurus:Glomerulus renal glomeruli TAO:0001288 Malphigian glomerulus BTO:0000530 Malpighian glomerulus Malpighian tuft glomerular capillary tuft ZFA:0001288 glomerular tuft glomerulus renis renal corpuscle 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 Portion of tissue, that consists of single layer of cells connected to each other by cell junctions. Examples: layer of glial cells; epithelium. consider adding to caro layer NCIT:C66831 layer of cells uberon cell sheath sheath of cells UBERON:0000119 cell layer Portion of tissue, that consists of single layer of cells connected to each other by cell junctions. Examples: layer of glial cells; epithelium. layer NCIT:C66831 A layer of thin, concentrically arranged cells with interspersed collagen that lies within the epineurium. (Nolte, J., The Human Brain 3rd edition) Connective tissue surrounding a fascicle[Wikipedia:Perineurium]. perineurial consider FBbt:00007090 (perineurium): The outer two layers of glial cells that cover the central nervous system and the nerves. The outer layer is the perineurial sheath (sometimes referred to as the perineurial sheath outer layer); the inner layer is the sub-perineural glial sheath (sometimes referred to as the perineurial sheath inner layer) BTO:0003153 EMAPA:37849 FMA:52585 NCIT:C33302 NCIT:C41407 NLXANAT:090205 UMLS:C0205890 uberon UBERON:0000121 perineurium http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray636.png FMA A layer of thin, concentrically arranged cells with interspersed collagen that lies within the epineurium. (Nolte, J., The Human Brain 3rd edition) NLXANAT:090205 Connective tissue surrounding a fascicle[Wikipedia:Perineurium]. consider FBbt:00007090 (perineurium): The outer two layers of glial cells that cover the central nervous system and the nerves. The outer layer is the perineurial sheath (sometimes referred to as the perineurial sheath outer layer); the inner layer is the sub-perineural glial sheath (sometimes referred to as the perineurial sheath inner layer) FBbt EMAPA:37849 MA:th UMLS:C0205890 ncithesaurus:Perineurium 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 loose connective tissue sheath surrounding each peripheral nerve. Composed mainly of colagen and fibroblasts, it forms a substantial covering over nerve trunks, then thins to an incomplete layer around smaller branches near their terminations. The epineurium is continuous centrally with the dura. Peripherally, it usually ends near the termination of a nerve fiber, but it may continue as the capsule of Meissner corpuscles and a few other encapsulated endings. Nolte, J. The Human Brain 3rd edition outermost layer of connective tissue surrounding a peripheral nerve. It includes the blood vessels supplying the nerve. It consists of adipose tissue and fibrocollagenous tissues[Wikipedia:Epineurium]. BTO:0003154 EMAPA:37848 FMA:12234 NCIT:C32528 NLXANAT:090203 UMLS:C0205889 uberon UBERON:0000124 epineurium http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray636.png FMA A loose connective tissue sheath surrounding each peripheral nerve. Composed mainly of colagen and fibroblasts, it forms a substantial covering over nerve trunks, then thins to an incomplete layer around smaller branches near their terminations. The epineurium is continuous centrally with the dura. Peripherally, it usually ends near the termination of a nerve fiber, but it may continue as the capsule of Meissner corpuscles and a few other encapsulated endings. Nolte, J. The Human Brain 3rd edition NLXANAT:090203 outermost layer of connective tissue surrounding a peripheral nerve. It includes the blood vessels supplying the nerve. It consists of adipose tissue and fibrocollagenous tissues[Wikipedia:Epineurium]. EMAPA:37848 MA:th UMLS:C0205889 ncithesaurus:Epineurium 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 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 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 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 Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid. BTO:0000068 CALOHA:TS-0034 EMAPA:36771 ENVO:02000021 EV:0100123 FMA:305905 GAID:1155 MA:0002893 MESH:D000653 NCIT:C13188 UMLS:C0002638 VHOG:0001267 uberon acqua amnii liquor amnii UBERON:0000173 amniotic fluid Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid. ENVO:02000021 MP:MP UMLS:C0002638 ncithesaurus:Amniotic_Fluid acqua amnii BTO:0000068 liquor amnii BTO:0000068 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 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 Ventral part (base region) of the telencephalon. BTO term refers specifically to the avian structure cjm 2009-04-18T12:12:27Z BTO:0003401 DMBA:15751 EFO:0003522 TAO:0000304 ZFA:0000304 area ventralis telencephali subpallium ventral telencephalon subpallium uberon UBERON:0000204 ventral part of telencephalon separated by cell-free region Ventral part (base region) of the telencephalon. GO:0021544 GO_REF:0000021 ISBN:0471888893 BTO term refers specifically to the avian structure BTO area ventralis telencephali ZFA:0000304 subpallium GO:0021544 ZFA:0000304 ventral telencephalon ZFA:0000304 subpallium BTO:0003401 NCBITaxon:8782 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 the thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected A thin but tough extraembryonic membrane of reptiles, birds and mammals that lines the chorion and contains the fEtus and the amniotic fluid around it. [Biology_Online][VHOG] Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] amniotic BTO:0000065 CALOHA:TS-0033 EHDAA2:0000116 EHDAA:136 EMAPA:16109 EV:0100122 FMA:80223 GAID:1298 MESH:A16.254.403.277 NCIT:C12365 UMLS:C0002630 VHOG:0000721 amnios uberon UBERON:0000305 amnion http://upload.wikimedia.org/wikipedia/commons/e/e7/Gray14.png ISBN:0073040584 ISBN:0073040584-table5.4 ISBN:0073040584-table5.4 the thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected MGI:csmith MP:0005029 A thin but tough extraembryonic membrane of reptiles, birds and mammals that lines the chorion and contains the fEtus and the amniotic fluid around it. [Biology_Online][VHOG] 2012-09-17 VHOG:0000721 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:0000721 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187 UMLS:C0002630 ncithesaurus:Amnion amnios 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 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 Cartilage pertaining to the tibia. This class represents a portion of cartilage tissue located in the tibia, *not* the cartilaginous condensation of an emrbyonic tibia BTO:0000207 FMA:33923 tibial cartilage uberon cartilage of tibia UBERON:0000313 portion of cartilage tissue in tibia Cartilage pertaining to the tibia. Dorlands_Medical_Dictionary:MerckSource cartilage of tibia FMA:33923 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 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 A fibrous membrane, which, in the neck, represents the supraspinal ligaments of the upper vertebrae. In humans it is a tendon-like structure that has developed independently in humans and other animals well adapted for running. In some four legged animals, particularly ungulates, the nuchal ligament serves to sustain the weight of the head As it is required for running, not all animals have a nuchal ligament BTO:0000952 EMAPA:19207 FMA:13427 ligament of neck ligamentum nuchae paddywhack uberon paxwax UBERON:0000351 nuchal ligament BTO C7 in humans A fibrous membrane, which, in the neck, represents the supraspinal ligaments of the upper vertebrae. ligament of neck FMA:13427 ligamentum nuchae FMA:13427 paddywhack NCBITaxon:9895 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 An epithelial tissue layer that lines much of the urinary tract, including the renal pelvis, the ureters, the bladder, and parts of the urethra. urothelial transitional epithelium BTO:0003906 CALOHA:TS-1096 EMAPA:37978 FMA:63914 FMA:67695 GAID:935 MESH:D019459 NCIT:C12884 NCIT:C13318 UMLS:C0225339 UMLS:C0227598 epithelium transitionale transitional epithelium uroepithelium uberon UBERON:0000365 urothelium Harnblase:Urothel.png An epithelial tissue layer that lines much of the urinary tract, including the renal pelvis, the ureters, the bladder, and parts of the urethra. transitional epithelium EMAPA:37978 MA:th UMLS:C0225339 ncithesaurus:Transitional_Epithelium UMLS:C0227598 ncithesaurus:Urothelium epithelium transitionale FMA:63914 transitional epithelium FMA:63914 uroepithelium FMA:67695 The corpus striatum (striated body) is a compound structure consisting of the caudate nucleus and the lentiform nucleus, which consists of the putamen and the globus pallidus[WP]. Thus, certain telencephalic characters - such as the presence of a pallium divided into lateral, dorsal, and medial formations and a subpallium divided into striatum and septum - appear to characterize all vertebrates. They are primitive characters and are homologous among all vertebrates.[well established][VHOG] The term has been used in a few different ways: * It is a pair of nuclear masses which form the basal ganglia, along with the subthalamic nucleus and the substantia nigra. * It may also refer to both the basal ganglia and internal capsule collectively.[2] UBERON:0010082 BAMS:CSTR BTO:0001311 CALOHA:TS-0183 EFO:0000381 EHDAA2:0000596 EMAPA:17549 EV:0100184 FMA:77616 GAID:667 MESH:A08.186.211.730.885.105.487 NCIT:C12448 UMLS:C0010097 VHOG:0001175 uberon striate body striated body UBERON:0000369 * According to the 1917 version of Gray's Anatomy, it is the combination of the lentiform nucleus (also known as the lenticular nucleus) and the caudate nucleus * According to BrainInfo it is a part of the basal ganglia comprising the globus pallidus and striatum corpus striatum http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray656.png MA The corpus striatum (striated body) is a compound structure consisting of the caudate nucleus and the lentiform nucleus, which consists of the putamen and the globus pallidus[WP]. Thus, certain telencephalic characters - such as the presence of a pallium divided into lateral, dorsal, and medial formations and a subpallium divided into striatum and septum - appear to characterize all vertebrates. They are primitive characters and are homologous among all vertebrates.[well established][VHOG] 2012-09-17 VHOG:0001175 VHOG DOI:10.1146/annurev.ne.04.030181.001505, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.487 Figure 14-10 UMLS:C0010097 ncithesaurus:Corpus_Striatum striate body BTO:0001311 striated body BTO:0001311 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 Apocrine sweat glands are sweat glands composed of a coiled secretory portion located at the junction of the dermis and subcutaneous fat, from which a straight portion inserts and secretes into the infundibular portion of the hair follicle. The ducts of apocrine glands open into the canals of hair follicles. The stimulus for the secretion of apocrine sweat glands is adrenaline, which is a hormone carried in the blood[WP]. A note of confusion is the difference between apocrine secretion and apocrine sweat gland. Apocrine secretion refers to the apical loss of a cell's membrane to create cell blebs, thus creating a secretory product. Apocrine sweat gland refers to a structure, not a secretion process. Apocrine sweat glands actually use a merocrine type secretion, or that mediated by exocytosis of secretory granules. When 'apocrine gland' is used without the word sweat, it is often referring to the gland which uses merocrine secretion, and not the secretion method. The important difference in apocrine sweat gland structure is its larger lumen, compared to the more narrow lumen of the eccrine sweat gland. In humans, apocrine sweat glands are found only in certain locations of the body: the axillae (armpits), the areola of the nipples, and the genitoanal region. BTO:0001458 EMAPA:37426 FMA:59155 MESH:D001050 NCIT:C32132 UMLS:C0930083 glandula sudorifera apocrina uberon UBERON:0000382 apocrine sweat gland FMA The term apocrine sweat gland is a misnomer. While it was once thought that apocrine sweat glands were true apocrine glands, it is now known that they use merocrine excretion. However, they have retained the original name Wikipedia Apocrine sweat glands are sweat glands composed of a coiled secretory portion located at the junction of the dermis and subcutaneous fat, from which a straight portion inserts and secretes into the infundibular portion of the hair follicle. The ducts of apocrine glands open into the canals of hair follicles. The stimulus for the secretion of apocrine sweat glands is adrenaline, which is a hormone carried in the blood[WP]. EMAPA:37426 MA:th UMLS:C0930083 ncithesaurus:Apocrine_Sweat_Gland glandula sudorifera apocrina 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 The group of nerve cell bodies that conveys auditory sensation from the organ of Corti to the hindbrain and resides on the cochlear part of the vestibulocochlear nerve (eighth cranial nerve)[MP]. distributed to the hair cells of the spiral organ. The cochlear fibers arise in bipolar cells in the spiral ganglion in the modiolus. in BTO this is part of the cochlear modiolus, but this leads to the CG being in both the nervous and skeletal systems BAMS:GcVIII BTO:0001688 EHDAA2:0002198 EMAPA:17572 FMA:53445 GAID:722 MA:0001085 MESH:D013136 VHOG:0001183 Corti's ganglion cochlear part of vestibulocochlear ganglion ganglion of Corti spiral ganglion vestibulocochlear VIII ganglion cochlear component uberon ganglion cochlearis ganglion spirale ganglion spirale cochleae spiral ganglion of cochlea vestibulocochlear ganglion cochlear component UBERON:0000395 cochlear ganglion http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray903.png cell bodies BTO-modified Wikipedia The group of nerve cell bodies that conveys auditory sensation from the organ of Corti to the hindbrain and resides on the cochlear part of the vestibulocochlear nerve (eighth cranial nerve)[MP]. distributed to the hair cells of the spiral organ. The cochlear fibers arise in bipolar cells in the spiral ganglion in the modiolus. MP:0002855 Corti's ganglion FMA:53445 cochlear part of vestibulocochlear ganglion ganglion of Corti FMA:53445 spiral ganglion FMA:53445 vestibulocochlear VIII ganglion cochlear component MA:0001085 ganglion cochlearis BTO:0001688 ganglion spirale ganglion spirale cochleae BTO:0001688 spiral ganglion of cochlea BTO:0001688 vestibulocochlear ganglion cochlear component EMAPA:17572 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 Any portion of cartilage tissue that is part of the sternum FMA:32567 cartilage of sternum uberon UBERON:0000398 Examples: cartilage of manubrium, cartilage of xiphoid process cartilage tissue of sternum Any portion of cartilage tissue that is part of the sternum cartilage of sternum FMA:32567 A mucosa that is part of a jejunum [Automatically generated definition]. BTO:0001742 CALOHA:TS-0495 EMAPA:27109 FMA:14949 MA:0003214 jejunal mucous membrane jejunum mucosa jejunum mucosa of organ jejunum mucous membrane jejunum organ mucosa mucosa of jejunum mucosa of organ of jejunum mucous membrane of jejunum organ mucosa of jejunum uberon UBERON:0000399 jejunal mucosa A mucosa that is part of a jejunum [Automatically generated definition]. OBOL:automatic jejunal mucous membrane FMA:14949 jejunum mucosa FMA:14949 jejunum mucosa of organ OBOL:automatic jejunum mucous membrane OBOL:automatic jejunum organ mucosa OBOL:automatic mucosa of jejunum FMA:14949 mucosa of organ of jejunum OBOL:automatic mucous membrane of jejunum OBOL:automatic organ mucosa of jejunum OBOL:automatic An epithelium that is part of a jejunum. BTO:0001743 CALOHA:TS-0494 EMAPA:18668 FMA:17232 MA:0003215 epithelium of jejunum uberon UBERON:0000400 jejunal epithelium FMA An epithelium that is part of a jejunum. OBOL:automatic 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 The outer covering of the calvaria. It is composed of several layers: SKIN; subcutaneous connective tissue; the occipitofrontal muscle which includes the tendonous galea aponeurotica; Loose connective tissue; and the pericranium (the PERIOSTEUM of the SKULL). BTO:0001809 CALOHA:TS-0896 EMAPA:37949 FMA:46494 GAID:80 MESH:D012535 NCIT:C89807 OpenCyc:Mx4rwNtaz5wpEbGdrcN5Y29ycA UMLS:C0036270 galen:Scalp uberon scalpus UBERON:0000403 scalp Double:cowlick.jpg http://upload.wikimedia.org/wikipedia/commons/5/55/Layers_of_the_scalp_and_meninges.png BTO The outer covering of the calvaria. It is composed of several layers: SKIN; subcutaneous connective tissue; the occipitofrontal muscle which includes the tendonous galea aponeurotica; Loose connective tissue; and the pericranium (the PERIOSTEUM of the SKULL). MESH:A01.456.810 EMAPA:37949 MA:th UMLS:C0036270 ncithesaurus:Scalp scalpus One of a a paired bundle of nerve fibers plus ganglia that run from the base of the skull to the coccyx. AAO:0010791 BAMS:S BTO:0001834 CALOHA:TS-2049 EV:0100374 FMA:6258 XAO:0000211 gangliated cord sympathetic chain sympathetic ganglionic chain uberon truncus sympathicus UBERON:0000407 sympathetic trunk http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray847.png FMA-abduced-lr One of a a paired bundle of nerve fibers plus ganglia that run from the base of the skull to the coccyx. gangliated cord sympathetic chain FMA:6258 sympathetic ganglionic chain truncus sympathicus 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 mesodermal signaling center of the hair follicle consisting of closely packed specialized mesenchymal fibroblasts. Framed by the enlarged bulb matrix in anagen. consider adding grouping class for TAO:0001995 ! papilla In humans, at the surface of the skin in hands and feet, they appear as epidermal or papillary ridges (colloquially known as fingerprints) Blood vessels in the dermal papillae nourish all hair follicles and bring nutrients and oxygen to the lower layers of epidermal cells. ncit has 'hair papilla' as part of hypodermis BTO:0001858 CALOHA:TS-0431 EMAPA:36484 FMA:70737 NCIT:C32710 NCIT:C83189 UMLS:C0221931 dermal papillae follicular papilla uberon dermal papilla cell hair follicle dermal papilla hair papilla papilla corii papilla dermatis papilla dermis papilla of corium papillae dermis skin papilla UBERON:0000412 dermal papilla http://upload.wikimedia.org/wikipedia/commons/3/34/Skin.jpg A mesodermal signaling center of the hair follicle consisting of closely packed specialized mesenchymal fibroblasts. Framed by the enlarged bulb matrix in anagen. ncit has 'hair papilla' as part of hypodermis ncit UMLS:C0221931 ncithesaurus:Dermal_Papilla dermal papillae follicular papilla FMA:70737 dermal papilla cell BTO:0001858 hair follicle dermal papilla MP:0010687 papilla corii BTO:0001858 papilla dermatis BTO:0001858 papilla dermis BTO:0001858 papilla of corium BTO:0001858 papillae dermis skin papilla BTO:0001858 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 A merocrine, unbranched, unbranched, coiled, tubular gland sweat gland. In humans, distributed over almost all of the body surface, and promote cooling by evaporation of their secretion. in mice, found only on footpads; in humans, entire body including soles and palms BTO:0002323 FMA:59154 GAID:945 MA:0003039 MESH:D004439 NCIT:C32490 UMLS:C0013492 glandula sudorifera eccrina glandula sudorifera merocrina uberon eccrine gland merocrine sweat gland UBERON:0000423 eccrine sweat gland MGI:anna A merocrine, unbranched, unbranched, coiled, tubular gland sweat gland. In humans, distributed over almost all of the body surface, and promote cooling by evaporation of their secretion. UMLS:C0013492 ncithesaurus:Eccrine_Sweat_Gland glandula sudorifera eccrina glandula sudorifera merocrina eccrine gland FMA:59154 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 A plexus of autonomic nerve fibers within the wall of the digestive tube, and made up of the submucosal, myenteric, and subserosal plexuses; it contains visceral afferent fibers, sympathetic postganglionic fibers, parasympathetic preganglionic and postganglionic fibers, and parasympathetic postganglionic cell bodies. UBERON:0012372 BTO:0002437 EMAPA:35446 FMA:77597 MA:0001147 enteric nerve plexus intrinsic nerve plexus plexus entericus plexus nervosus entericus sympathetic enteric nerve plexus uberon UBERON:0000429 enteric plexus A plexus of autonomic nerve fibers within the wall of the digestive tube, and made up of the submucosal, myenteric, and subserosal plexuses; it contains visceral afferent fibers, sympathetic postganglionic fibers, parasympathetic preganglionic and postganglionic fibers, and parasympathetic postganglionic cell bodies. BTO:0002437 enteric nerve plexus FMA:77597 intrinsic nerve plexus MA:0001147 plexus entericus BTO:0002437 plexus nervosus entericus FMA:77597 FMA:TA sympathetic enteric nerve plexus FMA:77597 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 . introducing part_of to 'cortex of lymph node' as in issue 7 introduces equivalencies; the part_of has instead been added to 'lymph node follicle' BTO:0002684 FMA:55222 NCIT:C33040 UMLS:C0229654 lymphoid nodule nodular lymphoid tissue uberon folliculus lymphaticus lymphatic follicle lymphatic nodule nodulus lymphaticus nodulus lymphoideus UBERON:0000444 lymphoid follicle FMA . UMLS:C0229654 ncithesaurus:Lymphoid_Follicle lymphoid nodule FMA:55222 nodular lymphoid tissue FMA:55222 folliculus lymphaticus BTO:0002684 lymphatic follicle BTO:0002684 lymphatic nodule BTO:0002684 nodulus lymphaticus BTO:0002684 nodulus lymphoideus BTO:0002684 Gray matter structure located on the midline of the forebrain consisting of the septum pellucidum (in some species) and the septal nuclei (Heimer, 1996). Subdivision of the telencephalon on the midline between the lateral ventricles which contains the septum pellucidum and the septal nuclei[FMA][FMA:61842]. Se septum BAMS:SA BAMS:SEP BAMS:Sep BAMS:Spt BIRNLEX:963 BM:Tel-Spt BTO:0002705 EMAPA:32837 FMA:61842 MA:0000924 MESH:A08.186.211.577.750 UMLS:C0752060 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=255 area septalis septal area septum (NN) telencephalon septum uberon massa praecommissuralis septal region septum pellucidum (BNA,PNA) septum telencephali UBERON:0000446 septum of telencephalon Gray matter structure located on the midline of the forebrain consisting of the septum pellucidum (in some species) and the septal nuclei (Heimer, 1996). BIRNLEX:963 Subdivision of the telencephalon on the midline between the lateral ventricles which contains the septum pellucidum and the septal nuclei[FMA][FMA:61842]. FMA:61842 Se septum BIRNLEX:963 UMLS:C0752060 BIRNLEX:963 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=255 BIRNLEX:963 area septalis FMA:61842 FMA:TA septal area FMA:61842 septum (NN) FMA:61842 telencephalon septum FMA:61842 massa praecommissuralis NeuroNames:255 septal region BAMS:SEP septum pellucidum (BNA,PNA) NeuroNames:255 septum telencephali NeuroNames:255 The layer located below the cerebral cortex that includes the forebrain, midbrain and hindbrain. BTO:0002858 FMA:242188 NCIT:C98712 UMLS:C0815008 cerebral medulla uberon subcortex UBERON:0000454 cerebral subcortex The layer located below the cerebral cortex that includes the forebrain, midbrain and hindbrain. ncithesaurus:Cerebral_Subcortex UMLS:C0815008 ncithesaurus:Cerebral_Subcortex cerebral medulla FMA:242188 subcortex BTO:0002858 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 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. 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 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 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 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 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 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 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 A muscle that acts on the pharynx[WP, vetted]. A pharyngeal muscle is any muscle that forms part of the pharynx[GO]. BTO:0001048 EFO:0003504 EMAPA:18963 FMA:46619 GAID:154 MA:0001797 MESH:D010609 NCIT:C13075 TAO:0000172 UMLS:C0031346 ZFA:0000172 branchial muscle muscle of pharynx muscle organ of pharynx pharynx muscle pharynx muscle organ uberon branchial muscles musculi pharyngis musculus pharyngis tunica muscularis pharyngis UBERON:0000933 Innervation notes: They are innervated by the pharyngeal branch of the Vagus nerve (CN X) with the exception of the stylopharyngeus muscle which is innervated by the glossopharyngeal nerve (CN IX).[WP] pharyngeal muscle http://upload.wikimedia.org/wikipedia/commons/3/35/Gray1030.png A muscle that acts on the pharynx[WP, vetted]. A pharyngeal muscle is any muscle that forms part of the pharynx[GO]. 2012-06-30 GO:0043282 does not quite work for some muscles such as stylopharyngeus GO GOC:go_curators UMLS:C0031346 ncithesaurus:Pharyngeal_Muscle branchial muscle ZFA:0000172 muscle organ of pharynx OBOL:automatic pharynx muscle organ OBOL:automatic branchial muscles TAO:0000172 musculi pharyngis musculus pharyngis BTO:0001048 tunica muscularis pharyngis Cranial nerve fiber tract which is comprised of retinal ganglion cell axons running posterior medially towards the optic chiasm, at which some of the axons cross the midline and after which the structure is termed the optic tract. Transmits visual information from the retina to the brain[ZFA]. Do not classify under 'cranial nerve', as this is not a true nerve - should be classified as evaginated sensory afferent[ISBN:0471888893] A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO] Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO] (...) 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 (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG] (relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon 2n optic nerve AAO:0010345 BAMS:2n BAMS:IIn BAMS:nII BIRNLEX:1640 CALOHA:TS-0713 DHBA:15544 EFO:0004258 EHDAA2:0001313 EHDAA:6788 EMAPA:17575 FMA:50863 GAID:831 HBA:9307 MA:0001097 MBA:848 MESH:D009900 NCIT:C12761 OpenCyc:Mx4rvVjLm5wpEbGdrcN5Y29ycA TAO:0000435 UMLS:C0029130 VHOG:0000543 XAO:0000188 ZFA:0000435 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=289 02 optic nerve cranial II nervus opticus nervus opticus [II] optic II optic II nerve optic nerve [II] second cranial nerve uberon CN-II nerve II optic UBERON:0000941 cranial nerve II EHDAA2 Cranial nerve fiber tract which is comprised of retinal ganglion cell axons running posterior medially towards the optic chiasm, at which some of the axons cross the midline and after which the structure is termed the optic tract. Transmits visual information from the retina to the brain[ZFA]. ISBN:0471209627 ISBN:0471888893 A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000435 TAO ZFIN:curator Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO] 2012-06-20 AAO:0010345 AAO AAO:EJS (...) 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 (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000543 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429, http://medical-dictionary.thefreedictionary.com/optic+stalk (relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon MA 2n BIRNLEX:1640 NIFSTD:NeuroNames_abbrevSource optic nerve FMA:50863 ZFA:0000435 UMLS:C0029130 BIRNLEX:1640 UMLS:C0029130 ncithesaurus:Optic_Nerve http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=289 BIRNLEX:1640 02 optic nerve AAO:0010345 nervus opticus nervus opticus [II] FMA:50863 FMA:TA optic II EHDAA2:0001313 optic II nerve EHDAA2:0001313 CN-II ZFA:0000435 nerve II NeuroNames:289 optic TAO:0000435 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. 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 stomach chamber uberon anterior intestine gaster mesenteron ventriculus 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 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 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] 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 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 Any of a number of short transversospinal muscles chiefly developed in cervical, lumbar, and thoracic regions, arising from the transverse process of one vertebra and inserted into the root of the spinous process of the next two or three vertebrae above, with nerve supply from the dorsal branches of the spinal nerve, and whose actions rotate the vertebral column. rotator muscle FMA:23081 uberon UBERON:0000951 rotator muscle of the vertebral column Any of a number of short transversospinal muscles chiefly developed in cervical, lumbar, and thoracic regions, arising from the transverse process of one vertebra and inserted into the root of the spinous process of the next two or three vertebrae above, with nerve supply from the dorsal branches of the spinal nerve, and whose actions rotate the vertebral column. rotator muscle FMA:23081 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 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 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 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 Any thin layer or plate. TODO - merge with cell layer? laminar laminar tissue uberon UBERON:0000957 lamina http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png Any thin layer or plate. 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 A decussation of the diencephalon where the fibers of the optic nerve cross The point at which fibers of the optic nerves cross.[AAO] The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG] AAO:0010622 BAMS:DC BAMS:OC BAMS:och BAMS:ox BIRNLEX:1416 BM:Tel-OCX DHBA:10644 DMBA:17783 EHDAA2:0001302 EHDAA:10227 EMAPA:17603 FMA:62045 GAID:832 HBA:9310 MA:0001098 MBA:117 MESH:D009897 NCIT:C90609 TAO:0000556 UMLS:C0029126 VHOG:0000190 XAO:0004071 ZFA:0000556 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=459 chiasma opticum decussation of optic nerve fibers optic chiasm uberon chiasma chiasma nervorum opticorum optic chiasm (Rufus of Ephesus) UBERON:0000959 optic chiasma http://upload.wikimedia.org/wikipedia/commons/b/b3/1543%2CVisalius%27OpticChiasma.jpg A decussation of the diencephalon where the fibers of the optic nerve cross MGI:llw2 MP:0009770 The point at which fibers of the optic nerves cross.[AAO] 2012-06-20 AAO:0010622 AAO AAO:DSM The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG] 2012-09-17 VHOG:0000190 VHOG DOI:10.1016/j.preteyeres.2005.04.005 Jeffery G, Erskine L, Variations in the architecture and development of the vertebrate optic chiasm. Progress in retinal and eye research (2005) UMLS:C0029126 BIRNLEX:1416 UMLS:C0029126 ncithesaurus:Optic_Chiasm http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=459 BIRNLEX:1416 chiasma opticum decussation of optic nerve fibers FMA:62045 optic chiasm chiasma NeuroNames:459 chiasma nervorum opticorum NeuroNames:459 optic chiasm (Rufus of Ephesus) NeuroNames:459 The thoracic ganglia are paravertebral ganglia. The thoracic portion of the sympathetic trunk typically has 12 thoracic ganglia. Emerging from the ganglia are thoracic splancic nerves (the cardiopulmonary, the greater, lesser, and least splanchic nerves) that help provide sympathetic innervation to abdominal structures. Also, the ganglia of the thoracic sympathetic trunk have both white and gray rami communicantes. The white rami carry sympathetic fibers arising in the spinal cord into the sympathetic trunk. [WP,unvetted]. BTO:0001831 EHDAA:4664 EMAPA:17158 FMA:6471 MA:0001159 NCIT:C52829 RETIRED_EHDAA2:0002012 UMLS:C0229010 VHOG:0000515 ganglion of thorax ganglion thoracicum splanchnicum thoracic paravertebral ganglion thoracic splanchnic ganglion thoracic sympathetic ganglion thorax ganglion uberon UBERON:0000961 thoracic ganglion http://upload.wikimedia.org/wikipedia/commons/3/3e/Gray849.png The thoracic ganglia are paravertebral ganglia. The thoracic portion of the sympathetic trunk typically has 12 thoracic ganglia. Emerging from the ganglia are thoracic splancic nerves (the cardiopulmonary, the greater, lesser, and least splanchic nerves) that help provide sympathetic innervation to abdominal structures. Also, the ganglia of the thoracic sympathetic trunk have both white and gray rami communicantes. The white rami carry sympathetic fibers arising in the spinal cord into the sympathetic trunk. [WP,unvetted]. UMLS:C0229010 ncithesaurus:Thoracic_Ganglion ganglion of thorax OBOL:automatic ganglion thoracicum splanchnicum FMA:6471 FMA:TA thoracic paravertebral ganglion MA:0001159 thorax ganglion OBOL:automatic 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 this term should be ceded to the arthropod anatomy ontology FBbt:00004114 MAT:0000204 MIAA:0000204 uberon UBERON:0000963 head sensillum 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 An organ that detects light. 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) 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 uberon light-detecting organ visual apparatus UBERON:0000970 eye An organ that detects light. visual apparatus EV:0100336 The smallest morphological and functional unit of the compound eye that consists of a usually limited and often constant number of rhabdomeric photoreceptor cells, cornea-secreting epithelial cells, and interommatidial pigment cells, and may additionally contain crystalline cone cells. ommatidial BTO:0001922 FBbt:00004510 HAO:0000666 MAT:0000143 MIAA:0000143 omatidium uberon omatidia UBERON:0000971 ommatidium The smallest morphological and functional unit of the compound eye that consists of a usually limited and often constant number of rhabdomeric photoreceptor cells, cornea-secreting epithelial cells, and interommatidial pigment cells, and may additionally contain crystalline cone cells. omatidia 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 A midventral endochondral skeletal element which represents the origin site of the pectoral muscles[PHENOSCAPE:ad]. in EMAPA and EHDAA2 this is part of the skeleton of pectoral girdle; the classic def of pectoral girdle (see WP) excludes the rib cage and sternum Single element that constitutes the postzonal area of the pectoral girdle.[AAO] relationship loss: part_of postzonal element (AAO:0000938)[AAO] Fishes lack a sternum. (...) A sternum is absent in the first fossil tetrapods, but it is present in modern amphibians. (...) Thus, a sternum occurs in some modern amphibians, birds, mammals and archosaurs. However, its absence in the common ancestors to these groups means that it has arisen independently several times within the field of the midventral connective tissue.[well established][VHOG] sternal It probably first evolved in early tetrapods as an extension of the pectoral girdle; it is not found in fish. In amphibians and reptiles it is typically a shield-shaped structure, often composed entirely of cartilage. It is absent in both turtles and snakes. In birds it is a relatively large bone and typically bears an enormous projecting keel to which the flight muscles are attached. Only in mammals does the sternum take on the elongated, segmented form seen in humans. In some mammals, such as opossums, the individual segments never fuse and remain separated by cartilagenous plates throughout life in birds, either ratite (no keel or carina) or carinate (keel and carina present) While its developmental origins are similar to the ribs (from the myospetum and septum of the trunk region), it is often associated with the pectoral skeleton, due to both function and physical connections (i.e. the coracoid of archosaurs). It may be a single element or a series of smaller structure (sternebrae). Based on Kardong 2012. [PHENOSCAPE:ad]. AAO:0000765 BTO:0001302 CALOHA:TS-0972 EHDAA2:0001914 EHDAA:9561 EMAPA:18344 FMA:7485 GAID:246 MA:0001331 MESH:D013249 NCIT:C12793 OpenCyc:Mx4rvVjO6JwpEbGdrcN5Y29ycA UMLS:C0038293 VHOG:0000856 galen:Sternum vertebrate sternum uberon breastbone UBERON:0000975 sternum http://upload.wikimedia.org/wikipedia/commons/1/12/Illu_thoracic_cage.jpg ISBN:0073040584 FMA A midventral endochondral skeletal element which represents the origin site of the pectoral muscles[PHENOSCAPE:ad]. PHENOSCAPE:ad Single element that constitutes the postzonal area of the pectoral girdle.[AAO] 2012-06-20 AAO:0000765 AAO AAO:LAP relationship loss: part_of postzonal element (AAO:0000938)[AAO] 2012-06-20 AAO:0000765 AAO Fishes lack a sternum. (...) A sternum is absent in the first fossil tetrapods, but it is present in modern amphibians. (...) Thus, a sternum occurs in some modern amphibians, birds, mammals and archosaurs. However, its absence in the common ancestors to these groups means that it has arisen independently several times within the field of the midventral connective tissue.[well established][VHOG] 2012-09-17 VHOG:0000856 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.294 While its developmental origins are similar to the ribs (from the myospetum and septum of the trunk region), it is often associated with the pectoral skeleton, due to both function and physical connections (i.e. the coracoid of archosaurs). It may be a single element or a series of smaller structure (sternebrae). Based on Kardong 2012. [PHENOSCAPE:ad]. WP UMLS:C0038293 ncithesaurus:Sternum breastbone BTO:0001302 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 The major preaxial endochondral bone in the posterior zeugopod[Phenoscape]. One of the two long bones of endochondral origin of the hind-epipodium; it is a straight, simple bone whose section is more or less rectangular at the ends and circular at its central portion.[AAO] AAO:0000890 BTO:0001252 CALOHA:TS-1048 EFO:0003054 EMAPA:19142 FMA:24476 GAID:204 MA:0001361 MESH:A02.835.232.500.883 NCIT:C12800 OpenCyc:Mx4rvtq3-ZwpEbGdrcN5Y29ycA UMLS:C0040184 galen:Tibia shankbone shinbone uberon UBERON:0000979 tibia http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray260.png The major preaxial endochondral bone in the posterior zeugopod[Phenoscape]. PHENOSCAPE:mah One of the two long bones of endochondral origin of the hind-epipodium; it is a straight, simple bone whose section is more or less rectangular at the ends and circular at its central portion.[AAO] 2012-06-20 AAO:0000890 AAO AAO:LAP UMLS:C0040184 ncithesaurus:Tibia shankbone shinbone 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 Vein that drains the axilla In human anatomy, the axillary vein is a large blood vessel that conveys blood from the lateral aspect of the thorax, axilla (armpit) and upper limb toward the heart. There is one axillary vein on each side of the body. Its origin is at the lower margin of the teres major muscle and a continuation of the brachial vein. Its tributaries include the basilic vein and cephalic vein, which are both superficial veins. It terminates at the lateral margin of the first rib, at which it becomes the subclavian vein. It is accompanied along its course by a similarly named artery, the axillary artery EMAPA:18758 FMA:13329 GAID:527 MA:0002084 MESH:D001367 NCIT:C32171 OpenCyc:Mx4rwLSHK5wpEbGdrcN5Y29ycA UMLS:C0004456 galen:AxillaryVein vena axillaris uberon subcostal vein UBERON:0000985 axillary vein http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray576.png Vein that drains the axilla In human anatomy, the axillary vein is a large blood vessel that conveys blood from the lateral aspect of the thorax, axilla (armpit) and upper limb toward the heart. There is one axillary vein on each side of the body. Its origin is at the lower margin of the teres major muscle and a continuation of the brachial vein. Its tributaries include the basilic vein and cephalic vein, which are both superficial veins. It terminates at the lateral margin of the first rib, at which it becomes the subclavian vein. It is accompanied along its course by a similarly named artery, the axillary artery WP UMLS:C0004456 ncithesaurus:Axillary_Vein vena axillaris 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 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 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 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 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 A group of axons linking two or more neuropils and having a common origin, termination[FBbt]. White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO) BIRNLEX:1649 EV:0100304 FBbt:00005100 FMA:83847 NLX:147822 axonal tract neuraxis tract tract of neuraxis nerve tract uberon nerve tract tract UBERON:0001018 WP says this is the analog of peripheral nerves in CNS. axon tract A group of axons linking two or more neuropils and having a common origin, termination[FBbt]. White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO) neuraxis tract FMA:83847 tract of neuraxis FMA:83847 nerve tract BIRNLEX:1649 A slender neuron projection bundle[FBbt]; A bundle of anatomical fibers, as of muscle or nerve (American Heritage Dictionary 4th ed). note FBbt class not disjoint from tract. Consider merging with 'neuron projection bundle' fascicle BIRNLEX:872 BTO:0002191 EMAPA:36605 FBbt:00005101 FMA:12235 NCIT:C32586 TGMA:0000088 UMLS:C1185741 fasciculus nerve bundle nerve fasciculus neural fasciculus uberon nerve fiber tract UBERON:0001019 nerve fasciculus A slender neuron projection bundle[FBbt]; A bundle of anatomical fibers, as of muscle or nerve (American Heritage Dictionary 4th ed). BIRNLEX:872 FBbt:00005101 fascicle FBbt:00005101 UMLS:C1185741 ncithesaurus:Fascicle fasciculus nerve bundle FMA:12235 nerve fasciculus FMA:12235 neural fasciculus FMA:12235 nerve fiber tract BTO:0002191 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 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 A tubule that extends from the posterior part of the digestive tract which absorbs solutes, water, and wastes from the surrounding hemolymph. Each tubule consists of a single layer of cells that is closed off at the distal end with the proximal end joining the alimentary canal at the junction between the midgut and hindgut[WP,modified]. this will be ceded to the Arthropod Anatomy Ontology It is unclear as to whether the Malpighian tubules of arachnids and those of the Uniramia are homologous or the result of convergent evolution.[Wikipedia:Malpighian_tubule_system] BTO:0000810 EFO:0000243 FBbt:00005786 GAID:1228 MAT:0000123 MESH:D008317 MIAA:0000123 TADS:0000163 TGMA:0001038 uberon Malphigian tube Malpighian tube tuba Malpighii UBERON:0001054 Malpighian tubule GO A tubule that extends from the posterior part of the digestive tract which absorbs solutes, water, and wastes from the surrounding hemolymph. Each tubule consists of a single layer of cells that is closed off at the distal end with the proximal end joining the alimentary canal at the junction between the midgut and hindgut[WP,modified]. Malphigian tube BTO:0000810 Malpighian tube UBERON:cjm tuba Malpighii BTO:0000810 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 A extension of a neural arches dorsal to the neural canal[TAO,modified]. Elaboration of the mid-dorsal keel into a posterior or posterolateral process.[AAO] Neural spines are extensions of neural arches dorsal to the neural canal in the median skeletogenous septum. Neural spines are typically unpaired median structures but can be paired in some instances, e.g., in the abdominal region of basal teleosts such as Leptolepis, Elops, Megalops, and Hiodon).[TAO] Small, posteriorly directed process at the posterior margin of each neural arch lamina; it is not a neural spine.[AAO] relationship loss: part_of mid-dorsal keel (AAO:0000735)[AAO] The spinous process of a vertebra is directed backward and downward from the junction of the laminae (in humans), and serves for the attachment of muscles and ligaments. In animals without an erect stance, the process points upward and may slant forward or backward. Spinous processes are exaggerated in some animals, such as the extinct Dimetrodon and Spinosaurus, where they form a sail- or finback. [Wikipedia:Spinous_process] spinous process AAO:0000705 EMAPA:25107 FMA:11948 MA:0001455 NCIT:C116112 TAO:0001336 ZFA:0001336 neuracanthe@fr processus spinosus processus spinosus vertebrae spinous process of vertebra vertebra spinous process épine neurale@fr uberon neural spine neural spines spine of verterba UBERON:0001076 neural spine http://upload.wikimedia.org/wikipedia/commons/4/48/Processusspinosusvertebrae.png A extension of a neural arches dorsal to the neural canal[TAO,modified]. TAO:0001336 Elaboration of the mid-dorsal keel into a posterior or posterolateral process.[AAO] 2012-06-20 AAO:0000705 AAO AAO:Pugener_and_Maglia_2008 Neural spines are extensions of neural arches dorsal to the neural canal in the median skeletogenous septum. Neural spines are typically unpaired median structures but can be paired in some instances, e.g., in the abdominal region of basal teleosts such as Leptolepis, Elops, Megalops, and Hiodon).[TAO] 2012-08-14 TAO:0001336 TAO ZFIN:curator Small, posteriorly directed process at the posterior margin of each neural arch lamina; it is not a neural spine.[AAO] 2012-06-20 AAO:0000739 AAO AAO:Pugener_2002 relationship loss: part_of mid-dorsal keel (AAO:0000735)[AAO] 2012-06-20 AAO:0000705 AAO neuracanthe@fr TAO:0001336 spinous process of vertebra FMA:11948 vertebra spinous process MA:0001455 épine neurale@fr TAO:0001336 neural spines ZFA:0001336 spine of verterba FMA:11948 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 The Pectoralis minor is a thin, triangular muscle, situated at the upper part of the chest, beneath the Pectoralis major. [WP,unvetted]. EHDAA2:0001425 EHDAA:8313 EMAPA:18180 FMA:13109 MA:0002355 NCIT:C33285 UMLS:C0224347 VHOG:0000902 pectoralis minor muscle supracoracoideus supracoracoideus muscle uberon musculus pectoralis minor UBERON:0001100 pectoralis minor Pectoralis:minor.png FMA third to fifth ribs near their costal cartilages dbpedia medial border and superior surface of the coracoid process of the scapula dbpedia The Pectoralis minor is a thin, triangular muscle, situated at the upper part of the chest, beneath the Pectoralis major. [WP,unvetted]. UMLS:C0224347 ncithesaurus:Pectoralis_Minor supracoracoideus supracoracoideus muscle musculus pectoralis minor A paired dermal or endochondral bone that is part of the pectoral girdle. The clavicle may be in contact with the interclavicle or coracoid and forms an attachment site for pectoral musculature. [PHENOSCAPE:ad]. Slender, paired bones of intramembranous origin that invest the anterior margins of the procoracoids.[AAO] relationship loss: part_of zonal element (AAO:0000936)[AAO] In early tetrapods, the connecting skull bone, the posttemporal, and adjoining shoulder bones, supracleithrum and postcleithrum (=anocleithrum), are absent, leaving a dermal shoulder girdle composed of the remaining ventral elements: the paired cleithrum and clavicle, and an unpaired midventral interclavicle that joins both halves of the girdle across the midline. (...) Several dermal elements of the shoulder persist in early synapsids. The clavicle and interclavicle are present in therapsids and monotremes, but in marsupials and placentals, the interclavicle is absent, the clavicle often is reduced in size, and the scapula becomes the predominant shoulder element.[well established][VHOG] clavicular The clavicle first appears as part of the skeleton in primitive bony fish, where it is associated with the pectoral fin; they also have a bone called the cleithrum. In such fish, the paired clavicles run behind and below the gills on each side, and are joined by a solid symphysis on the fish's underside. They are, however, absent in cartilagenous fish and in the vast majority of living bony fish, including all of the teleosts[ISBN 0-03-910284-X]. In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal. FMA and MA differ in whether they consider this part of the shoulder AAO:0000761 EMAPA:18721 FMA:13321 GAID:182 MA:0001329 MESH:D002968 MFMO:0000047 NCIT:C12695 OpenCyc:Mx4rvVjijZwpEbGdrcN5Y29ycA UMLS:C0008913 VHOG:0000849 VSAO:0005031 galen:Clavicle clavicle clavicula collar bone collarbone uberon UBERON:0001105 clavicle bone Pectoral:girdles-en.svg FMA mah ISBN:978-0-12-319060-4 from secondary cartilage of fusion ISBN:978-0-12-319060-4 A paired dermal or endochondral bone that is part of the pectoral girdle. The clavicle may be in contact with the interclavicle or coracoid and forms an attachment site for pectoral musculature. [PHENOSCAPE:ad]. PHENOSCAPE:ad Slender, paired bones of intramembranous origin that invest the anterior margins of the procoracoids.[AAO] 2012-06-20 AAO:0000761 AAO AAO:LAP relationship loss: part_of zonal element (AAO:0000936)[AAO] 2012-06-20 AAO:0000761 AAO In early tetrapods, the connecting skull bone, the posttemporal, and adjoining shoulder bones, supracleithrum and postcleithrum (=anocleithrum), are absent, leaving a dermal shoulder girdle composed of the remaining ventral elements: the paired cleithrum and clavicle, and an unpaired midventral interclavicle that joins both halves of the girdle across the midline. (...) Several dermal elements of the shoulder persist in early synapsids. The clavicle and interclavicle are present in therapsids and monotremes, but in marsupials and placentals, the interclavicle is absent, the clavicle often is reduced in size, and the scapula becomes the predominant shoulder element.[well established][VHOG] 2012-09-17 VHOG:0000849 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.330-333 and Figure 9.18 In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal. ISBN:978-0-12-319060-4 FMA and MA differ in whether they consider this part of the shoulder FMA UMLS:C0008913 ncithesaurus:Clavicle clavicle VSAO:0005031 clavicula VSAO:0005031 The latissimus dorsi is the larger, flat, dorso-lateral muscle on the trunk, posterior to the arm, and partly covered by the trapezius on its median dorsal region. [WP,unvetted]. In humans it inserts along a roughened line deep in the groove. In other mammals (most, I believe) it is an actual projection, the latissimus dorsi process [FEED:rd] [https://github.com/obophenotype/uberon/issues/1192] EFO:0003067 EHDAA2:0000932 EHDAA:8307 EMAPA:18178 FMA:13357 MA:0002331 NCIT:C33150 UMLS:C0224362 VHOG:0000930 dorsal latissimus muscle latissimi dorsi latissimus dorsi musculus latissimus dorsi uberon musculus latissimus dorsi UBERON:0001112 Dorsal group[Kardong] latissimus dorsi muscle Latissimus:dorsi.png EHDAA2 EHDAA2 spinous processes of thoracic T7-T12 thoracolumbar fascia iliac crest and inferior 3 or 4 ribs inferior angle of scapula dbpedia floor of intertubercular groove of the humerus dbpedia dbpedia dbpedia The latissimus dorsi is the larger, flat, dorso-lateral muscle on the trunk, posterior to the arm, and partly covered by the trapezius on its median dorsal region. [WP,unvetted]. UMLS:C0224362 ncithesaurus:Musculus_Latissimus_Dorsi latissimi dorsi musculus latissimus dorsi 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 The serratus ventralis is a muscle that originates on the surface of the upper eight or nine ribs at the side of the chest and inserts along the entire anterior length of the medial border of the scapula. [WP,unvetted]. EHDAA2:0001832 EHDAA:9463 EMAPA:18525 FMA:13397 MA:0002378 NCIT:C53014 OpenCyc:Mx4rvWn_D5wpEbGdrcN5Y29ycA UMLS:C1710059 VHOG:0000679 Boxer's muscle serratus anterior serratus anterior muscle serratus ventralis muscle uberon musculus serratus anterior serratus lateralis UBERON:0001125 serratus ventralis Serratus:anterior.png long thoracic nerve dbpedia EHDAA2 fleshy slips from the outer surface of upper 8 or 9 ribs dbpedia costal aspect of medial margin of the scapula dbpedia dbpedia The serratus ventralis is a muscle that originates on the surface of the upper eight or nine ribs at the side of the chest and inserts along the entire anterior length of the medial border of the scapula. [WP,unvetted]. UMLS:C1710059 ncithesaurus:Serratus_Ventralis serratus anterior VHOG:0000679 musculus serratus anterior serratus lateralis 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 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 fundus is the portion of the stomach that lies above the cardiac notch, and contains the fundic glands[GO, Kardong]. The greater curvature of the stomach. [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] BTO:0000502 EFO:0002554 EHDAA2:0001919 EHDAA:4844 EMAPA:17886 FMA:14559 GAID:320 MA:0001612 MESH:A03.492.766.419 NCIT:C12257 UMLS:C0017129 VHOG:0000421 galen:GastricFundus fundus gastricus (ventricularis) gastric fundus stomach fundus uberon fundus gastricus fundus gastricus ventricularis fundus ventricularis fundus ventriculi UBERON:0001160 fundus of stomach http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg The fundus is the portion of the stomach that lies above the cardiac notch, and contains the fundic glands[GO, Kardong]. GO:0014825 ISBN:0073040584 The greater curvature of the stomach. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000421 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:0000421 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 UMLS:C0017129 ncithesaurus:Fundus_of_the_Stomach fundus gastricus BTO:0000502 fundus gastricus ventricularis BTO:0000502 fundus ventricularis BTO:0000502 fundus ventriculi BTO:0000502 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 whole length of the small intestine except the superior part of the duodenum. It also supplies the cecum and the ascending part of the colon and about half the transverse part of the colon. It arises from the anterior surface of the aorta below the celiac artery at the level of the first lumbar vertebra. Origin: abdominal aorta; branches, inferior pancreaticoduodenal, jejunal, ileal, ileocolic, right colic, and middle colic arteries; distribution: small intestine, proximal half of colon BTO:0002303 EHDAA2:0001949 EHDAA:3358 EHDAA:5313 EMAPA:18619 FMA:14749 GAID:502 MA:0002005 MESH:D017538 NCIT:C33685 OpenCyc:Mx4rwE5KipwpEbGdrcN5Y29ycA UMLS:C0162861 VHOG:0000754 galen:SuperiorMesentericArtery superior mesenteric arterial tree uberon arteria mesenterica superior UBERON:0001182 superior mesenteric artery http://upload.wikimedia.org/wikipedia/commons/6/68/Gray1099.png http://upload.wikimedia.org/wikipedia/commons/c/c0/Superior_mesenteric_a.gif Mesenteric artery that supplies the whole length of the small intestine except the superior part of the duodenum. It also supplies the cecum and the ascending part of the colon and about half the transverse part of the colon. It arises from the anterior surface of the aorta below the celiac artery at the level of the first lumbar vertebra. MESH:A07.231.114.565.755 Origin: abdominal aorta; branches, inferior pancreaticoduodenal, jejunal, ileal, ileocolic, right colic, and middle colic arteries; distribution: small intestine, proximal half of colon BTO UMLS:C0162861 ncithesaurus:Superior_Mesenteric_Artery arteria mesenterica superior arteria mesenterica superior BTO:0002303 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 middle colic artery is a branch of the superior mesenteric artery that mostly supplies the transverse colon. It arises just below the pancreas, and, passing downward and forward between the layers of the transverse mesocolon, divides into two branches: right and left. The right branch anastomoses with the right colic artery The left branch anastomoses with the left colic artery, a branch of the inferior mesenteric artery. The arches thus formed are placed about two fingers' breadth from the transverse colon, to which they distribute branches. [WP,unvetted]. EMAPA:37106 FMA:14810 MA:0002007 NCIT:C52981 UMLS:C0226328 galen:MiddleColicArtery uberon arteria colica media UBERON:0001196 middle colic artery http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray537.png The middle colic artery is a branch of the superior mesenteric artery that mostly supplies the transverse colon. It arises just below the pancreas, and, passing downward and forward between the layers of the transverse mesocolon, divides into two branches: right and left. The right branch anastomoses with the right colic artery The left branch anastomoses with the left colic artery, a branch of the inferior mesenteric artery. The arches thus formed are placed about two fingers' breadth from the transverse colon, to which they distribute branches. [WP,unvetted]. EMAPA:37106 MA:th UMLS:C0226328 ncithesaurus:Middle_Colic_Artery arteria colica media The Ileocolic Artery is the lowest branch arising from the concavity of the superior mesenteric artery. It passes downward and to the right behind the peritoneum toward the right iliac fossa, where it divides into a superior and an inferior branch; the inferior anastomoses with the end of the superior mesenteric artery, the superior with the right colic artery. Supplies the cecum, ileum, and appendix. [WP,unvetted]. EMAPA:37083 FMA:14815 MA:0001970 NCIT:C32760 UMLS:C0226323 galen:IleocolicArtery uberon arteria ileocolica UBERON:0001197 ileocolic artery http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray536.png The Ileocolic Artery is the lowest branch arising from the concavity of the superior mesenteric artery. It passes downward and to the right behind the peritoneum toward the right iliac fossa, where it divides into a superior and an inferior branch; the inferior anastomoses with the end of the superior mesenteric artery, the superior with the right colic artery. Supplies the cecum, ileum, and appendix. [WP,unvetted]. EMAPA:37083 MA:th UMLS:C0226323 ncithesaurus:Ileo-colic_Artery arteria ileocolica 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 the protruding lymphoid tissue located on the mucosa of the intestine that is composed of densely packed B cell follicles Reptiles have accumulations of lymphocytes in their guts that may be primitive Peyer's patches (Zapata and Solas). FMA has [set of?] [aggregated,small] lymphoid [follice,nodule] of [colon, SI, I, etc] Pp is a syn for Aggregated lymphoid follicle of small intestine; but MA uses Pp as covering both SI and LI. MA also includes follicle as a part. WP says duodenum and jejunum lack PPs BTO:0001784 CALOHA:TS-0780 EFO:0001381 EMAPA:19028 GAID:950 MA:0000137 MESH:A10.549.598 NCIT:C12771 UMLS:C0031272 noduli lymphoidei aggregati uberon Peyers gland Peyers patch aggregated lymphoid follicle of intestine aggregated lymphoid nodule UBERON:0001211 Peyer's patch FMA MA check this the protruding lymphoid tissue located on the mucosa of the intestine that is composed of densely packed B cell follicles MESH:A10.549.600 MP:0000696 FMA has [set of?] [aggregated,small] lymphoid [follice,nodule] of [colon, SI, I, etc] FMA Pp is a syn for Aggregated lymphoid follicle of small intestine; but MA uses Pp as covering both SI and LI. MA also includes follicle as a part. WP says duodenum and jejunum lack PPs MA UMLS:C0031272 ncithesaurus:Peyer_s_Patch noduli lymphoidei aggregati Peyers gland BTO:0001784 Peyers patch BTO:0001784 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 A tributary of the superior mesenteric vein that drains the jejunum. EMAPA:37160 FMA:15402 MA:0002153 uberon venae jejunales UBERON:0001216 jejunal vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png FMA FMA/obol A tributary of the superior mesenteric vein that drains the jejunum. EMAPA:37160 MA:th venae jejunales 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 The ileocolic vein is a vein which drains the ileum, colon, and cecum. [WP,unvetted]. EMAPA:37150 FMA:15408 MA:0002141 NCIT:C53047 UMLS:C0226744 uberon vena ileocolica UBERON:0001219 ileocolic vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png The ileocolic vein is a vein which drains the ileum, colon, and cecum. [WP,unvetted]. EMAPA:37150 MA:th UMLS:C0226744 ncithesaurus:Ileocolic_Vein vena ileocolica 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 Tip of renal pyramid projecting into a minor calyx. BTO:0003925 EMAPA:35727 FMA:15622 MA:0002730 MESH:D007679 NCIT:C33460 UMLS:C0022666 galen:RenalPapilla kidney papilla uberon UBERON:0001228 renal papilla Kidney:PioM.png Tip of renal pyramid projecting into a minor calyx. UMLS:C0022666 ncithesaurus:Renal_Papilla kidney papilla MP:0011303 the structure containing the glomerular capsule and the glomerulus that serves as the initial blood-filtering component of a nephron A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO] A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO] The part of the nephron that filters blood.[TAO] BTO:0000333 CALOHA:TS-1317 EMAPA:28236 EMAPA:35726 EV:0100385 FMA:15625 MA:0000376 NCIT:C33456 TAO:0005281 UMLS:C0227635 VHOG:0001262 ZFA:0005281 Malphigian corpuscle Malpighian corpuscle corpusculum renale uberon corpusculum renis cortical renal corpuscle kidney corpuscle UBERON:0001229 Together, the Bowmans capsule and the glomerulus comprise the definitive renal corpuscle. http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron renal corpuscle Renal:corpuscle.svg MA ZFA the structure containing the glomerular capsule and the glomerulus that serves as the initial blood-filtering component of a nephron ISBN:0-683-40008-8 MP:0002827 A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO] 2012-11-28 BTO:0000333 BTO BTO:curator A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO] 2012-11-28 XAO:0000146 XAO XAO:curator The part of the nephron that filters blood.[TAO] 2012-08-14 TAO:0005281 TAO ZFIN:curator UMLS:C0227635 ncithesaurus:Renal_Corpuscle Malphigian corpuscle MA:0000376 Malpighian corpuscle ZFA:0005281 corpusculum renale corpusculum renis cortical renal corpuscle MA:0000376 kidney corpuscle A cup-like sac at the expanded beginning of a tubular component of a nephron that contains the glomerulus Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO] Fluids from blood in the glomerulus are collected in the Bowman's capsule and further processed along the nephron to form urine. This process is known as ultrafiltration[WP]. One fold of the S-shaped body gives rise to Bowman's capsule[GUDMAP] AAO:0010526 BTO:0002297 EMAPA:27973 EMAPA:28257 FMA:15626 KUPO:0001001 MA:0001660 NCIT:C32225 TAO:0005254 TAO:0005310 UMLS:C0524448 ZFA:0005254 ZFA:0005310 Bowman's capsule Bowmans capsule capsula glomerularis renal glomerular capsule uberon Bowman's capsule Malphigian capsule Malpighian capsule Mueller capsule Muellerian capsule capsula glomeruli pronephric glomerular capsule UBERON:0001230 glomerular capsule http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg A cup-like sac at the expanded beginning of a tubular component of a nephron that contains the glomerulus MGI:pvb MP:0002828 Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO] 2012-06-20 AAO:0010526 AAO AAO:BJB UMLS:C0524448 ncithesaurus:Bowman_s_Capsule Bowman's capsule Bowmans capsule KUPO:0001001 capsula glomerularis renal glomerular capsule TAO:0005254 Bowman's capsule TAO:0005254 Malphigian capsule BTO:0002297 Malpighian capsule UBERO:cjm Mueller capsule BTO:0002297 Muellerian capsule BTO:0002297 capsula glomeruli pronephric glomerular capsule TAO:0005310 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 A chromaffin paraganglion located at the bifurcation of the aorta or at the origin of the inferior mesenteric artery. EMAPA:18223 FMA:15647 GAID:444 MA:0001137 MESH:D010220 NCIT:C25316 UMLS:C0442134 organ of Zuckerkandl paraganglion of Zuckerkandl uberon para-aortic body paraganglia of Zuckerkandl UBERON:0001237 The largest chromaffin paraganglia, and the largest source of circulating catecholamines in the fetus and young infants, and gradually atrophies to microscopic loci[WP] paraaortic body http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png A chromaffin paraganglion located at the bifurcation of the aorta or at the origin of the inferior mesenteric artery. UMLS:C0442134 ncithesaurus:Paraaortic paraganglion of Zuckerkandl EMAPA:18223 paraganglia of Zuckerkandl 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 the tubular intestinal glands found in the mucosal membranes of the small intestine EMAPA:35777 FMA:15693 MA:0001552 NCIT:C33565 UMLS:C0227267 crypt of Lieberkuhn of small bowel crypt of Lieberkuhn of small intestine intestinal gland of small bowel intestinal gland of small intestine lieberkuhn crypt of small bowel lieberkuhn crypt of small intestine small bowel crypt of Lieberkuhn small bowel intestinal gland small bowel lieberkuhn crypt small intestinal crypt of Lieberkuhn small intestine crypt of Lieberkuhn small intestine intestinal gland small intestine lieberkuhn crypt uberon UBERON:0001241 crypt of Lieberkuhn of small intestine the tubular intestinal glands found in the mucosal membranes of the small intestine ISBN:0-683-40008-8 MP:0004841 UMLS:C0227267 ncithesaurus:Small_Intestinal_Crypt_of_Lieberkuhn crypt of Lieberkuhn of small bowel OBOL:automatic crypt of Lieberkuhn of small intestine OBOL:automatic intestinal gland of small bowel OBOL:automatic intestinal gland of small intestine OBOL:automatic lieberkuhn crypt of small bowel OBOL:automatic lieberkuhn crypt of small intestine OBOL:automatic small bowel crypt of Lieberkuhn OBOL:automatic small bowel intestinal gland OBOL:automatic small bowel lieberkuhn crypt OBOL:automatic small intestine crypt of Lieberkuhn OBOL:automatic small intestine intestinal gland OBOL:automatic small intestine lieberkuhn crypt 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 The area of the white pulp where the affinity maturation of B cells and the generation of memory B cells and plasma cells occur UBERON:0003969 EMAPA:35804 MA:0002672 NCIT:C33602 UMLS:C1519475 Malpighian body lymphatic follicle of spleen lymphoid follicle of spleen lymphoid nodule of spleen spleen B cell follicle spleen lymphoid follicle splenic B cell follicle splenic lymphatic follicle splenic lymphoid follicle uberon spleen lymphoid nodule UBERON:0001249 spleen lymphoid follicle CL:tm MA FMA The area of the white pulp where the affinity maturation of B cells and the generation of memory B cells and plasma cells occur CL:tm MP:0008470 UMLS:C1519475 ncithesaurus:Splenic_Lymphoid_Follicle Malpighian body FMA:15843 lymphatic follicle of spleen FMA:15843 lymphoid follicle of spleen FMA:15843 lymphoid nodule of spleen FMA:15843 spleen B cell follicle CL:tm spleen lymphoid follicle MA:0002672 splenic B cell follicle CL:tm splenic lymphatic follicle FMA:15843 spleen lymphoid nodule MA:0002672 the parenchymatous tissue network of the spleen that consists of loose plates or cords (sinuses) infiltrated with red blood cells where most of the blood filtration occurs and degenerate erythrocytes are removed from the circulation CALOHA:TS-1263 EMAPA:35806 FMA:15844 MA:0000756 NCIT:C12992 UMLS:C0229687 pulpa rubra red pulp spleen red pulp splenic red pulp uberon pulpa splenica UBERON:0001250 red pulp of spleen http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png the parenchymatous tissue network of the spleen that consists of loose plates or cords (sinuses) infiltrated with red blood cells where most of the blood filtration occurs and degenerate erythrocytes are removed from the circulation MGI:csmith MP:0002356 UMLS:C0229687 ncithesaurus:Splenic_Red_Pulp pulpa rubra FMA:15844 FMA:TA pulpa splenica the zone between the red and white pulp of the spleen containing numerous macrophages and lymphocytes, and a rich plexus of sinusoids supplied by white pulp arterioles carrying blood-borne antigens WP says - (Some sources consider it to be the part of red pulp which borders on the white pulp, while other sources consider it to be neither red pulp nor white pulp.) - we use the adjacency relation here so it overlaps neither. FMA considers this an anatomical line. marginal zone CALOHA:TS-2395 EMAPA:36650 FMA:15852 MA:0000755 NCIT:C49767 UMLS:C1711368 junctional zone of spleen spleen marginal zone uberon UBERON:0001251 marginal zone of spleen http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png the zone between the red and white pulp of the spleen containing numerous macrophages and lymphocytes, and a rich plexus of sinusoids supplied by white pulp arterioles carrying blood-borne antigens ISBN:0-683-40008-8 MP:0002362 WP says - (Some sources consider it to be the part of red pulp which borders on the white pulp, while other sources consider it to be neither red pulp nor white pulp.) - we use the adjacency relation here so it overlaps neither. FMA considers this an anatomical line. FMA marginal zone UMLS:C1711368 ncithesaurus:Marginal_Zone spleen marginal zone MA:0000755 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 The luminal epithelium of the tube that conducts the urine from the renal pelvis to the bladder[MP] MP treats ureter urothelium and ureter luminal urothelium as exact synonyms, yes MA treats these as distinct; see also: transitional epithelium vs urothelium EMAPA:28089 FMA:15897 MA:0002655 transitional epithelium of ureter ureter transitional epithelium ureter urothelium uberon ureter luminal urothelium UBERON:0001254 urothelium of ureter The luminal epithelium of the tube that conducts the urine from the renal pelvis to the bladder[MP] MP:0000535 MP treats ureter urothelium and ureter luminal urothelium as exact synonyms, yes MA treats these as distinct; see also: transitional epithelium vs urothelium MP ureter luminal urothelium MP:0000535 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 smooth triangular region of the wall of the urinary bladder formed by the two ureteral orifices and the internal urethral orifice; it is an area in which the muscle fibers are closely adherent to the mucosa The area is very sensitive to expansion and once stretched to a certain degree, the urinary bladder signals the brain of its need to empty. The signals become stronger as the bladder continues to fill. Embryologically, the trigone of the bladder is derived from the caudal end of mesonephric ducts, which is of mesodermal origin (the rest of the bladder is endodermal). In the female the mesonephric ducts regresses, causing the trigone to be less prominent, but still present EMAPA:35174 FMA:15910 MA:0002492 NCIT:C12331 UMLS:C0447586 galen:TrigoneOfUrinaryBladder Lieutaud's trigone bladder trigone deep trigone musculus trigoni vesicae profundus trigone of bladder trigonum vesicae urinary bladder trigone vesical trigone uberon dorsal bladder neck trigonum vesicae urinariae UBERON:0001257 trigone of urinary bladder Illu:bladder.jpg the smooth triangular region of the wall of the urinary bladder formed by the two ureteral orifices and the internal urethral orifice; it is an area in which the muscle fibers are closely adherent to the mucosa MGI:anna MP:0011768 Embryologically, the trigone of the bladder is derived from the caudal end of mesonephric ducts, which is of mesodermal origin (the rest of the bladder is endodermal). In the female the mesonephric ducts regresses, causing the trigone to be less prominent, but still present WP UMLS:C0447586 ncithesaurus:Bladder_Trigone musculus trigoni vesicae profundus FMA:15910 FMA:TA trigonum vesicae FMA:15910 FMA:TA dorsal bladder neck EMAPA:35174 trigonum vesicae urinariae 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 An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. 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 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 structure found in the red pulp of the spleen between the sinusoids, consisting of fibrils and connective tissue cells with a large population of monocytes and macrophages. These cords contain half of the human body's monocytes as a reserve so that after tissue injury these monocytes can move in and aid locally sourced monocytes in wound healing. Erythrocytes pass through the cords of Billroth before entering the sinusoids. The passage into the sinusoids may be seen as a bottleneck, where erythrocytes need to be flexible in order to pass through. In disorders of erythrocyte shape and/or flexibility, such as hereditary spherocytosis, erythrocytes fail to pass through and get phagocytosed, causing extravascular hemolysis. EMAPA:37752 FMA:16031 MA:0002671 NCIT:C33599 UMLS:C0735011 cord of Billroth cord of Bilroth uberon UBERON:0001266 splenic cord MA A structure found in the red pulp of the spleen between the sinusoids, consisting of fibrils and connective tissue cells with a large population of monocytes and macrophages. These cords contain half of the human body's monocytes as a reserve so that after tissue injury these monocytes can move in and aid locally sourced monocytes in wound healing. Erythrocytes pass through the cords of Billroth before entering the sinusoids. The passage into the sinusoids may be seen as a bottleneck, where erythrocytes need to be flexible in order to pass through. In disorders of erythrocyte shape and/or flexibility, such as hereditary spherocytosis, erythrocytes fail to pass through and get phagocytosed, causing extravascular hemolysis. EMAPA:37752 MA:th UMLS:C0735011 ncithesaurus:Splenic_Cord cord of Billroth cord of Bilroth FMA:16031 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 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 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 A narrow chalice-shaped cavity between the glomerular and capsular epithelium of the glomerular capsule of the kidney[TFD]. Between the visceral and parietal layers, into which the filtrate enters after passing through the podocytes' filtration slits[WP]. luminal region between the glomerular capsule visceral and parietal layers, into which filtrate enters after passing through the filtration barrier from the glomerular capillaries[MP] TODO - fix ZFA Space between the renal glomerulus and the glomerular capsule. Renal filtrate collects here then passes into the renal tubule.[TAO] EMAPA:27985 EMAPA:28263 FMA:17676 MA:0001664 NCIT:C33840 TAO:0005283 TAO:0005312 UMLS:C0227643 ZFA:0005283 ZFA:0005312 Bowman's space capsular space glomerular capsule space glomerular urinary space inter-glomerular space pronephric capsular space renal capsular space urinary space urinary space of renal corpuscle uberon Bowmanb%s space UBERON:0001286 Bowman's space A narrow chalice-shaped cavity between the glomerular and capsular epithelium of the glomerular capsule of the kidney[TFD]. Between the visceral and parietal layers, into which the filtrate enters after passing through the podocytes' filtration slits[WP]. luminal region between the glomerular capsule visceral and parietal layers, into which filtrate enters after passing through the filtration barrier from the glomerular capillaries[MP] MP:0011499 Space between the renal glomerulus and the glomerular capsule. Renal filtrate collects here then passes into the renal tubule.[TAO] 2012-08-14 TAO:0005283 TAO ZFIN:curator Space between the renal glomerulus and the glomerular capsule. Renal filtrate collects here then passes into the renal tubule.[TAO] 2012-08-14 TAO:0005312 TAO ZFIN:curator UMLS:C0227643 ncithesaurus:Urinary_Space capsular space glomerular capsule space MP:0011499 glomerular urinary space MP:0011499 inter-glomerular space ZFA:0005283 inter-glomerular space ZFA:0005312 pronephric capsular space ZFA:0005312 renal capsular space ZFA:0005283 urinary space of renal corpuscle EMAPA:28263 Bowmanb%s space TAO:0005312 The proximal convoluted tubule is the most proximal portion of the proximal tubule and extends from the glomerular capsule to the proximal straight tubule. Renal tubule that connects to the renal corpuscle.[TAO] CALOHA:TS-2198 EMAPA:28287 EV:0100388 FMA:17693 MA:0001669 NCIT:C33417 TAO:0005290 UMLS:C1514580 ZFA:0005290 proximal convoluted renal tubule tubulus contortus proximalis uberon 1st convoluted tubule PCT first convoluted tubule kidney proximal convoluted tubule renal proximal convoluted tubule tubulus contortus proximalis tubulus convolutus proximalis UBERON:0001287 proximal convoluted tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png MA MA uses subclass GOC:mtg_kidney_jan10 GO Wikipedia The proximal convoluted tubule is the most proximal portion of the proximal tubule and extends from the glomerular capsule to the proximal straight tubule. GO:0072019 Renal tubule that connects to the renal corpuscle.[TAO] 2012-08-14 TAO:0005290 TAO ZFIN:curator UMLS:C1514580 ncithesaurus:Proximal_Convoluted_Tube kidney proximal convoluted tubule EMAPA:28287 renal proximal convoluted tubule tubulus contortus proximalis tubulus convolutus proximalis the section of the renal tubule in the kidney medulla with a hairpin bend; consists of a descending limb and an ascending limb, and is situated between the proximal convoluted tubule to the distal convoluted tubule; it functions to reabsorb water and ions from the urine the definitions of some kidney parts (e.g. proximal straight tubule) refer to Henle's loop, even in species where this may not be present. Requires review. A highly specialized segment of the mammalian kidney tubules, that dips into the medulla. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.648, see_Liem_KF][VHOG] The structure differs considerably between species; there is a definite physical loop of Henle in the mammalian and avian renal systems but this seems to be absent in Xenopus. However, homologs of some, but not all, molecular markers (e.g. cldn8 and clcnk) of the mammalian loop of Henle were found to be present in the pronephros of the frog larva . The loop of Henle plays an important role in creating a concentration gradient in the medulla of the kidney. It is involved in reabsorption of filtered water and ions including sodium, potassium and calcium, and independently regulates both the volume and osmolarity of body fluids. BTO:0004608 EMAPA:19280 EV:0100390 FMA:17698 GAID:437 MA:0001675 MESH:D008138 NCIT:C33006 UMLS:C0023986 VHOG:0001270 Henle loop Henle's loop ansa nephroni uberon UBERON:0001288 loop of Henle http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png the section of the renal tubule in the kidney medulla with a hairpin bend; consists of a descending limb and an ascending limb, and is situated between the proximal convoluted tubule to the distal convoluted tubule; it functions to reabsorb water and ions from the urine MGI:csmith MP:0004755 A highly specialized segment of the mammalian kidney tubules, that dips into the medulla. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.648, see_Liem_KF][VHOG] 2012-09-17 VHOG:0001270 VHOG The structure differs considerably between species; there is a definite physical loop of Henle in the mammalian and avian renal systems but this seems to be absent in Xenopus. However, homologs of some, but not all, molecular markers (e.g. cldn8 and clcnk) of the mammalian loop of Henle were found to be present in the pronephros of the frog larva . The loop of Henle plays an important role in creating a concentration gradient in the medulla of the kidney. It is involved in reabsorption of filtered water and ions including sodium, potassium and calcium, and independently regulates both the volume and osmolarity of body fluids. UMLS:C0023986 ncithesaurus:Loop_of_Henle ansa nephroni the portion of the renal tubule that constitutes the proximal part of the loop of Henle, has low permeability to ions and urea, and is highly permeable to water; it consists of an initial short thick segment lined by low simple cuboidal epithelium and a long thin segment lined by simple squamous epithelium; however, this distinction is not as important physiologically as in the ascending limb, so often the two are treated as one structure descending limb EMAPA:35511 FMA:17705 MA:0001679 NCIT:C32456 UMLS:C0227657 descending limb of Henle's loop loop of Henle descending limb uberon UBERON:0001289 descending limb of loop of Henle http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png FMA FMA the portion of the renal tubule that constitutes the proximal part of the loop of Henle, has low permeability to ions and urea, and is highly permeable to water; it consists of an initial short thick segment lined by low simple cuboidal epithelium and a long thin segment lined by simple squamous epithelium; however, this distinction is not as important physiologically as in the ascending limb, so often the two are treated as one structure MGI:anna MP:0011341 UMLS:C0227657 ncithesaurus:Descending_Limb_of_the_Henle_s_Loop The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule. TODO - is S3 exactly coincident with PST? todo - ensure relationships work across species (loop of Henle) Portion of the renal tubule which is just posterior to the proximal convoluted tubule.[TAO] UBERON:0005166 BTO:0000055 EMAPA:29661 EMAPA:29669 FMA:17716 MA:0002614 TAO:0005291 ZFA:0005291 S3 thick descending limb of proximal tubule tubulus rectus proximalis uberon pars recta pars recta tubuli renalis proximal tubule segment 3 segment 3 of proximal tubule UBERON:0001290 proximal straight tubule MA MA MA uses subclass GOC:mtg_kidney_jan10 MA The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule. GO:0072020 Portion of the renal tubule which is just posterior to the proximal convoluted tubule.[TAO] 2012-08-14 TAO:0005291 TAO ZFIN:curator S3 GO:0072020 pars recta tubuli renalis BTO:0000055 proximal tubule segment 3 MA:0002614 segment 3 of proximal tubule EMAPA:29661 the distal sub-portion of the ascending loop of Henle which is lined by simple cuboidal epithelium and enters the renal cortex to empty a hypotonic filtrate into the distal convoluted tubule TODO - thick/thin check. Also - does the loop of Henle overlap the distal convoluted tubule? FMA divides DCT into straight and convoluted portions EMAPA:28396 EMAPA:29671 EMAPA:35512 FMA:17722 MA:0001677 ascending thick limb distal straight tubule loop of Henle ascending limb thick segment straight portion of distal convoluted renal tubule straight portion of distal convoluted tubule thick ascending limb thick ascending limb of Henle's loop thick ascending limb of distal tubule tubulus rectus distalis uberon tubulus rectus distalis UBERON:0001291 thick ascending limb of loop of Henle http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png MA the distal sub-portion of the ascending loop of Henle which is lined by simple cuboidal epithelium and enters the renal cortex to empty a hypotonic filtrate into the distal convoluted tubule MGI:anna MP:0011344 distal straight tubule MA:0001677 loop of Henle ascending limb thick segment MA:0001677 straight portion of distal convoluted tubule FMA:17722 thick ascending limb of distal tubule FMA:17722 tubulus rectus distalis FMA:17722 tubulus rectus distalis The first segment of the nephron lying just downstream from the loop of Henle, immediately after the macula densa. a portion of kidney nephron between the loop of Henle and the collecting duct system[Wikipedia:Distal_convoluted_tubule]. in humans it is responsible for the reabsorption of about 5% of filtered sodium via the thiazide-sensitive Na-Cl symporter. EMAPA:28393 EV:0100389 FMA:17721 MA:0001666 NCIT:C32469 UMLS:C0022676 distal convoluted renal tubule tubulus contortus distalis uberon second convoluted tubule tubulus contortus distalis tubulus convolutus distalis UBERON:0001292 distal convoluted tubule Kidney:nephron.png MA EMAPA GO MA-modified-from-isa The first segment of the nephron lying just downstream from the loop of Henle, immediately after the macula densa. GO:0072025 a portion of kidney nephron between the loop of Henle and the collecting duct system[Wikipedia:Distal_convoluted_tubule]. UMLS:C0022676 ncithesaurus:Distal_Convoluted_Tubule tubulus contortus distalis tubulus convolutus distalis The renal outer medulla is the region of the kidney that lies between the renal cortex and the renal inner medulla[GO]. BTO:0001746 CALOHA:TS-0508 EMAPA:28310 FMA:17733 MA:0001653 outer renal medulla outer zone of medulla of kidney outer zone of renal medulla renal outer medulla zona externa (medullaris renalis) zona externa medullae renalis uberon kidney outer medulla set of outer region of renal pyramids UBERON:0001293 outer medulla of kidney The renal outer medulla is the region of the kidney that lies between the renal cortex and the renal inner medulla[GO]. GOC:mtg_kidney_jan10 renal outer medulla BTO:0001746 zona externa (medullaris renalis) FMA:17733 FMA:TA zona externa medullae renalis FMA:17733 FMA:TA kidney outer medulla BTO:0001746 set of outer region of renal pyramids FMA:17733 Innermost region of the mammalian kidney. unique to mammals BTO:0001745 CALOHA:TS-0506 EMAPA:28349 FMA:17734 MA:0001652 inner renal medulla inner zone of medulla of kidney inner zone of renal medulla renal inner medulla set of inner region of renal pyramids zona interna (medullaris renalis) zona interna medullae renalis uberon kidney inner medulla UBERON:0001294 inner medulla of kidney Innermost region of the mammalian kidney. GO:0072053 unique to mammals GO:0072053 renal inner medulla BTO:0001745 zona interna (medullaris renalis) FMA:17734 FMA:TA zona interna medullae renalis FMA:17734 FMA:TA kidney inner medulla BTO:0001745 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 the smooth muscle coat of the uterus, which forms the main mass of the organ and surrounds and supports the endometrium The muscular wall of the uterus. [TFD][VHOG] In all mammals, the uterus develops as a specialization of the paramesonephric or Müllerian ducts, which gives rise to the infundibula, oviducts, uterus, cervix, and anterior vagina. Morphogenetic events common to development of all uteri include: 1) differentiation and growth of the myometrium, 2) differentiation and morphogenesis of the endometrial glands, and 3) organization and stratification of endometrial stroma. Uterine development is initiated in the fetus, but is only completed postnatally with differentiation and development of the endometrial glands.[well established][VHOG] myometrial The myometrium stretches (the smooth muscle cells expand in both size and number) during pregnancy to allow for the harboring of the pregnancy, and contracts in a coordinated fashion during the process of labor. After delivery the myometrium contracts to expel the placenta and reduce blood loss. BTO:0000907 CALOHA:TS-0652 EFO:0001970 EMAPA:29923 EV:0100116 FMA:17743 GAID:171 MA:0000391 MESH:D009215 NCIT:C12314 UMLS:C0027088 VHOG:0001281 tunica muscularis (myometrium) uberon tunica muscularis uterine myometrium uterine smooth muscle UBERON:0001296 myometrium Illu:cervix.jpg FMA the smooth muscle coat of the uterus, which forms the main mass of the organ and surrounds and supports the endometrium MESH:A02.633.570.500 MGI:brs MP:0008256 The muscular wall of the uterus. [TFD][VHOG] 2012-09-17 VHOG:0001281 VHOG In all mammals, the uterus develops as a specialization of the paramesonephric or Müllerian ducts, which gives rise to the infundibula, oviducts, uterus, cervix, and anterior vagina. Morphogenetic events common to development of all uteri include: 1) differentiation and growth of the myometrium, 2) differentiation and morphogenesis of the endometrial glands, and 3) organization and stratification of endometrial stroma. Uterine development is initiated in the fetus, but is only completed postnatally with differentiation and development of the endometrial glands.[well established][VHOG] 2012-09-17 VHOG:0001281 VHOG PMID:15471813 Spencer TE, Bazer FW, Uterine and placental factors regulating conceptus growth in domestic animals. Journal of Animal Science (2004) UMLS:C0027088 ncithesaurus:Myometrium tunica muscularis uterine myometrium BTO:0000907 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 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 spherical aggregation of cells in the ovary that contains a single oocyte[WP,modified]. TODO - align subtypes based on staging, which is taxon-specific Oocyte development of zebrafish has been divided into five stages based on morphological criteria and on physiological and biochemical events. Stage I follicles (less than 140 microns) are primary growth stage, stage II follicles (140-340 microns) are cortical alveolus stage, stage III (340-690 microns) are vitellogenesis, stage IV (690-730 microns) are oocyte maturation, and stage V follicles are matured egg. Selman et al, 1993.[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] These structures are periodically initiated to grow and develop, culminating in ovulation of usually a single competent oocyte in humans. These eggs/ova are only developed once every menstrual cycle (e.g. once a month in humans) The somatic cell component of the follicle produces hormones important for oocyte development and proper endocrine function BTO:0000475 CALOHA:TS-0726 EMAPA:35627 FMA:18640 GAID:371 MA:0001707 MAT:0000449 MESH:D006080 NCIT:C33244 TAO:0001110 UMLS:C0018120 VHOG:0001536 ZFA:0001110 follicle of ovary follicle of ovary viewed macroscopically ovary follicle uberon egg follicle folliculi ovarici primarii folliculi ovarici vesiculosi UBERON:0001305 ovarian follicle Primary:follicle-4.JPG http://upload.wikimedia.org/wikipedia/commons/c/ca/Human_ovarian_follicle.jpg Wikipedia A spherical aggregation of cells in the ovary that contains a single oocyte[WP,modified]. Oocyte development of zebrafish has been divided into five stages based on morphological criteria and on physiological and biochemical events. Stage I follicles (less than 140 microns) are primary growth stage, stage II follicles (140-340 microns) are cortical alveolus stage, stage III (340-690 microns) are vitellogenesis, stage IV (690-730 microns) are oocyte maturation, and stage V follicles are matured egg. Selman et al, 1993.[TAO] 2012-08-14 TAO:0001110 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:0001536 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) UMLS:C0018120 ncithesaurus:Ovarian_Follicle follicle of ovary viewed macroscopically FMA:18640 ovary follicle MA:0001707 egg follicle ZFA:0001110 folliculi ovarici primarii folliculi ovarici vesiculosi 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 internal iliac artery (formerly known as the hypogastric artery) is the main artery of the pelvis. [WP,unvetted]. BTO:0004667 EMAPA:17860 FMA:18808 MA:0001974 NCIT:C32845 UMLS:C0226364 galen:InternalIliacArtery uberon arteria iliaca interna hypogastric artery UBERON:0001309 internal iliac artery http://upload.wikimedia.org/wikipedia/commons/d/d3/Iliac_artery_bifurcation.PNG MA The internal iliac artery (formerly known as the hypogastric artery) is the main artery of the pelvis. [WP,unvetted]. UMLS:C0226364 ncithesaurus:Internal_Iliac_Artery arteria iliaca interna hypogastric artery BTO:0004667 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 lower urinary bladder. EMAPA:37089 FMA:18823 MA:0002079 NCIT:C52685 UMLS:C0226377 arteria vesicali inferior arteria vesicalis inferior uberon arteria vesicalis inferior UBERON:0001311 inferior vesical artery https://upload.wikimedia.org/wikipedia/commons/1/13/Inferiorvesical.png An artery that supplies blood to the lower urinary bladder. EMAPA:37089 MA:th UMLS:C0226377 ncithesaurus:Inferior_Vesical_Artery arteria vesicali inferior arteria vesicalis inferior arteria vesicalis inferior 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 inferred from artery EMAPA:37158 FMA:18890 MA:0002264 uberon UBERON:0001318 inferior vesical vein true MA EMAPA:37158 MA:th 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 Connective tissue consisting of fat-storing cells and arranged in lobular groups or along minor blood vessels[MP,modified] Adipose tissue, cells of which contain a single large lipid droplet. BTO:0001456 CALOHA:TS-1119 EFO:0000813 EMAPA:35926 FMA:20117 MA:0000058 MAT:0000199 MIAA:0000199 NCIT:C33889 UMLS:C1704223 adipocytus unigutturalis textus adiposus albus unilocular adipose tissue white fat uberon textus adiposus albus UBERON:0001347 white adipose tissue Connective tissue consisting of fat-storing cells and arranged in lobular groups or along minor blood vessels[MP,modified] ISBN:0-683-40008-8 MP:0005670 Adipose tissue, cells of which contain a single large lipid droplet. FMA UMLS:C1704223 ncithesaurus:White_Adipose_Tissue textus adiposus albus A thermogenic form of adipose tissue that is composed of brown adipocytes[MP,modified] Adipose tissue, cells of which contain multiple small lipid droplets.[FMA] especially abundant in newborns and in hibernating mammals thermogenesis BTO:0000156 CALOHA:TS-0099 EFO:0000812 EMAPA:19209 FMA:20118 GAID:921 MA:0000057 MAT:0000198 MESH:D002001 MIAA:0000198 NCIT:C32235 UMLS:C0006298 adipocytus multigutturalis brown fat multilocular adipose tissue textus adiposus fuscus uberon BAT textus adiposus fuscus UBERON:0001348 brown adipose tissue Brownfat:PETCT.jpg A thermogenic form of adipose tissue that is composed of brown adipocytes[MP,modified] MGI:smb MP:0011698 Adipose tissue, cells of which contain multiple small lipid droplets.[FMA] FMA UMLS:C0006298 ncithesaurus:Brown_Adipose_Tissue BAT textus adiposus fuscus 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 The part of the cerebral cortex that receives projections from the motor thalamus and which projects to motor neurons in the brainstem and spinal cord. The motor cortex corresponds to Brodmann's area 4 (MM). The primary motor cortex, or M1, is located on the precentral gyrus and on the anterior paracentral lobule on the medial surface of the brain. Of the three motor cortex areas, stimulation of the primary motor cortex requires the least amount of electrical current to elicit a movement. http://neuroscience.uth.tmc.edu/s3/chapter03.html TODO - in MA this is asserted to be part_of BOTH frontal and parietal cortex. in ABA these are disjoint. FMA makes no commitment beyond cerebral cortex. Wikipedia says frontal lobe. Check if species difference or difference in definition. Removed relationship: part_of UBERON:0001872 parietal lobe The part of the cerebral cortex that receives projections from the motor thalamus and which projects to motor neurons in the brainstem and spinal cord. The motor cortex corresponds to Brodmann's area 4 (MM). The primary motor cortex, or M1, is located on the precentral gyrus and on the anterior paracentral lobule on the medial surface of the brain. Of the three motor cortex areas, stimulation of the primary motor cortex requires the least amount of electrical current to elicit a movement. http://neuroscience.uth.tmc.edu/s3/chapter03.html the area of the frontal lobe that is involved with integration of voluntary movements and with speech.[MP] BAMS:M1 BAMS:MO BAMS:MOp BM:Tel-Cx-M1 BTO:0004348 DHBA:10162 EFO:0002472 EMAPA:35704 FMA:224854 MA:0000907 MBA:985 MESH:A08.186.211.730.885.213.270.548 NCIT:C97339 NLX:143555 UMLS:C0026607 motor cortex uberon Rolando's area excitable area gyrus precentralis motor area prefrontal gyrus primary motor area somatic motor areas somatomotor areas UBERON:0001384 primary motor cortex http://upload.wikimedia.org/wikipedia/commons/e/eb/Ba4.png MA Wikipedia The part of the cerebral cortex that receives projections from the motor thalamus and which projects to motor neurons in the brainstem and spinal cord. The motor cortex corresponds to Brodmann's area 4 (MM). The primary motor cortex, or M1, is located on the precentral gyrus and on the anterior paracentral lobule on the medial surface of the brain. Of the three motor cortex areas, stimulation of the primary motor cortex requires the least amount of electrical current to elicit a movement. http://neuroscience.uth.tmc.edu/s3/chapter03.html NLX:143555 The part of the cerebral cortex that receives projections from the motor thalamus and which projects to motor neurons in the brainstem and spinal cord. The motor cortex corresponds to Brodmann's area 4 (MM). The primary motor cortex, or M1, is located on the precentral gyrus and on the anterior paracentral lobule on the medial surface of the brain. Of the three motor cortex areas, stimulation of the primary motor cortex requires the least amount of electrical current to elicit a movement. http://neuroscience.uth.tmc.edu/s3/chapter03.html NLX:143555 the area of the frontal lobe that is involved with integration of voluntary movements and with speech.[MP] 2012-08-31 MP:0000800 MP MGI:csmith UMLS:C0026607 ncithesaurus:Primary_Motor_Cortex motor cortex FMA:224854 Rolando's area BTO:0004348 excitable area BTO:0004348 gyrus precentralis motor area BTO:0004348 prefrontal gyrus MP:0000798 primary motor area BAMS:MOp somatic motor areas BAMS:MO somatomotor areas BAMS:MO Artery that supplies the axilla In human anatomy, the axillary artery is a large blood vessel that conveys oxygenated blood to the lateral aspect of the thorax, the axilla (armpit) and the upper limb. Its origin is at the lateral margin of the first rib, before which it is called the subclavian artery. After passing the lower margin of teres major it becomes the brachial artery. EMAPA:18749 FMA:22654 GAID:473 MA:0002573 MESH:D001366 NCIT:C32169 OpenCyc:Mx4rwRh-vZwpEbGdrcN5Y29ycA UMLS:C0004455 galen:AxillaryArtery arteria axillaris axillary part of subclavian artery axillary part of trunk of subclavian artery uberon UBERON:0001394 axillary artery Axillary:limits.PNG Artery that supplies the axilla UMLS:C0004455 ncithesaurus:Axillary_Artery arteria axillaris axillary part of subclavian artery FMA:22654 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 outer layers of solid, hard bone that covers spongy bone; consists of parallel osteons containing mineral deposits and interstitial lamellae EMAPA:35250 FMA:24018 MA:0001461 NCIT:C52714 UMLS:C0222661 galen:CorticalBone bony cortex compact bone compact bone tissue cortical bone cortical bone tissue cortical region of bone substantia compacta substantia compacta (pars ossea) substantia corticalis uberon UBERON:0001439 MP distinguishes compact/cortical bone. in other AOs they are syns compact bone tissue the outer layers of solid, hard bone that covers spongy bone; consists of parallel osteons containing mineral deposits and interstitial lamellae ISBN:0-683-40008-8 MGI:hdene MP:0003797 UMLS:C0222661 ncithesaurus:Cortical_Bone bony cortex HP:0002753 compact bone MA:0001461 substantia compacta FMA:24018 FMA:TA substantia corticalis FMA:24018 FMA:TA 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 eyelid [Automatically generated definition]. EMAPA:37536 FMA:24760 MA:0001256 NCIT:C52718 UMLS:C0222088 blepharon zone of skin eyelid skin eyelid zone of skin zone of skin of blepharon zone of skin of eyelid uberon UBERON:0001457 skin of eyelid A zone of skin that is part of a eyelid [Automatically generated definition]. OBOL:automatic EMAPA:37536 MA:th UMLS:C0222088 ncithesaurus:Eyelid_Skin blepharon zone of skin OBOL:automatic eyelid zone of skin OBOL:automatic zone of skin of blepharon OBOL:automatic zone of skin of eyelid OBOL:automatic 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 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 segment of the hindlimb that corresponds to the joint connecting a hindlimb stylopod and zeugopod. BTO:0003595 CALOHA:TS-2220 EHDAA2:0000895 EHDAA:5159 EHDAA:6184 EMAPA:17493 FMA:24974 GAID:48 MA:0000046 MESH:D007717 OpenCyc:Mx4rvVjPKZwpEbGdrcN5Y29ycA VHOG:0000347 galen:Knee knee region uberon UBERON:0001465 knee http://upload.wikimedia.org/wikipedia/commons/8/8d/Male_Knee_by_David_Shankbone.jpg A segment of the hindlimb that corresponds to the joint connecting a hindlimb stylopod and zeugopod. 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 sternoclavicular articulation is a double arthrodial joint composed of two portions separated by an articular disc. The parts entering into its formation are the sternal end of the clavicle, the upper and lateral part of the manubrium sterni, and the cartilage of the first rib, visible from the outside as the suprasternal notch. The articular surface of the clavicle is much larger than that of the sternum, and is invested with a layer of cartilage, which is considerably thicker than that on the latter bone. The ligaments of this joint are: Articular capsule Anterior sternoclavicular ligament Posterior sternoclavicular ligament Interclavicular ligament Costoclavicular ligament Articular disk [WP,unvetted]. sternoclavicular EMAPA:19203 FMA:25883 GAID:270 MA:0001507 MESH:D013247 NCIT:C33615 OpenCyc:Mx4rv_eLJZwpEbGdrcN5Y29ycA OpenCyc:Mx4rwI-ZZpwpEbGdrcN5Y29ycA UMLS:C0038291 sterno clavicular joint sternoclavicular articulation uberon articulatio sternoclavicularis UBERON:0001469 sternoclavicular joint http://upload.wikimedia.org/wikipedia/commons/3/3f/Gray325.png FMA clavicular notch of the manubrium sterni sternal end of the clavicle and first rib The sternoclavicular articulation is a double arthrodial joint composed of two portions separated by an articular disc. The parts entering into its formation are the sternal end of the clavicle, the upper and lateral part of the manubrium sterni, and the cartilage of the first rib, visible from the outside as the suprasternal notch. The articular surface of the clavicle is much larger than that of the sternum, and is invested with a layer of cartilage, which is considerably thicker than that on the latter bone. The ligaments of this joint are: Articular capsule Anterior sternoclavicular ligament Posterior sternoclavicular ligament Interclavicular ligament Costoclavicular ligament Articular disk [WP,unvetted]. sternoclavicular UMLS:C0038291 ncithesaurus:Sternoclavicular_Joint sternoclavicular articulation articulatio sternoclavicularis 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 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 muscle of shoulder which attaches to the scapula, clavicle and humerus.[FMA,generalized] Muscle which originates as three heads, the pars externalis, pars clavicularis, and pars scapularis. The pars externalis originates from the lateral border of the omosternum and inserts on the distal portion of the humerus. The pars clavicularis originates from the ventro-lateral surface of the clavicle and inserts on the deltoid crest of the humerus. The pars scapularis originates from the lateral surface of the clavicle and inserts on the deltoid crest of the humerus.[AAO] AAO:0010716 EFO:0001412 EHDAA2:0000339 EMAPA:18177 FMA:32521 MA:0002286 NCIT:C32446 OpenCyc:Mx4rvVjdc5wpEbGdrcN5Y29ycA UMLS:C0224234 VHOG:0000846 deltoid muscle m. deltoideus musculus deltoideus uberon common shoulder muscle deltoideus deltoideus muscle musculus deltoideus UBERON:0001476 We use a generic definition that includes the deltoideus as represented in AAO: 'Muscle which originates as three heads, the pars externalis, pars clavicularis, and pars scapularis. The pars externalis originates from the lateral border of the omosternum and inserts on the distal portion of the humerus. The pars clavicularis originates from the ventro-lateral surface of the clavicle and inserts on the deltoid crest of the humerus. The pars scapularis originates from the lateral surface of the clavicle and inserts on the deltoid crest of the humerus'. Kardong: Dorsal group deltoid http://upload.wikimedia.org/wikipedia/commons/9/93/Deltoideus.png FMA EHDAA2 dbpedia EHDAA2 FMA the anterior border and upper surface of the lateral third of the clavicle acromion spine of the scapula dbpedia the anterior border and upper surface of the lateral third of the clavicle acromion spine of the scapula dbpedia the anterior border and upper surface of the lateral third of the clavicle acromion spine of the scapula dbpedia deltoid tuberosity of humerus dbpedia dbpedia A muscle of shoulder which attaches to the scapula, clavicle and humerus.[FMA,generalized] FMA:32521 Muscle which originates as three heads, the pars externalis, pars clavicularis, and pars scapularis. The pars externalis originates from the lateral border of the omosternum and inserts on the distal portion of the humerus. The pars clavicularis originates from the ventro-lateral surface of the clavicle and inserts on the deltoid crest of the humerus. The pars scapularis originates from the lateral surface of the clavicle and inserts on the deltoid crest of the humerus.[AAO] 2012-06-20 AAO:0010716 AAO AAO:MEJ UMLS:C0224234 ncithesaurus:Deltoid deltoid muscle m. deltoideus AAO:0010716 musculus deltoideus common shoulder muscle deltoideus deltoideus muscle musculus deltoideus A sesamoid element that is composed of bone tissue. sesamoid AEO:0000086 EHDAA2:0003086 EMAPA:36620 FMA:32672 GAID:210 MA:0001375 MESH:D012716 NCIT:C33541 UMLS:C0036846 galen:SessamoidBone ossa sesamoidea uberon UBERON:0001479 Sesamoids are often endochondral replacement elements and in addition to bone tissue, may also be composed of articular cartilage, fibrocartilage, hyaline cartilage, and calcified cartilage.[VSAO] sesamoid bone http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray350.png UBERON:cjm A sesamoid element that is composed of bone tissue. UMLS:C0036846 ncithesaurus:Sesamoid_Bone ossa sesamoidea 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 The knee joint joins the thigh with the leg and consists of two articulations: one between the femur and tibia, and one between the femur and patella. It is the largest and most complicated joint in the human body. The knee is a mobile trocho-ginglymus (i.e. a pivotal hinge joint), which permits flexion and extension as well as a slight medial and lateral rotation[WP,unvetted]. EFO:0001957 EMAPA:19137 FMA:35175 GAID:114 MA:0000471 MESH:D007719 NCIT:C32898 OpenCyc:Mx4rwCuaYZwpEbGdrcN5Y29ycA UMLS:C0022745 VHOG:0001003 galen:KneeJoint joint of knee uberon articulatio genus UBERON:0001485 knee joint http://upload.wikimedia.org/wikipedia/commons/c/ca/Knee.agr.jpg definitional The knee joint joins the thigh with the leg and consists of two articulations: one between the femur and tibia, and one between the femur and patella. It is the largest and most complicated joint in the human body. The knee is a mobile trocho-ginglymus (i.e. a pivotal hinge joint), which permits flexion and extension as well as a slight medial and lateral rotation[WP,unvetted]. UMLS:C0022745 ncithesaurus:Knee_Joint joint of knee OBOL:automatic articulatio genus 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 The axillary nerve is a nerve of the human body, that comes off the posterior cord of the brachial plexus at the level of the axilla (armpit) and carries nerve fibers from C5 and C6. The axillary nerve travels through the quadrangular space with the posterior circumflex humeral artery and vein. [WP,unvetted]. EMAPA:18802 FMA:37072 MA:0001166 NCIT:C52817 OpenCyc:Mx4rvgwMfpwpEbGdrcN5Y29ycA UMLS:C0228885 circumflex humeral nerve uberon auxillery nerve circumflex nerve nervus axillaris UBERON:0001493 axillary nerve Brachial:plexus.jpg http://upload.wikimedia.org/wikipedia/commons/e/ea/Brachial_plexus_2.svg MA The axillary nerve is a nerve of the human body, that comes off the posterior cord of the brachial plexus at the level of the axilla (armpit) and carries nerve fibers from C5 and C6. The axillary nerve travels through the quadrangular space with the posterior circumflex humeral artery and vein. [WP,unvetted]. UMLS:C0228885 ncithesaurus:Axillary_Nerve auxillery nerve circumflex nerve nervus axillaris nervus axillaris Muscles of the upper chest. The term may refer to one of two muscles, the pectoralis major and pectoralis minor. The former is a thick muscle in the anterior portion of the chest. Its action involves flexion, medial rotation, and adduction of the humerus. The latter is a thin muscle located beneath the pectoralis major. Its action involves lowering the scapula and raising the ribs. Muscle which is comprised of three heads. The anterior head is the portio epicoracoidea that originates on the epicoracoid cartilage and inserts on the deltoid crest of the humerus. The next more posterior head, portio sternalis, originates on the sternum and inserts in the groove next to the deltoid crest of the humerus. The most posterior head, portio abdominalis, arises from the M. rectus abdominis and inserts on the deltoid crest of the humerus.[AAO] AAO:0010727 BTO:0000023 CALOHA:TS-0751 EMAPA:35670 FMA:37349 GAID:153 MA:0002423 MESH:D010369 NCIT:C33286 UMLS:C0030747 M. pectoralis muscle of pectoral part of chest muscle of pectoral region uberon breast muscle pectoralis pectoralis group muscle pectoralis muscle UBERON:0001495 This currently groups the major and minor muscles (which have different attachment sites) as well as the AAO structure: Muscle which is comprised of three heads. The anterior head is the portio epicoracoidea that originates on the epicoracoid cartilage and inserts on the deltoid crest of the humerus. The next more posterior head, portio sternalis, originates on the sternum and inserts in the groove next to the deltoid crest of the humerus. The most posterior head, portio abdominalis, arises from the M. rectus abdominis and inserts on the deltoid crest of the humerus pectoral muscle Pectoralis:major.png FMA Muscles of the upper chest. The term may refer to one of two muscles, the pectoralis major and pectoralis minor. The former is a thick muscle in the anterior portion of the chest. Its action involves flexion, medial rotation, and adduction of the humerus. The latter is a thin muscle located beneath the pectoralis major. Its action involves lowering the scapula and raising the ribs. ncithesaurus:Pectoralis_Muscle Muscle which is comprised of three heads. The anterior head is the portio epicoracoidea that originates on the epicoracoid cartilage and inserts on the deltoid crest of the humerus. The next more posterior head, portio sternalis, originates on the sternum and inserts in the groove next to the deltoid crest of the humerus. The most posterior head, portio abdominalis, arises from the M. rectus abdominis and inserts on the deltoid crest of the humerus.[AAO] 2012-06-20 AAO:0010727 AAO AAO:MEJ UMLS:C0030747 ncithesaurus:Pectoralis_Muscle M. pectoralis AAO:0010727 muscle of pectoral part of chest FMA:37349 muscle of pectoral region FMA:37349 breast muscle BTO:0000023 pectoralis muscle BTO:0000023 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 the convex portion of the aorta between the ascending and descending parts of the aorta; branches from it include the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery; the brachiocephalic trunk further splits to form the right subclavian artery and the right common carotid artery Do not confuse with aortic arch The curving portion between the ascending aorta and the descending aorta, giving rise to the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery. [TFD][VHOG] The double systemic arch arches (left and right) present in amphibians and reptiles become reduced to a single systemic arch - the right in birds, the left in mammals.[well established][VHOG] birds have right aortic arch, mammals left. BTO:0000157 EFO:0002526 EHDAA2:0000132 EMAPA:17613 FMA:3768 GAID:471 MA:0000475 VHOG:0001196 arcus aortae uberon aortic arch thoracic aorta UBERON:0001508 arch of aorta http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg left arch 4 in human embryology.ch the convex portion of the aorta between the ascending and descending parts of the aorta; branches from it include the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery; the brachiocephalic trunk further splits to form the right subclavian artery and the right common carotid artery ISBN:0-683-40008-8 MP:0004113 The curving portion between the ascending aorta and the descending aorta, giving rise to the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery. [TFD][VHOG] 2012-09-17 VHOG:0001196 VHOG The double systemic arch arches (left and right) present in amphibians and reptiles become reduced to a single systemic arch - the right in birds, the left in mammals.[well established][VHOG] 2012-09-17 VHOG:0001196 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460 and p.461 Figure 12.20 arcus aortae FMA:3768 FMA:TA aortic arch FMA:3768 thoracic aorta GAID:471 A zone of skin that is part of a knee [Automatically generated definition]. EMAPA:18151 FMA:37800 MA:0000668 NCIT:C64859 UMLS:C0222275 knee skin knee zone of skin zone of skin of knee uberon UBERON:0001510 skin of knee A zone of skin that is part of a knee [Automatically generated definition]. OBOL:automatic UMLS:C0222275 ncithesaurus:Knee_Skin knee zone of skin OBOL:automatic zone of skin of knee 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 the short first aortic arch branch and divides into the right subclavian artery and the right common carotid artery innominate EFO:0002550 EHDAA2:0000835 EMAPA:17615 FMA:3932 GAID:476 MA:0001922 MESH:D016122 NCIT:C32814 OpenCyc:Mx4rv9mMTpwpEbGdrcN5Y29ycA UMLS:C0006094 galen:BrachioCephalicArtery brachiocephalic trunk innominate artery truncus brachiocephalicus uberon truncus brachiocephalicus UBERON:0001529 brachiocephalic artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg the short first aortic arch branch and divides into the right subclavian artery and the right common carotid artery MGI:csmith MP:0010663 innominate UMLS:C0006094 ncithesaurus:Innominate_Artery brachiocephalic trunk MA:0001922 innominate artery truncus brachiocephalicus FMA:3932 FMA:TA truncus brachiocephalicus 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 One of the curved arteries at the corticomedullary border of the kidney that arise from the interlobar arteries and give rise to the interlobular arteries. arcuate artery EMAPA:28215 FMA:70497 MA:0002583 renal arcuate artery uberon UBERON:0001552 kidney arcuate artery http://upload.wikimedia.org/wikipedia/commons/e/ee/Gray553.png MA One of the curved arteries at the corticomedullary border of the kidney that arise from the interlobar arteries and give rise to the interlobular arteries. MP:0011315 arcuate artery MA:0002583 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. 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 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 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 Nerve that carries information from the olfactory epithelium to the olfactory bulb[Butler and Hodos]. Nerve that carries information from the olfactory epithelium through the olfactory bulb to the olfactory cortex of the telencephalon.[AAO] Segment of neural tree organ which is continuous with the olfactory epithelium and an olfactory bulb[FMA:46787]. The 1st cranial nerve. The olfactory nerve conveys the sense of smell. It is formed by the axons of OLFACTORY RECEPTOR NEURONS which project from the olfactory epithelium (in the nasal epithelium) to the OLFACTORY BULB[MESH:A08.800.800.120.640]. 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] connects to main OB (in taxa where main/accessory distinction is important) 1n AAO:0010088 BAMS:1n BAMS:ln BIRNLEX:1319 BTO:0003648 EHDAA2:0001293 EHDAA:6672 EMAPA:17797 FMA:46787 GAID:830 HBA:9300 MA:0001096 MBA:840 MESH:D009832 NCIT:C12759 OpenCyc:Mx4rvZuXAJwpEbGdrcN5Y29ycA TAO:0000249 UMLS:C0028938 UMLS:C1268984 VHOG:0000703 XAO:0000426 ZFA:0000249 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=32 first cranial nerve nervus olfactorius [i] olfactory I olfactory i nerve olfactory nerve [I] uberon CN-I cranial nerve I fila olfactoria nerve I nerve of smell nervus olfactorius olfactoria fila olfactory fila UBERON:0001579 olfactory nerve http://upload.wikimedia.org/wikipedia/commons/b/be/Gray771.png ISBN:0471888893 ISBN:0471888893 Nerve that carries information from the olfactory epithelium to the olfactory bulb[Butler and Hodos]. ISBN:0471209627 Nerve that carries information from the olfactory epithelium through the olfactory bulb to the olfactory cortex of the telencephalon.[AAO] 2012-06-20 AAO:0010088 AAO AAO:DSM Segment of neural tree organ which is continuous with the olfactory epithelium and an olfactory bulb[FMA:46787]. FMA:46787 The 1st cranial nerve. The olfactory nerve conveys the sense of smell. It is formed by the axons of OLFACTORY RECEPTOR NEURONS which project from the olfactory epithelium (in the nasal epithelium) to the OLFACTORY BULB[MESH:A08.800.800.120.640]. MESH:A08.800.800.120.640 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:0000703 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 1n BIRNLEX:1319 NIFSTD:NeuroNames_abbrevSource UMLS:C0028938 BIRNLEX:1319 UMLS:C0028938 ncithesaurus:Olfactory_Nerve UMLS:C1268984 BIRNLEX:1319 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=32 BIRNLEX:1319 nervus olfactorius [i] FMA:46787 FMA:TA olfactory I EHDAA2:0001293 fila olfactoria BTO:0003648 nerve I NeuroNames:32 nerve of smell BTO:0003648 nervus olfactorius nervus olfactorius BTO:0003648 olfactoria fila NeuroNames:32 olfactory fila BTO:0003648 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 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 The occipital artery arises opposite the facial artery, its path is below the posterior belly of digastric to the occipital region. This artery supplies blood to the back of the scalp and sterno-mastoid muscles. Other muscles it supplies are deep muscles in the back and neck. [WP,unvetted]. EMAPA:37672 FMA:49586 MA:0002009 NCIT:C33194 OpenCyc:Mx4rwC1IFJwpEbGdrcN5Y29ycA UMLS:C0226117 uberon arteria occipitalis UBERON:0001613 occipital artery http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png The occipital artery arises opposite the facial artery, its path is below the posterior belly of digastric to the occipital region. This artery supplies blood to the back of the scalp and sterno-mastoid muscles. Other muscles it supplies are deep muscles in the back and neck. [WP,unvetted]. EMAPA:37672 MA:th UMLS:C0226117 ncithesaurus:Occipital_Artery arteria occipitalis 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 An artery that supplies the myocardium. BTO:0000290 CALOHA:TS-0176 EFO:0002551 EMAPA:19160 EV:0100383 FMA:49893 MA:0002453 NCIT:C12843 OpenCyc:Mx4rvoL56ZwpEbGdrcN5Y29ycA UMLS:C0205042 VHOG:0001557 ZFA:0005812 galen:CoronaryArtery coronary arterial tree uberon coronary vessel UBERON:0001621 coronary artery http://upload.wikimedia.org/wikipedia/commons/4/46/Gray492.png An artery that supplies the myocardium. UMLS:C0205042 ncithesaurus:Coronary_Artery coronary vessel ZFA:0005812 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 transmits sound and equilibrium (balance) information from the inner ear to the brain. Nerve primarily composed of special somatic afferent fibers innervating the inner ear, and is involved in balance, position, and hearing.[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] 8n AAO:0010473 BAMS:8n BAMS:VIIIn BAMS:nVIII BIRNLEX:890 BTO:0003490 EHDAA2:0002194 EMAPA:17801 FMA:50869 GAID:839 HBA:9331 MA:0001109 MBA:933 MESH:D000159 NCIT:C12996 OpenCyc:Mx4rvVjMFZwpEbGdrcN5Y29ycA TAO:0000247 UMLS:C0001162 UMLS:C1278835 VHOG:0000695 XAO:0003095 ZFA:0000247 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=553 CN-VIII VIII nerve VIIIth cranial nerve acoustic VIII nerve acoustic nerve acoustic nerve (Crosby) cochlear-vestibular nerve cochleovestibular nerve cranial nerve VIII eighth cranial nerve nervus vestibulocochlearis [viii] stato-acoustic nerve vestibulocochlear VIII nerve vestibulocochlear nerve [VIII] vestibulocochlear nerve tree uberon nervus octavus nervus statoacusticus nervus vestibulocochlearis octaval nerve statoacoustic nerve UBERON:0001648 vestibulocochlear nerve http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray789.png ISBN:0471888893 Cranial nerve that transmits sound and equilibrium (balance) information from the inner ear to the brain. ISBN:0471209627 Nerve primarily composed of special somatic afferent fibers innervating the inner ear, and is involved in balance, position, and hearing.[AAO] 2012-06-20 AAO:0010473 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:0000695 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 8n BIRNLEX:890 NIFSTD:NeuroNames_abbrevSource UMLS:C0001162 BIRNLEX:890 UMLS:C0001162 ncithesaurus:Vestibulocochlear_Nerve UMLS:C1278835 BIRNLEX:890 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=553 BIRNLEX:890 acoustic nerve FMA:50869 nervus vestibulocochlearis [viii] FMA:50869 FMA:TA nervus octavus NeuroNames:553 nervus statoacusticus NeuroNames:553 nervus vestibulocochlearis BTO:0003490 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 An unpaired bone situated at the base of the skull in front of the temporal bone and basilar part of the occipital bone. The sphenoid bone is one of the seven bones that articulate to form the orbit. Its shape somewhat resembles that of a butterfly or bat with its wings extended. part of viscerocranium (facial skeleton) in FMA CALOHA:TS-2343 EMAPA:18340 FMA:52736 GAID:230 MA:0001472 MESH:D013100 NCIT:C12790 OpenCyc:Mx4rwAU9XpwpEbGdrcN5Y29ycA UMLS:C0037884 os sphenoidale sphenoid sphenoidal bone uberon butterfly bone os sphenoidale os sphenoidum sphenoid complex UBERON:0001677 sphenoid bone http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg FMA orbito pre and basi sphenoid pterygoid process alisphenoid cjm An unpaired bone situated at the base of the skull in front of the temporal bone and basilar part of the occipital bone. The sphenoid bone is one of the seven bones that articulate to form the orbit. Its shape somewhat resembles that of a butterfly or bat with its wings extended. part of viscerocranium (facial skeleton) in FMA FMA UMLS:C0037884 ncithesaurus:Sphenoid_Bone os sphenoidale FMA:52736 FMA:TA butterfly bone os sphenoidale os sphenoidale os sphenoidum 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 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. 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 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 A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane blepharic palpebral In humans the upper and lower eyelid consists of the following layers, starting anteriorly: (1) skin, (2) a layer of subcutaneous connective tissue, (3) a layer of striated muscle fibres of the orbicularis muscle, (4) a layer of submuscular connective tissue, (5) a fibrous layer, including the tarsal plates, (6) a layer of smooth muscle, (7) the palpebral conjunctiva. Consider adding 'eye surface', like MA FMA divides this into skin, fascia, conjunctiva BTO:0002241 EHDAA2:0000487 EHDAA:9037 EMAPA:17829 EV:0100338 FMA:54437 GAID:72 MA:0000268 MESH:D005143 NCIT:C12713 OpenCyc:Mx4rvVi4m5wpEbGdrcN5Y29ycA UMLS:C0015426 VHOG:0000016 blepharon eye lid palpebra uberon blephara palpebrae UBERON:0001711 eyelid Eye:makeup.jpg multiple A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane Consider adding 'eye surface', like MA MA FMA divides this into skin, fascia, conjunctiva FMA UMLS:C0015426 ncithesaurus:Eyelid blephara palpebrae 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 Any of the nuclei of the cochlear nuclear complex. EMAPA:35248 FMA:54603 GAID:601 MA:0001012 MESH:D017626 NCIT:C12837 TAO:0002243 ZFA:0001638 cochlear VIII nucleus cochlear nucleus of acoustic nerve cochlear nucleus of eighth cranial nerve nucleus of cochlear nerve statoacoustic (VIII) nucleus uberon vestibulocochlear nucleus UBERON:0001720 cochlear nucleus http://upload.wikimedia.org/wikipedia/commons/5/52/Gray691.png Any of the nuclei of the cochlear nuclear complex. cochlear VIII nucleus MA:0001012 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. 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 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 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 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 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 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 A lymphoid follicle that contains a germinal center. FMA:55224 GAID:946 peripheral lymphoid tissue secondary lymphoid nodule secondary lymphoid tissue uberon UBERON:0001745 secondary nodular lymphoid tissue http://upload.wikimedia.org/wikipedia/commons/2/2f/Keimzentrum.jpg A lymphoid follicle that contains a germinal center. CL:tm 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 A dentine-like hypermineralized substance that covers the tooth tip. Enamel's primary mineral is hydroxylapatite, which is a crystalline calcium phosphate. Unlike dentin and bone, enamel does not contain collagen. Instead, it has two unique classes of proteins called amelogenins and enamelins[WP]. current classification under substance of tooth may be turned into taxon GCI (e.g. sharks have enamel in dermal denticles) Skeletal tissue that consists of an avascular, noncollagenous, hypermineralized matrix that is deposited by ameloblasts that are excluded from the matrix. Enamel develops from organic pre-enamel tissue that is replaced by a largely inorganic matrix.[VSAO] part_of tooth enamel organ in MA BTO:0001844 CALOHA:TS-1057 EMAPA:35303 FMA:55629 MA:0002543 MESH:A14.254.900.255 NCIT:C32505 UMLS:C0011350 VSAO:0000065 XAO:0004198 enamel of tooth enamel tissue tooth enamel uberon enameloid UBERON:0001752 enamel http://upload.wikimedia.org/wikipedia/commons/6/66/Enamelorgan11-17-05.jpg VSAO VSAO A dentine-like hypermineralized substance that covers the tooth tip. Enamel's primary mineral is hydroxylapatite, which is a crystalline calcium phosphate. Unlike dentin and bone, enamel does not contain collagen. Instead, it has two unique classes of proteins called amelogenins and enamelins[WP]. ZFIN:curator Skeletal tissue that consists of an avascular, noncollagenous, hypermineralized matrix that is deposited by ameloblasts that are excluded from the matrix. Enamel develops from organic pre-enamel tissue that is replaced by a largely inorganic matrix.[VSAO] 2012-08-14 VSAO:0000065 VSAO PSPUB:0000170 part_of tooth enamel organ in MA MA UMLS:C0011350 ncithesaurus:Enamel enamel tissue VSAO:curator Odontoid tissue that is deposited by cementoblasts onto dentine tissue and functions to attach teeth, odontodes and other odontogenic derivatives to bone tissue and the integument. Odontoid tissue that is deposited by cementoblasts onto dentine tissue and functions to attach teeth, odontodes and other odontogenic derivatives to bone tissue and the integument.[VSAO] Substance of tooth produced by cementoblasts; surrounds the dentine of the root of the tooth[FMA:55630]. Cementum, the supporting tissue that anchors mammalian and crocodylian teeth into their sockets, differs among species and can have features of dentine, of bone, and of calcified cartilage, as well as unique features. Cementum is deposited by cementoblasts onto existing dentine. As in bone and dentine, cementoblasts produce an organic matrix, the main constituent of which is collagen type I (Bosshardt, 2005), but cementum, dentine, and bone also share a number of important noncollagenous matrix components such as osteopontin, osteocalcin, bone sialoprotein, a2-HS- glycoprotein, dentine matrix protein, dentine sialoprotein, and den- tine phosphoprotein (McKee et al., 1996; Bosshardt, 2005). it has been argued that in all rodents and ruminants, cementum is a form of calcified cartilage[H&W] BTO:0002525 CALOHA:TS-2163 EMAPA:35203 FMA:55630 MA:0002541 MESH:A14.254.646.267 NCIT:C32276 UMLS:C0011343 VSAO:0000062 XAO:0004196 cement cement of tooth cementum cementum of tooth uberon bone of attachment UBERON:0001753 cementum The:Periodontium.jpg VSAO Wikipedia Odontoid tissue that is deposited by cementoblasts onto dentine tissue and functions to attach teeth, odontodes and other odontogenic derivatives to bone tissue and the integument. GO_REF:0000034 PSPUB:0000170 VSAO:0000062 Odontoid tissue that is deposited by cementoblasts onto dentine tissue and functions to attach teeth, odontodes and other odontogenic derivatives to bone tissue and the integument.[VSAO] 2012-08-14 VSAO:0000062 VSAO PSPUB:0000170 Substance of tooth produced by cementoblasts; surrounds the dentine of the root of the tooth[FMA:55630]. FMA:55630 UMLS:C0011343 ncithesaurus:Cementum cement FMA:55630 bone of attachment VSAO:0000062 The part in the center of a tooth made up of living soft tissue and cells called odontoblasts[WP]. Material in the center of the dentine of the mature tooth. In secondary teeth the pulp contains blood vessels and odontoblast.[TAO] The oral cavity of vertebrates is generally thought to arise as an ectodermal invagination. Consistent with this, oral teeth are proposed to arise exclusively from ectoderm, contributing to tooth enamel epithelium, and from neural crest derived mesenchyme, contributing to dentin and pulp (reference 1); 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 (reference 2).[uncertain][VHOG] BTO:0000339 CALOHA:TS-0195 EMAPA:35274 FMA:55631 GAID:1270 MA:0001599 MESH:A14.254.900.260 NCIT:C32451 TAO:0005141 UMLS:C0011399 VHOG:0001469 ZFA:0005141 pulp of tooth tooth pulp uberon dental pulp cell UBERON:0001754 dental pulp Tooth:Section.svg FMA ZFA The part in the center of a tooth made up of living soft tissue and cells called odontoblasts[WP]. Material in the center of the dentine of the mature tooth. In secondary teeth the pulp contains blood vessels and odontoblast.[TAO] 2012-08-14 TAO:0005141 TAO ZFIN:curator The oral cavity of vertebrates is generally thought to arise as an ectodermal invagination. Consistent with this, oral teeth are proposed to arise exclusively from ectoderm, contributing to tooth enamel epithelium, and from neural crest derived mesenchyme, contributing to dentin and pulp (reference 1); 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 (reference 2).[uncertain][VHOG] 2012-09-17 VHOG:0001469 VHOG DOI:10.1038/nature07304 Soukup V, Epperlein HH, Horacek I, Cerny R, Dual epithelial origin of vertebrate oral teeth. Nature (2008), 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) UMLS:C0011399 ncithesaurus:Dental_Pulp tooth pulp ZFA:0005141 dental pulp cell BTO:0000339 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 The tissues that invest or help to invest and support the teeth, including the periodontal ligament, gingivae, cementum, and alveolar and supporting bone[BTO]. FMA treats periodontium and periodontal ligament as the same BTO:0001021 CALOHA:TS-2380 GAID:216 MESH:A14.254.646 NCIT:C33304 UMLS:C0031093 uberon paradentium periodontal ligament periodontal membrane tooth supporting structure UBERON:0001758 periodontium The:Periodontium.jpg cjm cjm The tissues that invest or help to invest and support the teeth, including the periodontal ligament, gingivae, cementum, and alveolar and supporting bone[BTO]. BTO:0001021 FMA treats periodontium and periodontal ligament as the same FMA UMLS:C0031093 ncithesaurus:Periodontium paradentium MESH:A14.254.646 periodontal ligament FMA:56665 periodontal membrane MA:0002467 tooth supporting structure MESH:A14.254.646 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 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 Epithelial tube that transports milk[GO]. BTO:0002845 CALOHA:TS-2385 EMAPA:35538 FMA:58006 MA:0000791 NCIT:C32910 UMLS:C0222613 lactiferous duct lactiferous gland duct mammary gland duct uberon ductus lactiferi galactophorous duct galactophorous tubule lactiferous tubule mammilary duct UBERON:0001765 This structure regresses in most males mammary duct http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg Epithelial tube that transports milk[GO]. GO:0060603 UMLS:C0222613 ncithesaurus:Lactiferous_Duct lactiferous duct FMA:58006 lactiferous gland duct OBOL:automatic mammary gland duct MA:0000791 ductus lactiferi ductus lactiferi BTO:0002845 galactophorous duct galactophorous tubule BTO:0002845 lactiferous tubule BTO:0002845 mammilary duct 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 part of the lacrimal duct that connects the lacrimal punctum to the lacrimal sac. TODO - resolve lacrimal canaliculus vs lacrimal duct EMAPA:37624 FMA:58245 MA:0001294 NCIT:C32907 UMLS:C0459631 uberon canaliculus lacrimalis UBERON:0001770 lacrimal canaliculus FMA The part of the lacrimal duct that connects the lacrimal punctum to the lacrimal sac. EMAPA:37624 MA:th UMLS:C0459631 ncithesaurus:Lacrimal_Canaliculus canaliculus lacrimalis 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 A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup[ZFA]. the pigmented cell layer just outside the neurosensory retina that nourishes retinal visual cells, and is firmly attached to the underlying choroid and overlying retinal visual cells[WP]. A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup. Kimmel et al, 1995.[TAO] The monolayer of pigmented epithelium covering the neural retina.[AAO] (...) 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:0011096 BTO:0001177 CALOHA:TS-0869 EHDAA2:0001465 EHDAA:4765 EMAPA:17172 EMAPA:35738 FMA:58627 MA:0000279 MA:0003173 NCIT:C33470 TAO:0000144 UMLS:C0035322 VHOG:0000536 XAO:0003217 ZFA:0000144 outer pigmented layer of retina pigment epithelium of retina pigmented retina epithelium pigmented retinal epithelium retinal pigment epithelium retinal pigmented epithelium stratum pigmentosum (retina) stratum pigmentosum retinae uberon PRE RPE epithelium, retinal pigment p. pigmentosa retinae pigmented epithelium pigmented retina retinal pigment layer stratum pigmentosa retinae UBERON:0001782 pigmented layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png Wikipedia A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup[ZFA]. the pigmented cell layer just outside the neurosensory retina that nourishes retinal visual cells, and is firmly attached to the underlying choroid and overlying retinal visual cells[WP]. ZFIN:curator A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000144 TAO ZFIN:curator The monolayer of pigmented epithelium covering the neural retina.[AAO] 2012-06-20 AAO:0011096 AAO ZFA:0000144 (...) 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:0000536 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 UMLS:C0035322 ncithesaurus:Retinal_Pigment_Epithelium retinal pigment epithelium MP:0005201 retinal pigmented epithelium ZFA:0000144 stratum pigmentosum retinae FMA:58627 FMA:TA epithelium, retinal pigment BTO:0001177 p. pigmentosa retinae retinal pigment layer VHOG:0000536 stratum pigmentosa retinae 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 The layer within the retina where the photoreceptor cell receptor segments reside. (...) 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] we follow MA and ZFA in subdividing this into inner and outer segments EMAPA:35686 FMA:58680 MA:0001308 NCIT:C32954 TAO:0000143 UMLS:C0229206 VHOG:0001165 XAO:0003215 ZFA:0000143 retina photoreceptor layer retinal photoreceptor layer stratum segmentorum externorum et internorum (retina) stratum segmentorum externorum et internorum retinae uberon layer of rods and cones retinal photoreceptor layers UBERON:0001787 photoreceptor layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png The layer within the retina where the photoreceptor cell receptor segments reside. ZFA:0000143 (...) 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:0001165 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 we follow MA and ZFA in subdividing this into inner and outer segments MA UMLS:C0229206 ncithesaurus:Layer_of_the_Rods_and_Cones retinal photoreceptor layer ZFA:0000143 stratum segmentorum externorum et internorum retinae FMA:58680 FMA:TA retinal photoreceptor layers ZFA:0000143 The row of jucntional complexes between the plasma membranes of rod segments and the Muller glia cells; this barrier separates the layer of inner and outer segments of the rods and cones from the outer nuclear layer and forms a blood-retina barrier[MP]. EMAPA:36518 FMA:58683 MA:0001309 NCIT:C33235 TAO:0001331 UMLS:C1518685 XAO:0003224 ZFA:0001331 external limiting lamina of retina external limiting membrane external limiting membrane of retina outer limiting membrane outer limiting membrane of retina retina external limiting lamina retina outer limiting membrane stratum limitans externum (retina) stratum limitans externum retinae uberon BRB blood retina barrier outer limiting membranes UBERON:0001788 outer limiting layer of retina MA The row of jucntional complexes between the plasma membranes of rod segments and the Muller glia cells; this barrier separates the layer of inner and outer segments of the rods and cones from the outer nuclear layer and forms a blood-retina barrier[MP]. MP:0010236 UMLS:C1518685 ncithesaurus:Outer_Limiting_Membrane external limiting membrane ZFA:0001331 outer limiting membrane XAO:0003224 retina outer limiting membrane MP:0010236 stratum limitans externum retinae FMA:58683 FMA:TA BRB blood retina barrier outer limiting membranes ZFA:0001331 The layer within the retina where the photoreceptor cell bodies reside. (...) 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] outer nuclear layer BAMS:Ronl BTO:0005600 EMAPA:19157 FMA:58684 MA:0001315 NCIT:C33236 TAO:0001464 UMLS:C0229210 VHOG:0001170 XAO:0003219 ZFA:0001464 neural retina outer nuclear layer retina outer nuclear layer retinal outer nuclear layer stratum nucleare externum (retina) stratum nucleare externum retinae ONL uberon external nuclear layer layer of outer granules retina, outer nuclear layer retinal outer nuclear layers UBERON:0001789 outer nuclear layer of retina The layer within the retina where the photoreceptor cell bodies reside. ZFA:0001464 (...) 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:0001170 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 UMLS:C0229210 ncithesaurus:Outer_Nuclear_Layer_of_Retina neural retina outer nuclear layer EMAPA:19157 stratum nucleare externum retinae FMA:58684 FMA:TA external nuclear layer BTO:0005600 layer of outer granules BTO:0005600 retina, outer nuclear layer BAMS:Ronl retinal outer nuclear layers ZFA:0001464 The layer within the retina where the bipolar cells synapse with the photoreceptor cells[ZFA]. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells[GO]. The layer within the retina where the bipolar cells synapse with the photoreceptor cells.[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 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] external plexiform layer BAMS:Ropl BTO:0003174 EMAPA:35744 FMA:58685 MA:0001316 NCIT:C33237 TAO:0001330 UMLS:C0229217 VHOG:0001171 XAO:0003218 ZFA:0001330 outer plexiform layer retina outer plexiform layer retinal outer plexiform layer stratum plexiforme externum stratum plexiforme externum retinae OPL uberon retina, outer plexiform layer retinal outer plexiform layers UBERON:0001790 outer plexiform layer of retina The layer within the retina where the bipolar cells synapse with the photoreceptor cells[ZFA]. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells[GO]. ZFA:0001330 The layer within the retina where the bipolar cells synapse with the photoreceptor cells.[TAO] 2012-08-14 TAO:0001330 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 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:0001171 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 external plexiform layer BTO:0003174 UMLS:C0229217 ncithesaurus:Outer_Plexiform_Layer outer plexiform layer BTO:0003174 stratum plexiforme externum retinae FMA:58685 FMA:TA OPL retina, outer plexiform layer BAMS:Ropl retinal outer plexiform layers ZFA:0001330 Cytoarchitectural layer of retina containing closely packed cell bodies, the majority of which are bipolar cells (adapted from Wikipedia). The layer of the retina composed of the cell bodies of bipolar cells, horizontal cells, and some of the cell bodies of amacrine cells[BTO:0003176]. (...) 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] BAMS:Rinl BTO:0003176 EMAPA:19155 FMA:58686 MA:0001311 NCIT:C32808 NLX:93816 NLXANAT:1005031 TAO:0000119 UMLS:C0229211 VHOG:0001167 XAO:0003221 ZFA:0000119 inner nuclear layer intermediate cell layer neural retina inner nuclear layer retina inner nuclear layer retinal inner nuclear layer stratum nucleare internum stratum nucleare internum retinae INL uberon layer of inner granules retina, inner nuclear layer UBERON:0001791 AO notes NLXANAT:1005031 appears to be retired inner nuclear layer of retina Cytoarchitectural layer of retina containing closely packed cell bodies, the majority of which are bipolar cells (adapted from Wikipedia). NLX:93816 The layer of the retina composed of the cell bodies of bipolar cells, horizontal cells, and some of the cell bodies of amacrine cells[BTO:0003176]. BTO:0003176 (...) 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:0001167 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 UMLS:C0229211 ncithesaurus:Inner_Nuclear_Layer intermediate cell layer ZFA:0000119 neural retina inner nuclear layer EMAPA:19155 stratum nucleare internum retinae FMA:58686 FMA:TA layer of inner granules NLX:93816 retina, inner nuclear layer BAMS:Rinl Cytoarchitectural layer of retina that contains somata of retinal ganglion cells, bounded by the stratum opticum and the inner plexiform layer a layer of the retina that consists of retinal ganglion cells[WP]. innermost nuclear layer of the retina, which contains neurons that project axons through the optic nerve to the brain[Wikipedia:Ganglion_cell_layer]. (...) 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] NIFSTD class appears to be retired in nlx[http://neurolex.org/wiki/Nlx_anat_1005030] ganglion cell layer BAMS:Rgcl BTO:0003398 CALOHA:TS-0867 EMAPA:35739 FMA:58687 MA:0001310 NCIT:C32652 NLX:36500 NLXANAT:1005030 TAO:0000024 VHOG:0001166 XAO:0003223 ZFA:0000024 GCL layer RGC layer ganglionic cell layer of retina retina ganglion cell layer retina ganglion layer retinal ganglion cell layer retinal ganglion layer stratum ganglionicum (retina) uberon retina, ganglion cell layer stratum ganglionicum retinae UBERON:0001792 ganglionic layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png FMA FMA Cytoarchitectural layer of retina that contains somata of retinal ganglion cells, bounded by the stratum opticum and the inner plexiform layer NLX:36500 a layer of the retina that consists of retinal ganglion cells[WP]. innermost nuclear layer of the retina, which contains neurons that project axons through the optic nerve to the brain[Wikipedia:Ganglion_cell_layer]. (...) 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:0001166 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 NIFSTD class appears to be retired in nlx[http://neurolex.org/wiki/Nlx_anat_1005030] NIF ganglion cell layer FMA:58687 ZFA:0000024 ganglionic cell layer of retina FMA:58687 retinal ganglion layer MP:0008510 stratum ganglionicum (retina) FMA:58687 retina, ganglion cell layer BAMS:Rgcl stratum ganglionicum retinae layer of the retina formed by expansion of the fibers of the optic nerve (...) 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] UBERON:0005888 nerve fiber layer DMBA:15652 EMAPA:18591 FMA:58688 MA:0001314 TAO:0002212 VHOG:0001169 XAO:0003220 ZFA:0001619 layer of nerve fibers of retina layer of nerve fibres of retina optic fiber layer retina nerve fiber layer stratum neurofibrarum (retina) stratum neurofibrarum retinae stratum opticum of retina uberon neural retina nerve fibre layer optic fiber layer optic fiber layers stratum neurofibrum retinae UBERON:0001793 nerve fiber layer of retina FMA layer of the retina formed by expansion of the fibers of the optic nerve ISBN:0-914294-08-3 MGI:smb (...) 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:0001169 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 nerve fiber layer ZFA:0001619 optic fiber layer DMBA:15652 stratum neurofibrarum retinae FMA:58688 FMA:TA neural retina nerve fibre layer EMAPA:18591 optic fiber layer VHOG:0001169 optic fiber layers TAO:0002212 stratum neurofibrum retinae The row of fused Muller cell processes and astrocytes that separates the retinal nerve fiber layer from the vitreous[MP]. TODO - check frog/fish Membrane on the apical surface of the retina. The retinal vasculature becomes adhered to the apical surface of the ILM by 30dpf[ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3]. ILM EMAPA:36519 FMA:58689 MA:0001313 NCIT:C32807 TAO:0001029 UMLS:C1512783 XAO:0003222 ZFA:0001029 inner limiting membrane inner limiting membrane of retina internal limiting lamina of retina internal limiting membrane of retina retina inner limiting membrane retina internal limiting lamina stratum limitans internum retinae uberon inner limiting membranes UBERON:0001794 inner limiting layer of retina MA The row of fused Muller cell processes and astrocytes that separates the retinal nerve fiber layer from the vitreous[MP]. MP:0010235 Membrane on the apical surface of the retina. The retinal vasculature becomes adhered to the apical surface of the ILM by 30dpf[ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3]. ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3 ILM ZFA:0001029 UMLS:C1512783 ncithesaurus:Inner_Limiting_Membrane inner limiting membrane XAO:0003222 retina inner limiting membrane MP:0010235 stratum limitans internum retinae FMA:58689 FMA:TA inner limiting membranes ZFA:0001029 Cytoarchitectural layer of the retina that is made up of a dense reticulum of fibrils formed by interlaced dendrites of retinal ganglion cells and cells of the inner nuclear layer (adapted from Wikipedia) The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells[GO][GO:0010842]. The layer within the retina where the bipolar cells synapse with the dendrites of the ganglion cells.[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 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] http://neurolex.org/wiki/Nlx_anat_1005032 appears to be retired BAMS:Ripl BTO:0003175 EMAPA:35741 FMA:58704 MA:0001312 NCIT:C32809 NLX:20558 NLXANAT:1005032 TAO:0001329 UMLS:C0229221 VHOG:0001168 XAO:0003225 ZFA:0001329 retina inner plexiform layer retinal inner plexiform layer stratum plexiforme internum IPL uberon inner plexiform layer internal plexiform layer of retina retina, inner plexiform layer retinal internal plexiform layer stratum plexifome internum stratum plexiforme internum retinae UBERON:0001795 inner plexiform layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png Cytoarchitectural layer of the retina that is made up of a dense reticulum of fibrils formed by interlaced dendrites of retinal ganglion cells and cells of the inner nuclear layer (adapted from Wikipedia) NLX:20558 The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells[GO][GO:0010842]. GO:0010842 The layer within the retina where the bipolar cells synapse with the dendrites of the ganglion cells.[TAO] 2012-08-14 TAO:0001329 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 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:0001168 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 UMLS:C0229221 ncithesaurus:Inner_Plexiform_Layer stratum plexiforme internum FMA:58704 IPL inner plexiform layer BTO:0003175 internal plexiform layer of retina NLXANAT:1005032 retina, inner plexiform layer BAMS:Ripl retinal internal plexiform layer NLXANAT:1005032 stratum plexifome internum BTO:0003175 stratum plexiforme internum retinae 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 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 Trunk ganglion which is part of a bilaterally paired set of sympathetic ganglia located anterior and lateral to the spinal cord. UBERON:0005466 EHDAA2:0001403 EHDAA:5635 FMA:5891 MA:0003100 TAO:0001556 ZFA:0001556 ganglion of sympathetic trunk ganglion trunci sympathetici ganglion trunci sympathici sympathetic chain ganglion uberon ganglia of sympathetic trunk ganglia trunci sympathici paravertebral ganglia paravertebral ganglion sympathetic chain ganglia UBERON:0001807 paravertebral ganglion http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray847.png ZFA Trunk ganglion which is part of a bilaterally paired set of sympathetic ganglia located anterior and lateral to the spinal cord. ZFIN:curator ganglion trunci sympathetici ganglion trunci sympathici FMA:5891 FMA:TA ganglia of sympathetic trunk ganglia trunci sympathici paravertebral ganglia FMA:80128 paravertebral ganglion sympathetic chain ganglia Anatomical junction where subdivisions of two or more neural trees interconnect with one another to form a network through which nerve fibers of the constituent nerve trees become regrouped; together with other nerve plexuses, nerves and ganglia, it constitutes the peripheral nervous system. Examples: cervical nerve plexus, brachial nerve plexus, sacral nerve plexus[FMA]. in FMA this is a subtype of junction rather than tissue plexus AEO:0000138 BTO:0000205 EHDAA2:0003138 EHDAA:3780 EMAPA:37683 FMA:5901 MA:0002407 NCIT:C12929 UMLS:C0501403 uberon UBERON:0001810 nerve plexus Anatomical junction where subdivisions of two or more neural trees interconnect with one another to form a network through which nerve fibers of the constituent nerve trees become regrouped; together with other nerve plexuses, nerves and ganglia, it constitutes the peripheral nervous system. Examples: cervical nerve plexus, brachial nerve plexus, sacral nerve plexus[FMA]. FMA:5901 in FMA this is a subtype of junction rather than tissue FMA EMAPA:37683 MA:th UMLS:C0501403 ncithesaurus:Nerve_Plexus the mucous membrane that lines the inner surface of the eyelids and the front of the eyeball conjunctival AAO:0010343 BTO:0003415 CALOHA:TS-2232 EFO:0000374 EMAPA:18233 EV:0100340 FMA:59011 GAID:898 MA:0000265 MESH:A09.371.192 NCIT:C12341 UMLS:C0009758 XAO:0000182 conjunctivae conjunctivas tunica conjunctiva wall of conjunctival sac uberon UBERON:0001811 conjunctiva http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png FMA cjm MA ISBN:0781772214 the mucous membrane that lines the inner surface of the eyelids and the front of the eyeball MESH:A09.371.060.200 MGI:csmith MP:0001310 UMLS:C0009758 ncithesaurus:Conjunctiva conjunctivae XAO:0000182 conjunctivas XAO:0000182 tunica conjunctiva FMA:TA wall of conjunctival sac FMA:59011 an intermingling of fiber fascicles from adjacent spinal nerves to form a network. To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles.[well established][VHOG] EHDAA2:0001899 EMAPA:16987 FMA:5903 MA:0000235 NCIT:C49601 UMLS:C0228603 VHOG:0000925 plexus nervorum spinalium plexus of spinal nerves somatic nerve plexus spinal nerve plexus uberon UBERON:0001813 spinal nerve plexus an intermingling of fiber fascicles from adjacent spinal nerves to form a network. To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles.[well established][VHOG] 2012-09-17 VHOG:0000926 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.436 UMLS:C0228603 ncithesaurus:Spinal_Nerve_Plexus plexus nervorum spinalium FMA:5903 FMA:TA plexus of spinal nerves FMA:5903 somatic nerve plexus FMA:5903 spinal nerve plexus FMA:5903 An arrangement of nerve fibers, running from the spine where it proceeds through the neck then the axilla and into the arm where it innervates skin and muscle. [WP,modified]. check superclass - nerve vs collection of fibers vs junction; note that FMA also has 'brachial autonomic nerve plexus' A nerve plexus originating from the anterior branches of the last four cervical and the first thoracic spinal nerves, giving off many of the principal nerves of the shoulder, chest, and arms. [TFD][VHOG] To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles.[well established][VHOG] EHDAA2:0000180 EHDAA:3782 EMAPA:16988 FMA:5906 GAID:842 MA:0001180 MESH:D001917 NCIT:C12682 OpenCyc:Mx4rwNWmO5wpEbGdrcN5Y29ycA UMLS:C0006090 VHOG:0000372 brachial plexus uberon plexus brachialis UBERON:0001814 brachial nerve plexus http://upload.wikimedia.org/wikipedia/commons/3/3a/Gray808.png http://upload.wikimedia.org/wikipedia/commons/c/c9/Brachial_plexus_color.svg An arrangement of nerve fibers, running from the spine where it proceeds through the neck then the axilla and into the arm where it innervates skin and muscle. [WP,modified]. UBERON:cjm A nerve plexus originating from the anterior branches of the last four cervical and the first thoracic spinal nerves, giving off many of the principal nerves of the shoulder, chest, and arms. [TFD][VHOG] 2012-09-17 VHOG:0000372 VHOG To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles.[well established][VHOG] 2012-09-17 VHOG:0000372 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.436 UMLS:C0006090 ncithesaurus:Brachial_Plexus brachial plexus MA:0001180 plexus brachialis plexus brachialis An arrangement of nerve fibers, running from the spine that travels to the pelvic appendage where it innervates skin and muscle. BAMS:lsp EHDAA2:0001040 EHDAA:4673 EMAPA:17587 FMA:5907 GAID:849 MA:0001181 MESH:D008160 NCIT:C52805 OpenCyc:Mx4rvzYo75wpEbGdrcN5Y29ycA UMLS:C0024093 VHOG:0000926 lumbosacral plexus plexus lumbosacralis uberon plexus lumbosacralis UBERON:0001815 lumbosacral nerve plexus http://upload.wikimedia.org/wikipedia/commons/8/8d/Gray822.png An arrangement of nerve fibers, running from the spine that travels to the pelvic appendage where it innervates skin and muscle. UBERON:cjm UMLS:C0024093 ncithesaurus:Lumbosacral_Plexus plexus lumbosacralis FMA:5907 FMA:TA plexus lumbosacralis A nerve plexus that is part of an autonomic nervous system [Automatically generated definition]. EMAPA:18224 FMA:5910 MA:0000221 autonomic plexus plexus autonomicus plexus nervosus visceralis plexus visceralis visceral nerve plexus visceral plexus uberon UBERON:0001816 autonomic nerve plexus A nerve plexus that is part of an autonomic nervous system [Automatically generated definition]. OBOL:automatic plexus autonomicus FMA:5910 FMA:TA plexus nervosus visceralis FMA:5910 FMA:TA plexus visceralis FMA:5910 FMA:TA 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 The fibrous investing tissue, covered by keratinized epithelium, that immediately surrounds a tooth and is contiguous with its periodontal ligament and with the mucosal tissues of the mouth[Glossary of Periodontal Terms 2001]. FMA has a 3-level breakdown of jaws into: region, jaw (skeleton+gums), skeleton. gingival BTO:0000519 CALOHA:TS-2074 EFO:0001925 EMAPA:35945 EV:0100064 FMA:59762 GAID:1257 MA:0000342 MESH:A14.254.646.480 NCIT:C32677 OpenCyc:Mx4rvViWnZwpEbGdrcN5Y29ycA UMLS:C0017562 VHOG:0001269 galen:Gingiva gum gum tissue gums uberon gingival mucosa UBERON:0001828 gingiva Tooth:Section.svg ISBN:0013002015 The fibrous investing tissue, covered by keratinized epithelium, that immediately surrounds a tooth and is contiguous with its periodontal ligament and with the mucosal tissues of the mouth[Glossary of Periodontal Terms 2001]. ISBN:0013002015 UMLS:C0017562 ncithesaurus:Gingiva gum FMA:59762 gum tissue 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 One of three half-circular, interconnected tubes located inside each ear[WP]. Fluid-filled toroidal spaces, arranged orthogonally to each other in the ear, that detect angular accelerations. (See Anatomical Atlas entry for semicircular canals by T. Whitfield.)[TAO] In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. These ducts are sometimes called canals, but technically the term semicircular canal applies to the spaces in the osseus labyrinth in which the semicircular ducts lie.[uncertain][VHOG] detects angular acceleration MA divides this into osseous and duct. In FMA, this is systemically part of the bony labyrinth. Note this is an anatomical space in ZFA. The MA treatment has advantages for representing the neuroepithelium, which should not be part of bone. Also check duct vs canal AAO:0011098 BTO:0003383 CALOHA:TS-2164 EMAPA:32832 EV:0100365 FMA:60186 GAID:776 MA:0000249 MESH:D012665 NCIT:C33527 TAO:0000431 UMLS:C0036622 VHOG:0001144 XAO:0000198 ZFA:0000431 semicircular canals uberon canalis semicircularis ductus semicirculares scc semicircular ducts UBERON:0001840 semicircular canal http://upload.wikimedia.org/wikipedia/commons/3/33/Balance_Disorder_Illustration_A.png GO OG One of three half-circular, interconnected tubes located inside each ear[WP]. Fluid-filled toroidal spaces, arranged orthogonally to each other in the ear, that detect angular accelerations. (See Anatomical Atlas entry for semicircular canals by T. Whitfield.)[TAO] 2012-08-14 TAO:0000431 TAO ZFIN:curator In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. These ducts are sometimes called canals, but technically the term semicircular canal applies to the spaces in the osseus labyrinth in which the semicircular ducts lie.[uncertain][VHOG] 2012-09-17 VHOG:0001144 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.414 MA divides this into osseous and duct. In FMA, this is systemically part of the bony labyrinth. Note this is an anatomical space in ZFA. The MA treatment has advantages for representing the neuroepithelium, which should not be part of bone. Also check duct vs canal MA UMLS:C0036622 ncithesaurus:Semicircular_Canal semicircular canals TAO:0000431 canalis semicircularis ductus semicirculares BTO:0003383 FMA:71880 FMA:TA scc TAO:0000431 semicircular ducts XAO:0000198 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 Transudate contained in the osseous labyrinth outside the membranous labyrinth.[FMA] EMAPA:36549 FMA:60908 GAID:1185 MA:0002529 MESH:A12.207.571.678 NCIT:C33297 TAO:0005413 UMLS:C0031059 ZFA:0005413 uberon liquor cotunnii perilympha UBERON:0001845 perilymph Wikipedia Transudate contained in the osseous labyrinth outside the membranous labyrinth.[FMA] FMA:FMA UMLS:C0031059 ncithesaurus:Perilymph liquor cotunnii perilympha 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 Organ with organ cavity which consists of the vestibular labyrinth and the cochlear labyrinth. The membranous labyrinth is lodged within the bony labyrinth and has the same general form; it is, however, considerably smaller and is partly separated from the bony walls by a quantity of fluid, the perilymph.[FMA, WP] A system of communicating epithelial sacs and ducts within the bony labyrinth, containing the endolymph. [TFD][VHOG] 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] inner ear has parts membranous and osseuous/bony labyrinth. it's not clear where the EMAPA term 'labyrinth' belong, we place them here for now UBERON:0010113 AAO:0011060 EHDAA2:0000899 EHDAA:4698 EMAPA:17815 EV:0100367 FMA:61022 MA:0000242 NCIT:C33090 UMLS:C0458700 VHOG:0000729 XAO:0000194 labyrinthus membranaceus uberon UBERON:0001849 membranous labyrinth http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray924.png FMA MA Organ with organ cavity which consists of the vestibular labyrinth and the cochlear labyrinth. The membranous labyrinth is lodged within the bony labyrinth and has the same general form; it is, however, considerably smaller and is partly separated from the bony walls by a quantity of fluid, the perilymph.[FMA, WP] FMA:61022 A system of communicating epithelial sacs and ducts within the bony labyrinth, containing the endolymph. [TFD][VHOG] 2012-09-17 VHOG:0000729 VHOG 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:0000729 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.366 inner ear has parts membranous and osseuous/bony labyrinth. it's not clear where the EMAPA term 'labyrinth' belong, we place them here for now EMAPA UMLS:C0458700 ncithesaurus:Membranous_Labyrinth labyrinthus membranaceus 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 the larger of the two otolith organs in the vestibule The portion of the membranous labyrinth of the ear into which the semicircular ducts find their outlet. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus.[well established][VHOG] AAO:0000625 AAO:0011109 BTO:0001807 EHDAA2:0002153 EHDAA:4726 EMAPA:17293 EV:0100368 FMA:61113 MA:0000247 NCIT:C33844 TAO:0000700 UMLS:C0042158 VHOG:0000289 XAO:0000195 ZFA:0000700 membranous labyrinth utricle utricle utriculus utriculus (labyrinthus vestibularis) uberon UBERON:0001853 XAO/AAO to be checked - see https://github.com/seger/aao/issues/5; AAO has both utricle and utriculus; these are generally considered synonyms - e.g. http://www.fishbase.org/glossary/Glossary.php?q=utriculus utricle of membranous labyrinth Wikipedia ZFA the larger of the two otolith organs in the vestibule ISBN:0-8036-0655-9 MGI:smb MP:0006090 The portion of the membranous labyrinth of the ear into which the semicircular ducts find their outlet. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] 2012-09-17 VHOG:0000289 VHOG In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus.[well established][VHOG] 2012-09-17 VHOG:0000289 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414 UMLS:C0042158 ncithesaurus:Utricle utriculus ZFA:0000700 the smaller of the two otolith organs in the vestibule The most ventral chamber of the membranous labyrinth. [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 gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. (...) In all gnathostomes, the utriculus connects ventrally with a larger sac, called the sacculus (...) .[well established][VHOG] AAO:0000550 BTO:0001805 EHDAA2:0001769 EHDAA:4712 EMAPA:17290 EV:0100369 FMA:61116 MA:0000246 NCIT:C33503 TAO:0000428 UMLS:C0036029 VHOG:0000374 XAO:0000196 ZFA:0000428 membranous labyrinth saccule saccule sacculus sacculus (labyrinthus vestibularis) uberon sacculus UBERON:0001854 XAO/AAO to be checked - see https://github.com/seger/aao/issues/5 saccule of membranous labyrinth http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg Wikipedia ZFA the smaller of the two otolith organs in the vestibule ISBN:0-8036-0655-9 MGI:smb MP:0006089 The most ventral chamber of the membranous labyrinth. [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:0000374 VHOG In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. (...) In all gnathostomes, the utriculus connects ventrally with a larger sac, called the sacculus (...) .[well established][VHOG] 2012-09-17 VHOG:0000374 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414 UMLS:C0036029 ncithesaurus:Saccule sacculus ZFA:0000428 sacculus An endolymph filled cavity inside the cochlea, located in between the scala tympani and the scala vestibuli, separated by the basilar membrane and Reissner's membrane (the vestibular membrane) respectively. Houses the organ of Corti[WP]. TODO - check cochlear duct vs cochlear aqueduct vs scala media The coiled portion of the membranous labyrinth located inside the cochlea. It contains endolymph. [TFD][VHOG] In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. (...) In all gnathostomes, the utriculus connects ventrally with a larger sac, called the sacculus (...) In most groups of gnathostomes, the caudoventral evagination of the sacculus forms a small lagena, and in some diapsids and mammals the lagena develops into a longer duct. The lagena becomes greatly elongated in therians and coils to form the cochlear duct.[well established][VHOG] BIRNLEX:2562 BTO:0001692 CALOHA:TS-0152 EHDAA2:0000262 EHDAA:4718 EMAPA:17598 FMA:61119 GAID:874 MA:0000243 MESH:D003053 NCIT:C32335 UMLS:C1281166 UMLS:C1323110 VHOG:0000507 Reissner's canal Reissners canal cochlea duct cochlear duct scala medias uberon cochlear aqueduct ductus cochlearis membranous cochlea scala media scala of Loewenberg UBERON:0001855 cochlear duct of membranous labyrinth http://upload.wikimedia.org/wikipedia/commons/b/bc/Gray928.png FMA MA An endolymph filled cavity inside the cochlea, located in between the scala tympani and the scala vestibuli, separated by the basilar membrane and Reissner's membrane (the vestibular membrane) respectively. Houses the organ of Corti[WP]. The coiled portion of the membranous labyrinth located inside the cochlea. It contains endolymph. [TFD][VHOG] 2012-09-17 VHOG:0000507 VHOG In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. (...) In all gnathostomes, the utriculus connects ventrally with a larger sac, called the sacculus (...) In most groups of gnathostomes, the caudoventral evagination of the sacculus forms a small lagena, and in some diapsids and mammals the lagena develops into a longer duct. The lagena becomes greatly elongated in therians and coils to form the cochlear duct.[well established][VHOG] 2012-09-17 VHOG:0000507 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414 UMLS:C1281166 BIRNLEX:2562 UMLS:C1323110 BIRNLEX:2562 UMLS:C1323110 ncithesaurus:Cochlear_Duct Reissner's canal FMA:61119 Reissners canal BIRNLEX:2562 cochlea duct BIRNLEX:2562 scala medias BIRNLEX:2562 ductus cochlearis ductus cochlearis BTO:0001692 membranous cochlea BTO:0001692 scala media scala of Loewenberg BTO:0001692 Any of the three loop-shaped membranous inner tubular parts of the semicircular canals that are about one-fourth the diameter of the corresponding outer bony canals, that communicate at each end with the utricle, and that have near one end an expanded ampulla containing an area of sensory epithelium TODO - check canal vs duct. see Wikipedia:File:Gray927.png In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus (...); Gnathostome ears have a horizontal semicircular duct. This brings their complement to three semicircular ducts, a pattern retained throughout gnathostome evolution.[well established][VHOG] EMAPA:32830 FMA:61122 MA:0000251 NCIT:C33528 UMLS:C1323109 VHOG:0000238 uberon ductus semicirculares membranous semicircular canal UBERON:0001856 semicircular duct MA FMA MA Any of the three loop-shaped membranous inner tubular parts of the semicircular canals that are about one-fourth the diameter of the corresponding outer bony canals, that communicate at each end with the utricle, and that have near one end an expanded ampulla containing an area of sensory epithelium In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus (...); Gnathostome ears have a horizontal semicircular duct. This brings their complement to three semicircular ducts, a pattern retained throughout gnathostome evolution.[well established][VHOG] 2012-09-17 VHOG:0000238 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414 and p.58 UMLS:C1323109 ncithesaurus:Semicircular_Duct ductus semicirculares FMA:71880 FMA:TA membranous semicircular canal MA:0000251 The part of the membranous labyrinth that includes the utricle and saccule lodged within the vestibule and the semicircular ducts lodged eccentrically in the corresponding canals. vestibular component BTO:0001856 CALOHA:TS-0479 EHDAA2:0000832 EHDAA:4706 EMAPA:17286 EMAPA:17815 FMA:61255 MA:0000245 NCIT:C33871 UMLS:C0042606 XAO:0004145 inner ear vestibular component uberon labyrinthus vestibularis vestibular apparatus UBERON:0001862 vestibular labyrinth The part of the membranous labyrinth that includes the utricle and saccule lodged within the vestibule and the semicircular ducts lodged eccentrically in the corresponding canals. BTO:0001856 UMLS:C0042606 ncithesaurus:Vestibular_Labyrinth inner ear vestibular component EHDAA2:0000832 labyrinthus vestibularis BTO:0001856 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 Part of the hippocampal formation forming a 'V' or 'U' shaped structure with the opening bounded by hippocampal area CA3. It consists of 3 layers from superficial to deep: molecular, granule cell and polymorphic or hilar layer. The dentate gyrus is one of two interlocking gyri of the hippocampus. It contains granule cells, which project to the pyramidal cells and interneurons of the CA3 region of the ammon gyrus[GO][GO:0021542]. BAMS:DG BIRNLEX:1178 BM:Tel-DG BTO:0002496 BTO:0002615 CALOHA:TS-2388 DHBA:10295 DMBA:16115 EFO:0001366 EMAPA:19037 FMA:61922 GAID:624 HBA:12891 MA:0000190 MBA:726 MESH:A08.186.211.577.405.200 NCIT:C32452 UMLS:C0152314 area dentata dentate area (dentate gyrus) dentate gyrus fascia dentata uberon dentate area gyrus dentatus hippocampal dentate gyrus UBERON:0001885 BTO says dentate gyrus = fascia dentata + hilus. Note that GO classifies dentate gyrus development under hippocampus development dentate gyrus of hippocampal formation http://upload.wikimedia.org/wikipedia/commons/a/ab/HippocampalRegions.jpg MA Part of the hippocampal formation forming a 'V' or 'U' shaped structure with the opening bounded by hippocampal area CA3. It consists of 3 layers from superficial to deep: molecular, granule cell and polymorphic or hilar layer. BIRNLEX:1178 The dentate gyrus is one of two interlocking gyri of the hippocampus. It contains granule cells, which project to the pyramidal cells and interneurons of the CA3 region of the ammon gyrus[GO][GO:0021542]. GO:0021542 UMLS:C0152314 ncithesaurus:Dentate_Gyrus dentate area (dentate gyrus) DHBA:10295 dentate area DHBA:10295 gyrus dentatus gyrus dentatus BTO:0002496 hippocampal dentate gyrus BTO:0002496 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 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 Diencephalic white matter (tract) which is comprised of retinal ganglion cell axons after which they have passed through the optic chiasm[ZFA]. Predominantly white matter structure found in diencephalon consisting of fibers originating in the retina. The optic tract is considered to extend from the point of the optic chiasm and terminates largely, although not exclusively, in the lateral geniculate complex. Other fibers end in the superior colliculus and other structures in the diencephalon, midbrain and brainstem (MM)[NIF]. relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII 'continuous_with' BAMS:opt BIRNLEX:1684 BM:Tel-OT DHBA:10589 DMBA:17785 EMAPA:16678 EMAPA:35617 FMA:62046 GAID:735 HBA:9309 MA:0001099 MBA:125 MESH:D014795 NCIT:C33218 TAO:0000252 UMLS:C0152405 VHOG:0001164 XAO:0004101 ZFA:0000252 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=460 optic lemniscus uberon optic tracts tractus optici tractus opticus visual pathway UBERON:0001908 optic tract http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png Diencephalic white matter (tract) which is comprised of retinal ganglion cell axons after which they have passed through the optic chiasm[ZFA]. Predominantly white matter structure found in diencephalon consisting of fibers originating in the retina. The optic tract is considered to extend from the point of the optic chiasm and terminates largely, although not exclusively, in the lateral geniculate complex. Other fibers end in the superior colliculus and other structures in the diencephalon, midbrain and brainstem (MM)[NIF]. NIFSTD ZFIN:curator UMLS:C0152405 BIRNLEX:1684 UMLS:C0152405 ncithesaurus:Optic_Tract http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=460 BIRNLEX:1684 optic tracts ZFA:0000252 tractus optici NeuroNames:460 tractus opticus visual pathway GAID:735 A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males. Originally this was classified as a female reproductive structure, as it was in the MP in 2011 Any of the milk-producing apocrine glands typically occurring in pairs in female mammals and consisting of lobes containing clusters of alveoli with a system of ducts to convey the milk to an external nipple or teat. [TFD][VHOG] The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG] mammary A mouse mammary gland contains a single duct or sinus, forming 5-10 secondary ducts The male Dayak fruit bat has lactating mammary glands The mammary glands of humans are in the thoracid/breast region. In other mammals they may be located elsewhere on the mammary ridges. The BTO class represents the combination of nipple plus lobe The FMA class represents an individule lobe. The nipple is not a part The MA class represents a composite structure, including the nipple, fat, connective tissue, smooth muscle as parts BTO:0000817 CALOHA:TS-0595 EFO:0000854 EMAPA:17759 EV:0100125 FMA:286452 MA:0000145 MAT:0000073 MESH:D008321 MIAA:0000073 NCIT:C12367 OpenCyc:Mx4rvVjVq5wpEbGdrcN5Y29ycA UMLS:C0929301 VHOG:0000398 glandula mammaria lactiferous gland lobe of breast milk patch uberon Brustdruese dug glandula mammaria lobe of mammary gland mamma mammae UBERON:0001911 mammary gland http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males. BTO:0000817 Any of the milk-producing apocrine glands typically occurring in pairs in female mammals and consisting of lobes containing clusters of alveoli with a system of ducts to convey the milk to an external nipple or teat. [TFD][VHOG] 2012-09-17 VHOG:0000398 VHOG The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG] 2012-09-17 VHOG:0000398 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224 UMLS:C0929301 ncithesaurus:Mammary_Gland glandula mammaria FMA:57983 FMA:TA lactiferous gland FMA:62088 milk patch NCBITaxon:9255 Brustdruese BTO:0000817 dug glandula mammaria lobe of mammary gland FMA:62088 mamma BTO:0000817 mammae Organ component of the mammary gland which consists of an aggregate of mammary alveoli that communicate with a lobular lactiferous duct.[FMA] TODO - ensure correct terminology for lobes/lobules. In mouse there are no distinct lobes (ISBN:0123813611), here lobule appears to be synonymous with acinus EMAPA:36634 FMA:62090 MA:0000793 acinus of mammary gland lactiferous acinus lactiferous gland lobule lactiferous lobule lobule of lactiferous gland lobule of mammary gland mammary acinus mammary gland lobule uberon UBERON:0001912 lobule of mammary gland FMA Organ component of the mammary gland which consists of an aggregate of mammary alveoli that communicate with a lobular lactiferous duct.[FMA] FMA:62090 acinus of mammary gland FMA:62090 lactiferous acinus FMA:62090 lactiferous gland lobule FMA:62090 lactiferous lobule FMA:62090 lobule of lactiferous gland FMA:62090 lobule of mammary gland FMA:62090 mammary acinus FMA:62090 mammary gland lobule MA:0000793 An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. to axiomatize the different forms of mammary gland secretion an ontology of the phases of pregnancy/lactation is required. Using the existing GO def of lactation is circular. The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG] ncit:Milk refers specifically to cow milk BTO:0000868 CALOHA:TS-0636 EMAPA:36540 ENVO:02000031 EV:0100126 FMA:62100 GAID:1230 MA:0002552 MAT:0000056 MESH:A13.622 MIAA:0000056 NCIT:C13401 OpenCyc:Mx4rvVjGZJwpEbGdrcN5Y29ycA UMLS:C1511310 VHOG:0001263 galen:Milk mammary gland milk uberon UBERON:0001913 milk An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG] 2012-09-17 VHOG:0001263 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224 ncit:Milk refers specifically to cow milk ncit UMLS:C1511310 ncithesaurus:Breast_Fluid_or_Secretion 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 Nucleus in the anterior part of the hypothalamus. (MSH) * one of the magnocellular hypothalamic nuclei, an elongated plate of large, deeply staining cells located close to the third ventricle in the anterior hypothalamic area; major source of oxytocin and to a lesser extent, of antidiuretic hormone, neurohormones, which are carried to the neurohypophysis along the paraventriculohypophysial tract. (CSP) Pa BAMS:PAH BAMS:PVH BAMS:Pa BIRNLEX:1407 BM:Die-Hy-PAH BTO:0002476 DHBA:10476 EFO:0002469 EMAPA:35665 EV:0100229 FMA:62320 GAID:643 HBA:12905 MA:0000848 MBA:38 MESH:A08.186.211.730.385.357.342.400 UMLS:C0030532 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=387 filiform nucleus paraventricular hypothalamic nucleus paraventricular nucleus uberon nuclei paraventriculares nuclei paraventricularis hypothalami nucleus filiformis nucleus hypothalami filiformis nucleus hypothalami paraventricularis nucleus paraventricularis hypothalami paraventricular nucleus hypothalamus (Malone) paraventricular nucleus of the hypothalamus parvocellular hypothalamic nucleus subcommissural nucleus (Ziehen) UBERON:0001930 paraventricular nucleus of hypothalamus http://upload.wikimedia.org/wikipedia/commons/e/ef/PVNss.jpg http://upload.wikimedia.org/wikipedia/en/thumb/e/ef/PVNss.jpg/200px-PVNss.jpg Nucleus in the anterior part of the hypothalamus. (MSH) * one of the magnocellular hypothalamic nuclei, an elongated plate of large, deeply staining cells located close to the third ventricle in the anterior hypothalamic area; major source of oxytocin and to a lesser extent, of antidiuretic hormone, neurohormones, which are carried to the neurohypophysis along the paraventriculohypophysial tract. (CSP) BIRNLEX:1407 Pa BIRNLEX:1407 NIFSTD:NeuroNames_abbrevSource UMLS:C0030532 BIRNLEX:1407 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=387 BIRNLEX:1407 nuclei paraventriculares NeuroNames:387 nuclei paraventricularis hypothalami nucleus filiformis NeuroNames:387 nucleus hypothalami filiformis NeuroNames:387 nucleus hypothalami paraventricularis NeuroNames:387 nucleus paraventricularis hypothalami BTO:0002476 paraventricular nucleus hypothalamus (Malone) NeuroNames:387 paraventricular nucleus of the hypothalamus NeuroNames:387 parvocellular hypothalamic nucleus BAMS:PVH subcommissural nucleus (Ziehen) NeuroNames:387 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 A stratified squamous epithelium consisting of a basal layer; it is keratinized or parakeratinized[BTO]. In humans: 15% orthokeratinized, 75% parakeratinized, 10% non-keratinized; diurnal; decreased keratinization with age. Note that in FMA this is classified as keratinized squamous - this perhaps refers to the epithelium of the attached or free gingiva BTO:0004998 FMA:62423 MA:0001576 NCIT:C49239 UMLS:C1179154 epithelial tissue of gingiva epithelium of gingiva gingiva epithelial tissue gingiva epithelium uberon UBERON:0001949 gingival epithelium A stratified squamous epithelium consisting of a basal layer; it is keratinized or parakeratinized[BTO]. BTO:0004998 UMLS:C1179154 ncithesaurus:Gingival_Epithelium epithelial tissue of gingiva OBOL:automatic gingiva epithelial tissue OBOL:automatic gingiva epithelium OBOL:automatic 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 A part of the brain consisting of a three layered cortex located in the forebrain bordering the medial surface of the lateral ventricle. The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum. hippocampal Non-mammalian species do not have a brain structure that looks like the mammalian hippocampus, but they have one that is considered homologous to it. The hippocampus, as pointed out above, is essentially the medial edge of the cortex. Only mammals have a fully developed cortex, but the structure it evolved from, called the pallium, is present in all vertebrates, even the most primitive ones such as the lamprey or hagfish. The pallium is usually divided into three zones: medial, lateral, and dorsal. The medial pallium forms the precursor of the hippocampus. It does not resemble the hippocampus visually, because the layers are not warped into an S shape or enwrapped by the dentate gyrus, but the homology is indicated by strong chemical and functional affinities. There is now evidence that these hippocampal-like structures are involved in spatial cognition in birds, reptiles, and fish. In birds, the correspondence is sufficiently well established that most anatomists refer to the medial pallial zone as the 'avian hippocampus'. The story for fish is more complex. In teleost fish (which make up the great majority of existing species), the forebrain is distorted in comparison to other types of vertebrates: most neuroanatomists believe that the teleost forebrain is essentially everted, like a sock turned inside-out, so that structures that lie in the interior, next to the ventricles, for most vertebrates, are found on the outside in teleost fish, and vice versa. One of the consequences of this is that the medial pallium ('hippocampal' zone) of a typical vertebrate is thought to correspond to the lateral pallium of a typical fish. Several types of fish (particularly goldfish) have been shown experimentally to have strong spatial memory abilities, even forming 'cognitive maps' of the areas they inhabit.[WP] UBERON:0003940 UBERON:0004165 BAMS:CA BIRNLEX:721 BM:Tel-CAM BTO:0003705 CALOHA:TS-0460 DHBA:10296 DMBA:16124 EFO:0000530 EHDAA2:0004443 EMAPA:32772 EMAPA:32845 EV:0100180 FMA:62493 GAID:623 MA:0000191 MAT:0000114 MBA:375 MESH:A08.186.211.577.405 MIAA:0000114 NCIT:C12444 NCIT:C32374 OpenCyc:Mx4rv3piFJwpEbGdrcN5Y29ycA PBA:128012244 UMLS:C0019564 VHOG:0001177 Ammon's horn ammon gyrus ammon horn hippocampus major hippocampus proper hippocampus proprius uberon Ammon horn fields Ammons horn cornu ammonis hippocampus UBERON:0001954 Ammon's horn http://upload.wikimedia.org/wikipedia/commons/2/2e/Gray739-emphasizing-hippocampus.png FMA ABA FMA A part of the brain consisting of a three layered cortex located in the forebrain bordering the medial surface of the lateral ventricle. The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum. BIRNLEX:721 UMLS:C0019564 BIRNLEX:721 UMLS:C0019564 ncithesaurus:Hippocampus Ammon's horn GO:0021541 ammon gyrus GO:0021541 ammon horn BIRNLEX:721 hippocampus proper BIRNLEX:721 hippocampus proprius FMA:62493 FMA:TA Ammon horn fields BAMS:CA Ammons horn BTO:0003705 cornu ammonis GO:0021541 hippocampus MA:0000191 An epithelium that is part of a respiratory bronchiole [Automatically generated definition]. EMAPA:35730 FMA:62498 MA:0001773 NCIT:C48943 UMLS:C1179179 bronchiolus respiratorius epithelial tissue bronchiolus respiratorius epithelium epithelial tissue of bronchiolus respiratorius epithelial tissue of respiratory bronchiole epithelium of bronchiolus respiratorius respiratory bronchiole epithelial tissue respiratory bronchiole epithelium uberon UBERON:0001955 epithelium of respiratory bronchiole An epithelium that is part of a respiratory bronchiole [Automatically generated definition]. OBOL:automatic UMLS:C1179179 ncithesaurus:Respiratory_Bronchiole_Epithelium bronchiolus respiratorius epithelial tissue OBOL:automatic bronchiolus respiratorius epithelium OBOL:automatic epithelial tissue of bronchiolus respiratorius OBOL:automatic epithelial tissue of respiratory bronchiole OBOL:automatic epithelium of bronchiolus respiratorius OBOL:automatic respiratory bronchiole epithelial tissue OBOL:automatic 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 the parenchymatous tissue of the spleen that surrounds splenic blood vessels, consists of compact masses of lymphatic cells and is where foreign material removed from the blood is used to initiate an immune reaction that results in the production of antibodies The white pulp contains T cells, B cells and accessory cells. The function of the white pulp is to mount an immunological response to antigens within the blood. The white pulp is present in the form of a periarteriolar lymphoid sheath. This sheath contains B cell follicles and T cells. At the edge of the T zone is a region known as the marginal zone where larger lymphocytes and antigen presenting dendritic cells are located. [Wikipedia:White_pulp] CALOHA:TS-1264 EMAPA:35809 FMA:62805 MA:0000762 NCIT:C12993 UMLS:C0229686 pulpa alba spleen white pulp splenic white pulp white pulp uberon noduli lymphoidei splenici UBERON:0001959 white pulp of spleen http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png the parenchymatous tissue of the spleen that surrounds splenic blood vessels, consists of compact masses of lymphatic cells and is where foreign material removed from the blood is used to initiate an immune reaction that results in the production of antibodies MGI:csmith MP:0002357 UMLS:C0229686 ncithesaurus:Splenic_White_Pulp pulpa alba FMA:62805 FMA:TA noduli lymphoidei splenici 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 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 the tubular intestinal glands found in the mucosal membranes In histology, an intestinal crypt, also crypt of LieberkC<hn and intestinal gland, is a gland found in the epithelial lining of the small intestine and colon. The crypts secrete various enzymes, including sucrase and maltase, along with endopeptidases and exopeptidases. Also new epithelium is formed here, keeping in mind that the epithelium at this site is frequently worn away by the passing food. Loss of proliferation control in the crypts is thought to lead to colorectal cancer. The basal portion of the Crypt contains multipotent stem cells. At each mitosis one daughter remains a stem cell while the other differentiates and migrates up the side of the crypt and eventually the villus. Goblet cells are among the cells produced in this fashion[Wikipedia:Intestinal_crypt]. Most fish lack intestinal glands that extend into the mucosa, Gadidae (Jacobshagen 1937) and Macrouridae (Geisterdoerfer 1973( have glands at the base of surface folds throughout intestine - these have been called crypts, but cell types are the same as for surface epithelium. Crypts have been described in salamander midguts (Reeder 1964) some reptiles (Luppa 1977) and some birds (Ziswiler and Farner 1972). Reptile crypts are less developed than birds and mammals, with epithelium similar to the surface. Avian crypts vary from those with absorprive and goblet cells to those that have cells with basophilic granules intestinal gland EMAPA:35266 FMA:63621 MA:0001535 NCIT:C32411 UMLS:C1621887 Lieberkuhn crypt Lieberkuhn gland Lieberkuhn's gland Lieberkuhn's glands crypt of Lieberkuhn crypt of Lieberkühn crypts of Lieberkühn follicles of lieberkuhn intestinal crypt intestinal crypts lieberkuhn crypt uberon intestinal gland of Lieberkuhn UBERON:0001983 crypt of Lieberkuhn http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg the tubular intestinal glands found in the mucosal membranes ISBN:0-683-40008-8 MP:0000490 In histology, an intestinal crypt, also crypt of LieberkC<hn and intestinal gland, is a gland found in the epithelial lining of the small intestine and colon. The crypts secrete various enzymes, including sucrase and maltase, along with endopeptidases and exopeptidases. Also new epithelium is formed here, keeping in mind that the epithelium at this site is frequently worn away by the passing food. Loss of proliferation control in the crypts is thought to lead to colorectal cancer. The basal portion of the Crypt contains multipotent stem cells. At each mitosis one daughter remains a stem cell while the other differentiates and migrates up the side of the crypt and eventually the villus. Goblet cells are among the cells produced in this fashion[Wikipedia:Intestinal_crypt]. Most fish lack intestinal glands that extend into the mucosa, Gadidae (Jacobshagen 1937) and Macrouridae (Geisterdoerfer 1973( have glands at the base of surface folds throughout intestine - these have been called crypts, but cell types are the same as for surface epithelium. Crypts have been described in salamander midguts (Reeder 1964) some reptiles (Luppa 1977) and some birds (Ziswiler and Farner 1972). Reptile crypts are less developed than birds and mammals, with epithelium similar to the surface. Avian crypts vary from those with absorprive and goblet cells to those that have cells with basophilic granules ISBN:9780521617147 intestinal gland UMLS:C1621887 ncithesaurus:Crypts_of_the_Lieberkuhn Lieberkuhn's glands crypts of Lieberkühn intestinal crypts intestinal gland of Lieberkuhn FMA:63621 A crypt of lieberkuhn that is part of a large intestine [Automatically generated definition]. EMAPA:35465 FMA:63622 MA:0001544 NCIT:C32924 UMLS:C1179777 intestinal gland of large intestine large intestinal crypt of Lieberkuhn large intestine crypt of Lieberkuhn large intestine intestinal gland large intestine lieberkuhn crypt lieberkuhn crypt of large intestine uberon UBERON:0001984 crypt of Lieberkuhn of large intestine A crypt of lieberkuhn that is part of a large intestine [Automatically generated definition]. OBOL:automatic UMLS:C1179777 ncithesaurus:Large_Intestinal_Crypt_of_the_Lieberkuhn intestinal gland of large intestine OBOL:automatic large intestine intestinal gland OBOL:automatic large intestine lieberkuhn crypt OBOL:automatic lieberkuhn crypt of large intestine OBOL:automatic 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 The upper layer of the dermis beneath the epidermis, composed of dense irregular connective tissue[ncit,modified]. todo - check tissue composition Dense irregular connective tissue of the skin that consists of fibroblasts, various connective tissue cell types, and collagen, predominantly type III. EMAPA:35282 FMA:64776 MA:0000800 MA:0000802 NCIT:C33630 NCIT:C94819 UMLS:C0221930 UMLS:C0682598 corpus papillary dermis papillary layer papillary dermis papillary layer papillary layer of dermis stratum papillare stratum papillare (dermis) stratum papillare corii stratum papillare dermis superficial dermis uberon dermal papillary layer stratum papillare UBERON:0001992 papillary layer of dermis http://upload.wikimedia.org/wikipedia/commons/b/b4/Normal_Epidermis_and_Dermis_with_Intradermal_Nevus_10x.JPG WP FMA-text The upper layer of the dermis beneath the epidermis, composed of dense irregular connective tissue[ncit,modified]. ncithesaurus:Papillary_Dermis Dense irregular connective tissue of the skin that consists of fibroblasts, various connective tissue cell types, and collagen, predominantly type III. FMA:64776 UMLS:C0221930 ncithesaurus:Stratum_Papillare UMLS:C0682598 ncithesaurus:Papillary_Dermis corpus papillary MP:0009545 dermis papillary layer MA:0000800 papillary layer MP:0009545 papillary layer of dermis FMA:64776 stratum papillare MP:0009545 stratum papillare (dermis) FMA:64776 FMA:TA stratum papillare corii MP:0009545 stratum papillare dermis FMA:64776 FMA:TA superficial dermis MA:0000802 superficial dermis MP:0009545 dermal papillary layer EMAPA:35282 stratum papillare The thicker, deeper layer of the dermis, comprised of criss-crossing collagen fibers that form a strong elastic network and also containing blood and lymph vessels, nerves and nerve endings, and hair follicles EMAPA:35283 FMA:64778 MA:0000801 NCIT:C33631 NCIT:C94818 UMLS:C0682599 UMLS:C1514988 dermis reticular layer dermis stratum reticulare reticular dermis stratum reticulare stratum reticulare dermis uberon dermal reticular layer stratum reticulare UBERON:0001993 reticular layer of dermis FMA The thicker, deeper layer of the dermis, comprised of criss-crossing collagen fibers that form a strong elastic network and also containing blood and lymph vessels, nerves and nerve endings, and hair follicles ISBN:0-683-40008-8 MP:0005081 UMLS:C0682599 ncithesaurus:Reticular_Dermis UMLS:C1514988 ncithesaurus:Stratum_Reticulare stratum reticulare stratum reticulare dermis FMA:64778 FMA:TA dermal reticular layer EMAPA:35283 stratum reticulare 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 intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns. A mixture of white fibrous tissue and cartilaginous tissue in various proportions. It owes its flexibility and toughness to the former of these constituents, and its elasticity to the latter. It is the only type of cartilage that contains type I collagen in addition to the normal type I[Wikipedia:Fibrocartilage]I Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel without a well-defined perichondrium[FMA:64784]. Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns.[VSAO] fibrocartilaginous FMA:64784 MA:0000108 NCIT:C32599 UMLS:C0684077 VSAO:0000103 XAO:0004028 galen:Fibrocartilage fibrocartilage tissue stratified cartilage tissue uberon UBERON:0001995 The white fibrocartilages admit of arrangement into four groups-interarticular, connecting, circumferential, and stratiform -- WP. EDITOR NOTE: TODO add mineralized fibrocartilage http://upload.wikimedia.org/wikipedia/commons/2/2e/Gray295.png Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns. GO_REF:0000034 PSPUB:0000170 VSAO:0000103 A mixture of white fibrous tissue and cartilaginous tissue in various proportions. It owes its flexibility and toughness to the former of these constituents, and its elasticity to the latter. It is the only type of cartilage that contains type I collagen in addition to the normal type I[Wikipedia:Fibrocartilage]I Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel without a well-defined perichondrium[FMA:64784]. FMA:64784 Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns.[VSAO] 2012-08-14 VSAO:0000103 VSAO PSPUB:0000170 UMLS:C0684077 ncithesaurus:Fibrocartilage fibrocartilage tissue stratified cartilage tissue 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 A sensory epithelium inside the nasal cavity that is responsible for detecting odors[WP]. Sensory lining of the medial wall, roof and anterior aspects of the main olfactory cavity (cavum principale).[AAO] relationship loss: part_of principal cavity (AAO:0000992)[AAO] UBERON:0004853 AAO:0010158 BIRNLEX:2703 BTO:0000108 CALOHA:TS-0703 EFO:0001972 EHDAA2:0001228 EHDAA:4774 EMAPA:17606 FMA:64803 MA:0001325 MAT:0000445 NCIT:C33203 TAO:0000554 UMLS:C0599332 VHOG:0000985 ZFA:0000554 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1900 main olfactory epithelium nasal cavity olfactory epithelium olfactory membrane olfactory sensory epithelium sensory olfactory epithelium uberon MOE nasal epithelium nasal sensory epithelium pseudostratified main olfactory epithelium UBERON:0001997 Genes: V1Rs, Trpc2 present in lamprey olfactory epithelium http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray857.png NIFSTD A sensory epithelium inside the nasal cavity that is responsible for detecting odors[WP]. Sensory lining of the medial wall, roof and anterior aspects of the main olfactory cavity (cavum principale).[AAO] 2012-06-20 AAO:0010158 AAO AAO:DSM relationship loss: part_of principal cavity (AAO:0000992)[AAO] 2012-06-20 AAO:0010158 AAO UMLS:C0599332 BIRNLEX:2703 UMLS:C0599332 ncithesaurus:Olfactory_Epithelium http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1900 BIRNLEX:2703 main olfactory epithelium NCBIBook:NBK55971 nasal cavity olfactory epithelium MA:0001325 olfactory membrane BIRNLEX:2703 MOE NCBIBook:NBK55971 pseudostratified main olfactory epithelium 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 The enteric nervous system is composed of two ganglionated neural plexuses in the gut wall which form one of the three major divisions of the autonomic nervous system. The enteric nervous system innervates the gastrointestinal tract, the pancreas, and the gall bladder. It contains sensory neurons, interneurons, and motor neurons. Thus the circuitry can autonomously sense the tension and the chemical environment in the gut and regulate blood vessel tone, motility, secretions, and fluid transport. The system is itself governed by the central nervous system and receives both parasympathetic and sympathetic innervation[GO]. most sources classify this as autonomic, but in FMA it is placed directly under nervous system. BAMS:ENS BIRNLEX:1166 BTO:0002506 CALOHA:TS-2093 EFO:0000895 EHDAA2:0004202 EMAPA:26922 FMA:66070 GAID:799 MA:0000222 MAT:0000102 MESH:D017615 MIAA:0000102 TAO:0001155 UMLS:C0206111 ZFA:0001155 PNS - enteric enteric PNS uberon UBERON:0002005 enteric nervous system cjm FMA MA NIF ZFA-isa-changed Wikipedia ZFA The enteric nervous system is composed of two ganglionated neural plexuses in the gut wall which form one of the three major divisions of the autonomic nervous system. The enteric nervous system innervates the gastrointestinal tract, the pancreas, and the gall bladder. It contains sensory neurons, interneurons, and motor neurons. Thus the circuitry can autonomously sense the tension and the chemical environment in the gut and regulate blood vessel tone, motility, secretions, and fluid transport. The system is itself governed by the central nervous system and receives both parasympathetic and sympathetic innervation[GO]. GO:0048484 most sources classify this as autonomic, but in FMA it is placed directly under nervous system. FMA UMLS:C0206111 BIRNLEX:1166 PNS - enteric EFO:0000895 enteric PNS EFO:0000895 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 A plexus of nerves situated at the base of the heart that innervate the heart. EMAPA:37460 FMA:6628 MA:0001138 NCIT:C52833 UMLS:C0459528 autonomic nerve plexus of heart autonomic plexus of heart cardiac plexus heart autonomic nerve plexus heart autonomic plexus plexus cardiacus uberon UBERON:0002008 cardiac nerve plexus http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png A plexus of nerves situated at the base of the heart that innervate the heart. EMAPA:37460 MA:th UMLS:C0459528 ncithesaurus:Cardiac_Nerve_Plexus autonomic nerve plexus of heart OBOL:automatic autonomic plexus of heart OBOL:automatic heart autonomic nerve plexus OBOL:automatic heart autonomic plexus OBOL:automatic plexus cardiacus The thoracodorsal artery is a branch of the subscapular artery. It travels inferiorly with the thoracodorsal nerve and supplies the latissimus dorsi. [WP,unvetted]. EMAPA:37129 FMA:66320 MA:0002065 NCIT:C53018 UMLS:C0933449 uberon arteria thoracodorsalis UBERON:0002011 thoracodorsal artery Latissimus:dorsi.png The thoracodorsal artery is a branch of the subscapular artery. It travels inferiorly with the thoracodorsal nerve and supplies the latissimus dorsi. [WP,unvetted]. EMAPA:37129 MA:th UMLS:C0933449 ncithesaurus:Thoracodorsal_Artery arteria thoracodorsalis 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 deepest layer of the epidermis, which is composed of dividing stem cells and anchoring cells replaces damaged cells on outside of body consisting of non-keratinized, viable cells, in contrast to the outer (upper) layer of epidermis made up of keratinized, anucleated, non-viable cells Malpighian layer rete Malphighii rete Malpighii stratum Malpighi stratum basale stratum germinosum AAO:0010598 BTO:0000438 EMAPA:32779 FMA:67540 MA:0000803 NCIT:C33466 NCIT:C33623 TAO:0001180 UMLS:C0221925 XAO:0000041 ZFA:0001180 basal cell layer of epidermis basal epidermal layer epidermal basal stratum epidermis stratum basale stratum basalis of epidermis stratum germinativum stratum germinosum of epidermis uberon basal cell layer of skin basal layer of epidermis epidermis basal layer epidermis sensorial layer epidermis stratum germinativum UBERON:0002025 stratum basale of epidermis the deepest layer of the epidermis, which is composed of dividing stem cells and anchoring cells ISBN:0-683-40008-8 MP:0001231 Malpighian layer rete Malphighii stratum Malpighi UMLS:C0221925 ncithesaurus:Stratum_Basale basal cell layer of epidermis FMA:67540 basal epidermal layer ZFA:0001180 epidermal basal stratum TAO:0001180 epidermis sensorial layer XAO:0000041 the layer of polyhedral cells in the epidermis found between the stratum granulosum and stratum basale; shrinkage and adhesion of these cells gives a spiny or prickly appearance Has cells that produce and secrete bipolar lipids which prevent evaporation, helping to 'water-proof' the skin. Keratinization begins in the stratum spinosum. [Wikipedia:Stratum_spinosum] Malpighian layer stratum Malpighii BTO:0000435 EMAPA:32785 FMA:67542 MA:0000807 NCIT:C12850 UMLS:C0221924 epidermis stratum spinosum prickle cell layer of epidermis squamous cell layer of epidermis stratum spinosum uberon epidermis prickle cell layer prickle cell layer UBERON:0002026 stratum spinosum of epidermis the layer of polyhedral cells in the epidermis found between the stratum granulosum and stratum basale; shrinkage and adhesion of these cells gives a spiny or prickly appearance ISBN:0-683-40008-8 MP:0001236 Malpighian layer stratum Malpighii UMLS:C0221924 ncithesaurus:Stratum_Spinosum prickle cell layer of epidermis FMA:67542 prickle cell layer BTO:0000435 the outer layer of the epidermis, consisting of several layers of flat keratinized non-nucleated cells The keratinized outermost layer of the epidermis, which is periodically shed.[AAO] some oral epitehlium also has cornified layer / stratum corneum horny layer keratinized squame layer stratum corneum AAO:0010597 BTO:0000344 CALOHA:TS-0981 EMAPA:32787 FMA:67545 MA:0000804 NCIT:C33625 UMLS:C0221921 cornified layer epidermis stratum corneum horny layer of epidermis keratinized squame layer of epidermis uberon stratum corneum epidermidis UBERON:0002027 stratum corneum of epidermis Epidermal:layers.png http://upload.wikimedia.org/wikipedia/commons/2/20/Skinlayers.png the outer layer of the epidermis, consisting of several layers of flat keratinized non-nucleated cells ISBN:0-683-40008-8 MP:0001240 The keratinized outermost layer of the epidermis, which is periodically shed.[AAO] 2012-06-20 AAO:0010597 AAO AAO:CAM horny layer BTO:0000344 UMLS:C0221921 ncithesaurus:Stratum_Corneum horny layer of epidermis FMA:67545 stratum corneum epidermidis 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 Projection of skin containing the outlets for 15-20 lactiferous ducts arranged cylindrically around the tip. a male mouse has no nipples - mammary tissue regresses during embryonic development FMA makes this part of the breast, whereas in MA it is part of the mammary gland - BTO:0000821 CALOHA:TS-2234 EMAPA:36508 FMA:67771 GAID:35 MA:0000796 MESH:D009558 NCIT:C12299 OpenCyc:Mx4rvVjKi5wpEbGdrcN5Y29ycA UMLS:C0028109 galen:Nipple papilla mammae papilla of breast thele thelium papillary part of breast teat uberon papilla mammaria UBERON:0002030 nipple http://upload.wikimedia.org/wikipedia/commons/5/59/Female_nipple_profile.jpg Stedmans Projection of skin containing the outlets for 15-20 lactiferous ducts arranged cylindrically around the tip. FMA:67771 FMA makes this part of the breast, whereas in MA it is part of the mammary gland - FMA UMLS:C0028109 ncithesaurus:Nipple papilla mammae MP:0009723 thele MP:0009723 thelium MP:0009723 papilla mammaria 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 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 Predominantly gray matter midbrain structure lying dorsal to the crus cerebri and ventral to the midbrain tegmentum. It is divided into a dorsal, cellularly compact region known as the pars compacta and a more ventrally located, containing more loosely packed cells, the pars reticulata. The most lateral region of the reticulata is identified as the pars lateralis (MM). TODO - In BTO and NIF, part of basal ganglion which is part of telencephalon - but this is inconsistent with being part of midbrain, if these are spatially disjoint, as in ABA Subdivision of the midbrain anterior to the midbrain tegmentum which contains darkly pigmented neurons[FMA][FMA:67947]. (...) the substantia nigra first appears in reptiles and is best developed in primates.[well established][VHOG] SN BAMS:SN BIRNLEX:789 BTO:0000143 CALOHA:TS-0990 DHBA:12251 EFO:0000922 EHDAA2:0004711 EMAPA:35835 EV:0100247 FMA:67947 GAID:581 HBA:9072 MA:0000210 MAT:0000504 MESH:A08.186.211.132.659.687 NCIT:C12453 UMLS:C0038590 UMLS:C1269578 VHOG:0001573 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=536 Soemmering's substance nucleus of basis pedunculi uberon nucleus pigmentosus subthalamo-peduncularis substancia nigra substantia nigra (Soemmerringi) UBERON:0002038 substantia nigra http://upload.wikimedia.org/wikipedia/commons/5/5f/Midbraincrosssection.png NIF FMA-abduced-lr Predominantly gray matter midbrain structure lying dorsal to the crus cerebri and ventral to the midbrain tegmentum. It is divided into a dorsal, cellularly compact region known as the pars compacta and a more ventrally located, containing more loosely packed cells, the pars reticulata. The most lateral region of the reticulata is identified as the pars lateralis (MM). BIRNLEX:789 Subdivision of the midbrain anterior to the midbrain tegmentum which contains darkly pigmented neurons[FMA][FMA:67947]. FMA:67947 (...) the substantia nigra first appears in reptiles and is best developed in primates.[well established][VHOG] 2012-09-17 VHOG:0001573 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.336 SN BIRNLEX:789 NIFSTD:NeuroNames_abbrevSource UMLS:C0038590 BIRNLEX:789 UMLS:C0038590 ncithesaurus:Substantia_Nigra UMLS:C1269578 BIRNLEX:789 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=536 BIRNLEX:789 nucleus pigmentosus subthalamo-peduncularis NeuroNames:536 substancia nigra substantia nigra (Soemmerringi) NeuroNames:536 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 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 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] 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 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 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 the narrow subcapsular outer zone of the adrenal cortex where aldosterone is produced BTO:0000048 CALOHA:TS-0017 EMAPA:35115 FMA:69225 GAID:449 MA:0001891 MESH:D015384 adrenal gland zona glomerulosa zona glomerulosa zona glomerulosa of suprarenal gland uberon glomerulosa UBERON:0002053 zona glomerulosa of adrenal gland http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png MA the narrow subcapsular outer zone of the adrenal cortex where aldosterone is produced MESH:A06.407.071.140.960 MGI:llw2 MP:0008293 adrenal gland zona glomerulosa MA:0001891 glomerulosa BTO:0000048 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 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 The umbilical vein is a blood vessel present during fetal development that carries oxygenated blood from the placenta to the growing fetus. [WP,unvetted]. BTO:0001509 CALOHA:TS-1082 EFO:0001940 EHDAA:1034 EHDAA:488 EMAPA:16243 EMAPA:16375 EV:0100392 FMA:70317 GAID:542 MA:0002249 MESH:D014471 NCIT:C33830 OpenCyc:Mx4rdu17MmWaEd2AAABQjYGu0g RETIRED_EHDAA2:0002107 UMLS:C0041637 uberon vena umbilicalis UBERON:0002066 umbilical vein http://upload.wikimedia.org/wikipedia/commons/e/ee/Gray502.png The umbilical vein is a blood vessel present during fetal development that carries oxygenated blood from the placenta to the growing fetus. [WP,unvetted]. UMLS:C0041637 ncithesaurus:Umbilical_Vein vena umbilicalis 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 the layer of flattened cells containing basophilic granules of keratohyalin and lying just above the stratum spinosum (spiny layer) of the epidermis BTO:0000361 EMAPA:32786 FMA:70344 MA:0000805 NCIT:C33627 UMLS:C0221923 epidermis stratum granulosum granular layer of epidermis stratum granulosum uberon epidermis granular layer UBERON:0002069 stratum granulosum of epidermis the layer of flattened cells containing basophilic granules of keratohyalin and lying just above the stratum spinosum (spiny layer) of the epidermis ISBN:0-683-40008-8 MP:0001239 UMLS:C0221923 ncithesaurus:Stratum_Granulosum granular layer of epidermis FMA:70344 stratum granulosum BTO:0000361 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 smooth and glossy outer protective cell layer of hair shaft EMAPA:35388 FMA:70933 MA:0000157 hair cuticle uberon UBERON:0002076 cuticle of hair smooth and glossy outer protective cell layer of hair shaft MGI:llw2 MP:0003810 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 companion vein of the thoracodorsal artery, draining the apical part of the latissimus dorsi and merging with the circumflex scapular vein to form a subscapular vein EMAPA:37198 FMA:71213 MA:0002238 uberon UBERON:0002089 thoracodorsal vein FMA/obol companion vein of the thoracodorsal artery, draining the apical part of the latissimus dorsi and merging with the circumflex scapular vein to form a subscapular vein EMAPA:37198 MA:th 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 the organ that functions to filter blood and to store red corpuscles and platelets 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 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 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]. 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 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. 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 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 duodenum to the ileum TODO consider ZFA:0001323 mid intestine, see also small intestine The first two fifth of the small intestine beyond the duodenum. It extends from the end of the duodenum to the ileum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] jejunal The jejunum is the middle 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 middle intestine or mid-gut may be used instead of jejunum.[Wikipedia:Jejunum] BTO:0000657 CALOHA:TS-0496 EFO:0001333 EMAPA:18666 EV:0100074 FMA:7207 GAID:318 MA:0000340 MAT:0000045 MESH:A03.492.411.620.625 MIAA:0000045 NCIT:C12388 OpenCyc:Mx4rwATkPJwpEbGdrcN5Y29ycA UMLS:C0022378 VHOG:0000053 galen:Jejunum uberon intestinum jejunum mid-intestine middle intestine UBERON:0002115 jejunum http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg 3 cjm Wikipedia the portion of the small intestine that extends from the duodenum to the ileum MGI:monikat MP:0004002 The first two fifth of the small intestine beyond the duodenum. It extends from the end of the duodenum to the ileum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000053 VHOG UMLS:C0022378 ncithesaurus:Jejunum intestinum jejunum BTO:0000657 mid-intestine middle intestine BTO:0000657 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 small terminal dilation of the alveolar ducts around which the alveoli form pocket-like clusters UBERON:0008871 BTO:0000061 EMAPA:35119 FMA:7317 MA:0000418 NCIT:C32057 OpenCyc:Mx4rwCvh75wpEbGdrcN5Y29ycA UMLS:C0225691 pulmonary alveolar sac sacculus alveolaris uberon air sac UBERON:0002169 alveolar sac MA FMA The small terminal dilation of the alveolar ducts around which the alveoli form pocket-like clusters MP:0010902 UMLS:C0225691 ncithesaurus:Alveolar_Sac pulmonary alveolar sac MP:0010902 sacculus alveolaris FMA:7317 air sac MP:0010902 the respiratory conducting tubes distal to the respiratory bronchiole that lead to the alveolar sacs and the alveoli In human anatomy, respiratory bronchioles exists proximal to the alveolar ducts. The epithelial lining consists of smooth muscle knobs covered by nonciliated, simple cuboidal cells. The smooth muscle constricts under parasympathetic innervation and relax under sympathetic innervation EMAPA:32694 FMA:7341 MA:0000417 NCIT:C32056 OpenCyc:Mx4rvXmfV5wpEbGdrcN5Y29ycA UMLS:C0391892 alveolar duct ductus alveolaris respiratory alveolar duct uberon UBERON:0002173 pulmonary alveolar duct http://upload.wikimedia.org/wikipedia/commons/8/8f/Gray975.png the respiratory conducting tubes distal to the respiratory bronchiole that lead to the alveolar sacs and the alveoli ISBN:0-683-40008-8 MGI:cwg MP:0002271 UMLS:C0391892 ncithesaurus:Alveolar_Duct alveolar duct MA:0000417 ductus alveolaris FMA:7341 FMA:TA The white substance of the spinal cord lying on either side between the ventral median fissure and the ventral roots of the spinal nerves. FMA:74003 NLX:379 TAO:0000605 ZFA:0000605 anterior funiculus anterior funiculus of spinal cord anterior white column of spinal cord funiculus anterior medullae spinalis ventral funiculus ventral funiculus of spinal cord ventral white column of spinal cord uberon ventral funiculi UBERON:0002180 ventral funiculus of spinal cord http://upload.wikimedia.org/wikipedia/commons/d/dc/Medulla_spinalis_-_Section_-_English.svg FMA-abduced-lr The white substance of the spinal cord lying on either side between the ventral median fissure and the ventral roots of the spinal nerves. anterior white column of spinal cord FMA:74003 funiculus anterior medullae spinalis FMA:74003 FMA:TA ventral funiculus ZFA:0000605 ventral white column of spinal cord FMA:74003 ventral funiculi ZFA:0000605 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 bronchiole that is the first segment of the respiratory zone. mice have few or none of these structures, with the terminal bronchioles transitioning directly to the alveolary ducts BTO:0003222 EMAPA:35729 FMA:7412 MA:0000423 NCIT:C33465 OpenCyc:Mx4rwS6ki5wpEbGdrcN5Y29ycA UMLS:C1261270 bronchiolus respiratorii bronchiolus respiratorius uberon UBERON:0002188 respiratory bronchiole Alveoli:diagram.png ISBN:0123813611 A bronchiole that is the first segment of the respiratory zone. ISBN:0123813611 mice have few or none of these structures, with the terminal bronchioles transitioning directly to the alveolary ducts ISBN:0123813611 UMLS:C1261270 ncithesaurus:Respiratory_Bronchiole bronchiolus respiratorii bronchiolus respiratorius FMA:7412 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 Part of the hippocampal formation that is bounded by the entorhinal cortex and area CA1. It is characterized on the CA1 border by an abrupt widening of the pyramidal cell layer. A molecular layer is present that is continuous with that of CA1, although the stratum radiatum is no longer present. The stratum oriens is also not present. adapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 468) subicular The pyramidal neurons in the subiculum exhibit transitions between two modes of action potential output: bursting and single spiking. The transitions between these two modes is thought to be important for routing information out of the hippocampus. It is the site responsible for ictal activity in some cases of human epilepsy. It has also been implicated in working memory and drug addiction.[Wikipedia:Subiculum] In ABA SUB is part of the retrohippocampal region, along with the entorhinal area. this is in the hippocampal formation but not the hippocampal region in DHBA subicular cortex is divided into subiculum, prosubiculum and supracallosal subiculum BAMS:S BAMS:SUB BIRNLEX:1305 BM:Tel-Cx-SB BTO:0003087 DHBA:10301 DHBA:10302 DMBA:16163 EMAPA:35832 FMA:74414 HBA:12896 MA:0000960 MBA:502 NCIT:C33648 PBA:10054 PBA:128012354 UMLS:C0152316 subicular cortex subiculum hippocampi uberon gyrus parahippocampalis subiculum cornu ammonis UBERON:0002191 subiculum Hippocampus:(brain).jpg NIFSTD Part of the hippocampal formation that is bounded by the entorhinal cortex and area CA1. It is characterized on the CA1 border by an abrupt widening of the pyramidal cell layer. A molecular layer is present that is continuous with that of CA1, although the stratum radiatum is no longer present. The stratum oriens is also not present. adapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 468) BIRNLEX:1305 In ABA SUB is part of the retrohippocampal region, along with the entorhinal area. this is in the hippocampal formation but not the hippocampal region ABA UMLS:C0152316 ncithesaurus:Subiculum subicular cortex BIRNLEX:1305 subiculum hippocampi FMA:74414 gyrus parahippocampalis BTO:0003087 subiculum cornu ammonis BTO:0003087 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 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 One of two hemispherical bulges on the base of the posterior hypothalamus (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed., 2005, pg 455). MMB BAMS:MB BAMS:MBO BAMS:mmb BIRNLEX:865 DHBA:15546 DMBA:15723 EMAPA:35542 FMA:74877 GAID:652 HBA:12909 MA:0000174 MBA:331 MESH:A08.186.211.730.385.357.362.500 NCIT:C33052 TAO:0000334 UMLS:C0024670 UMLS:C1305759 ZFA:0000334 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=412 corpus mamillare uberon corpora mamillaria corpora mammillaria corpus mamillare corpus mamillaris corpus mammillare mammillary area UBERON:0002206 mammillary body http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1180.png ABA GO definition One of two hemispherical bulges on the base of the posterior hypothalamus (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed., 2005, pg 455). BIRNLEX:865 Hardisty, p. 320-1 MMB BIRNLEX:865 NIFSTD:NeuroNames_abbrevSource UMLS:C0024670 BIRNLEX:865 UMLS:C0024670 ncithesaurus:Mamillary_Body UMLS:C1305759 BIRNLEX:865 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=412 BIRNLEX:865 corpus mamillare ZFA:0000334 corpora mamillaria NeuroNames:412 corpora mammillaria NeuroNames:412 corpus mamillare corpus mamillaris NeuroNames:412 corpus mammillare NeuroNames:412 mammillary area DMBA:Mam 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 A continuation of the neuron projection bundle component of a nerve inside, crossing or immediately outside the central nervous system. We consider cranial nerve roots to be primarily CNS structures, but model spinal nerve roots as PNS structures, due to the existence of ganglia on the roots. The continuation of the neurite bundle and associated glia of a nerve, inside the central nervous system[FBbt:00007602, FBC:DOS]. FMA has 'central zone of nerve' which is the superclass of cranial nerve tracts, which the FMA sometimes calls roots FMA:5981 FMA:82524 NCIT:C54024 NLX:144250 UMLS:C0228084 initial segment of nerve radix nervi uberon UBERON:0002211 nerve root A continuation of the neuron projection bundle component of a nerve inside, crossing or immediately outside the central nervous system. The continuation of the neurite bundle and associated glia of a nerve, inside the central nervous system[FBbt:00007602, FBC:DOS]. FBbt:00007602, FBC:DOS FMA has 'central zone of nerve' which is the superclass of cranial nerve tracts, which the FMA sometimes calls roots FMA UMLS:C0228084 ncithesaurus:Nerve_Root initial segment of nerve radix nervi the oval neuroepithelial sensory receptor in the anterior wall of the saccule; hair cells of the neuroepithelium support the statoconial membrane and have terminal arborizations of vestibular nerve fibers around their bodies EMAPA:35534 FMA:74944 MA:0001201 NCIT:C33045 TAO:0007000 UMLS:C0229468 XAO:0004136 ZFA:0007000 macula of membranous labyrinth saccule macula of saccule macula of sacculus (labyrinthus vestibularis) macula saccule macula sacculi membranous labyrinth saccule macula saccular macula saccular macula of membranous labyrinth saccule macula saccule of membranous labyrinth macula sacculus (labyrinthus vestibularis) macula uberon macula sacculi saccular maculs UBERON:0002212 macula of saccule of membranous labyrinth the oval neuroepithelial sensory receptor in the anterior wall of the saccule; hair cells of the neuroepithelium support the statoconial membrane and have terminal arborizations of vestibular nerve fibers around their bodies MGI:anna MP:0004330 UMLS:C0229468 ncithesaurus:Macula_of_Saccule macula of membranous labyrinth saccule OBOL:automatic macula of sacculus (labyrinthus vestibularis) OBOL:automatic macula saccule ZFA:0007000 macula sacculi FMA:74944 FMA:TA membranous labyrinth saccule macula OBOL:automatic saccular macula ZFA:0007000 saccule macula OBOL:automatic saccule of membranous labyrinth macula OBOL:automatic sacculus (labyrinthus vestibularis) macula OBOL:automatic macula sacculi 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 the neuroepithelial sensory receptor in the inferolateral wall of the utricle; hair cells of the neuroepithelium support the statoconial membrane and have terminal arborizations of vestibular nerve fibers around their bodies; normally sensitive to linear acceleration in the longitudinal axis of the body and to gravitational influences EFO:0003474 EMAPA:35535 FMA:74960 MA:0001203 NCIT:C33046 TAO:0000030 UMLS:C0229451 ZFA:0000030 macula of membranous labyrinth utricle macula of utricle macula of utriculus (labyrinthus vestibularis) macula utricle macula utriculi membranous labyrinth utricle macula utricle macula utricle of membranous labyrinth macula utriculus (labyrinthus vestibularis) macula uberon macula utriculi maculae utricle utricular macula UBERON:0002214 macula of utricle of membranous labyrinth http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg the neuroepithelial sensory receptor in the inferolateral wall of the utricle; hair cells of the neuroepithelium support the statoconial membrane and have terminal arborizations of vestibular nerve fibers around their bodies; normally sensitive to linear acceleration in the longitudinal axis of the body and to gravitational influences MGI:anna MP:0004333 UMLS:C0229451 ncithesaurus:Macula_of_Utricle macula of membranous labyrinth utricle OBOL:automatic macula of utriculus (labyrinthus vestibularis) OBOL:automatic macula utricle ZFA:0000030 macula utriculi FMA:74960 FMA:TA membranous labyrinth utricle macula OBOL:automatic utricle macula OBOL:automatic utricle of membranous labyrinth macula OBOL:automatic utriculus (labyrinthus vestibularis) macula OBOL:automatic macula utriculi maculae utricle ZFA:0000030 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 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 The organ of Corti (or spiral organ) is the organ in the inner ear of mammals that contains auditory sensory cells, or 'hair cells.' [WP,unvetted]. The auditory hair cells in tetrapods are located in the inner ear in a structure known as the basilar papilla. In mammals this structure (along with some related structure) is called the organ of Corti.[well established][VHOG] in basal early lizards, organized into 3 tonotopically organized areas, the outer areas lack a tectorial membrane[ISBN:9780387714691] BIRNLEX:2526 BTO:0001691 CALOHA:TS-0717 EFO:0001364 EMAPA:19061 EV:0100364 FMA:75715 GAID:772 MA:0001193 NCIT:C33223 UMLS:C0029207 VHOG:0001567 ncithesaurus:Spiral_Organ_of_Corti cochlear spiral organ organum spirale spiral organ spiral organ of Corti uberon Corti's organ auditory papilla auditory papillae basilar papilla organ of Corti papilla basilaris UBERON:0002227 spiral organ of cochlea http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png http://upload.wikimedia.org/wikipedia/commons/c/cb/Cochlea-crosssection.svg MA The organ of Corti (or spiral organ) is the organ in the inner ear of mammals that contains auditory sensory cells, or 'hair cells.' [WP,unvetted]. The auditory hair cells in tetrapods are located in the inner ear in a structure known as the basilar papilla. In mammals this structure (along with some related structure) is called the organ of Corti.[well established][VHOG] 2012-09-17 VHOG:0001567 VHOG ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.33 UMLS:C0029207 BIRNLEX:2526 UMLS:C0029207 ncithesaurus:Organ_of_Corti organum spirale Corti's organ BTO:0001691 auditory papilla ISBN:9780387714691 auditory papillae ISBN:9780387714691 basilar papilla XAO:0003145 papilla basilaris XAO:0003145 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 A rib that is ventrally connected to the sternum. EMAPA:37774 FMA:7592 MA:0001419 OpenCyc:Mx4rv4-iWJwpEbGdrcN5Y29ycA costa vera uberon costae verae UBERON:0002237 true rib http://upload.wikimedia.org/wikipedia/commons/3/3d/Gray115.png A rib that is ventrally connected to the sternum. ISBN:0073040584 EMAPA:37774 MA:th costae verae 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 thought to supplement the olfactory system in receiving pheromonic communication. The sensory part of the organ is in two long, thin sacs, situated on either side of the nasal septum at its base. An organ thought to supplement the olfactory system in receiving pheromonic communication. The sensory part of the organ is in two long, thin sacs, situated on either side of the nasal septum at its base. [TFD][VHOG] (...) the vomeronasal organ is known only in some tetrapods. It is absent in most turtles, crocodiles, birds, some bats, and aquatic mammals. In amphibians, it is in a recessed area off the main nasal cavity. (...) In mammals possesing this organ, it is an isolated area of olfactory membrane within the nasal cavity that is usually connected to the mouth via the nasopalatine duct (reference 1); The opinions concerning the presence and functioning of the vomeronasal organ in humans are controversial. The vomeronasal cavities appear early in human foetuses. (...) Historical examination of the nasal septum revealed the presence of vomeronasal cavities in approximately 70% of adults. In contrast to the situation in other mammals, the organ is not supported by a rigid tube of bone or cartilage (reference 2); (...) the best evidence for the homology of the human VNO to that of other primates (and of mammals in general) is ontogenetic in nature, based on a common embryonic origin from a thickening (vomeronasal primordium) on the medial aspect of each olfactory pit (reference 3); (...) suggesting that lungfish possess a region homologous to the accessory olfactory bulb of tetrapods. Based on these results, it seems appropriate to refer to the recess epithelium as a primordium of the vomeronasal organ (reference 4). [debated][VHOG] Generally formed only in tetrapods; lungfish have rudimentary VN organs; true VN organs are not normally found in recent fishes, birds, aquatic reptiles, aquatic mammals (Bertmar 1980). Humans: Its presence in many animals has been widely studied and the importance of the vomeronasal system to the role of reproduction and social behavior (through influence on anterior hypothalamus) has been shown in many studies. Its presence and functionality in humans was controversial, though most studies agree the organ regresses during fetal development. Many genes essential for VNO function in animals (such as TRPC2) are non-functional in humans (Liman ER. Use it or lose it: molecular evolution of sensory signaling in primates. Pflugers Arch. 2006;453(2):125-31.) AAO:0000997 BTO:0002608 EFO:0001934 EHDAA2:0002211 EHDAA:7865 EMAPA:17612 FMA:77280 GAID:354 MA:0000289 MESH:A04.531.591.940 VHOG:0000665 XAO:0000272 Jacobson's organ organon vomeronasale organum vomeronasale uberon VNO organ of Jacobsen UBERON:0002255 vomeronasal organ http://upload.wikimedia.org/wikipedia/commons/8/84/Gray51.png Wikipedia EHDAA2-abduced An organ thought to supplement the olfactory system in receiving pheromonic communication. The sensory part of the organ is in two long, thin sacs, situated on either side of the nasal septum at its base. VHOG:0000665 An organ thought to supplement the olfactory system in receiving pheromonic communication. The sensory part of the organ is in two long, thin sacs, situated on either side of the nasal septum at its base. [TFD][VHOG] 2012-09-17 VHOG:0000665 VHOG (...) the vomeronasal organ is known only in some tetrapods. It is absent in most turtles, crocodiles, birds, some bats, and aquatic mammals. In amphibians, it is in a recessed area off the main nasal cavity. (...) In mammals possesing this organ, it is an isolated area of olfactory membrane within the nasal cavity that is usually connected to the mouth via the nasopalatine duct (reference 1); The opinions concerning the presence and functioning of the vomeronasal organ in humans are controversial. The vomeronasal cavities appear early in human foetuses. (...) Historical examination of the nasal septum revealed the presence of vomeronasal cavities in approximately 70% of adults. In contrast to the situation in other mammals, the organ is not supported by a rigid tube of bone or cartilage (reference 2); (...) the best evidence for the homology of the human VNO to that of other primates (and of mammals in general) is ontogenetic in nature, based on a common embryonic origin from a thickening (vomeronasal primordium) on the medial aspect of each olfactory pit (reference 3); (...) suggesting that lungfish possess a region homologous to the accessory olfactory bulb of tetrapods. Based on these results, it seems appropriate to refer to the recess epithelium as a primordium of the vomeronasal organ (reference 4). [debated][VHOG] 2012-09-17 VHOG:0000665 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.669 (ref.1), http://www.ncbi.nlm.nih.gov/pubmed/9866877 Doving KB, Trotier D, Review: Structure and function of the vomeronasal organ. The Journal of Experimental Biology (1998) (ref.2), DOI:10.1046/j.1469-7580.2001.19810077.x Smith TD, Siegel MI, Bonar CJ, Bhatnagar KP, Mooney MP, Burrows AM, Smith MA, Maico LM, The existence of the vomeronasal organ in postnatal chimpanzees and evidence for its homology with that of humans. J Anat (2001) (ref.3) , DOI:10.1002/ar.22415 Nakamuta S, Nakamuta N, Taniguchi K, Taniguchi K, Histological and ultrastructural characteristics of the primordial vomeronasal organ in lungfish. Anat Rec (Hoboken) (2012) (ref.4) Jacobson's organ XAO:0000272 organon vomeronasale organum vomeronasale VNO VHOG:0000665 The pronounced, dorsolaterally oriented ridge of grey matter in each lateral half of the spinal cord[MP]. the dorsal (more towards the back) grey matter of the spinal cord. It receives several types of sensory information from the body, including light touch, proprioception, and vibration. This information is sent from receptors of the skin, bones, and joints through sensory neurons whose cell bodies lie in the dorsal root ganglion[WP]. The dorsal region of the mature spinal cord contains neurons that process and relay sensory input[GO]. dorsal grey horn dorsal horn dorsal region of mature spinal cord dorsal region of spinal cord dorsal spinal cord BAMS:DH BIRNLEX:2667 BM:SpC-DH EMAPA:18574 EMAPA:35790 FMA:256530 MA:0001119 NCIT:C32473 TAO:0000649 UMLS:C0228564 UMLS:C0228575 VHOG:0001287 ZFA:0000649 columna grisea posterior medullae spinalis cornu dorsale cornu posterius medullae spinalis dorsal gray column of spinal cord dorsal gray horn dorsal gray matter of spinal cord dorsal grey column of spinal cord dorsal horn spinal cord posterior gray column of spinal cord posterior gray horn of spinal cord posterior grey column of spinal cord posterior horn of spinal cord spinal cord dorsal horn spinal cord posterior horn uberon dorsal horn of the spinal cord spinal cord dorsal horns UBERON:0002256 dorsal horn of spinal cord http://upload.wikimedia.org/wikipedia/commons/d/dc/Medulla_spinalis_-_Section_-_English.svg FMA-abduced-lr lexical The pronounced, dorsolaterally oriented ridge of grey matter in each lateral half of the spinal cord[MP]. the dorsal (more towards the back) grey matter of the spinal cord. It receives several types of sensory information from the body, including light touch, proprioception, and vibration. This information is sent from receptors of the skin, bones, and joints through sensory neurons whose cell bodies lie in the dorsal root ganglion[WP]. The dorsal region of the mature spinal cord contains neurons that process and relay sensory input[GO]. GO:0021516 MP:0006282 dorsal grey horn EMAPA:18574 dorsal horn ZFA:0000649 UMLS:C0228564 BIRNLEX:2667 UMLS:C0228575 ncithesaurus:Dorsal_Horn_of_the_Spinal_Cord columna grisea posterior medullae spinalis FMA:256530 FMA:TA cornu dorsale ZFA:0000649 cornu posterius medullae spinalis dorsal gray column of spinal cord FMA:256530 dorsal gray horn BIRNLEX:2667 dorsal gray matter of spinal cord FMA:256530 dorsal horn spinal cord ZFA:0000649 posterior gray column of spinal cord FMA:256530 posterior gray horn of spinal cord FMA:256530 posterior horn of spinal cord spinal cord posterior horn BIRNLEX:2667 dorsal horn of the spinal cord BAMS:DH spinal cord dorsal horns The ventral grey column of the spinal cord[MP]. The neurons of the ventral region of the mature spinal cord participate in motor output[GO]. The anterior horn of the spinal cord (or anterior cornu, or anterior column, or ventral horn) is the ventral (front) grey matter section of the spinal cord. The anterior horn contains motor neurons that affect the axial muscles while the posterior horn receives information regarding touch and sensation. The anterior horn is where the cell bodies of alpha motorneurons are located[Wikipedia:Anterior_horn_of_spinal_cord]. BAMS:VH BIRNLEX:2668 BTO:0005151 EMAPA:18575 EMAPA:35794 FMA:256541 MA:0001134 NCIT:C33859 TAO:0000702 UMLS:C0228569 UMLS:C0228590 VHOG:0001288 ZFA:0000702 anterior gray column of spinal cord anterior gray horn of spinal cord anterior grey column of spinal cord anterior horn columna grisea anterior medullae spinalis spinal cord anterior horn spinal cord ventral horn ventral gray column of spinal cord ventral gray matter of spinal cord ventral grey column of spinal cord ventral grey horn ventral horn spinal cord ventral region of spinal cord ventral spinal cord uberon anterior column anterior column of the spinal cord anterior horn (spinal cord) cornu anterius medullae spinalis ventral horn of the spinal cord ventral horns spinal cord UBERON:0002257 ventral horn of spinal cord FMA-abduced-lr lexical The ventral grey column of the spinal cord[MP]. The neurons of the ventral region of the mature spinal cord participate in motor output[GO]. GO:0021517 MP:0005112 The anterior horn of the spinal cord (or anterior cornu, or anterior column, or ventral horn) is the ventral (front) grey matter section of the spinal cord. The anterior horn contains motor neurons that affect the axial muscles while the posterior horn receives information regarding touch and sensation. The anterior horn is where the cell bodies of alpha motorneurons are located[Wikipedia:Anterior_horn_of_spinal_cord]. UMLS:C0228569 BIRNLEX:2668 UMLS:C0228590 ncithesaurus:Ventral_Horn_of_the_Spinal_Cord anterior gray column of spinal cord FMA:256541 anterior gray horn of spinal cord FMA:256541 anterior horn BIRNLEX:2668 columna grisea anterior medullae spinalis FMA:256541 FMA:TA spinal cord anterior horn BIRNLEX:2668 ventral gray column of spinal cord FMA:256541 ventral gray matter of spinal cord FMA:256541 ventral grey horn BIRNLEX:2668 ventral horn spinal cord ZFA:0000702 anterior column anterior column of the spinal cord anterior horn (spinal cord) cornu anterius medullae spinalis ventral horn of the spinal cord BAMS:VH ventral horns spinal cord VHOG:0001288 The dorsal roots contain afferent sensory axons. The dorsal roots of each side continue outwards, along the way forming a dorsal root ganglion (also called a spinal ganglion). In anatomy and neurology, the dorsal root (or posterior root) is the afferent sensory root of a spinal nerve. At the distal end of the dorsal root is the dorsal root ganglion, which contains the neuron cell bodies of the nerve fibres conveyed by the root. If the dorsal root of a spinal nerve were severed it would lead to numbness in certain areas of the body. The lateral division of the dorsal root contains lightly myelinated and unmyelinated axons of small diameter. These transmit pain and temperature sensation from the body. These fibers cross through the anterior white commissure to form the Anterior lateral system in the lateral funiculus. The medial division of the dorsal root contains myelinated axons of larger diameter. These transmit information of discriminative touch, pressure, vibration, and conscious proprioception originating from spinal levels C2 through S5. These fibers are pushed in towards the posterior medial sulcus to form the fasciculus gracilis and the fasciculus cuneatus. [WP,unvetted][Wikipedia:Posterior_root_of_spinal_nerve]. BAMS:drt BTO:0000360 FMA:5980 NCIT:C32477 NLXANAT:20090208 TAO:0000652 UMLS:C0205955 ZFA:0000652 dorsal root dorsal root of spinal nerve dorsal spinal nerve root dorsal spinal root posterior root of spinal nerve radix dorsalis radix posterior (nervus spinalis) radix sensoria (nervus spinalis) sensory root of spinal nerve uberon dorsal roots radix posterior radix posterior nervi spinalis root dorsali nervi spinalis root sensoria nervi spinalis sensory spinal root UBERON:0002261 dorsal root of spinal cord Spinal:nerve.svg FMA The dorsal roots contain afferent sensory axons. The dorsal roots of each side continue outwards, along the way forming a dorsal root ganglion (also called a spinal ganglion). NLXANAT:20090208 In anatomy and neurology, the dorsal root (or posterior root) is the afferent sensory root of a spinal nerve. At the distal end of the dorsal root is the dorsal root ganglion, which contains the neuron cell bodies of the nerve fibres conveyed by the root. If the dorsal root of a spinal nerve were severed it would lead to numbness in certain areas of the body. The lateral division of the dorsal root contains lightly myelinated and unmyelinated axons of small diameter. These transmit pain and temperature sensation from the body. These fibers cross through the anterior white commissure to form the Anterior lateral system in the lateral funiculus. The medial division of the dorsal root contains myelinated axons of larger diameter. These transmit information of discriminative touch, pressure, vibration, and conscious proprioception originating from spinal levels C2 through S5. These fibers are pushed in towards the posterior medial sulcus to form the fasciculus gracilis and the fasciculus cuneatus. [WP,unvetted][Wikipedia:Posterior_root_of_spinal_nerve]. UMLS:C0205955 ncithesaurus:Dorsal_Root_of_the_Spinal_Nerve dorsal root ZFA:0000652 dorsal root of spinal nerve FMA:5980 dorsal spinal nerve root FMA:5980 posterior root of spinal nerve radix dorsalis ZFA:0000652 radix posterior (nervus spinalis) FMA:5980 radix sensoria (nervus spinalis) FMA:5980 sensory root of spinal nerve FMA:5980 dorsal roots BAMS:drt radix posterior radix posterior nervi spinalis BTO:0000360 root dorsali nervi spinalis BTO:0000360 root sensoria nervi spinalis BTO:0000360 sensory spinal root BTO:0000360 A bulbous anterior projection of the olfactory lobe that is the place of termination of the olfactory nerves and is especially well developed in lower vertebrates (as fishes)[BTO]. Part of the rostral part of the cerebrum where axons of olfactory cells from the nasal mucosa terminate. Projects onto olfactory parts of pallium via olfactory tracts Part of the telencephalon comprised of anterior outgrowths of either of the cerebral hemispheres in which the olfactory nerve exits.[AAO] Segment of neural tree organ which is continuous with a set of olfactory nerves and an olfactory tract[FMA:77624]. The part of the forebrain in which the olfactory nerves end and the olfactory tracts originate. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 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] In most vertebrates, the olfactory bulb is the most rostral (forward) part of the brain. In humans, however, the olfactory bulb is on the inferior (bottom) side of the brain. The olfactory bulb is supported and protected by the cribriform plate which in mammals, separates it from the olfactory epithelium, and which is perforated by olfactory nerve axons. The bulb is divided into two distinct structures, the main olfactory bulb, and the accessory olfactory bulb Note that in uberon 'main olfactory bulb' is a separate class, but some ontologies may treat this as partially synonymous. The distinction may only make sense in tetrapods with a vomeronasal organ (olfactory nerves terminate in OB in fishes and in main OB in tetrapods - Butler and Hodos) the olfactory bulbs develop as bilateral evaginations from a region of the prosencephalic neural plate intercalated between the septal and the cortical anlagen (Cobos et al. 2001b, Rubenstein et al. 1998). Comparing the structure of the olfactory bulb among vertebrate species, such as the leopard frog and the lab mouse, reveals that they all share the same fundamental layout(WP). AAO:0010165 BAMS:DLB BAMS:OB BAMS:Olf BIRNLEX:1137 BM:Tel-OB BTO:0000961 CALOHA:TS-0702 DHBA:10307 EHDAA2:0004705 EMAPA:32809 EV:0100173 FMA:77624 GAID:633 HBA:9303 MA:0000194 MESH:A08.186.211.577.699.573 NCIT:C28401 TAO:0000402 UMLS:C0028936 VHOG:0000033 XAO:0004180 ZFA:0000402 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=279 bulbus olfactorius uberon bulbus olfactorius bulbus olfactorius (Morgagni) olfactory lobe olfactory lobe (Barr & Kiernan) UBERON:0002264 olfactory bulb http://upload.wikimedia.org/wikipedia/commons/d/d2/1543%2CVesalius%27OlfactoryBulbs.jpg http://upload.wikimedia.org/wikipedia/commons/f/f9/1543,Vesalius%27OlfactoryBulbs.jpg ISBN:0471888893 A bulbous anterior projection of the olfactory lobe that is the place of termination of the olfactory nerves and is especially well developed in lower vertebrates (as fishes)[BTO]. BTO:0000961 Part of the rostral part of the cerebrum where axons of olfactory cells from the nasal mucosa terminate. Projects onto olfactory parts of pallium via olfactory tracts ISBN:0471888893 Part of the telencephalon comprised of anterior outgrowths of either of the cerebral hemispheres in which the olfactory nerve exits.[AAO] 2012-06-20 AAO:0010165 AAO AAO:BJB Segment of neural tree organ which is continuous with a set of olfactory nerves and an olfactory tract[FMA:77624]. FMA:77624 The part of the forebrain in which the olfactory nerves end and the olfactory tracts originate. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000033 VHOG 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:0000033 VHOG DOI:10.1146/annurev.ne.04.030181.001505 Northcutt RG, Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. (1981) In most vertebrates, the olfactory bulb is the most rostral (forward) part of the brain. In humans, however, the olfactory bulb is on the inferior (bottom) side of the brain. The olfactory bulb is supported and protected by the cribriform plate which in mammals, separates it from the olfactory epithelium, and which is perforated by olfactory nerve axons. The bulb is divided into two distinct structures, the main olfactory bulb, and the accessory olfactory bulb WP UMLS:C0028936 BIRNLEX:1137 UMLS:C0028936 ncithesaurus:Olfactory_Bulb http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=279 BIRNLEX:1137 bulbus olfactorius bulbus olfactorius bulbus olfactorius (Morgagni) NeuroNames:279 olfactory lobe ZFA:0000402 olfactory lobe (Barr & Kiernan) NeuroNames:279 White matter tract that contains projections from the olfactory bulb to other parts of the brain A nervelike, white band composed primarily of nerve fibres originating from the mitral cells and tufted cells of the olfactory bulb but also containing the scattered cells of the anterior olfactory nucleus[BTO:0003647]. The olfactory tract is a bundle of axons connecting the mitral and tufted cells of the olfactory bulb to several target regions in the brain, including piriform cortex, amygdala, and entorhinal cortex. It is a narrow white band, triangular on coronal section, the apex being directed upward. It lies in the olfactory sulcus on the inferior surface of the frontal lobe, and divides posteriorly into two striæ, a medial olfactory stria and a lateral olfactory stria.[Wikipedia]. Tract of brain which is continuous with olfactory bulb and the cerebral cortex.[FMA] White matter tract that contains projections from the olfactory bulb to the olfactory cortex (Maryann Martone) in animals with a long snout, the olfactory tract is long, whereas it is short in short-snouted animals such as primates. In some birds the tract per se does not exist as the bulb is connected directly to the cerebral hemisphere.[ISBN:0471888893] The definition was adapted from the NIFSTD class which has been retired. It has been generalized so it is applicable to various different kinds of olfactory tracts found in different taxa. BAMS:olf BIRNLEX:1663 BTO:0003647 DHBA:12073 DHBA:12074 EMAPA:35615 FMA:77626 HBA:9302 MA:0000975 NCIT:C33207 UMLS:C0162435 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=283 uberon olfactory peduncle olfactory stalk pedunclulus olfactorius tractus olfactorium tractus olfactorius UBERON:0002265 olfactory tract http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray732.png White matter tract that contains projections from the olfactory bulb to other parts of the brain BIRNLEX:1663 ISBN:0471888893 A nervelike, white band composed primarily of nerve fibres originating from the mitral cells and tufted cells of the olfactory bulb but also containing the scattered cells of the anterior olfactory nucleus[BTO:0003647]. BTO:0003647 The olfactory tract is a bundle of axons connecting the mitral and tufted cells of the olfactory bulb to several target regions in the brain, including piriform cortex, amygdala, and entorhinal cortex. It is a narrow white band, triangular on coronal section, the apex being directed upward. It lies in the olfactory sulcus on the inferior surface of the frontal lobe, and divides posteriorly into two striæ, a medial olfactory stria and a lateral olfactory stria.[Wikipedia]. Tract of brain which is continuous with olfactory bulb and the cerebral cortex.[FMA] FMA White matter tract that contains projections from the olfactory bulb to the olfactory cortex (Maryann Martone) deprecated class BIRNLEX:1663 The definition was adapted from the NIFSTD class which has been retired. It has been generalized so it is applicable to various different kinds of olfactory tracts found in different taxa. cjm ISBN:0471888893 UMLS:C0162435 ncithesaurus:Olfactory_Tract http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=283 BIRNLEX:1663 olfactory peduncle BTO:0003647 olfactory stalk NeuroNames:283 pedunclulus olfactorius NeuroNames:283 tractus olfactorium NeuroNames:283 tractus olfactorius tractus olfactorius BTO:0003647 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 BAMS:PVZ EMAPA:35421 FMA:77682 MA:0000846 MBA:157 VHOG:0000623 hypothalamus periventricular zone zona periventricularis hypothalamicae uberon periventricular zone of the hypothalamus UBERON:0002271 periventricular zone of hypothalamus zona periventricularis hypothalamicae FMA:77682 FMA:TA periventricular zone of the hypothalamus BAMS:PVZ BAMS:MEZ BAMS:MZ EMAPA:35419 FMA:77683 MA:0000837 MBA:467 hypothalamus medial zone zona medialis hypothalamicae uberon hypothalamic medial zone behavioral control column medial zone of the hypothalamus UBERON:0002272 medial zone of hypothalamus zona medialis hypothalamicae FMA:77683 FMA:TA hypothalamic medial zone behavioral control column BAMS:MEZ medial zone of the hypothalamus BAMS:MEZ medial zone of the hypothalamus BAMS:MZ 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 The osseous spiral lamina consists of two plates of bone, and between these are the canals for the transmission of the filaments of the acoustic nerve. On the upper plate of that part of the lamina which is outside the vestibular membrane, the periosteum is thickened to form the limbus spiralis (or limbus laminæ spiralis), this ends externally in a concavity, the sulcus spiralis internus, which represents, on section, the form of the letter C. [WP,unvetted]. EMAPA:35496 FMA:77721 MA:0001191 limbus lamina spiralis limbus laminae spiralis limbus laminae spiralis osseae spiral limbus lamina uberon spiral limbus UBERON:0002276 lamina of spiral limbus http://upload.wikimedia.org/wikipedia/commons/a/a5/Gray930.png MA The osseous spiral lamina consists of two plates of bone, and between these are the canals for the transmission of the filaments of the acoustic nerve. On the upper plate of that part of the lamina which is outside the vestibular membrane, the periosteum is thickened to form the limbus spiralis (or limbus laminæ spiralis), this ends externally in a concavity, the sulcus spiralis internus, which represents, on section, the form of the letter C. [WP,unvetted]. limbus lamina spiralis MA:0001191 limbus laminae spiralis FMA:77721 spiral limbus lamina FMA:77721 The fluid-filled space separating the membranous from the osseous labyrinth. BTO:0002083 FMA:77745 ZFA:0005459 uberon Retzius space cisterna perilymphatica spatium perilymphaticum UBERON:0002278 perilymphatic space ZFA The fluid-filled space separating the membranous from the osseous labyrinth. Dorlands_Medical_Dictionary:MerckSource cisterna perilymphatica spatium perilymphaticum The upper portion of the spiral ligament contains numerous capillary loops and small blood vessels, and is termed the stria vascularis. It produces endolymph for the scala media, one of the three fluid-filled compartments of the cochlea. [WP,unvetted]. represented as a wall in FMA. MESH def implies part of spiral ligament but better represented as adjacency / overlaps BIRNLEX:2525 BTO:0001819 CALOHA:TS-0982 EFO:0001644 EMAPA:35827 FMA:77832 GAID:875 MA:0001198 MESH:D013316 UMLS:C0229477 psalterial cord stria vascularis stria vascularis of cochlea vascular stripe of cochlear duct uberon stria vascularis ductus cochlearis vascular stria of cochlear duct UBERON:0002282 stria vascularis of cochlear duct http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png FMA MA The upper portion of the spiral ligament contains numerous capillary loops and small blood vessels, and is termed the stria vascularis. It produces endolymph for the scala media, one of the three fluid-filled compartments of the cochlea. [WP,unvetted]. represented as a wall in FMA. MESH def implies part of spiral ligament but better represented as adjacency / overlaps FMA UMLS:C0229477 BIRNLEX:2525 psalterial cord MP:0000048 stria vascularis of cochlea FMA:77832 vascular stripe of cochlear duct MP:0000048 stria vascularis ductus cochlearis BTO:0001819 vascular stria of cochlear duct BTO:0001819 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 division of the spiral canal of the cochlea that contains the organ of Corti (the neuroepithelial receptor organ for hearing) TODO - check cochlear duct vs cochlear aqueduct vs scala media EHDAA2:0000262 EMAPA:35751 FMA:79789 MA:0002458 uberon cochlear duct UBERON:0002295 located in between the scala tympani and the scala vestibuli, separated by the basilar membrane and Reissner's membrane (the vestibular membrane) respectively. Scala media houses the organ of Corti. [Wikipedia:Scala_media] scala media http://upload.wikimedia.org/wikipedia/commons/b/bc/Gray928.png MA FMA the division of the spiral canal of the cochlea that contains the organ of Corti (the neuroepithelial receptor organ for hearing) MGI:anna MP:0003169 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 Spherical outcropping of the respiratory bronchioles and primary site of gas exchange with the blood. Alveoli are particular to mammalian lungs. Different structures are involved in gas exchange in other vertebrates[WP]. alveolus BTO:0000060 CALOHA:TS-0031 EFO:0001985 EMAPA:32682 EV:0100043 FMA:7318 GAID:349 MA:0000420 MESH:D011650 VHOG:0001445 alveolus pulmonis lung alveolus pulmonary alveolus respiratory alveolus uberon alveoli alveolus pulmonis respiratory alveoli UBERON:0002299 alveolus of lung Alveolus:diagram.svg FMA Spherical outcropping of the respiratory bronchioles and primary site of gas exchange with the blood. Alveoli are particular to mammalian lungs. Different structures are involved in gas exchange in other vertebrates[WP]. alveolus pulmonis pulmonary alveolus FMA:7318 alveoli BTO:0000060 alveolus pulmonis respiratory alveoli 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 An anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. a microscopic structure in the kidney, which regulates the function of each nephron. The juxtaglomerular apparatus is named for its proximity to the glomerulus: it is found between the vascular pole of the renal corpuscle and the returning distal convoluted tubule of the same nephron. This location is critical to its function in regulating renal blood flow and glomerular filtration rate. The three cellular components of the apparatus are the macula densa, extraglomerular mesangial cells, and juxtaglomerular cells (also known as granular cells)[WP]. BTO:0005157 EMAPA:30449 FMA:83599 GAID:432 MA:0002546 MESH:D007606 NCIT:C32891 UMLS:C0022445 complexus juxtaglomerularis juxtaglomerular complex uberon UBERON:0002303 juxtaglomerular apparatus MA An anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. a microscopic structure in the kidney, which regulates the function of each nephron. The juxtaglomerular apparatus is named for its proximity to the glomerulus: it is found between the vascular pole of the renal corpuscle and the returning distal convoluted tubule of the same nephron. This location is critical to its function in regulating renal blood flow and glomerular filtration rate. The three cellular components of the apparatus are the macula densa, extraglomerular mesangial cells, and juxtaglomerular cells (also known as granular cells)[WP]. GO:0072206 UMLS:C0022445 ncithesaurus:Juxtaglomerular_Apparatus complexus juxtaglomerularis juxtaglomerular complex MP:0002829 One of the three layers of the dentate gyrus of the hippocampal formation. the basic trilaminar structure of the dentate gyrus is common across all species studied, with relatively minimal phylogenetic variation[PMC2492885] EMAPA:35278 FMA:83678 MA:0002429 dentate gyrus cell layer dentate gyrus layer uberon UBERON:0002304 layer of dentate gyrus One of the three layers of the dentate gyrus of the hippocampal formation. PMCID:PMC2492885 The layers of the laminar structure of the hippocampus. TODO - check NIF xref BIRNLEX:1192 EMAPA:35407 FMA:277842 FMA:83679 MA:0002427 cytoarchitectural fields of hippocampal formation hippocampus layer uberon hippocampus proper layer layer of cornu ammonis UBERON:0002305 layer of hippocampus The layers of the laminar structure of the hippocampus. MP:0000813 cytoarchitectural fields of hippocampal formation BIRNLEX:1192 hippocampus proper layer FMA:83679 layer of cornu ammonis FMA:83679 mucus produced in the nasal cavity, by the respiratory segment of the nasal mucosa. TODO - split nasal vs respiratory tract? protects the olfactory epithelium and allows odors to dissolve so that they can be detected by olfactory receptor neurons BTO:0003603 CALOHA:TS-0658 EMAPA:36552 FMA:83688 MA:0002535 NCIT:C52551 UMLS:C0225392 uberon respiratory mucus UBERON:0002306 nasal mucus mucus produced in the nasal cavity, by the respiratory segment of the nasal mucosa. UMLS:C0225392 ncithesaurus:Nasal_Mucus respiratory mucus BTO:0003603 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 Regional part of fornix consisting of a prominent white matter structure adjacent to the hippocampus on the ventricular side continuous with the alveus. Near the splenium the fimbria separates from the hippocampus as the crus of the fornix. [adapted from Wikipedia] (MM: 2006-10-26). fimbria BAMS:FI BAMS:fi BIRNLEX:1502 BM:Tel-FI DHBA:10575 DMBA:17766 EMAPA:35345 FMA:83866 HBA:9253 MA:0000949 MBA:603 NCIT:C32606 UMLS:C0152315 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=187 fimbria hippocampus fimbria of hippocampus fimbria of the fornix fimbria-fornix hippocampal fimbria neuraxis fimbria uberon fimbria (Vieussens) fimbria fornicis fimbria hippocampi fimbria of fornix fimbria of the hippocampus UBERON:0002310 hippocampus fimbria http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray749.png Need to determine whether the fimbria is part of the fornix. Sometimes the language suggests it isn't always thought of that way, but I see no useful reason why it should be separate; it all forms one continuous white matter tract. Neuronames and others include this as part of the hippocampal formation (MM) NIFSTD MA NIFSTD Regional part of fornix consisting of a prominent white matter structure adjacent to the hippocampus on the ventricular side continuous with the alveus. Near the splenium the fimbria separates from the hippocampus as the crus of the fornix. [adapted from Wikipedia] (MM: 2006-10-26). BIRNLEX:1502 fimbria BIRNLEX:1502 UMLS:C0152315 BIRNLEX:1502 UMLS:C0152315 ncithesaurus:Fimbria http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=187 BIRNLEX:1502 fimbria of hippocampus FMA:83866 fimbria of the fornix BIRNLEX:1502 fimbria-fornix BIRNLEX:1502 hippocampal fimbria MP:0009324 fimbria (Vieussens) NeuroNames:187 fimbria fornicis NeuroNames:187 fimbria hippocampi fimbria hippocampi NeuroNames:187 fimbria of fornix NeuroNames:187 fimbria of the hippocampus NeuroNames:187 A cytoarchitectural term denoting the layer of the hippocampus in which pyramidal cells are predominant. Its location is superficial to the Stratum oriens; it is deep to the Stratum radiatum in area CA1 and area CA2 and deep to the Stratum lucidum in area CA3 (Stephan-75) (NeuroNames). this layer changes in its depthwise spatial relation across its extent UBERON:0005369 BAMS:Py BIRNLEX:1444 BTO:0001066 EMAPA:35409 FMA:83895 MA:0000956 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=156 pyramidal cell layer of the hippocampus pyramidal layer of hippocampus stratum pyramidale stratum pyramidale hippocampi uberon gyrus occipitalis inferior gyrus occipitalis tertius hippocampal pyramidal cell layer hippocampal pyramidal layer hippocampus pyramidal cell layer hippocampus stratum pyramidale UBERON:0002313 hippocampus pyramidal layer A cytoarchitectural term denoting the layer of the hippocampus in which pyramidal cells are predominant. Its location is superficial to the Stratum oriens; it is deep to the Stratum radiatum in area CA1 and area CA2 and deep to the Stratum lucidum in area CA3 (Stephan-75) (NeuroNames). BIRNLEX:1444 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=156 BIRNLEX:1444 pyramidal cell layer of the hippocampus BIRNLEX:1444 pyramidal layer of hippocampus FMA:83895 stratum pyramidale BIRNLEX:1444 stratum pyramidale hippocampi BIRNLEX:1444 gyrus occipitalis inferior NeuroNames:156 gyrus occipitalis tertius NeuroNames:156 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 Neural tissue consisting of myelinated axons connecting grey matter areas of the central nervous system. Cell part cluster consisting predominantly of neurites in the brain and the spinal cord[FMA:83929]. Multi-tissue structure comprised largely of myelinated axons.[TAO] The myelination of axons by glial cells was the last major step in the evolution of cells in the vertebrate nervous system, and white-matter tracts are key to the architecture of the mammalian brain.[well established][VHOG] nlx_anat_101177 seems to have been lost in the transition from NIFGA to Neurolex AEO:0000139 AEO:0001011 EMAPA:35927 FMA:83929 HBA:9218 MA:0001135 NCIT:C33892 NLX:412 NLXANAT:101177 OpenCyc:Mx4rwOAsDZwpEbGdrcN5Y29ycA PBA:294022044 TAO:0000145 TAO:0002142 TAO:0002143 UMLS:C0682708 VHOG:0001764 ZFA:0001682 CNS tract/commissure neuronal white matter white matter of neuraxis white substance uberon CNS tracts and commissures CNS white matter substantia alba white mater UBERON:0002316 white matter Spinal:nerve.svg http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg Neural tissue consisting of myelinated axons connecting grey matter areas of the central nervous system. Cell part cluster consisting predominantly of neurites in the brain and the spinal cord[FMA:83929]. FMA:83929 Multi-tissue structure comprised largely of myelinated axons.[TAO] 2012-08-14 TAO:0002142 TAO ZFIN:curator The myelination of axons by glial cells was the last major step in the evolution of cells in the vertebrate nervous system, and white-matter tracts are key to the architecture of the mammalian brain.[well established][VHOG] 2012-09-17 VHOG:0001764 VHOG DOI:10.1038/nature09614 Nave KA, Myelination and support of axonal integrity by glia. Nature (2010) nlx_anat_101177 seems to have been lost in the transition from NIFGA to Neurolex NIF https://github.com/SciCrunch/NIF-Ontology/issues/83 UMLS:C0682708 ncithesaurus:White_Matter CNS tract/commissure ZFA:0001682 neuronal white matter AEO:0001011 white matter of neuraxis FMA:83929 CNS tracts and commissures TAO:0000145 CNS white matter TAO:0002143 substantia alba white mater VHOG:0001764 The regions of the spinal cord that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites. BAMS:SCwhite DHBA:146035088 EMAPA:35795 FMA:83945 MA:0000910 NCIT:C33893 UMLS:C0458457 spinal cord white matter spinal cord white matter of neuraxis spinal cord white substance substantia alba medullae spinalis white matter of neuraxis of spinal cord white substance of spinal cord uberon UBERON:0002318 white matter of spinal cord The regions of the spinal cord that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites. MP:0008027 UMLS:C0458457 ncithesaurus:White_Matter_of_the_Spinal_Cord spinal cord white matter of neuraxis OBOL:automatic spinal cord white substance OBOL:automatic substantia alba medullae spinalis FMA:83945 FMA:TA white matter of neuraxis of spinal cord OBOL:automatic white substance of spinal cord OBOL:automatic The inner layer of the glomerulus, within the basement membrane surrounding the glomerular capillaries. mesangial WP considers this the same as glomerular mesangium. In MA, glomerular and extraglomerular are distingsuished. FMA class has no definition and is a type of stroma, which is inconsistent with our classification of this here. BTO:0002494 EMAPA:28248 EMAPA:36561 FMA:84139 MA:0002617 NCIT:C33101 UMLS:C0017655 uberon UBERON:0002319 mesangium The inner layer of the glomerulus, within the basement membrane surrounding the glomerular capillaries. WP considers this the same as glomerular mesangium. In MA, glomerular and extraglomerular are distingsuished. FMA class has no definition and is a type of stroma, which is inconsistent with our classification of this here. MA EMAPA:36561 MA:th UMLS:C0017655 ncithesaurus:Mesangium A thin membrane which helps to support the capillary loops in a renal glomerulus. It is connective tissue composed of mesangial cells - myofibroblasts phenotypically related to vascular smooth muscle cells (muscle, smooth, vascular), phagocytes and the mesangial extracellular matrix. EMAPA:27961 EMAPA:28248 FMA:84140 GAID:430 MA:0002606 MESH:A05.810.453.736.520.380 uberon UBERON:0002320 glomerular mesangium GO A thin membrane which helps to support the capillary loops in a renal glomerulus. It is connective tissue composed of mesangial cells - myofibroblasts phenotypically related to vascular smooth muscle cells (muscle, smooth, vascular), phagocytes and the mesangial extracellular matrix. MESH:A05.810.453.736.520.380 the tissue comprised of mesangial cells that fill the triangular space between the macula densa and the afferent and efferent arterioles of the juxtaglomerular apparatus check MA part_ofs - should be spatially disjoint from renal glomerulus? EMAPA:28278 FMA:84141 MA:0002602 uberon UBERON:0002321 extraglomerular mesangium MA MA the tissue comprised of mesangial cells that fill the triangular space between the macula densa and the afferent and efferent arterioles of the juxtaglomerular apparatus ISBN:0-683-40008-8 MP:0011340 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 macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus[GO]. not part of a nephron or distal tubule in MA and FMA BTO:0003940 EMAPA:28399 FMA:86333 MA:0002603 NCIT:C33043 UMLS:C0227662 uberon UBERON:0002335 macula densa MA GO The macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus[GO]. GO:0072024 not part of a nephron or distal tubule in MA and FMA MA UMLS:C0227662 ncithesaurus:Macula_Densa 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 part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node[GO]. Subdivision of conducting system of heart at the junction of the right atrium and the superior vena cava, around the sinoatrial nodal branch of right coronary artery and is continuous with the internodal tract[FMA]. BTO:0004358 EHDAA2:0004184 EMAPA:35772 FMA:9477 GAID:561 MA:0000097 MESH:D012849 NCIT:C33555 OpenCyc:Mx4rOhejDGMcEd2AAABQjYGu0g TAO:0005069 UMLS:C0037189 ZFA:0005069 Koch's node SA nodal muscle tissue SA node cardiac pacemaker node of Keith-Flack nodus sinuatrialis sinoatrial node sinu-atrial node sinuatrial nodal muscle tissue sinuatrial node sinus node sinus node of Keith and Flack uberon nodus sinuatrialis UBERON:0002351 WP:Heart states: "The SA node is found in all amniotes but not in more primitive vertebrates. In these animals, the muscles of the heart are relatively continuous and the sinus venosus coordinates the beat which passes in a wave through the remaining chambers. Indeed, since the sinus venosus is incorporated into the right atrium in amniotes, it is likely homologous with the SA node. In teleosts, with their vestigial sinus venosus, the main centre of coordination is, instead, in the atrium.". Note however that ZFA has SA node. sinoatrial node http://upload.wikimedia.org/wikipedia/commons/d/d2/Sinoatrial_node_low_mag.jpg http://upload.wikimedia.org/wikipedia/commons/d/de/Sinoatrial_node_2_low_mag.jpg cjm ZFA The part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node[GO]. Subdivision of conducting system of heart at the junction of the right atrium and the superior vena cava, around the sinoatrial nodal branch of right coronary artery and is continuous with the internodal tract[FMA]. GO:0003163 UMLS:C0037189 ncithesaurus:Sinoatrial_Node Koch's node FMA:9477 SA nodal muscle tissue FMA:9477 SA node FMA:9477 cardiac pacemaker FMA:9477 node of Keith-Flack FMA:9477 nodus sinuatrialis FMA:9477 FMA:TA sinoatrial node FMA:9477 sinu-atrial node FMA:9477 sinuatrial nodal muscle tissue FMA:9477 sinuatrial node FMA:9477 sinus node FMA:9477 sinus node of Keith and Flack FMA:9477 nodus sinuatrialis An area of conducting tissue between the atria and the ventricles of the heart that conducts the normal electrical impulse from the atria to the ventricles. 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. Furthermore, within the ventricular component a compact outer myocardial component and an interiorly localized extensive trabecular component can be distinguished. The specific activation of the ventricle adds to its complexity as follows. The depolarizing impulse travels rapidly from the atrioventricular node toward the apex and then toward the conal region, achieving activation from apex to base.[uncertain][VHOG] BTO:0005689 EFO:0000276 EHDAA2:0004183 EMAPA:35153 FMA:9478 GAID:558 MA:0000095 MAT:0000498 MESH:D001283 NCIT:C32161 OpenCyc:Mx4rMfD91mMcEd2AAABQjYGu0g TAO:0005070 UMLS:C0004247 VHOG:0001474 ZFA:0005070 AV nodal muscle tissue AV node Aschoff-Tawara node atrioventricular nodal muscle tissue node of Tawara nodus atrioventricularis uberon A-V node atrio-ventricular node atriovetricular node downstream pacemaker nodus atrioventricularis UBERON:0002352 atrioventricular node http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png http://upload.wikimedia.org/wikipedia/commons/9/92/Gray501.png cjm An area of conducting tissue between the atria and the ventricles of the heart that conducts the normal electrical impulse from the atria to the ventricles. UBERON:cjm 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. Furthermore, within the ventricular component a compact outer myocardial component and an interiorly localized extensive trabecular component can be distinguished. The specific activation of the ventricle adds to its complexity as follows. The depolarizing impulse travels rapidly from the atrioventricular node toward the apex and then toward the conal region, achieving activation from apex to base.[uncertain][VHOG] 2012-09-17 VHOG:0001474 VHOG DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003) UMLS:C0004247 ncithesaurus:Atrioventricular_Node AV nodal muscle tissue FMA:9478 AV node FMA:9478 MA:0000095 Aschoff-Tawara node FMA:9478 atrioventricular nodal muscle tissue FMA:9478 node of Tawara FMA:9478 nodus atrioventricularis FMA:TA A-V node EMAPA:35153 atrio-ventricular node EMAPA:35153 atriovetricular node TAO:0005070 downstream pacemaker ZFA:0005070 nodus atrioventricularis A part of the His-Purkinje system that transmits signals from the AV node to the cardiac Purkinje fibers[GO] EMAPA:35152 FMA:9484 GAID:559 MA:0002576 MESH:D002036 NCIT:C32160 OpenCyc:Mx4rUv1WcGPJEd2AAABQjYGu0g UMLS:C0006382 galen:BundleOfHis AV bundle AVB His bundle atrio-ventricular bundle atrioventricular bundle atrioventricular bundle muscle tissue atrioventricular fasciculus bundle of His fasciculus atrioventricularis uberon A-V bundle UBERON:0002353 bundle of His http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png http://upload.wikimedia.org/wikipedia/commons/b/b6/ECG_Principle_fast.gif cjm GO A part of the His-Purkinje system that transmits signals from the AV node to the cardiac Purkinje fibers[GO] GO:0003166 GOC:mtg_heart UMLS:C0006382 ncithesaurus:Atrioventricular_Bundle AVB atrio-ventricular bundle EMAPA:35152 atrioventricular bundle muscle tissue FMA:9484 atrioventricular fasciculus FMA:9484 bundle of His FMA:9484 GO:0003166 fasciculus atrioventricularis A-V bundle EMAPA:35152 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 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 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 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. 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 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 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 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 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 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 A large superficial muscle that extends longitudinally from the occipital bone to the lower thoracic vertebrae and laterally to the spine of the scapula (shoulder blade). Its functions are to move the scapulae and support the arm. The trapezius has three functional regions: the superior region (descending part), which supports the weight of the arm; the intermediate region (transverse part), which retracts the scapulae; and the inferior region (ascending part), which medially rotates and depresses the scapulae. [WP,unvetted]. The sternomastoid and the three parts of the trapezius are branchiomeric muscles that have secondarily acquired an attachment to the pectoral girdle. They evolved from the fish cucullaris.[well established][VHOG] EMAPA:18183 FMA:9626 MA:0002398 NCIT:C33809 UMLS:C0224361 VHOG:0000834 trapezius uberon musculus trapezius spinotrapezius UBERON:0002380 trapezius muscle http://upload.wikimedia.org/wikipedia/commons/6/60/Trapezius.png external occipital protuberance nuchal ligament medial superior nuchal line spinous processes of vertebrae C7-T12 dbpedia external occipital protuberance nuchal ligament medial superior nuchal line spinous processes of vertebrae C7-T12 dbpedia posterior border of the lateral third of the clavicle acromion process and spine of scapula dbpedia posterior border of the lateral third of the clavicle acromion process and spine of scapula dbpedia dbpedia dbpedia A large superficial muscle that extends longitudinally from the occipital bone to the lower thoracic vertebrae and laterally to the spine of the scapula (shoulder blade). Its functions are to move the scapulae and support the arm. The trapezius has three functional regions: the superior region (descending part), which supports the weight of the arm; the intermediate region (transverse part), which retracts the scapulae; and the inferior region (ascending part), which medially rotates and depresses the scapulae. [WP,unvetted]. The sternomastoid and the three parts of the trapezius are branchiomeric muscles that have secondarily acquired an attachment to the pectoral girdle. They evolved from the fish cucullaris.[well established][VHOG] 2012-09-17 VHOG:0000834 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.345 UMLS:C0224361 ncithesaurus:Trapezius_Muscle musculus trapezius spinotrapezius The pectoralis major is a thick, fan-shaped muscle, situated at the upper front of the chest wall. It makes up the bulk of the chest muscles in the male and lies under the breast in the female. Underneath the pectoralis major is the pectoralis minor, a thin, triangular muscle. [WP,unvetted]. EHDAA2:0001424 EHDAA:8311 EMAPA:18179 FMA:9627 MA:0002354 NCIT:C33284 UMLS:C0585574 VHOG:0000895 pectoralis major muscle pectoralis major muscle structure uberon musculus pectoralis major UBERON:0002381 pectoralis major Pectoralis:major.png FMA lateral pectoral nerve and medial pectoral nerveClavicular head: C5 and C6Sternocostal head: C7 C8 and T1 dbpedia anterior surface of the sternum and the superior six costal cartilages and the aponeurosis of the external oblique muscle dbpedia anterior surface of the medial half of the clavicle dbpedia Lateral lip of intertubercular groove of the humerus dbpedia The pectoralis major is a thick, fan-shaped muscle, situated at the upper front of the chest wall. It makes up the bulk of the chest muscles in the male and lies under the breast in the female. Underneath the pectoralis major is the pectoralis minor, a thin, triangular muscle. [WP,unvetted]. UMLS:C0585574 ncithesaurus:Pectoralis_Major musculus pectoralis major 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 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 An individual member of a collection of basal ganglia. Basal ganglia are subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum[NIF,modified]. it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the set of all BGs-singular. it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done. BTO:0000235 CALOHA:TS-1149 DHBA:10332 EFO:0000904 FMA:62514 basal ganglion of telencephalon uberon basal ganglia basal nucleus nuclei basales UBERON:0002420 basal ganglion http://upload.wikimedia.org/wikipedia/commons/1/1b/Basal_Ganglia_and_Related_Structures.svg FMA BTO An individual member of a collection of basal ganglia. Basal ganglia are subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum[NIF,modified]. BIRNLEX:826 basal ganglia basal nucleus MA:0000184 nuclei basales Hippocampus (proper) plus dentate gyrus and subiculum[definition derived from NIF comments and ontology alignment]. The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum BTO:0000601 is placed here since it includes the DG. GO also includes dentate gyrus development as part of hippocampus development, so we assume when GO says 'hippocampus' it means 'hippocampal formation'. In ABA HPF = (.. subiculum) + HIP, HIP = DG + AH. BAMS:HPF BAMS:Hi BAMS:HiF BIRNLEX:715 BM:Tel-HF BTO:0000601 DHBA:10294 EMAPA:35405 FMA:74038 HBA:4249 MA:0000189 MBA:1089 PBA:4003 UMLS:C0175202 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=177 hippocampus (Crosby) hippocampus uberon archipallium formatio hippocampi major hippocampus primal cortex seahorse UBERON:0002421 hippocampal formation MBA-indirect NIFSTD Hippocampus (proper) plus dentate gyrus and subiculum[definition derived from NIF comments and ontology alignment]. The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum NIF BTO:0000601 is placed here since it includes the DG. GO also includes dentate gyrus development as part of hippocampus development, so we assume when GO says 'hippocampus' it means 'hippocampal formation'. In ABA HPF = (.. subiculum) + HIP, HIP = DG + AH. BTO UMLS:C0175202 BIRNLEX:715 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=177 BIRNLEX:715 hippocampus BTO:0000601 GO:0021766 archipallium MA:0000189 formatio hippocampi NeuroNames:177 major hippocampus BTO:0000601 primal cortex MA:0000189 seahorse NeuroNames:177 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 region of the forebrain consisting of the caudate nucleus, putamen and fundus striati.[GO]. striatal FMA divides 'striatum of neuraxis' into 4, neostriatum is seperate class. In NIF these are synonyms. TODO - check striatum vs corpus striatum see Wikipedia:Striatum#History. Check caudoputamen BAMS:STR BAMS:Str BAMS:Striatum BIRNLEX:1672 BM:N BTO:0000418 DHBA:10333 DMBA:15851 EFO:0000109 EMAPA:17549 FMA:77618 FMA:83683 HBA:4277 MA:0000891 MBA:477 MESH:A08.186.211.730.885.105.487.550 NCIT:C111122 PBA:10080 UMLS:C0162512 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=225 ncithesaurus:Striatum neostriatum neuraxis striatum striate nucleus striatum striatum of neuraxis uberon caudate putamen corpus striatum corpus striatum (Zilles) dorsal striatum striated nucleus UBERON:0002435 striatum http://upload.wikimedia.org/wikipedia/commons/3/33/BrainCaudatePutamen.svg GO BTO NIFSTD A region of the forebrain consisting of the caudate nucleus, putamen and fundus striati.[GO]. GOC:jl FMA divides 'striatum of neuraxis' into 4, neostriatum is seperate class. In NIF these are synonyms. TODO - check striatum vs corpus striatum see Wikipedia:Striatum#History. Check caudoputamen FMA UMLS:C0162512 BIRNLEX:1672 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=225 BIRNLEX:1672 neostriatum GO:0021756 neostriatum BIRNLEX:1672 neuraxis striatum FMA:83683 striate nucleus GO:0021756 striatum BIRNLEX:1672 striatum of neuraxis FMA:83683 caudate putamen BIRNLEX:1672 corpus striatum MA:0000891 corpus striatum (Zilles) NeuroNames:225 dorsal striatum BIRNLEX:1672 striated nucleus BTO:0000418 White matter that is part of a cerebral hemisphere. sometimes the term 'cerebral white matter' may be used generically but here is refers specifically to the white matter in a hemisphere The BTO class is inconsistent as it is part of the brain and spinal cord. BAMS:cw BIRNLEX:711 BTO:0000236 CALOHA:TS-2362 EMAPA:35237 FMA:241998 FMA:256174 FMA:61822 MA:0000945 NCIT:C49347 UMLS:C0152295 UMLS:C1284115 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=189 cerebral hemisphere white matter cerebral white matter white matter structure of cerebral hemisphere uberon hemisphere white matter region of cerebral white matter substantia medullaris cerebri UBERON:0002437 cerebral hemisphere white matter White matter that is part of a cerebral hemisphere. The BTO class is inconsistent as it is part of the brain and spinal cord. BTO UMLS:C0152295 BIRNLEX:711 UMLS:C0152295 ncithesaurus:Cerebral_White_Matter UMLS:C1284115 BIRNLEX:711 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=189 BIRNLEX:711 cerebral white matter MA:0000945 white matter structure of cerebral hemisphere FMA:61822 region of cerebral white matter FMA:256174 substantia medullaris cerebri NeuroNames:189 EMAPA:37719 FMA:65265 MA:0001175 right axillary neural trunk trunk of right axillary nerve uberon circumflex nerve trunk UBERON:0002442 axillary nerve trunk EMAPA:37719 MA:th trunk of right axillary nerve FMA:65265 circumflex nerve trunk MA:0001175 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 A large sesamoid bone found in the distal femur/proximal tibial region of the hindlimb of tetrapods. The patella is the attachment site for proximal hindlimb tendons.[PHENOSCAPE:ad] patellar EMAPA:35668 FMA:24485 GAID:203 MA:0001374 MESH:A02.835.232.500.624 NCIT:C33282 UMLS:C0030647 galen:Patella uberon knee bone knee cap patella UBERON:0002446 The patella, also known as the knee cap or kneepan, is the largest sesamoid bone in the human body. The primary functional role of the patella is knee extension. The patella has convergently evolved in placental mammals and birds; marsupials have only rudimentary, non-ossified patellae. In more primitive tetrapods, including living amphibians and reptiles, the muscle tendons from the upper leg are attached directly to the tibia, and the patella is not present. See also: fabella. patella Knee:diagram.svg FMA A large sesamoid bone found in the distal femur/proximal tibial region of the hindlimb of tetrapods. The patella is the attachment site for proximal hindlimb tendons.[PHENOSCAPE:ad] PHENOSCAPE:ad UMLS:C0030647 ncithesaurus:Patella knee bone FMA:24485 knee cap patella The maternal uterine-derived portion of the placenta TODO - check mp syn formed under the influence of progesterone and forms highly-characteristic cells. [Wikipedia:Decidua] BTO:0001360 CALOHA:TS-0193 EMAPA:35269 FMA:85538 GAID:378 MA:0001722 MAT:0000290 MESH:D003656 MIAA:0000290 NCIT:C32425 UMLS:C0011106 decidous membrane uberon decidua basalis endometrium extraembryonic part of placenta extraembryonic placenta maternal decidual layer maternal part of placenta maternal placenta placenta maternal decidual layer uterine decidua UBERON:0002450 decidua http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray33.png FMA maternal MA The maternal uterine-derived portion of the placenta MP:0004256 UMLS:C0011106 ncithesaurus:Decidua decidous membrane FMA:85538 extraembryonic part of placenta extraembryonic placenta maternal decidual layer MP:0004256 maternal part of placenta maternal placenta EMAPA:35269 maternal placenta GOC:dph uterine decidua BTO:0001360 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 the bone that is situated in the orbit on either side of the presphenoid; it generally forms a part of the sphenoid in the adult, and may be independent in the young Endochondral ossification of the lateral sides of the braincase.[AAO] Large median unpaired cartilage bone consisting of two diverging plates. Positioned medial to the eye. The orbitosphenoid develops from the Trabeculae communis and forms the anterior and anterolateral boundary of the orbital foramen and constitutes a significant part of the sidewalls and floor of the cranial cavity. Bordered by the lateral ethmoid anteriorly, and the pterosphenoid posteriorly, The orbitosphenoid may extend ventrally to meet the parasphenoid. In the adult, the orbitosphenoid is fused ventrally to the parasphenoid via a thin sheet of bone.[TAO] relationship loss: develops_from taenia marginalis anterior (TAO:0001505)[TAO] relationship loss: overlaps orbitosphenoid-lateral ethmoid joint (TAO:0001941)[TAO] relationship loss: overlaps orbitosphenoid-prootic joint (TAO:0001794)[TAO] relationship loss: overlaps pterosphenoid-orbitosphenoid joint (TAO:0001831)[TAO] relationship loss: part_of braincase and otic capsule skeleton (AAO:0000052)[AAO] relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: develops_from neurocranium (UBERON:0001703)[TAO] relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: part_of neurocranium (UBERON:0001703)[TAO] AAO:0000345 EMAPA:18719 FMA:52869 MA:0002773 TAO:0000253 VHOG:0001153 ZFA:0000253 ala minor (os sphenoidale) ala minor ossis sphenoidalis conchosphénocïde@fr ingrassia's process lesser wing of sphenoid lesser wing of sphenoidal bone orbito-sphénocïde@fr orbitosphenoid bone uberon alae parvae lesser wing of sphenoid bone orbitosphenoids UBERON:0002478 orbitosphenoid http://upload.wikimedia.org/wikipedia/commons/3/35/Gray145.png FMA-abduced-lr the bone that is situated in the orbit on either side of the presphenoid; it generally forms a part of the sphenoid in the adult, and may be independent in the young ISBN:0-683-40008-8 MP:0004457 Endochondral ossification of the lateral sides of the braincase.[AAO] 2012-06-20 AAO:0000345 AAO AAO:LAP Large median unpaired cartilage bone consisting of two diverging plates. Positioned medial to the eye. The orbitosphenoid develops from the Trabeculae communis and forms the anterior and anterolateral boundary of the orbital foramen and constitutes a significant part of the sidewalls and floor of the cranial cavity. Bordered by the lateral ethmoid anteriorly, and the pterosphenoid posteriorly, The orbitosphenoid may extend ventrally to meet the parasphenoid. In the adult, the orbitosphenoid is fused ventrally to the parasphenoid via a thin sheet of bone.[TAO] 2012-08-14 TAO:0000253 TAO ZFIN:curator relationship loss: develops_from taenia marginalis anterior (TAO:0001505)[TAO] 2012-08-14 TAO:0000253 TAO relationship loss: overlaps orbitosphenoid-lateral ethmoid joint (TAO:0001941)[TAO] 2012-08-14 TAO:0000253 TAO relationship loss: overlaps orbitosphenoid-prootic joint (TAO:0001794)[TAO] 2012-08-14 TAO:0000253 TAO relationship loss: overlaps pterosphenoid-orbitosphenoid joint (TAO:0001831)[TAO] 2012-08-14 TAO:0000253 TAO relationship loss: part_of braincase and otic capsule skeleton (AAO:0000052)[AAO] 2012-06-20 AAO:0000345 AAO relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: develops_from neurocranium (UBERON:0001703)[TAO] 2012-08-14 TAO:0000253 TAO relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: part_of neurocranium (UBERON:0001703)[TAO] 2012-08-14 TAO:0000253 TAO ala minor (os sphenoidale) FMA:52869 ala minor ossis sphenoidalis FMA:52869 FMA:TA conchosphénocïde@fr TAO:0000253 ingrassia's process FMA:52869 lesser wing of sphenoid FMA:52869 lesser wing of sphenoidal bone FMA:52869 orbito-sphénocïde@fr TAO:0000253 orbitosphenoid bone alae parvae lesser wing of sphenoid bone MA:0002773 orbitosphenoids ZFA:0000253 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 Bone tissue that has a regular parallel alignment of collagen into sheets (lamellae) and is mechanically strong. EMAPA:37625 FMA:224806 MA:0002781 galen:LamellarBone uberon UBERON:0002482 histological classification, lamellar vs woven. Note that only FMA has woven lamellar bone Bone tissue that has a regular parallel alignment of collagen into sheets (lamellae) and is mechanically strong. EMAPA:37625 MA:th the medullary cavities of the bones where bone marrow is stored Located in the main shaft (cortical bone) of a long bone (diaphysis) (consisting mostly of compact bone), the medullary cavity has walls composed of spongy bone (cancellous bone) and is lined with a thin, vascular membrane (endosteum)[Wikipedia:Bone_marrow_of_ovaryry_cavity] not clear if the FMA intends to have two classes. MP:0000065: 'the medullary cavities of the bones.'. NCITA also has 'medullary bone' FMA:75147 FMA:83698 MA:0002783 cavity of cancellous bone marrow cavity medullary cavity uberon UBERON:0002484 bone marrow cavity the medullary cavities of the bones where bone marrow is stored ISBN:0-683-40008-8 MP:0000065 not clear if the FMA intends to have two classes. MP:0000065: 'the medullary cavities of the bones.'. NCITA also has 'medullary bone' FMA marrow cavity FMA:83698 medullary cavity FMA:83698 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 Region of the scapula where the latter meets with the clavicle: attachment point of the clavicle to the scapula in some taxa. Anterior rounded projection of the pars acromialis of the scapula.[AAO] relationship loss: part_of pars acromialis (AAO:0000752)[AAO] AAO:0000826 EMAPA:25119 FMA:23260 GAID:187 MA:0002805 MESH:D000174 NCIT:C32048 OpenCyc:Mx4rvmrF8pwpEbGdrcN5Y29ycA UMLS:C0001209 VSAO:0005067 acromion process scapular acromion uberon acromion of scapula acromion of the scapula UBERON:0002497 acromion http://upload.wikimedia.org/wikipedia/commons/7/79/Gray206.png Region of the scapula where the latter meets with the clavicle: attachment point of the clavicle to the scapula in some taxa. VSAO:0005067 Anterior rounded projection of the pars acromialis of the scapula.[AAO] 2012-06-20 AAO:0000826 AAO AAO:LAP relationship loss: part_of pars acromialis (AAO:0000752)[AAO] 2012-06-20 AAO:0000826 AAO UMLS:C0001209 ncithesaurus:Acromion acromion process VSAO:0005067 scapular acromion VSAO:0005067 acromion of scapula acromion of the scapula a rough elevation at the middle of the lateral side of the shaft of the humerus to which the deltoid muscle attaches In basal Tetrapodomorph lineages often the deltoid process and the pectoral processes are separate and thus should not be made exact synonyms to the deltopectoral crest.[PHENOSCAPE:ad] AAO:0000736 EMAPA:25052 FMA:23418 MA:0002808 crista ventralis deltoid crest deltoid eminence deltoid impression deltoid tuberosity deltoid tuberosity of humerus tuberositas deltoidea tuberositas deltoidea (corpus humeri) tuberositas deltoidea humeri uberon crista ventralis humeri deltoid process pectoral process UBERON:0002498 deltopectoral crest http://upload.wikimedia.org/wikipedia/commons/a/a7/HumerusFront.png a rough elevation at the middle of the lateral side of the shaft of the humerus to which the deltoid muscle attaches ISBN:0-683-40008-8 MP:0004353 crista ventralis AAO:0000736 deltoid crest AAO:0000736 MP:0004353 deltoid eminence MP:0004353 deltoid impression MP:0004353 deltoid tuberosity FMA:23418 deltoid tuberosity of humerus FMA:23418 tuberositas deltoidea FMA:23418 FMA:TA tuberositas deltoidea humeri crista ventralis humeri AAO:0000736 deltoid process MP:0004353 The labyrinth is 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. It is named by analogy with the mythical maze that imprisoned the Minotaur, because of its appearance. 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]. we follow the FMA in placing this in the membranous labyrinth. Notes: The labyrinth can be divided by layer or by region. Bony vs. membranous / Vestibular vs. cochlear BTO:0004686 EMAPA:36569 FMA:61259 MA:0002809 NCIT:C32336 UMLS:C0931689 uberon UBERON:0002499 cochlear labyrinth http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png FMA The labyrinth is 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. It is named by analogy with the mythical maze that imprisoned the Minotaur, because of its appearance. 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:C0931689 ncithesaurus:Cochlear_Labyrinth 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 A transient endocrine gland that develops from the postovulatory or atretic follicles and secretes progesterone; it is thought to be related to egg retention[PMID]. maintains the endometrium in mammals[WP]. A corpus luteum is known in hagfish (100), Squalus (101), and salamander (100) but not lamprey (102). There are no data for Branchiostoma and Ciona, and given that they are multiple spawners, there is no a priori reason to conclude that they lack a corpus luteum BTO:0000292 CALOHA:TS-0181 EMAPA:29886 FMA:18619 GAID:369 MA:0002834 MESH:D003338 NCIT:C26465 UMLS:C0010092 corpora lutea corpus luteum of ovary ovarian corpus luteum uberon luteal gland UBERON:0002512 corpus luteum http://upload.wikimedia.org/wikipedia/commons/5/57/Folliclesinovary.jpg MA A transient endocrine gland that develops from the postovulatory or atretic follicles and secretes progesterone; it is thought to be related to egg retention[PMID]. maintains the endometrium in mammals[WP]. A corpus luteum is known in hagfish (100), Squalus (101), and salamander (100) but not lamprey (102). There are no data for Branchiostoma and Ciona, and given that they are multiple spawners, there is no a priori reason to conclude that they lack a corpus luteum UMLS:C0010092 ncithesaurus:Corpus_Luteum corpora lutea luteal gland BTO:0000292 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 thick fibrous membrane that closely invests the entire surface of a bone except the articular cartilage at synovial joints periosteal BTO:0001022 EMAPA:35681 FMA:24041 GAID:925 MA:0002838 MESH:D010521 NCIT:C13184 UMLS:C0031110 galen:PeriOsteum uberon UBERON:0002515 periosteum Bone:growth.png the thick fibrous membrane that closely invests the entire surface of a bone except the articular cartilage at synovial joints ISBN:0-683-40008-8 MP:0010971 UMLS:C0031110 ncithesaurus:Periosteum 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 the crystalline particles composed of calcium carbonate and a protein which adhere to the gelatinous membrane of the maculae of the utricle and saccule (otolithic membrane) Representation of utricle, sacule and otoliths in correspondence to other ontologies may require review. In EHDAA2, saccule and utricle are epithelia In fishes, as in other vertebrates, the vestibular end-organs are divided into a gravity receptor system, with three subdivisions and an angular acceleration receptor system. The gravity receptor system on each side consists of utricular, saccular, and lagenar maculae, each covered by an otolith (reference 1); (...)considerations have led to our rethinking issues related to the origin of several aspects of vertebrate hearing, and to the view that many basic auditory functions evolved very early in vertebrate history, and that the functions observed in more `advanced' vertebrates, such as birds and mammals, are frequently modifications of themes first encountered in fishes, and perhaps even more ancestral animals (reference 2).[well established][VHOG] EFO:0003539 GAID:883 MA:0002841 MESH:D012444 TAO:0000559 VHOG:0001676 ZFA:0000559 uberon otolith organs saccule and utricle utricle and saccule UBERON:0002518 otolith organ http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg the crystalline particles composed of calcium carbonate and a protein which adhere to the gelatinous membrane of the maculae of the utricle and saccule (otolithic membrane) ISBN:0-683-40008-8 MGI:llw2 MP:0002894 In fishes, as in other vertebrates, the vestibular end-organs are divided into a gravity receptor system, with three subdivisions and an angular acceleration receptor system. The gravity receptor system on each side consists of utricular, saccular, and lagenar maculae, each covered by an otolith (reference 1); (...)considerations have led to our rethinking issues related to the origin of several aspects of vertebrate hearing, and to the view that many basic auditory functions evolved very early in vertebrate history, and that the functions observed in more `advanced' vertebrates, such as birds and mammals, are frequently modifications of themes first encountered in fishes, and perhaps even more ancestral animals (reference 2).[well established][VHOG] 2012-09-17 VHOG:0001676 VHOG PMID:11581521 Moorman SJ, Development of sensory systems in zebrafish (Danio rerio). ILAR Journal (2001), DOI:10.1016/S0378-5955(00)00168-4 Fay RR, Popper AN, Evolution of hearing in vertebrates: the inner ears and processing. Hearing research (2000) otolith organs ZFA:0000559 saccule and utricle MESH:A09.246.631.909.625 utricle and saccule MESH:A09.246.631.909.625 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 Sense organ embedded in the integument and consisting of one or a cluster of sensory neurons and associated sensory structures, support cells and glial cells forming a single organised unit with a largely bona-fide boundary.[FBbt] this term should be ceded to the arthropod anatomy ontology BTO:0001237 EFO:0000939 FBbt:00007152 HAO:0000933 MAT:0000163 MIAA:0000163 TGMA:0000540 sensillum uberon UBERON:0002536 arthropod sensillum Sense organ embedded in the integument and consisting of one or a cluster of sensory neurons and associated sensory structures, support cells and glial cells forming a single organised unit with a largely bona-fide boundary.[FBbt] FBbt:00007152 sensillum FBbt:00007152 HAO:0000933 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 line of sensory organs and associated structures along the sides of fish and amphibia that detect vibrations and pressure changes. we model this as being potentially inclusive of lateral line scales, and thus overlapping with the skeletal system. This is to accomodate TAO A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. (See Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO] Sensory system which develops from a specialized series of dorsolateral ectodermal placodes named lateral line placodes.[AAO] relationship loss: is_formed_by lateral line receptor organ (AAO:0001001)[AAO] The mechanosensory lateral line system is widely distributed in aquatic anamniotes. It was apparently present in the earliest vertebrates, as it has been identified in agnathans, cartilaginous fishes, bony fishes, lungfishes, the crossopterygian Latimeria, and aquatic amphibians.[well established][VHOG] AAO:0000269 AAO:0000975 EFO:0000941 MAT:0000249 MIAA:0000249 TAO:0000034 VHOG:0001243 XAO:0000095 ZFA:0000034 uberon lateral line organs lateral line stitches lateral-line organs ll UBERON:0002540 lateral line system A line of sensory organs and associated structures along the sides of fish and amphibia that detect vibrations and pressure changes. ISBN:0471209627 ISBN:0815318960 A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. (See Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO] 2012-08-14 TAO:0000034 TAO ZFIN:curator Sensory system which develops from a specialized series of dorsolateral ectodermal placodes named lateral line placodes.[AAO] 2012-06-20 AAO:0000975 AAO AAO:EJS relationship loss: is_formed_by lateral line receptor organ (AAO:0001001)[AAO] 2012-06-20 AAO:0000975 AAO The mechanosensory lateral line system is widely distributed in aquatic anamniotes. It was apparently present in the earliest vertebrates, as it has been identified in agnathans, cartilaginous fishes, bony fishes, lungfishes, the crossopterygian Latimeria, and aquatic amphibians.[well established][VHOG] 2012-09-17 VHOG:0001243 VHOG ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.195 lateral line organs VHOG:0001243 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 Part of cerebral hemisphere located on the medial surface, forming a ring around the brain stem BAMS:LL BAMS:Limbic_lobe BIRNLEX:1128 CALOHA:TS-2061 DHBA:12155 FMA:72719 HBA:4219 UMLS:C0458337 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=834 fornicate gyrus grande lobe limbique of Broca limbic lobe (carpenter) uberon fornicate convolution fornicate lobe gyrus fornicatus lobus limbicus UBERON:0002600 limbic lobe http://upload.wikimedia.org/wikipedia/commons/7/7e/Human_brain_inferior-medial_view_description.JPG FMA Part of cerebral hemisphere located on the medial surface, forming a ring around the brain stem BIRNLEX:1128 UMLS:C0458337 BIRNLEX:1128 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=834 BIRNLEX:1128 fornicate gyrus FMA:72719 fornicate convolution NeuroNames:834 fornicate lobe NeuroNames:834 gyrus fornicatus NeuroNames:834 lobus limbicus The cochlear nuclei consist of: (a) the dorsal cochlear nucleus, corresponding to the tuberculum acusticum on the dorso-lateral surface of the inferior peduncle; and (b) the ventral or accessory cochlear nucleus, placed between the two divisions of the nerve, on the ventral aspect of the inferior peduncle. [WP,unvetted]. WP says 'The CN is located at the dorso-lateral side of the brainstem, spanning the junction of the pons and medulla.'. MA places this in pons, other sources the medulla BAMS:CN BIRNLEX:1151 BM:Me-Co DHBA:12437 EV:0100260 FMA:72240 HBA:9528 MBA:607 UMLS:C0152411 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=720 cochlear nuclei uberon nuclei cochleares UBERON:0002610 cochlear nuclear complex http://upload.wikimedia.org/wikipedia/commons/5/52/Gray691.png MA FMA The cochlear nuclei consist of: (a) the dorsal cochlear nucleus, corresponding to the tuberculum acusticum on the dorso-lateral surface of the inferior peduncle; and (b) the ventral or accessory cochlear nucleus, placed between the two divisions of the nerve, on the ventral aspect of the inferior peduncle. [WP,unvetted]. UMLS:C0152411 BIRNLEX:1151 UMLS:C0152411 ncithesaurus:Cochlear_Nuclei http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=720 BIRNLEX:1151 cochlear nuclei FMA:72240 nuclei cochleares 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 Collection of nerve cells in the medial forebrain lying generally in front of the anterior commissure (Maryann Martone). Any of the groups of neural nuclei situated in the septal region which have afferent and cholinergic efferent connections with a variety of forebrain and brainstem areas including the hippocampus, the lateral hypothalamus, the tegmentum, and the amygdala. The septal nuclei are structures in the middle anteroventral cerebrum that are composed of medium-size neurons grouped into medial, lateral, and posterior groups. The septal nuclei receive reciprocal connections from the olfactory bulb, hippocampus, amygdala, hypothalamus, midbrain, habenula, cingulate gyrus, and thalamus. The septal nuclei play a role in reward and reinforcement along with the nucleus accumbens. In the 1950s, Olds &amp; Milner showed that rats with electrodes implanted in this area will self-stimulate repeatedly in order to experience a euphoric feeling (i.e. press a bar to receive electrical current that will stimulate the neurons). [WP,unvetted][Wikipedia:Septal_nuclei]. in NIFSTD this is the mereological sum of the individual complexes - in MA it is the superclass BAMS:SptN BIRNLEX:1313 DHBA:10350 EHDAA2:0004709 EMAPA:35763 FMA:61845 GAID:637 HBA:13002 MA:0002978 MESH:A08.186.211.577.750.800 UMLS:C0036687 parolfactory nuclei septal nuclei septal nucleus uberon nuclei septales UBERON:0002663 septal nuclear complex NIFSTD Collection of nerve cells in the medial forebrain lying generally in front of the anterior commissure (Maryann Martone). BIRNLEX:1313 Any of the groups of neural nuclei situated in the septal region which have afferent and cholinergic efferent connections with a variety of forebrain and brainstem areas including the hippocampus, the lateral hypothalamus, the tegmentum, and the amygdala. MP:0012682 The septal nuclei are structures in the middle anteroventral cerebrum that are composed of medium-size neurons grouped into medial, lateral, and posterior groups. The septal nuclei receive reciprocal connections from the olfactory bulb, hippocampus, amygdala, hypothalamus, midbrain, habenula, cingulate gyrus, and thalamus. The septal nuclei play a role in reward and reinforcement along with the nucleus accumbens. In the 1950s, Olds &amp; Milner showed that rats with electrodes implanted in this area will self-stimulate repeatedly in order to experience a euphoric feeling (i.e. press a bar to receive electrical current that will stimulate the neurons). [WP,unvetted][Wikipedia:Septal_nuclei]. in NIFSTD this is the mereological sum of the individual complexes - in MA it is the superclass NIF UMLS:C0036687 BIRNLEX:1313 parolfactory nuclei FMA:61845 septal nuclei FMA:61845 septal nucleus MA:0002978 nuclei septales The corticospinal fibers that arise from the pyramidal cells within the cerebral cortex layer V of the precentral motor area, the premotor area and the postcentral gyrus, then descend into and through the medulla to form the lateral corticospinal tract and the anterior corticospinal tract. UBERON:0004095 pyramidal tract BAMS:P BIRNLEX:1464 BM:CST BM:Me-PyT DHBA:12776 DMBA:17756 EMAPA:36600 FMA:72634 GAID:702 HBA:265505574 MBA:190 MBA:784 MESH:D011712 UMLS:C0034229 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=800 corticospinal fibers fasciculus cerebro-spinalis fasciculus pyramidalis fibrae corticospinales pyramid (Willis) tractus cortico-spinalis tractus corticospinalis tractus pyramidalis uberon UBERON:0002707 corticospinal tract http://upload.wikimedia.org/wikipedia/commons/a/ac/Gray684.png In NIFSTD this is a tract of brain but this leads to issues due to its overlap with the spinal cord The corticospinal fibers that arise from the pyramidal cells within the cerebral cortex layer V of the precentral motor area, the premotor area and the postcentral gyrus, then descend into and through the medulla to form the lateral corticospinal tract and the anterior corticospinal tract. ISBN:0-683-40008-8 MP:0002878 pyramidal tract BIRNLEX:1464 MP:0002878 UMLS:C0034229 BIRNLEX:1464 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=800 BIRNLEX:1464 corticospinal fibers NeuroNames:1320 fasciculus cerebro-spinalis NeuroNames:1320 fasciculus pyramidalis NeuroNames:800 fibrae corticospinales NeuroNames:1320 pyramid (Willis) NeuroNames:800 tractus cortico-spinalis NeuroNames:1320 tractus corticospinalis tractus corticospinalis NeuroNames:1320 tractus pyramidalis NeuroNames:800 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 Either of the two roots that come of the vestibulocochlear nerve BAMS:8nf BIRNLEX:1519 BIRNLEX:1636 DHBA:12868 DMBA:17746 FMA:72499 central part of vestibulocochlear nerve fibrae nervi statoacustici root of vestibulocochlear nerve statoacoustic nerve fibers vestibulocochlear nerve fibers vestibulocochlear nerve roots vestibulocochlear nerve tract uberon UBERON:0002731 vestibulocochlear nerve root FMA Either of the two roots that come of the vestibulocochlear nerve central part of vestibulocochlear nerve FMA:72499 fibrae nervi statoacustici FMA:72499 FMA:TA root of vestibulocochlear nerve DHBA:12868 statoacoustic nerve fibers FMA:72499 vestibulocochlear nerve fibers FMA:72499 vestibulocochlear nerve roots FMA:72499 vestibulocochlear nerve tract FMA:72499 A region of the brain consisting of ventral and rostral subcortical regions of the telencephalon, including among others, the basal ganglia, septal nuclei, amygdala, ventral pallidum, substantia innominata, and basal nucleus of Meynert. BAMS:Basal_forebrain BIRNLEX:1560 BM:Tel-BF BTO:0002444 DHBA:10349 EMAPA:35164 FMA:77700 HBA:4300 PBA:128012976 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1997 uberon basal forebrain area pars basalis telencephali UBERON:0002743 basal forebrain http://upload.wikimedia.org/wikipedia/commons/a/a4/Basal_Forebrain_Monakhos_2007.png BTO A region of the brain consisting of ventral and rostral subcortical regions of the telencephalon, including among others, the basal ganglia, septal nuclei, amygdala, ventral pallidum, substantia innominata, and basal nucleus of Meynert. BIRNLEX:1560 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1997 BIRNLEX:1560 basal forebrain area NeuroNames:1997 pars basalis telencephali 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 The part of the hypothalamus posterior to the middle region consisting of several nuclei including the medial mamillary nucleus, lateral mamillary nucleus, and posterior hypothalamic nucleus (posterior hypothalamic area). The posterior hypothalamic area is concerned with control of sympathetic responses and is sensitive to conditions of decreasing temperature and controls the mechanisms for the conservation and increased production of heat. PHR BAMS:PH BAMS:PHR BIRNLEX:1651 FMA:62029 GAID:651 HBA:4665 MESH:A08.186.211.730.385.357.362 UMLS:C0020670 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=411 mammillary level of hypothalamus mammillary region posterior hypothalamus uberon hypothalamus posterior regio hypothalamica posterior UBERON:0002770 posterior hypothalamic region The part of the hypothalamus posterior to the middle region consisting of several nuclei including the medial mamillary nucleus, lateral mamillary nucleus, and posterior hypothalamic nucleus (posterior hypothalamic area). The posterior hypothalamic area is concerned with control of sympathetic responses and is sensitive to conditions of decreasing temperature and controls the mechanisms for the conservation and increased production of heat. MESH:A08.186.211.730.385.357.362 PHR BIRNLEX:1651 NIFSTD:NeuroNames_abbrevSource UMLS:C0020670 BIRNLEX:1651 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=411 BIRNLEX:1651 mammillary level of hypothalamus FMA:62029 mammillary region FMA:62029 posterior hypothalamus FMA:62029 hypothalamus posterior NeuroNames:411 regio hypothalamica posterior NeuroNames:411 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 limbic lobe that is part of a left cerebral hemisphere. BIRNLEX:1780 FMA:72981 uberon UBERON:0002804 left limbic lobe A limbic lobe that is part of a left cerebral hemisphere. OBOL:automatic A limbic lobe that is part of a right cerebral hemisphere. BIRNLEX:1781 FMA:72980 uberon UBERON:0002805 right limbic lobe A limbic lobe that is part of a right cerebral hemisphere. OBOL:automatic 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 the group of neuron cell bodies associated with the eighth cranial nerve during embryogenesis; splits in later development to form the cochlear and vestibular ganglia Consider follow MA naming scheme. The sensory ganglion of the ear. (See Anatomical Atlas entry for statoacoustic ganglion by T. Whitfield.)[TAO] (During the development of the inner ear in a vertebrate embryo) 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.[well established][VHOG] The cell bodies of the cochlear nerve lie within the central aspect of the cochlea and are collectively known as the spiral ganglion. This name reflects the fact that the cell bodies, considered as a unit, have a spiral (or perhaps more accurately, a helical) shape, reflecting the shape of the cochlea. The terms 'cochlear nerve fiber' and 'spiral ganglion cell' are used, to some degree, interchangeably, although the former may be used to more specifically refer to the central axons of the cochlear nerve. These central axons exit the cochlea at its base, where it forms a nerve trunk. In humans, this aspect of the nerve is roughly one inch in length. It projects centrally to the brainstem, where its fibers synapse with the cell bodies of the cochlear nucleus SAG BIRNLEX:2564 EFO:0003543 EHDAA2:0002196 EHDAA:5569 EHDAA:6653 EMAPA:16982 EMAPA:17571 MA:0001084 TAO:0000588 UMLS:C0037959 VHOG:0000696 XAO:0004142 ZFA:0000588 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=496 acoustic ganglion VIII acoustico-vestibular VIII ganglion auditory ganglion gVIII ganglion VIII statoacoustic (VIII) ganglion statoacoustic ganglia statoacoustic ganglion vestibulocochlear VIII ganglion uberon acoustic ganglion auditory ganglion nucleus nervi oculomotorii ventrolateralis nucleus nervi oculomotorii, pars ventralis statoacoustic VIII ganglion vestibulocochlear ganglia UBERON:0002827 vestibulocochlear ganglion ZFA ZFA NCBIBook:NBK53175 EHDAA2 the group of neuron cell bodies associated with the eighth cranial nerve during embryogenesis; splits in later development to form the cochlear and vestibular ganglia MGI:smb MP:0003703 The sensory ganglion of the ear. (See Anatomical Atlas entry for statoacoustic ganglion by T. Whitfield.)[TAO] 2012-08-14 TAO:0000588 TAO ZFIN:curator (During the development of the inner ear in a vertebrate embryo) 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.[well established][VHOG] 2012-09-17 VHOG:0000696 VHOG PMID:21452441 Park BY, Saint-Jeannet JP, Induction and Segregation of the Vertebrate Cranial Placodes. Developmental Biology (2010) The cell bodies of the cochlear nerve lie within the central aspect of the cochlea and are collectively known as the spiral ganglion. This name reflects the fact that the cell bodies, considered as a unit, have a spiral (or perhaps more accurately, a helical) shape, reflecting the shape of the cochlea. The terms 'cochlear nerve fiber' and 'spiral ganglion cell' are used, to some degree, interchangeably, although the former may be used to more specifically refer to the central axons of the cochlear nerve. These central axons exit the cochlea at its base, where it forms a nerve trunk. In humans, this aspect of the nerve is roughly one inch in length. It projects centrally to the brainstem, where its fibers synapse with the cell bodies of the cochlear nucleus SAG ZFA:0000588 UMLS:C0037959 BIRNLEX:2564 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=496 BIRNLEX:2564 acoustic ganglion VIII EMAPA:16982 acoustico-vestibular VIII ganglion EHDAA2:0002196 auditory ganglion ZFA:0000588 gVIII ZFA:0000588 statoacoustic (VIII) ganglion ZFA:0000588 statoacoustic ganglia ZFA:0000588 statoacoustic ganglion XAO:0004142 vestibulocochlear VIII ganglion MA:0001084 acoustic ganglion VHOG:0000696 auditory ganglion BIRNLEX:2564 nucleus nervi oculomotorii ventrolateralis NeuroNames:496 nucleus nervi oculomotorii, pars ventralis NeuroNames:496 statoacoustic VIII ganglion VHOG:0000696 vestibulocochlear ganglia XAO:0004142 BIRNLEX:2599 FMA:6005 UMLS:C0457466 cervical dorsal root ganglion cervical spinal ganglion uberon UBERON:0002834 cervical dorsal root ganglion UMLS:C0457466 BIRNLEX:2599 cervical dorsal root ganglion FMA:6005 cervical spinal ganglion FMA:6005 A dorsal root ganglion that is part of a thorax [Automatically generated definition]. BIRNLEX:2600 FMA:6006 UMLS:C0457467 dorsal root ganglion of thorax ganglion of dorsal root of thorax ganglion spinalis of thorax thoracic dorsal root ganglion thoracic spinal ganglion thorax dorsal root ganglion thorax ganglion of dorsal root thorax ganglion spinalis uberon UBERON:0002835 thoracic dorsal root ganglion A dorsal root ganglion that is part of a thorax [Automatically generated definition]. OBOL:automatic UMLS:C0457467 BIRNLEX:2600 dorsal root ganglion of thorax OBOL:automatic ganglion of dorsal root of thorax OBOL:automatic ganglion spinalis of thorax OBOL:automatic thoracic dorsal root ganglion FMA:6006 thoracic spinal ganglion FMA:6006 thorax dorsal root ganglion OBOL:automatic thorax ganglion of dorsal root OBOL:automatic thorax ganglion spinalis OBOL:automatic 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 A cellular layer of the dentate gyrus enclosed by the granule cell layer. A number of cell types are located in the polymorphic layer but the most prominent is the mossy cell. TODO: add mossy cell BAMS:PoDG BAMS:po BIRNLEX:4128 EMAPA:35280 MA:0002864 MBA:10704 NLX:42439 uberon CA4 polymorph layer of the dentate gyrus UBERON:0002928 dentate gyrus polymorphic layer A cellular layer of the dentate gyrus enclosed by the granule cell layer. A number of cell types are located in the polymorphic layer but the most prominent is the mossy cell. PMCID:PMC2492885 CA4 polymorph layer of the dentate gyrus BAMS:PoDG The granular layer is the innermost layer of the cerebellar cortex. This layer contains densely packed small neurons, mostly granule cells. Some Golgi cells are found at the outer border. Granule neurons send parallel fibers to the upper molecular layer, where they synapse with Purkinje cell dendrites. Mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons at cerebellar glomeruli in the granule cell layer. BIRNLEX:779 BTO:0004425 CALOHA:TS-1247 EMAPA:35217 FMA:83140 MA:0000993 MBA:1143 NCIT:C49138 UMLS:C1708253 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=363 cerebellar granular layer cerebellar granule cell layer cerebellar granule layer cerebellum granule cell layer cerebellum granule layer granule cell layer of cerebellar cortex stratum granulosum cerebelli stratum granulosum corticis cerebelli uberon granular layer of cerebellum UBERON:0002956 granular layer of cerebellar cortex The granular layer is the innermost layer of the cerebellar cortex. This layer contains densely packed small neurons, mostly granule cells. Some Golgi cells are found at the outer border. Granule neurons send parallel fibers to the upper molecular layer, where they synapse with Purkinje cell dendrites. Mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons at cerebellar glomeruli in the granule cell layer. GO:0021681 UMLS:C1708253 ncithesaurus:Granular_Layer_of_the_Cerebellum http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=363 BIRNLEX:779 cerebellar granular layer GO:0021681 cerebellum granule cell layer MA:0000993 granule cell layer of cerebellar cortex BIRNLEX:779 stratum granulosum cerebelli BTO:0004425 stratum granulosum corticis cerebelli FMA:83140 FMA:TA granular layer of cerebellum BTO:0004425 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 nerve fiber that is part of a trigeminal nerve. BAMS:5nf BIRNLEX:974 FMA:72501 UMLS:C0175452 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=607 central part of trigeminal nerve trigeminal nerve fibers trigeminal nerve tract uberon fibrae nervi trigemini UBERON:0003041 trigeminal nerve fibers A nerve fiber that is part of a trigeminal nerve. OBOL:automatic UMLS:C0175452 BIRNLEX:974 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=607 BIRNLEX:974 central part of trigeminal nerve FMA:72501 trigeminal nerve fibers FMA:72501 trigeminal nerve tract FMA:72501 fibrae nervi trigemini NeuroNames:607 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 the narrow, proximal portion of the optic vesicle which connects the embryonic eye and forebrain The evagination from the neural tube of the developing embryo which develops the optic cup at its extremity; the stalk persists as the optic nerve. [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.[well established][VHOG] AAO:0011077 EHDAA2:0001318 EHDAA:3816 EMAPA:16678 NCIT:C34235 TAO:0000137 UMLS:C0231107 VHOG:0000223 XAO:0000475 ZFA:0000137 uberon optic stalks pedunculus opticus UBERON:0003098 optic stalk http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png EHDAA2 the narrow, proximal portion of the optic vesicle which connects the embryonic eye and forebrain ISBN:0-914294-08-3 MP:0004268 The evagination from the neural tube of the developing embryo which develops the optic cup at its extremity; the stalk persists as the optic nerve. [TFD][VHOG] 2012-09-17 VHOG:0000223 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.[well established][VHOG] 2012-09-17 VHOG:0000223 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 UMLS:C0231107 ncithesaurus:Optic_Stalk optic stalks ZFA:0000137 pedunculus opticus 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. 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. 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 a posterolateral part of the cranium and structurally supports the vestibuloauditory system.[TAO] Anatomical cluster that is a posterolateral part of the neurocranium and structurally supports the vestibuloauditory system.[AAO] relationship loss: overlaps hyomandibular-otic region joint (TAO:0001947)[TAO] UBERONREF:0000007 has this as a syn for otic capsule AAO:0010208 TAO:0000189 XAO:0003175 ZFA:0000189 uberon cranial vault UBERON:0003110 otic region Anatomical cluster that is a posterolateral part of the cranium and structurally supports the vestibuloauditory system.[TAO] 2012-08-14 TAO:0000189 TAO TAO:MAH Anatomical cluster that is a posterolateral part of the neurocranium and structurally supports the vestibuloauditory system.[AAO] 2012-06-20 AAO:0010208 AAO AAO:EJS relationship loss: overlaps hyomandibular-otic region joint (TAO:0001947)[TAO] 2012-08-14 TAO:0000189 TAO cranial vault ZFA:0000189 Anatomical cluster that forms the floor and sidewalls of the middle part of the cranium. Anatomical cluster that forms the floor and sidewalls of the middle part of the neurocranium.[AAO] AAO:0010207 TAO:0000290 XAO:0003174 ZFA:0000290 uberon UBERON:0003111 sphenoid region Anatomical cluster that forms the floor and sidewalls of the middle part of the cranium. TAO:0000290 UBERONREF:0000007 Anatomical cluster that forms the floor and sidewalls of the middle part of the neurocranium.[AAO] 2012-06-20 AAO:0010207 AAO AAO:EJS 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 A respiratory airway that is part of an open tracheal system. trachea FBbt:00005043 SPD:0000434 TADS:0000315 invertebrate trachea uberon UBERON:0003127 open tracheal system trachea A respiratory airway that is part of an open tracheal system. trachea FBbt:00005043 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 barrier in the choroid plexus located in the lateral, third, and fourth brain ventricles that controls the entrance of substances into the cerebrospinal fluid from the blood[MP]. blood-CSF barrier uberon UBERON:0003210 blood-cerebrospinal fluid barrier barrier in the choroid plexus located in the lateral, third, and fourth brain ventricles that controls the entrance of substances into the cerebrospinal fluid from the blood[MP]. MP:0006088 blood-CSF barrier MP:0006088 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 A sac-like structure that is found in the mature gland[GO]. EMAPA:36566 FMA:73285 MA:0002760 alveolus of lactiferous gland alveolus of lobe of breast alveolus of lobe of mammary gland alveolus of mammary gland lactiferous alveolus lactiferous gland alveolus lobe of breast alveolus lobe of mammary gland alveolus mammary alveolus uberon mammary alveoli UBERON:0003214 mammary gland alveolus A sac-like structure that is found in the mature gland[GO]. GO:0060749 alveolus of lactiferous gland OBOL:automatic alveolus of lobe of breast OBOL:automatic alveolus of lobe of mammary gland OBOL:automatic alveolus of mammary gland OBOL:automatic lobe of breast alveolus OBOL:automatic lobe of mammary gland alveolus OBOL:automatic mammary alveoli organ part that has the form of a hollow cavity[WP]. alveolar EFO:0002513 EV:0100043 FMA:82493 NCIT:C12986 OpenCyc:Mx4rwN8NFZwpEbGdrcN5Y29ycA UMLS:C0034051 uberon UBERON:0003215 alveolus organ part that has the form of a hollow cavity[WP]. UMLS:C0034051 ncithesaurus:Alveolus 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 knee [Automatically generated definition]. EHDAA2:0000896 EHDAA:5161 EHDAA:6186 EMAPA:17494 VHOG:0000810 epithelial tissue of knee knee epithelial tissue knee epithelium uberon UBERON:0003232 epithelium of knee EHDAA2 An epithelium that is part of a knee [Automatically generated definition]. OBOL:automatic epithelial tissue of knee OBOL:automatic knee epithelial tissue OBOL:automatic knee 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 utricle of membranous labyrinth [Automatically generated definition]. TODO - check relationships w.r.t macula EHDAA:4730 EMAPA:17295 EMAPA:17298 EMAPA:17301 EMAPA:17820 EMAPA:17823 FMA:75604 MA:0001204 RETIRED_EHDAA2:0002155 VHOG:0000634 epithelial tissue of membranous labyrinth utricle epithelial tissue of utricle epithelial tissue of utricle of membranous labyrinth epithelial tissue of utriculus (labyrinthus vestibularis) epithelium of membranous labyrinth utricle epithelium of utricle of membranous labyrinth epithelium of utriculus (labyrinthus vestibularis) membranous labyrinth utricle epithelial tissue membranous labyrinth utricle epithelium utricle epithelial tissue utricle epithelium utricle of membranous labyrinth epithelial tissue utricle of membranous labyrinth epithelium utriculus (labyrinthus vestibularis) epithelial tissue utriculus (labyrinthus vestibularis) epithelium epithelium of macula of utricle of membranous labyrinth uberon UBERON:0003241 epithelium of utricle FMA FMA An epithelium that is part of a utricle of membranous labyrinth [Automatically generated definition]. OBOL:automatic epithelial tissue of membranous labyrinth utricle OBOL:automatic epithelial tissue of utricle OBOL:automatic epithelial tissue of utricle of membranous labyrinth OBOL:automatic epithelial tissue of utriculus (labyrinthus vestibularis) OBOL:automatic epithelium of membranous labyrinth utricle OBOL:automatic epithelium of utricle of membranous labyrinth OBOL:automatic epithelium of utriculus (labyrinthus vestibularis) OBOL:automatic membranous labyrinth utricle epithelial tissue OBOL:automatic membranous labyrinth utricle epithelium OBOL:automatic utricle epithelial tissue OBOL:automatic utricle epithelium OBOL:automatic utricle of membranous labyrinth epithelial tissue OBOL:automatic utricle of membranous labyrinth epithelium OBOL:automatic utriculus (labyrinthus vestibularis) epithelial tissue OBOL:automatic utriculus (labyrinthus vestibularis) epithelium OBOL:automatic epithelium of macula of utricle of membranous labyrinth FMA:75604 An epithelium that is part of a saccule of membranous labyrinth [Automatically generated definition]. TODO - check relationships w.r.t macula EHDAA:4724 EMAPA:17292 FMA:75605 MA:0001202 RETIRED_EHDAA2:0001771 VHOG:0000633 epithelial tissue of membranous labyrinth saccule epithelial tissue of saccule epithelial tissue of saccule of membranous labyrinth epithelial tissue of sacculus (labyrinthus vestibularis) epithelium of membranous labyrinth saccule epithelium of saccule of membranous labyrinth epithelium of sacculus (labyrinthus vestibularis) membranous labyrinth saccule epithelial tissue membranous labyrinth saccule epithelium saccule epithelial tissue saccule epithelium saccule of membranous labyrinth epithelial tissue saccule of membranous labyrinth epithelium sacculus (labyrinthus vestibularis) epithelial tissue sacculus (labyrinthus vestibularis) epithelium uberon epithelium of macula of saccule of membranous labyrinth UBERON:0003242 epithelium of saccule An epithelium that is part of a saccule of membranous labyrinth [Automatically generated definition]. OBOL:automatic epithelial tissue of membranous labyrinth saccule OBOL:automatic epithelial tissue of saccule OBOL:automatic epithelial tissue of saccule of membranous labyrinth OBOL:automatic epithelial tissue of sacculus (labyrinthus vestibularis) OBOL:automatic epithelium of membranous labyrinth saccule OBOL:automatic epithelium of saccule of membranous labyrinth OBOL:automatic epithelium of sacculus (labyrinthus vestibularis) OBOL:automatic membranous labyrinth saccule epithelial tissue OBOL:automatic membranous labyrinth saccule epithelium OBOL:automatic saccule epithelial tissue OBOL:automatic saccule epithelium OBOL:automatic saccule of membranous labyrinth epithelial tissue OBOL:automatic saccule of membranous labyrinth epithelium OBOL:automatic sacculus (labyrinthus vestibularis) epithelial tissue OBOL:automatic sacculus (labyrinthus vestibularis) epithelium OBOL:automatic epithelium of macula of saccule of membranous labyrinth FMA:75605 An epithelium that is part of a cochlear duct of membranous labyrinth [Automatically generated definition]. EHDAA:4722 EMAPA:17600 RETIRED_EHDAA2:0000264 VHOG:0000640 Reissner's canal epithelial tissue Reissner's canal epithelium cochlear duct epithelial tissue cochlear duct epithelium cochlear duct of membranous labyrinth epithelial tissue cochlear duct of membranous labyrinth epithelium epithelial tissue of Reissner's canal epithelial tissue of cochlear duct epithelial tissue of cochlear duct of membranous labyrinth epithelium of Reissner's canal epithelium of cochlear duct of membranous labyrinth uberon UBERON:0003243 epithelium of cochlear duct An epithelium that is part of a cochlear duct of membranous labyrinth [Automatically generated definition]. OBOL:automatic Reissner's canal epithelial tissue OBOL:automatic Reissner's canal epithelium OBOL:automatic cochlear duct epithelial tissue OBOL:automatic cochlear duct epithelium OBOL:automatic cochlear duct of membranous labyrinth epithelial tissue OBOL:automatic cochlear duct of membranous labyrinth epithelium OBOL:automatic epithelial tissue of Reissner's canal OBOL:automatic epithelial tissue of cochlear duct OBOL:automatic epithelial tissue of cochlear duct of membranous labyrinth OBOL:automatic epithelium of Reissner's canal OBOL:automatic epithelium of cochlear duct of membranous labyrinth OBOL:automatic the epithelial layer of the luminal surfaces of the mammary gland BTO:0001430 CALOHA:TS-0593 EHDAA2:0001057 EHDAA:6526 EMAPA:17760 FMA:74445 MA:0000792 NCIT:C12937 UMLS:C0596882 VHOG:0001088 epithelium of lactiferous gland lactiferous gland epithelium mammary epithelium mammary gland epithelial tissue mammary gland epithelium uberon UBERON:0003244 epithelium of mammary gland EHDAA2 Wikipathways:WP2062 the epithelial layer of the luminal surfaces of the mammary gland MGI:csmith MP:0009504 UMLS:C0596882 ncithesaurus:Mammary_Epithelium epithelium of lactiferous gland FMA:74445 lactiferous gland epithelium FMA:74445 mammary epithelium BTO:0001430 mammary gland epithelial tissue OBOL:automatic mammary gland 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 we make the germ layer relationship develops_from, as currently the germ layers are declared to be purely embryonic. TODO - check. WP:Amnion - In the human embryo the earliest stages of the formation of the amnion have not been observed; in the youngest embryo which has been studied the amnion was already present as a closed sac, and appears in the inner cell-mass as a cavity. This cavity is roofed in by a single stratum of flattened, ectodermal cells, the amniotic ectoderm, and its floor consists of the prismatic ectoderm of the embryonic disk-the continuity between the roof and floor being established at the margin of the embryonic disk. Outside the amniotic ectoderm is a thin layer of mesoderm, which is continuous with that of the somatopleure and is connected by the body-stalk with the mesodermal lining of the chorion. UBERON:0008359 BTO:0000897 EHDAA2:0000117 EHDAA:138 EMAPA:16110 VHOG:0000621 amnion ectoderm amnionic ectoderm uberon amnion epithelium UBERON:0003254 amniotic ectoderm EHDAA2 EHDAA2 EHDAA2 amnion ectoderm EHDAA2:0000117 amnion ectoderm OBOL:automatic amnionic ectoderm amnionic ectoderm ISBN:9780878932504 amnion epithelium BTO:0000897 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 amnion. we make the germ layer relationship develops_from, as currently the germ layers are declared to be purely embryonic. TODO - check. WP:Amnion - In the human embryo the earliest stages of the formation of the amnion have not been observed; in the youngest embryo which has been studied the amnion was already present as a closed sac, and appears in the inner cell-mass as a cavity. This cavity is roofed in by a single stratum of flattened, ectodermal cells, the amniotic ectoderm, and its floor consists of the prismatic ectoderm of the embryonic disk-the continuity between the roof and floor being established at the margin of the embryonic disk. Outside the amniotic ectoderm is a thin layer of mesoderm, which is continuous with that of the somatopleure and is connected by the body-stalk with the mesodermal lining of the chorion. UBERON:0003411 EHDAA2:0000118 EHDAA:140 EMAPA:16111 EMAPA:16265 VHOG:0000622 amnion mesenchyme amnion mesoderm amnionic mesoderm mesenchyme of amnion uberon amnionic mesenchyme amnionic mesoderm UBERON:0003262 amniotic mesoderm EHDAA2 EHDAA2 A mesenchyme that is part of a amnion. OBOL:automatic amnion mesenchyme EHDAA2:0000118 amnion mesoderm OBOL:automatic amnionic mesoderm mesenchyme of amnion EMAPA:16265 amnionic mesenchyme EMAPA:16265 amnionic mesoderm EMAPA:16111 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 knee [Automatically generated definition]. EHDAA2:0000898 EHDAA:5163 EHDAA:6188 EMAPA:17495 VHOG:0001070 knee mesenchyme uberon UBERON:0003321 mesenchyme of knee Mesenchyme that is part of a developing knee [Automatically generated definition]. OBOL:automatic knee 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 mammary gland. EHDAA2:0001058 EHDAA:6528 EMAPA:17761 VHOG:0001087 lactiferous gland mesenchyme lobe of breast mesenchyme lobe of mammary gland mesenchyme mammary gland mesenchyme mammary mesenchyme mesenchyme of lactiferous gland mesenchyme of lobe of breast mesenchyme of lobe of mammary gland uberon UBERON:0003326 mesenchyme of mammary gland Mesenchyme that is part of a developing mammary gland. OBOL:automatic lactiferous gland mesenchyme OBOL:automatic lobe of breast mesenchyme OBOL:automatic lobe of mammary gland mesenchyme OBOL:automatic mammary gland mesenchyme OBOL:automatic mesenchyme of lactiferous gland OBOL:automatic mesenchyme of lobe of breast OBOL:automatic mesenchyme of lobe of mammary gland 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 submucosa that is part of a jejunum [Automatically generated definition]. EMAPA:27111 FMA:14950 jejunal submucosa jejunum submucosa uberon UBERON:0003333 submucosa of jejunum A submucosa that is part of a jejunum [Automatically generated definition]. OBOL:automatic jejunal submucosa FMA:14950 jejunum 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 serous membrane that is part of a jejunum [Automatically generated definition]. EMAPA:27115 FMA:14955 jejunal serosa jejunum serosa jejunum serous membrane serous membrane of jejunum visceral peritoneum of jejunum uberon UBERON:0003337 serosa of jejunum A serous membrane that is part of a jejunum [Automatically generated definition]. OBOL:automatic jejunal serosa FMA:14955 jejunum serosa OBOL:automatic jejunum serous membrane OBOL:automatic serous membrane of jejunum OBOL:automatic visceral peritoneum of jejunum FMA:14955 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 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 epithelium that is part of a vomeronasal organ [Automatically generated definition]. TODO - add cell types EHDAA2:0004102 EMAPA:18444 FMA:301283 MA:0001328 Jacobson's organ epithelial tissue Jacobson's organ epithelium epithelial tissue of Jacobson's organ epithelial tissue of vomeronasal organ epithelium of Jacobson's organ vomeronasal epithelium vomeronasal organ epithelial tissue vomeronasal organ epithelium vomeronasal organ sensory epithelium uberon UBERON:0003367 epithelium of vomeronasal organ EHDAA2 EHDAA2 An epithelium that is part of a vomeronasal organ [Automatically generated definition]. OBOL:automatic Jacobson's organ epithelial tissue OBOL:automatic Jacobson's organ epithelium OBOL:automatic epithelial tissue of Jacobson's organ OBOL:automatic epithelial tissue of vomeronasal organ OBOL:automatic epithelium of Jacobson's organ OBOL:automatic vomeronasal epithelium EHDAA2:0004102 vomeronasal organ epithelial tissue OBOL:automatic vomeronasal organ epithelium OBOL:automatic vomeronasal organ sensory epithelium MA:0001328 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 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 mesentery that is part of a jejunum [Automatically generated definition]. EMAPA:18670 FMA:14651 jejunal mesentery jejunum mesentery mesojejunum uberon UBERON:0003398 mesentery of jejunum A mesentery that is part of a jejunum [Automatically generated definition]. OBOL:automatic mesojejunum 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 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 vomeronasal organ [Automatically generated definition]. EHDAA2:0004103 EMAPA:18445 Jacobson's organ mesenchyme mesenchyme of Jacobson's organ vomeronasal mesenchyme vomeronasal organ mesenchyme uberon UBERON:0003421 mesenchyme of vomeronasal organ EHDAA2 EHDAA2 Mesenchyme that is part of a developing vomeronasal organ [Automatically generated definition]. OBOL:automatic Jacobson's organ mesenchyme OBOL:automatic mesenchyme of Jacobson's organ OBOL:automatic vomeronasal mesenchyme EHDAA2:0004103 vomeronasal organ mesenchyme OBOL:automatic 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 A nerve that innervates an eyelid. EMAPA:37535 MA:0001255 blepharon nerve nerve of blepharon nerve of eyelid palpebral nerve uberon UBERON:0003437 eyelid nerve A nerve that innervates an eyelid. EMAPA:37535 MA:th blepharon nerve OBOL:automatic nerve of blepharon OBOL:automatic nerve of eyelid OBOL:automatic palpebral nerve 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 Peyer's patch that is part of a large intestine. requires expert attention EMAPA:35468 FMA:15658 MA:0001550 Peyer's patch of large intestine large intestine Peyer's patch uberon solitary lymphatic follicle of large intestine solitary lymphoid follicle of subdivision of large intestine UBERON:0003453 large intestine Peyer's patch A Peyer's patch that is part of a large intestine. OBOL:automatic Peyer's patch of large intestine OBOL:automatic large intestine Peyer's patch OBOL:automatic solitary lymphatic follicle of large intestine FMA:15658 solitary lymphoid follicle of subdivision of large intestine FMA:15658 nodular lymphoid structures on the serosal surface of the small intestine. add subtypes for jejunum, ileum Peyer's patch EMAPA:35782 FMA:15054 MA:0001557 Peyer's patch of small bowel Peyer's patch of small intestine aggregated lymphoid follicle of small intestine noduli lymphoidei aggregati intestini tenuis small bowel Peyer's patch small intestine Peyer's patch uberon UBERON:0003454 small intestine Peyer's patch ncithesaurus nodular lymphoid structures on the serosal surface of the small intestine. Peyer's patch FMA:15054 Peyer's patch of small bowel OBOL:automatic Peyer's patch of small intestine OBOL:automatic aggregated lymphoid follicle of small intestine FMA:15054 noduli lymphoidei aggregati intestini tenuis FMA:76466 small bowel Peyer's patch OBOL:automatic small intestine Peyer's patch OBOL:automatic A loop of Henle that is part of a inner medulla of kidney [Automatically generated definition]. EMAPA:28352 MA:0002623 kidney inner medulla loop of Henle loop of Henle, inner medullary portion uberon UBERON:0003455 inner renal medulla loop of Henle A loop of Henle that is part of a inner medulla of kidney [Automatically generated definition]. OBOL:automatic kidney inner medulla loop of Henle MA:0002623 loop of Henle, inner medullary portion EMAPA:28352 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 A lactiferous gland that is part of the abdominal region [Automatically generated definition]. Female mice normally have five pairs of nipples and mammary glands, three in the thoracic and two in the abdominal region. (There is an additional abdominal pair in female rats.) http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml EMAPA:36507 MA:0000787 abdomen lactiferous gland abdomen lobe of breast abdomen lobe of mammary gland abdomen mammary gland lactiferous gland of abdomen lobe of breast of abdomen lobe of mammary gland of abdomen mammary gland of abdomen uberon UBERON:0003488 abdominal mammary gland A lactiferous gland that is part of the abdominal region [Automatically generated definition]. OBOL:automatic abdomen lactiferous gland OBOL:automatic abdomen lobe of breast OBOL:automatic abdomen lobe of mammary gland OBOL:automatic abdomen mammary gland OBOL:automatic lactiferous gland of abdomen OBOL:automatic lobe of breast of abdomen OBOL:automatic lobe of mammary gland of abdomen OBOL:automatic mammary gland of abdomen 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 eyelid [Automatically generated definition]. EMAPA:37388 MA:0001250 blepharon blood vessel blood vessel of blepharon blood vessel of eyelid uberon UBERON:0003510 eyelid blood vessel A blood vessel that is part of a eyelid [Automatically generated definition]. OBOL:automatic EMAPA:37388 MA:th blepharon blood vessel OBOL:automatic blood vessel of blepharon OBOL:automatic blood vessel of eyelid OBOL:automatic 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 An alveolar duct that is part of a right lung [Automatically generated definition]. EMAPA:35819 MA:0001785 NCIT:C49277 UMLS:C1709958 alveolar duct of right lung uberon UBERON:0003536 right lung alveolar duct An alveolar duct that is part of a right lung [Automatically generated definition]. OBOL:automatic UMLS:C1709958 ncithesaurus:Right_Lung_Alveolar_Duct alveolar duct of right lung OBOL:automatic An alveolar duct that is part of a left lung [Automatically generated definition]. EMAPA:19183 MA:0001776 NCIT:C49250 UMLS:C1708672 alveolar duct of left lung uberon UBERON:0003537 Mice have 1 left lobe left lung alveolar duct An alveolar duct that is part of a left lung [Automatically generated definition]. OBOL:automatic UMLS:C1708672 ncithesaurus:Left_Lung_Alveolar_Duct alveolar duct of left lung OBOL:automatic 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 respiratory bronchiole that is part of a right lung [Automatically generated definition]. EMAPA:36637 MA:0001788 NCIT:C49285 UMLS:C1709960 bronchiolus respiratorius of right lung respiratory bronchiole of right lung right lung bronchiolus respiratorius uberon UBERON:0003542 right lung respiratory bronchiole A respiratory bronchiole that is part of a right lung [Automatically generated definition]. OBOL:automatic UMLS:C1709960 ncithesaurus:Right_Lung_Respiratory_Bronchiole bronchiolus respiratorius of right lung OBOL:automatic respiratory bronchiole of right lung OBOL:automatic right lung bronchiolus respiratorius OBOL:automatic A respiratory bronchiole that is part of a left lung [Automatically generated definition]. EMAPA:36635 MA:0001779 NCIT:C49254 UMLS:C1708674 bronchiolus respiratorius of left lung left lung bronchiolus respiratorius respiratory bronchiole of left lung uberon UBERON:0003543 left lung respiratory bronchiole A respiratory bronchiole that is part of a left lung [Automatically generated definition]. OBOL:automatic UMLS:C1708674 ncithesaurus:Left_Lung_Respiratory_Bronchiole bronchiolus respiratorius of left lung OBOL:automatic left lung bronchiolus respiratorius OBOL:automatic respiratory bronchiole of left lung OBOL:automatic The regions of the brain that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites. EMAPA:35187 HBA:9218 MA:0000820 NCIT:C49334 UMLS:C1706995 brain white matter of neuraxis brain white substance white matter of brain white matter of neuraxis of brain white substance of brain uberon UBERON:0003544 brain white matter The regions of the brain that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites. MP:0008026 UMLS:C1706995 ncithesaurus:Brain_White_Matter brain white matter of neuraxis OBOL:automatic brain white substance OBOL:automatic white matter of brain OBOL:automatic white matter of neuraxis of brain OBOL:automatic white substance of brain OBOL:automatic A macula densa that is part of a distal convoluted tubule [Automatically generated definition]. MA:0001668 uberon UBERON:0003546 distal convoluted tubule macula densa MA A macula densa that is part of a distal convoluted tubule [Automatically generated definition]. 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 knee [Automatically generated definition]. EMAPA:37326 MA:0000667 connective tissue of knee knee portion of connective tissue uberon UBERON:0003577 knee connective tissue A portion of connective tissue that is part of a knee [Automatically generated definition]. OBOL:automatic EMAPA:37326 MA:th connective tissue of knee OBOL:automatic knee portion of connective tissue 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 eyelid [Automatically generated definition]. EMAPA:37532 MA:0001251 NCIT:C49482 UMLS:C1707989 blepharon connective tissue connective tissue of blepharon connective tissue of eyelid uberon UBERON:0003581 eyelid connective tissue A portion of connective tissue that is part of a eyelid [Automatically generated definition]. OBOL:automatic EMAPA:37532 MA:th UMLS:C1707989 ncithesaurus:Eyelid_Connective_Tissue blepharon connective tissue OBOL:automatic connective tissue of blepharon OBOL:automatic connective tissue of eyelid 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 The fibrous supportive tissue of the mammary gland. EMAPA:35537 FMA:74479 FMA:74483 MA:0002897 connective tissue of lactiferous gland connective tissue of lobe of breast connective tissue of lobe of mammary gland connective tissue of mammary gland lactiferous gland connective tissue lactiferous gland portion of connective tissue lactiferous gland stroma mammary gland stroma mammary stroma stroma of lactiferous gland uberon UBERON:0003584 mammary gland connective tissue The fibrous supportive tissue of the mammary gland. MP:0009507 connective tissue of lactiferous gland OBOL:automatic connective tissue of lobe of breast OBOL:automatic connective tissue of lobe of mammary gland OBOL:automatic connective tissue of mammary gland OBOL:automatic lactiferous gland connective tissue OBOL:automatic lactiferous gland portion of connective tissue OBOL:automatic lactiferous gland stroma mammary gland stroma mammary stroma stroma of lactiferous gland FMA:74483 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 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 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 A muscle that attaches to an eyelid. The muscle in the orbit of the eye that lifts the upper eyelid[ncithesaurus:Eyelid_Muscle]. MA:0000269 NCIT:C52803 UMLS:C1707990 blepharon muscle organ eyelid muscle organ muscle organ of blepharon muscle organ of eyelid uberon UBERON:0003660 eyelid muscle A muscle that attaches to an eyelid. The muscle in the orbit of the eye that lifts the upper eyelid[ncithesaurus:Eyelid_Muscle]. ncithesaurus:Eyelid_Muscle UMLS:C1707990 ncithesaurus:Eyelid_Muscle blepharon muscle organ OBOL:automatic eyelid muscle organ OBOL:automatic muscle organ of blepharon OBOL:automatic muscle organ of eyelid OBOL:automatic 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 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 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 A fold of peritoneum originating at the stomach and supporting the viscera. omental CALOHA:TS-2004 EV:0100084 FMA:14650 GAID:23 MESH:A01.047.025.600.573 NCIT:C33209 UMLS:C0028977 galen:Omentum uberon UBERON:0003688 omentum A fold of peritoneum originating at the stomach and supporting the viscera. ncithesaurus:Omentum UMLS:C0028977 ncithesaurus:Omentum 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 Any joint connecting the acromonion of the scapula and clavicle. The gliding joint formed by the outer extremity of the clavicle and the inner margin of the acromion process of the scapula. FMA:25898 GAID:249 MESH:D000173 NCIT:C32047 OpenCyc:Mx4rwHhmSJwpEbGdrcN5Y29ycA UMLS:C0001208 uberon acromioclavicular articulation articulatio acromioclavicularis scapuloclavicular articulation UBERON:0003692 acromioclavicular joint http://upload.wikimedia.org/wikipedia/commons/3/3b/Gray326.png FMA Any joint connecting the acromonion of the scapula and clavicle. The gliding joint formed by the outer extremity of the clavicle and the inner margin of the acromion process of the scapula. MESH:A02.835.583.032 UMLS:C0001208 ncithesaurus:Acromioclavicular_Joint acromioclavicular articulation articulatio acromioclavicularis scapuloclavicular articulation 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 sensory organs in muscle that are involved in the stretch reflex. FMA:83607 GAID:819 MESH:A08.800.550.700.500.500 NCIT:C13824 UMLS:C0027871 neuromuscular spindle uberon muscle stretch receptor neuromuscular spindle UBERON:0003718 muscle spindle The sensory organs in muscle that are involved in the stretch reflex. MP:0004069 UMLS:C0027871 ncithesaurus:Muscle_Spindle neuromuscular spindle FMA:83607 muscle stretch receptor GAID:819 neuromuscular spindle GAID:819 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 An arrangement of nerve fibers, running from the spine that travels to the head and neck where it innervates skin and muscle. BAMS:cep FMA:5904 GAID:847 MESH:D002572 OpenCyc:Mx4rvkEE3JwpEbGdrcN5Y29ycA cervical nerve plexus cervical plexus plexus cervicalis uberon plexus cervicalis UBERON:0003725 cervical nerve plexus http://upload.wikimedia.org/wikipedia/commons/2/20/Gray784.png An arrangement of nerve fibers, running from the spine that travels to the head and neck where it innervates skin and muscle. UBERON:cjm cervical nerve plexus FMA:5904 cervical plexus FMA:5904 plexus cervicalis FMA:5904 FMA:TA plexus cervicalis 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 posterior part of a vertebra that consists of a pair of pedicles and a pair of laminae, and supports seven processes: four articular processes, two transverse processes one spinous process[WP]. ZFA: A neural arch encloses the neural canal and typically meets its partner to form a neural spine. . A neural arch encloses the neural canal and typically meets its partner to form a neural spine. The neural arch can be a replacement ossification of the basidorsal cartilage or can form directly in membrane bone.[TAO] Bony arch perched on the vertebral centrum; successive arches enclose the neural canal that surrounds and protects the spinal cord dorsally.[AAO] the dorsal bony and/or cartilaginous part of a vertebra, consisting of a pair of pedicles, a pair of laminae, and seven processes (four articular processes, two transverse processes, and one spinous process) relationship loss: develops_from basidorsal (TAO:0001060)[TAO] (...) certain common components [of vertebral structure] are found in nearly all vertebrate. A representative vertebra has a vertebral arch or neural arch, which extends dorsally around the spinal cord.[well established][VHOG] tiny neural arches present in Hagfish (which lack a true vertebraal column). The neural arch can be a replacement ossification of the basidorsal cartilage or can form directly in membrane bone vertebra neural arch AAO:0000725 EFO:0003618 FMA:11946 MA:0001453 NCIT:C32138 OpenCyc:Mx4rwKYHvZwpEbGdrcN5Y29ycA TAO:0001066 UMLS:C0223076 VHOG:0001670 ZFA:0001066 arcus vertebra arcus vertebrae arcus vertebrae (vertebralis) dorsal arcocentrum uberon arcus vertebrae vertebra dorsal arch UBERON:0003861 neural arch http://upload.wikimedia.org/wikipedia/commons/3/30/Gray82.png posterior part of a vertebra that consists of a pair of pedicles and a pair of laminae, and supports seven processes: four articular processes, two transverse processes one spinous process[WP]. ZFA: A neural arch encloses the neural canal and typically meets its partner to form a neural spine. . A neural arch encloses the neural canal and typically meets its partner to form a neural spine. The neural arch can be a replacement ossification of the basidorsal cartilage or can form directly in membrane bone.[TAO] 2012-08-14 TAO:0001066 TAO ZFIN:curator Bony arch perched on the vertebral centrum; successive arches enclose the neural canal that surrounds and protects the spinal cord dorsally.[AAO] 2012-06-20 AAO:0000725 AAO AAO:Pugener_2002 the dorsal bony and/or cartilaginous part of a vertebra, consisting of a pair of pedicles, a pair of laminae, and seven processes (four articular processes, two transverse processes, and one spinous process) MP:0004599:csmith relationship loss: develops_from basidorsal (TAO:0001060)[TAO] 2012-08-14 TAO:0001066 TAO (...) certain common components [of vertebral structure] are found in nearly all vertebrate. A representative vertebra has a vertebral arch or neural arch, which extends dorsally around the spinal cord.[well established][VHOG] 2012-09-17 VHOG:0001670 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.270 vertebra neural arch MA:0001453 UMLS:C0223076 ncithesaurus:Arch_of_the_Vertebra arcus vertebra arcus vertebrae arcus vertebrae (vertebralis) FMA:11946 dorsal arcocentrum ZFA:0001066 arcus vertebrae vertebra dorsal arch MA:0001453 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 wide vessels in the spleen that drain into trabecular veins[WP]. Whereas man and the rat are in the 'sinusal' group, the mouse belongs in the 'nonsinusal' group. The red pulp of spleens of rat, dog, man, and many other mammals contains an elaborate plexus of sinuses; that of mouse, cat, pig and others has no true sinuses and relatively few veins leading from the meshes into collecting veins - http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml FMA:63199 sinusoidal blood vessel of spleen uberon sinusoid of red pulp of spleen UBERON:0003910 splenic sinusoid wide vessels in the spleen that drain into trabecular veins[WP]. sinusoidal blood vessel of spleen OBOL:automatic sinusoid of red pulp of spleen FMA:63199 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 White matter that is part of a diencephalon [Automatically generated definition]. UBERON:0023148 BIRNLEX:1678 FMA:83931 TAO:0000338 ZFA:0000338 diencephalic tract/commissure diencephalic tracts and commissures predominantly white regional part of diencephalon white matter of diencephalon uberon UBERON:0003931 diencephalic white matter White matter that is part of a diencephalon [Automatically generated definition]. OBOL:automatic diencephalic tract/commissure ZFA:0000338 diencephalic tracts and commissures TAO:0000338 predominantly white regional part of diencephalon BIRNLEX:1678 white matter of diencephalon FMA:83931 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 placental layers where embryonic blood vessels are surrounded by trophoblast cells and maternal blood Mouse-human differences: The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively ... The mouse placental labyrinth is composed of an intricate network of maternal blood spaces and embryonal blood vessels. Maternal and embryonal blood is separated by a placental barrier that consists of four cellular layers: layer I trophoblasts line the maternal lacunae, trophoblasts in layers II and III form syncytial-like layers, and endothelial cells line the embryonic vessels[DOI: 10.1073/pnas.96.14.8138 ] labyrinthine layer labyrinthine layer of placenta placental labyrinth uberon UBERON:0003946 placenta labyrinth http://placentation.ucsd.edu/placenta.html The placental layers where embryonic blood vessels are surrounded by trophoblast cells and maternal blood MP:0001716 labyrinthine layer GO:0060713 labyrinthine layer of placenta GO:0060713 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 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 blood vessels of the layer of the placenta where embryonic and maternal blood vessels interdigitate placental labyrinth vascular network vasculature of placenta labyrinth uberon placental vasculature UBERON:0003970 placental labyrinth vasculature blood vessels of the layer of the placenta where embryonic and maternal blood vessels interdigitate MP:0008803 placental vasculature OBOL:automatic 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]. In mammals, the uterine tube infundibulum is part of the fallopian tube. In birds, where there is no fallopian tube, the uterine tube infundibulum is part of the oviduct. 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]. In mammals, the uterine tube infundibulum is part of the fallopian tube. In birds, where there is no fallopian tube, the uterine tube infundibulum is part of the oviduct. 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 subclasses of motor neurons which are organized into longitudinally oriented columns that occupy distinct and, in some cases, discontinuous domains along the rostrocaudal axis of the spinal cord; motor neurons within a single column send their axons to a common peripheral target uberon UBERON:0003990 spinal cord motor column The subclasses of motor neurons which are organized into longitudinally oriented columns that occupy distinct and, in some cases, discontinuous domains along the rostrocaudal axis of the spinal cord; motor neurons within a single column send their axons to a common peripheral target MP:0009685 . TODO - check isa parentage EMAPA:37917 NLXANAT:20090402 cytoarchitectural part of olfactory bulb uberon UBERON:0004001 olfactory bulb layer . MP:0009946 EMAPA:37917 MA:th cytoarchitectural part of olfactory bulb NLXANAT:20090402 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 The transient proliferative population of neurons that expands exponentially during late prenatal development; it is a continuous germinal zone distinct from the ventricular zone that surrounds the brain ventricles[MP]. contributes significantly in building up the GABAergic cortical cell population[WP] GE SVZ embryonic GE embryonic SVZ subventricular zone DHBA:10549 EMAPA:32665 PBA:128012818 embryonic subventricular zone embryonic/fetal subventricular zone fetal subventricular zone subependymal layer uberon UBERON:0004023 ganglionic eminence The transient proliferative population of neurons that expands exponentially during late prenatal development; it is a continuous germinal zone distinct from the ventricular zone that surrounds the brain ventricles[MP]. MP:0004274 GE SVZ MP:0004274 embryonic GE embryonic SVZ subventricular zone DHBA:SZ embryonic subventricular zone MP:0004274 subependymal layer MP:0004274 A distinct elevation of a transient proliferating cell mass of the fetal subventricular zone; this mass contributes most of its cells to the neocortex; however, hippocampal neurons, thalamus, septum and olfactory bulb neurons are also partly derived from the MGE. MGE DHBA:10550 EMAPA:37471 PBA:128012834 uberon UBERON:0004024 medial ganglionic eminence A distinct elevation of a transient proliferating cell mass of the fetal subventricular zone; this mass contributes most of its cells to the neocortex; however, hippocampal neurons, thalamus, septum and olfactory bulb neurons are also partly derived from the MGE. MP:0004276 MGE EMAPA:37471 MA:th The caudally located, distinct elevation of a transient proliferating cell mass of the fetal subventricular zone, located adjacent to the lateral ventricle CGE DHBA:10552 EFO:0001911 EMAPA:37469 PBA:128012846 uberon UBERON:0004026 caudal ganglionic eminence The caudally located, distinct elevation of a transient proliferating cell mass of the fetal subventricular zone, located adjacent to the lateral ventricle MP:0004278 EMAPA:37469 MA:th 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 nodules of small undifferentiated B lymphocytes and follicular dendritic cells located in the spleen white pulp FMA:15843 is classified as primary follicle so it belongs here EMAPA:37960 FMA:15843 primary spleen B cell follicle uberon UBERON:0004041 spleen primary B follicle The nodules of small undifferentiated B lymphocytes and follicular dendritic cells located in the spleen white pulp MP:0008471 FMA:15843 is classified as primary follicle so it belongs here FMA EMAPA:37960 MA:th primary spleen B cell follicle CL:tm The nodules of antigen-activated, differentiating B cells, follicular dendritic cells, antigen-presenting T cells and macrophages in the spleen white pulp EMAPA:37961 secondary spleen B cell follicle splenic secondary B cell follicle uberon UBERON:0004042 spleen secondary B follicle CL:tm The nodules of antigen-activated, differentiating B cells, follicular dendritic cells, antigen-presenting T cells and macrophages in the spleen white pulp MP:0008472 EMAPA:37961 MA:th secondary spleen B cell follicle CL:tm splenic secondary B cell follicle MP:0008472 The spherical enlargement at the base of each semicircular canal where they connect with the utricle, containing the crista ampullaris which detects movement of the fluid within the canals TODO check duct vs canal. Also check FMA - has many subtypes of semicircular canal such as 'ampulla of anterior semicircular canal' EMAPA:32831 MA:0002770 uberon ampullae osseae membraneous ampulla of the semicircular duct semicircular duct ampulla UBERON:0004043 semicircular canal ampulla http://upload.wikimedia.org/wikipedia/commons/6/65/Vestibular_system%27s_semicircular_canal-_a_cross-section.jpg MA The spherical enlargement at the base of each semicircular canal where they connect with the utricle, containing the crista ampullaris which detects movement of the fluid within the canals MP:0008488 ampullae osseae membraneous ampulla of the semicircular duct MP:0008488 semicircular duct ampulla MA:0002770 The extraembryonic tissue that is responsible for the proper orientation of the anterior-posterior axis of the embryo and for appropriate patterning of adjacent embryonic tissue BTO:0003361 EMAPA:36068 uberon AVE UBERON:0004044 anterior visceral endoderm The extraembryonic tissue that is responsible for the proper orientation of the anterior-posterior axis of the embryo and for appropriate patterning of adjacent embryonic tissue MP:0008533 AVE BTO:0003361 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 subclasses of motor neurons which project their axons to axial muscles that lie close to the vertebral column; motor neurons in the lateral subdivision of the MMC project their axons to body wall muscles uberon UBERON:0004059 spinal cord medial motor column The subclasses of motor neurons which project their axons to axial muscles that lie close to the vertebral column; motor neurons in the lateral subdivision of the MMC project their axons to body wall muscles MP:0009686 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 lexical 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 The central area of the two limbs of a horseshoe-shaped mesenchymal swelling that lie medial to the olfactory placode or pit in the future nasal region of the embryo; it joins with the ipsilateral maxillary prominence in the formation of half of the upper jaw, and the nasal tip and philtrum of the upper lip develop from it Fusion of right and left medial nasal processes forms a primary palate rostrally and the nasal septum caudally. The incisive bone, including upper incisor teeth and the rostral up- per lip, are derived from the primary palate. The nasal septum consists of bone, cartilage, and a patch of soft tissue membrane that separates right & left halves of the nasal cavity. EHDAA2:0001076 EHDAA:4792 EMAPA:16808 FMA:295858 VHOG:0000804 medial nasal process medial-nasal process prominentia nasalis medialis uberon medial nasal swelling nasomedial prominence UBERON:0004068 medial nasal prominence http://upload.wikimedia.org/wikipedia/commons/8/85/Gray45.png EHDAA2 Wikipedia lexical The central area of the two limbs of a horseshoe-shaped mesenchymal swelling that lie medial to the olfactory placode or pit in the future nasal region of the embryo; it joins with the ipsilateral maxillary prominence in the formation of half of the upper jaw, and the nasal tip and philtrum of the upper lip develop from it MP:0009903 medial nasal process EHDAA2:0001076 medial-nasal process EMAPA:16808 prominentia nasalis medialis medial nasal swelling nasomedial prominence 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 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 one of the two jaw ridges either on the roof of the mouth between the upper teeth and the hard palate or on the bottom of the mouth behind the lower teeth[WP]. The alveolar ridges contain the sockets (alveoli) of the teeth[HP]. in BTO, this is part of an embryo BTO:0001383 EMAPA:35118 FMA:313923 GAID:215 MA:0003119 MESH:D000539 NCIT:C89749 UMLS:C0447411 alveolar body alveolar bone alveolar margin alveolar process margo alveolaris uberon UBERON:0004103 alveolar ridge Wikipedia one of the two jaw ridges either on the roof of the mouth between the upper teeth and the hard palate or on the bottom of the mouth behind the lower teeth[WP]. The alveolar ridges contain the sockets (alveoli) of the teeth[HP]. HP:0006477 in BTO, this is part of an embryo BTO UMLS:C0447411 ncithesaurus:Alveolar_Ridge alveolar body MP:0004189 alveolar bone MP:0004189 margo alveolaris The outer or sperficial part of the humerus. FMA:31542 compact bone of humerus cortex of the humerus humerus compact bone humerus cortical bone uberon UBERON:0004109 cortex of humerus The outer or sperficial part of the humerus. PHENOSCAPE:ad compact bone of humerus FMA:31542 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 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 cartilage that will provide a scaffold for mineralization of endochondral bones as they elongate or grow. uberon growth plate UBERON:0004129 growth plate cartilage cartilage that will provide a scaffold for mineralization of endochondral bones as they elongate or grow. GO:0003417 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 In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO]. TODO - ensure definition works across species. BTO:0001498 CALOHA:TS-0509 EMAPA:28281 MA:0002611 MESH:D007687 kidney proximal tubule proximal kidney tubule renal proximal tubule uberon UBERON:0004134 proximal tubule GO GO In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO]. GO:0072014 kidney proximal tubule MA:0002611 proximal kidney tubule MESH:A05.810.453.736.560.570 The distal tubule is a nephron tubule that consists of the distal convoluted tubule and distal straight tubule segments BTO:0000482 CALOHA:TS-0504 EMAPA:28387 MA:0002633 MESH:D007686 kidney distal tubule renal distal tubule uberon UBERON:0004135 distal tubule The distal tubule is a nephron tubule that consists of the distal convoluted tubule and distal straight tubule segments GO:0072017 kidney distal tubule MA:0002633 The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules TODO - check for applicability across species FMA:17718 renal intermediate tubule tubulus attenuatus uberon UBERON:0004136 intermediate tubule FMA The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules GO:0072018 tubulus attenuatus FMA:17718 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 The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles the intraventricular conduction system from the bundle of His to the distal Purkinje fibers, which carries the impulse to the ventricles. HPS His-Purkinji network VCS ventricular conduction system uberon UBERON:0004146 His-Purkinje system cjm GO The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles GO:0003164 the intraventricular conduction system from the bundle of His to the distal Purkinje fibers, which carries the impulse to the ventricles. HPS 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 A jaw muscle that arises from cranial mesenchyme and is innervated by cranial nerves. The branchiomeric muscle is derived from cranial mesoderm and controls facial expression, pharyngeal and laryngeal function, operating the jaw. Branchiomeric muscles of mammals correspond to the musculature of fish[GO][GO:0014707]. It has been hypothesized that Haikouella must have been powered by branchiomeric muscles, as in living craniates, rather than by water moving through the pharynx via ciliary currents, as in lancelets[http://icb.oxfordjournals.org/content/42/4/743.full] XAO:0004325 branchial head muscle branchiomeric skeletal muscle uberon UBERON:0004164 branchiomeric muscle ISBN:0073040584 A jaw muscle that arises from cranial mesenchyme and is innervated by cranial nerves. ISBN:0073040584 The branchiomeric muscle is derived from cranial mesoderm and controls facial expression, pharyngeal and laryngeal function, operating the jaw. Branchiomeric muscles of mammals correspond to the musculature of fish[GO][GO:0014707]. GO:0014707 branchial head muscle XAO:0004325 branchiomeric skeletal muscle GO:0014707 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 A saclike structure of the prostate gland, comprised of at least three cell layers: an innermost layer of secretory columnar luminal epithelium, a middle layer of squamous basal epithelium that also contains neuroendocrine cells, transit amplifying cells, and stem cells, and an outer layer of smooth muscle intermixed with other stromal cells the muscle layer is implicitly treated as outside the acinus Concurrent with branching morphogenesis, the solid cords of epithelium formed by budding arborize and differentiate postnatally into glandular acin. The basic prostate architecture is established by puberty and acquires secretory function thereafter[PMID:18977204] FMA:66808 prostatic acinus prostatic follicle uberon UBERON:0004179 prostate glandular acinus FMA GO A saclike structure of the prostate gland, comprised of at least three cell layers: an innermost layer of secretory columnar luminal epithelium, a middle layer of squamous basal epithelium that also contains neuroendocrine cells, transit amplifying cells, and stem cells, and an outer layer of smooth muscle intermixed with other stromal cells GO:0060525 prostatic acinus FMA:66808 prostatic follicle FMA:66808 The mammary fat is an adipose structure in the gland that is invaded by the mammary ducts EMAPA:35539 MA:0002911 adipose tissue of lactiferous gland adipose tissue of mammary gland fat tissue of lactiferous gland fat tissue of lobe of breast fat tissue of lobe of mammary gland fat tissue of mammary gland fatty tissue of lactiferous gland fatty tissue of lobe of breast fatty tissue of lobe of mammary gland fatty tissue of mammary gland lactiferous gland adipose tissue lactiferous gland fat tissue lactiferous gland fatty tissue lobe of breast adipose tissue lobe of breast fat tissue lobe of breast fatty tissue lobe of mammary gland adipose tissue lobe of mammary gland fat tissue lobe of mammary gland fatty tissue mammary gland adipose tissue mammary gland fat tissue mammary gland fatty tissue uberon UBERON:0004180 mammary gland fat The mammary fat is an adipose structure in the gland that is invaded by the mammary ducts GO:0060611 adipose tissue of lactiferous gland OBOL:automatic adipose tissue of mammary gland OBOL:automatic fat tissue of lactiferous gland OBOL:automatic fat tissue of lobe of breast OBOL:automatic fat tissue of lobe of mammary gland OBOL:automatic fat tissue of mammary gland OBOL:automatic fatty tissue of lactiferous gland OBOL:automatic fatty tissue of lobe of breast OBOL:automatic fatty tissue of lobe of mammary gland OBOL:automatic fatty tissue of mammary gland OBOL:automatic lactiferous gland adipose tissue OBOL:automatic lactiferous gland fat tissue OBOL:automatic lactiferous gland fatty tissue OBOL:automatic lobe of breast adipose tissue OBOL:automatic lobe of breast fat tissue OBOL:automatic lobe of breast fatty tissue OBOL:automatic lobe of mammary gland adipose tissue OBOL:automatic lobe of mammary gland fat tissue OBOL:automatic lobe of mammary gland fatty tissue OBOL:automatic mammary gland adipose tissue OBOL:automatic mammary gland fat tissue OBOL:automatic mammary gland fatty tissue OBOL:automatic The solid cord of epithelial cells that emerges from the mammary bud and grows down from the primary mammary mesenchyme and into a second stromal compartment, the fat pad precursor, beneath the dermis. in female mouse embryos, the primary mammary cord (aka 'mammary sprout') is formed between E15.5 and E16.5; once the primary cord reaches the adipocytes of the fat pad (around E16), it begins to branch in a characteristic dichotomous fashion to form the initial ductal tree lactiferous gland cord mammary cord uberon mammary sprout UBERON:0004182 mammary gland cord The solid cord of epithelial cells that emerges from the mammary bud and grows down from the primary mammary mesenchyme and into a second stromal compartment, the fat pad precursor, beneath the dermis. MP:0013725 The embryonic vessels grow through the layer to come in close contact with the maternal blood supply blood vessel of labyrinthine layer blood vessel of labyrinthine layer of placenta blood vessel of placenta labyrinth labyrinthine layer blood vessel labyrinthine layer of placenta blood vessel placenta labyrinth blood vessel uberon UBERON:0004183 placental labyrinth blood vessel The embryonic vessels grow through the layer to come in close contact with the maternal blood supply GO:0060716 blood vessel of labyrinthine layer OBOL:automatic blood vessel of labyrinthine layer of placenta OBOL:automatic blood vessel of placenta labyrinth OBOL:automatic labyrinthine layer blood vessel GO:0060716 labyrinthine layer of placenta blood vessel OBOL:automatic placenta labyrinth blood vessel OBOL:automatic 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 The mitral cell layer is composed of pyramidal neurons whose cell bodies are located between the granule cell layer and the plexiform layer NIF divides this into main and accessory BAMS:Mi BTO:0001108 DHBA:11329 DMBA:15912 EMAPA:35611 MA:0000973 NLXANAT:100201 OB mitral cell layer mitral cell body layer mitral cell layer uberon mitral cell layer of the olfactory bulb olfactory bulb main mitral cell body layer UBERON:0004186 olfactory bulb mitral cell layer The mitral cell layer is composed of pyramidal neurons whose cell bodies are located between the granule cell layer and the plexiform layer GO:0061034 NIF divides this into main and accessory NIF OB mitral cell layer DMBA:OB mitral cell body layer NLXANAT:100201 mitral cell layer BTO:0001108 mitral cell layer of the olfactory bulb BAMS:Mi olfactory bulb main mitral cell body layer NLXANAT:100201 The glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus. The glomerular epithelium consists of both parietal and visceral epithelium. Metanephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros. TODO - check - GO says outer, BTO says inner. Make this a superclass BTO:0001515 EMAPA:35458 MA:0002847 epithelium of glomerulus epithelium of kidney glomerulus epithelium of renal glomerulus kidney glomerular epithelium uberon glomerular epithelial cell UBERON:0004188 glomerular epithelium The glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus. The glomerular epithelium consists of both parietal and visceral epithelium. Metanephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros. GO:0072010 kidney glomerular epithelium MA:0002847 glomerular epithelial cell BTO:0001515 The glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus BTO:0004631 endothelium of renal glomerulus renal glomerulus endothelium uberon UBERON:0004189 glomerular endothelium The glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus GO:0072011 endothelium of renal glomerulus OBOL:automatic renal glomerulus endothelium OBOL:automatic The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus glomerulus vasculature renal glomerulus vascular network renal glomerulus vasculature vascular network of renal glomerulus vasculature of renal glomerulus uberon UBERON:0004190 renal glomerulus vasculature The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus GO:0072012 glomerulus vasculature OBOL:automatic renal glomerulus vascular network OBOL:automatic renal glomerulus vasculature OBOL:automatic vascular network of renal glomerulus OBOL:automatic vasculature of renal glomerulus OBOL:automatic A sub-portion of the loop of Henle in the nephron of the kidney that is permeable to ions but not to water check relationship to distal tubule EMAPA:28328 EMAPA:28361 FMA:17720 MA:0001678 ascending limb thin segment of loop of Henle ascending thin limb pars ascendens (tubulus attenuatus) thin ascending limb thin ascending limb of loop of Henle uberon UBERON:0004193 loop of Henle ascending limb thin segment http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png A sub-portion of the loop of Henle in the nephron of the kidney that is permeable to ions but not to water GO:0072021 ascending thin limb FMA:17720 pars ascendens (tubulus attenuatus) FMA:17720 thin ascending limb EMAPA:28328 The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron EMAPA:27681 ZFA:0005588 CSB uberon UBERON:0004198 comma-shaped body cjm ZFA The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron GO:0072049 CSB The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron TODO EMAPA:27756 ZFA:0005589 SSB stage II nephron uberon UBERON:0004199 S-shaped body cjm GO The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron GO:0072050 SSB stage II nephron 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 inner stripe is a deep, centrally located portion of the renal outer medulla and is traversed by thick and thin portions of nephron tubules EMAPA:29675 FMA:76663 MA:0002626 inner stripe inner stripe of medulla of kidney inner stripe of outer medulla inner stripe of renal medulla outer medulla inner stripe stria interna medullae renalis uberon UBERON:0004201 kidney outer medulla inner stripe The inner stripe is a deep, centrally located portion of the renal outer medulla and is traversed by thick and thin portions of nephron tubules GO:0072057 inner stripe GO:0072057 inner stripe of medulla of kidney FMA:76663 inner stripe of outer medulla EMAPA:29675 inner stripe of renal medulla FMA:76663 outer medulla inner stripe MA:0002626 stria interna medullae renalis FMA:76663 FMA:TA The outer stripe is the region of the kidney that lies distal to the line of termination of the straight renal tubules EMAPA:29663 FMA:76662 MA:0002629 outer medulla outer stripe outer stripe outer stripe of medulla of kidney outer stripe of outer medulla outer stripe of renal medulla stria externa medullae renalis uberon UBERON:0004202 kidney outer medulla outer stripe The outer stripe is the region of the kidney that lies distal to the line of termination of the straight renal tubules GO:0072058 outer medulla outer stripe MA:0002629 outer stripe GO:0072058 outer stripe of medulla of kidney FMA:76662 outer stripe of outer medulla EMAPA:29663 outer stripe of renal medulla FMA:76662 stria externa medullae renalis FMA:76662 FMA:TA 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 The outer medullary collecting duct is the portion of the collecting duct that lies in the renal outer medulla UBERON:0005186 EMAPA:28346 MA:0002599 kidney outer medulla collecting duct outer renal medulla collecting duct uberon UBERON:0004204 outer medullary collecting duct The outer medullary collecting duct is the portion of the collecting duct that lies in the renal outer medulla GO:0072060 kidney outer medulla collecting duct MA:0002599 outer renal medulla collecting duct MA:0002599 The inner medullary collecting duct is the portion of the collecting duct that lies in the renal inner medulla UBERON:0005187 BTO:0004544 EMAPA:28370 MA:0002598 inner renal medulla collecting duct kidney inner medulla collecting duct uberon papillary collecting duct UBERON:0004205 inner medullary collecting duct The inner medullary collecting duct is the portion of the collecting duct that lies in the renal inner medulla GO:0072061 inner renal medulla collecting duct MA:0002598 kidney inner medulla collecting duct MA:0002598 papillary collecting duct MA:0002598 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 the small branching blood vessels in the kidney glomerulus that receives blood from the kidney afferent arterioles; these capillaries are under high pressure for filtering within the glomerulus Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO] EMAPA:28245 FMA:274259 MA:0002587 NCIT:C32684 TAO:0005284 UMLS:C0226356 ZFA:0005284 blood capillary of renal glomerulus capillary of renal glomerulus capillary vessel of renal glomerulus renal glomerulus blood capillary renal glomerulus capillary renal glomerulus capillary vessel uberon glomerular capillaries glomerular capillary system UBERON:0004212 glomerular capillary the small branching blood vessels in the kidney glomerulus that receives blood from the kidney afferent arterioles; these capillaries are under high pressure for filtering within the glomerulus MGI:csmith MP:0011320 Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO] 2012-08-14 TAO:0005284 TAO ZFIN:ZDB-PUB-000824-1 ZFIN:curator UMLS:C0226356 ncithesaurus:Glomerular_Capillary blood capillary of renal glomerulus OBOL:automatic capillary of renal glomerulus OBOL:automatic capillary vessel of renal glomerulus OBOL:automatic renal glomerulus blood capillary OBOL:automatic renal glomerulus capillary OBOL:automatic renal glomerulus capillary vessel OBOL:automatic glomerular capillaries glomerular capillary system MA:0002587 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 trigone of urinary bladder [Automatically generated definition]. EMAPA:28649 MA:0001700 Lieutaud's trigone involuntary muscle Lieutaud's trigone non-striated muscle Lieutaud's trigone smooth muscle Lieutaud's trigone smooth muscle tissue deep trigone involuntary muscle deep trigone non-striated muscle deep trigone smooth muscle deep trigone smooth muscle tissue involuntary muscle of Lieutaud's trigone involuntary muscle of deep trigone involuntary muscle of trigone of bladder involuntary muscle of trigone of urinary bladder involuntary muscle of urinary bladder trigone involuntary muscle of vesical trigone non-striated muscle of Lieutaud's trigone non-striated muscle of deep trigone non-striated muscle of trigone of bladder non-striated muscle of trigone of urinary bladder non-striated muscle of urinary bladder trigone non-striated muscle of vesical trigone smooth muscle of Lieutaud's trigone smooth muscle of deep trigone smooth muscle of trigone of bladder smooth muscle of trigone of urinary bladder smooth muscle of urinary bladder trigone smooth muscle of vesical trigone smooth muscle tissue of Lieutaud's trigone smooth muscle tissue of deep trigone smooth muscle tissue of trigone of bladder smooth muscle tissue of trigone of urinary bladder smooth muscle tissue of urinary bladder trigone smooth muscle tissue of vesical trigone trigone of bladder involuntary muscle trigone of bladder non-striated muscle trigone of bladder smooth muscle trigone of bladder smooth muscle tissue trigone of urinary bladder involuntary muscle trigone of urinary bladder non-striated muscle trigone of urinary bladder smooth muscle trigone of urinary bladder smooth muscle tissue urinary bladder trigone involuntary muscle urinary bladder trigone muscle urinary bladder trigone non-striated muscle urinary bladder trigone smooth muscle tissue vesical trigone involuntary muscle vesical trigone non-striated muscle vesical trigone smooth muscle vesical trigone smooth muscle tissue uberon UBERON:0004229 urinary bladder trigone smooth muscle A portion of smooth muscle tissue that is part of a trigone of urinary bladder [Automatically generated definition]. OBOL:automatic Lieutaud's trigone involuntary muscle OBOL:automatic Lieutaud's trigone non-striated muscle OBOL:automatic Lieutaud's trigone smooth muscle OBOL:automatic Lieutaud's trigone smooth muscle tissue OBOL:automatic deep trigone involuntary muscle OBOL:automatic deep trigone non-striated muscle OBOL:automatic deep trigone smooth muscle OBOL:automatic deep trigone smooth muscle tissue OBOL:automatic involuntary muscle of Lieutaud's trigone OBOL:automatic involuntary muscle of deep trigone OBOL:automatic involuntary muscle of trigone of bladder OBOL:automatic involuntary muscle of trigone of urinary bladder OBOL:automatic involuntary muscle of urinary bladder trigone OBOL:automatic involuntary muscle of vesical trigone OBOL:automatic non-striated muscle of Lieutaud's trigone OBOL:automatic non-striated muscle of deep trigone OBOL:automatic non-striated muscle of trigone of bladder OBOL:automatic non-striated muscle of trigone of urinary bladder OBOL:automatic non-striated muscle of urinary bladder trigone OBOL:automatic non-striated muscle of vesical trigone OBOL:automatic smooth muscle of Lieutaud's trigone OBOL:automatic smooth muscle of deep trigone OBOL:automatic smooth muscle of trigone of bladder OBOL:automatic smooth muscle of trigone of urinary bladder OBOL:automatic smooth muscle of urinary bladder trigone OBOL:automatic smooth muscle of vesical trigone OBOL:automatic smooth muscle tissue of Lieutaud's trigone OBOL:automatic smooth muscle tissue of deep trigone OBOL:automatic smooth muscle tissue of trigone of bladder OBOL:automatic smooth muscle tissue of trigone of urinary bladder OBOL:automatic smooth muscle tissue of urinary bladder trigone OBOL:automatic smooth muscle tissue of vesical trigone OBOL:automatic trigone of bladder involuntary muscle OBOL:automatic trigone of bladder non-striated muscle OBOL:automatic trigone of bladder smooth muscle OBOL:automatic trigone of bladder smooth muscle tissue OBOL:automatic trigone of urinary bladder involuntary muscle OBOL:automatic trigone of urinary bladder non-striated muscle OBOL:automatic trigone of urinary bladder smooth muscle OBOL:automatic trigone of urinary bladder smooth muscle tissue OBOL:automatic urinary bladder trigone involuntary muscle OBOL:automatic urinary bladder trigone muscle MA:0001700 urinary bladder trigone non-striated muscle OBOL:automatic urinary bladder trigone smooth muscle tissue OBOL:automatic vesical trigone involuntary muscle OBOL:automatic vesical trigone non-striated muscle OBOL:automatic vesical trigone smooth muscle OBOL:automatic vesical trigone 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 a mammary gland [Automatically generated definition]. EMAPA:37669 MA:0000795 smooth muscle tissue of mammary gland uberon UBERON:0004235 mammary gland smooth muscle A portion of smooth muscle tissue that is part of a mammary gland [Automatically generated definition]. OBOL:automatic EMAPA:37669 MA:th smooth muscle tissue of mammary gland 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 An endothelium that is part of a glomerular capillary. MA:0001658 NCIT:C32522 UMLS:C0227647 renal glomerulus capillary endothelium uberon UBERON:0004294 glomerular capillary endothelium An endothelium that is part of a glomerular capillary. OBOL:automatic UMLS:C0227647 ncithesaurus:Endothelium_of_the_Glomerular_Capillary renal glomerulus capillary endothelium 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 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 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 tibia [Automatically generated definition]. EMAPA:37771 FMA:33112 MA:0003113 tibial epiphysis uberon UBERON:0004383 epiphysis of tibia An epiphysis that is part of a tibia [Automatically generated definition]. OBOL:automatic EMAPA:37771 MA:th tibial epiphysis FMA:33112 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 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 periosteum that is part of a epiphysis [Automatically generated definition]. FMA:32687 epiphysis periosteum uberon UBERON:0004403 periosteum of epiphysis A periosteum that is part of a epiphysis [Automatically generated definition]. OBOL:automatic epiphysis periosteum FMA:32687 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 tibia [Automatically generated definition]. FMA:33116 distal end of tibia lower end of tibia uberon UBERON:0004405 distal epiphysis of tibia A distal epiphysis that is part of a tibia [Automatically generated definition]. OBOL:automatic distal end of tibia FMA:33116 lower end of tibia FMA:33116 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 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 the collection of muscles that acts on the pharynx. FMA:264609 TAO:0001307 ZFA:0001307 pharyngeal musculature uberon set of muscles of pharynx UBERON:0004467 See comments for 'pharyngeal muscle' musculature of pharynx the collection of muscles that acts on the pharynx. pharyngeal musculature TAO:0001307 set of muscles of pharynx FMA:264609 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 deltoid [Automatically generated definition]. FMA:261732 uberon skeletal muscle tissue of deltoid muscle UBERON:0004500 skeletal muscle tissue of deltoid A portion of skeletal muscle tissue that is part of a deltoid [Automatically generated definition]. OBOL:automatic skeletal muscle tissue of deltoid muscle FMA:261732 A portion of skeletal muscle tissue that is part of a trapezius [Automatically generated definition]. FMA:261938 uberon skeletal muscle tissue of trapezius muscle UBERON:0004509 skeletal muscle tissue of trapezius A portion of skeletal muscle tissue that is part of a trapezius [Automatically generated definition]. OBOL:automatic skeletal muscle tissue of trapezius muscle FMA:261938 A portion of skeletal muscle tissue that is part of a pectoralis major [Automatically generated definition]. FMA:261968 uberon skeletal muscle tissue of pectoralis major muscle UBERON:0004510 skeletal muscle tissue of pectoralis major A portion of skeletal muscle tissue that is part of a pectoralis major [Automatically generated definition]. OBOL:automatic skeletal muscle tissue of pectoralis major muscle FMA:261968 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 portion of smooth muscle tissue that is part of a respiratory bronchiole [Automatically generated definition]. FMA:261055 uberon UBERON:0004517 smooth muscle tissue of respiratory bronchiole A portion of smooth muscle tissue that is part of a respiratory 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 The capsule surrounding the inner ear mechanism. developmental relationships need to be checked Skeletal elements surrounding the membranous labyrinth of the inner ear. Sensory capsules anterolateral to and confluent with occipital arch.[AAO] The cartilage capsule surrounding the inner ear mechanism; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony. [Biology_online][VHOG] relationship loss: part_of occipito-petrosal (AAO:0010831)[AAO] relationship loss: part_of otic and occipital (AAO:0000993)[AAO] Otic capsules develop around the parts of the ear that lie within the chondrocranium. This part of the ear, known as the inner ear, is composed of the semicircular ducts and associated sacs that contain the receptive cells for equilibrium and hearing (reference 1); (...) considerations have led to our rethinking issues related to the origin of several aspects of vertebrate hearing, and to the view that many basic auditory functions evolved very early in vertebrate history, and that the functions observed in more `advanced' vertebrates, such as birds and mammals, are frequently modifications of themes first encountered in fishes, and perhaps even more ancestral animals.[well established][VHOG] in elasmobranchs, it remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans) otic capsule skeletal element AAO:0010143 VHOG:0000854 otic capsule otic capsule element otic capsule endochondral element uberon auditory capsule otic region periotic periotic capsule UBERON:0004637 otic capsule The capsule surrounding the inner ear mechanism. Skeletal elements surrounding the membranous labyrinth of the inner ear. Sensory capsules anterolateral to and confluent with occipital arch.[AAO] 2012-06-20 AAO:0010143 AAO AAO:EJS The cartilage capsule surrounding the inner ear mechanism; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony. [Biology_online][VHOG] 2012-09-17 VHOG:0000854 VHOG relationship loss: part_of occipito-petrosal (AAO:0010831)[AAO] 2012-06-20 AAO:0010143 AAO relationship loss: part_of otic and occipital (AAO:0000993)[AAO] 2012-06-20 AAO:0010143 AAO Otic capsules develop around the parts of the ear that lie within the chondrocranium. This part of the ear, known as the inner ear, is composed of the semicircular ducts and associated sacs that contain the receptive cells for equilibrium and hearing (reference 1); (...) considerations have led to our rethinking issues related to the origin of several aspects of vertebrate hearing, and to the view that many basic auditory functions evolved very early in vertebrate history, and that the functions observed in more `advanced' vertebrates, such as birds and mammals, are frequently modifications of themes first encountered in fishes, and perhaps even more ancestral animals.[well established][VHOG] 2012-09-17 VHOG:0000854 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.235, DOI:10.1016/S0378-5955(00)00168-4 Fay RR, Popper AN, Evolution of hearing in vertebrates: the inner ears and processing. Hearing research (2000) in elasmobranchs, it remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans) Biology-Online otic capsule skeletal element otic capsule ZFA:0001500 otic capsule element otic capsule endochondral element auditory capsule VHOG:0000854 periotic capsule VHOG:0000854 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 blood vessels that branch from the kidney interlobular artery, convey blood to the glomerular capillaries, and play an important role in the regulation of blood pressure as a part of the tubuloglomerular feedback mechanism EMAPA:28230 EMAPA:28266 FMA:77042 MA:0002579 TAO:0002139 ZFA:0005307 afferent arteriole afferent glomerular arteriole afferent glomerular arteriole of kidney arteriola glomerularis afferens renis kidney afferent arteriole uberon arteriola glomerularis afferens UBERON:0004639 renal afferent arteriole http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png the blood vessels that branch from the kidney interlobular artery, convey blood to the glomerular capillaries, and play an important role in the regulation of blood pressure as a part of the tubuloglomerular feedback mechanism ISBN:0-683-40008-8 MGI:csmith MP:0011312 afferent arteriole MA:0002579 afferent glomerular arteriole ZFA:0005307 afferent glomerular arteriole of kidney FMA:77042 arteriola glomerularis afferens renis FMA:77042 FMA:TA kidney afferent arteriole MP:0011312 arteriola glomerularis afferens the blood vessels that convey blood from the glomerulocapillary network to the capillary bed of the proximal convoluted tubule EMAPA:28233 EMAPA:28275 FMA:77043 MA:0002585 TAO:0002140 ZFA:0005308 arteriola glomerularis efferens renis efferent arteriole efferent glomerular arteriole efferent glomerular arteriole of kidney kidney efferent arteriole uberon arteriola glomerularis efferens capsulae renalis UBERON:0004640 renal efferent arteriole http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png the blood vessels that convey blood from the glomerulocapillary network to the capillary bed of the proximal convoluted tubule ISBN:0-683-40008-8 MGI:csmith MP:0011313 arteriola glomerularis efferens renis FMA:77043 FMA:TA efferent arteriole MA:0002585 efferent glomerular arteriole ZFA:0005308 efferent glomerular arteriole of kidney FMA:77043 kidney efferent arteriole MP:0011313 arteriola glomerularis efferens capsulae renalis 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 epithelial lining of the luminal space of the urinary bladder. 5-7 cell layers thick in contracted bladder, 2-3 cells thick in distended bladder; lines renal pelvis, ureters, bladder, most of urethra but not distal urethra urothelium BTO:0001694 CALOHA:TS-1088 EMAPA:28601 FMA:15936 MA:0001693 NCIT:C13318 UMLS:C0225339 bladder transitional cell epithelium transitional epithelium of urinary bladder urinary bladder transitional epithelium urothelium of urinary bladder uberon epithelium of bladder transitional epithelium UBERON:0004645 urinary bladder urothelium The epithelial lining of the luminal space of the urinary bladder. MP:0000540 urothelium BTO:0001245 UMLS:C0225339 ncithesaurus:Transitional_Epithelium bladder transitional cell epithelium FMA:15936 transitional epithelium of urinary bladder FMA:15936 urinary bladder transitional epithelium FMA:15936 urothelium of urinary bladder FMA:15936 epithelium of bladder EMAPA:28601 transitional epithelium MA:0001693 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 A nerve root that extends_fibers_into a trigeminal nerve. TODO - check ZFA BIRNLEX:1346 DHBA:12865 DMBA:17739 FMA:52610 TAO:0000192 ZFA:0000192 radix descendens nervi trigemini root of trigeminal V nerve root of trigeminal nerve trigeminal nerve root trigeminal neural root uberon descending trigeminal root UBERON:0004673 trigeminal nerve root FMA A nerve root that extends_fibers_into a trigeminal nerve. OBOL:automatic radix descendens nervi trigemini ZFA:0000192 root of trigeminal V nerve Obol:cjm root of trigeminal nerve FMA:52610 trigeminal nerve root BIRNLEX:1346 trigeminal neural root FMA:52610 descending trigeminal root TAO:0000192 A nerve root that extends_fibers_into a facial nerve. BAMS:7n BAMS:7nf BIRNLEX:1513 DHBA:12862 DMBA:17742 FMA:53418 central part of facial nerve facial nerve fibers facial nerve root facial neural root fibrae nervi facialis root of facial nerve uberon facial nerve or its root facial nerve/root UBERON:0004674 facial nerve root FMA A nerve root that extends_fibers_into a facial nerve. OBOL:automatic central part of facial nerve FMA:53418 facial nerve fibers FMA:53418 facial nerve root BIRNLEX:1513 facial neural root FMA:53418 fibrae nervi facialis FMA:53418 FMA:TA root of facial nerve FMA:53418 facial nerve or its root BAMS:7n facial nerve/root BAMS:7n A nerve root that extends_fibers_into a hypoglossal nerve. UBERON:0022760 BAMS:12n BAMS:12nf BIRNLEX:1288 BIRNLEX:1588 DHBA:12886 DMBA:17750 FMA:72632 central part of hypoglossal nerve fibrae nervi hypoglossi hypoglossal nerve fiber bundle hypoglossal nerve fibers hypoglossal nerve root hypoglossal nerve tract root of hypoglossal nerve uberon central part of hypoglossal nerve hypoglossal nerve fibers hypoglossal nerve/ root root of hypoglossal nerve UBERON:0004675 hypoglossal nerve root FMA A nerve root that extends_fibers_into a hypoglossal nerve. OBOL:automatic central part of hypoglossal nerve FMA:72632 fibrae nervi hypoglossi FMA:72632 FMA:TA hypoglossal nerve fiber bundle BIRNLEX:1288 hypoglossal nerve fiber bundle BIRNLEX:1288 hypoglossal nerve fibers FMA:72632 hypoglossal nerve root BIRNLEX:1588 hypoglossal nerve tract FMA:72632 root of hypoglossal nerve FMA:72632 central part of hypoglossal nerve BIRNLEX:1288 hypoglossal nerve fibers BIRNLEX:1288 hypoglossal nerve/ root BAMS:12n root of hypoglossal nerve BIRNLEX:1288 The molecular layer of the dentate gyrus that is bounded by the pial surface superficially and the dentate gyrus granule cell layer deep. It is divided into 2 or more sublayers. BAMS:Mol BAMS:mo BIRNLEX:4127 EMAPA:35279 FMA:83677 MA:0003122 MBA:10703 dentate gyrus molecular layer molecular layer of dentate gyrus stratum moleculare gyri dentati uberon molecular layer of the dentate gyrus UBERON:0004679 dentate gyrus molecular layer The molecular layer of the dentate gyrus that is bounded by the pial surface superficially and the dentate gyrus granule cell layer deep. It is divided into 2 or more sublayers. BIRNLEX:4127 dentate gyrus molecular layer BIRNLEX:4127 molecular layer of dentate gyrus FMA:83677 stratum moleculare gyri dentati FMA:83677 FMA:TA molecular layer of the dentate gyrus BAMS:Mol 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 the specialized epithelium of the Peyer's patch EMAPA:36506 MA:0000731 peyer's patch epithelium uberon UBERON:0004693 Peyer's patch epithelium the specialized epithelium of the Peyer's patch ISBN:0-8153-1691-7 MGI:cwg MP:0002388 peyer's patch epithelium MA:0000731 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 Area of the Peyer's patch where B cells proliferate and differentiate into plasma cells EMAPA:35684 MA:0000734 NCIT:C49600 UMLS:C1711398 uberon UBERON:0004697 Peyer's patch germinal center Area of the Peyer's patch where B cells proliferate and differentiate into plasma cells MP:0002391 UMLS:C1711398 ncithesaurus:Peyer_s_Patch_Germinal_Center 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 ring of fibrocartilage and fibrous tissue forming the circumference of the intervertebral disc; surrounds the nucleus pulposus, which is prone to herniation when the annulus fibrosus is compromised. annulus fibrosus BTO:0003629 EMAPA:32670 FMA:13551 MA:0000111 anulus fibrosus (diskus intervertebralis) anulus fibrosus of intervertebral disk uberon annulus fibrosus of intervertebral disc fibrous ring of intervertebral disc UBERON:0004715 annulus fibrosus disci intervertebralis http://upload.wikimedia.org/wikipedia/commons/d/d9/Cervical_vertebra_english.png The ring of fibrocartilage and fibrous tissue forming the circumference of the intervertebral disc; surrounds the nucleus pulposus, which is prone to herniation when the annulus fibrosus is compromised. BTO:0003629 annulus fibrosus MA:0000111 anulus fibrosus (diskus intervertebralis) FMA:13551 anulus fibrosus of intervertebral disk FMA:13551 annulus fibrosus of intervertebral disc BTO:0003629 fibrous ring of intervertebral disc BTO:0003629 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 Any of the veins that parallel the arcuate arteries, receive blood from the interlobular veins and straight venules, and terminate in the interlobar veins. arcuate vein EMAPA:28221 FMA:272193 FMA:321527 MA:0002593 arciform vein of kidney arcuate vein of kidney renal arcuate vein venae arcuatae renis uberon arcuate veins UBERON:0004719 kidney arcuate vein Kidney:PioM.png Any of the veins that parallel the arcuate arteries, receive blood from the interlobular veins and straight venules, and terminate in the interlobar veins. ISBN:0-683-40008-8 MP:0011325 arcuate vein MA:0002593 arciform vein of kidney MP:0011325 arcuate vein of kidney MP:0011325 renal arcuate vein MP:0011325 venae arcuatae renis arcuate veins The crista ampullaris is the sensory organ of rotation located in the semicircular canal of the inner ear. The function of the crista ampullaris is to sense angular acceleration and deceleration. EMAPA:32791 FMA:77714 MA:0002771 NCIT:C32063 UMLS:C0229465 ampullary crest of semicircular duct uberon ampullary crest cristae ampullares UBERON:0004721 crista ampullaris http://upload.wikimedia.org/wikipedia/commons/e/ec/Semicircular_canal_-_ampulla.png MA The crista ampullaris is the sensory organ of rotation located in the semicircular canal of the inner ear. The function of the crista ampullaris is to sense angular acceleration and deceleration. UMLS:C0229465 ncithesaurus:Ampullary_Crest ampullary crest of semicircular duct FMA:77714 ampullary crest MA:0002771 cristae ampullares The branches of the arcuate arteries of the kidney that radiate outward throught the renal columns and supply the glomeruli[MP]. The first set of renal bloodvessels, the interlobular arteries (or cortical radiate arteries, or cortical radial arteries), are given off at right angles from the side of the arcuate arteries looking toward the cortical substance, and pass directly outward between the medullary rays to reach the fibrous tunic, where they end in the capillary network of this part. These vessels do not anastomose with each other, but form what are called end-arteries. In their outward course they give off lateral branches; these are the afferent vessels for the renal corpuscles; they enter the capsule, and end in the glomerulus. From each tuft the corresponding efferent vessel arises, and, having made its egress from the capsule near to the point where the afferent vessel enters, breaks up into a number of branches, which form a dense plexus within Bowman's capsule. EMAPA:28212 FMA:70498 MA:0002584 NCIT:C32826 UMLS:C1512856 interlobular renal artery kidney interlobular artery uberon arteriae corticales radiatae arteriae interlobulares renis cortical radial arteries interlobular renal interlobular artery UBERON:0004723 interlobular artery http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png The branches of the arcuate arteries of the kidney that radiate outward throught the renal columns and supply the glomeruli[MP]. The first set of renal bloodvessels, the interlobular arteries (or cortical radiate arteries, or cortical radial arteries), are given off at right angles from the side of the arcuate arteries looking toward the cortical substance, and pass directly outward between the medullary rays to reach the fibrous tunic, where they end in the capillary network of this part. These vessels do not anastomose with each other, but form what are called end-arteries. In their outward course they give off lateral branches; these are the afferent vessels for the renal corpuscles; they enter the capsule, and end in the glomerulus. From each tuft the corresponding efferent vessel arises, and, having made its egress from the capsule near to the point where the afferent vessel enters, breaks up into a number of branches, which form a dense plexus within Bowman's capsule. MP:0011316 UMLS:C1512856 ncithesaurus:Interlobular_Artery interlobular renal artery FMA:70498 kidney interlobular artery MP:0011316 arteriae corticales radiatae arteriae interlobulares renis cortical radial arteries interlobular renal interlobular artery FMA:70498 In the blood supply of the kidney, the vasa recta renis (or straight arteries of kidney, or straight arterioles of kidney) form a series of straight capillaries in the medulla. They lie parallel to the loop of Henle. These vessels branch off the efferent arterioles of juxtamedullary nephrons (those nephrons closest to the medulla), enter the medulla, and surround the loop of Henle. TODO - is this a vein or set of veins? in MA it is a venous blood vessel EMAPA:30043 FMA:72006 MA:0002595 galen:ArteriaeRectae arteriolae rectae renis kidney vasa recta renal medullary capillary set of straight arterioles of kidney straight arterioles of kidney vasa recta of kidney vasa recta renis uberon arteria recta arteriae rectae arteriolae rectae renis arteriolae recti vasa rectae UBERON:0004726 vasa recta Kidney:nephron.png In the blood supply of the kidney, the vasa recta renis (or straight arteries of kidney, or straight arterioles of kidney) form a series of straight capillaries in the medulla. They lie parallel to the loop of Henle. These vessels branch off the efferent arterioles of juxtamedullary nephrons (those nephrons closest to the medulla), enter the medulla, and surround the loop of Henle. arteriolae rectae renis FMA:72006 FMA:TA kidney vasa recta MP:0011324 renal medullary capillary EMAPA:30043 set of straight arterioles of kidney FMA:72006 straight arterioles of kidney FMA:72006 vasa recta of kidney FMA:72006 vasa recta renis FMA:72006 FMA:TA arteria recta arteriae rectae arteriolae rectae renis arteriolae recti vasa rectae A nerve in the head that carries signals from the cochlea of the inner ear to the brain. It is part of the vestibulocochlear nerve, the 8th cranial nerve which is found in higher vertebrates; the other portion of the 8th cranial nerve is the vestibular nerve which carries spatial orientation information from the semicircular canals. The cochlear nerve is a sensory nerve, one which conducts to the brain information about the environment, in this case acoustic energy impinging on the tympanic membrane. The cochlear nerve arises from within the cochlea and extends to the brainstem, where its fibers make contact with the cochlear nucleus, the next stage of neural processing in the auditory system[WP]. cochlear component BAMS:cVIIIn BM:VIIIN BTO:0003490 EHDAA2:0002195 EMAPA:17802 FMA:53431 GAID:723 MA:0001110 MBA:948 MESH:D003056 NCIT:C12697 OpenCyc:Mx4rwIhQfZwpEbGdrcN5Y29ycA UMLS:C0009201 VHOG:0001182 auditory nerve cochlear root of acoustic nerve cochlear root of eighth cranial nerve vestibulocochlear VIII nerve cochlear component uberon nervus vestibulocochlearis vestibulocochlear nerve cochlear component UBERON:0004727 cochlear nerve A nerve in the head that carries signals from the cochlea of the inner ear to the brain. It is part of the vestibulocochlear nerve, the 8th cranial nerve which is found in higher vertebrates; the other portion of the 8th cranial nerve is the vestibular nerve which carries spatial orientation information from the semicircular canals. The cochlear nerve is a sensory nerve, one which conducts to the brain information about the environment, in this case acoustic energy impinging on the tympanic membrane. The cochlear nerve arises from within the cochlea and extends to the brainstem, where its fibers make contact with the cochlear nucleus, the next stage of neural processing in the auditory system[WP]. UMLS:C0009201 ncithesaurus:Cochlear_Nerve auditory nerve FMA:53431 cochlear root of acoustic nerve FMA:53431 cochlear root of eighth cranial nerve FMA:53431 vestibulocochlear VIII nerve cochlear component MA:0001110 nervus vestibulocochlearis BTO:0003490 vestibulocochlear nerve cochlear component EMAPA:17802 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 glomerulus of the mature vertebrate kidney, or metanephros. VHOG:0001242 glomerulus of metanephros uberon UBERON:0004736 metanephric glomerulus glomerulus of the mature vertebrate kidney, or metanephros. GO:0072224 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 juxtaglomerular apparatus of the mature vertebrate kidney, or metanephros. juxtaglomerular apparatus of metanephros uberon UBERON:0004738 metanephric juxtaglomerular apparatus true juxtaglomerular apparatus of the mature vertebrate kidney, or metanephros. GO:0072206 The glomus forms from the splanchnic intermediate mesoderm and is the vascularized filtration unit, filtering the blood before it enters the tubules. The glomus is external to the nephron and extends over more than one body segment. a glomus differs from a glomerulus in that each vascular glomus services several tubules Paired highly vascularized portion of the pronephros. Left and right glomeruli are fused at the midline. Begins to function between 40 and 48hpf. Drummond, 2000.[TAO] The teleost pronephros shares many essential features with the amphibian pronephros including its derivation from mesoderm associated with the coelom and the derivation of the glomerular blood supply from the medial dorsal aorta. However, unlike the pronephros of amphibians, which have an external glomus and tubules with nephrostomes open to the coelom, the mature teleost pronephros has no connection to the body cavity and instead functions as a closed system (reference 1); This variation in nephron types [with external glomeruli that open into the coelom and with internal glomeruli that do not connect with the coelom] and their pattern of distribution suggest an evolutionary sequence. Ancestral craniates probably had an external glomerulus and nephrostomes, as do the first few to develop in very primitive craniates. (...) The mechanism would become more efficient as the coelomic recess into which each glomerulus discharged became a part of the tubule, that is, grew around the glomerulus as a renal capsule. The glomerulus becomes internal. The nephrostomes were lost during subsequent evolution, leaving the type of renal tubule found in most vertebrates (reference 2).[well established][VHOG] GO treats glomus and pronephric glomerulus differently UBERON:0004191 AAO:0011049 TAO:0001557 VHOG:0001237 XAO:0000318 ZFA:0001557 glomerulus of pronephros glomus uberon corpuscle glomera pronephric glomera pronephric glomeruli pronephric glomus UBERON:0004739 pronephric glomerulus XAO The glomus forms from the splanchnic intermediate mesoderm and is the vascularized filtration unit, filtering the blood before it enters the tubules. The glomus is external to the nephron and extends over more than one body segment. GO:0072013 GOC:mtg_kidney_jan10 XAO:0000318 a glomus differs from a glomerulus in that each vascular glomus services several tubules ISBN:0073040584 Paired highly vascularized portion of the pronephros. Left and right glomeruli are fused at the midline. Begins to function between 40 and 48hpf. Drummond, 2000.[TAO] 2012-08-14 TAO:0001557 TAO ZFIN:curator The teleost pronephros shares many essential features with the amphibian pronephros including its derivation from mesoderm associated with the coelom and the derivation of the glomerular blood supply from the medial dorsal aorta. However, unlike the pronephros of amphibians, which have an external glomus and tubules with nephrostomes open to the coelom, the mature teleost pronephros has no connection to the body cavity and instead functions as a closed system (reference 1); This variation in nephron types [with external glomeruli that open into the coelom and with internal glomeruli that do not connect with the coelom] and their pattern of distribution suggest an evolutionary sequence. Ancestral craniates probably had an external glomerulus and nephrostomes, as do the first few to develop in very primitive craniates. (...) The mechanism would become more efficient as the coelomic recess into which each glomerulus discharged became a part of the tubule, that is, grew around the glomerulus as a renal capsule. The glomerulus becomes internal. The nephrostomes were lost during subsequent evolution, leaving the type of renal tubule found in most vertebrates (reference 2).[well established][VHOG] 2012-09-17 VHOG:0001237 VHOG PMID:9806915 Drummond IA, Majumdar A, Hentschel H, Elger M, Solnica-Krezel L, Schier AF, Neuhauss SCF, Stemple DL, Zwartkruis F, Rangini Z, Driever W, Fishman MC, Early development of the zebrafish pronephros and analysis of mutations affecting pronephric function. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.636 GO treats glomus and pronephric glomerulus differently GO glomus XAO:0000318 corpuscle XAO:0000318 glomera XAO:0000318 pronephric glomera VHOG:0001237 pronephric glomeruli VHOG:0001237 pronephric glomus VHOG:0001237 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 Replacement bone tissue that forms within cartilage[VSAO, modified]. the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type EMAPA:35304 MA:0002836 uberon UBERON:0004763 endochondral bone tissue Replacement bone tissue that forms within cartilage[VSAO, modified]. GO:0001958 VSAO:0000145 the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type MA 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 vasa recta that is part of a outer medulla of kidney [Automatically generated definition]. EMAPA:36560 MA:0002597 kidney outer medulla vasa recta kidney outer renal medulla vasa recta outer medulla of kidney vasa recta outer zone of medulla of kidney vasa recta outer zone of renal medulla vasa recta vasa recta of outer medulla of kidney vasa recta of outer renal medulla vasa recta of outer zone of medulla of kidney vasa recta of outer zone of renal medulla uberon UBERON:0004775 outer renal medulla vasa recta A vasa recta that is part of a outer medulla of kidney [Automatically generated definition]. OBOL:automatic kidney outer medulla vasa recta MP:0011330 kidney outer renal medulla vasa recta MP:0011330 outer medulla of kidney vasa recta OBOL:automatic outer zone of medulla of kidney vasa recta OBOL:automatic outer zone of renal medulla vasa recta OBOL:automatic vasa recta of outer medulla of kidney OBOL:automatic vasa recta of outer renal medulla OBOL:automatic vasa recta of outer zone of medulla of kidney OBOL:automatic vasa recta of outer zone of renal medulla OBOL:automatic A vasa recta that is part of a inner medulla of kidney [Automatically generated definition]. EMAPA:36559 MA:0002596 inner medulla of kidney vasa recta inner zone of medulla of kidney vasa recta inner zone of renal medulla vasa recta set of inner region of renal pyramids vasa recta vasa recta of inner medulla of kidney vasa recta of inner renal medulla vasa recta of inner zone of medulla of kidney vasa recta of inner zone of renal medulla vasa recta of set of inner region of renal pyramids uberon UBERON:0004776 inner renal medulla vasa recta A vasa recta that is part of a inner medulla of kidney [Automatically generated definition]. OBOL:automatic inner medulla of kidney vasa recta OBOL:automatic inner zone of medulla of kidney vasa recta OBOL:automatic inner zone of renal medulla vasa recta OBOL:automatic set of inner region of renal pyramids vasa recta OBOL:automatic vasa recta of inner medulla of kidney OBOL:automatic vasa recta of inner renal medulla OBOL:automatic vasa recta of inner zone of medulla of kidney OBOL:automatic vasa recta of inner zone of renal medulla OBOL:automatic vasa recta of set of inner region of renal pyramids OBOL:automatic 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 An urothelium that is part of a urethra [Automatically generated definition]. EMAPA:35896 MA:0001687 NCIT:C49310 UMLS:C1710585 urethra uroepithelium uroepithelium of urethra urothelium of urethra uberon UBERON:0004787 urethra urothelium An urothelium that is part of a urethra [Automatically generated definition]. OBOL:automatic UMLS:C1710585 ncithesaurus:Urethra_Transitional_Cell_Epithelium urethra uroepithelium OBOL:automatic uroepithelium of urethra OBOL:automatic urothelium of urethra OBOL:automatic the epithelial lining of the luminal space of the kidney pelvis EMAPA:28077 FMA:263264 MA:0002632 NCIT:C54556 UMLS:C1709899 kidney pelvis transitional epithelium kidney pelvis uroepithelium pelvis of ureter uroepithelium pelvis of ureter urothelium renal pelvis transitional epithelium renal pelvis uroepithelium renal pelvis urothelium transitional epithelium of kidney pelvis transitional epithelium of renal pelvis uroepithelium of kidney pelvis uroepithelium of pelvis of ureter uroepithelium of renal pelvis urothelium of kidney pelvis urothelium of pelvis of ureter urothelium of renal pelvis uberon pelvic urothelium UBERON:0004788 kidney pelvis urothelium the epithelial lining of the luminal space of the kidney pelvis MGI:csmith MP:0011336 UMLS:C1709899 ncithesaurus:Renal_Pelvis_Urothelium kidney pelvis transitional epithelium OBOL:automatic kidney pelvis uroepithelium OBOL:automatic pelvis of ureter uroepithelium OBOL:automatic pelvis of ureter urothelium OBOL:automatic renal pelvis transitional epithelium OBOL:automatic renal pelvis uroepithelium OBOL:automatic renal pelvis urothelium OBOL:automatic transitional epithelium of kidney pelvis OBOL:automatic transitional epithelium of renal pelvis FMA:263264 uroepithelium of kidney pelvis OBOL:automatic uroepithelium of pelvis of ureter OBOL:automatic uroepithelium of renal pelvis OBOL:automatic urothelium of kidney pelvis OBOL:automatic urothelium of pelvis of ureter OBOL:automatic urothelium of renal pelvis OBOL:automatic pelvic urothelium EMAPA:28077 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 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 The epithelial layer of the alveoli[MP]. The layer of cells covering the lining of the tiny air sacs at the end of the bronchioles[BTO]. BTO:0003511 EMAPA:35121 FMA:63915 MA:0001771 NCIT:C12867 alveolus epithelial tissue alveolus epithelium epithelial tissue of alveolus epithelium of alveolus epithelium of pulmonary alveolus pulmonary alveolar epithelium pulmonary alveolus epithelium uberon alveolar epithelium UBERON:0004821 pulmonary alveolus epithelium FMA FMA The epithelial layer of the alveoli[MP]. The layer of cells covering the lining of the tiny air sacs at the end of the bronchioles[BTO]. BTO:0003511 MP:0010898 alveolus epithelial tissue OBOL:automatic alveolus epithelium MA:0001771 epithelial tissue of alveolus OBOL:automatic epithelium of alveolus OBOL:automatic epithelium of pulmonary alveolus FMA:63915 pulmonary alveolar epithelium FMA:63915 pulmonary alveolus epithelium MP:0010898 alveolar epithelium EMAPA:35121 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 An alveolus that is part of a right lung [Automatically generated definition]. EMAPA:35997 MA:0001786 NCIT:C49278 UMLS:C1709959 alveolus of right lung uberon UBERON:0004861 right lung alveolus An alveolus that is part of a right lung [Automatically generated definition]. OBOL:automatic UMLS:C1709959 ncithesaurus:Right_Lung_Alveolus alveolus of right lung OBOL:automatic An alveolus that is part of a left lung [Automatically generated definition]. EMAPA:19182 MA:0001777 NCIT:C49251 UMLS:C1708673 alveolus of left lung alveolus of lobe of left lung uberon UBERON:0004862 left lung alveolus An alveolus that is part of a left lung [Automatically generated definition]. OBOL:automatic UMLS:C1708673 ncithesaurus:Left_Lung_Alveolus alveolus of left lung OBOL:automatic alveolus of lobe of left lung 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 Visceral endoderm, a population of extraembyonic endoderm, is an extraembryonic tissue that functions in a regulatory capacity but does not contribute directly to the formation of any adult organs[PMID:15905405]. primitive endoderm-derived tissue which remains in contact with and surrounds the extra-embryonic ectoderm and the epiblast and provides signals for the differentiation and patterning of the epiblast; a small number of visceral endoderm cells also contribute to the endoderm of the embryonic gut[MP]. Gilbert uses visceral endoderm as a synonym for primitive endoderm/hypoblast BTO:0003487 EMAPA:16058 uberon UBERON:0004877 visceral endoderm BTO Visceral endoderm, a population of extraembyonic endoderm, is an extraembryonic tissue that functions in a regulatory capacity but does not contribute directly to the formation of any adult organs[PMID:15905405]. primitive endoderm-derived tissue which remains in contact with and surrounds the extra-embryonic ectoderm and the epiblast and provides signals for the differentiation and patterning of the epiblast; a small number of visceral endoderm cells also contribute to the endoderm of the embryonic gut[MP]. MP:0011186 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 A the thin septum that separates adjacent pulmonary alveoli, containing connective tissue constituents of the respiratory tissue and the capillary network of the blood supply of the lung. BTO:0003149 EMAPA:35433 MA:0000421 NCIT:C49473 UMLS:C1706784 alveolar septum uberon septum interalveolare UBERON:0004893 interalveolar septum A the thin septum that separates adjacent pulmonary alveoli, containing connective tissue constituents of the respiratory tissue and the capillary network of the blood supply of the lung. LG:0012625 UMLS:C1706784 ncithesaurus:Alveolar_Septum alveolar septum septum interalveolare BTO:0003149 A wall that contains the alveoli part of wall in FMA UBERON:0008872 BTO:0002543 EMAPA:35120 FMA:14117 MA:0002568 NCIT:C13085 UMLS:C0225695 pulmonary alveolar wall pulmonary interalveolar septum wall of pulmonary alveolus uberon alveolus wall UBERON:0004894 alveolar wall A wall that contains the alveoli LG:0012626 MP:0010903 part of wall in FMA FMA UMLS:C0225695 ncithesaurus:Alveolar_Wall pulmonary alveolar wall FMA:14117 pulmonary interalveolar septum FMA:14117 wall of pulmonary alveolus FMA:14117 alveolus wall EMAPA:35120 Alveolar smooth muscle is a type of non-striated muscle, found within the walls of the alveolus EMAPA:35122 MA:0002759 uberon UBERON:0004895 alveolar smooth muscle Alveolar smooth muscle is a type of non-striated muscle, found within the walls of the alveolus LG:0012628 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 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 fundus of stomach [Automatically generated definition]. EMAPA:27153 FMA:17058 fundus gastricus (ventricularis) submucosa fundus of stomach submucosa stomach fundus submucosa submucosa of fundus gastricus (ventricularis) submucosa of stomach fundus uberon UBERON:0004933 submucosa of fundus of stomach A submucosa that is part of a fundus of stomach [Automatically generated definition]. OBOL:automatic fundus gastricus (ventricularis) submucosa OBOL:automatic fundus of stomach submucosa OBOL:automatic stomach fundus submucosa OBOL:automatic submucosa of fundus gastricus (ventricularis) OBOL:automatic submucosa of stomach fundus 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 trigone of urinary bladder [Automatically generated definition]. EMAPA:32304 FMA:17852 Lieutaud ' s trigone submucosa deep trigone submucosa submucosa of Lieutaud ' s trigone submucosa of deep trigone submucosa of trigone of bladder submucosa of urinary bladder trigone submucosa of vesical trigone trigone of bladder submucosa trigone of urinary bladder submucosa urinary bladder trigone submucosa vesical trigone submucosa uberon UBERON:0004944 submucosa of trigone of urinary bladder A submucosa that is part of a trigone of urinary bladder [Automatically generated definition]. OBOL:automatic Lieutaud ' s trigone submucosa OBOL:automatic deep trigone submucosa OBOL:automatic submucosa of Lieutaud ' s trigone OBOL:automatic submucosa of deep trigone OBOL:automatic submucosa of trigone of bladder OBOL:automatic submucosa of urinary bladder trigone OBOL:automatic submucosa of vesical trigone OBOL:automatic trigone of bladder submucosa OBOL:automatic trigone of urinary bladder submucosa OBOL:automatic urinary bladder trigone submucosa OBOL:automatic vesical trigone submucosa OBOL:automatic 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 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 fundus of stomach [Automatically generated definition]. EMAPA:27151 FMA:17053 fundus gastricus (ventricularis) mucosa fundus gastricus (ventricularis) mucosa of organ fundus gastricus (ventricularis) mucous membrane fundus gastricus (ventricularis) organ mucosa fundus of stomach mucosa fundus of stomach mucosa of organ fundus of stomach mucous membrane fundus of stomach organ mucosa mucosa of fundus gastricus (ventricularis) mucosa of organ of fundus gastricus (ventricularis) mucosa of organ of fundus of stomach mucosa of organ of stomach fundus mucosa of stomach fundus mucous membrane of fundus gastricus (ventricularis) mucous membrane of fundus of stomach mucous membrane of stomach fundus organ mucosa of fundus gastricus (ventricularis) organ mucosa of fundus of stomach organ mucosa of stomach fundus stomach fundus mucosa stomach fundus mucosa of organ stomach fundus mucous membrane stomach fundus organ mucosa uberon UBERON:0004994 mucosa of fundus of stomach A mucosa that is part of a fundus of stomach [Automatically generated definition]. OBOL:automatic fundus gastricus (ventricularis) mucosa OBOL:automatic fundus gastricus (ventricularis) mucosa of organ OBOL:automatic fundus gastricus (ventricularis) mucous membrane OBOL:automatic fundus gastricus (ventricularis) organ mucosa OBOL:automatic fundus of stomach mucosa OBOL:automatic fundus of stomach mucosa of organ OBOL:automatic fundus of stomach mucous membrane OBOL:automatic fundus of stomach organ mucosa OBOL:automatic mucosa of fundus gastricus (ventricularis) OBOL:automatic mucosa of organ of fundus gastricus (ventricularis) OBOL:automatic mucosa of organ of fundus of stomach OBOL:automatic mucosa of organ of stomach fundus OBOL:automatic mucosa of stomach fundus OBOL:automatic mucous membrane of fundus gastricus (ventricularis) OBOL:automatic mucous membrane of fundus of stomach OBOL:automatic mucous membrane of stomach fundus OBOL:automatic organ mucosa of fundus gastricus (ventricularis) OBOL:automatic organ mucosa of fundus of stomach OBOL:automatic organ mucosa of stomach fundus OBOL:automatic stomach fundus mucosa OBOL:automatic stomach fundus mucosa of organ OBOL:automatic stomach fundus mucous membrane OBOL:automatic stomach fundus 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 trigone of urinary bladder [Automatically generated definition]. FMA:17847 Lieutaud ' s trigone mucosa Lieutaud ' s trigone mucosa of organ Lieutaud ' s trigone mucous membrane Lieutaud ' s trigone organ mucosa deep trigone mucosa deep trigone mucosa of organ deep trigone mucous membrane deep trigone organ mucosa mucosa of Lieutaud ' s trigone mucosa of deep trigone mucosa of organ of Lieutaud ' s trigone mucosa of organ of deep trigone mucosa of organ of trigone of bladder mucosa of organ of trigone of urinary bladder mucosa of organ of urinary bladder trigone mucosa of organ of vesical trigone mucosa of trigone of bladder mucosa of urinary bladder trigone mucosa of vesical trigone mucous membrane of Lieutaud ' s trigone mucous membrane of deep trigone mucous membrane of trigone of bladder mucous membrane of trigone of urinary bladder mucous membrane of urinary bladder trigone mucous membrane of vesical trigone organ mucosa of Lieutaud ' s trigone organ mucosa of deep trigone organ mucosa of trigone of bladder organ mucosa of trigone of urinary bladder organ mucosa of urinary bladder trigone organ mucosa of vesical trigone trigone of bladder mucosa trigone of bladder mucosa of organ trigone of bladder mucous membrane trigone of bladder organ mucosa trigone of urinary bladder mucosa trigone of urinary bladder mucosa of organ trigone of urinary bladder mucous membrane trigone of urinary bladder organ mucosa urinary bladder trigone mucosa urinary bladder trigone mucosa of organ urinary bladder trigone mucous membrane urinary bladder trigone organ mucosa vesical trigone mucosa vesical trigone mucosa of organ vesical trigone mucous membrane vesical trigone organ mucosa uberon UBERON:0005009 mucosa of trigone of urinary bladder A mucosa that is part of a trigone of urinary bladder [Automatically generated definition]. OBOL:automatic Lieutaud ' s trigone mucosa OBOL:automatic Lieutaud ' s trigone mucosa of organ OBOL:automatic Lieutaud ' s trigone mucous membrane OBOL:automatic Lieutaud ' s trigone organ mucosa OBOL:automatic deep trigone mucosa OBOL:automatic deep trigone mucosa of organ OBOL:automatic deep trigone mucous membrane OBOL:automatic deep trigone organ mucosa OBOL:automatic mucosa of Lieutaud ' s trigone OBOL:automatic mucosa of deep trigone OBOL:automatic mucosa of organ of Lieutaud ' s trigone OBOL:automatic mucosa of organ of deep trigone OBOL:automatic mucosa of organ of trigone of bladder OBOL:automatic mucosa of organ of trigone of urinary bladder OBOL:automatic mucosa of organ of urinary bladder trigone OBOL:automatic mucosa of organ of vesical trigone OBOL:automatic mucosa of trigone of bladder OBOL:automatic mucosa of urinary bladder trigone OBOL:automatic mucosa of vesical trigone OBOL:automatic mucous membrane of Lieutaud ' s trigone OBOL:automatic mucous membrane of deep trigone OBOL:automatic mucous membrane of trigone of bladder OBOL:automatic mucous membrane of trigone of urinary bladder OBOL:automatic mucous membrane of urinary bladder trigone OBOL:automatic mucous membrane of vesical trigone OBOL:automatic organ mucosa of Lieutaud ' s trigone OBOL:automatic organ mucosa of deep trigone OBOL:automatic organ mucosa of trigone of bladder OBOL:automatic organ mucosa of trigone of urinary bladder OBOL:automatic organ mucosa of urinary bladder trigone OBOL:automatic organ mucosa of vesical trigone OBOL:automatic trigone of bladder mucosa OBOL:automatic trigone of bladder mucosa of organ OBOL:automatic trigone of bladder mucous membrane OBOL:automatic trigone of bladder organ mucosa OBOL:automatic trigone of urinary bladder mucosa OBOL:automatic trigone of urinary bladder mucosa of organ OBOL:automatic trigone of urinary bladder mucous membrane OBOL:automatic trigone of urinary bladder organ mucosa OBOL:automatic urinary bladder trigone mucosa OBOL:automatic urinary bladder trigone mucosa of organ OBOL:automatic urinary bladder trigone mucous membrane OBOL:automatic urinary bladder trigone organ mucosa OBOL:automatic vesical trigone mucosa OBOL:automatic vesical trigone mucosa of organ OBOL:automatic vesical trigone mucous membrane OBOL:automatic vesical trigone organ mucosa OBOL:automatic 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 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 lacrimal canaliculus [Automatically generated definition]. FMA:85366 lacrimal canalicular mucosa lacrimal canaliculus mucosa lacrimal canaliculus mucosa of organ lacrimal canaliculus mucous membrane lacrimal canaliculus organ mucosa mucosa of organ of lacrimal canaliculus mucous membrane of lacrimal canaliculus organ mucosa of lacrimal canaliculus uberon UBERON:0005029 mucosa of lacrimal canaliculus A mucosa that is part of a lacrimal canaliculus [Automatically generated definition]. OBOL:automatic lacrimal canalicular mucosa FMA:85366 lacrimal canaliculus mucosa OBOL:automatic lacrimal canaliculus mucosa of organ OBOL:automatic lacrimal canaliculus mucous membrane OBOL:automatic lacrimal canaliculus organ mucosa OBOL:automatic mucosa of organ of lacrimal canaliculus OBOL:automatic mucous membrane of lacrimal canaliculus OBOL:automatic organ mucosa of lacrimal canaliculus OBOL:automatic 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 mucosa that is part of a respiratory bronchiole [Automatically generated definition]. FMA:263238 bronchiolus respiratorius mucosa bronchiolus respiratorius mucosa of organ bronchiolus respiratorius mucous membrane bronchiolus respiratorius organ mucosa mucosa of bronchiolus respiratorius mucosa of organ of bronchiolus respiratorius mucosa of organ of respiratory bronchiole mucous membrane of bronchiolus respiratorius mucous membrane of respiratory bronchiole organ mucosa of bronchiolus respiratorius organ mucosa of respiratory bronchiole respiratory bronchiole mucosa respiratory bronchiole mucosa of organ respiratory bronchiole mucous membrane respiratory bronchiole organ mucosa uberon UBERON:0005041 mucosa of respiratory bronchiole A mucosa that is part of a respiratory bronchiole [Automatically generated definition]. OBOL:automatic bronchiolus respiratorius mucosa OBOL:automatic bronchiolus respiratorius mucosa of organ OBOL:automatic bronchiolus respiratorius mucous membrane OBOL:automatic bronchiolus respiratorius organ mucosa OBOL:automatic mucosa of bronchiolus respiratorius OBOL:automatic mucosa of organ of bronchiolus respiratorius OBOL:automatic mucosa of organ of respiratory bronchiole OBOL:automatic mucous membrane of bronchiolus respiratorius OBOL:automatic mucous membrane of respiratory bronchiole OBOL:automatic organ mucosa of bronchiolus respiratorius OBOL:automatic organ mucosa of respiratory bronchiole OBOL:automatic respiratory bronchiole mucosa OBOL:automatic respiratory bronchiole mucosa of organ OBOL:automatic respiratory bronchiole mucous membrane OBOL:automatic respiratory 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 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 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 The descending thin limb is a part of the loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the loop of Henle[GO]. UBERON:0005165 EMAPA:35514 FMA:17719 MA:0002625 descending thin limb of loop of Henle loop of Henle descending thin limb loop of Henle thin descending limb pars descendens (tubulus attenuatus) thin descending limb uberon descending limb of Henle's loop descending limb of loop of Henle thin descending limb of loop of Henle thin descending limb of the loop of Henle thin descending loop of Henle UBERON:0005096 descending thin limb http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png The descending thin limb is a part of the loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the loop of Henle[GO]. GO:0072022 loop of Henle thin descending limb MA:0002625 pars descendens (tubulus attenuatus) FMA:17719 descending limb of Henle's loop descending limb of loop of Henle thin descending limb of loop of Henle thin descending limb of the loop of Henle thin descending loop of Henle The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO]. BTO:0004539 EMAPA:27758 EMAPA:27790 EMAPA:28011 MA:0002610 connecting tubule kidney connecting tubule uberon tubulus renalis arcuatus UBERON:0005097 renal connecting tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png Wikipedia The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO]. GO:0072027 connecting tubule MA:0002610 kidney connecting tubule MA:0002610 tubulus renalis arcuatus 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 ascending thin limb is a segment of a nephron tubule in the metanephros lying in the inner medulla that is permeable to ions but not to water and has a simple epithelium; active transepithelial solute transport is absent[GO]. uberon UBERON:0005114 metanephric ascending thin limb The metanephric ascending thin limb is a segment of a nephron tubule in the metanephros lying in the inner medulla that is permeable to ions but not to water and has a simple epithelium; active transepithelial solute transport is absent[GO]. GO:0072218 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 It extends to the tip of the metanephric loop of Henle[GO]. uberon UBERON:0005116 metanephric descending thin limb true It extends to the tip of the metanephric loop of Henle[GO]. GO:0072220 The metanephric distal convoluted tubule is a portion of the metanephric nephron tubule that connects the metanephric loop of Henle to the collecting duct[GO]. VHOG:0001569 uberon UBERON:0005117 metanephric distal convoluted tubule true The metanephric distal convoluted tubule is a portion of the metanephric nephron tubule that connects the metanephric loop of Henle to the collecting duct[GO]. GO:0072221 The metanephric glomerular mesangium is the thin membrane connective tissue composed of mesangial cells in the metanephros, which helps to support the capillary loops in a renal glomerulus[GO]. uberon UBERON:0005119 metanephric glomerular mesangium true The metanephric glomerular mesangium is the thin membrane connective tissue composed of mesangial cells in the metanephros, which helps to support the capillary loops in a renal glomerulus[GO]. GO:0072223 The metanephric macula densa is an area of specialized cells in the distal tubule of the metanephros that makes contact with the vascular pole of the glomerulus[GO]. uberon UBERON:0005122 metanephric macula densa true The metanephric macula densa is an area of specialized cells in the distal tubule of the metanephros that makes contact with the vascular pole of the glomerulus[GO]. GO:0072227 The metanephric proximal convoluted tubule is the most proximal portion of the metanephric proximal tubule and extends from the metanephric glomerular capsule to the metanephric proximal straight tubule[GO]. VHOG:0001570 uberon UBERON:0005124 metanephric proximal convoluted tubule true The metanephric proximal convoluted tubule is the most proximal portion of the metanephric proximal tubule and extends from the metanephric glomerular capsule to the metanephric proximal straight tubule[GO]. GO:0072229 The metanephric proximal straight tubule is the part of the metanephric descending limb that extends from the metanephric proximal convoluted tubule to the metanephric descending thin tubule[GO]. TODO - place mammalian xrefs here rather than at parent uberon UBERON:0005125 metanephric proximal straight tubule true The metanephric proximal straight tubule is the part of the metanephric descending limb that extends from the metanephric proximal convoluted tubule to the metanephric descending thin tubule[GO]. GO:0072230 At the macula densa, the thick ascending limb connects to the distal convoluted tubule[GO]. uberon UBERON:0005127 metanephric thick ascending limb At the macula densa, the thick ascending limb connects to the distal convoluted tubule[GO]. GO:0072233 The metanephric distal tubule is a metanephric nephron tubule that begins at the metanephric macula densa and extends to the metanephric connecting tubule[GO]. UBERON:0005150 uberon UBERON:0005129 metanephric distal tubule The metanephric distal tubule is a metanephric nephron tubule that begins at the metanephric macula densa and extends to the metanephric connecting tubule[GO]. GO:0072235 The metanephric loop of Henle is a metanephric nephron tubule that connects the proximal convoluted tubule to the distal convoluted tubule in the metanephros[GO]. uberon UBERON:0005130 metanephric loop of Henle The metanephric loop of Henle is a metanephric nephron tubule that connects the proximal convoluted tubule to the distal convoluted tubule in the metanephros[GO]. GO:0072236 The metanephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the metanephric glomerulus[GO]. UBERON:0005143 uberon UBERON:0005133 metanephric glomerulus vasculature true The metanephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the metanephric glomerulus[GO]. GO:0072239 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 A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros[GO]. uberon UBERON:0005135 metanephric glomerular epithelium true A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros[GO]. GO:0072244 The metanephric glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus of the metanephros[GO]. uberon UBERON:0005136 metanephric glomerular endothelium true The metanephric glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus of the metanephros[GO]. GO:0072264 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 This process pertains to the initial formation of a structure from unspecified parts[GO]. uberon UBERON:0005144 metanephric glomerular capillary true This process pertains to the initial formation of a structure from unspecified parts[GO]. GO:0072277 The metanephric comma-shaped body is the precursor structure to the metanephric S-shaped body that contributes to the morphogenesis of a nephron in the metanephros[GO]. uberon UBERON:0005145 metanephric comma-shaped body The metanephric comma-shaped body is the precursor structure to the metanephric S-shaped body that contributes to the morphogenesis of a nephron in the metanephros[GO]. GO:0072278 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 The metanephric S-shaped body is the successor of the metanephric comma-shaped body that contributes to the morphogenesis of a nephron in the metanephros[GO]. uberon UBERON:0005148 metanephric S-shaped body true The metanephric S-shaped body is the successor of the metanephric comma-shaped body that contributes to the morphogenesis of a nephron in the metanephros[GO]. GO:0072284 The metanephric connecting tubule is a tubular segment of the metanephric nephron; it connects the distal convoluted tubule to the collecting duct in the metanephros[GO]. uberon UBERON:0005149 metanephric connecting tubule The metanephric connecting tubule is a tubular segment of the metanephric nephron; it connects the distal convoluted tubule to the collecting duct in the metanephros[GO]. GO:0072286 The metanephric proximal tubule is a metanephric nephron tubule that connects Bowman's capsule to the descending thin limb of the loop of Henle in the metanephros. It has a brush border epithelial morphology[GO]. UBERON:0005131 uberon UBERON:0005151 metanephric proximal tubule true The metanephric proximal tubule is a metanephric nephron tubule that connects Bowman's capsule to the descending thin limb of the loop of Henle in the metanephros. It has a brush border epithelial morphology[GO]. GO:0072288 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 An open tracheal system is a respiratory system, a branched network of epithelial tubes that supplies oxygen to target tissues via spiracles. An example of this is found in Drosophila melanogaster. tracheal system BTO:0003870 FBbt:00005024 SPD:0000427 TADS:0000043 invertebrate tracheal system open tracheal system uberon UBERON:0005155 open tracheal system An open tracheal system is a respiratory system, a branched network of epithelial tubes that supplies oxygen to target tissues via spiracles. An example of this is found in Drosophila melanogaster. GO:0007424 tracheal system FBbt:00005024 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 The distal part of the loop of Henle that is impermeable to water and actively pumps sodium out of the filtrate to generate the hypertonic interstitium that drives countercurrent exchange; it consists of an initial very thin segment lined by simple squamous epithelium followed by a distal thick segment lined by simple cuboidal epithelium[MP]. TODO - thick/thin check. Also relationship to distal tubule. We need a home for MA:0002634-renal straight tubule ascending limb EMAPA:35510 FMA:17717 MA:0001676 NCIT:C32154 UMLS:C0227658 ascending limb of Henle's loop loop of Henle ascending limb uberon distal straight tubule UBERON:0005164 ascending limb of loop of Henle The distal part of the loop of Henle that is impermeable to water and actively pumps sodium out of the filtrate to generate the hypertonic interstitium that drives countercurrent exchange; it consists of an initial very thin segment lined by simple squamous epithelium followed by a distal thick segment lined by simple cuboidal epithelium[MP]. MP:0011342 UMLS:C0227658 ncithesaurus:Ascending_Limb_of_the_Henle_s_Loop loop of Henle ascending limb MP:0011342 The terminal portions of the medullary collecting ducts are the papillary ducts, which end at the renal papilla and empty into a minor calyx. BTO:0004540 EMAPA:35655 MA:0001646 papillary duct papillary duct of kidney renal papillary duct uberon Bellini's duct duct of Bellini UBERON:0005167 papillary duct The terminal portions of the medullary collecting ducts are the papillary ducts, which end at the renal papilla and empty into a minor calyx. Bellini's duct MP:0011331 Any of the veins that parallel the interlobular arteries, receiving blood from the peritubular capillary plexus and empty into the arcuate veins EMAPA:28218 FMA:71634 MA:0002594 interlobular vein venae interlobulares renis uberon interlobular veins of kidney set of interlobular veins of kidney venae interlobulares renis UBERON:0005168 renal interlobular vein http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png Any of the veins that parallel the interlobular arteries, receiving blood from the peritubular capillary plexus and empty into the arcuate veins ISBN:0-683-40008-8 MP:0011326 interlobular vein MA:0002594 venae interlobulares renis FMA:71634 FMA:TA interlobular veins of kidney FMA:71634 set of interlobular veins of kidney FMA:71634 venae interlobulares renis connective tissue between the cellular elements of a structure. specify differentia from stroma interstital FMA:86301 interstitium uberon UBERON:0005169 interstitial tissue FMA connective tissue between the cellular elements of a structure. 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 germinal center that is part of the spleen. The spleen germinal center is located in a secondary B follicle in the white pulp of the spleen. EMAPA:35803 MA:0000764 NCIT:C49760 UMLS:C1710156 germinal center of spleen spleen GC spleen follicle center splenic germinal center uberon UBERON:0005196 spleen germinal center CL:tm A germinal center that is part of the spleen. The spleen germinal center is located in a secondary B follicle in the white pulp of the spleen. CL:tm UMLS:C1710156 ncithesaurus:Spleen_Germinal_Center spleen GC MP:0008474 spleen follicle center MP:0008474 splenic germinal center MP:0008474 A mammary gland that is part of a cervical region. mice have a single pair of cervical mammary glands MA:0000789 uberon UBERON:0005199 cervical mammary gland A mammary gland that is part of a cervical region. OBOL:automatic A lactiferous gland that is located in the thoracic region/breast. Most primates have one pair of mammary glands, which are thoracic. lactiferous gland mammary gland EHDAA2:0001056 EHDAA:6524 EMAPA:36633 FMA:62088 MA:0000797 breast mammary gland uberon anterior mammary gland UBERON:0005200 thoracic mammary gland BTO A lactiferous gland that is located in the thoracic region/breast. lactiferous gland FMA:62088 mammary gland FMA:62088 anterior mammary gland A macula densa that is part of an ascending limb of loop of Henle [Automatically generated definition]. TODO - unify terminology - check DST = TAL? Note EMAPA class appears to refer to this segment EMAPA:28399 MA:0002604 uberon UBERON:0005202 distal straight tubule macula densa MA MA A macula densa that is part of an ascending limb of loop of Henle [Automatically generated definition]. OBOL:automatic 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 tissue surrounding the loop of Henle in the renal medulla. It functions in renal water reabsorption by building up a high hypertonicity, which draws water out of the thin descending limb of the loop of Henle and the collecting duct system. This hypertonicity, in turn, is created by an efflux of urea from the inner medullary collecting duct. EMAPA:18326 MA:0002619 kidney medulla interstitium renal medullary interstitial tissue renal medullary interstitium medullary interstitium uberon medullary stroma UBERON:0005211 renal medulla interstitium tissue surrounding the loop of Henle in the renal medulla. kidney medulla interstitium MA:0002619 renal medullary interstitium EMAPA:18326 medullary interstitium medullary stroma EMAPA:18326 The male gonad containing two functional parts: the SEMINIFEROUS TUBULES for the production and transport of male germ cells (SPERMATOGENESIS) and the interstitial compartment containing LEYDIG CELLS that produce ANDROGENS.. EMAPA:18687 MA:0002713 interstitium of testis interstitium of the testis testis - interstitial testis interstitial tissue testis interstitium uberon UBERON:0005212 Leydig cell region of testis The male gonad containing two functional parts: the SEMINIFEROUS TUBULES for the production and transport of male germ cells (SPERMATOGENESIS) and the interstitial compartment containing LEYDIG CELLS that produce ANDROGENS.. MESH:A05.360.444.849 interstitium of testis interstitium of the testis EMAPA:18687 testis - interstitial testis interstitial tissue MA:0002713 testis interstitium A portion of interstitial tissue that is part of a outer medulla of kidney [Automatically generated definition]. EMAPA:28337 MA:0002621 kidney outer medulla interstitium outer medullary interstitium uberon UBERON:0005213 outer renal medulla interstitium MA A portion of interstitial tissue that is part of a outer medulla of kidney [Automatically generated definition]. OBOL:automatic kidney outer medulla interstitium MA:0002621 outer medullary interstitium EMAPA:28337 A portion of interstitial tissue that is part of a inner medulla of kidney [Automatically generated definition]. EMAPA:28364 MA:0002620 inner medullary interstitium kidney inner medulla interstitium uberon papillary interstitium UBERON:0005214 inner renal medulla interstitium MA A portion of interstitial tissue that is part of a inner medulla of kidney [Automatically generated definition]. OBOL:automatic inner medullary interstitium EMAPA:28364 kidney inner medulla interstitium MA:0002620 papillary interstitium EMAPA:28364 The interstitial compartment of the kidney, comprising the extravascular intertubular spaces of the renal parenchyma, with their attendant cellular elements and extracellular substances, bounded on all sides by epithelial and vascular basement membranes. See https://sourceforge.net/p/geneontology/ontology-requests/10941/ The interstitium is necessarily involved in all intrarenal exchange processes since the reabsorption and secretion of fluid and solutes implicates a transit across the interstitial compartment. The fibroblasts in the interstitium provide the 'skeleton' of the tissue and maintain the three-dimensional architecture of the tissue. EMAPA:28518 FMA:70983 MA:0002616 NCIT:C33459 interstitial tissue of kidney renal interstitial tissue renal interstitium renal stroma stroma of kidney uberon kidney interstitium group UBERON:0005215 kidney interstitium The interstitial compartment of the kidney, comprising the extravascular intertubular spaces of the renal parenchyma, with their attendant cellular elements and extracellular substances, bounded on all sides by epithelial and vascular basement membranes. renal interstitium FMA:70983 renal stroma FMA:70983 stroma of kidney FMA:70983 kidney interstitium group EMAPA:28518 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 medial nasal prominence [Automatically generated definition]. EHDAA2:0001078 EMAPA:16809 FMA:312675 VHOG:0000803 uberon UBERON:0005233 medial-nasal process ectoderm An ectoderm that is part of a medial nasal prominence [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 compartment of the renal cortex situated between basement membranes of epithelia and vessels that contains two contiguous cellular networks in mutual contact, one formed by interstitial fibroblasts, the other by dendritic cells. In the renal cortex, interstitial fibroblasts produce erythropoietin and are distinguished from other interstitial cells by their prominent F-actin cytoskeleton, abundance of rough endoplasmic reticulum, and by ecto-5'-nucleotidase expression in their plasma membrane. The resident dendritic cells belong to the mononuclear phagocyte system and fulfil a sentinel function. They are characterized by their expression of MHC class II and CD11c. EMAPA:28136 MA:0002608 kidney cortex interstitium renal cortical interstitial tissue uberon cortical stroma UBERON:0005270 renal cortex interstitium MA A compartment of the renal cortex situated between basement membranes of epithelia and vessels that contains two contiguous cellular networks in mutual contact, one formed by interstitial fibroblasts, the other by dendritic cells. In the renal cortex, interstitial fibroblasts produce erythropoietin and are distinguished from other interstitial cells by their prominent F-actin cytoskeleton, abundance of rough endoplasmic reticulum, and by ecto-5'-nucleotidase expression in their plasma membrane. The resident dendritic cells belong to the mononuclear phagocyte system and fulfil a sentinel function. They are characterized by their expression of MHC class II and CD11c. kidney cortex interstitium MA:0002608 cortical stroma EMAPA:28136 The part of the renal cortex nearest to the medulla. EMAPA:37623 FMA:74288 KUPO:0001008 MA:0001648 inner cortex of kidney inner renal cortex juxtamedullary cortex of kidney uberon UBERON:0005271 juxtamedullary cortex FMA KUPO The part of the renal cortex nearest to the medulla. EMAPA:37623 MA:th inner cortex of kidney FMA:74288 inner renal cortex KUPO:0001008 juxtamedullary cortex of kidney FMA:74288 the tiny blood vessels that receive blood from the efferent arterioles of the glomerulus, and interact with superficial cortical nephrons allowing reabsorption and secretion between blood and the inner lumen of the nephron; peritubular capillaries are situated around the tubule and are at low pressure EMAPA:36558 MA:0002588 uberon UBERON:0005272 peritubular capillary the tiny blood vessels that receive blood from the efferent arterioles of the glomerulus, and interact with superficial cortical nephrons allowing reabsorption and secretion between blood and the inner lumen of the nephron; peritubular capillaries are situated around the tubule and are at low pressure MGI:csmith MP:0011321 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 mammary placode is a transient lens shaped structure that will give rise to the mammary bud proper[GO]. TODO develops_from in mouse, five pairs of symmetrically positioned mammary placodes (three thoracic and two inguinal) form at reproducible locations along the mammary line at E11.5; the individual pairs develop asynchronously and in a distinct order; pair 3 is first, followed by pair 4, then by pairs 1 and 5 (which develop together), and finally by pair 2; the orientation of placodal cells is not uniform, suggesting that placodes are formed by migration of cells from the mammary line; between E11.5 and E12.5, each mammary placode expands and invaginates into the underlying mesenchyme to form an early bulb-shaped mammary bud[MP] EMAPA:35541 uberon mammary anlage UBERON:0005311 mammary placode NCBIBook:NBK53175 Stedmans The mammary placode is a transient lens shaped structure that will give rise to the mammary bud proper[GO]. GO:0060596 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 The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. uberon UBERON:0005320 mesonephric juxtaglomerular apparatus The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. GO:0061212 . 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 macula densa is an area of specialized cells in the distal tubule of the mesonephros that makes contact with the vascular pole of the glomerulus[GO]. uberon UBERON:0005324 mesonephric macula densa true The mesonephric macula densa is an area of specialized cells in the distal tubule of the mesonephros that makes contact with the vascular pole of the glomerulus[GO]. GO:0061220 The mesonephric glomerulus is a capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the mature vertebrate kidney, or mesonephros[GO]. A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated.[AAO] In animals in which the mesonephros is the terminal kidney, such as amphibians and fish, the final organ is very complex, containing a large number of nephrons, most of which have an internal glomerulus.[well established][VHOG] XAO/AAO class belongs here, as it refers to mesonephric structure glomerulus AAO:0010388 EMAPA:30568 VHOG:0001238 XAO:0000146 uberon UBERON:0005325 mesonephric glomerulus The mesonephric glomerulus is a capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the mature vertebrate kidney, or mesonephros[GO]. GO:0061224 A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated.[AAO] 2012-06-20 AAO:0010388 AAO AAO:BJB In animals in which the mesonephros is the terminal kidney, such as amphibians and fish, the final organ is very complex, containing a large number of nephrons, most of which have an internal glomerulus.[well established][VHOG] 2012-09-17 VHOG:0001238 VHOG ISBN:978-0127224411 Vize PD, Woolf AS, Bard JBL, The kidney: From normal development to congenital disease (2003) p.3 XAO/AAO class belongs here, as it refers to mesonephric structure XAO glomerulus AAO:0010388 The mesonephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the mesonephric glomerulus[GO]. uberon UBERON:0005326 mesonephric glomerulus vasculature true The mesonephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the mesonephric glomerulus[GO]. GO:0061231 A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the mesonephros[GO]. uberon UBERON:0005327 mesonephric glomerular epithelium true A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the mesonephros[GO]. GO:0061232 The mesonephric comma-shaped body is the precursor structure to the mesonephric S-shaped body that contributes to the morphogenesis of a nephron in the mesonephros[GO]. uberon UBERON:0005328 mesonephric comma-shaped body The mesonephric comma-shaped body is the precursor structure to the mesonephric S-shaped body that contributes to the morphogenesis of a nephron in the mesonephros[GO]. GO:0061236 A mesonephric nephron tubule is an epithelial tube that is part of the mesonephric nephron, the functional part of the mesonephros[GO]. mesonephric renal tubule uberon UBERON:0005329 mesonephric nephron tubule A mesonephric nephron tubule is an epithelial tube that is part of the mesonephric nephron, the functional part of the mesonephros[GO]. GO:0061240 mesonephric renal tubule 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 The mesonephric S-shaped body is the successor of the mesonephric comma-shaped body that contributes to the morphogenesis of a nephron in the mesonephros[GO]. uberon UBERON:0005332 mesonephric S-shaped body The mesonephric S-shaped body is the successor of the mesonephric comma-shaped body that contributes to the morphogenesis of a nephron in the mesonephros[GO]. GO:0061244 A bulb of epithelial cells that forms from the mammary placode that develops into the mammary gland. produced along the length of the embryonic mammary ridge these buds represent the future locations of the mammary glands. Invagination of ectoderm at each bud leads to the development of epithelial diverticula, later maturing as lactiferous ducts UBERON:0004181 EMAPA:35536 lactiferous gland bud mammary gland bud uberon mammary primordium milk bud UBERON:0005333 mammary bud A bulb of epithelial cells that forms from the mammary placode that develops into the mammary gland. produced along the length of the embryonic mammary ridge these buds represent the future locations of the mammary glands. Invagination of ectoderm at each bud leads to the development of epithelial diverticula, later maturing as lactiferous ducts mammary gland bud GO:0060648 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 The lobe at the anterior part of each cerebral hemisphere, responsible for olfactory functions. Part of the telencephalon, comprised of paired anterior outgrowths of either of the cerebral hemispheres in which the olfactory nerve exits. In Xenopus,the olfactory bulbs begin to fuse at NF stage 50, fusion is complete around NF stage 58. The cerebral vein loops around the olfactory bulb by NF stage 43[XAO:0004180]. (In mammals) Odorant detection is mediated by millions of olfactory sensory neurons located in the olfactory epithelium lining the nasal cavity. These neurons transmit sensory signals to the olfactory bulb of the brain, which in turn sends signals to the olfactory cortex.[well established][VHOG] BTO:0001362 EFO:0000108 EHDAA2_RETIRED:0001294 EHDAA:5480 EMAPA:17778 MA:0002413 MIAA:0000116 NCIT:C33204 UMLS:C0178780 VHOG:0000833 uberon UBERON:0005366 olfactory lobe The lobe at the anterior part of each cerebral hemisphere, responsible for olfactory functions. UBERON:cjm Part of the telencephalon, comprised of paired anterior outgrowths of either of the cerebral hemispheres in which the olfactory nerve exits. In Xenopus,the olfactory bulbs begin to fuse at NF stage 50, fusion is complete around NF stage 58. The cerebral vein loops around the olfactory bulb by NF stage 43[XAO:0004180]. XAO:0004180 (In mammals) Odorant detection is mediated by millions of olfactory sensory neurons located in the olfactory epithelium lining the nasal cavity. These neurons transmit sensory signals to the olfactory bulb of the brain, which in turn sends signals to the olfactory cortex.[well established][VHOG] 2012-09-17 VHOG:0000833 VHOG DOI:10.1111/j.1753-4887.2004.tb00097.x Buck LB, Olfactory receptors and odor coding in mammals. Nutrition Reviews (2008) UMLS:C0178780 ncithesaurus:Olfactory_Lobe Layer that is part of the CA fields of the hippocampus consisting of a narrow relatively cell free layer located deep to the pyramidal cell layer extending through areas CA1, CA2 and CA3. (adapted from Paxinos The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995) BAMS:Or BIRNLEX:4113 EMAPA:35412 FMA:83893 MA:0000958 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=157 oriens layer of hippocampus oriens layer of the hippocampus polymorphic layer of hippocampus polymorphic layer of the hippocampus stratum oriens stratum oriens hippocampi uberon gyrus cuneus UBERON:0005371 hippocampus stratum oriens Layer that is part of the CA fields of the hippocampus consisting of a narrow relatively cell free layer located deep to the pyramidal cell layer extending through areas CA1, CA2 and CA3. (adapted from Paxinos The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995) BIRNLEX:4113 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=157 BIRNLEX:4113 oriens layer of hippocampus BIRNLEX:4113 oriens layer of the hippocampus BIRNLEX:4113 polymorphic layer of hippocampus BIRNLEX:4113 polymorphic layer of the hippocampus BIRNLEX:4113 stratum oriens BIRNLEX:4113 stratum oriens hippocampi FMA:83893 FMA:TA gyrus cuneus NeuroNames:157 The layer located immediately above the pyramidal cell layer in CA2 and CA1 and superficial to the stratum lucidum in CA3. Suprapyramidal region in which CA3 to CA3 associational connections and CA3 to CA1 Schaffer collateral connections are located. contains septal and commissural fibers. It also contains Schaffer collateral fibers, which are the projection forward from CA3 to CA1. Some interneurons that can be found in more superficial layers can also be found here, including basket cells, bistratified cells, and radial trilaminar cells BAMS:Rad BIRNLEX:1298 EMAPA:35413 FMA:83894 MA:0000959 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=158 radiate layer of hippocampus stratum radiatum stratum radiatum hippocampi uberon stratum radiatum of the hippocampus UBERON:0005372 hippocampus stratum radiatum The layer located immediately above the pyramidal cell layer in CA2 and CA1 and superficial to the stratum lucidum in CA3. Suprapyramidal region in which CA3 to CA3 associational connections and CA3 to CA1 Schaffer collateral connections are located. BIRNLEX:1298 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=158 BIRNLEX:1298 radiate layer of hippocampus FMA:83894 stratum radiatum BIRNLEX:1298 stratum radiatum hippocampi FMA:83894 FMA:TA stratum radiatum of the hippocampus BAMS:Rad the area of white matter of the spinal cord located on either side of the ventral (anterior) medial fissure The ventral ridge of gray matter in each half of the spinal cord. [TFD][VHOG] in MA, this is a subclass of white matter, but in WP/Gray's, the anterior column is a synonym of the grey matter section. is this the same as funiculus? See lateral column. EV:0100326 MA:0002751 VHOG:0001622 anterior column spinal cord anterior column ventral column uberon UBERON:0005375 spinal cord ventral column the area of white matter of the spinal cord located on either side of the ventral (anterior) medial fissure ISBN:0-683-40008-8 MP:0009679 The ventral ridge of gray matter in each half of the spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0001622 VHOG in MA, this is a subclass of white matter, but in WP/Gray's, the anterior column is a synonym of the grey matter section. is this the same as funiculus? See lateral column. MA Cytoarchitectural part of the olfactory bulb, lying superior to the mitral cell layer and inferior to the glomerular layer. The EPL is mostly neuropil composed almost entirely of mitral and tulfted cell dendrites and granule cell dendrites and their synaptic inputs. external plexiform layer BAMS:EPl BTO:0001319 DMBA:15913 EMAPA:35607 MA:0000969 NLXANAT:20090403 olfactory bulb main external plexiform layer uberon EPL OB outer plexiform layer external plexiform layer of the olfactory bulb UBERON:0005376 olfactory bulb external plexiform layer Cytoarchitectural part of the olfactory bulb, lying superior to the mitral cell layer and inferior to the glomerular layer. The EPL is mostly neuropil composed almost entirely of mitral and tulfted cell dendrites and granule cell dendrites and their synaptic inputs. NLXANAT:20090403 external plexiform layer BTO:0001319 olfactory bulb main external plexiform layer NLXANAT:20090403 EPL BTO:0001319 OB outer plexiform layer DMBA:OB-Opl external plexiform layer of the olfactory bulb BAMS:EPl The glomerular layer is the most superficial layer, consisting of mitral cell dendritic arborizations (glomeruli), olfactory nerve fibers, and periglomerular cells. Periglomerular cells contact multiple mitral cell dendrites within the glomeruli and provide lateral inhibition of neighboring glomeruli while allowing excitation of a specific mitral cell dendritic tree. Each mitral cell is contacted by at least 1000 olfactory nerve fibers[BTO]. Portion of tissue which is located in between the primary olfactory fiber layer and the external cellular layer of the olfactory bulb[ZFA]. glomerular layer BAMS:Gl BTO:0001317 DHBA:11327 EMAPA:35608 MA:0000970 MBA:212 NLXANAT:1005007 TAO:0000357 ZFA:0000357 olfactory bulb main glomerulus stratum glomerulosum bulbi olfactorii uberon glomerular layer of the olfactory bulb UBERON:0005377 olfactory bulb glomerular layer The glomerular layer is the most superficial layer, consisting of mitral cell dendritic arborizations (glomeruli), olfactory nerve fibers, and periglomerular cells. Periglomerular cells contact multiple mitral cell dendrites within the glomeruli and provide lateral inhibition of neighboring glomeruli while allowing excitation of a specific mitral cell dendritic tree. Each mitral cell is contacted by at least 1000 olfactory nerve fibers[BTO]. Portion of tissue which is located in between the primary olfactory fiber layer and the external cellular layer of the olfactory bulb[ZFA]. BTO:0001317 glomerular layer BTO:0001317 ZFA:0000357 olfactory bulb main glomerulus NLXANAT:1005007 stratum glomerulosum bulbi olfactorii ZFA:0000357 glomerular layer of the olfactory bulb BAMS:Gl Granule cell layer is also called the DG principal cell layer. This one of the three layers of dentate gyrus that lies deep to the molecular layer and is made of densely packed layer that is four to eight granule cells thick. BAMS:DG-sg BAMS:GrDG BAMS:sg BIRNLEX:4129 DMBA:16122 EMAPA:35276 FMA:83146 MA:0000946 MBA:632 DG granule cell layer granular layer of dentate gyrus stratum granulare gyri dentati uberon dentate gyrus, granule cell layer granular layer of the dentate gyrus UBERON:0005381 dentate gyrus granule cell layer Granule cell layer is also called the DG principal cell layer. This one of the three layers of dentate gyrus that lies deep to the molecular layer and is made of densely packed layer that is four to eight granule cells thick. BIRNLEX:4129 DG granule cell layer BIRNLEX:4129 granular layer of dentate gyrus FMA:83146 stratum granulare gyri dentati FMA:83146 FMA:TA dentate gyrus, granule cell layer BAMS:DG-sg granular layer of the dentate gyrus BAMS:GrDG 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 epithelium that is part of the respiratory segment of the nasal mucosa [Automatically generated definition]. EHDAA2:0001230 EHDAA:6807 EMAPA:17607 MA:0001326 NCIT:C49262 UMLS:C1709152 uberon UBERON:0005385 nasal cavity respiratory epithelium An epithelium that is part of the respiratory segment of the nasal mucosa [Automatically generated definition]. OBOL:automatic UMLS:C1709152 ncithesaurus:Nasal_Cavity_Respiratory_Epithelium That portion of the nasal mucosa containing the sensory endings for olfaction; the organ of smell[MESH]. The olfactory mucosa is located in the upper region of the nasal cavity and is made up of the olfactory epithelium and the underlying lamina propria, connective tissue containing fibroblasts, blood vessels, Bowman's glands and bundles of fine axons from the olfactory neurons. The mucus protects the olfactory epithelium and allows odors to dissolve so that they can be detected by olfactory receptor neurons. Electron microscopy studies show that Bowman's glands contain cells with large secretory vesicles. The exact composition of the secretions from Bowman's glands is unclear, but there is evidence that Bowman's glands do not produce odorant binding protein[WP][Wikipedia:Olfactory_mucosa]. CALOHA:TS-2197 EMAPA:37918 FMA:77199 GAID:303 MESH:D009831 NCIT:C33205 UMLS:C0028937 olfactory area of nasal mucosa olfactory mucosa olfactory part of nasal mucosa olfactory zone of nasal mucosa pars olfactoria tunicae mucosae nasi uberon pars olfactoria tunicae mucosae nasi UBERON:0005386 olfactory segment of nasal mucosa That portion of the nasal mucosa containing the sensory endings for olfaction; the organ of smell[MESH]. MESH:A04.531.520.573 The olfactory mucosa is located in the upper region of the nasal cavity and is made up of the olfactory epithelium and the underlying lamina propria, connective tissue containing fibroblasts, blood vessels, Bowman's glands and bundles of fine axons from the olfactory neurons. The mucus protects the olfactory epithelium and allows odors to dissolve so that they can be detected by olfactory receptor neurons. Electron microscopy studies show that Bowman's glands contain cells with large secretory vesicles. The exact composition of the secretions from Bowman's glands is unclear, but there is evidence that Bowman's glands do not produce odorant binding protein[WP][Wikipedia:Olfactory_mucosa]. EMAPA:37918 MA:th UMLS:C0028937 ncithesaurus:Olfactory_Mucosa olfactory area of nasal mucosa FMA:77199 olfactory part of nasal mucosa FMA:77199 olfactory zone of nasal mucosa FMA:77199 pars olfactoria tunicae mucosae nasi FMA:77199 FMA:TA pars olfactoria tunicae mucosae nasi 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. The most superficial layer of the neocortex characterized by a paucity of cell bodies. ABA:CTX1 BTO:0004906 EMAPA:35255 FMA:83900 MA:0000897 NCIT:C33137 NLXANAT:090807 PBA:294021786 UMLS:C1709063 cerebral cortex, layer 1 lamina molecularis isocorticis [lamina I] layer 1 of neocortex layer I of neocortex molecular layer of cerebral cortex molecular layer of isocortex [layer i] molecular layer of neocortex neocortex layer 1 neocortex layer I neocortex molecular layer neocortex plexiform layer plexiform layer of neocortex uberon molecular layer plexiform layer UBERON:0005390 cortical layer I NBK10047 The most superficial layer of the neocortex characterized by a paucity of cell bodies. NLXANAT:090807 UMLS:C1709063 ncithesaurus:Molecular_Layer cerebral cortex, layer 1 ABA:CTX1 lamina molecularis isocorticis [lamina I] FMA:83900 FMA:TA layer 1 of neocortex NLXANAT:090807 layer I of neocortex NLXANAT:090807 molecular layer of cerebral cortex ncithesaurus:Molecular_layer molecular layer of isocortex [layer i] FMA:83900 molecular layer of neocortex FMA:83900 molecular layer of neocortex NLXANAT:090807 neocortex layer 1 NLXANAT:090807 neocortex layer I NLXANAT:090807 neocortex molecular layer NLXANAT:090807 neocortex plexiform layer NLXANAT:090807 plexiform layer of neocortex NLXANAT:090807 Layer of neocortex lying just deep to molecular layer characterized by numerous small cell bodies. ABA:CTX2 EMAPA:35256 FMA:77804 MA:0000898 NCIT:C32557 NLXANAT:090808 PBA:294021800 UMLS:C1517039 cerebral cortex, layer 2 external granular layer of isocortex [layer II] external granular layer of neocortex external granule cell layer of neocortex lamina granularis externa isocorticis [lamina ii] layer II of neocortex neocortex layer 2 neocortex layer II uberon EGL external granular cell layer external granular layer external granular layer of cerebral cortex external granule cell layer granule cell layer of cerebral cortex UBERON:0005391 cortical layer II BRAINSPAN Layer of neocortex lying just deep to molecular layer characterized by numerous small cell bodies. NLXANAT:090808 UMLS:C1517039 ncithesaurus:External_Granular_Layer cerebral cortex, layer 2 ABA:CTX2 external granular layer of isocortex [layer II] FMA:77804 external granular layer of neocortex FMA:77804 external granule cell layer of neocortex NLXANAT:090808 lamina granularis externa isocorticis [lamina ii] FMA:77804 FMA:TA layer II of neocortex NLXANAT:090808 neocortex layer 2 NLXANAT:090808 neocortex layer II NLXANAT:090808 EGL Layer of neocortex lying deep to the external granule cell layer defined cytoarchitecturally by numerous small pyramidal neurons. ABA:CTX3 EMAPA:35257 FMA:77810 MA:0000899 NCIT:C32571 NLXANAT:090809 PBA:294021824 UMLS:C1517046 cerebral cortex, layer 3 external pyramidal cell layer external pyramidal cell layer of neocortex external pyramidal layer of isocortex [layer iii] external pyramidal layer of neocortex lamina pyramidalis externa isocorticis [lamina iii] layer 3 of neocortex layer III of neocortex neocortex external pyramidal cell layer neocortex layer 3 neocortex layer III uberon external pyramidal layer of cerebral cortex isocortex, deep supragranular pyramidal layer lamina pyramidalis externa layer of medium-sized and large pyramidal cells pyramidal layer UBERON:0005392 cortical layer III BRAINSPAN Layer of neocortex lying deep to the external granule cell layer defined cytoarchitecturally by numerous small pyramidal neurons. NLXANAT:090809 UMLS:C1517046 ncithesaurus:External_Pyramidal_Cell_Layer cerebral cortex, layer 3 ABA:CTX3 external pyramidal cell layer FMA:77810 external pyramidal cell layer of neocortex NLXANAT:090809 external pyramidal layer of isocortex [layer iii] FMA:77810 external pyramidal layer of neocortex FMA:77810 lamina pyramidalis externa isocorticis [lamina iii] FMA:77810 FMA:TA layer 3 of neocortex NLXANAT:090809 layer III of neocortex NLXANAT:090809 neocortex external pyramidal cell layer NLXANAT:090809 neocortex layer 3 NLXANAT:090809 neocortex layer III NLXANAT:090809 external pyramidal layer of cerebral cortex ncithesaurus:External_Pyramidal_Cell_Layer isocortex, deep supragranular pyramidal layer NeuroNames:2448 lamina pyramidalis externa NeuroNames:2448 layer of medium-sized and large pyramidal cells NeuroNames:2448 Layer of neocortex lying deep to the external pyramidal cell layer defined cytoarchitecturally by the presence of numerous small cells ... Relatively undeveloped in some mammals such as the tenrec. ABA:CTX4 EMAPA:35258 FMA:77811 MA:0000900 NCIT:C32844 NLXANAT:090810 PBA:294021852 UMLS:C1512872 cerebral cortex, layer 4 internal granular layer of isocortex [layer iv] internal granular layer of neocortex internal granule cell layer of neocortex lamina granularis interna isocorticis [lamina iv] layer 4 of neocortex layer IV of neocortex neocortex internal granule cell layer neocortex layer 4 neocortex layer IV neocortical internal granule cell layer neocortical layer IV uberon internal granular layer UBERON:0005393 cortical layer IV BRAINSPAN Layer of neocortex lying deep to the external pyramidal cell layer defined cytoarchitecturally by the presence of numerous small cells NLXANAT:090810 ... Relatively undeveloped in some mammals such as the tenrec. ISBN:0471888893 UMLS:C1512872 ncithesaurus:Internal_Granular_Layer cerebral cortex, layer 4 ABA:CTX4 internal granular layer of isocortex [layer iv] FMA:77811 internal granular layer of neocortex FMA:77811 internal granule cell layer of neocortex NLXANAT:090810 lamina granularis interna isocorticis [lamina iv] FMA:77811 FMA:TA layer 4 of neocortex NLXANAT:090810 layer IV of neocortex NLXANAT:090810 neocortex internal granule cell layer NLXANAT:090810 neocortex layer 4 NLXANAT:090810 neocortex layer IV NLXANAT:090810 neocortical internal granule cell layer NLXANAT:090810 neocortical layer IV NLXANAT:090810 Layer of neocortex lying deep to the internal granule cell layer (layer 4) defined cytoarchitecturally by the predominance of large pyramidal cell bodies ABA:CTX5 EMAPA:35259 FMA:77812 MA:0000901 NCIT:C32653 NLXANAT:090811 PBA:294021878 UMLS:C1517447 betz' cells cerebral cortex, layer 5 internal pyramidal cell layer of neocortex internal pyramidal layer of isocortex [layer v] internal pyramidal layer of neocortex lamina pyramidalis interna isocorticis [lamina v] layer 5 of neocortex layer V of neocortex neocortex internal pyramidal cell layer neocortex layer 5 neocortex layer V neocortical layer 5 neocortical layer V uberon deep layer of large pyramidal cells ganglionic layer ganglionic layer of cerebral cortex inner layer of large pyramidal cells internal pyramidal layer isocortex, infragranular pyramidal layer lamina ganglionaris lamina pyramidalis interna UBERON:0005394 cortical layer V BRAINSPAN Layer of neocortex lying deep to the internal granule cell layer (layer 4) defined cytoarchitecturally by the predominance of large pyramidal cell bodies NLXANAT:090811 UMLS:C1517447 ncithesaurus:Ganglionic_Layer betz' cells FMA:77812 cerebral cortex, layer 5 ABA:CTX5 internal pyramidal cell layer of neocortex NLXANAT:090811 internal pyramidal layer of isocortex [layer v] FMA:77812 internal pyramidal layer of neocortex FMA:77812 lamina pyramidalis interna isocorticis [lamina v] FMA:77812 FMA:TA layer 5 of neocortex NLXANAT:090811 layer V of neocortex NLXANAT:090811 neocortex internal pyramidal cell layer NLXANAT:090811 neocortex layer 5 NLXANAT:090811 neocortex layer V NLXANAT:090811 neocortical layer 5 NLXANAT:090811 neocortical layer V NLXANAT:090811 deep layer of large pyramidal cells NeuroNames:2450 inner layer of large pyramidal cells NeuroNames:2450 internal pyramidal layer NeuroNames:2450 isocortex, infragranular pyramidal layer NeuroNames:2450 lamina ganglionaris NeuroNames:2450 lamina pyramidalis interna NeuroNames:2450 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 The adipose capsule of kidney (or perinephric fat or perirenal fat) is a structure between the renal fascia and renal capsule, and may be regarded as a part of the latter. A different structure, the pararenal fat, is the adipose tissue superficial to the renal fascia. TODO - split perinephric / perirenal EMAPA:36495 FMA:15876 FMA:20502 MA:0002975 perirenal fascia uberon adipose capsule of kidney capsula adiposa renis fatty capsule of kidney perinephric fat periphrenic fascia perirenal fascia perirenal fat capsule perirenal fat pad UBERON:0005406 perirenal fat Illu:kidney.jpg The adipose capsule of kidney (or perinephric fat or perirenal fat) is a structure between the renal fascia and renal capsule, and may be regarded as a part of the latter. A different structure, the pararenal fat, is the adipose tissue superficial to the renal fascia. perirenal fascia FMA:20502 adipose capsule of kidney MA:0002975 capsula adiposa renis fatty capsule of kidney MA:0002975 perinephric fat MA:0002975 periphrenic fascia MA:0002975 perirenal fascia MA:0002975 perirenal fat capsule MA:0002975 perirenal fat pad 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 otic capsule endochondral element that is composed primarily of cartilage tissue. Bilaterally paired cartilage encasing the semicircular canals of the inner ear.[TAO] relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: develops_from neurocranium (UBERON:0001703)[TAO] relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: part_of neurocranium (UBERON:0001703)[TAO] In elasmobranchs, the otic capsule remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans). todo - check EMAPA UBERON:0010351 EHDAA2:0001333 EHDAA:4704 EMAPA:17596 EMAPA:18803 EMAPA:37467 TAO:0001500 ZFA:0001500 auditory capsule otic capsule cartilage element uberon UBERON:0005410 cartilaginous otic capsule EHDAA2 A otic capsule endochondral element that is composed primarily of cartilage tissue. OBOL:automatic Bilaterally paired cartilage encasing the semicircular canals of the inner ear.[TAO] 2012-08-14 TAO:0001500 TAO ZFIN:curator relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: develops_from neurocranium (UBERON:0001703)[TAO] 2012-08-14 TAO:0001500 TAO relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: part_of neurocranium (UBERON:0001703)[TAO] 2012-08-14 TAO:0001500 TAO EMAPA:37467 MA:th auditory capsule ZFA:0001500 the cartilage or bony capsule surrounding the inner ear mechanism In elasmobranchs, the otic capsule remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans) EMAPA:17596 EMAPA:37466 MA:0000252 otic capsule bone uberon UBERON:0005411 bony otic capsule EHDAA2 the cartilage or bony capsule surrounding the inner ear mechanism ISBN:0-683-40008-8 MP:0000039 EMAPA:37466 MA:th 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 outer layer of the optic cup and will become the retinal pigmented epithelium. (...) 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] EHDAA2:0001306 EMAPA:16677 TAO:0000064 VHOG:0000492 ZFA:0000064 future RPE future retinal pigmented epithelium optic cup outer layer outer layer optic cup presumptive pigmented epithelia uberon future PRE future pigmented layer future pigmented retinal epithelium presumptive pigmented epithelium UBERON:0005424 presumptive retinal pigmented epithelium Portion of tissue that is the outer layer of the optic cup and will become the retinal pigmented epithelium. 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:0000492 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 optic cup outer layer EHDAA2:0001306 outer layer optic cup ZFA:0000064 presumptive pigmented epithelia ZFA:0000064 future PRE EMAPA:16677 future pigmented layer EMAPA:16677 future pigmented retinal epithelium EMAPA:16677 presumptive pigmented epithelium TAO:0000064 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 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 The foramen rotundum is a circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa. A circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa.vity. [Wikipedia:Foramen_rotundum][VHOG] It is suggested that the mammalian lamina ascendens arose from an upgrowth of the root of the quadrate ramus of the epipterygoid in cynodonts, separating foramen rotundum from foramen ovale.[well established][VHOG] todo - check placement of AAO class AAO:0000194 EHDAA2:0000552 EHDAA:10629 EMAPA:18712 FMA:53154 VHOG:0001543 uberon foramen rotundum of the skull foramen rotundum ossis sphenoidalis round foramen UBERON:0005446 foramen rotundum http://upload.wikimedia.org/wikipedia/commons/3/35/Gray145.png The foramen rotundum is a circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa. A circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa.vity. [Wikipedia:Foramen_rotundum][VHOG] 2012-09-17 VHOG:0001543 VHOG It is suggested that the mammalian lamina ascendens arose from an upgrowth of the root of the quadrate ramus of the epipterygoid in cynodonts, separating foramen rotundum from foramen ovale.[well established][VHOG] 2012-09-17 VHOG:0001543 VHOG PMID:1018003 Presley R, Steel FLD, On the homology of the alisphenoid. Journal of Anatomy (1976) todo - check placement of AAO class AAO foramen rotundum of the skull foramen rotundum ossis sphenoidalis round foramen VHOG:0001543 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 An umbilical vein that is in the left side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0000967 EMAPA:16358 EMAPA:16377 FMA:70320 uberon UBERON:0005459 left umbilical vein An umbilical vein that is in the left side of a multicellular organism. OBOL:automatic 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 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 An umbilical vein that is in the right side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0001761 EMAPA:16359 EMAPA:16378 FMA:70319 uberon UBERON:0005471 right umbilical vein An umbilical vein that is in the right side of a multicellular organism. OBOL:automatic 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 simple columnar epithelium that is part of a fundus of stomach. EHDAA2:0001921 EMAPA:17888 FMA:17277 VHOG:0000878 epithelium of fundus of stomach gastric epithelium of fundus gastric fundus epithelium uberon UBERON:0005477 stomach fundus epithelium A simple columnar epithelium that is part of a fundus of stomach. OBOL:automatic epithelium of fundus of stomach FMA:17277 gastric epithelium of fundus FMA:17277 gastric fundus epithelium FMA:17277 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 A venous channel found between layers of dura mater in the brain. Receives blood from internal and external veins of the brain, receive cerebrospinal fluid (CSF) from the subarachnoid space, and ultimately empty into the internal jugular vein. the MA placement should be checked EHDAA2:0002169 EHDAA:6491 EMAPA:18634 FMA:50762 MA:0002113 NCIT:C102627 VHOG:0001004 cranial dural venous sinus dural sinus dural vein dural venous sinus venous dural venous dural sinus uberon s. durae matris UBERON:0005486 venous dural sinus Gray488:blue.gif FMA A venous channel found between layers of dura mater in the brain. Receives blood from internal and external veins of the brain, receive cerebrospinal fluid (CSF) from the subarachnoid space, and ultimately empty into the internal jugular vein. cranial dural venous sinus FMA:50762 dural sinus FMA:50762 dural vein MA:0002113 dural venous sinus FMA:50762 venous dural EHDAA:6491 venous dural sinus EHDAA2:0002169 s. durae matris 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 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 A orbitosphenoid endochondral element that is composed primarily of cartilage tissue. EHDAA2:0001329 EHDAA:9554 uberon sphenoid lesser wing cartilage element UBERON:0005687 orbitosphenoid cartilage element EHDAA2 EHDAA2 EHDAA2 A orbitosphenoid endochondral element that is composed primarily of cartilage tissue. OBOL:automatic sphenoid lesser wing cartilage element EHDAA2:0001329 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 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 An opening in the skull through which cranial nerve II passes.[MP]. An aperture in the root of the lesser wing of the sphenoid bone transmitting the optic nerve. [TFD][VHOG] Foramen in the orbital region of the neurocranium for the passage of the optic nerve (cranial nerve II).[TAO] The short canal through the orbitosphenoid bone at the apex of the orbit that gives passage to the optic nerve and the opthalmic artery UBERON:0006269 AAO:0000342 EHDAA2:0001312 EHDAA:10646 EMAPA:18716 FMA:54774 TAO:0002025 VHOG:0001408 ZFA:0005428 optic canal optic foramen optic nerve (II) foramen optic nerve foramen uberon canalis opticus foramen opticum ossis sphenoidalis UBERON:0005745 In teleost fishes the opening is wider that in mammals. Due to the longer and deeper shape in mammals, this is usually called the optic canal; sometimes the term optic foramen may be used for the opening of the canal, but here we use this term to denote the entire space together with surrounding bone surface. optic foramen Orbita:mensch.jpg FMA-abduced-lr An opening in the skull through which cranial nerve II passes.[MP]. ISBN:0-683-40008-8 MP:0010704 An aperture in the root of the lesser wing of the sphenoid bone transmitting the optic nerve. [TFD][VHOG] 2012-09-17 VHOG:0001408 VHOG Foramen in the orbital region of the neurocranium for the passage of the optic nerve (cranial nerve II).[TAO] 2012-08-14 TAO:0002025 TAO TAO:wd The short canal through the orbitosphenoid bone at the apex of the orbit that gives passage to the optic nerve and the opthalmic artery MP:0010704 MP optic canal optic foramen optic nerve (II) foramen ZFA:0005428 ZFIN:ZDB-PUB-961014-192 optic nerve foramen TAO:0002025 canalis opticus foramen opticum ossis sphenoidalis The capillary loops of the kidney that normally function as a filtration unit[MP]. ...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus EMAPA:28239 uberon glomerular capillary tuft glomerulus UBERON:0005749 glomerular tuft Wikipedia The capillary loops of the kidney that normally function as a filtration unit[MP]. MP:0005325 ...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus GudMap glomerulus EMAPA:28239 A single layer of simple squamous epithelium in the glomerular capsule. Does not function in filtration[UBERON]. outer layer of the glomerular capsule composed of a single layer of simple squamous epithelium[MP] TODO - check this. BTO has podocytes under here Simple squamous epithelium that lines the capsule of the renal glomerulus.[TAO] BTO:0002296 EMAPA:27979 EMAPA:28260 EMAPA:35969 FMA:74272 MA:0002605 NCIT:C33271 TAO:0005253 UMLS:C0227645 ZFA:0005253 Bowman's parietal epithelium capsular epithelium glomerular capsule parietal layer outer layer of glomerular capsule parietal capsular epithelium parietal epithelial layer parietal epithelium of Bowman's capsule parietal layer of Bowman capsule parietal layer of Bowman's capsule parietal layer of glomerular capsule renal glomerular capsule epithelium uberon kidney parietal epithelium UBERON:0005750 glomerular parietal epithelium A single layer of simple squamous epithelium in the glomerular capsule. Does not function in filtration[UBERON]. outer layer of the glomerular capsule composed of a single layer of simple squamous epithelium[MP] MP:0011498 Simple squamous epithelium that lines the capsule of the renal glomerulus.[TAO] 2012-08-14 TAO:0005253 TAO ZFIN:curator UMLS:C0227645 ncithesaurus:Parietal_Layer_of_Bowman_s_Capsule Bowman's parietal epithelium MP:0011498 capsular epithelium BTO:0002296 glomerular capsule parietal layer FMA:74272 outer layer of glomerular capsule FMA:74272 parietal capsular epithelium MP:0011498 parietal epithelial layer ZFA:0005253 parietal epithelium of Bowman's capsule MP:0011498 parietal layer of Bowman's capsule MP:0011498 parietal layer of glomerular capsule FMA:74272 parietal layer of glomerular capsule MP:0011498 renal glomerular capsule epithelium ZFA:0005253 kidney parietal epithelium EMAPA:35969 The inner, or visceral, layer of the renal glomerular capsule, overlying the capillaries, composed of podocytes, and separated from the outer, or parietal, layer by the capsular (Bowman's) space[BTO]. Lies just above the thickened glomerular basement membrane and is made of podocytes. Beneath the visceral layer lie the glomerular capillaries[WP]. inner layer of the glomerular capsule surrounding the capillary endothelial cells and composed of highly specialized epithelial cells (podocytes) that are separated by filtration slits; the visceral layer is separated from the outer parietal layer by the urinary space (also known as the Bowman's or capsular space)[MP] TODO - check - the BTO class 'glomerular epithelium' is the visceral layer. But GO uses 'glomerular epithelium' as the mereological sum of P+V layers FMA:74273 NCIT:C33879 UMLS:C0227644 Bowman's visceral epithelium glomerular capsule visceral layer inner epithelial layer of Bowman's capsule podocyte layer of Bowman's capsule visceral epithelium of Bowman's capsule visceral layer of Bowman's capsule visceral layer of glomerular capsule uberon UBERON:0005751 visceral layer of glomerular capsule The inner, or visceral, layer of the renal glomerular capsule, overlying the capillaries, composed of podocytes, and separated from the outer, or parietal, layer by the capsular (Bowman's) space[BTO]. Lies just above the thickened glomerular basement membrane and is made of podocytes. Beneath the visceral layer lie the glomerular capillaries[WP]. inner layer of the glomerular capsule surrounding the capillary endothelial cells and composed of highly specialized epithelial cells (podocytes) that are separated by filtration slits; the visceral layer is separated from the outer parietal layer by the urinary space (also known as the Bowman's or capsular space)[MP] BTO:0001515 MP:0011497 UMLS:C0227644 ncithesaurus:Visceral_Layer_of_Bowman_s_Capsule Bowman's visceral epithelium MP:0011497 glomerular capsule visceral layer MP:0011497 inner epithelial layer of Bowman's capsule podocyte layer of Bowman's capsule visceral epithelium of Bowman's capsule visceral epithelium of Bowman's capsule MP:0011497 visceral layer of Bowman's capsule MP:0011497 visceral layer of glomerular capsule MP:0011497 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. The ridge of mesoderm covered with endoderm that in the early developing embryo partitions the endodermal cloaca into the primary urogenital sinus (ventrally) and the anorectal canal of the hindgut (dorsally); the urorectal septum eventually fuses with the cloacal membrane, dividing it into a dorsal anal membrane and a larger ventral urogenital membrane - this area of fusion is represented in the adult by the perineal body[MP]. todo - use to define cloacal septation in GO A ridge of mesoderm covered with endoderm that in the early developing embryo divides the endodermal cloaca into the urogenital sinus and the rectum. [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] EHDAA2:0002152 EHDAA:5921 EMAPA:17212 MA:0003235 NCIT:C34323 UMLS:C1519838 VHOG:0000018 septum urorectale urorectal fold urorectal membrane uberon cloacal septum UBERON:0005760 urorectal septum http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray992.png MA EHDAA2 The ridge of mesoderm covered with endoderm that in the early developing embryo partitions the endodermal cloaca into the primary urogenital sinus (ventrally) and the anorectal canal of the hindgut (dorsally); the urorectal septum eventually fuses with the cloacal membrane, dividing it into a dorsal anal membrane and a larger ventral urogenital membrane - this area of fusion is represented in the adult by the perineal body[MP]. MP:anna A ridge of mesoderm covered with endoderm that in the early developing embryo divides the endodermal cloaca into the urogenital sinus and the rectum. [TFD][VHOG] 2012-09-17 VHOG:0000018 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:0000018 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.388-89 and Figure 300 UMLS:C1519838 ncithesaurus:Urorectal_Septum septum urorectale urorectal fold MP:anna urorectal membrane MP:anna cloacal septum VHOG:0000018 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 the layer of extracellular matrix that lies between the endothelium of the glomerular capillaries and the podocytes of the inner or visceral layer of the Bowman capsule; it is a fusion of the endothelial cell and podocyte basal laminas and acts as a physical barrier and an ion-selective filter Membrane between the mesonephric podocytes and the renal glomerular capillaries. It is a trilaminar structure composed of the fused basement membranes of the glomerular capillaries and basement membrane of the podocytes. The capillary membranes touch the GBM at contact points that are separated by pores. The membrane is semi-permeable allowing water and small molecules to pass into the renal capsular space.[TAO] GBM EMAPA:28251 EMAPA:30965 FMA:74274 MA:0001659 NCIT:C32683 TAO:0005285 UMLS:C0599297 ZFA:0005285 glomerular capillary basement membrane glomerular filtration membrane uberon UBERON:0005777 glomerular basement membrane http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png true the layer of extracellular matrix that lies between the endothelium of the glomerular capillaries and the podocytes of the inner or visceral layer of the Bowman capsule; it is a fusion of the endothelial cell and podocyte basal laminas and acts as a physical barrier and an ion-selective filter MGI:anna MP:0011348 Membrane between the mesonephric podocytes and the renal glomerular capillaries. It is a trilaminar structure composed of the fused basement membranes of the glomerular capillaries and basement membrane of the podocytes. The capillary membranes touch the GBM at contact points that are separated by pores. The membrane is semi-permeable allowing water and small molecules to pass into the renal capsular space.[TAO] 2012-08-14 TAO:0005285 TAO ZFIN:ZDB-PUB-000824-1 GBM UMLS:C0599297 ncithesaurus:Glomerular_Basement_Membrane glomerular capillary basement membrane MA:0001659 glomerular filtration membrane ZFA:0005285 Middle layer of the glomerular basement membrane. lamina densa FMA:74276 NCIT:C32916 TAO:0005286 UMLS:C1235665 ZFA:0005286 lamina densa of glomerular basement membrane middle layer of glomerular basement membrane uberon UBERON:0005787 lamina densa of glomerular basement membrane Middle layer of the glomerular basement membrane. ZFIN:curator lamina densa ZFA:0005286 UMLS:C1235665 ncithesaurus:Lamina_Densa lamina densa of glomerular basement membrane FMA:74276 middle layer of glomerular basement membrane FMA:74276 Layer of the glomerular basement membrane adjacent to the glomerular capillary. FMA:74277 NCIT:C32920 TAO:0005287 UMLS:C1517719 ZFA:0005287 internal layer of glomerular basement membrane lamina interna of glomerular basement membrane uberon UBERON:0005788 lamina rara interna Layer of the glomerular basement membrane adjacent to the glomerular capillary. ZFIN:curator UMLS:C1517719 ncithesaurus:Lamina_Rara_Interna internal layer of glomerular basement membrane FMA:74277 lamina interna of glomerular basement membrane FMA:74277 Layer of the glomerular basement membrane adjacent to the podocytes and capsular space. FMA:74275 NCIT:C32919 TAO:0005288 UMLS:C1517718 ZFA:0005288 external layer of glomerular basement membrane lamina externa of glomerular basement membrane uberon UBERON:0005789 lamina rara externa Layer of the glomerular basement membrane adjacent to the podocytes and capsular space. ZFIN:curator UMLS:C1517718 ncithesaurus:Lamina_Rara_Externa external layer of glomerular basement membrane FMA:74275 lamina externa of glomerular basement membrane FMA:74275 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 The outer or sperficial part of a bone of the manus. uberon UBERON:0005809 cortex of manus bone The outer or sperficial part of a bone of the manus. PHENOSCAPE:ad A round nodule, small eminence, or warty outgrowth found on bones, skin, or within the lungs in tuberculosis. They are also found on the leading edge of Humpback Whale's flippers, improving fluid flow over the flipper's surface[WP]. AAO:0010605 BTO:0002173 FMA:75429 uberon UBERON:0005813 tubercle A round nodule, small eminence, or warty outgrowth found on bones, skin, or within the lungs in tuberculosis. They are also found on the leading edge of Humpback Whale's flippers, improving fluid flow over the flipper's surface[WP]. A fascicle that is part of a spinal cord. FMA:75799 spinal cord fasciculus uberon UBERON:0005837 fasciculus of spinal cord A fascicle that is part of a spinal cord. OBOL:automatic spinal cord fasciculus FMA:75799 A fascicle that is part of a brain. FMA:83844 brain fasciculus uberon UBERON:0005838 fasciculus of brain A fascicle that is part of a brain. OBOL:automatic brain fasciculus FMA:83844 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 A serous sac which is the aggregate of the conjunctiva plus the conjunctival space EMAPA:18233 FMA:20291 conjunctiva serous sac subbrillar sac uberon UBERON:0005908 conjunctival sac FMA FMA HPO:pr MA A serous sac which is the aggregate of the conjunctiva plus the conjunctival space subbrillar sac NCBITaxon:8570 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 Thickening of the proximal end of the hair follicle. Contains rapidly proliferating, rather undifferentiated matrix cells (transient amplifying cells), melanocytes and outer root sheath cells. EMAPA:18770 FMA:70666 MA:0000161 NCIT:C32706 UMLS:C0221962 hair bulb hair follicle bulb coat hair bulb uberon UBERON:0005932 bulb of hair follicle https://github.com/obophenotype/mouse-anatomy-ontology/issues/56 Thickening of the proximal end of the hair follicle. Contains rapidly proliferating, rather undifferentiated matrix cells (transient amplifying cells), melanocytes and outer root sheath cells. UMLS:C0221962 ncithesaurus:Hair_Bulb hair bulb FMA:70666 hair follicle bulb FMA:70666 coat hair bulb MA:0000161 . EMAPA:18772 FMA:294628 MA:0000162 uberon UBERON:0005933 hair root sheath . A multilayered tube composed of terminally differentiated hair follicle keratinocytes that is surrounded by the outer root sheath; the layers of the inner root sheath include the companion layer, Henle's layer, Huxley's layer and the inner root sheath cuticle[MP]. BTO:0003971 EMAPA:32792 FMA:70935 MA:0000779 hair follicle inner root sheath inner root sheath of hair follicle inner sheath of hair follicle internal root sheath of hair follicle uberon inner root sheath UBERON:0005941 hair inner root sheath A multilayered tube composed of terminally differentiated hair follicle keratinocytes that is surrounded by the outer root sheath; the layers of the inner root sheath include the companion layer, Henle's layer, Huxley's layer and the inner root sheath cuticle[MP]. MP:0010685 hair follicle inner root sheath MP:0010685 inner root sheath of hair follicle FMA:70935 inner sheath of hair follicle FMA:70935 internal root sheath of hair follicle FMA:70935 inner root sheath BTO:0003971 A stratified epithelium that surrounds the hair follicle that merges proximally with the basal layer of the interfollicular epidermis and distally with the hair bulb. BTO:0003969 EMAPA:32793 FMA:70943 MA:0000780 NCIT:C62490 external root sheath of hair follicle hair follicle outer root sheath outer root sheath of hair follicle uberon ORS outer hair sheath outer root sheath UBERON:0005942 hair outer root sheath A stratified epithelium that surrounds the hair follicle that merges proximally with the basal layer of the interfollicular epidermis and distally with the hair bulb. external root sheath of hair follicle FMA:70943 hair follicle outer root sheath BTO:0003969 outer root sheath of hair follicle FMA:70943 ORS BTO:0003969 outer root sheath BTO:0003969 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 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 vertical crest of the interior wall of the right atrium that lies to the right of the sinus of the vena cava and separates this from the remainder of the right atrium EMAPA:37837 FMA:9236 crista terminalis atrii dextri crista terminalis cordis crista terminalis of right atrium uberon UBERON:0005979 crista terminalis The vertical crest of the interior wall of the right atrium that lies to the right of the sinus of the vena cava and separates this from the remainder of the right atrium MP:0010495 EMAPA:37837 MA:th crista terminalis atrii dextri FMA:9236 FMA:TA crista terminalis cordis FMA:9236 crista terminalis of right atrium FMA:9236 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 left branch of the atrioventricular bundle that separates at the bundle of His, descends the septal wall of the left ventricle and connects to the terminal Purkinje fiber[MP]. EMAPA:37358 FMA:9487 galen:LeftBundleBranch LBB crus sinistrum (fasciculi atrioventricularis) crus sinistrum fasciculi atrioventricularis left branch of atrioventricular bundle left bundle branch left bundle branch of bundle of His left bundle of atrioventricular bundle left crus of atrioventricular bundle left posterior branch left posterior bundle uberon UBERON:0005986 left bundle branch The left branch of the atrioventricular bundle that separates at the bundle of His, descends the septal wall of the left ventricle and connects to the terminal Purkinje fiber[MP]. MP:0010566 EMAPA:37358 MA:th LBB crus sinistrum (fasciculi atrioventricularis) FMA:9487 crus sinistrum fasciculi atrioventricularis FMA:9487 FMA:TA left bundle branch MP:0010566 left bundle branch of bundle of His HP:0005172 left bundle of atrioventricular bundle MP:0010566 left crus of atrioventricular bundle MP:0010566 left posterior branch MP:0010566 left posterior bundle MP:0010566 The right branch of the atrioventricular bundle that separates just below the bundle of His, descends the septal wall of the right ventricle and connects to the terminal Purkinje fibers[MP]. EMAPA:37359 FMA:9486 galen:RightBundleBranch RBB crus dextrum (fasciculi atrioventricularis) crus dextrum fasciculi atrioventricularis right branch of atrioventricular bundle right bundle right bundle branch right bundle branch of bundle of His right right crus of atrioventricular bundle right ventricular bundle uberon UBERON:0005987 right bundle branch The right branch of the atrioventricular bundle that separates just below the bundle of His, descends the septal wall of the right ventricle and connects to the terminal Purkinje fibers[MP]. MP:0010567 EMAPA:37359 MA:th RBB crus dextrum (fasciculi atrioventricularis) FMA:9486 crus dextrum fasciculi atrioventricularis FMA:9486 FMA:TA right bundle FMA:9486 MP:0010567 right bundle branch FMA:9486 right right crus of atrioventricular bundle MP:0010567 right ventricular bundle MP:0010567 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 The bulb region adjacent to the dermal papilla that contains rapidly proliferating matrix cells that give rise to the various cell lineages of the hair shaft and inner root sheath EMAPA:37878 FMA:70772 germinal matrix of hair bulb lower part of bulb of hair follicle lower zone of bulb of hair follicle uberon UBERON:0006004 hair follicle matrix region The bulb region adjacent to the dermal papilla that contains rapidly proliferating matrix cells that give rise to the various cell lineages of the hair shaft and inner root sheath MP:0010686 EMAPA:37878 MA:th germinal matrix of hair bulb FMA:70772 lower part of bulb of hair follicle FMA:70772 lower zone of bulb of hair follicle FMA:70772 A ring of ribrous tissue that surrounds the atrioventricular and arterial orifices TODO - compare with ZFA atrioventricular ring, part of the conduction system BTO:0003628 EMAPA:37422 FMA:9497 anulus fibrosus of heart uberon Lower's ring annulus fibrosus cordis anulus fibrosus cordis aortic annulus atrioventricular ring coronary tendon fibrous ring of heart UBERON:0006008 fibrous ring of heart A ring of ribrous tissue that surrounds the atrioventricular and arterial orifices EMAPA:37422 MA:th anulus fibrosus of heart FMA:9497 Lower's ring BTO:0003628 annulus fibrosus cordis anulus fibrosus cordis aortic annulus atrioventricular ring BTO:0003628 coronary tendon BTO:0003628 fibrous ring of heart 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 One of the cartilaginous structures surrounding the embryonic spinal cord, formed by the dorsal growth of the dorsolateral arcualia; it is the primordium of the vertebral arch. BTO:0001763 uberon neural arch primordium UBERON:0006063 cartilaginous neural arch One of the cartilaginous structures surrounding the embryonic spinal cord, formed by the dorsal growth of the dorsolateral arcualia; it is the primordium of the vertebral arch. BTO:0001763 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 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 base or posterior surface of the urinary bladder contains the trigone of the bladder and the outlet where urine empties through the internal urethral orifice. fundus of bladder EHDAA2:0000582 EHDAA:9330 EMAPA:35173 EMAPA_RETIRED:18322 FMA:15908 MA:0001694 NCIT:C48939 UMLS:C0447584 VHOG:0001184 base of urinary bladder fundus vesicae urinary bladder base urinary bladder fundus urinary bladder fundus region uberon bladder dome UBERON:0006082 fundus of urinary bladder EHDAA2-modified EHDAA2 The base or posterior surface of the urinary bladder contains the trigone of the bladder and the outlet where urine empties through the internal urethral orifice. MP:0011785 fundus of bladder FMA:15908 UMLS:C0447584 ncithesaurus:Bladder_Fundus base of urinary bladder FMA:15908 fundus vesicae FMA:15908 FMA:TA urinary bladder base MP:0011785 urinary bladder fundus FMA:15908 urinary bladder fundus region MA:0001694 bladder dome EMAPA:35173 The deep nuclei of telencephalic origin found in the basal region of the forebrain BAMS:BG BAMS:BNC BIRNLEX:1629 EV:0100182 UMLS:C0004781 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=224 basal nuclei basal nuclei of the forebrain uberon basal ganglia basal ganglia (anatomic) corpus striatum (Savel'ev) ganglia basales UBERON:0006098 basal nuclear complex The deep nuclei of telencephalic origin found in the basal region of the forebrain BIRNLEX:1629 UMLS:C0004781 BIRNLEX:1629 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=224 BIRNLEX:1629 basal nuclei BIRNLEX:1629 basal nuclei of the forebrain BIRNLEX:1629 basal ganglia BIRNLEX:1629 basal ganglia (anatomic) NeuroNames:224 corpus striatum (Savel'ev) NeuroNames:224 ganglia basales NeuroNames:224 BIRNLEX:2553 EMAPA:35801 FMA:75371 MA:0003176 UMLS:C0009198 UMLS:C0458767 cochlear canal spiral canal of cochlea wall of cochlea uberon spiral vessel UBERON:0006106 cochlear canal UMLS:C0009198 BIRNLEX:2553 UMLS:C0458767 BIRNLEX:2553 cochlear canal BIRNLEX:2553 spiral canal of cochlea BIRNLEX:2553 wall of cochlea FMA:75371 spiral vessel MA:0003176 A funiculus of neuraxis that is part of a spinal cord. FMA:77460 spinal cord funiculus white column of spinal cord uberon UBERON:0006127 funiculus of spinal cord A funiculus of neuraxis that is part of a spinal cord. OBOL:automatic spinal cord funiculus FMA:77460 white column of spinal cord FMA:77460 The cerebrospinal nerves consist of numerous nerve fibers collected together and enclosed in membranous sheaths. A small bundle of fibers, enclosed in a tubular sheath, is called a funiculus; if the nerve is of small size, it may consist only of a single funiculus; but if large, the funiculi are collected together into larger bundles or fasciculi, which are bound together in a common membranous investment. Examples include: Anterior funiculus of the spinal cord Lateral funiculus of the spinal cord Posterior funiculus of the spinal cord Funiculus solitarius of the medulla Funiculus separans FMA:76738 uberon UBERON:0006133 funiculus of neuraxis The cerebrospinal nerves consist of numerous nerve fibers collected together and enclosed in membranous sheaths. A small bundle of fibers, enclosed in a tubular sheath, is called a funiculus; if the nerve is of small size, it may consist only of a single funiculus; but if large, the funiculi are collected together into larger bundles or fasciculi, which are bound together in a common membranous investment. Examples include: Anterior funiculus of the spinal cord Lateral funiculus of the spinal cord Posterior funiculus of the spinal cord Funiculus solitarius of the medulla Funiculus separans A threadlike extension of a nerve cell and consists of an axon and myelin sheath (if it is myelinated) in the nervous system. There are nerve fibers in the central nervous system and peripheral nervous system. A nerve fiber may be myelinated and/or unmyelinated. In the central nervous system (CNS), myelin by oligodendroglia cells is formed. Schwann cells form myelin in the peripheral nervous system (PNS). Schwann cells also make a thin covering in an axon without myelin (in the PNS). A peripheral nerve fiber contains an axon, myelin sheath, schwann cells and its endoneurium. There are no endoneurium and schwann cells in the central nervous system. neurofibrous BAMS:nfi FMA:5914 MESH:A08.663.542 nerve fibre neurofibra neurofibrum uberon nerve fibers neurofibra UBERON:0006134 nerve fiber A threadlike extension of a nerve cell and consists of an axon and myelin sheath (if it is myelinated) in the nervous system. There are nerve fibers in the central nervous system and peripheral nervous system. A nerve fiber may be myelinated and/or unmyelinated. In the central nervous system (CNS), myelin by oligodendroglia cells is formed. Schwann cells form myelin in the peripheral nervous system (PNS). Schwann cells also make a thin covering in an axon without myelin (in the PNS). A peripheral nerve fiber contains an axon, myelin sheath, schwann cells and its endoneurium. There are no endoneurium and schwann cells in the central nervous system. nerve fibre FMA:5914 neurofibra FMA:5914 FMA:TA neurofibrum FMA:5914 nerve fibers BAMS:nfi neurofibra Axons of neurons encased in a lipoproteinaceous material called myelin. (MeSH) consider adding link to UBERON:0002316 ! white matter of neuraxis http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html, http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=6134604, Wikipedia:Myelin#Invertebrate_myelin FMA:5915 GAID:745 MESH:A08.663.542.512 NCIT:C12627 UMLS:C0027750 uberon UBERON:0006135 myelinated nerve fiber Axons of neurons encased in a lipoproteinaceous material called myelin. (MeSH) ncithesaurus:Myelinated_Nerve_Fiber UMLS:C0027750 ncithesaurus:Myelinated_Nerve_Fiber FMA:5916 GAID:767 MESH:A08.663.542.756 NCIT:C33835 UMLS:C0501409 non-myelinated nerve fiber uberon UBERON:0006136 unmyelinated nerve fiber UMLS:C0501409 ncithesaurus:Unmyelinated_Nerve_Fiber non-myelinated nerve fiber FMA:5916 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 pronephros proximal tubule uberon UBERON:0006173 pronephric proximal tubule pronephros proximal tubule GO:0039011 uberon UBERON:0006175 pronephric distal tubule The mesonephric glomerular mesangium is the thin membrane connective tissue composed of mesangial cells in the mesonephros, which helps to support the capillary loops in a renal glomerulus uberon UBERON:0006182 mesonephric glomerular mesangium true The mesonephric glomerular mesangium is the thin membrane connective tissue composed of mesangial cells in the mesonephros, which helps to support the capillary loops in a renal glomerulus GO:0061247 . uberon UBERON:0006183 mesonephric glomerular capillary true . GO:0061249 The mesonephric connecting tubule is a tubular segment of the mesonephric nephron; it connects the distal tubule to the collecting duct in the mesonephros uberon UBERON:0006189 mesonephric connecting tubule The mesonephric connecting tubule is a tubular segment of the mesonephric nephron; it connects the distal tubule to the collecting duct in the mesonephros GO:0061272 The mesonephric distal tubule is a mesonephric nephron tubule that begins at the macula densa and extends to the mesonephric connecting tubule ZFA has terms for developing tubule uberon UBERON:0006190 mesonephric distal tubule The mesonephric distal tubule is a mesonephric nephron tubule that begins at the macula densa and extends to the mesonephric connecting tubule GO:0061273 ZFA has terms for developing tubule ZFA The mesonephric proximal tubule extends from the capsule to the distal tubule ZFA has terms for developing tubule uberon UBERON:0006192 mesonephric proximal tubule The mesonephric proximal tubule extends from the capsule to the distal tubule GO:0061275 ZFA has terms for developing tubule ZFA 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 EHDAA2:0000340 EHDAA:6002 EMAPA:17749 uberon UBERON:0006219 deltoid pre-muscle mass EHDAA2 EHDAA2 EHDAA2 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 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 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 EHDAA2:0000897 EHDAA:8467 EMAPA:17740 uberon UBERON:0006256 knee joint primordium 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 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 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. 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 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 One of eight distinct lateral lines in the 4-day larva. A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. check XAO/AAO One of eight distinct lateral lines in the 4-day larva. A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. (See Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO] relationship loss: develops_from posterior lateral line primordium (TAO:0001157)[TAO] relationship loss: part_of posterior lateral line system (TAO:0001471)[TAO] AAO:0011024 EFO:0003595 HBA:4413 TAO:0000944 XAO:0000465 ZFA:0000944 pll uberon UBERON:0006334 posterior lateral line lexical One of eight distinct lateral lines in the 4-day larva. A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. ZFA:0000944 One of eight distinct lateral lines in the 4-day larva. A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. (See Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO] 2012-08-14 TAO:0000944 TAO ZFIN:curator relationship loss: develops_from posterior lateral line primordium (TAO:0001157)[TAO] 2012-08-14 TAO:0000944 TAO relationship loss: part_of posterior lateral line system (TAO:0001471)[TAO] 2012-08-14 TAO:0000944 TAO pll ZFA:0000944 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 A peritubular capillary that is part of a outer medulla of kidney. EMAPA:35461 MA:0002589 kidney outer medulla peritubular capillary uberon UBERON:0006341 outer renal medulla peritubular capillary A peritubular capillary that is part of a outer medulla of kidney. OBOL:automatic kidney outer medulla peritubular capillary MA:0002589 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 . EMAPA:29671 MA:0002628 distal straight tubule premacula segment kidney medulla loop of Henle ascending limb thick segment medullary thick ascending limb of Henle's loop renal medulla loop of Henle ascending limb thick segment renal medulla thick ascending limb uberon UBERON:0006376 premacula segment of distal straight tubule MA MA MA . distal straight tubule premacula segment MA:0002628 kidney medulla loop of Henle ascending limb thick segment MA:th medullary thick ascending limb of Henle's loop MA:th renal medulla loop of Henle ascending limb thick segment MA:th renal medulla thick ascending limb MA:th 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 ring of fibrous or fibrocartilaginous tissue (as of an intervertebral disk or surrounding an orifice of the heart). anulus BTO:0003627 EMAPA:32670 FMA:76704 anulus fibrosus fibrocartilaginous ring uberon fibrous ring UBERON:0006444 annulus fibrosus A ring of fibrous or fibrocartilaginous tissue (as of an intervertebral disk or surrounding an orifice of the heart). BTO:0003627 anulus BTO:0003627 anulus fibrosus FMA:76704 fibrocartilaginous ring fibrous ring BTO:0003627 System pertaining to a bronchus and alveoli. BTO:0000136 CALOHA:TS-1296 EMAPA:32692 MA:0000416 pulmonary alveolar system uberon bronchoalveolar system UBERON:0006524 alveolar system System pertaining to a bronchus and alveoli. BTO:0000136 pulmonary alveolar system MP:0010899 bronchoalveolar system BTO:0000136 EMAPA:19001 MA:0001775 uberon UBERON:0006525 left lung alveolar system EMAPA:35717 MA:0001784 uberon UBERON:0006526 right lung alveolar system 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 Any region of a nephron tubule that is convoluted. Examples: distal convoluted tubule, proximal convoluted tuble. EMAPA:35725 MA:0001665 NCIT:C49479 UMLS:C1707510 convoluted tubule kidney convoluted tubule uberon UBERON:0006534 renal convoluted tubule Any region of a nephron tubule that is convoluted. Examples: distal convoluted tubule, proximal convoluted tuble. UMLS:C1707510 ncithesaurus:Convoluted_Tubule kidney convoluted tubule MA:0001665 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 substance that is secreted by a mammary gland. The substance may differ depending on phase, with colostrum produced during pregancy/early lactation, and milk produced afterwards. EMAPA:36538 MA:0002505 uberon lactiferous gland fluid lactiferous gland secretion mammary gland fluid mammary gland secreted fluid mammary gland secretion secretion of mammary gland UBERON:0006539 mammary gland fluid/secretion A substance that is secreted by a mammary gland. The substance may differ depending on phase, with colostrum produced during pregancy/early lactation, and milk produced afterwards. A loop of Henle that is part of a kidney outer medulla inner stripe. EMAPA:29679 MA:0002627 uberon UBERON:0006541 outer medulla inner stripe loop of Henle A loop of Henle that is part of a kidney outer medulla inner stripe. OBOL:automatic A loop of Henle that is part of a kidney outer medulla outer stripe. EMAPA:29665 MA:0002630 uberon UBERON:0006542 outer medulla outer stripe loop of Henle A loop of Henle that is part of a kidney outer medulla outer stripe. OBOL:automatic 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 An organ system subdivision that is the part of the lymphoid system that excludes the lymphatic vessels.. FMA:74623 non-lymphatic lymphoid system uberon UBERON:0006561 non-lymphatic part of lymphoid system An organ system subdivision that is the part of the lymphoid system that excludes the lymphatic vessels.. non-lymphatic lymphoid system FMA:74623 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 Transudate located within the osseus labyrinth. Otolymph can be further classified with respect to whether it is within the membranous labyrinth (endolymph) or outside the mebranous labyrinth (perilymph). Fluids found within the osseous labyrinth (PERILYMPH) and the membranous labyrinth (ENDOLYMPH) of the inner ear. (From Gray's Anatomy, 30th American ed, p1328, 1332[MESH:A12.207.571]) UBERON:0007793 EMAPA:36547 GAID:1183 MA:0002527 MESH:A12.207.571 NCIT:C33231 UMLS:C1518679 uberon labyrinthine fluid UBERON:0006586 otolymph FMA-abduced Transudate located within the osseus labyrinth. Otolymph can be further classified with respect to whether it is within the membranous labyrinth (endolymph) or outside the mebranous labyrinth (perilymph). Fluids found within the osseous labyrinth (PERILYMPH) and the membranous labyrinth (ENDOLYMPH) of the inner ear. (From Gray's Anatomy, 30th American ed, p1328, 1332[MESH:A12.207.571]) MESH:A12.207.571 UMLS:C1518679 ncithesaurus:Otolymph labyrinthine fluid MESH:A12.207.571 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 AAO:0000472 EFO:0003462 TAO:0001334 ZFA:0001334 future enteric nervous system uberon UBERON:0006600 presumptive enteric nervous system NCBIBook:NBK10065 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 A sheet of extracellular matrix. Aponeuroses are layers of flat broad tendons. They have a shiny, whitish-silvery color, and are histologically similar to tendons, but are very sparingly supplied with blood vessels and nerves. When dissected, aponeuroses are papery, and peel off by sections. The primary regions with thick aponeurosis is in the ventral abdominal region, the dorsal lumbar region, and in the palmar region. Their primary function is to join muscles and the body parts the muscles act upon[Wikipedia:Aponeurosis]. in ZFA, aponeuroses are subtypes of tendons, but this is inconsistent with tendons being muscle-bone connections AEO:0000092 EHDAA2:0003092 FMA:9722 NCIT:C32133 UMLS:C0225205 ZFA:0005652 uberon aponeuroses aponeurotic UBERON:0006614 aponeurosis http://upload.wikimedia.org/wikipedia/commons/e/e6/Aponeurosis.png FMA FMA A sheet of extracellular matrix. AEO:0000092 Aponeuroses are layers of flat broad tendons. They have a shiny, whitish-silvery color, and are histologically similar to tendons, but are very sparingly supplied with blood vessels and nerves. When dissected, aponeuroses are papery, and peel off by sections. The primary regions with thick aponeurosis is in the ventral abdominal region, the dorsal lumbar region, and in the palmar region. Their primary function is to join muscles and the body parts the muscles act upon[Wikipedia:Aponeurosis]. in ZFA, aponeuroses are subtypes of tendons, but this is inconsistent with tendons being muscle-bone connections ZFA UMLS:C0225205 ncithesaurus:Aponeurosis aponeuroses aponeurotic A large vein or channel for the circulation of venous blood check if it is valid to group ZFA class here. MA:0000070 NCIT:C12877 UMLS:C0226504 ZFA:0007072 uberon blood sinus UBERON:0006615 venous sinus A large vein or channel for the circulation of venous blood UMLS:C0226504 ncithesaurus:Venous_Sinus blood sinus ZFA:0007072 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 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 The galea aponeurotica (epicranial aponeurosis, aponeurosis epicranialis) is a tough layer of dense fibrous tissue which covers the upper part of the cranium; behind, it is attached, in the interval between its union with the Occipitales, to the external occipital protuberance and highest nuchal lines of the occipital bone; in front, it forms a short and narrow prolongation between its union with the Frontales. On either side it gives origin to the Auriculares anterior and superior; in this situation it loses its aponeurotic character, and is continued over the temporal fascia to the zygomatic arch as a layer of laminated areolar tissue. It is closely connected to the integument by the firm, dense, fibro-fatty layer which forms the superficial fascia of the scalp: it is attached to the pericranium by loose cellular tissue, which allows the aponeurosis, carrying with it the integument to move through a considerable distance. EMAPA:19210 FMA:46768 aponeurosis epicranialis aponeurosis of epicranius epicranial aponeurosis epicranius aponeurosis galea aponeurotica uberon cranial aponeurosis epicranial aponeurosis galea aponeurosis galea aponeurotica; aponeurosis epicranialis galeal aponeurosis UBERON:0006661 epicranial aponeurosis http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray378.png FMA The galea aponeurotica (epicranial aponeurosis, aponeurosis epicranialis) is a tough layer of dense fibrous tissue which covers the upper part of the cranium; behind, it is attached, in the interval between its union with the Occipitales, to the external occipital protuberance and highest nuchal lines of the occipital bone; in front, it forms a short and narrow prolongation between its union with the Frontales. On either side it gives origin to the Auriculares anterior and superior; in this situation it loses its aponeurotic character, and is continued over the temporal fascia to the zygomatic arch as a layer of laminated areolar tissue. It is closely connected to the integument by the firm, dense, fibro-fatty layer which forms the superficial fascia of the scalp: it is attached to the pericranium by loose cellular tissue, which allows the aponeurosis, carrying with it the integument to move through a considerable distance. aponeurosis epicranialis FMA:46768 FMA:TA aponeurosis of epicranius FMA:46768 epicranial aponeurosis FMA:46768 epicranius aponeurosis FMA:46768 galea aponeurotica FMA:46768 cranial aponeurosis epicranial aponeurosis galea aponeurosis galea aponeurotica; aponeurosis epicranialis galeal aponeurosis 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 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 the central cone shaped core of spongy bone about which turns the spiral canal modiolus BTO:0001693 EMAPA:35575 FMA:61278 MA:0001182 NCIT:C33135 UMLS:C0229503 cochlea modiolus modiolus cochleae modiolus of cochlea uberon columella cochleae UBERON:0006723 cochlear modiolus http://upload.wikimedia.org/wikipedia/commons/1/16/Gray921.png MA the central cone shaped core of spongy bone about which turns the spiral canal ISBN:0-683-40008-8 MGI:anna MP:0003309 modiolus MA:0001182 UMLS:C0229503 ncithesaurus:Modiolus cochlea modiolus FMA:61278 modiolus cochleae FMA:61278 FMA:TA modiolus of cochlea FMA:61278 columella cochleae BTO:0001693 A spiral thickening of the fibrous lining of the cochlear wall. Spiral ligament secures the membranous cochlear duct to the bony spiral canal of the cochlea. Its spiral ligament fibrocytes function in conjunction with the stria vascularis to mediate cochlear ion homeostasis. this is not classified as a ligament in FMA UBERON:0028186 BIRNLEX:2524 EMAPA:35798 FMA:77834 MA:0001192 MESH:D055493 ligamentum spirale ductus cochlearis spiral cochlear ligament spiral ligament of cochlea spiral ligament of cochlear duct uberon UBERON:0006725 spiral ligament MESH-def A spiral thickening of the fibrous lining of the cochlear wall. Spiral ligament secures the membranous cochlear duct to the bony spiral canal of the cochlea. Its spiral ligament fibrocytes function in conjunction with the stria vascularis to mediate cochlear ion homeostasis. this is not classified as a ligament in FMA FMA ligamentum spirale ductus cochlearis spiral cochlear ligament spiral ligament of cochlea BIRNLEX:2524 spiral ligament of cochlear duct FMA:77834 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 Layer of nonkeratinized squamous epithelium lining the conjunctiva, overlying scleral tissue BTO:0005131 EFO:0001916 FMA:62131 NCIT:C32365 UMLS:C1179037 conjunctiva epithelium conjunctival epithelium uberon UBERON:0006763 epithelium of conjunctiva FMA BTO Layer of nonkeratinized squamous epithelium lining the conjunctiva, overlying scleral tissue UMLS:C1179037 ncithesaurus:Conjunctival_Epithelium conjunctiva epithelium FMA:62131 conjunctival epithelium BTO:0005131 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 open tracheal system trachea. tracheal lumen FBbt:00007410 uberon UBERON:0006832 lumen of open tracheal system trachea An anatomical space that surrounded_by a open tracheal system trachea. OBOL:automatic tracheal lumen FBbt:00007410 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 Vein that is central to a lobule in the liver. central vein FMA:17544 NCIT:C32281 TAO:0005168 ZFA:0005168 terminal branch of hepatic vein terminal hepatic venule vena centralis (hepar) uberon UBERON:0006841 central vein of liver Vein that is central to a lobule in the liver. ZFA:0005168 central vein ZFA:0005168 terminal branch of hepatic vein FMA:17544 terminal hepatic venule FMA:17544 vena centralis (hepar) FMA:17544 The initial segment of a cranial nerve, leaving the central nervous system. recommend asserting under this class rather than relying on inference, as relations may change FMA:52609 TAO:0002190 ZFA:0001663 cranial nerve root cranial neural root uberon UBERON:0006843 root of cranial nerve The initial segment of a cranial nerve, leaving the central nervous system. cranial nerve root FMA:52609 cranial neural root FMA:52609 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 peritubular capillary that is part of a cortex of kidney. EMAPA:37488 MA:0002590 kidney cortex peritubular capillary uberon UBERON:0006851 renal cortex peritubular capillary A peritubular capillary that is part of a cortex of kidney. OBOL:automatic EMAPA:37488 MA:th kidney cortex peritubular capillary MA:0002590 A region of nephron tubule that is part of a cortex of kidney. EMAPA:18976 MA:0002609 kidney cortex tubule uberon cortical tubule UBERON:0006853 renal cortex tubule MA A region of nephron tubule that is part of a cortex of kidney. OBOL:automatic kidney cortex tubule MA:0002609 cortical tubule MA:0002609 . EMAPA:28402 MA:0002615 cortical thick ascending limb of Henle's loop kidney cortex loop of Henle ascending limb thick segment renal cortex loop of Henle ascending limb thick segment renal cortex thick ascending limb uberon UBERON:0006854 distal straight tubule postmacula segment MA . cortical thick ascending limb of Henle's loop MA:th kidney cortex loop of Henle ascending limb thick segment MA:th renal cortex loop of Henle ascending limb thick segment MA:th renal cortex thick ascending limb MA:th 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 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 An epithelium that is part of a vestibular labyrinth. BTO:0005581 EMAPA:32884 EMAPA:35921 FMA:75606 MA:0002892 RETIRED_EHDAA2:0000834 epithelium of vestibular labyrinth inner ear vestibular component epithelium vestibular sensory epithelium uberon UBERON:0006932 vestibular epithelium An epithelium that is part of a vestibular labyrinth. OBOL:automatic epithelium of vestibular labyrinth OBOL:automatic inner ear vestibular component epithelium RETIRED_EHDAA2:0000834 vestibular sensory epithelium FMA:75606 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 An epithelium that is part of a crista ampullaris. FMA:75636 MA:0002870 epithelium of crista of ampulla of semicircular duct of membranous labyrinth uberon ampullary crest neuroepithelium UBERON:0006935 crista ampullaris neuroepithelium FMA MA An epithelium that is part of a crista ampullaris. OBOL:automatic epithelium of crista of ampulla of semicircular duct of membranous labyrinth FMA:75636 ampullary crest neuroepithelium MA:0002870 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 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 distal part of adenohypophysis: the part that makes up the main body of the gland. Region of the adenohypophysis which produces the follicle-stimulating hormone, luteinizing hormone, prolactin, thyrotropin, and adrenocorticotropin.[AAO] The anterior part of the adenohypophysis. [TFD][VHOG] 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] DHP pars anterior AAO:0010542 BAMS:DHP BIRNLEX:1022 BTO:0001787 EHDAA2:0001416 EHDAA:7532 EMAPA:17515 FMA:74630 MA:0000854 TAO:0001195 UMLS:C0175322 VHOG:0000244 ZFA:0001195 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=410 distal part of hypophysis pars anterior of adenohypophysis pars distalis (glandula pituitaria) pars distalis adenohypophysis pars distalis of anterior lobe of pituitary gland pars glandularis of adenohypophysis uberon anterior lobe distal part of the hypophysis pars distalis pars distalis (hypophysis) pars distalis adenohypophyseos pars distalis lobi anterioris hypophyseos pars glandularis UBERON:0006964 pars distalis of adenohypophysis MA The distal part of adenohypophysis: the part that makes up the main body of the gland. Dorlands_Medical_Dictionary:MerckSource Region of the adenohypophysis which produces the follicle-stimulating hormone, luteinizing hormone, prolactin, thyrotropin, and adrenocorticotropin.[AAO] 2012-06-20 AAO:0010542 AAO AAO:BJB The anterior part of the adenohypophysis. [TFD][VHOG] 2012-09-17 VHOG:0000244 VHOG 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:0000244 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 DHP BIRNLEX:1022 NIFSTD:NeuroNames_abbrevSource pars anterior EHDAA2:0001416 MA:0000854 ZFA:0001195 UMLS:C0175322 BIRNLEX:1022 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=410 BIRNLEX:1022 distal part of hypophysis BIRNLEX:1022 pars anterior of adenohypophysis FMA:74630 pars distalis (glandula pituitaria) FMA:74630 FMA:TA pars distalis adenohypophysis FMA:74630 FMA:TA pars distalis of anterior lobe of pituitary gland FMA:74630 pars glandularis of adenohypophysis FMA:74630 anterior lobe MA:0000854 distal part of the hypophysis NeuroNames:410 pars distalis MA:0000854 pars distalis (hypophysis) NeuroNames:410 pars distalis adenohypophyseos BTO:0001787 pars distalis lobi anterioris hypophyseos BTO:0001787 pars glandularis MA:0000854 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 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 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 Portion of tissue that consists of the precursors of the pronephric glomus or glomerulus; derived from the medial portion of the pronephric intermediate mesoderm. XAO:0000110 uberon corpuscle glomerulus UBERON:0007128 glomeral mesenchyme Portion of tissue that consists of the precursors of the pronephric glomus or glomerulus; derived from the medial portion of the pronephric intermediate mesoderm. ISBN:0815318960 corpuscle XAO:0000110 glomerulus XAO:0000110 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 EMAPA:25125 FMA:23800 scapular angle uberon UBERON:0007172 angle of scapula https://github.com/obophenotype/uberon/issues/58 scapular angle FMA:23800 The lateral border (or axillary border, or margin) is the thickest of the three borders of the scapula. It begins above at the lower margin of the glenoid cavity, and inclines obliquely downward and backward to the inferior angle. Immediately below the glenoid cavity is a rough impression, the infraglenoid tuberosity, about 2.5 cm. in length, which gives origin to the long head of the Triceps brachii; in front of this is a longitudinal groove, which extends as far as the lower third of this border, and affords origin to part of the Subscapularis. The inferior third is thin and sharp, and serves for the attachment of a few fibers of the Teres major behind, and of the Subscapularis in front. EMAPA:25126 FMA:23239 axillary border of scapula lateral border of scapula margo lateralis (scapula) margo lateralis scapulae uberon lateral part of scapula UBERON:0007173 lateral border of scapula EMAPA-modified lexical The lateral border (or axillary border, or margin) is the thickest of the three borders of the scapula. It begins above at the lower margin of the glenoid cavity, and inclines obliquely downward and backward to the inferior angle. Immediately below the glenoid cavity is a rough impression, the infraglenoid tuberosity, about 2.5 cm. in length, which gives origin to the long head of the Triceps brachii; in front of this is a longitudinal groove, which extends as far as the lower third of this border, and affords origin to part of the Subscapularis. The inferior third is thin and sharp, and serves for the attachment of a few fibers of the Teres major behind, and of the Subscapularis in front. axillary border of scapula FMA:23239 lateral border of scapula FMA:23239 margo lateralis (scapula) FMA:23239 margo lateralis scapulae FMA:23239 FMA:TA lateral part of scapula FMA:23239 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 lexical 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 An angle of the scapula formed by the union of the vertebral and axillary borders; its dorsal surface affords attachment to the Teres major and frequently to a few fibers of the Latissimus dorsi.[WP,unvetted] EMAPA:25128 FMA:13315 angulus inferior (scapula) angulus inferior scapulae uberon UBERON:0007175 inferior angle of scapula EMAPA-modified An angle of the scapula formed by the union of the vertebral and axillary borders; its dorsal surface affords attachment to the Teres major and frequently to a few fibers of the Latissimus dorsi.[WP,unvetted] angulus inferior (scapula) FMA:13315 angulus inferior scapulae 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 The osseous cochlea is the bony foundation that forms the small shell arrangement for the cochlear nerve. TODO - check this. in MA, cochlea is not part of the bony labyrinth EMAPA:35620 MA:0000239 uberon UBERON:0007223 osseus cochlea The osseous cochlea is the bony foundation that forms the small shell arrangement for the cochlear nerve. 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 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 proximal convoluted tubule that is part of a pronephros. TAO:0002238 ZFA:0001620 uberon UBERON:0007298 pronephric proximal convoluted tubule A proximal convoluted tubule that is part of a pronephros. OBOL:automatic 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 glomerular capillary that is part of a pronephros. TAO:0005309 ZFA:0005309 uberon UBERON:0007306 pronephric glomerular capillary true A glomerular capillary that is part of a pronephros. OBOL:automatic A glomerular basement membrane that is part of a pronephros. TAO:0005313 ZFA:0005313 pronephric glomerular filtration membrane uberon UBERON:0007307 pronephric glomerular basement membrane true A glomerular basement membrane that is part of a pronephros. OBOL:automatic pronephric glomerular filtration membrane ZFA:0005313 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 blood vessels supplying the stria vascularis in the cochlea of the inner ear. stria vascularis blood vessels uberon stria vascularis blood vessel UBERON:0007352 stria vascularis vasculature blood vessels supplying the stria vascularis in the cochlea of the inner ear. MP:0004368 stria vascularis blood vessel MP:0004368 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 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 Nerve fibers crossing the midline of the neuraxis relative to their point of origin, on a course to from one level of the nervous system to another. (CUMBO, Heimer, L. The Human Brain, 2nd ed., 1995, pg 6) chiasm chiasma decussation FMA:83858 NCIT:C28351 NLX:144064 decussation of neuraxis neuraxis chiasm neuraxis chiasma neuraxis decussation uberon UBERON:0007418 neural decussation Nerve fibers crossing the midline of the neuraxis relative to their point of origin, on a course to from one level of the nervous system to another. (CUMBO, Heimer, L. The Human Brain, 2nd ed., 1995, pg 6) NLX:144064 decussation of neuraxis FMA:83858 neuraxis decussation FMA:83858 A neural decussation that is part of a diencephalon. FMA:62446 diencephalon decussation uberon UBERON:0007425 decussation of diencephalon FMA Obol A neural decussation that is part of a diencephalon. OBOL:automatic diencephalon decussation FMA:62446 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 MA does treat internal/external limiting membranes as layers - these are classified as laminae. We do not follow this convention. However, we do following MA is grouping these terms together MA:0001318 retina lamina uberon UBERON:0007619 limiting membrane of retina UBERON MA does treat internal/external limiting membranes as layers - these are classified as laminae. We do not follow this convention. However, we do following MA is grouping these terms together MA retina lamina MA:0001318 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 Layer of hippocampus area CA3 lying superficial to the pyramidal cell layer that contains mossy fiber axons projecting from the dentate gyrus. A slight thickening in this layer marks the border in some species between areas CA2 and CA3. dapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 460) stratum lucidum BAMS:SLu BIRNLEX:4108 EMAPA:35411 NCIT:C33629 OldNeuroNames:-975815906 UMLS:C0221922 uberon stratum lucidum hippocampi stratum lucidum hippocampus UBERON:0007637 hippocampus stratum lucidum Layer of hippocampus area CA3 lying superficial to the pyramidal cell layer that contains mossy fiber axons projecting from the dentate gyrus. A slight thickening in this layer marks the border in some species between areas CA2 and CA3. dapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 460) BIRNLEX:4108 stratum lucidum BIRNLEX:4108 OldNeuroNames:-975815906 BIRNLEX:4108 UMLS:C0221922 ncithesaurus:Stratum_Lucidum stratum lucidum hippocampi stratum lucidum hippocampus BAMS:SLu Regional part of fornix consisting of a thin layer of white matter on the surface of the hippocampal formation, bordering the wall of the lateral ventricle and composed of white, myelinated fibers. The alveus arises from cell bodies in the subiculum and hippocampus, and eventually merges with the fimbria of the hippocampus. The fimbria goes on to become the fornix (MM: 2006-10-26). TODO - check xref: NCIT:C32058 ! Alveus BAMS:Alv BAMS:alv BIRNLEX:1510 DHBA:10570 FMA:83867 HBA:9234 MBA:466 NCIT:C32058 UMLS:C0228247 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=186 alveus alveus of hippocampus neuraxis alveus uberon CA2 alveus alveus hippocampi alveus of fornix alveus of the hippocampus UBERON:0007639 hippocampus alveus NIFSTD Regional part of fornix consisting of a thin layer of white matter on the surface of the hippocampal formation, bordering the wall of the lateral ventricle and composed of white, myelinated fibers. The alveus arises from cell bodies in the subiculum and hippocampus, and eventually merges with the fimbria of the hippocampus. The fimbria goes on to become the fornix (MM: 2006-10-26). BIRNLEX:1510 UMLS:C0228247 BIRNLEX:1510 UMLS:C0228247 ncithesaurus:Alveus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=186 BIRNLEX:1510 alveus BIRNLEX:1510 alveus of hippocampus FMA:83867 neuraxis alveus FMA:83867 CA2 alveus BAMS:alv alveus hippocampi NeuroNames:186 alveus of fornix BAMS:alv alveus of the hippocampus BAMS:alv 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 consider moving MA:0000377 renal tubule here, as it includes the various segments (proximal etc) as subclasses, not parts FMA:17692 renal tubule region uberon region of renal tubule UBERON:0007685 region of nephron tubule consider moving MA:0000377 renal tubule here, as it includes the various segments (proximal etc) as subclasses, not parts MA renal tubule region FMA:17692 region of renal tubule FMA:17692 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 An axon tract that is part of a spinal cord. FMA:75683 NCIT:C12995 UMLS:C1519456 spinal cord tract uberon UBERON:0007699 tract of spinal cord cjm An axon tract that is part of a spinal cord. OBOL:automatic UMLS:C1519456 ncithesaurus:Spinal_Cord_Tract spinal cord tract FMA:75683 An axon tract that is part of a brain. the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts FMA:83848 brain tract uberon landmark tracts UBERON:0007702 tract of brain cjm An axon tract that is part of a brain. OBOL:automatic brain tract FMA:83848 landmark tracts DMBA:tracts 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 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 An endothelium that is part of a umbilical vein. BTO:0001416 CALOHA:TS-1081 uberon UBERON:0007777 umbilical vein endothelium BTO An endothelium that is part of a umbilical vein. 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 A sesamoid bone that is part of a manus. FMA:42353 sesamoid bone of hand uberon UBERON:0007997 sesamoid bone of manus FMA A sesamoid bone that is part of a manus. OBOL:automatic sesamoid bone of hand FMA:42353 A sesamoid bone that is part of a pes. FMA:45096 sesamoid bone of foot uberon UBERON:0008000 sesamoid bone of pes FMA A sesamoid bone that is part of a pes. OBOL:automatic sesamoid bone of foot FMA:45096 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 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 clavicle that is in the right side of a entire appendicular skeleton. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:13322 uberon UBERON:0008255 right clavicle FMA A clavicle that is in the right side of a entire appendicular skeleton. OBOL:automatic A clavicle that is in the left side of a entire appendicular skeleton. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:13323 uberon UBERON:0008256 left clavicle FMA A clavicle that is in the left side of a entire appendicular skeleton. OBOL:automatic The fibrous connective tissue that surrounds the root of a tooth, separating it from and attaching it to the alveolar bone. It extends from the base of the gingival mucosa to the fundus of the bony socket, and its main function is to hold the tooth in its socket[BTO]. The collagen fibers, running from the cementum to the alveolar bone, that suspend a tooth in its socket; they include apical, oblique, horizontal, and alveolar crest fibers, indicating that the orientation of the fibers varies at different levels[http://www.drugs.com/dict/desmodentium.html]. The fibrous connective tissue that surrounds the root of a tooth, separating it from and attaching it to the alveolar bone. It extends from the base of the gingival mucosa to the fundus of the bony socket, and its main function is to hold the tooth in its socket[BTO]. It consist of cells, extracellular compartment of fibers. The cells are fibroblast, epithelial, undifferentiated mesenchymal cells, bone and cementum cells. The extracellular compartment consists of collagen fibers bundles embedded in ground substance. The PDL substance has been estimated to be 70% water and is thought to have a significant effect on the tooth's ability to withstand stress loads[WP][BTO:0001020, Wikipedia:Periodontal_fiber, https://github.com/obophenotype/uberon/issues/21]. FMA treats periodontium and periodontal ligament as the same; it has a separate class desmodentium, which we place here even though it is classified as fetal in FMA BTO:0001020 CALOHA:TS-0763 EMAPA:35679 FMA:56665 GAID:1259 MA:0002467 fibra periodontalis periodontal fiber periodontal fibre uberon PDL alveolar periosteum alveolodental ligament alveolodental membrane desmodontium odontoperiosteum paradentium peridental membrane peridontal fiber peridontal fibre peridontal ligament peridontal ligament fiber peridontal ligament fibre peridontal membrane peridontium periodontium UBERON:0008266 periodontal ligament The:Periodontium.jpg FMA-moved BTO The fibrous connective tissue that surrounds the root of a tooth, separating it from and attaching it to the alveolar bone. It extends from the base of the gingival mucosa to the fundus of the bony socket, and its main function is to hold the tooth in its socket[BTO]. BTO:0001020 The collagen fibers, running from the cementum to the alveolar bone, that suspend a tooth in its socket; they include apical, oblique, horizontal, and alveolar crest fibers, indicating that the orientation of the fibers varies at different levels[http://www.drugs.com/dict/desmodentium.html]. The fibrous connective tissue that surrounds the root of a tooth, separating it from and attaching it to the alveolar bone. It extends from the base of the gingival mucosa to the fundus of the bony socket, and its main function is to hold the tooth in its socket[BTO]. It consist of cells, extracellular compartment of fibers. The cells are fibroblast, epithelial, undifferentiated mesenchymal cells, bone and cementum cells. The extracellular compartment consists of collagen fibers bundles embedded in ground substance. The PDL substance has been estimated to be 70% water and is thought to have a significant effect on the tooth's ability to withstand stress loads[WP][BTO:0001020, Wikipedia:Periodontal_fiber, https://github.com/obophenotype/uberon/issues/21]. FMA treats periodontium and periodontal ligament as the same; it has a separate class desmodentium, which we place here even though it is classified as fetal in FMA FMA fibra periodontalis periodontal fiber periodontal fibre PDL alveolar periosteum BTO:0001020 alveolodental ligament BTO:0001020 alveolodental membrane BTO:0001020 desmodontium BTO:0001020 odontoperiosteum BTO:0001020 paradentium BTO:0001020 peridental membrane BTO:0001020 peridontal fiber peridontal fibre peridontal ligament fiber peridontal ligament fibre peridontal membrane BTO:0001020 peridontium BTO:0001020 periodontium FMA:56665 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 BTO:0003122 uberon UBERON:0008339 microvascular endothelium BTO 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 jejunum. FMA:63301 uberon UBERON:0008343 intestinal villus of jejunum An intestinal villus in the jejunum. 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 The cells lining the proximal tubule are cuboidal epithelial cells with deep basal membrane invaginations that provide a large basal surface area. The long microvilli (the brush border) lining the tubule lumen, maximize luminal surface area and make these cells ideally suited for both reabsorptive and secretory functions. See https://github.com/obophenotype/uberon/issues/1305 BTO:0003576 FMA:64808 epithelium of proximal convoluted tubule epithelium of proximal renal tubule proximal renal tubule epithelium proximale tubular epithelium uberon proximal tubule epithelium UBERON:0008404 proximal tubular epithelium The cells lining the proximal tubule are cuboidal epithelial cells with deep basal membrane invaginations that provide a large basal surface area. The long microvilli (the brush border) lining the tubule lumen, maximize luminal surface area and make these cells ideally suited for both reabsorptive and secretory functions. Renal_Physiology:Section_7 _Chapter_3 epithelium of proximal convoluted tubule FMA:64808 epithelium of proximal renal tubule FMA:64808 proximal renal tubule epithelium FMA:64808 proximale tubular epithelium BTO:0003576 proximal tubule epithelium BTO:0003576 An epithelium that is part of a distal tubule. See https://github.com/obophenotype/uberon/issues/1305 BTO:0003948 uberon distal tubule epithelium UBERON:0008408 distal tubular epithelium BTO An epithelium that is part of a distal tubule. OBOL:automatic distal tubule epithelium BTO:0003948 A ridge of epidermal cells that will form the mammary placodes. consider splitting ridge (precursor) and milk line These buds are either located in the thoracic region in primates, in the inguinal area in ungulates or along the entire length of the trunk in rodents and pigs. In humans, milk lines appear in the seventh week of embryonic development The first manifestation of the mammary gland in many mammals is an elevated ridge or milk line, which then fragments into individual buds in specific regions lateral of the dorsal midline. After initial development of the milk lines they go into remission. in mouse, mammary gland development begins shortly after mid-gestation (about E10.5); epidermal cells within the milk line become columnar and multilayered, defining a ridge that protrudes above and below the plane of the single-layered primitive epidermis or periderm; by E11.5, five pairs of lens-shaped placodes form along the mammary line at the site of each future nipple.[MP] EMAPA:18541 mammary fold mammary gland ridge uberon mammary line milk line UBERON:0008425 mammary ridge A ridge of epidermal cells that will form the mammary placodes. GOC:dph mammary fold mammary gland ridge EMAPA:18541 mammary line milk line 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 thoracic vertebra. FMA:9143 uberon UBERON:0008432 thoracic vertebral foramen A vertebral foramen that is part of a thoracic vertebra. OBOL:automatic A neural arch that is part of a cervical vertebra. FMA:23893 arch of cervical vertebra uberon UBERON:0008434 cervical vertebral arch A neural arch that is part of a cervical vertebra. OBOL:automatic arch of cervical vertebra FMA:23893 A neural arch that is part of a thoracic vertebra. FMA:9151 arch of thoracic vertebra uberon UBERON:0008436 thoracic vertebral arch A neural arch that is part of a thoracic vertebra. OBOL:automatic arch of thoracic vertebra FMA:9151 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 A proximal epiphysis that is part of a tibia. FMA:33113 NCIT:C32722 UMLS:C0932431 head of tibia proximal end of tibia proximal tibial epiphysis upper end of tibia uberon UBERON:0008772 proximal epiphysis of tibia A proximal epiphysis that is part of a tibia. OBOL:automatic UMLS:C0932431 ncithesaurus:Head_of_the_Tibia head of tibia FMA:33113 proximal end of tibia FMA:33113 upper end of tibia FMA:33113 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 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 The distinguishing cell types of the lung alveolar tissue, including pulmonary epithelial cells (pneumocytes), alveolar capillary endothelial cells, interstitial cells (fibroblasts) and alveolar macrophages EMAPA:37942 uberon UBERON:0008870 pulmonary alveolar parenchyma The distinguishing cell types of the lung alveolar tissue, including pulmonary epithelial cells (pneumocytes), alveolar capillary endothelial cells, interstitial cells (fibroblasts) and alveolar macrophages MP:0010901 EMAPA:37942 MA:th The part of the airway consisting of a respiratory bronchiole and all of its branches EMAPA:37941 FMA:7313 NCIT:C33426 UMLS:C0225696 acinus pulmonaris arbor alveolaris lobulus pulmonis primarius primary pulmonary lobule respiratory lobule uberon UBERON:0008874 pulmonary acinus FMA The part of the airway consisting of a respiratory bronchiole and all of its branches MP:0010911 EMAPA:37941 MA:th UMLS:C0225696 ncithesaurus:Pulmonary_Acinus acinus pulmonaris FMA:7313 FMA:TA arbor alveolaris FMA:7313 FMA:TA lobulus pulmonis primarius FMA:7313 FMA:TA primary pulmonary lobule FMA:7313 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 multi-layer basement membrane between the dermis and epidermis that serves to adhere the dermis and epidermis, provide mechanical support for the epidermis, and forms a barrier to cells and large molecules across the junction EMAPA:37866 FMA:70963 NCIT:C62356 dermal-epidermal junction dermo-epidermal junction dermoepidermal junction epidermal dermol junction uberon UBERON:0008877 epidermal-dermal junction MP The multi-layer basement membrane between the dermis and epidermis that serves to adhere the dermis and epidermis, provide mechanical support for the epidermis, and forms a barrier to cells and large molecules across the junction MP:0011159 EMAPA:37866 MA:th dermal-epidermal junction FMA:70963 dermoepidermal junction FMA:70963 Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue. Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue.[VSAO] Newly formed organic bone matrix secreted by osteoblasts, that exists prior to calcification; it is comprised mainly of type I collagen fibers, chondroitin sulfate and osteocalci[ISBN:0-683-40008-8]n Note that in VSAO this was classified both as tissue and acellular extracellular matrix. Consider also the AEO class 'bone condensation'. is_a intercellular matrix in FMA. EMAPA:37923 FMA:66830 NCIT:C33228 UMLS:C0682561 VSAO:0000046 XAO:0004035 galen:Osteoid osteoid tissue pre-bone prebone prebone tissue uberon UBERON:0008883 osteoid Active:osteoblasts.jpg VSAO Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue. GO_REF:0000034 VSAO:0000046 Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue.[VSAO] 2012-08-14 VSAO:0000046 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 Newly formed organic bone matrix secreted by osteoblasts, that exists prior to calcification; it is comprised mainly of type I collagen fibers, chondroitin sulfate and osteocalci[ISBN:0-683-40008-8]n ISBN:0-683-40008-8 MP:0010924 Note that in VSAO this was classified both as tissue and acellular extracellular matrix. Consider also the AEO class 'bone condensation'. is_a intercellular matrix in FMA. VSAO EMAPA:37923 MA:th UMLS:C0682561 ncithesaurus:Osteoid osteoid tissue pre-bone PSPUB:0000170 prebone VSAO:curator prebone tissue FMA:66830 MP:0002113 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 Volcano-shaped lateral line sensory organ located in characteristic positions within the skin epithelium and containing hair cells and their support elements. Type of mechanoreceptive organ of the lateral line which are arranged in lines on the body surface. These organs are constituted by hair cells and supporting cells and it is located in the epidermis with its hair cells exposed to the surface. Absent in some caecilians. These receptors receive afferent and efferent innervations.[AAO] Volcano-shaped lateral line sensory organ located in characteristic positions within the skin epithelium and containing hair cells and their support elements. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO] relationship loss: part_of lateral line receptor organ (AAO:0001001)[AAO] relationship loss: subclass lateral line receptor (AAO:0010705)[AAO] lateral line organ AAO:0001004 EFO:0003513 TAO:0000243 ZFA:0000243 cyatocïde@fr lateral line neuromast neuromast organ neuromaste superficiel@fr neuromasts uberon UBERON:0008904 neuromast ZFA Volcano-shaped lateral line sensory organ located in characteristic positions within the skin epithelium and containing hair cells and their support elements. ZFIN:ZDB-PUB-961014-576 Type of mechanoreceptive organ of the lateral line which are arranged in lines on the body surface. These organs are constituted by hair cells and supporting cells and it is located in the epidermis with its hair cells exposed to the surface. Absent in some caecilians. These receptors receive afferent and efferent innervations.[AAO] 2012-06-20 AAO:0001004 AAO AAO:EJS Volcano-shaped lateral line sensory organ located in characteristic positions within the skin epithelium and containing hair cells and their support elements. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO] 2012-08-14 TAO:0000243 TAO ZFIN:curator relationship loss: part_of lateral line receptor organ (AAO:0001001)[AAO] 2012-06-20 AAO:0001004 AAO relationship loss: subclass lateral line receptor (AAO:0010705)[AAO] 2012-06-20 AAO:0001004 AAO lateral line organ ZFA:0000243 cyatocïde@fr TAO:0000243 lateral line neuromast ZFA:0000243 neuromast organ PHENOSCAPE:wd neuromaste superficiel@fr TAO:0000243 neuromasts ZFA:0000243 Cranial nerves that carry afferent and efferent fibers for the lateral line system. Any of the sensory nerves that innervate mechano- and electroreceptors of the lateral line system. The lateral line nerves may be separated in two components, anterior and posterior, in relation to the position of its roots with respect to the otic capsule. These nerves develop from lateral line placodes.[AAO] relationship loss: innervates lateral line receptor organ (AAO:0001001)[AAO] relationship type change: part_of_proxy lateral line system (AAO:0000975) CHANGED TO: part_of lateral line system (UBERON:0002540)[AAO] AAO:0010077 TAO:0001479 ZFA:0001479 lateral line nerves uberon UBERON:0008906 lateral line nerve NCBIBook:NBK53175 Cranial nerves that carry afferent and efferent fibers for the lateral line system. ZFIN:curator Any of the sensory nerves that innervate mechano- and electroreceptors of the lateral line system. The lateral line nerves may be separated in two components, anterior and posterior, in relation to the position of its roots with respect to the otic capsule. These nerves develop from lateral line placodes.[AAO] 2012-06-20 AAO:0010077 AAO AAO:SIQ relationship loss: innervates lateral line receptor organ (AAO:0001001)[AAO] 2012-06-20 AAO:0010077 AAO relationship type change: part_of_proxy lateral line system (AAO:0000975) CHANGED TO: part_of lateral line system (UBERON:0002540)[AAO] 2012-06-20 AAO:0010077 AAO lateral line nerves ZFA:0001479 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 . uberon UBERON:0008921 substratum of layer of retina . UBERON:CL_meeting_20110725 A retinal neural layer that is immediately adjacent to the inner nuclear layer and comprises 20 percent of the inner plexiform layer of retina. CP:0000113 uberon UBERON:0008922 sublaminar layer S1 A retinal neural layer that is immediately adjacent to the inner nuclear layer and comprises 20 percent of the inner plexiform layer of retina. GOC:tfm A retinal neural layer that is immediately adjacent to the S1 and S3 layers and comprises 20 percent of the inner plexiform layer of retina. CP:0000114 uberon UBERON:0008923 sublaminar layer S2 A retinal neural layer that is immediately adjacent to the S1 and S3 layers and comprises 20 percent of the inner plexiform layer of retina. GOC:tfm A retinal neural layer that is immediately adjacent to the S2 and S4 layers and comprises 20 percent of the inner plexiform layer of retina. CP:0000115 uberon UBERON:0008924 sublaminar layer S3 A retinal neural layer that is immediately adjacent to the S2 and S4 layers and comprises 20 percent of the inner plexiform layer of retina. GOC:tfm A retinal neural layer that is immediately adjacent to the S3 and S5 layer and comprises 20 percent of the inner plexiform layer of retina. CP:0000116 uberon UBERON:0008925 sublaminar layer S4 A retinal neural layer that is immediately adjacent to the S3 and S5 layer and comprises 20 percent of the inner plexiform layer of retina. GOC:tfm A retinal neural layer that is immediately adjacent to the retinal ganglion cell layer and comprises 20 percent of the ganglion plexiform layer of retina. CP:0000117 uberon UBERON:0008926 sublaminar layer S5 A retinal neural layer that is immediately adjacent to the retinal ganglion cell layer and comprises 20 percent of the ganglion plexiform layer of retina. GOC:tfm One of sublaminar layers S1 or S2. CP:0000118 uberon UBERON:0008927 sublaminar layers S1 or S2 One of sublaminar layers S1 or S2. GOC:tfm One of sublaminar layers S2 or S3. CP:0000119 uberon UBERON:0008928 sublaminar layers S2 or S3 One of sublaminar layers S2 or S3. GOC:tfm One of sublaminar layers S4 or S5. CP:0000120 uberon UBERON:0008929 sublaminar layers S4 or S5 One of sublaminar layers S4 or S5. GOC:tfm 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 A sac containing the developing tooth and its odontogenic organ. The dental follicle (DF) differentiates into the periodontal ligament. In addition, it may be the precursor of other cells of the periodontium, including osteoblasts, cementoblasts and fibroblasts. They develop into the alveolar bone, the cementum with Sharpey's fibers and the periodontal ligament fibers respectively. BTO:0000337 EMAPA:35275 MA:0003121 NCIT:C34138 uberon dental sac tooth follicle UBERON:0008969 dental follicle A sac containing the developing tooth and its odontogenic organ. The dental follicle (DF) differentiates into the periodontal ligament. In addition, it may be the precursor of other cells of the periodontium, including osteoblasts, cementoblasts and fibroblasts. They develop into the alveolar bone, the cementum with Sharpey's fibers and the periodontal ligament fibers respectively. dental sac MA:0003121 tooth follicle BTO:0000337 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 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 Any region of a nephron tubule that is straight. Examples: distal convoluted tubule, proximal convoluted tuble. EMAPA:37489 MA:0002634 kidney straight tubule straight tubule uberon UBERON:0009035 renal straight tubule Any region of a nephron tubule that is straight. Examples: distal convoluted tubule, proximal convoluted tuble. EMAPA:37489 MA:th kidney straight tubule MA:0002634 A germinal center that is located in a lymph node germinal center BTO:0003671 CALOHA:TS-1269 EMAPA:35528 MA:0002989 NCIT:C49757 uberon lymph node activated zone lymph node central zone lymph node light zone lymph node nodule UBERON:0009039 lymph node germinal center MA A germinal center that is located in a lymph node CL:tm germinal center BTO:0003671 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 This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medullar parallel to the descending limb KUPO:0001003 uberon UBERON:0009089 inner medulla vasa recta descending limb KUPO This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medullar parallel to the descending limb CL This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medullar parallel to the descending limb KUPO:0001004 uberon UBERON:0009090 outer medulla vasa recta descending limb KUPO This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medullar parallel to the descending limb CL This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the ascending limb KUPO:0001005 uberon UBERON:0009091 vasa recta ascending limb KUPO This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the ascending limb CL This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medulla parallel to the ascending limb KUPO:0001006 uberon UBERON:0009092 inner medulla vasa recta ascending limb KUPO This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medulla parallel to the ascending limb CL This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medulla parallel to the ascending limb KUPO:0001007 uberon UBERON:0009093 outer medulla vasa recta ascending limb KUPO This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medulla parallel to the ascending limb CL KUPO:0001009 papillary tip papillary tips uberon UBERON:0009095 tip of renal papilla KUPO papillary tip KUPO:0001009 papillary tips KUPO:0001009 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 An ectodermal placode that will develop into the components of the lateral line system TODO - compare with protoneuromast Specialized series of dorsolateral ectodermal placodes.[AAO] AAO:0010718 XAO:0000440 uberon lateral line placodes UBERON:0009128 lateral line placode ISBN:0471888893 An ectodermal placode that will develop into the components of the lateral line system Specialized series of dorsolateral ectodermal placodes.[AAO] 2012-06-20 AAO:0010718 AAO AAO:SIQ lateral line placodes XAO:0000440 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 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 A sphenoid endochondral element that is composed primarily of a pre-cartilage condensation. EHDAA2:0003446 EMAPA:18015 uberon UBERON:0009191 sphenoid bone pre-cartilage condensation EHDAA2 EHDAA2 EHDAA2 EHDAA2 A sphenoid endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic A sphenoid endochondral element that is composed primarily of cartilage tissue. EHDAA2:0001888 sphenoid bone cartilage condensation uberon UBERON:0009193 sphenoid cartilage element EHDAA2 A sphenoid endochondral element that is composed primarily of cartilage tissue. OBOL:automatic sphenoid bone cartilage condensation EHDAA2:0001888 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 This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the descending limb KUPO:0001002 uberon UBERON:0009202 vasa recta descending limb KUPO This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the descending limb CL Mesenchyme that is part of a medial nasal prominence. EHDAA2:0001077 EMAPA:16810 FMA:312659 uberon UBERON:0009204 medial nasal process mesenchyme EHDAA2 lexical Mesenchyme that is part of a medial nasal prominence. OBOL:automatic 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 lexical 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 The axilla is the area directly under the joint where the forelimb connects to the shoulder. axillary CALOHA:TS-2208 EFO:0001395 FMA:24864 MESH:D001365 NCIT:C12674 UMLS:C0004454 galen:Axilla arm pit armpit axillary region regio axillaris uberon armpits axilla axillae axillary region oxter underarm UBERON:0009472 axilla http://upload.wikimedia.org/wikipedia/commons/f/f2/Gray411.png FMA The axilla is the area directly under the joint where the forelimb connects to the shoulder. UMLS:C0004454 ncithesaurus:Axilla arm pit armpit axillary region FMA:24864 regio axillaris FMA:TA armpits axilla axillae axillary region oxter underarm 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 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 A proximal straight tubule that is part of a pronephros. TAO:0002239 ZFA:0001621 uberon proximal straight tubules UBERON:0009622 pronephric proximal straight tubule true A proximal straight tubule that is part of a pronephros. ZFIN:ZDB-PUB-071029-9 proximal straight tubules TAO:0002239 The paired bundles of nerve fibers entering and leaving the spinal cord at each segment. The dorsal and ventral nerve roots join to form the mixed segmental spinal nerves. The dorsal roots are generally afferent, formed by the central projections of the spinal (dorsal root) ganglia sensory cells, and the ventral roots efferent, comprising the axons of spinal motor and autonomic preganglionic neurons. There are, however, some exceptions to this afferent/efferent rule. ZFA has part_of to spinal cord but this causes spatial disjointness violations (CNS/PNS) BTO:0000883 DHBA:146035120 FMA:14060 GAID:717 MESH:D013126 NCIT:C12791 UMLS:C0037940 ZFA:0005578 root of spinal nerve spinal neural root spinal root uberon UBERON:0009623 spinal nerve root FMA The paired bundles of nerve fibers entering and leaving the spinal cord at each segment. The dorsal and ventral nerve roots join to form the mixed segmental spinal nerves. The dorsal roots are generally afferent, formed by the central projections of the spinal (dorsal root) ganglia sensory cells, and the ventral roots efferent, comprising the axons of spinal motor and autonomic preganglionic neurons. There are, however, some exceptions to this afferent/efferent rule. MESH:A08.800.800.720.725 ZFA has part_of to spinal cord but this causes spatial disjointness violations (CNS/PNS) ZFA UMLS:C0037940 ncithesaurus:Spinal_Nerve_Root root of spinal nerve FMA:14060 spinal neural root FMA:14060 spinal root BTO:0000883 A spinal nerve root that is part of a thoracic nerve. BIRNLEX:836 FMA:14064 nerve root part of thoracic spinal cord thoracic nerve root thoracic neural root uberon UBERON:0009630 root of thoracic nerve A spinal nerve root that is part of a thoracic nerve. OBOL:automatic nerve root part of thoracic spinal cord NIF:NIF thoracic nerve root FMA:14064 thoracic neural root FMA:14064 BIRNLEX:955 FMA:16422 NCIT:C12893 UMLS:C0581631 cervical neural root cervical spinal root nerve root part of cervical spinal cord root of cervical spinal nerve uberon UBERON:0009632 root of cervical nerve UMLS:C0581631 ncithesaurus:Cervical_Spinal_Nerve_Root cervical neural root FMA:16422 cervical spinal root FMA:16422 nerve root part of cervical spinal cord NIF:NIF root of cervical spinal nerve FMA:16422 uberon orbitosphenoid center UBERON:0009638 merge with sphenoid lesser wing cartilage element? orbitosphenoid ossification center EMAPA:35878 MA:0001859 uberon UBERON:0009644 trachea non-cartilage connective tissue MA 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 eyelid connective tissue that is part of a hypodermis. EMAPA:37533 FMA:63975 MA:0001252 NCIT:C49226 UMLS:C1707991 uberon superficial fascia of eyelid UBERON:0009648 eyelid subcutaneous connective tissue A eyelid connective tissue that is part of a hypodermis. OBOL:automatic EMAPA:37533 MA:th UMLS:C1707991 ncithesaurus:Eyelid_Subcutaneous_Connective_Tissue superficial fascia of eyelid FMA:63975 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 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 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 The primordial mass of tissue formed by the merging of the medial nasal prominences of the embryo; it contributes to the intermaxillary portion of the upper jaw, the prolabial portion of the upper lip, and the primary palate. requires verification. Note EHDAA2 has this as coming from both lateral and medial prominences. See also: median cleft lip EHDAA2:0000868 EHDAA:7856 FMA:295872 uberon globular process globular processes of his intermaxillary segment UBERON:0009714 intermaxillary process EHDAA2-modified inconsistent EHDAA2 EHDAA2 The primordial mass of tissue formed by the merging of the medial nasal prominences of the embryo; it contributes to the intermaxillary portion of the upper jaw, the prolabial portion of the upper lip, and the primary palate. globular process globular processes of his intermaxillary segment 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 One of sublaminar layers S3 or S4. CP:0001040 uberon UBERON:0009731 sublaminar layers S3 or S4 One of sublaminar layers S3 or S4. GOC:plr One of sublaminar layers S1, S2, or S5. CP:0001041 uberon UBERON:0009732 sublaminar layers S1 or S2 or S5 One of sublaminar layers S1, S2, or S5. GOC:plr One of sublaminar layers S1, S2, or S3. CP:0001042 uberon UBERON:0009733 sublaminar layers S1 or S2 or S3 One of sublaminar layers S1, S2, or S3. GOC:plr One of sublaminar layers S2, S3, or S4. CP:0001043 uberon UBERON:0009734 sublaminar layers S2 or S3 or S4 One of sublaminar layers S2, S3, or S4. GOC:plr One of sublaminar layers S1, S3, or S4. CP:0001044 uberon UBERON:0009735 sublaminar layers S1 or S3 or S4 One of sublaminar layers S1, S3, or S4. GOC:plr One of sublaminar layers S3, S4, or S5. CP:0001045 uberon UBERON:0009736 sublaminar layers S3 or S4 or S5 One of sublaminar layers S3, S4, or S5. GOC:plr One of sublaminar layers S1, S2, S3, or S4. CP:0001046 uberon UBERON:0009737 sublaminar layers S1 or S2 or S3 or S4 One of sublaminar layers S1, S2, S3, or S4. GOC:plr 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 EMAPA:35113 FMA:69086 MA:0001887 adrenal cortical region uberon region of adrenal cortex UBERON:0009753 adrenal gland cortex zone MA adrenal cortical region FMA:69086 region of adrenal cortex FMA:69086 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 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 thin layer of connective tissue that lines the surface of the bony tissue that forms the medullary cavity of long bones endosteal FMA:32692 NCIT:C13183 UMLS:C0222658 uberon UBERON:0009859 endosteum http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg A thin layer of connective tissue that lines the surface of the bony tissue that forms the medullary cavity of long bones UMLS:C0222658 ncithesaurus:Endosteum 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 cortical nephrogenic niche cortical nephrogenic zone uberon nephrogenic tissue UBERON:0009871 nephrogenic zone Outer portion of the renal cortex. Site of formation of medullary and cortical elements. cortical nephrogenic niche cortical nephrogenic zone 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 One of a number of vertical folds, produced by an infolding of the mucous membrane and some of the muscular tissue in the upper half of the lumen of the anal canal[WP] FMA:15713 NCIT:C32067 UMLS:C0227428 column of Morgagni uberon columnae anales UBERON:0009882 anal column https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png One of a number of vertical folds, produced by an infolding of the mucous membrane and some of the muscular tissue in the upper half of the lumen of the anal canal[WP] UMLS:C0227428 ncithesaurus:Anal_Column column of Morgagni FMA:15713 columnae anales 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 A nerve root that extends_fibers_into a nerve connecting eye with brain. TODO - check. See comments for optic tract. FMA also has medial root. BIRNLEX:1328 FMA:84573 optic nerve root optic tract root root of optic tract uberon UBERON:0009906 root of optic nerve FMA A nerve root that extends_fibers_into a nerve connecting eye with brain. OBOL:automatic optic nerve root BIRNLEX:1328 optic tract root FMA:84573 root of optic tract FMA:84573 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 loose collection of neurons that reside in the rostral medulla close to the medullary surface, ventral and immediately caudal of nVII, that are crucial for CO2 sensing in the brain DHBA:12531 DMBA:17327 MA:0003022 uberon UBERON:0009918 retrotrapezoid nucleus The loose collection of neurons that reside in the rostral medulla close to the medullary surface, ventral and immediately caudal of nVII, that are crucial for CO2 sensing in the brain MP:0011406 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 check if the NIF class is actually a grouping class plexiform layer NLXANAT:20090405 uberon UBERON:0009950 olfactory bulb plexiform layer NIFSTD plexiform layer NLXANAT:20090405 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 A vertebrate nasal chemosensory system that is responsible for detecting intraspecific pheromonal cues as well as environmental odorants check relationship to olfactory system. Evolution: The morphological components of the VNS are found only in tetrapods, but the genetic components of the system have been found in teleost fish, in addition to tetrapods. In tetrapods, the VNS was thought to be the olfactory system for detecting pheromones, while the main olfactory system detected general odorants (Scalia and Winans 1975). However, experimental evidence suggests that there is not such a clear functional distinction (Restrepo et al. 2004; Baxi, Dorries, and Eisthen 2006; Spehr et al. 2006; Kelliher 2007). Sea lampreys produce unique bile acids which act as pheromones both in migration and mate finding (Li, Sorensen, and Gallaher 1995; Li et al. 2002; Siefkes and Li 2004). However, bile acids in teleost fish are known to require components of the main olfactory signal transduction pathway (Hansen et al. 2003), and interruption of the VNS signal transduction pathway had no effect on bile acid olfactory response (Hansen et al. 2003)[Grus - EVOLUTION OF THE VOMERONASAL SYSTEM VIEWED THROUGH SYSTEM-SPECIFIC GENES] uberon UBERON:0009954 vomeronasal system A vertebrate nasal chemosensory system that is responsible for detecting intraspecific pheromonal cues as well as environmental odorants 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 conducting pathway in the conducting tissue of heart through which electrical activity spreads from the SA node to the AV node. include 3 subtypes? evidence is sparse [http://www.gpnotebook.co.uk/simplepage.cfm?ID=-483065798] There is some functional evidence for the existence of specialized conducting pathways within the atria (termed internodal tracts), although this is controversial FMA:9479 interatrial conduction tract internodal conduction tract internodal fasciculus internodal tract muscle tissue uberon UBERON:0009966 internodal tract cjm FMA A conducting pathway in the conducting tissue of heart through which electrical activity spreads from the SA node to the AV node. evidence is sparse [http://www.gpnotebook.co.uk/simplepage.cfm?ID=-483065798] There is some functional evidence for the existence of specialized conducting pathways within the atria (termed internodal tracts), although this is controversial internodal fasciculus FMA:9479 internodal tract muscle tissue FMA:9479 EMAPA:37751 FMA:62815 MA:0000761 NCIT:C33605 UMLS:C1179415 sinus lienalis sinus splenicus splenic sinus venous sinus of red pulp of spleen uberon UBERON:0009967 spleen venous sinus cjm MA EMAPA:37751 MA:th UMLS:C1179415 ncithesaurus:Splenic_Sinus sinus lienalis FMA:TA sinus splenicus FMA:TA splenic sinus FMA:62815 venous sinus of red pulp of spleen FMA:62815 FMA:64804 stato-acoustic epithelium uberon UBERON:0009969 statoacoustic epithelium FMA stato-acoustic epithelium FMA:64804 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 one of the gastric glands that secretes the hydrochloric acid of the gastric juice[Stedman's]. FMA has this as part of both the fundus and the body, but these are largely spatially disjoint. gastric gland FMA:14921 FMA:14923 acid gland glandula gastrica propria main gastric gland oxyntic gland principal gland of fundus of stomach uberon Wassman gland gastric follicle UBERON:0009971 principal gastric gland FMA one of the gastric glands that secretes the hydrochloric acid of the gastric juice[Stedman's]. MP:0003892 FMA has this as part of both the fundus and the body, but these are largely spatially disjoint. FMA gastric gland MP:0003892 acid gland glandula gastrica propria FMA:14921 main gastric gland FMA:14921 oxyntic gland FMA:14921 principal gland of fundus of stomach FMA:14923 Wassman gland MP:0003892 gastric follicle MP:0003892 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 vascularized and branched structures arising from the rodent trophoblast-derived epithelium that allow an increase its surface area for the efficient exchange of nutrients and wastes between the maternal and fetal circulation villous of placental labyrinth uberon placental labyrinth villi UBERON:0010005 placental labyrinth villous MP The vascularized and branched structures arising from the rodent trophoblast-derived epithelium that allow an increase its surface area for the efficient exchange of nutrients and wastes between the maternal and fetal circulation MP:0011522 placental labyrinth villi A regional part of brain consisting of multiple brain regions that are not related through a simple volummetric part of hierarchy, e.g., basal ganglia[NIF]. May be obsoleted. FMA:256381 NLXANAT:20090509 uberon set of nuclei of neuraxis UBERON:0010009 aggregate regional part of brain A regional part of brain consisting of multiple brain regions that are not related through a simple volummetric part of hierarchy, e.g., basal ganglia[NIF]. NLXANAT:20090509 set of nuclei of neuraxis FMA:256381 Subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum. it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the collection of all BGs-singular. it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done. All nuclei of the mammalian basal ganglia are also present in the oldest vertebrates.[well established][VHOG] BAMS:BG BIRNLEX:826 BM:Tel-BG DHBA:10331 EMAPA:32673 FMA:84013 GAID:617 HBA:4275 HBA:4276 MA:0000184 MBA:623 MESH:A08.186.211.730.885.105 NCIT:C12447 PBA:128012596 PBA:4001 UMLS:C0004781 VHOG:0001696 basal ganglia basal ganglia set basal nuclei (basal ganglia) set of basal ganglia uberon basal nuclei cerebral nuclei set of basal nuclei subcortical nuclei UBERON:0010011 collection of basal ganglia FMA FMA MA NIF Subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum. BIRNLEX:826 All nuclei of the mammalian basal ganglia are also present in the oldest vertebrates.[well established][VHOG] 2012-09-17 VHOG:0001696 VHOG DOI:10.1016/j.cub.2011.05.001 Stephenson-Jones M, Samuelsson E, Ericsson J, Robertson B, Grillner S, Evolutionary conservation of the basal ganglia as a common vertebrate mechanism for action selection. Current Biology (2011) UMLS:C0004781 ncithesaurus:Basal_Ganglia basal ganglia FMA:84013 basal ganglia set FMA:84013 basal nuclei (basal ganglia) PBA:BN set of basal ganglia FMA:84013 cerebral nuclei NeuroNames:2677 set of basal nuclei FMA:84013 subcortical nuclei NeuroNames:2677 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 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 The fundus glands (or fundic glands, or gastric glands) are found in the body and fundus of the stomach. They are simple tubes, two or more of which open into a single duct. Consider FMA:14923 ! Principal gland of fundus of stomach. Added part_of to mucosa to be consistent with FMA pattern (note that Kardong places this in the glandular epithelium) EMAPA:27161 NCIT:C32643 UMLS:C0017130 fundal gland fundus gland gastric fundal gland gastric fundus gland gastric gland of fundus of stomach uberon glandulae gastricae UBERON:0010038 fundic gastric gland http://upload.wikimedia.org/wikipedia/commons/d/d7/Fundic_gland_polyp_%281%29.jpg The fundus glands (or fundic glands, or gastric glands) are found in the body and fundus of the stomach. They are simple tubes, two or more of which open into a single duct. UMLS:C0017130 ncithesaurus:Fundic_Gland glandulae gastricae 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 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 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 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 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 The lateral line consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head and body of all fishes and most amphibians. The lateral line develops from cranial ectodermal placodes situated behind the ear and between the eye and ear. AAO:0011128 TAO:0001469 XAO:0004002 ZFA:0001469 lateral lines uberon UBERON:0010202 lateral line ZFA ZFA The lateral line consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head and body of all fishes and most amphibians. The lateral line develops from cranial ectodermal placodes situated behind the ear and between the eye and ear. ZFA:0001469 lateral lines ZFA:0001469 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 An exocrine gland whose secretions are excreted via exocytosis from secretory cells into an epithelial-walled duct or ducts and thence onto a bodily surface or into the lumen; the gland releases its product and no part of the gland is lost or damaged. merocrine BTO:0002324 MA:0003041 uberon UBERON:0010243 merocrine gland An exocrine gland whose secretions are excreted via exocytosis from secretory cells into an epithelial-walled duct or ducts and thence onto a bodily surface or into the lumen; the gland releases its product and no part of the gland is lost or damaged. MGI:anna MP:0013544 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. A single extraembryonic epithelium, which closes the germband dorsally. May be obsoleted once added to insect ontology. Coordinate with cell type in CL BTO:0004800 EFO:0000250 FBbt:00000095 uberon amnion-serosa UBERON:0010302 amnioserosa A single extraembryonic epithelium, which closes the germband dorsally. amnion-serosa BTO:0004800 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 One of the three major regions of the conjunctiva. FMA:59023 conjunctiva region region of conjunctiva uberon UBERON:0010305 subdivision of conjunctiva One of the three major regions of the conjunctiva. region of conjunctiva FMA:59023 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 Mesenchyme that is part of a developing eyelid. EMAPA:32759 uberon UBERON:0010330 eyelid mesenchyme Mesenchyme that is part of a developing eyelid. 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 A otic capsule endochondral element that is composed primarily of a pre-cartilage condensation. EHDAA2:0000833 otic capsule anlage uberon UBERON:0010349 otic capsule pre-cartilage condensation A otic capsule endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic 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 An arch-shaped structure of the vertebra that extends dorsally (neural arch) or ventrally (hemal arch) from the vertebral centrum (...) certain common components [of vertebral structure] are found in nearly all vertebrate. A representative vertebra has a vertebral arch or neural arch, which extends dorsally around the spinal cord.[well established][VHOG] Note that humans do not have hemal arches, so VA=NA for FMA EMAPA:36614 FMA:11946 arch of vertebra arcus vertebrae (vertebralis) vertebra arch vertebral arch uberon UBERON:0010358 arch of centrum of vertebra FMA An arch-shaped structure of the vertebra that extends dorsally (neural arch) or ventrally (hemal arch) from the vertebral centrum (...) certain common components [of vertebral structure] are found in nearly all vertebrate. A representative vertebra has a vertebral arch or neural arch, which extends dorsally around the spinal cord.[well established][VHOG] 2012-09-17 VHOG:0001670 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.270 Note that humans do not have hemal arches, so VA=NA for FMA FMA arch of vertebra FMA:11946 arcus vertebrae (vertebralis) FMA:11946 vertebra arch MA:0001453 vertebral arch FMA:11946 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 A vasculature that is part of a conjunctiva. FMA:70887 conjunctival veins conjunctival veins set set of conjunctival veins venae conjunctivales uberon UBERON:0010366 conjunctival vasculature A vasculature that is part of a conjunctiva. OBOL:automatic conjunctival veins FMA:70887 conjunctival veins set FMA:70887 set of conjunctival veins FMA:70887 venae conjunctivales FMA:TA A vein that is part of a conjunctiva. conjunctival blood vessel FMA:70887 uberon UBERON:0010367 conjunctival vein A vein that is part of a conjunctiva. OBOL:automatic 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 the neurons that innervate the esophagus, stomach, small and large bowel EMAPA:37479 MA:0001145 uberon UBERON:0010380 enteric nerve the neurons that innervate the esophagus, stomach, small and large bowel MGI:csmith MP:0001046 EMAPA:37479 MA:th A lymphoid follicle that is part of a Peyer's patch. MA:0000732 peyer's patch follicle uberon UBERON:0010386 Peyer's patch follicle A lymphoid follicle that is part of a Peyer's patch. OBOL:automatic peyer's patch follicle MA:0000732 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 An unstimulated network of follicular dendritic cells and small resting B cells in the lymph node cortex. EMAPA:35530 FMA:312350 MA:0000743 primary follicle of lymph node uberon UBERON:0010395 lymph node primary follicle An unstimulated network of follicular dendritic cells and small resting B cells in the lymph node cortex. MP:0002345 Any layer of the epidermis that is superior to the stratum basale suprabasal layer EMAPA:35315 MA:0000808 suprabasal cell layer of skin suprabasal layer of epidermis uberon UBERON:0010402 epidermis suprabasal layer Any layer of the epidermis that is superior to the stratum basale MP:0001233 suprabasal layer MP:0001233 The part of the future brain that is derived from the mantle layer of the neural tube not clear if the MA/EMAPA classes refer specifically to the cortical subset. DHBA class incldues non-neocortex derivatives so it belongs here brain marginal zone DHBA:10508 EMAPA:32680 MA:0000812 uberon UBERON:0010403 brain marginal zone The part of the future brain that is derived from the mantle layer of the neural tube not clear if the MA/EMAPA classes refer specifically to the cortical subset. DHBA class incldues non-neocortex derivatives so it belongs here MA brain marginal zone MA:0000812 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 part of the secondary follicle in which naive B cells reside along with some helper T cells, macrophages and follicular dendritic cells; these are displaced by the expanding germinal centre and form a 'mantle' around it EMAPA:37661 MA:0002990 lymph node B cell corona lymph node dark zone lymph node follicular mantle lymph node inactive zone lymph node peripheral zone uberon UBERON:0010420 lymph node follicular corona MA A part of the secondary follicle in which naive B cells reside along with some helper T cells, macrophages and follicular dendritic cells; these are displaced by the expanding germinal centre and form a 'mantle' around it MP:MP EMAPA:37661 MA:th lymph node B cell corona CL:tm lymph node dark zone CL:tm lymph node follicular mantle MA:0002990 lymph node inactive zone CL:tm lymph node peripheral zone CL:tm The area of the (spleen) secondary B follicle that surrounds the germinal center and harbors the small recirculating B lymphocytes B cell domain of the spleen B lymphocyte domain of the spleen lymphocytic corona splenic corona EMAPA:37962 follicle mantle spleen B cell corona spleen B-cell corona spleen lymphocytic corona splenic B cell corona uberon spleen mantle zone UBERON:0010421 spleen B cell corona CL:tm The area of the (spleen) secondary B follicle that surrounds the germinal center and harbors the small recirculating B lymphocytes CL:tm B cell domain of the spleen MP:0002360 lymphocytic corona CL:tm MP:0002360 splenic corona CL:tm EMAPA:37962 MA:th follicle mantle MP:0002360 spleen B cell corona MP:0002360 spleen B-cell corona MP:0002360 spleen lymphocytic corona CL:tm MP:0002360 splenic B cell corona MP:0002360 spleen mantle zone CL:tm MP:0002360 A lymphoid follicle containing naive B cells The cortex of lymph nodes, the white pulp of spleen, and mucosa associated lymphoid tissue all have these primary follicles FMA:55223 primary lymphoid follicle primary lymphoid nodule uberon primary follicle UBERON:0010422 primary nodular lymphoid tissue FMA A lymphoid follicle containing naive B cells CL:tm primary lymphoid nodule FMA:55223 A primary nodular lymphoid tissue that is part of a tonsil. FMA:86018 uberon lymphoid nodule of tonsil UBERON:0010423 primary lymphoid nodule of tonsil FMA A primary nodular lymphoid tissue that is part of a tonsil. OBOL:automatic lymphoid nodule of tonsil FMA:86018 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 An organ that is capable of detecting electrical stimulus electric sense organ electroreception organ uberon UBERON:0010521 electroreceptor organ An organ that is capable of detecting electrical stimulus 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 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 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 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 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 orbitosphenoid endochondral element that is composed primarily of a pre-cartilage condensation. EHDAA2:0003449 uberon UBERON:0010728 sphenoid lesser wing pre-cartilage condensation EHDAA2 EHDAA2 A orbitosphenoid endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic 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 lymphoid follicle that is part of a lymph node. EMAPA:35527 MA:0000742 follicle of lymph node uberon UBERON:0010748 lymph node follicle issues/7 MP-def A lymphoid follicle that is part of a lymph node. OBOL:automatic A secondary follicle that is located in a lymph node EMAPA:35531 FMA:312352 MA:0000744 uberon UBERON:0010753 lymph node secondary follicle MA A secondary follicle that is located in a lymph node CL:tm A collection of activated B cells at the center of a secondary follicle, formed after B cells become activated and migrate to the center. BTO:0003671 EV:0100051 MESH:D018858 NCIT:C13337 UMLS:C0282491 central zone of follice light zone of follicle reaction center of follicle uberon lymhpoid nodule nodule UBERON:0010754 A germinal center is a specialized microenvironment formed when activated B cells enter lymphoid follicles. Germinal centers are the foci for B cell proliferation and somatic hypermutation.[GO] germinal center Germinal:center.svg A collection of activated B cells at the center of a secondary follicle, formed after B cells become activated and migrate to the center. CL:tm UMLS:C0282491 ncithesaurus:Germinal_Center central zone of follice CL:tm light zone of follicle CL:tm reaction center of follicle CL:tm lymhpoid nodule CL:tm nodule CL:tm The part of the secondary follicle that surrounds the germinal center. consider making terminology consistent amongst subclasses - see https://github.com/obophenotype/uberon/issues/7 NCIT:C33053 UMLS:C1512987 dark zone of follicle inactive zone of follicle peripheral zone of follicle uberon B cell corona mantle zone UBERON:0010755 secondary follicle corona The part of the secondary follicle that surrounds the germinal center. CL:tm UMLS:C1512987 ncithesaurus:Mantle_Zone dark zone of follicle CL:tm inactive zone of follicle CL:tm peripheral zone of follicle CL:tm 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 cartilaginous condensation that has the potential to develop into a clavicle. In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal. EMAPA:18342 uberon UBERON:0010843 clavicle cartilage element A cartilaginous condensation that has the potential to develop into a clavicle. OBOL:automatic In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal. ISBN:978-0-12-319060-4 A pre-cartilage condensation that has the potential to develop into a clavicle. In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal. EMAPA:18026 uberon UBERON:0010844 clavicle pre-cartilage condensation A pre-cartilage condensation that has the potential to develop into a clavicle. OBOL:automatic In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal. ISBN:978-0-12-319060-4 A cartilaginous condensation that has the potential to develop into a tibia. EMAPA:18155 uberon UBERON:0010849 tibia cartilage element EMAPA A cartilaginous condensation that has the potential to develop into a tibia. OBOL:automatic A pre-cartilage condensation that has the potential to develop into a tibia. EHDAA2:0002036 uberon UBERON:0010850 tibia pre-cartilage condensation A pre-cartilage condensation that has the potential to develop into a tibia. OBOL:automatic 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 A primordium that develops into a clavicle bone. EHDAA2:0000254 clavicle primordium uberon UBERON:0010905 lateral part derives from a fish dermal bone while the medial part comes from a spur off the manubrium endochondral bone[JB] clavicle bone primordium EHDAA2 EHDAA2 mah shown in mouse PMC1352163 A primordium that develops into a clavicle bone. Skeletal element that is often isolated, small, and variable in composition. VSAO:0000132 uberon UBERON:0010911 Ossicles are composed of a combination skeletal tissues, including bone, calcified cartilage, hyaline cartilage, etc, and exhibit variable development across species. Ossicles are not necessarily jointed, and examples include the menisci of synovial joints, 'Panda's thumb' (radial sesamoid), cardiac skeletal elements, sclerotic bones, middle ear ossicles, and sesamoids. ossicle VSAO Skeletal element that is often isolated, small, and variable in composition. PSPUB:0000169 VSAO:0000132 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 A muscle organ that attaches_to a clavicle and attaches_to a occipital bone. EMAPA:37688 MA:0002276 NCIT:C52895 cleido-occipitalis cleido-occipitalis muscle cleidooccipital uberon UBERON:0010948 Some studies have indicated a supernumerary cleido-occipital muscle more or less separate from the sterno-cleido-mastoid muscle; The frequency of cleido-occipital muscle occurrence has been reported up to 33% cleidooccipital muscle A muscle organ that attaches_to a clavicle and attaches_to a occipital bone. OBOL:automatic EMAPA:37688 MA:th cleidooccipital MA:0002276 A muscle organ that has_muscle_insertion a occipital bone and has_muscle_origin a sternum. EMAPA:37702 MA:0002385 NCIT:C53069 UMLS:C1710196 sternooccipital uberon UBERON:0010949 sternooccipital muscle A muscle organ that has_muscle_insertion a occipital bone and has_muscle_origin a sternum. OBOL:automatic EMAPA:37702 MA:th UMLS:C1710196 ncithesaurus:Sternooccipital sternooccipital MA:0002385 EHDAA2:0002079 uberon UBERON:0010955 trapezius pre-muscle mass EHDAA2 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 EHDAA2:0000933 uberon UBERON:0010982 latissimus dorsi pre-muscle mass EHDAA2 EHDAA2 EHDAA2 EHDAA2:0000993 uberon UBERON:0010983 levator scapulae pre-muscle mass EHDAA2 EHDAA2 EHDAA2 EHDAA2:0001423 uberon UBERON:0010984 pectoral pre-muscle mass EHDAA2 EHDAA2 EHDAA2 EHDAA2:0001833 EHDAA:5992 serratus anterior pre-muscle mass uberon UBERON:0010986 serratus ventralis pre-muscle mass EHDAA2 EHDAA2 EHDAA2 serratus anterior pre-muscle mass EHDAA2:0001833 A thin layer of cartilage, usually hyaline, on the articular surface of bones in synovial joints. AEO:0000179 BTO:0001572 CALOHA:TS-0055 EFO:0001902 EMAPA:35149 FMA:12264 GAID:101 MA:0000487 MESH:A02.165.165 NCIT:C32144 UMLS:C0007303 galen:ArticularCartilage articular cartilage cartilago articularis uberon hyaline cartilage joint-associated cartilage UBERON:0010996 articular cartilage of joint MA Wikipedia A thin layer of cartilage, usually hyaline, on the articular surface of bones in synovial joints. BTO:0001572 UMLS:C0007303 ncithesaurus:Articular_Cartilage articular cartilage MA:0000487 cartilago articularis FMA:12264 hyaline cartilage BTO:0001572 joint-associated cartilage AEO:0000179 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 channel containing perilymph passing through the temporal bone, connecting the scala tympani of the cochlea to the subarachnoid space. relationship to FMA class unclear Duct that contains perilymph[ZFA:0005461, ZFIN:curator]. AAO:0000136 EMAPA:35677 FMA:77822 MA:0000248 ZFA:0005461 ductus perilymphaticus uberon cochlear aqueduct perilymphatic duct perilymphatic space UBERON:0011060 perilymphatic channel MA A channel containing perilymph passing through the temporal bone, connecting the scala tympani of the cochlea to the subarachnoid space. MESH:A09.246.631.246.280 Duct that contains perilymph[ZFA:0005461, ZFIN:curator]. ZFA:0005461, ZFIN:curator ductus perilymphaticus AAO:0000136 cochlear aqueduct FMA:77822 MESH:A09.246.631.246.280 perilymphatic duct MESH:A09.246.631.246.280 perilymphatic space MA:0000248 A ligament that is part of a knee joint. FMA:44580 knee joint ligament uberon UBERON:0011088 ligament of knee joint A ligament that is part of a knee joint. OBOL:automatic knee joint ligament FMA:44580 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 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 Ossicle that is part of the appendicular skeleton. VSAO:0000131 XAO:0004194 ossicle of appendicular skeleton uberon UBERON:0011141 Examples of appendicular ossicles include the patella and meniscus of the knee joint. appendicular ossicle Ossicle that is part of the appendicular skeleton. PSPUB:0000169 VSAO:0000131 ossicle of appendicular skeleton OBOL:automatic Ossicle that is part of the axial skeleton. VSAO:0000133 ossicle of axial skeleton ossicle of postcranial-axial skeleton uberon vertebral ossicle UBERON:0011142 Examples of axial ossicles include the ossified tendons adjacent to the neural spines of the vertebral column. axial ossicle Ossicle that is part of the axial skeleton. PSPUB:0000169 VSAO:0000133 ossicle of axial skeleton OBOL:automatic ossicle of postcranial-axial skeleton OBOL:automatic vertebral ossicle OBOL:automatic 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 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 An epithelium that is part of a crypt of Lieberkuhn. FMA has classes for subdivisions of this epithelium crypt epithelium NCIT:C83191 UMLS:C2826787 intestinal crypt epithelium uberon UBERON:0011184 epithelium of crypt of Lieberkuhn An epithelium that is part of a crypt of Lieberkuhn. OBOL:automatic FMA has classes for subdivisions of this epithelium FMA UMLS:C2826787 ncithesaurus:Crypt_Epithelium 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 root of cranial nerve that is part of a vagus nerve. FMA distinguishes between roots and rootlets - we mix the two here rX BIRNLEX:1456 DHBA:12888 DMBA:17748 FMA:6213 ZFA:0007011 rootlet of vagus nerve vagal root vagus nerve root vagus root uberon vagus neural rootlet UBERON:0011213 root of vagus nerve A root of cranial nerve that is part of a vagus nerve. OBOL:automatic FMA distinguishes between roots and rootlets - we mix the two here FMA rX ZFA:0007011 rootlet of vagus nerve FMA:6213 vagal root ZFA:0007011 vagus nerve root BIRNLEX:1456 vagus root ZFA:0007011 vagus neural rootlet FMA:6213 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 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. 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 pharyngeal aponeurosis (or pharyngobasilar fascia, or fibrous coat), is situated between the mucous and muscular layers. It is thick above where the muscular fibers are wanting, and is firmly connected to the basilar portion of the occipital and the petrous portions of the temporal bones. As it descends it diminishes in thickness, and is gradually lost. It is strengthened posteriorly by a strong fibrous band, which is attached above to the pharyngeal spine on the under surface of the basilar portion of the occipital bone, and passes downward, forming a median raphe, which gives attachment to the Constrictores pharyngis. FMA:55074 pharyngeal aponeurosis uberon pharyngeal aponeurosis UBERON:0011289 pharyngobasilar fascia FMA The pharyngeal aponeurosis (or pharyngobasilar fascia, or fibrous coat), is situated between the mucous and muscular layers. It is thick above where the muscular fibers are wanting, and is firmly connected to the basilar portion of the occipital and the petrous portions of the temporal bones. As it descends it diminishes in thickness, and is gradually lost. It is strengthened posteriorly by a strong fibrous band, which is attached above to the pharyngeal spine on the under surface of the basilar portion of the occipital bone, and passes downward, forming a median raphe, which gives attachment to the Constrictores pharyngis. pharyngeal aponeurosis FMA:55074 pharyngeal aponeurosis 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 partion of white matter that is part of a telencephalon. This can be further subdivided in some species, for example, into hemisphere white matter and the corpus callosum. CNS white matter that is part of the telencephalon[ZFA:0000597]. UBERON:0013202 UBERON:0022550 BIRNLEX:1075 FMA:83930 HBA:9219 HBA:9230 TAO:0000597 ZFA:0000597 predominantly white regional part of telencephalon telencephalic tract/commissure telencephalic white matter telencephalic tracts uberon UBERON:0011299 white matter of telencephalon A partion of white matter that is part of a telencephalon. This can be further subdivided in some species, for example, into hemisphere white matter and the corpus callosum. CNS white matter that is part of the telencephalon[ZFA:0000597]. ZFA:0000597 predominantly white regional part of telencephalon BIRNLEX:1075 telencephalic tract/commissure ZFA:0000597 telencephalic white matter HBA:TELWM telencephalic tracts TAO:0000597 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 Odontogenic tissue that is avascular non-mineralized matrix that is deposited by preameloblast and ameloblasts that are excluded from the matrix. VSAO:0000066 XAO:0004202 pre-enamel tissue preenamel tissue uberon UBERON:0011588 pre-enamel VSAO Odontogenic tissue that is avascular non-mineralized matrix that is deposited by preameloblast and ameloblasts that are excluded from the matrix. GO_REF:0000034 PSPUB:0000170 VSAO:0000066 pre-enamel tissue VSAO:curator preenamel 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 An axon tract that is part of a diencephalon. FMA:62447 diencephalon tract uberon UBERON:0011591 tract of diencephalon An axon tract that is part of a diencephalon. OBOL:automatic diencephalon tract FMA:62447 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 A gingiva that is part of a lower jaw region. EMAPA:18967 FMA:59764 NCIT:C54204 gum of lower jaw gum of mandible lower gingiva lower jaw gingiva uberon lower gum lower jaw gum mandibular gum UBERON:0011602 gingiva of lower jaw A gingiva that is part of a lower jaw region. OBOL:automatic gum of lower jaw EMAPA:18967 lower jaw gingiva FMA:59764 lower jaw gum FMA:59764 mandibular gum FMA:59764 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 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 . 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 mammary gland. FMA:74438 lactiferous gland acinus uberon UBERON:0011856 acinus of lactiferous gland An acinus that is part of a mammary gland. OBOL:automatic lactiferous gland acinus FMA:74438 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 skeletal ligament that is part of a sternoclavicular joint. FMA:63980 ligamentum sternoclavicularis sternoclavicular joint ligament uberon UBERON:0011875 ligament of sternoclavicular joint A skeletal ligament that is part of a sternoclavicular joint. OBOL:automatic ligamentum sternoclavicularis sternoclavicular joint ligament FMA:63980 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 The the continuous basement membrane found within the membranous labyrinth of the cochlea, known to extend from the limbus, down to the inner sulcus, across the basilar membrane, up to the external sulcus to the spiral prominence and radiating into the spiral ligament ensheathing the root cell processes EMAPA:37830 basement membrane of cochlear labyrinth cochlea basement membrane uberon UBERON:0011922 cochlear basement membrane The the continuous basement membrane found within the membranous labyrinth of the cochlea, known to extend from the limbus, down to the inner sulcus, across the basilar membrane, up to the external sulcus to the spiral prominence and radiating into the spiral ligament ensheathing the root cell processes MP:0004598 EMAPA:37830 MA:th Nerve fibers which project from the central nervous system to autonomic ganglia. In the sympathetic division most preganglionic fibers originate with neurons in the intermediolateral column of the spinal cord, exit via ventral roots from upper thoracic through lower lumbar segments, and project to the paravertebral ganglia; there they either terminate in synapses or continue through the splanchnic nerves to the prevertebral ganglia. In the parasympathetic division the fibers originate in neurons of the brain stem and sacral spinal cord. In both divisions the principal transmitter is acetylcholine but peptide cotransmitters may also be released. FMA:5923 MESH:A08.663.542.122 NCIT:C12624 preganglionic nerve fiber uberon preganglionic autonomic fibre UBERON:0011925 preganglionic autonomic fiber Nerve fibers which project from the central nervous system to autonomic ganglia. In the sympathetic division most preganglionic fibers originate with neurons in the intermediolateral column of the spinal cord, exit via ventral roots from upper thoracic through lower lumbar segments, and project to the paravertebral ganglia; there they either terminate in synapses or continue through the splanchnic nerves to the prevertebral ganglia. In the parasympathetic division the fibers originate in neurons of the brain stem and sacral spinal cord. In both divisions the principal transmitter is acetylcholine but peptide cotransmitters may also be released. MESH:A08.663.542.122 preganglionic nerve fiber FMA:5923 A cholinergic axonal fiber projecting from the CNS to a sympathetic ganglion uberon sympathetic preganglionic fiber UBERON:0011927 preganglionic sympathetic fiber A cholinergic axonal fiber projecting from the CNS to a sympathetic ganglion MP:0008310 sympathetic preganglionic fiber MP:0008310 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 A skeletal ligament that connects a tibia and connects a tarsal skeleton. FMA:44055 deltoid collateral ligament of ankle joint deltoid ligament of ankle joint ligamentum collaterale mediale (articulatio talocruralis) ligamentum collaterale mediale articulationis talocruralis ligamentum deltoideum ligamentum deltoideum (articulatio talocruralis) medial collateral ligament of ankle joint uberon UBERON:0011972 medial ligament of ankle joint A skeletal ligament that connects a tibia and connects a tarsal skeleton. OBOL:automatic deltoid collateral ligament of ankle joint FMA:44055 deltoid ligament of ankle joint FMA:44055 ligamentum collaterale mediale (articulatio talocruralis) FMA:44055 ligamentum collaterale mediale articulationis talocruralis FMA:44055 FMA:TA ligamentum deltoideum FMA:TA ligamentum deltoideum (articulatio talocruralis) FMA:44055 medial collateral ligament of ankle joint FMA:44055 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 A cartilaginous condensation that has the potential to develop into a patella. Note some sources have this as intramembranous EMAPA:19140 uberon UBERON:0012080 patella cartilage element A cartilaginous condensation that has the potential to develop into a patella. OBOL:automatic A pre-cartilage condensation that has the potential to develop into a patella. EMAPA:18510 uberon UBERON:0012081 patella pre-cartilage condensation EMAPA A pre-cartilage condensation that has the potential to develop into a patella. OBOL:automatic 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 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 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 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 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 Small bodies containing chromaffin cells occurring outside of the adrenal medulla, most commonly near the sympathetic ganglia and in organs such as the kidney, liver, heart and gonads. paraganglion CALOHA:TS-2358 MESH:D010233 NCIT:C94826 UMLS:C0030419 uberon chromaffin body chromaffin paraganglia chromaffin paraganglion UBERON:0012279 chromaffin paraganglion Small bodies containing chromaffin cells occurring outside of the adrenal medulla, most commonly near the sympathetic ganglia and in organs such as the kidney, liver, heart and gonads. MESH:A06.224.736 paraganglion ncithesaurus:Paraganglion UMLS:C0030419 ncithesaurus:Paraganglion chromaffin body MESH:A06.224.736 chromaffin paraganglia MESH:A06.224.736 chromaffin paraganglion MESH:A06.224.736 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 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 nerve plexus that is part of a sympathetic nervous system. EMAPA:37617 MA:0001160 uberon UBERON:0012373 sympathetic nerve plexus A nerve plexus that is part of a sympathetic nervous system. OBOL:automatic EMAPA:37617 MA:th 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 jejunum. FMA:14951 muscularis externa of jejunum uberon jejunal smooth muscle muscularis propria of jejunum smooth muscle of jejunum UBERON:0012377 muscle layer of jejunum A muscular coat that is part of a jejunum. OBOL:automatic muscularis externa of jejunum FMA:14951 jejunal smooth muscle muscularis propria of jejunum smooth muscle of jejunum 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 endothelium that is part of a peritubular capillary. peritubular endothelium peritubular capillary endothelium uberon UBERON:0012441 endothelium of peritubular capillary A endothelium that is part of a peritubular capillary. OBOL:automatic 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 serous membrane that is part of a fundus of stomach. EMAPA:27157 FMA:17073 visceral peritoneum of fundus of stomach uberon UBERON:0012503 serosa of fundus of stomach A serous membrane that is part of a fundus of stomach. OBOL:automatic visceral peritoneum of fundus of stomach FMA:17073 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 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 Glands of Moll, also known as ciliary glands, are modified apocrine sweat glands that are found on the margin of the eyelid. They are next to the base of the eyelashes, and anterior to the Meibomian glands within the distal eyelid margin. These glands are relatively large and tubular-shaped. The glands of Moll are named after Dutch oculist Jacob Anton Moll (1832-1914). Glands of Moll empty into the adjacent lashes. Glands of Moll and Zeis secrete lipid that adds to the superficial layer of the tear film, retarding evaporation. The glands of Moll are prone to infection and blockage of its duct with sebum and cell debris. Blockage of the gland's duct causes swelling which can manifest itself as a stye. FMA:59159 NCIT:C32679 Moll's gland ciliary gland ciliary gland of moll ciliary sweat gland of eyelid gland of Moll uberon UBERON:0013228 sweat gland of eyelid Glands of Moll, also known as ciliary glands, are modified apocrine sweat glands that are found on the margin of the eyelid. They are next to the base of the eyelashes, and anterior to the Meibomian glands within the distal eyelid margin. These glands are relatively large and tubular-shaped. The glands of Moll are named after Dutch oculist Jacob Anton Moll (1832-1914). Glands of Moll empty into the adjacent lashes. Glands of Moll and Zeis secrete lipid that adds to the superficial layer of the tear film, retarding evaporation. The glands of Moll are prone to infection and blockage of its duct with sebum and cell debris. Blockage of the gland's duct causes swelling which can manifest itself as a stye. Moll's gland FMA:59159 ciliary gland FMA:59159 ciliary gland of moll FMA:59159 ciliary sweat gland of eyelid FMA:59159 gland of Moll FMA:59159 Any gland that is part of an eyelid. This includes sebaceous glands (Zeis gland, tarsal gland) and sweat glands (Moll's gland). gland of eyelid uberon UBERON:0013229 eyelid gland Any gland that is part of an eyelid. This includes sebaceous glands (Zeis gland, tarsal gland) and sweat glands (Moll's gland). Any of the sebaceous glands that are in the eyelid. Examples: gland of Zeis (services eyelashes), gland of Meibom (tarsal gland - unconnected to eyelids). uberon UBERON:0013231 sebaceous gland of eyelid Any of the sebaceous glands that are in the eyelid. Examples: gland of Zeis (services eyelashes), gland of Meibom (tarsal gland - unconnected to eyelids). 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 A diaphysis that is part of a tibia. The body of the tibia has three borders and three surfaces[Wikipedia:Body_of_tibia]. EMAPA:37770 FMA:33125 MA:0003049 body of tibia corpus tibiae shaft of tibia tibial diaphysis uberon body of the tibia shaft of tibia UBERON:0013280 diaphysis of tibia A diaphysis that is part of a tibia. OBOL:automatic The body of the tibia has three borders and three surfaces[Wikipedia:Body_of_tibia]. EMAPA:37770 MA:th body of tibia FMA:33125 corpus tibiae FMA:TA shaft of tibia FMA:33125 tibial diaphysis FMA:33125 body of the tibia shaft of tibia 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 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 An intestinal crypt that is located in the ileum. EMAPA:37839 FMA:269061 ileal crypt ileal crypt of Lieberkuhn ileal intestinal crypt uberon UBERON:0013481 crypt of Lieberkuhn of ileum FMA An intestinal crypt that is located in the ileum. EMAPA:37839 MA:th An intestinal crypt that is located in the duodenum. EMAPA:37838 FMA:269063 duodenal crypt duodenal crypt of Lieberkuhn uberon UBERON:0013482 crypt of Lieberkuhn of duodenum FMA An intestinal crypt that is located in the duodenum. EMAPA:37838 MA:th An intestinal crypt that is located in the jejunum. EMAPA:37840 FMA:269065 jejunal crypt jejunal crypt of Lieberkuhn uberon UBERON:0013483 crypt of Lieberkuhn of jejunum FMA An intestinal crypt that is located in the jejunum. EMAPA:37840 MA:th An intestinal crypt that is located in the colon. The colonic crypts of Lieberkühn are straight and unbranched and lined largely with goblet cells. colonic crypt colonic crypt of Lieberkuhn uberon UBERON:0013485 crypt of Lieberkuhn of colon An intestinal crypt that is located in the colon. The colonic crypts of Lieberkühn are straight and unbranched and lined largely with goblet cells. An intestinal crypt that is located in the appendix. appendiceal crypt appendiceal crypt of Lieberkuhn uberon UBERON:0013486 crypt of Lieberkuhn of appendix An intestinal crypt that is located in the appendix. requires verification EHDAA2:0004313 EMAPA:17570 vestibulocochlear VIII ganglion complex vestibulocochlear ganglion complex uberon vestibular VIII ganglion complex UBERON:0013498 vestibulo-cochlear VIII ganglion complex vestibular VIII ganglion complex EHDAA2:0004313 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 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 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. Ossicle that develops within bands of dense, regular connective tissue (e.g., tendons and ligaments). Sesamoids are generally located proximate to a bony prominence, over which the dense regular connective tissue wraps, and/or a joint or articulation. VSAO:0000137 sesamoid uberon UBERON:0013631 Sesamoids are often endochondral replacement elements and in addition to bone tissue, may also be composed of articular cartilage, fibrocartilage, hyaline cartilage, and calcified cartilage. sesamoid element VSAO VSAO Ossicle that develops within bands of dense, regular connective tissue (e.g., tendons and ligaments). Sesamoids are generally located proximate to a bony prominence, over which the dense regular connective tissue wraps, and/or a joint or articulation. PSPUB:0000169 VSAO:0000137 sesamoid VSAO:0000137 A sesamoid element that is composed primarily of cartilage tissue. FMA:55379 cartilago sesamoidea sesamoid cartilage of cricopharyngeal ligament uberon UBERON:0013632 sesamoid cartilage A sesamoid element that is composed primarily of cartilage tissue. OBOL:automatic cartilago sesamoidea FMA:55379 sesamoid cartilage of cricopharyngeal ligament FMA:55379 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 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 Periosteum that is part of a skull. FMA:76623 periosteum externum cranii uberon UBERON:0013687 pericranium Periosteum that is part of a skull. OBOL:automatic periosteum externum cranii FMA:76623 FMA:TA A germinal center that is part of a tonsil. consider adding related terms, e.g. secondary lymphoid tissue of tonsil The germinal center or reaction center is the activated center of a lymphoid follicle in secondary lymphoid tissue where B-lymphocytes are stimulated by antigens and helper T cells (T-lymphocytes, helper-inducer) are stimulated to generate memory cells. Here, the germinal center of a tonsil[TS-1288]. CALOHA:TS-1288 uberon tonsil reaction center UBERON:0013688 tonsil germinal center A germinal center that is part of a tonsil. OBOL:automatic The germinal center or reaction center is the activated center of a lymphoid follicle in secondary lymphoid tissue where B-lymphocytes are stimulated by antigens and helper T cells (T-lymphocytes, helper-inducer) are stimulated to generate memory cells. Here, the germinal center of a tonsil[TS-1288]. TS-1288 tonsil reaction center CALOHA:TS-1288 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 A strand of hair that is part of a axilla. FMA:54253 axilla hair axillary hair hair of axilla uberon UBERON:0013699 strand of axillary hair A strand of hair that is part of a axilla. OBOL:automatic axillary hair FMA:54253 hair of axilla FMA:54253 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 metaphysis that is part of a tibia. EMAPA:37772 FMA:33135 MA:0003106 tibial metaphysis uberon UBERON:0013750 metaphysis of tibia A metaphysis that is part of a tibia. OBOL:automatic EMAPA:37772 MA:th tibial metaphysis FMA:33135 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 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 nipple that is in_the_left_side_of a body proper. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:223695 uberon UBERON:0013772 left nipple A nipple that is in_the_left_side_of a body proper. OBOL:automatic A nipple that is in_the_right_side_of a body proper. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:223693 uberon UBERON:0013773 right nipple A nipple that is in_the_right_side_of a body proper. OBOL:automatic 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 Sweat that is produced by the glands of the axilla. FMA:63085 axillary sweat uberon UBERON:0014393 sweat of axilla Sweat that is produced by the glands of the axilla. axillary sweat FMA:63085 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 lamina of neuraxis neuraxis lamina FMA:83856 uberon UBERON:0014530 white matter lamina of neuraxis lamina of neuraxis FMA:83856 neuraxis lamina FMA:83856 diencephalon lamina lamina of diencephalon FMA:62449 uberon UBERON:0014531 white matter lamina of diencephalon diencephalon lamina FMA:62449 lamina of diencephalon FMA:62449 cerebral hemisphere lamina lamina of cerebral hemisphere FMA:67951 uberon UBERON:0014532 white matter lamina of cerebral hemisphere cerebral hemisphere lamina FMA:67951 lamina of cerebral hemisphere FMA:67951 The white laminae of cerebellum is subdivision of the cerebellar cortex comprised of myelinated axons lying deep to the granule cell layer of the cerebellar cortex. BIRNLEX:1105 UMLS:C0228472 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=163 lamina alba of cerebellar cortex laminae albae of cerebellar cortex white lamina of cerebellum white laminae of cerebellum uberon isthmus cinguli isthmus gyri cingulatus isthmus gyri cinguli isthmus of gyrus fornicatus isthmus of the cingulate gyrus isthmus-2 laminae albae of cerebellar cortex UBERON:0014540 white matter lamina of cerebellum The white laminae of cerebellum is subdivision of the cerebellar cortex comprised of myelinated axons lying deep to the granule cell layer of the cerebellar cortex. UMLS:C0228472 BIRNLEX:1105 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=163 BIRNLEX:1105 white laminae of cerebellum BIRNLEX:1105 isthmus cinguli NeuroNames:163 isthmus gyri cingulatus NeuroNames:163 isthmus gyri cinguli NeuroNames:163 isthmus of gyrus fornicatus NeuroNames:163 isthmus of the cingulate gyrus NeuroNames:163 isthmus-2 NeuroNames:163 laminae albae of cerebellar cortex BIRNLEX:1105 A dorsal horn of spinal cord that is part of a thoracic spinal cord. BIRNLEX:1404 UMLS:C0228628 thoracic spinal cord dorsal horn uberon thoracic spinal cord posterior horn UBERON:0014609 thoracic spinal cord dorsal horn A dorsal horn of spinal cord that is part of a thoracic spinal cord. OBOL:automatic UMLS:C0228628 BIRNLEX:1404 thoracic spinal cord dorsal horn BIRNLEX:1404 thoracic spinal cord posterior horn BIRNLEX:1404 A ventral horn of spinal cord that is part of a thoracic spinal cord. BIRNLEX:1410 UMLS:C0228632 UMLS:C1288552 thoracic spinal cord ventral horn uberon thoracic spinal cord anterior horn UBERON:0014610 thoracic spinal cord ventral horn A ventral horn of spinal cord that is part of a thoracic spinal cord. OBOL:automatic UMLS:C0228632 BIRNLEX:1410 UMLS:C1288552 BIRNLEX:1410 thoracic spinal cord ventral horn BIRNLEX:1410 thoracic spinal cord anterior horn BIRNLEX:1410 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 white matter of spinal cord that is part of a cervical spinal cord. BIRNLEX:1531 UMLS:C0228616 cervical spinal cord white matter uberon UBERON:0014614 cervical spinal cord white matter A white matter of spinal cord that is part of a cervical spinal cord. OBOL:automatic UMLS:C0228616 BIRNLEX:1531 cervical spinal cord white matter BIRNLEX:1531 A nerve root that is part of a accessory XI nerve. c11n BAMS:c11n BIRNLEX:1580 DHBA:12883 DMBA:17749 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=703 accessory nerve root root of accessory nerve uberon accessory portion of spinal accessory nerve bulbar accessory nerve bulbar part of accessory nerve cranial accessory nerve cranial part of accessory nerve cranial part of the accessory nerve cranial portion of eleventh cranial nerve internal branch of accessory nerve nerve XI (cranialis) pars vagalis of nervus accessorius radices craniales nervi accessorii UBERON:0014615 accessory nerve root A nerve root that is part of a accessory XI nerve. OBOL:automatic c11n BIRNLEX:1580 NIFSTD:NeuroNames_abbrevSource http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=703 BIRNLEX:1580 accessory nerve root BIRNLEX:1580 accessory portion of spinal accessory nerve NeuroNames:703 bulbar accessory nerve NeuroNames:703 bulbar part of accessory nerve NeuroNames:703 cranial accessory nerve NeuroNames:703 cranial part of accessory nerve BAMS:c11n cranial part of the accessory nerve NeuroNames:703 cranial portion of eleventh cranial nerve NeuroNames:703 internal branch of accessory nerve NeuroNames:703 nerve XI (cranialis) NeuroNames:703 pars vagalis of nervus accessorius NeuroNames:703 radices craniales nervi accessorii NeuroNames:703 A dorsal horn of spinal cord that is part of a cervical spinal cord. BIRNLEX:1673 UMLS:C0228611 cervical spinal cord dorsal horn uberon cervical spinal cord posterior horn UBERON:0014620 cervical spinal cord dorsal horn A dorsal horn of spinal cord that is part of a cervical spinal cord. OBOL:automatic UMLS:C0228611 BIRNLEX:1673 cervical spinal cord dorsal horn BIRNLEX:1673 cervical spinal cord posterior horn BIRNLEX:1673 A ventral horn of spinal cord that is part of a cervical spinal cord. BIRNLEX:1680 UMLS:C0228615 UMLS:C1278740 cervical spinal cord ventral horn uberon cervical spinal cord anterior horn UBERON:0014621 cervical spinal cord ventral horn A ventral horn of spinal cord that is part of a cervical spinal cord. OBOL:automatic UMLS:C0228615 BIRNLEX:1680 UMLS:C1278740 BIRNLEX:1680 cervical spinal cord ventral horn BIRNLEX:1680 cervical spinal cord anterior horn BIRNLEX:1680 A dorsal root of spinal cord that overlaps a cervical spinal cord. BIRNLEX:964 UMLS:C1278751 dorsal nerve root of cervical spinal cord uberon posterior nerve root of cervical spinal cord UBERON:0014635 dorsal nerve root of cervical spinal cord NIFSTD A dorsal root of spinal cord that overlaps a cervical spinal cord. OBOL:automatic UMLS:C1278751 BIRNLEX:964 dorsal nerve root of cervical spinal cord BIRNLEX:964 posterior nerve root of cervical spinal cord BIRNLEX:964 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 A white matter of spinal cord that is part of a thoracic spinal cord. BIRNLEX:999 UMLS:C0228633 UMLS:C1288557 thoracic spinal cord white matter uberon UBERON:0014637 thoracic spinal cord white matter A white matter of spinal cord that is part of a thoracic spinal cord. OBOL:automatic UMLS:C0228633 BIRNLEX:999 UMLS:C1288557 BIRNLEX:999 thoracic spinal cord white matter BIRNLEX:999 A white matter that is part of a medulla oblongata. BAMS:mw BIRNLEX:1024 BIRNLEX:1414 FMA:83944 substantia alba medullae oblongatae white matter of medulla white substance of medulla uberon medullary white matter UBERON:0014649 white matter of medulla oblongata A white matter that is part of a medulla oblongata. OBOL:automatic substantia alba medullae oblongatae FMA:TA white matter of medulla FMA:83944 white substance of medulla FMA:83944 medullary white matter BAMS:mw The angular vein formed by the junction of the frontal vein and supraorbital vein, runs obliquely downward, on the side of the root of the nose, to the level of the lower margin of the orbit, where it becomes the anterior facial vein. It receives the external nasal veins of the ala nasi, and communicates with the superior ophthalmic vein through the nasofrontal vein, thus establishing an important anastomosis between the anterior facial vein and the cavernous sinus. FMA:50893 uberon UBERON:0014686 angular vein The angular vein formed by the junction of the frontal vein and supraorbital vein, runs obliquely downward, on the side of the root of the nose, to the level of the lower margin of the orbit, where it becomes the anterior facial vein. It receives the external nasal veins of the ala nasi, and communicates with the superior ophthalmic vein through the nasofrontal vein, thus establishing an important anastomosis between the anterior facial vein and the cavernous sinus. 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. A blood vessel that drains from from an eyelid. FMA:51997 uberon palpebral veins venae palpebrales UBERON:0014769 palpebral vein A blood vessel that drains from from an eyelid. palpebral veins venae palpebrales An artery that supplies blood to an eyelid. In humans, the eyelids are supplied with blood by two arches on each upper and lower lid. The arches are formed by anastamoses of the lateral palpebral arteries and medial palpebral arteries, branching off from the lacrimal artery and ophthalmic artery, respectively. In amphibians, the eyelids may be supplied by branches of the lateral pretrosal arteries.[cjm] uberon UBERON:0014770 palpebral artery An artery that supplies blood to an eyelid. 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 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 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 White matter that is part of a brainstem [Automatically generated definition]. EMAPA:35189 FMA:282112 MA:0002741 uberon brain stem white matter brainstem tract/commissure brainstem tracts brainstem tracts and commissures UBERON:0014891 brainstem white matter White matter that is part of a brainstem [Automatically generated definition]. OBOL:automatic brain stem white matter EMAPA:35189 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 developing superficial cortical layer located just under the pia matter, develops from the marginal layer of the neural tube and becomes cortical layer I in humans develops into cortical layer I EMAPA temporally divides this into zone and layer. TODO - unify this with marginal layers in EHDAA2 MZ marginal zone EMAPA:17546 EMAPA:32713 PBA:294021774 cortical marginal layer cortical marginal zone future cortical layer I uberon cerebral cortex marginal zone UBERON:0014935 cerebral cortex marginal layer developing superficial cortical layer located just under the pia matter, develops from the marginal layer of the neural tube and becomes cortical layer I MP:0000792 EMAPA temporally divides this into zone and layer. TODO - unify this with marginal layers in EHDAA2 EMAPA MZ BRAINSPAN:BRAINSPAN MZ MP:0000792 marginal zone PBA:294021774 cortical marginal layer cortical marginal zone MP:0000792 future cortical layer I cerebral cortex marginal zone EMAPA:32713 these layers primarily refer to the mammalian future neocortex uberon UBERON:0014950 layer of developing cerebral cortex EMAPA The major preaxial endochondral element in the posterior zeugopod[Phenoscape]. tibia skeletal element tibia element uberon UBERON:0015004 tibia endochondral element The major preaxial endochondral element in the posterior zeugopod[Phenoscape]. PHENOSCAPE:mah tibia skeletal element tibia element 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 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 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 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 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 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 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 orbitosphenoid bone or its cartilage or pre-cartilage precursor. orbitosphenoid skeletal element orbitosphenoid element uberon UBERON:0015059 orbitosphenoid endochondral element A orbitosphenoid bone or its cartilage or pre-cartilage precursor. orbitosphenoid skeletal element orbitosphenoid element A sphenoid bone or its cartilage or pre-cartilage precursor. sphenoid bone skeletal element sphenoid element uberon UBERON:0015060 sphenoid endochondral element A sphenoid bone or its cartilage or pre-cartilage precursor. sphenoid bone skeletal element sphenoid 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. A anatomical space that is enclosed by a conjunctiva. FMA:59083 cavity of conjunctival sac conjunctival sac cavity subconjunctival space subbrillar space uberon UBERON:0015155 conjunctival space A anatomical space that is enclosed by a conjunctiva. OBOL:automatic cavity of conjunctival sac FMA:59083 conjunctival sac cavity FMA:59083 subbrillar space NCBITaxon:8570 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 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 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 axilla. EMAPA:37349 FMA:37322 MA:0003087 NCIT:C116164 axillary skin skin of axilla uberon UBERON:0015474 axilla skin A zone of skin that is part of a axilla. OBOL:automatic EMAPA:37349 MA:th axillary skin FMA:37322 skin of axilla FMA:37322 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 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 The portion of the nasal mucosa that is part of the respiratory system. lined with ciliated pseudostratified columnar epithelium (respiratory epithelium). The respiratory segment has a very vascularized lamina propria allowing the venous plexuses of the conchal mucosa to engorge with blood, restricting airflow and causing air to be directed to the other side of the nose. FMA:77198 pars respiratoria tunicae mucosae nasi respiratory zone of nasal mucosa uberon UBERON:0015786 respiratory segment of nasal mucosa The portion of the nasal mucosa that is part of the respiratory system. lined with ciliated pseudostratified columnar epithelium (respiratory epithelium). The respiratory segment has a very vascularized lamina propria allowing the venous plexuses of the conchal mucosa to engorge with blood, restricting airflow and causing air to be directed to the other side of the nose. pars respiratoria tunicae mucosae nasi FMA:77198 FMA:TA respiratory zone of nasal mucosa FMA:77198 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:24023 uberon central medullary cavity of long bone UBERON:0016413 medullary cavity of long bone central medullary cavity of long bone FMA:24023 A compact bone tissue that is part of a bone tissue of long bone. FMA:32674 uberon UBERON:0016422 compact bone of long bone A compact bone tissue that is part of a bone tissue of long bone. OBOL:automatic A compact bone tissue that is part of a diaphysis. FMA:32678 uberon UBERON:0016423 compact bone of diaphysis A compact bone tissue that is part of a diaphysis. OBOL:automatic 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 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 A anatomical space that is enclosed by a fundus of stomach. EMAPA:18382 FMA:17077 cavity of fundus of stomach lumen of fundus of stomach lumen of stomach fundus uberon UBERON:0016502 stomach fundus lumen A anatomical space that is enclosed by a fundus of stomach. OBOL:automatic cavity of fundus of stomach FMA:17077 lumen of fundus of stomach FMA:17077 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 lamina propria that is part of a mucosa of fundus of stomach. EMAPA:27163 FMA:17500 lamina propria mucosae of fundus of stomach uberon UBERON:0016511 lamina propria of fundus of stomach A lamina propria that is part of a mucosa of fundus of stomach. OBOL:automatic lamina propria mucosae of fundus of stomach FMA:FMA 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 anatomical space that is part of a jejunum. EMAPA:18729 FMA:14590 jejunal lumen jejunum lumen uberon UBERON:0016517 lumen of jejunum A anatomical space that is part of a jejunum. OBOL:automatic jejunal lumen FMA:FMA jejunum lumen 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 FMA:256176 uberon UBERON:0016527 white matter of cerebral lobe A white matter of cerebral lobe that is part of a frontal lobe. FMA:256178 frontal lobe white matter uberon UBERON:0016528 white matter of frontal lobe A white matter of cerebral lobe that is part of a frontal lobe. OBOL:automatic 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 A white matter of cerebral lobe that is part of a parietal lobe. FMA:256184 uberon UBERON:0016531 white matter of parietal lobe A white matter of cerebral lobe that is part of a parietal lobe. OBOL:automatic A white matter of cerebral lobe that is part of a temporal lobe. FMA:256186 uberon UBERON:0016534 white matter of temporal lobe A white matter of cerebral lobe that is part of a temporal lobe. OBOL:automatic A white matter of cerebral lobe that is part of a limbic lobe. FMA:261091 uberon UBERON:0016536 white matter of limbic lobe A white matter of cerebral lobe that is part of a limbic lobe. OBOL:automatic 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 FMA:242234 cortex of limbic lobe limbic lobe cortex uberon gray matter of limbic lobe UBERON:0016542 limbic cortex cortex of limbic lobe FMA:242234 limbic lobe cortex FMA:242234 gray matter of limbic lobe FMA:242234 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 A layer of of the central nervous system that is composed of white matter. white matter layer FMA:83898 CNS white matter layer white matter layer of neuraxis uberon UBERON:0016549 central nervous system white matter layer A layer of of the central nervous system that is composed of white matter. white matter layer of neuraxis FMA:83898 uberon UBERON:0016550 spinal cord column 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 white matter that is part of the midbrain. DHBA:10650 FMA:83936 HBA:265505382 mesencephalic white matter uberon UBERON:0016554 white matter of midbrain A white matter that is part of the midbrain. OBOL:automatic mesencephalic white matter HBA:MESWM 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. 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 A periosteum that is part of a long bone. FMA:32677 long bone periosteum uberon UBERON:0016896 periosteum of long bone A periosteum that is part of a long bone. OBOL:automatic long bone periosteum FMA:32677 A bony structure embedded in skin, roughly equivalent to osteoderms. http://purl.bioontology.org/ontology/provisional/3b77fb04-1e62-43af-a84b-5d5eb7388525 http://purl.bioontology.org/ontology/provisional/bdc28b9d-8fe6-4175-ae67-002f61493279 bony tubercle uberon bony tubercles UBERON:0017163 skin bony tubercle A bony structure embedded in skin, roughly equivalent to osteoderms. PHENOSCAPE:Nizar bony tubercles UBERONTEMP:3b77fb04-1e62-43af-a84b-5d5eb7388525 A sesamoid element that is part of a tarsal skeleton. http://purl.bioontology.org/ontology/provisional/c97fd8d8-cf3e-4326-938d-bea58477423d uberon tarsal sesamoid UBERON:0017261 intertarsal sesamoid A sesamoid element that is part of a tarsal skeleton. OBOL:automatic FMA:52568 paired dural venous sinus uberon UBERON:0017635 paired venous dural sinus paired dural venous sinus FMA:52568 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 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 kidney interstitium that is part of a left kidney. FMA:74271 left renal stroma stroma of left kidney uberon UBERON:0018113 left kidney interstitium A kidney interstitium that is part of a left kidney. OBOL:automatic left renal stroma FMA:74271 stroma of left kidney FMA:74271 A kidney interstitium that is part of a right kidney. FMA:74270 right renal stroma stroma of right kidney uberon UBERON:0018114 right kidney interstitium A kidney interstitium that is part of a right kidney. OBOL:automatic right renal stroma FMA:74270 stroma of right kidney FMA:74270 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 A renal cortex interstitium that is part of a left kidney. cortical interstitial tissue of left kidney uberon UBERON:0018117 left renal cortex interstitium A renal cortex interstitium that is part of a left kidney. OBOL:automatic A renal cortex interstitium that is part of a right kidney. cortical interstitial tissue of right kidney uberon UBERON:0018118 right renal cortex interstitium A renal cortex interstitium that is part of a right kidney. OBOL:automatic A renal medulla interstitium that is part of a left kidney. medullary interstitial tissue of left kidney uberon UBERON:0018119 left renal medulla interstitium A renal medulla interstitium that is part of a left kidney. OBOL:automatic A renal medulla interstitium that is part of a right kidney. medullary interstitial tissue of right kidney uberon UBERON:0018120 right renal medulla interstitium A renal medulla interstitium that is part of a right kidney. OBOL:automatic 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 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 sweat gland that is part of a axilla. axillary apocrine sweat gland sweat gland of axilla uberon UBERON:0018232 axillary sweat gland ISBN:0123813611 A sweat gland that is part of a axilla. OBOL:automatic axillary apocrine sweat gland sweat gland of axilla 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 branch of the superior mesenteric artery that supplies the jejunum. FMA:14808 uberon jejunal branch of superior mesenteric artery UBERON:0018255 jejunal artery A branch of the superior mesenteric artery that supplies the jejunum. jejunal branch of superior mesenteric artery FMA:14808 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 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 A white matter that is part of the hindbrain. DHBA:10668 FMA:268636 uberon UBERON:0019258 white matter of hindbrain A white matter that is part of the hindbrain. OBOL:automatic A white matter that is part of the forebrain. DHBA:10557 FMA:268634 uberon UBERON:0019261 white matter of forebrain A white matter that is part of the forebrain. OBOL:automatic A white matter that is part of the myelencephalon. HBA:9298 myelencephalic white matter uberon UBERON:0019262 white matter of myelencephalon A white matter that is part of the myelencephalon. OBOL:automatic myelencephalic white matter HBA:MYWM 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 FMA:83939 HBA:9287 uberon UBERON:0019291 white matter of metencephalon FMA:83940 uberon UBERON:0019292 white matter of pons UBERON:0025819 BIRNLEX:1069 FMA:83942 HBA:265505486 pontine white matter tracts predominantly white regional part of pontine tegmentum substantia alba tegmenti pontis white matter of pontile tegmentum white substance of pontile tegmentum uberon UBERON:0019293 white matter of pontine tegmentum pontine white matter tracts HBA:PoWM predominantly white regional part of pontine tegmentum BIRNLEX:1069 substantia alba tegmenti pontis FMA:TA white matter of pontile tegmentum FMA:83942 white substance of pontile tegmentum FMA:83942 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 BIRNLEX:1533 DHBA:12887 DMBA:17747 glossopharyngeal nerve root uberon UBERON:0019310 glossopharyngeal nerve root glossopharyngeal nerve root BIRNLEX:1533 The initial segment of an olfactory nerve, leaving the central nervous system. BIRNLEX:1632 olfactory nerve root uberon UBERON:0019311 root of olfactory nerve The initial segment of an olfactory nerve, leaving the central nervous system. olfactory nerve root BIRNLEX:1632 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:260712 cerebral fascicle cerebral fasciculus nerve fascicle of telencephalon telencephalic fascicle telencephalic nerve fascicle uberon UBERON:0022248 cerebral nerve fasciculus cerebral fascicle FMA:260712 cerebral fasciculus FMA:260712 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 FMA:63243 epithelium of small intestinal crypt of Lieberkuhn uberon wall of small intestinal crypt of Lieberkuhn UBERON:0022280 epithelium of crypt of Lieberkuhn of small intestine epithelium of small intestinal crypt of Lieberkuhn FMA:63243 wall of small intestinal crypt of Lieberkuhn FMA:63243 FMA:63628 uberon UBERON:0022281 epithelium of crypt of Lieberkuhn of large intestine 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 Note that in some lamination schemes, more particularly so in primates, this layer is referred to as layer IV thus resulting in some confusion when compared to the present scheme where the lamina dissecans is referred to layer IV[DOI:10.1155/2008/381243] NLX:144263 uberon primary motor cortex lamina V primary motor cortex layer V UBERON:0022315 primary motor cortex layer 5 nlx nlx primary motor cortex lamina V NLX:144263 primary motor cortex layer V NLX:144263 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 The layer of endometrial epithelium adjacent to the myometrium. FMA:86493 NCIT:C32642 functional layer of endometrium stratum functionalis of endometrium uberon UBERON:0022356 outer layer of endometrium The layer of endometrial epithelium adjacent to the myometrium. functional layer of endometrium FMA:86493 stratum functionalis of endometrium FMA:86493 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 mammary gland duct that is part of a male organism. This structure typically regresses. uberon UBERON:0022360 male mammary gland duct A mammary gland duct that is part of a male organism. This structure typically regresses. 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 A set of neural structures that subserve a specific function, e.g., visual system this class was inherited from NIFSTD as part of the replacement of NIFSTD with Uberon. It may be obsoleted in the future NLXANAT:090802 neural system uberon UBERON:0023879 neural system A set of neural structures that subserve a specific function, e.g., visual system NLXANAT:090802 neural system NLXANAT:090802 White matter that lies deep to the granular cell layer of the cerebellar cortex. It contains afferents to the cerebellar cortex and axons that run between the cerebellar cortex and the deep cerebellar nuclei. NLXANAT:20081249 white matter of the cerebellar cortex uberon UBERON:0024045 white matter of the cerebellar cortex White matter that lies deep to the granular cell layer of the cerebellar cortex. It contains afferents to the cerebellar cortex and axons that run between the cerebellar cortex and the deep cerebellar nuclei. NLXANAT:20081249 white matter of the cerebellar cortex NLXANAT:20081249 white matter of the cerebellar cortex NLXANAT:20081249 BIRNLEX:749 thalamic fiber tracts uberon UBERON:0025261 thalamic fiber tract thalamic fiber tracts BIRNLEX:749 thalamic fiber tracts BIRNLEX:749 The part of the central nervous system that is involved with movement. NLXANAT:090805 motor system uberon UBERON:0025525 It consists of the pyramidal and extrapyramidal system motor system NIFSTD The part of the central nervous system that is involved with movement. motor system NLXANAT:090805 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 Telencephalic white matter which extends between the olfactory bulb and the ipsilateral dorsal telencephalon and carries secondary olfactory fibers. From Neuroanatomy of the Zebrafish Brain. TAO:0000229 ZFA:0000229 uberon lateral olfactory tract tractus olfactorius lateralis UBERON:0034730 olfactory tract linking bulb to ipsilateral dorsal telencephalon Telencephalic white matter which extends between the olfactory bulb and the ipsilateral dorsal telencephalon and carries secondary olfactory fibers. From Neuroanatomy of the Zebrafish Brain. ZFA:0000229 lateral olfactory tract ZFA:0000229 tractus olfactorius lateralis ZFA:0000229 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 2 Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. CARO:0020000 uberon UBERON:0034923 disconnected anatomical group CARO Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. CARO:0020000 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. An enlarged chamber in the blood sinus capable of accumulating a large volume of blood. ZFA:0007073 blood sinus cavity blood sinus lumen uberon UBERON:0034940 venous sinus cavity An enlarged chamber in the blood sinus capable of accumulating a large volume of blood. GOC:YMB ZFA:0007073 blood sinus cavity ZFA:0007073 blood sinus lumen ZFA:0007073 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 A cluster of neuroendocrine cells derived from neural crest. Paraganglia may be chromaffin or nonchromaffin corresponding portion of CL needs fixed FMA:15648 uberon paraganglia UBERON:0034978 paraganglion (generic) cjm A cluster of neuroendocrine cells derived from neural crest. Paraganglia may be chromaffin or nonchromaffin paraganglia 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:28322 loop of Henle, outer medullary portion uberon UBERON:0034996 outer renal medulla loop of Henle loop of Henle, outer medullary portion EMAPA:28322 EMAPA:35460 loop of Henle of renal medulla loop of Henle, medullary portion uberon UBERON:0034997 renal medulla loop of Henle loop of Henle of renal medulla EMAPA:35460 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 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 an eyelid [Automatically generated definition]. EMAPA:32758 MA:0003163 uberon UBERON:0035034 eyelid epithelium An epithelium that is part of an eyelid [Automatically generated definition]. OBOL:automatic 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:70617 ductal part of eccrine sweat gland uberon UBERON:0035073 duct of eccrine sweat gland ductal part of eccrine sweat gland FMA:70617 FMA:70643 ductal part of apocrine sweat gland uberon UBERON:0035074 duct of apocrine sweat gland ductal part of apocrine sweat gland FMA:70643 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 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 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 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 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 ensure pit organ classifies here uberon UBERON:0035555 lateral line sense organ 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. Tubular connection between the epidermal surface and the most distal part of the inner root sheath. Contains the hair shaft. uberon UBERON:0035610 hair canal Tubular connection between the epidermal surface and the most distal part of the inner root sheath. Contains the hair shaft. 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 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 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. The corticobulbar and corticospinal tracts combined. pyramidal tract uberon UBERON:0036224 corticobulbar and corticospinal tracts NIFSTD The corticobulbar and corticospinal tracts combined. pyramidal tract BIRNLEX:1464 MP:0002878 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 Parenchymal tissue that consists of the alveoli, grape-like clusters where milk is stored, and branching ducts, which are tubular canals carrying gladular secretions. lactiferous gland parenchyma mammary gland parenchyma parenchyma of lactiferous gland uberon UBERON:0036245 parenchyma of mammary gland Parenchymal tissue that consists of the alveoli, grape-like clusters where milk is stored, and branching ducts, which are tubular canals carrying gladular secretions. BGEE:ann 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:14179 coronary arterial wall uberon UBERON:0036328 wall of coronary artery FMA FMA coronary arterial wall FMA:14179 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:15089 brachiocephalic arterial wall uberon UBERON:0036351 wall of brachiocephalic artery FMA FMA brachiocephalic arterial wall FMA:15089 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:79837 membranous labyrinth wall uberon UBERON:0037191 wall of membranous labyrinth FMA FMA membranous labyrinth wall FMA:79837 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 FMA:54242 neck hair uberon UBERON:0037458 hair of neck neck hair FMA:54242 FMA:54243 limb hair uberon UBERON:0037459 hair of limb limb hair FMA:54243 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 The parenchyma of the spleen, consisting of lymphocytes and macrophages. It lies between the splenic trabecula. Red pulp is the part suffused with blood and white pulp consists of areas of lymphatic tissue where there are sleeves of lymphocytes and macrophages. EMAPA:35805 FMA:15845 MA:0002487 NCIT:C33603 UMLS:C0229691 Malpighian corpuscles pulp of spleen splenic pulp uberon UBERON:1000023 spleen pulp FMA The parenchyma of the spleen, consisting of lymphocytes and macrophages. It lies between the splenic trabecula. Red pulp is the part suffused with blood and white pulp consists of areas of lymphatic tissue where there are sleeves of lymphocytes and macrophages. ncithesaurus:Splenic_Pulp UMLS:C0229691 ncithesaurus:Splenic_Pulp Malpighian corpuscles FMA:15845 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 An anatomical junction between two parts of the digestive tract. 2021-02-05T11:19:31Z uberon UBERON:1100000 digestive tract junction An anatomical junction between two parts of the digestive tract. ORCID:0000-0002-7073-9172 Ganglion that develops from a cranial ectodermal placode and contains sensory neurons that innervate a lateral line. EFO:0003493 TAO:0000120 XAO:0004457 ZFA:0000120 LLG lateral line ganglia uberon UBERON:2000120 lateral line ganglion Ganglion that develops from a cranial ectodermal placode and contains sensory neurons that innervate a lateral line. ZFA:0000120 ZFA:curator LLG TAO:0000120 lateral line ganglia TAO:0000120 Cranial nerve which enters the brain between cranial nerves VIII and IX; contains afferents and sensory efferents to the posterior lateral line ganglion and middle ganglion. Fibers from the posterior lateral line ganglion innervate the occipital dorsal lateral line and trunk lateral lines. 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:0000175 caudal lateral line nerve uberon/phenoscape-anatomy posterior lateral line nerve Cranial nerve which enters the brain between cranial nerves VIII and IX; contains afferents and sensory efferents to the posterior lateral line ganglion and middle ganglion. Fibers from the posterior lateral line ganglion innervate the occipital dorsal lateral line and trunk lateral lines. ZFIN:curator caudal lateral line nerve TAO:0000175 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:0000228 lateral line primordia llp uberon/phenoscape-anatomy lateral line primordium lateral line primordia TAO:0000228 llp TAO:0000228 Cranial nerve which enters the brain between cranial nerves VI and VII; contains afferents and sensory efferents to the anterior lateral line ganglia. 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:0000425 rostral lateral line nerve uberon/phenoscape-anatomy anterior lateral line nerve Cranial nerve which enters the brain between cranial nerves VI and VII; contains afferents and sensory efferents to the anterior lateral line ganglia. ZFIN:curator rostral lateral line nerve TAO:0000425 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 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:0001156 uberon uberon/phenoscape-anatomy UBERON:2001156 posterior lateral line placode lexical The posterior lateral line ganglion develops from a cranial ectodermal placode and contains sensory neurons that innervate the posterior lateral line system. 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:0001314 uberon uberon/phenoscape-anatomy UBERON:2001314 posterior lateral line ganglion lexical The posterior lateral line ganglion develops from a cranial ectodermal placode and contains sensory neurons that innervate the posterior lateral line system. ZFIN:curator Dorsolateral placode that gives rise to the anterior lateral line. Lateral line placode that gives rise to the anterior lateral line nerve[XAO:0004221, XAO:EJS]. EFO:0003461 TAO:0001316 XAO:0004221 ZFA:0001316 uberon anterior lateral line placodes pre-auditory lateral line placode UBERON:2001316 anterior lateral line placode lexical Dorsolateral placode that gives rise to the anterior lateral line. ZFA:0001316 ZFA:curator Lateral line placode that gives rise to the anterior lateral line nerve[XAO:0004221, XAO:EJS]. XAO:EJS anterior lateral line placodes ZFA:0001316 pre-auditory lateral line placode XAO:0004221 The anteror lateral line ganglia develops from cranial ectodermal placodes and contain sensory neurons that innervate the anterior lateral line system. EFO:0003683 TAO:0001391 ZFA:0001391 none uberon anterior lateral line ganglia UBERON:2001391 anterior lateral line ganglion lexical The anteror lateral line ganglia develops from cranial ectodermal placodes and contain sensory neurons that innervate the anterior lateral line system. ZFIN:curator anterior lateral line ganglia TAO:0001391 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:0001431 uberon/phenoscape-anatomy primitive olfactory epithelium 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 The anterior lateral line system develops from cranial ectodermal placodes, situated between the eye and the ear, that give rise to both the neuromasts and the anterior lateral line sensory nerves that innervate the neuromasts. The anterior lateral line system consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians and are innervated by several lateral line nerves, which project to the hindbrain. The anterior lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. EFO:0003691 TAO:0001468 ZFA:0001468 uberon UBERON:2001468 anterior lateral line system lexical The anterior lateral line system develops from cranial ectodermal placodes, situated between the eye and the ear, that give rise to both the neuromasts and the anterior lateral line sensory nerves that innervate the neuromasts. The anterior lateral line system consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians and are innervated by several lateral line nerves, which project to the hindbrain. The anterior lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. ZFIN:curator The anterior lateral line consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians. The anterior lateral line develops from cranial ectodermal placodes situated between the eye and ear. TAO:0001470 ZFA:0001470 uberon UBERON:2001470 anterior lateral line lexical The anterior lateral line consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians. The anterior lateral line develops from cranial ectodermal placodes situated between the eye and ear. ZFIN:curator The posterior lateral line system develops from cranial ectodermal placodes, situated behind the ear, that give rise to both the neuromasts and the posterior lateral line sensory nerves that innervate the neuromasts. The posterior lateral line system consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians. The neuromasts are innervated by several lateral line nerves, which project primarily to the hindbrain. The posterior mechanosensory lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. 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:0001471 uberon/phenoscape-anatomy posterior lateral line system lexical The posterior lateral line system develops from cranial ectodermal placodes, situated behind the ear, that give rise to both the neuromasts and the posterior lateral line sensory nerves that innervate the neuromasts. The posterior lateral line system consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians. The neuromasts are innervated by several lateral line nerves, which project primarily to the hindbrain. The posterior mechanosensory lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. ZFIN:curator A migrating group of cells originating from an anterior lateral line placode. The primordium deposits neuromasts and interneuromasts between them during its migration. 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:0005117 anterior lateral line primordia uberon/phenoscape-anatomy anterior lateral line primordium A migrating group of cells originating from an anterior lateral line placode. The primordium deposits neuromasts and interneuromasts between them during its migration. ZFIN:curator anterior lateral line primordia TAO:0005117 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:0005227 uberon/phenoscape-anatomy immature neuromast proto neuromast proto-neuromast protoneuromast immature neuromast TAO:0005227 proto neuromast TAO:0005227 proto-neuromast TAO:0005227 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 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 lateral line nucleus 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 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 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 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 zone of skin that is part of a scalp. http://orcid.org/0000-0001-9897-3238 FMA:24757 adult scalp zone of skin scalp skin scalp zone of skin zone of skin of adult scalp zone of skin of scalp uberon UBERON:8300000 skin of scalp A zone of skin that is part of a scalp. 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 Any of the metabolic zones found in the hepatic acinus. Liver tissue is heterogenous at the level of morphometry and histochemistry. This heterogeneity is linked to the position of a cell within the functional unit of the tissue, which, in turn, is related to the blood supply: Cells located in the upstream zone differ from those in the downstream zone with respect to subcellular structures, key enzymes, translocators, and receptors and, therefore, have different metabolic capacities. This is the basis for "metabolic zonation", a concept first proposed for carbohydrate metabolism and later expanded to include amino acid and ammonia metabolism, xenobiotic metabolism, protective metabolism, and formation of plasma proteins. http://orcid.org/0000-0003-2034-601X 202z-09-29T15:45:36Z hepatic acinus metabolic zone uberon UBERON:8400005 metabolic zone of liver Any of the metabolic zones found in the hepatic acinus. Liver tissue is heterogenous at the level of morphometry and histochemistry. This heterogeneity is linked to the position of a cell within the functional unit of the tissue, which, in turn, is related to the blood supply: Cells located in the upstream zone differ from those in the downstream zone with respect to subcellular structures, key enzymes, translocators, and receptors and, therefore, have different metabolic capacities. This is the basis for "metabolic zonation", a concept first proposed for carbohydrate metabolism and later expanded to include amino acid and ammonia metabolism, xenobiotic metabolism, protective metabolism, and formation of plasma proteins. hepatic acinus metabolic zone The region of the liver lobule that is closest to the portal triad. http://orcid.org/0000-0003-2034-601X 2020-10-05T12:56:57Z uberon hepatic acinus zone 1 UBERON:8400006 liver lobule periportal region The region of the liver lobule that is closest to the portal triad. hepatic acinus zone 1 The region of the liver lobule that is closest to the central vein. http://orcid.org/0000-0003-2034-601X 2020-10-05T15:43:18Z uberon hepatic acinus zone 3 UBERON:8400007 liver lobule centrilobular region The region of the liver lobule that is closest to the central vein. hepatic acinus zone 3 The region of the liver lobule that is between the periportal and centrilobular regions. http://orcid.org/0000-0003-2034-601X 2020-10-05T15:52:22Z uberon hepatic acinus zone 2 UBERON:8400008 liver lobule midzonal region The region of the liver lobule that is between the periportal and centrilobular regions. hepatic acinus zone 2 Hepatic serous coat; peritoneal covering of the liver, enclosing almost all except for a triangular area on its posterior surface (the "bare area of the liver") and a smaller area where the liver and gallbladder are in direct contact. https://orcid.org/0000-0003-2034-601X serosa of liver tunica serosa hepatis uberon UBERON:8400021 liver serosa Hepatic serous coat; peritoneal covering of the liver, enclosing almost all except for a triangular area on its posterior surface (the "bare area of the liver") and a smaller area where the liver and gallbladder are in direct contact. serosa of liver FMA:15811 tunica serosa hepatis LATIN Subserosal tissue of liver. A zone of areolar connective tissue lying beneath the serous coat of the liver and distinguished with difficulty from the fibrous capsule of Glisson. https://orcid.org/0000-0003-2034-601X hepatic subserosa subserosal tissue of liver subserous layer of liver tela subserosa (hepar) tela subserosa hepatis uberon UBERON:8400023 liver subserosa Subserosal tissue of liver. A zone of areolar connective tissue lying beneath the serous coat of the liver and distinguished with difficulty from the fibrous capsule of Glisson. FMA:15812 tela subserosa (hepar) FMA:15821 tela subserosa hepatis Region of liver parenchyma immediately below the capsule. This region is frequently specified in pathology diagnoses. https://orcid.org/0000-0003-2034-601X liver subcapsular region liver subcapsular tissue subcapsular tissue of liver uberon UBERON:8400024 subcapsular region of liver Region of liver parenchyma immediately below the capsule. This region is frequently specified in pathology diagnoses. liver subcapsular region liver subcapsular tissue subcapsular tissue of liver The anatomical junction between the duodenum and the jejunum. FMA:15957 TA2:2952 WikipediaVersioned:Duodenojejunal_flexure&oldid=937307798 duodeno-jejunal flexure duodenojejunal flexure duodenojejunal junction flexura duodenojejunalis uberon UBERON:8410000 duodeno-jejunal junction The anatomical junction between the duodenum and the jejunum. flexura duodenojejunalis The anatomical junction between the descending colon and the sigmoid colon. http://orcid.org/0000-0002-2825-0621 sigmoid junction descending-sigmoid colon junction descending-sigmoid junction uberon UBERON:8410016 descending sigmoid junction The anatomical junction between the descending colon and the sigmoid colon. A portal vein that drains the descending colon. It is a tributary of the inferior mesenteric vein, and follows the path of its corresponding artery, the left colic artery. http://orcid.org/0000-0002-2825-0621 FMA:15394 uberon UBERON:8410017 left colic vein A portal vein that drains the descending colon. It is a tributary of the inferior mesenteric vein, and follows the path of its corresponding artery, the left colic artery. WikipediaVersioned:Left_colic_vein&oldid=964575339 A portal vein that drains the ascending colon. It is a tributary of the superior mesenteric vein, and travels with its corresponding artery, the right colic artery. http://orcid.org/0000-0002-2825-0621 FMA:15407 uberon UBERON:8410018 right colic vein A portal vein that drains the ascending colon. It is a tributary of the superior mesenteric vein, and travels with its corresponding artery, the right colic artery. WikipediaVersioned:Right_colic_vein&oldid=870898828 The area where the jejunum ends and the ileum part of the intestine begins. Although there is no clear distinct section, the ileum is narrower and has smaller villi than the jejunum. http://orcid.org/0000-0002-2825-0621 jejunoileal junction uberon UBERON:8410019 jejuno-ileal junction The area where the jejunum ends and the ileum part of the intestine begins. Although there is no clear distinct section, the ileum is narrower and has smaller villi than the jejunum. An anatomical junction between two parts of the intestine. http://orcid.org/0000-0002-2825-0621 junction of intestine uberon UBERON:8410024 intestinal junction An anatomical junction between two parts of the intestine. ORCID:0000-0002-7073-9172 A vein where lymph node venules condense and which exits at the lymph node hilum. It is also called hilar vein. http://orcid.org/0000-0002-2825-0621 hilar vein of lymph node vein of lymph node uberon UBERON:8410033 lymph node vein A vein where lymph node venules condense and which exits at the lymph node hilum. It is also called hilar vein. WikipediaVersioned:Lymph_node&oldid=1001655735#Structure An artery that enters the lymph node at the hilum and branches into smaller arterioles. artery of lymph node hilar artery of lymph node uberon UBERON:8410034 lymph node artery An artery that enters the lymph node at the hilum and branches into smaller arterioles. WikipediaVersioned:Lymph_node&oldid=1001655735#Structure A protein coding gene BCL6 in human. gene HGNC:1001 Category=external. BCL6 (human) A protein coding gene BCL6 in human. PRO:DNx A protein coding gene RNASE2 in human. gene HGNC:10045 Category=external. RNASE2 (human) A protein coding gene RNASE2 in human. PRO:DNx A protein coding gene RNASE3 in human. gene HGNC:10046 Category=external. RNASE3 (human) A protein coding gene RNASE3 in human. PRO:DNx A protein coding gene RORC in human. gene HGNC:10260 Category=external. RORC (human) A protein coding gene RORC in human. PRO:DNx A protein coding gene RUNX1 in human. gene HGNC:10471 Category=external. RUNX1 (human) A protein coding gene RUNX1 in human. PRO:DNx A protein coding gene CXCR5 in human. gene HGNC:1060 Category=external. CXCR5 (human) A protein coding gene CXCR5 in human. PRO:DNx A protein coding gene SDC1 in human. gene HGNC:10658 Category=external. SDC1 (human) A protein coding gene SDC1 in human. PRO:DNx A protein coding gene SELL in human. gene HGNC:10720 Category=external. SELL (human) A protein coding gene SELL in human. PRO:DNx A protein coding gene SIGLEC5 in human. gene HGNC:10874 Category=external. SIGLEC5 (human) A protein coding gene SIGLEC5 in human. PRO:DNx A protein coding gene SLAMF1 in human. gene HGNC:10903 Category=external. SLAMF1 (human) A protein coding gene SLAMF1 in human. PRO:DNx A protein coding gene SIGLEC1 in human. gene HGNC:11127 Category=external. SIGLEC1 (human) A protein coding gene SIGLEC1 in human. PRO:DNx A protein coding gene SNCG in human. gene HGNC:11141 Category=external. SNCG (human) A protein coding gene SNCG in human. PRO:DNx A protein coding gene BST2 in human. gene HGNC:1119 Category=external. BST2 (human) A protein coding gene BST2 in human. PRO:DNx A protein coding gene SPI1 in human. gene HGNC:11241 Category=external. SPI1 (human) A protein coding gene SPI1 in human. PRO:DNx A protein coding gene SPN in human. gene HGNC:11249 Category=external. SPN (human) A protein coding gene SPN in human. PRO:DNx A protein coding gene SST in human. gene HGNC:11329 Category=external. SST (human) A protein coding gene SST in human. PRO:DNx A protein coding gene TAL1 in human. gene HGNC:11556 Category=external. TAL1 (human) A protein coding gene TAL1 in human. PRO:DNx A protein coding gene TBX21 in human. gene HGNC:11599 Category=external. TBX21 (human) A protein coding gene TBX21 in human. PRO:DNx A protein coding gene TFRC in human. gene HGNC:11763 Category=external. TFRC (human) A protein coding gene TFRC in human. PRO:DNx A protein coding gene THBD in human. gene HGNC:11784 Category=external. THBD (human) A protein coding gene THBD in human. PRO:DNx A protein coding gene THY1 in human. gene HGNC:11801 Category=external. THY1 (human) A protein coding gene THY1 in human. PRO:DNx A protein coding gene TNFRSF11A in human. gene HGNC:11908 Category=external. TNFRSF11A (human) A protein coding gene TNFRSF11A in human. PRO:DNx A protein coding gene CD27 in human. gene HGNC:11922 Category=external. CD27 (human) A protein coding gene CD27 in human. PRO:DNx A protein coding gene CD40LG in human. gene HGNC:11935 Category=external. CD40LG (human) A protein coding gene CD40LG in human. PRO:DNx A protein coding gene TRPC3 in human. gene HGNC:12335 Category=external. TRPC3 (human) A protein coding gene TRPC3 in human. PRO:DNx A protein coding gene ACP5 in human. gene HGNC:124 Category=external. ACP5 (human) A protein coding gene ACP5 in human. PRO:DNx A protein coding gene VIP in human. gene HGNC:12693 Category=external. VIP (human) A protein coding gene VIP in human. PRO:DNx A protein coding gene VPREB1 in human. gene HGNC:12709 Category=external. VPREB1 (human) A protein coding gene VPREB1 in human. PRO:DNx A protein coding gene CLEC4C in human. gene HGNC:13258 Category=external. CLEC4C (human) A protein coding gene CLEC4C in human. PRO:DNx A protein coding gene NETO1 in human. gene HGNC:13823 Category=external. NETO1 (human) A protein coding gene NETO1 in human. PRO:DNx A protein coding gene CLEC6A in human. gene HGNC:14556 Category=external. CLEC6A (human) A protein coding gene CLEC6A in human. PRO:DNx A protein coding gene CLEC7A in human. gene HGNC:14558 Category=external. CLEC7A (human) A protein coding gene CLEC7A in human. PRO:DNx A protein coding gene IRX6 in human. gene HGNC:14675 Category=external. IRX6 (human) A protein coding gene IRX6 in human. PRO:DNx A protein coding gene LILRA4 in human. gene HGNC:15503 Category=external. LILRA4 (human) A protein coding gene LILRA4 in human. PRO:DNx A protein coding gene CCK in human. gene HGNC:1569 Category=external. CCK (human) A protein coding gene CCK in human. PRO:DNx A protein coding gene CD93 in human. gene HGNC:15855 Category=external. CD93 (human) A protein coding gene CD93 in human. PRO:DNx A protein coding gene CCR1 in human. gene HGNC:1602 Category=external. CCR1 (human) A protein coding gene CCR1 in human. PRO:DNx A protein coding gene CCR2 in human. gene HGNC:1603 Category=external. CCR2 (human) A protein coding gene CCR2 in human. PRO:DNx A protein coding gene CCR3 in human. gene HGNC:1604 Category=external. CCR3 (human) A protein coding gene CCR3 in human. PRO:DNx A protein coding gene CCR4 in human. gene HGNC:1605 Category=external. CCR4 (human) A protein coding gene CCR4 in human. PRO:DNx A protein coding gene CCR5 in human. gene HGNC:1606 Category=external. CCR5 (human) A protein coding gene CCR5 in human. PRO:DNx A protein coding gene CCR6 in human. gene HGNC:1607 Category=external. CCR6 (human) A protein coding gene CCR6 in human. PRO:DNx A protein coding gene CCR7 in human. gene HGNC:1608 Category=external. CCR7 (human) A protein coding gene CCR7 in human. PRO:DNx A protein coding gene LAMP5 in human. gene HGNC:16097 Category=external. LAMP5 (human) A protein coding gene LAMP5 in human. PRO:DNx A protein coding gene CD14 in human. gene HGNC:1628 Category=external. CD14 (human) A protein coding gene CD14 in human. PRO:DNx A protein coding gene CD163 in human. gene HGNC:1631 Category=external. CD163 (human) A protein coding gene CD163 in human. PRO:DNx A protein coding gene CD19 in human. gene HGNC:1633 Category=external. CD19 (human) A protein coding gene CD19 in human. PRO:DNx A protein coding gene CD1A in human. gene HGNC:1634 Category=external. CD1A (human) A protein coding gene CD1A in human. PRO:DNx A protein coding gene CD1C in human. gene HGNC:1636 Category=external. CD1C (human) A protein coding gene CD1C in human. PRO:DNx A protein coding gene CD1D in human. gene HGNC:1637 Category=external. CD1D (human) A protein coding gene CD1D in human. PRO:DNx A protein coding gene CD2 in human. gene HGNC:1639 Category=external. CD2 (human) A protein coding gene CD2 in human. PRO:DNx A protein coding gene CD209 in human. gene HGNC:1641 Category=external. CD209 (human) A protein coding gene CD209 in human. PRO:DNx A protein coding gene CD22 in human. gene HGNC:1643 Category=external. CD22 (human) A protein coding gene CD22 in human. PRO:DNx A protein coding gene CD24 in human. gene HGNC:1645 Category=external. CD24 (human) A protein coding gene CD24 in human. PRO:DNx A protein coding gene CD28 in human. gene HGNC:1653 Category=external. CD28 (human) A protein coding gene CD28 in human. PRO:DNx A protein coding gene CD33 in human. gene HGNC:1659 Category=external. CD33 (human) A protein coding gene CD33 in human. PRO:DNx A protein coding gene CD34 in human. gene HGNC:1662 Category=external. CD34 (human) A protein coding gene CD34 in human. PRO:DNx A protein coding gene CD36 in human. gene HGNC:1663 Category=external. CD36 (human) A protein coding gene CD36 in human. PRO:DNx A protein coding gene CD38 in human. gene HGNC:1667 Category=external. CD38 (human) A protein coding gene CD38 in human. PRO:DNx A protein coding gene CD3E in human. gene HGNC:1674 Category=external. CD3E (human) A protein coding gene CD3E in human. PRO:DNx A protein coding gene CD4 in human. gene HGNC:1678 Category=external. CD4 (human) A protein coding gene CD4 in human. PRO:DNx A protein coding gene CD44 in human. gene HGNC:1681 Category=external. CD44 (human) A protein coding gene CD44 in human. PRO:DNx A protein coding gene CD48 in human. gene HGNC:1683 Category=external. CD48 (human) A protein coding gene CD48 in human. PRO:DNx A protein coding gene CD5 in human. gene HGNC:1685 Category=external. CD5 (human) A protein coding gene CD5 in human. PRO:DNx A protein coding gene CD68 in human. gene HGNC:1693 Category=external. CD68 (human) A protein coding gene CD68 in human. PRO:DNx A protein coding gene CD69 in human. gene HGNC:1694 Category=external. CD69 (human) A protein coding gene CD69 in human. PRO:DNx A protein coding gene CD7 in human. gene HGNC:1695 Category=external. CD7 (human) A protein coding gene CD7 in human. PRO:DNx A protein coding gene CD80 in human. gene HGNC:1700 Category=external. CD80 (human) A protein coding gene CD80 in human. PRO:DNx A protein coding gene CD83 in human. gene HGNC:1703 Category=external. CD83 (human) A protein coding gene CD83 in human. PRO:DNx A protein coding gene CD84 in human. gene HGNC:1704 Category=external. CD84 (human) A protein coding gene CD84 in human. PRO:DNx A protein coding gene CD86 in human. gene HGNC:1705 Category=external. CD86 (human) A protein coding gene CD86 in human. PRO:DNx A protein coding gene CD8A in human. gene HGNC:1706 Category=external. CD8A (human) A protein coding gene CD8A in human. PRO:DNx A protein coding gene CD8B in human. gene HGNC:1707 Category=external. CD8B (human) A protein coding gene CD8B in human. PRO:DNx A protein coding gene CD9 in human. gene HGNC:1709 Category=external. CD9 (human) A protein coding gene CD9 in human. PRO:DNx A protein coding gene TMED1 in human. gene HGNC:17291 Category=external. TMED1 (human) A protein coding gene TMED1 in human. PRO:DNx A protein coding gene CDH1 in human. gene HGNC:1748 Category=external. CDH1 (human) A protein coding gene CDH1 in human. PRO:DNx A protein coding gene CDH5 in human. gene HGNC:1764 Category=external. CDH5 (human) A protein coding gene CDH5 in human. PRO:DNx A protein coding gene CD207 in human. gene HGNC:17935 Category=external. CD207 (human) A protein coding gene CD207 in human. PRO:DNx A protein coding gene IL17RB in human. gene HGNC:18015 Category=external. IL17RB (human) A protein coding gene IL17RB in human. PRO:DNx A protein coding gene A4GALT in human. gene HGNC:18149 Category=external. A4GALT (human) A protein coding gene A4GALT in human. PRO:DNx A protein coding gene CD244 in human. gene HGNC:18171 Category=external. CD244 (human) A protein coding gene CD244 in human. PRO:DNx A protein coding gene CEACAM8 in human. gene HGNC:1820 Category=external. CEACAM8 (human) A protein coding gene CEACAM8 in human. PRO:DNx A protein coding gene CEBPA in human. gene HGNC:1833 Category=external. CEBPA (human) A protein coding gene CEBPA in human. PRO:DNx A protein coding gene CEBPE in human. gene HGNC:1836 Category=external. CEBPE (human) A protein coding gene CEBPE in human. PRO:DNx A protein coding gene CHRNA7 in human. gene HGNC:1960 Category=external. CHRNA7 (human) A protein coding gene CHRNA7 in human. PRO:DNx A protein coding gene COL1A1 in human. gene HGNC:2197 Category=external. COL1A1 (human) A protein coding gene COL1A1 in human. PRO:DNx A protein coding gene NTNG1 in human. gene HGNC:23319 Category=external. NTNG1 (human) A protein coding gene NTNG1 in human. PRO:DNx A protein coding gene CR1 in human. gene HGNC:2334 Category=external. CR1 (human) A protein coding gene CR1 in human. PRO:DNx A protein coding gene CR2 in human. gene HGNC:2336 Category=external. CR2 (human) A protein coding gene CR2 in human. PRO:DNx A protein coding gene CSF1R in human. gene HGNC:2433 Category=external. CSF1R (human) A protein coding gene CSF1R in human. PRO:DNx A protein coding gene CTLA4 in human. gene HGNC:2505 Category=external. CTLA4 (human) A protein coding gene CTLA4 in human. PRO:DNx A protein coding gene CTSK in human. gene HGNC:2536 Category=external. CTSK (human) A protein coding gene CTSK in human. PRO:DNx A protein coding gene CX3CR1 in human. gene HGNC:2558 Category=external. CX3CR1 (human) A protein coding gene CX3CR1 in human. PRO:DNx A protein coding gene CXCR4 in human. gene HGNC:2561 Category=external. CXCR4 (human) A protein coding gene CXCR4 in human. PRO:DNx A protein coding gene DNTT in human. gene HGNC:2983 Category=external. DNTT (human) A protein coding gene DNTT in human. PRO:DNx A protein coding gene EGR2 in human. gene HGNC:3239 Category=external. EGR2 (human) A protein coding gene EGR2 in human. PRO:DNx A protein coding gene ADGRE1 in human. gene HGNC:3336 Category=external. ADGRE1 (human) A protein coding gene ADGRE1 in human. PRO:DNx A protein coding gene ENG in human. gene HGNC:3349 Category=external. ENG (human) A protein coding gene ENG in human. PRO:DNx A protein coding gene ENPEP in human. gene HGNC:3355 Category=external. ENPEP (human) A protein coding gene ENPEP in human. PRO:DNx A protein coding gene ENPP3 in human. gene HGNC:3358 Category=external. ENPP3 (human) A protein coding gene ENPP3 in human. PRO:DNx A protein coding gene EOMES in human. gene HGNC:3372 Category=external. EOMES (human) A protein coding gene EOMES in human. PRO:DNx A protein coding gene EPX in human. gene HGNC:3423 Category=external. EPX (human) A protein coding gene EPX in human. PRO:DNx A protein coding gene FCER1A in human. gene HGNC:3609 Category=external. FCER1A (human) A protein coding gene FCER1A in human. PRO:DNx A protein coding gene FCER2 in human. gene HGNC:3612 Category=external. FCER2 (human) A protein coding gene FCER2 in human. PRO:DNx A protein coding gene FCGR1A in human. gene HGNC:3613 Category=external. FCGR1A (human) A protein coding gene FCGR1A in human. PRO:DNx A protein coding gene FCGR2B in human. gene HGNC:3618 Category=external. FCGR2B (human) A protein coding gene FCGR2B in human. PRO:DNx A protein coding gene FLT3 in human. gene HGNC:3765 Category=external. FLT3 (human) A protein coding gene FLT3 in human. PRO:DNx A protein coding gene FOS in human. gene HGNC:3796 Category=external. FOS (human) A protein coding gene FOS in human. PRO:DNx A protein coding gene FPR1 in human. gene HGNC:3826 Category=external. FPR1 (human) A protein coding gene FPR1 in human. PRO:DNx A protein coding gene FUT4 in human. gene HGNC:4015 Category=external. FUT4 (human) A protein coding gene FUT4 in human. PRO:DNx A protein coding gene GATA1 in human. gene HGNC:4170 Category=external. GATA1 (human) A protein coding gene GATA1 in human. PRO:DNx A protein coding gene GATA2 in human. gene HGNC:4171 Category=external. GATA2 (human) A protein coding gene GATA2 in human. PRO:DNx A protein coding gene GATA3 in human. gene HGNC:4172 Category=external. GATA3 (human) A protein coding gene GATA3 in human. PRO:DNx A protein coding gene GFAP in human. gene HGNC:4235 Category=external. GFAP (human) A protein coding gene GFAP in human. PRO:DNx A protein coding gene GP1BA in human. gene HGNC:4439 Category=external. GP1BA (human) A protein coding gene GP1BA in human. PRO:DNx A protein coding gene PTGDR2 in human. gene HGNC:4502 Category=external. PTGDR2 (human) A protein coding gene PTGDR2 in human. PRO:DNx A protein coding gene CXCR3 in human. gene HGNC:4540 Category=external. CXCR3 (human) A protein coding gene CXCR3 in human. PRO:DNx A protein coding gene GYPA in human. gene HGNC:4702 Category=external. GYPA (human) A protein coding gene GYPA in human. PRO:DNx A protein coding gene GZMB in human. gene HGNC:4709 Category=external. GZMB (human) A protein coding gene GZMB in human. PRO:DNx A protein coding gene HBZ in human. gene HGNC:4835 Category=external. HBZ (human) A protein coding gene HBZ in human. PRO:DNx A protein coding gene HLA-DRA in human. gene HGNC:4947 Category=external. HLA-DRA (human) A protein coding gene HLA-DRA in human. PRO:DNx A protein coding gene ANPEP in human. gene HGNC:500 Category=external. ANPEP (human) A protein coding gene ANPEP in human. PRO:DNx A protein coding gene ICOS in human. gene HGNC:5351 Category=external. ICOS (human) A protein coding gene ICOS in human. PRO:DNx A protein coding gene IGLL1 in human. gene HGNC:5870 Category=external. IGLL1 (human) A protein coding gene IGLL1 in human. PRO:DNx A protein coding gene IL1RL1 in human. gene HGNC:5998 Category=external. IL1RL1 (human) A protein coding gene IL1RL1 in human. PRO:DNx A protein coding gene IL2RA in human. gene HGNC:6008 Category=external. IL2RA (human) A protein coding gene IL2RA in human. PRO:DNx A protein coding gene IL2RB in human. gene HGNC:6009 Category=external. IL2RB (human) A protein coding gene IL2RB in human. PRO:DNx A protein coding gene IL3RA in human. gene HGNC:6012 Category=external. IL3RA (human) A protein coding gene IL3RA in human. PRO:DNx A protein coding gene IL5RA in human. gene HGNC:6017 Category=external. IL5RA (human) A protein coding gene IL5RA in human. PRO:DNx A protein coding gene IL7R in human. gene HGNC:6024 Category=external. IL7R (human) A protein coding gene IL7R in human. PRO:DNx A protein coding gene CXCR1 in human. gene HGNC:6026 Category=external. CXCR1 (human) A protein coding gene CXCR1 in human. PRO:DNx A protein coding gene CXCR2 in human. gene HGNC:6027 Category=external. CXCR2 (human) A protein coding gene CXCR2 in human. PRO:DNx A protein coding gene FOXP3 in human. gene HGNC:6106 Category=external. FOXP3 (human) A protein coding gene FOXP3 in human. PRO:DNx A protein coding gene ITGA2 in human. gene HGNC:6137 Category=external. ITGA2 (human) A protein coding gene ITGA2 in human. PRO:DNx A protein coding gene ITGA2B in human. gene HGNC:6138 Category=external. ITGA2B (human) A protein coding gene ITGA2B in human. PRO:DNx A protein coding gene ITGA4 in human. gene HGNC:6140 Category=external. ITGA4 (human) A protein coding gene ITGA4 in human. PRO:DNx A protein coding gene ITGAE in human. gene HGNC:6147 Category=external. ITGAE (human) A protein coding gene ITGAE in human. PRO:DNx A protein coding gene ITGAM in human. gene HGNC:6149 Category=external. ITGAM (human) A protein coding gene ITGAM in human. PRO:DNx A protein coding gene ITGAX in human. gene HGNC:6152 Category=external. ITGAX (human) A protein coding gene ITGAX in human. PRO:DNx A protein coding gene ITGB7 in human. gene HGNC:6162 Category=external. ITGB7 (human) A protein coding gene ITGB7 in human. PRO:DNx A protein coding gene KDR in human. gene HGNC:6307 Category=external. KDR (human) A protein coding gene KDR in human. PRO:DNx A protein coding gene KIT in human. gene HGNC:6342 Category=external. KIT (human) A protein coding gene KIT in human. PRO:DNx A protein coding gene KLRB1 in human. gene HGNC:6373 Category=external. KLRB1 (human) A protein coding gene KLRB1 in human. PRO:DNx A protein coding gene KLRC1 in human. gene HGNC:6374 Category=external. KLRC1 (human) A protein coding gene KLRC1 in human. PRO:DNx A protein coding gene KLRD1 in human. gene HGNC:6378 Category=external. KLRD1 (human) A protein coding gene KLRD1 in human. PRO:DNx A protein coding gene KLRG1 in human. gene HGNC:6380 Category=external. KLRG1 (human) A protein coding gene KLRG1 in human. PRO:DNx A protein coding gene LCN2 in human. gene HGNC:6526 Category=external. LCN2 (human) A protein coding gene LCN2 in human. PRO:DNx A protein coding gene LGALS1 in human. gene HGNC:6561 Category=external. LGALS1 (human) A protein coding gene LGALS1 in human. PRO:DNx A protein coding gene LHX3 in human. gene HGNC:6595 Category=external. LHX3 (human) A protein coding gene LHX3 in human. PRO:DNx A protein coding gene ARG1 in human. gene HGNC:663 Category=external. ARG1 (human) A protein coding gene ARG1 in human. PRO:DNx A protein coding gene LTF in human. gene HGNC:6720 Category=external. LTF (human) A protein coding gene LTF in human. PRO:DNx A protein coding gene LUM in human. gene HGNC:6724 Category=external. LUM (human) A protein coding gene LUM in human. PRO:DNx A protein coding gene LY75 in human. gene HGNC:6729 Category=external. LY75 (human) A protein coding gene LY75 in human. PRO:DNx A protein coding gene NCR1 in human. gene HGNC:6731 Category=external. NCR1 (human) A protein coding gene NCR1 in human. PRO:DNx A protein coding gene NCR2 in human. gene HGNC:6732 Category=external. NCR2 (human) A protein coding gene NCR2 in human. PRO:DNx A protein coding gene MARCO in human. gene HGNC:6895 Category=external. MARCO (human) A protein coding gene MARCO in human. PRO:DNx A protein coding gene MEIS2 in human. gene HGNC:7001 Category=external. MEIS2 (human) A protein coding gene MEIS2 in human. PRO:DNx A protein coding gene MERTK in human. gene HGNC:7027 Category=external. MERTK (human) A protein coding gene MERTK in human. PRO:DNx A protein coding gene MME in human. gene HGNC:7154 Category=external. MME (human) A protein coding gene MME in human. PRO:DNx A protein coding gene MPO in human. gene HGNC:7218 Category=external. MPO (human) A protein coding gene MPO in human. PRO:DNx A protein coding gene MRC1 in human. gene HGNC:7228 Category=external. MRC1 (human) A protein coding gene MRC1 in human. PRO:DNx A protein coding gene MS4A1 in human. gene HGNC:7315 Category=external. MS4A1 (human) A protein coding gene MS4A1 in human. PRO:DNx A protein coding gene MSR1 in human. gene HGNC:7376 Category=external. MSR1 (human) A protein coding gene MSR1 in human. PRO:DNx A protein coding gene MYB in human. gene HGNC:7545 Category=external. MYB (human) A protein coding gene MYB in human. PRO:DNx A protein coding gene NCAM1 in human. gene HGNC:7656 Category=external. NCAM1 (human) A protein coding gene NCAM1 in human. PRO:DNx A protein coding gene NFKB2 in human. gene HGNC:7795 Category=external. NFKB2 (human) A protein coding gene NFKB2 in human. PRO:DNx A protein coding gene PAX5 in human. gene HGNC:8619 Category=external. PAX5 (human) A protein coding gene PAX5 in human. PRO:DNx A protein coding gene PDCD1 in human. gene HGNC:8760 Category=external. PDCD1 (human) A protein coding gene PDCD1 in human. PRO:DNx A protein coding gene PDGFRA in human. gene HGNC:8803 Category=external. PDGFRA (human) A protein coding gene PDGFRA in human. PRO:DNx A protein coding gene PLAUR in human. gene HGNC:9053 Category=external. PLAUR (human) A protein coding gene PLAUR in human. PRO:DNx A protein coding gene PRF1 in human. gene HGNC:9360 Category=external. PRF1 (human) A protein coding gene PRF1 in human. PRO:DNx A protein coding gene PRG2 in human. gene HGNC:9362 Category=external. PRG2 (human) A protein coding gene PRG2 in human. PRO:DNx A protein coding gene PROM1 in human. gene HGNC:9454 Category=external. PROM1 (human) A protein coding gene PROM1 in human. PRO:DNx A protein coding gene SIRPA in human. gene HGNC:9662 Category=external. SIRPA (human) A protein coding gene SIRPA in human. PRO:DNx A protein coding gene PTPRC in human. gene HGNC:9666 Category=external. PTPRC (human) A protein coding gene PTPRC in human. PRO:DNx A protein coding gene PVALB in human. gene HGNC:9704 Category=external. PVALB (human) A protein coding gene PVALB in human. PRO:DNx A protein coding gene RAG1 in human. gene HGNC:9831 Category=external. RAG1 (human) A protein coding gene RAG1 in human. PRO:DNx A protein coding gene RAG2 in human. gene HGNC:9832 Category=external. RAG2 (human) A protein coding gene RAG2 in human. PRO:DNx A protein coding gene Cd86 in mouse. gene MGI:101773 Category=external. Cd86 (mouse) A protein coding gene Cd86 in mouse. PRO:DNx A protein coding gene Cd80 in mouse. gene MGI:101775 Category=external. Cd80 (mouse) A protein coding gene Cd80 in mouse. PRO:DNx A protein coding gene Klra4 in mouse. gene MGI:101904 Category=external. Klra4 (mouse) A protein coding gene Klra4 in mouse. PRO:DNx A protein coding gene Klra3 in mouse. gene MGI:101905 Category=external. Klra3 (mouse) A protein coding gene Klra3 in mouse. PRO:DNx A protein coding gene Klra1 in mouse. gene MGI:101907 Category=external. Klra1 (mouse) A protein coding gene Klra1 in mouse. PRO:DNx A protein coding gene Lhx3 in mouse. gene MGI:102673 Category=external. Lhx3 (mouse) A protein coding gene Lhx3 in mouse. PRO:DNx A protein coding gene Klra8 in mouse. gene MGI:102968 Category=external. Klra8 (mouse) A protein coding gene Klra8 in mouse. PRO:DNx A protein coding gene Ccr7 in mouse. gene MGI:103011 Category=external. Ccr7 (mouse) A protein coding gene Ccr7 in mouse. PRO:DNx A protein coding gene Prg2 in mouse. gene MGI:103294 Category=external. Prg2 (mouse) A protein coding gene Prg2 in mouse. PRO:DNx A protein coding gene Cxcr5 in mouse. gene MGI:103567 Category=external. Cxcr5 (mouse) A protein coding gene Cxcr5 in mouse. PRO:DNx A protein coding gene Cebpe in mouse. gene MGI:103572 Category=external. Cebpe (mouse) A protein coding gene Cebpe in mouse. PRO:DNx A protein coding gene Ccr3 in mouse. gene MGI:104616 Category=external. Ccr3 (mouse) A protein coding gene Ccr3 in mouse. PRO:DNx A protein coding gene Ccr1 in mouse. gene MGI:104618 Category=external. Ccr1 (mouse) A protein coding gene Ccr1 in mouse. PRO:DNx A protein coding gene Rorc in mouse. gene MGI:104856 Category=external. Rorc (mouse) A protein coding gene Rorc in mouse. PRO:DNx A protein coding gene Pdcd1 in mouse. gene MGI:104879 Category=external. Pdcd1 (mouse) A protein coding gene Pdcd1 in mouse. PRO:DNx A protein coding gene Cdh5 in mouse. gene MGI:105057 Category=external. Cdh5 (mouse) A protein coding gene Cdh5 in mouse. PRO:DNx A protein coding gene Cxcr2 in mouse. gene MGI:105303 Category=external. Cxcr2 (mouse) A protein coding gene Cxcr2 in mouse. PRO:DNx A protein coding gene Ccr2 in mouse. gene MGI:106185 Category=external. Ccr2 (mouse) A protein coding gene Ccr2 in mouse. PRO:DNx A protein coding gene Tmed1 in mouse. gene MGI:106201 Category=external. Tmed1 (mouse) A protein coding gene Tmed1 in mouse. PRO:DNx A protein coding gene Enpep in mouse. gene MGI:106645 Category=external. Enpep (mouse) A protein coding gene Enpep in mouse. PRO:DNx A protein coding gene Ly75 in mouse. gene MGI:106662 Category=external. Ly75 (mouse) A protein coding gene Ly75 in mouse. PRO:DNx A protein coding gene Cd93 in mouse. gene MGI:106664 Category=external. Cd93 (mouse) A protein coding gene Cd93 in mouse. PRO:DNx A protein coding gene Ly76 in mouse. gene MGI:106910 Category=external. Ly76 (mouse) A protein coding gene Ly76 in mouse. PRO:DNx A protein coding gene Adgre1 in mouse. gene MGI:106912 Category=external. Adgre1 (mouse) A protein coding gene Adgre1 in mouse. PRO:DNx A protein coding gene Ccr5 in mouse. gene MGI:107182 Category=external. Ccr5 (mouse) A protein coding gene Ccr5 in mouse. PRO:DNx A protein coding gene Bcl6 in mouse. gene MGI:107187 Category=external. Bcl6 (mouse) A protein coding gene Bcl6 in mouse. PRO:DNx A protein coding gene Fpr1 in mouse. gene MGI:107443 Category=external. Fpr1 (mouse) A protein coding gene Fpr1 in mouse. PRO:DNx A protein coding gene Cd38 in mouse. gene MGI:107474 Category=external. Cd38 (mouse) A protein coding gene Cd38 in mouse. PRO:DNx A protein coding gene Ly6a in mouse. gene MGI:107527 Category=external. Ly6a (mouse) A protein coding gene Ly6a in mouse. PRO:DNx A protein coding gene Klrb1c in mouse. gene MGI:107538 Category=external. Klrb1c (mouse) A protein coding gene Klrb1c in mouse. PRO:DNx A protein coding gene Epx in mouse. gene MGI:107569 Category=external. Epx (mouse) A protein coding gene Epx in mouse. PRO:DNx A protein coding gene Cd1d1 in mouse. gene MGI:107674 Category=external. Cd1d1 (mouse) A protein coding gene Cd1d1 in mouse. PRO:DNx A protein coding gene Ctsk in mouse. gene MGI:107823 Category=external. Ctsk (mouse) A protein coding gene Ctsk in mouse. PRO:DNx A protein coding gene Ccr4 in mouse. gene MGI:107824 Category=external. Ccr4 (mouse) A protein coding gene Ccr4 in mouse. PRO:DNx A protein coding gene Cd36 in mouse. gene MGI:107899 Category=external. Cd36 (mouse) A protein coding gene Cd36 in mouse. PRO:DNx A protein coding gene Sirpa in mouse. gene MGI:108563 Category=external. Sirpa (mouse) A protein coding gene Sirpa in mouse. PRO:DNx A protein coding gene Meis2 in mouse. gene MGI:108564 Category=external. Meis2 (mouse) A protein coding gene Meis2 in mouse. PRO:DNx A protein coding gene Cd244 in mouse. gene MGI:109294 Category=external. Cd244 (mouse) A protein coding gene Cd244 in mouse. PRO:DNx A protein coding gene Lum in mouse. gene MGI:109347 Category=external. Lum (mouse) A protein coding gene Lum in mouse. PRO:DNx A protein coding gene Ly6g in mouse. gene MGI:109440 Category=external. Ly6g (mouse) A protein coding gene Ly6g in mouse. PRO:DNx A protein coding gene Trpc3 in mouse. gene MGI:109526 Category=external. Trpc3 (mouse) A protein coding gene Trpc3 in mouse. PRO:DNx A protein coding gene Cxcr4 in mouse. gene MGI:109563 Category=external. Cxcr4 (mouse) A protein coding gene Cxcr4 in mouse. PRO:DNx A protein coding gene Nfkb2 in mouse. gene MGI:1099800 Category=external. Nfkb2 (mouse) A protein coding gene Nfkb2 in mouse. PRO:DNx A protein coding gene Prom1 in mouse. gene MGI:1100886 Category=external. Prom1 (mouse) A protein coding gene Prom1 in mouse. PRO:DNx A protein coding gene Klrd1 in mouse. gene MGI:1196275 Category=external. Klrd1 (mouse) A protein coding gene Klrd1 in mouse. PRO:DNx A protein coding gene Eomes in mouse. gene MGI:1201683 Category=external. Eomes (mouse) A protein coding gene Eomes in mouse. PRO:DNx A protein coding gene Cxcr3 in mouse. gene MGI:1277207 Category=external. Cxcr3 (mouse) A protein coding gene Cxcr3 in mouse. PRO:DNx A protein coding gene Itgae in mouse. gene MGI:1298377 Category=external. Itgae (mouse) A protein coding gene Itgae in mouse. PRO:DNx A protein coding gene Sncg in mouse. gene MGI:1298397 Category=external. Sncg (mouse) A protein coding gene Sncg in mouse. PRO:DNx A protein coding gene Marco in mouse. gene MGI:1309998 Category=external. Marco (mouse) A protein coding gene Marco in mouse. PRO:DNx A protein coding gene Tnfrsf11a in mouse. gene MGI:1314891 Category=external. Tnfrsf11a (mouse) A protein coding gene Tnfrsf11a in mouse. PRO:DNx A protein coding gene Cd83 in mouse. gene MGI:1328316 Category=external. Cd83 (mouse) A protein coding gene Cd83 in mouse. PRO:DNx A protein coding gene Ptgdr2 in mouse. gene MGI:1330275 Category=external. Ptgdr2 (mouse) A protein coding gene Ptgdr2 in mouse. PRO:DNx A protein coding gene Gp1ba in mouse. gene MGI:1333744 Category=external. Gp1ba (mouse) A protein coding gene Gp1ba in mouse. PRO:DNx A protein coding gene Ccr6 in mouse. gene MGI:1333797 Category=external. Ccr6 (mouse) A protein coding gene Ccr6 in mouse. PRO:DNx A protein coding gene Cx3cr1 in mouse. gene MGI:1333815 Category=external. Cx3cr1 (mouse) A protein coding gene Cx3cr1 in mouse. PRO:DNx A protein coding gene Ncr1 in mouse. gene MGI:1336212 Category=external. Ncr1 (mouse) A protein coding gene Ncr1 in mouse. PRO:DNx A protein coding gene Cd84 in mouse. gene MGI:1336885 Category=external. Cd84 (mouse) A protein coding gene Cd84 in mouse. PRO:DNx A protein coding gene Csf1r in mouse. gene MGI:1339758 Category=external. Csf1r (mouse) A protein coding gene Csf1r in mouse. PRO:DNx A protein coding gene Sdc1 in mouse. gene MGI:1349162 Category=external. Sdc1 (mouse) A protein coding gene Sdc1 in mouse. PRO:DNx A protein coding gene Slamf1 in mouse. gene MGI:1351314 Category=external. Slamf1 (mouse) A protein coding gene Slamf1 in mouse. PRO:DNx A protein coding gene Il17rb in mouse. gene MGI:1355292 Category=external. Il17rb (mouse) A protein coding gene Il17rb in mouse. PRO:DNx A protein coding gene Klrg1 in mouse. gene MGI:1355294 Category=external. Klrg1 (mouse) A protein coding gene Klrg1 in mouse. PRO:DNx A protein coding gene Icos in mouse. gene MGI:1858745 Category=external. Icos (mouse) A protein coding gene Icos in mouse. PRO:DNx A protein coding gene Clec4n in mouse. gene MGI:1861231 Category=external. Clec4n (mouse) A protein coding gene Clec4n in mouse. PRO:DNx A protein coding gene Clec7a in mouse. gene MGI:1861431 Category=external. Clec7a (mouse) A protein coding gene Clec7a in mouse. PRO:DNx A protein coding gene Tbx21 in mouse. gene MGI:1888984 Category=external. Tbx21 (mouse) A protein coding gene Tbx21 in mouse. PRO:DNx A protein coding gene Foxp3 in mouse. gene MGI:1891436 Category=external. Foxp3 (mouse) A protein coding gene Foxp3 in mouse. PRO:DNx A protein coding gene Cd209b in mouse. gene MGI:1916415 Category=external. Cd209b (mouse) A protein coding gene Cd209b in mouse. PRO:DNx A protein coding gene Bst2 in mouse. gene MGI:1916800 Category=external. Bst2 (mouse) A protein coding gene Bst2 in mouse. PRO:DNx A protein coding gene Cd200r3 in mouse. gene MGI:1921853 Category=external. Cd200r3 (mouse) A protein coding gene Cd200r3 in mouse. PRO:DNx A protein coding gene Lamp5 in mouse. gene MGI:1923411 Category=external. Lamp5 (mouse) A protein coding gene Lamp5 in mouse. PRO:DNx A protein coding gene Irx6 in mouse. gene MGI:1927642 Category=external. Irx6 (mouse) A protein coding gene Irx6 in mouse. PRO:DNx A protein coding gene Ntng1 in mouse. gene MGI:1934028 Category=external. Ntng1 (mouse) A protein coding gene Ntng1 in mouse. PRO:DNx A protein coding gene Cd163 in mouse. gene MGI:2135946 Category=external. Cd163 (mouse) A protein coding gene Cd163 in mouse. PRO:DNx A protein coding gene Enpp3 in mouse. gene MGI:2143702 Category=external. Enpp3 (mouse) A protein coding gene Enpp3 in mouse. PRO:DNx A protein coding gene Cd207 in mouse. gene MGI:2180021 Category=external. Cd207 (mouse) A protein coding gene Cd207 in mouse. PRO:DNx A protein coding gene Neto1 in mouse. gene MGI:2180216 Category=external. Neto1 (mouse) A protein coding gene Neto1 in mouse. PRO:DNx A protein coding gene A4galt in mouse. gene MGI:3512453 Category=external. A4galt (mouse) A protein coding gene A4galt in mouse. PRO:DNx A protein coding gene Ly6c2 in mouse. gene MGI:3712069 Category=external. Ly6c2 (mouse) A protein coding gene Ly6c2 in mouse. PRO:DNx A protein coding gene Anpep in mouse. gene MGI:5000466 Category=external. Anpep (mouse) A protein coding gene Anpep in mouse. PRO:DNx A protein coding gene Acp5 in mouse. gene MGI:87883 Category=external. Acp5 (mouse) A protein coding gene Acp5 in mouse. PRO:DNx A protein coding gene Arg1 in mouse. gene MGI:88070 Category=external. Arg1 (mouse) A protein coding gene Arg1 in mouse. PRO:DNx A protein coding gene Cck in mouse. gene MGI:88297 Category=external. Cck (mouse) A protein coding gene Cck in mouse. PRO:DNx A protein coding gene Cd14 in mouse. gene MGI:88318 Category=external. Cd14 (mouse) A protein coding gene Cd14 in mouse. PRO:DNx A protein coding gene Cd19 in mouse. gene MGI:88319 Category=external. Cd19 (mouse) A protein coding gene Cd19 in mouse. PRO:DNx A protein coding gene Cd2 in mouse. gene MGI:88320 Category=external. Cd2 (mouse) A protein coding gene Cd2 in mouse. PRO:DNx A protein coding gene Ms4a1 in mouse. gene MGI:88321 Category=external. Ms4a1 (mouse) A protein coding gene Ms4a1 in mouse. PRO:DNx A protein coding gene Cd22 in mouse. gene MGI:88322 Category=external. Cd22 (mouse) A protein coding gene Cd22 in mouse. PRO:DNx A protein coding gene Cd24a in mouse. gene MGI:88323 Category=external. Cd24a (mouse) A protein coding gene Cd24a in mouse. PRO:DNx A protein coding gene Cd27 in mouse. gene MGI:88326 Category=external. Cd27 (mouse) A protein coding gene Cd27 in mouse. PRO:DNx A protein coding gene Cd28 in mouse. gene MGI:88327 Category=external. Cd28 (mouse) A protein coding gene Cd28 in mouse. PRO:DNx A protein coding gene Cd34 in mouse. gene MGI:88329 Category=external. Cd34 (mouse) A protein coding gene Cd34 in mouse. PRO:DNx A protein coding gene Cd3e in mouse. gene MGI:88332 Category=external. Cd3e (mouse) A protein coding gene Cd3e in mouse. PRO:DNx A protein coding gene Cd4 in mouse. gene MGI:88335 Category=external. Cd4 (mouse) A protein coding gene Cd4 in mouse. PRO:DNx A protein coding gene Cd40lg in mouse. gene MGI:88337 Category=external. Cd40lg (mouse) A protein coding gene Cd40lg in mouse. PRO:DNx A protein coding gene Cd44 in mouse. gene MGI:88338 Category=external. Cd44 (mouse) A protein coding gene Cd44 in mouse. PRO:DNx A protein coding gene Cd48 in mouse. gene MGI:88339 Category=external. Cd48 (mouse) A protein coding gene Cd48 in mouse. PRO:DNx A protein coding gene Cd5 in mouse. gene MGI:88340 Category=external. Cd5 (mouse) A protein coding gene Cd5 in mouse. PRO:DNx A protein coding gene Cd68 in mouse. gene MGI:88342 Category=external. Cd68 (mouse) A protein coding gene Cd68 in mouse. PRO:DNx A protein coding gene Cd69 in mouse. gene MGI:88343 Category=external. Cd69 (mouse) A protein coding gene Cd69 in mouse. PRO:DNx A protein coding gene Cd7 in mouse. gene MGI:88344 Category=external. Cd7 (mouse) A protein coding gene Cd7 in mouse. PRO:DNx A protein coding gene Cd8a in mouse. gene MGI:88346 Category=external. Cd8a (mouse) A protein coding gene Cd8a in mouse. PRO:DNx A protein coding gene Cd8b1 in mouse. gene MGI:88347 Category=external. Cd8b1 (mouse) A protein coding gene Cd8b1 in mouse. PRO:DNx A protein coding gene Cd9 in mouse. gene MGI:88348 Category=external. Cd9 (mouse) A protein coding gene Cd9 in mouse. PRO:DNx A protein coding gene Cdh1 in mouse. gene MGI:88354 Category=external. Cdh1 (mouse) A protein coding gene Cdh1 in mouse. PRO:DNx A protein coding gene Col1a1 in mouse. gene MGI:88467 Category=external. Col1a1 (mouse) A protein coding gene Col1a1 in mouse. PRO:DNx A protein coding gene Cr2 in mouse. gene MGI:88489 Category=external. Cr2 (mouse) A protein coding gene Cr2 in mouse. PRO:DNx A protein coding gene Ctla4 in mouse. gene MGI:88556 Category=external. Ctla4 (mouse) A protein coding gene Ctla4 in mouse. PRO:DNx A protein coding gene Egr2 in mouse. gene MGI:95296 Category=external. Egr2 (mouse) A protein coding gene Egr2 in mouse. PRO:DNx A protein coding gene Eng in mouse. gene MGI:95392 Category=external. Eng (mouse) A protein coding gene Eng in mouse. PRO:DNx A protein coding gene Fcer1a in mouse. gene MGI:95494 Category=external. Fcer1a (mouse) A protein coding gene Fcer1a in mouse. PRO:DNx A protein coding gene Fcer2a in mouse. gene MGI:95497 Category=external. Fcer2a (mouse) A protein coding gene Fcer2a in mouse. PRO:DNx A protein coding gene Fcgr1 in mouse. gene MGI:95498 Category=external. Fcgr1 (mouse) A protein coding gene Fcgr1 in mouse. PRO:DNx A protein coding gene Fcgr2 in mouse. gene MGI:95499 Category=external. Fcgr2 (mouse) A protein coding gene Fcgr2 in mouse. PRO:DNx A protein coding gene Fcgr3 in mouse. gene MGI:95500 Category=external. Fcgr3 (mouse) A protein coding gene Fcgr3 in mouse. PRO:DNx A protein coding gene Flt3 in mouse. gene MGI:95559 Category=external. Flt3 (mouse) A protein coding gene Flt3 in mouse. PRO:DNx A protein coding gene Fos in mouse. gene MGI:95574 Category=external. Fos (mouse) A protein coding gene Fos in mouse. PRO:DNx A protein coding gene Fut4 in mouse. gene MGI:95594 Category=external. Fut4 (mouse) A protein coding gene Fut4 in mouse. PRO:DNx A protein coding gene Gata1 in mouse. gene MGI:95661 Category=external. Gata1 (mouse) A protein coding gene Gata1 in mouse. PRO:DNx A protein coding gene Gata2 in mouse. gene MGI:95662 Category=external. Gata2 (mouse) A protein coding gene Gata2 in mouse. PRO:DNx A protein coding gene Gata3 in mouse. gene MGI:95663 Category=external. Gata3 (mouse) A protein coding gene Gata3 in mouse. PRO:DNx A protein coding gene Gfap in mouse. gene MGI:95697 Category=external. Gfap (mouse) A protein coding gene Gfap in mouse. PRO:DNx A protein coding gene H2-Ea in mouse. gene MGI:95900 Category=external. H2-Ea (mouse) A protein coding gene H2-Ea in mouse. PRO:DNx A protein coding gene Hba-x in mouse. gene MGI:96019 Category=external. Hba-x (mouse) A protein coding gene Hba-x in mouse. PRO:DNx A protein coding gene Hbb-b1 in mouse. gene MGI:96021 Category=external. Hbb-b1 (mouse) A protein coding gene Hbb-b1 in mouse. PRO:DNx A protein coding gene Il2ra in mouse. gene MGI:96549 Category=external. Il2ra (mouse) A protein coding gene Il2ra in mouse. PRO:DNx A protein coding gene Il2rb in mouse. gene MGI:96550 Category=external. Il2rb (mouse) A protein coding gene Il2rb in mouse. PRO:DNx A protein coding gene Il3ra in mouse. gene MGI:96553 Category=external. Il3ra (mouse) A protein coding gene Il3ra in mouse. PRO:DNx A protein coding gene Il5ra in mouse. gene MGI:96558 Category=external. Il5ra (mouse) A protein coding gene Il5ra in mouse. PRO:DNx A protein coding gene Il7r in mouse. gene MGI:96562 Category=external. Il7r (mouse) A protein coding gene Il7r in mouse. PRO:DNx A protein coding gene Itga2 in mouse. gene MGI:96600 Category=external. Itga2 (mouse) A protein coding gene Itga2 in mouse. PRO:DNx A protein coding gene Itga2b in mouse. gene MGI:96601 Category=external. Itga2b (mouse) A protein coding gene Itga2b in mouse. PRO:DNx A protein coding gene Itga4 in mouse. gene MGI:96603 Category=external. Itga4 (mouse) A protein coding gene Itga4 in mouse. PRO:DNx A protein coding gene Itgam in mouse. gene MGI:96607 Category=external. Itgam (mouse) A protein coding gene Itgam in mouse. PRO:DNx A protein coding gene Itgax in mouse. gene MGI:96609 Category=external. Itgax (mouse) A protein coding gene Itgax in mouse. PRO:DNx A protein coding gene Itgb7 in mouse. gene MGI:96616 Category=external. Itgb7 (mouse) A protein coding gene Itgb7 in mouse. PRO:DNx A protein coding gene Kit in mouse. gene MGI:96677 Category=external. Kit (mouse) A protein coding gene Kit in mouse. PRO:DNx A protein coding gene Kdr in mouse. gene MGI:96683 Category=external. Kdr (mouse) A protein coding gene Kdr in mouse. PRO:DNx A protein coding gene Lcn2 in mouse. gene MGI:96757 Category=external. Lcn2 (mouse) A protein coding gene Lcn2 in mouse. PRO:DNx A protein coding gene Lgals1 in mouse. gene MGI:96777 Category=external. Lgals1 (mouse) A protein coding gene Lgals1 in mouse. PRO:DNx A protein coding gene Ltf in mouse. gene MGI:96837 Category=external. Ltf (mouse) A protein coding gene Ltf in mouse. PRO:DNx A protein coding gene Mertk in mouse. gene MGI:96965 Category=external. Mertk (mouse) A protein coding gene Mertk in mouse. PRO:DNx A protein coding gene Mme in mouse. gene MGI:97004 Category=external. Mme (mouse) A protein coding gene Mme in mouse. PRO:DNx A protein coding gene Mpo in mouse. gene MGI:97137 Category=external. Mpo (mouse) A protein coding gene Mpo in mouse. PRO:DNx A protein coding gene Mrc1 in mouse. gene MGI:97142 Category=external. Mrc1 (mouse) A protein coding gene Mrc1 in mouse. PRO:DNx A protein coding gene Myb in mouse. gene MGI:97249 Category=external. Myb (mouse) A protein coding gene Myb in mouse. PRO:DNx A protein coding gene Ncam1 in mouse. gene MGI:97281 Category=external. Ncam1 (mouse) A protein coding gene Ncam1 in mouse. PRO:DNx A protein coding gene Pax5 in mouse. gene MGI:97489 Category=external. Pax5 (mouse) A protein coding gene Pax5 in mouse. PRO:DNx A protein coding gene Pdgfra in mouse. gene MGI:97530 Category=external. Pdgfra (mouse) A protein coding gene Pdgfra in mouse. PRO:DNx A protein coding gene Prf1 in mouse. gene MGI:97551 Category=external. Prf1 (mouse) A protein coding gene Prf1 in mouse. PRO:DNx A protein coding gene Plaur in mouse. gene MGI:97612 Category=external. Plaur (mouse) A protein coding gene Plaur in mouse. PRO:DNx A protein coding gene Pvalb in mouse. gene MGI:97821 Category=external. Pvalb (mouse) A protein coding gene Pvalb in mouse. PRO:DNx A protein coding gene Rag1 in mouse. gene MGI:97848 Category=external. Rag1 (mouse) A protein coding gene Rag1 in mouse. PRO:DNx A protein coding gene Rag2 in mouse. gene MGI:97849 Category=external. Rag2 (mouse) A protein coding gene Rag2 in mouse. PRO:DNx A protein coding gene Msr1 in mouse. gene MGI:98257 Category=external. Msr1 (mouse) A protein coding gene Msr1 in mouse. PRO:DNx A protein coding gene Sell in mouse. gene MGI:98279 Category=external. Sell (mouse) A protein coding gene Sell in mouse. PRO:DNx A protein coding gene Spi1 in mouse. gene MGI:98282 Category=external. Spi1 (mouse) A protein coding gene Spi1 in mouse. PRO:DNx A protein coding gene Sst in mouse. gene MGI:98326 Category=external. Sst (mouse) A protein coding gene Sst in mouse. PRO:DNx A protein coding gene Spn in mouse. gene MGI:98384 Category=external. Spn (mouse) A protein coding gene Spn in mouse. PRO:DNx A protein coding gene Il1rl1 in mouse. gene MGI:98427 Category=external. Il1rl1 (mouse) A protein coding gene Il1rl1 in mouse. PRO:DNx A protein coding gene Tal1 in mouse. gene MGI:98480 Category=external. Tal1 (mouse) A protein coding gene Tal1 in mouse. PRO:DNx A protein coding gene Dntt in mouse. gene MGI:98659 Category=external. Dntt (mouse) A protein coding gene Dntt in mouse. PRO:DNx A protein coding gene Thbd in mouse. gene MGI:98736 Category=external. Thbd (mouse) A protein coding gene Thbd in mouse. PRO:DNx A protein coding gene Thy1 in mouse. gene MGI:98747 Category=external. Thy1 (mouse) A protein coding gene Thy1 in mouse. PRO:DNx A protein coding gene Tfrc in mouse. gene MGI:98822 Category=external. Tfrc (mouse) A protein coding gene Tfrc in mouse. PRO:DNx A protein coding gene Vip in mouse. gene MGI:98933 Category=external. Vip (mouse) A protein coding gene Vip in mouse. PRO:DNx A protein coding gene Cd33 in mouse. gene MGI:99440 Category=external. Cd33 (mouse) A protein coding gene Cd33 in mouse. PRO:DNx A protein coding gene Cebpa in mouse. gene MGI:99480 Category=external. Cebpa (mouse) A protein coding gene Cebpa in mouse. PRO:DNx A protein coding gene Siglec1 in mouse. gene MGI:99668 Category=external. Siglec1 (mouse) A protein coding gene Siglec1 in mouse. PRO:DNx A protein coding gene Chrna7 in mouse. gene MGI:99779 Category=external. Chrna7 (mouse) A protein coding gene Chrna7 in mouse. PRO:DNx A protein coding gene Runx1 in mouse. gene MGI:99852 Category=external. Runx1 (mouse) A protein coding gene Runx1 in mouse. PRO:DNx 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 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 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).