From 3eb45e5d2034f1610eb6185557d31229fef4c78c Mon Sep 17 00:00:00 2001 From: Nicole Vasilevsky Date: Thu, 20 Jan 2022 13:09:30 -0800 Subject: [PATCH] update uberon import --- src/ontology/imports/uberon_import.owl | 194253 +++++++++++++++------- 1 file changed, 136076 insertions(+), 58177 deletions(-) diff --git a/src/ontology/imports/uberon_import.owl b/src/ontology/imports/uberon_import.owl index fd79f1e..89ea022 100644 --- a/src/ontology/imports/uberon_import.owl +++ b/src/ontology/imports/uberon_import.owl @@ -1,6 +1,7 @@ - + @@ -42,7 +46,7 @@ - + @@ -64,6 +68,9 @@ MESH PMID:11433360 Placental development: lessons from mouse mutants PMID:16417468 Forgotten and novel aspects in pancreas development, Pieler and Chen + aggregates AAO from 13:04:2012 + aggregates TAO from 09:08:2012 + aggregates VSAO from 16:07:2012 http://wiki.phenotypercn.org/wg/phenotypercn/index.php?title=Neural_Crest_Workshop http://wiki.phenotypercn.org/wiki/August_2012_Notes https://docs.google.com/document/d/16JZOuH9sh_a8uIXA4cqg0Q1H6MV5yCj3-rhuKsZoV_U/edit @@ -71,7 +78,7 @@ https://docs.google.com/document/d/1cPWBqrl_Qy7XHEWFqtR_PgQX61yRkgGuLaiDpnEXxkE/edit https://docs.google.com/document/d/1r9kNPpFYGdu0SpJDLyFAVQczBlG0wAZCBMd18gG3Ot8/edit# https://docs.google.com/spreadsheet/ccc?key=0Aj8NJdyb-leqdDM0R3hTVTRHRExDVjRCSkZEbDc5N1E#gid=0 - 2021-02-15 + 2022-01-20 @@ -87,17 +94,77 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + definition + definition - + + + IAO:0000116 + uberon + editor_note + true + editor_note + + editor note + editor note + + + + + + + + + + + + + + + + + + + @@ -107,12 +174,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -125,6 +240,30 @@ + + + + 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 + + + + + + + + + + @@ -143,6 +282,12 @@ + + + + + + @@ -209,9 +354,43 @@ - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + @@ -351,6 +530,14 @@ + + + + + + + + @@ -364,6 +551,24 @@ + + + + + + + + + + + + + + + + + + @@ -394,6 +599,12 @@ + + + + + + @@ -406,12 +617,24 @@ + + + + + + + + + + + + @@ -500,6 +723,18 @@ + + + + + + + + + + + + @@ -512,6 +747,12 @@ + + + + + + @@ -536,6 +777,24 @@ + + + + + + + + + + + + + + + + + + @@ -554,6 +813,12 @@ + + + + + + @@ -574,6 +839,12 @@ + + + + + + @@ -586,6 +857,12 @@ + + + + + + @@ -612,13 +889,47 @@ + + 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 + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + 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 @@ -626,12 +937,39 @@ + + 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 + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + 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 @@ -639,14 +977,25 @@ + + - X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) + + + + + + + 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. BFO:0000062 is preceded by takes place after uberon preceded_by preceded_by + preceded by + preceded by preceded_by @@ -667,12 +1016,55 @@ + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + BFO:0000067 + uberon + contains_process + contains_process + contains process + contains process @@ -680,20 +1072,29 @@ + - 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 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 extends through an organism from head end to opposite end of body or tail. + 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 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 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 extends through an organism from head end to opposite end of body or tail. + BSPO:cjm + + + + + 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. @@ -702,13 +1103,23 @@ + + + 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 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 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). + BSPO:cjm + @@ -723,13 +1134,21 @@ + 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 extends through an organism from back (e.g. spinal column) to front (e.g. belly). 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 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 extends through an organism from back (e.g. spinal column) to front (e.g. belly). + BSPO:cjm + @@ -743,14 +1162,22 @@ + 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 extends through an organism from head end to opposite end of body or tail. 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 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 extends through an organism from head end to opposite end of body or tail. + BSPO:cjm + @@ -763,13 +1190,22 @@ + + x proximal to y iff x is closer to the point of attachment with the body than y. 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 proximal_to + + + + x proximal to y iff x is closer to the point of attachment with the body than y. + BSPO:cjm + @@ -783,13 +1219,21 @@ + 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 extends through an organism from back (e.g. spinal column) to front (e.g. belly). 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 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 extends through an organism from back (e.g. spinal column) to front (e.g. belly). + BSPO:cjm + @@ -802,19 +1246,21 @@ + 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 deep_to Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. - + BSPO:cjm @@ -822,18 +1268,79 @@ + Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:0000108 uberon superficial_to superficial_to + superficial to superficial_to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. - + BSPO:cjm + + + + + + + + + + X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion. + 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 + 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 two left and right portions, X is part of the left portion. + BSPO:PATO_mtg_2009 + + + + + 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 two left and right portions, X is part of the right portion. + 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 + 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 two left and right portions, X is part of the right 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:PATO_mtg_2009 @@ -842,13 +1349,21 @@ + X posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion. 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 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 + @@ -862,13 +1377,21 @@ + X anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion. 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 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 + @@ -884,10 +1407,12 @@ X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. + x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion. BSPO:0000124 uberon in_proximal_side_of in_proximal_side_of + in proximal side of in_proximal_side_of @@ -896,6 +1421,12 @@ 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 in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion. + BSPO:PATO_mtg_2009 + @@ -904,10 +1435,12 @@ X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. + x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion. BSPO:0000125 uberon in_distal_side_of in_distal_side_of + in distal side of in_distal_side_of @@ -916,6 +1449,12 @@ 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 distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion. + BSPO:PATO_mtg_2009 + @@ -923,18 +1462,26 @@ - 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 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 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 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 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 + UBERON:cjm + + + + + 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. @@ -944,17 +1491,31 @@ - X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y + X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y + 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 proximalmost_part_of - X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y + X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y + + + + + + X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y + https://orcid.org/0000-0002-6601-2165 + + + + + X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y. @@ -965,11 +1526,14 @@ + This relation holds when both the deep_to and ajdacent_to relationship similarly hold. + x immediately deep to y iff x deep_to y and x is contiguous with y. BSPO:0001107 uberon immediately_deep_to immediately_deep_to + immediately deep to immediately_deep_to @@ -978,6 +1542,12 @@ This relation holds when both the deep_to and ajdacent_to relationship similarly hold. + + + + x immediately deep to y iff x deep_to y and x is contiguous with y. + BSPO:curators + @@ -985,30 +1555,195 @@ - X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y + X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y + 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 distalmost_part_of - X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y + X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y + + + + + + X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y + https://orcid.org/0000-0002-6601-2165 + + + + + X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y. + + + + + X intersects median plane of iff X crosses the midine plane of Y. + 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 + intersects_midsagittal_plane_of + + + + + + + + + + x immediately superficial to y iff x superficial to y and x is contiguous with y. + BSPO:0015014 + uberon + immediately_superficial_to + immediately_superficial_to + immediately superficial to + immediately_superficial_to + + + + + x immediately superficial to y iff x superficial to y and x is contiguous with y. + BSPO:curators + + + + + + + + + X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion. + BSPO:0015101 + uberon + in_dorsal_side_of + in_dorsal_side_of + in dorsal side of + in_dorsal_side_of + + + + + X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion. + BSPO:cjm + + + + + + + + + + + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + characteristic of + + + + + + + Inverse of characteristic_of RO:0000053 uberon bearer_of bearer_of - bearer of + has characteristic + + + + + + + + + + + a relation between a continuant and a process, in which the continuant is somehow involved in the process + RO:0000056 + uberon + participates_in + participates_in + participates in + + + + + + + + + + + + + + a relation between a process and a continuant, in which the continuant is somehow involved in the process + has participant + + + + + + + + + + + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + function of + + + + + + + + + + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + quality of + + + + + + + + + + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + role of + + + + + + + + + + + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + has function @@ -1017,11 +1752,48 @@ + + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence RO:0000086 uberon has_quality has_quality - has quality + has quality + + + + + + + + + + + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + inverse of has disposition + disposition of @@ -1029,11 +1801,29 @@ + + + a relation between two independent continuants, the location and the target, in which the target is entirely within the location RO:0001015 uberon location_of location_of - location_of + location of + + + + + + + + + + + + + + + contained in @@ -1045,7 +1835,7 @@ uberon contains contains - contains + contains @@ -1053,11 +1843,66 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + a relation between two independent continuants, the target and the location, in which the target is entirely within the location RO:0001025 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. + + + + + + + + + + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + RO:0002000 + uberon + boundary_of + boundary_of + 2D boundary of @@ -1065,12 +1910,45 @@ + + + + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity RO:0002002 uberon has_boundary has_boundary - has boundary + has 2D boundary + + + + + + + + + + + + + + + RO:0002005 + nerve supply + uberon + innervated_by + innervated_by + http://code.google.com/p/obo-relations/issues/detail?id=6 + innervated_by + + + + + + nerve supply + FMA:85999 + @@ -1078,12 +1956,193 @@ + + + + + + + + + + + + + X outer_layer_of Y iff: +. X :continuant that bearer_of some PATO:laminar +. X part_of Y +. exists Z :surface +. X has_boundary Z +. Z boundary_of Y + +has_boundary: http://purl.obolibrary.org/obo/RO_0002002 +boundary_of: http://purl.obolibrary.org/obo/RO_0002000 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 + 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. + 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. + 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. + has positive regulatory component activity + + + + + + + + + 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. + has component process + + + + + + + + + + directly 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. + 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. + 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. + 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 + + + + + + + + + before or simultaneous with + + + + + + + + + + + + Relation between occurrents, shares start and end boundaries. + RO:0002082 + coincides_with + is_equal_to + uberon + simultaneous_with + simultaneous_with + simultaneous with + + + + + Relation between occurrents, shares start and end boundaries. + + Allen:is_equal_to + + + + + + + + + + ends after @@ -1092,7 +2151,12 @@ - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + + + + + + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y). 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 @@ -1102,7 +2166,7 @@ uberon immediately_preceded_by immediately_preceded_by - immediately_preceded_by + immediately preceded by @@ -1120,15 +2184,219 @@ + + + + + + + + + immediately precedes + + + + + + + + + + + + + + + + + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + BFO_0000051 some (BFO_0000050 some ?Y) + RO:0002131 + uberon + overlaps + overlaps + overlaps + + + + + + + + + true + + + + + + + + + + + + + Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. +T innervates some R +Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + RO:0002134 + uberon + innervates + innervates + http://code.google.com/p/obo-relations/issues/detail?id=6 + innervates + + + + + + + + X continuous_with Y if and only if X and Y share a fiat boundary. RO:0002150 uberon continuous_with continuous_with - continuous_with + continuous with + + + + + + + + + S only_in_taxon T iff: S SubClassOf in_taxon only T. + 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. + RO:0002160 + uberon + only_in_taxon + only_in_taxon + only in taxon + + + + + S only_in_taxon T iff: S SubClassOf in_taxon only T. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + RO:0002162 + uberon + in_taxon + in_taxon + in taxon + + + + + + + + + A is spatially_disjoint_from B if and only if they have no parts in common + spatially disjoint from @@ -1136,14 +2404,34 @@ + + + + + + + + + + + + + + + + + + + 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 @@ -1158,13 +2446,22 @@ + + + + + + + + Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. + c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect) RO:0002176 uberon connects connects - connects + connects @@ -1178,15 +2475,24 @@ + + + + + + + + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. RO:0002177 uberon attaches_to_part_of attaches_to_part_of - attaches_to_part_of + attached to part of @@ -1197,6 +2503,40 @@ true + + + + + + + + true + + + + + + + + + + Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. + relation between an artery and the structure is supplies with blood. + RO:0002178 + arterial supply of + uberon + supplies + supplies + source: FMA + supplies + + + + + + arterial supply of + FMA:86003 + @@ -1205,6 +2545,7 @@ + Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. RO:0002179 drains blood from drains from @@ -1212,7 +2553,21 @@ drains drains source: Wikipedia - drains + drains + + + + + + + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + RO:0002180 + uberon + has_component + has_component + has component @@ -1221,8 +2576,11 @@ + + + @@ -1231,11 +2589,18 @@ + + 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 - develops_from + This is the transitive form of the develops from relation + develops from @@ -1243,31 +2608,202 @@ + + + + inverse of develops from RO:0002203 uberon develops_into develops_into - develops_into + develops into + + + + + + + + + + + + + + + + + + + + + + + + + + Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. + RO:0002207 + uberon + directly_develops_from + directly_develops_from + directly develops from + + + + + + + + + inverse of directly develops from + directly develops into + + + + + + + + + + + + + + + + + + + + + + + + + process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. + RO:0002211 + 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. + RO:0002212 + 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. + RO:0002213 + 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 + + + + + + + + + + + + + + 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. + RO:0002216 + uberon + 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 + x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x + x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y. RO:0002219 uberon surrounded_by surrounded_by - surrounded_by + surrounded by - x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y + x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y. @@ -1276,13 +2812,17 @@ + - x adjacent_to y iff: x and y share a boundary + + + 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. RO:0002220 uberon adjacent_to adjacent_to - adjacent_to + adjacent to @@ -1290,33 +2830,47 @@ - inverse of surrounded_by + + inverse of surrounded by + inverse of surrounded_by. RO:0002221 uberon surrounds surrounds - surrounds + surrounds - inverse of surrounded_by + inverse of surrounded_by. + + + + + + temporally related to + + + + + Relation between occurrents, shares a start boundary with. + inverse of starts with RO:0002223 uberon starts starts - starts + starts @@ -1332,12 +2886,52 @@ + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. RO:0002224 uberon starts_with starts_with - starts with + starts with + + + + + + + + + + + + + x develops from part of y if and only if there exists some z such that x develops from z and z is part of y + RO:0002225 + uberon + develops_from_part_of + develops_from_part_of + develops from part of + + + + + + + + + + + + + + x develops_in y if x is located in y whilst x is developing + RO:0002226 + uberon + develops_in + develops_in + This relation take from EHDAA2 - precise semantics yet to be defined + develops in @@ -1346,13 +2940,16 @@ + + Relation between occurrents, shares an end boundary with. + inverse of ends with RO:0002229 finishes uberon ends ends - ends + ends @@ -1369,60 +2966,137 @@ + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. RO:0002230 uberon ends_with ends_with - ends with + ends with - + - - + + + + - - + + - RO:0002254 - uberon - has_developmental_contribution_from - has_developmental_contribution_from - has developmental contribution from + x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y + has start location - + - - + + + + - - + + - RO:0002255 - uberon - developmentally_contributes_to - developmentally_contributes_to - developmentally_contributes_to + x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y + has end location - + + + + + + + + + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + has input + + + + + + + + + + + + + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. + has output + + + + + + + + + + + + + + + + + x has developmental contribution from y iff x has some part z such that z develops from y + RO:0002254 + uberon + has_developmental_contribution_from + has_developmental_contribution_from + has developmental contribution from + + + + + + + + + + + + + + inverse of has developmental contribution from + RO:0002255 + uberon + developmentally_contributes_to + developmentally_contributes_to + developmentally contributes to + + + + + + + + + t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T RO:0002256 uberon developmentally_induced_by developmentally_induced_by sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F) - developmentally_induced_by + developmentally induced by @@ -1433,14 +3107,314 @@ + + + + + + Inverse of developmentally induced by + developmentally induces + + + + + + + + + + + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p + RO:0002258 + uberon + developmentally_preceded_by + developmentally_preceded_by + developmentally preceded by + + + + + + + + + + + + + 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 + + + + + + + + + + + + + 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. + acts upstream of or within + + + + + + x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else RO:0002285 uberon developmentally_replaces developmentally_replaces - developmentally_replaces + developmentally replaces + + + + + + + + + Inverse of developmentally preceded by + developmentally succeeded by + + + + + + + + + + + + + part of developmental precursor of + + + + + + + + + + causally upstream of, positive effect + + + + + + + + + + causally upstream of, negative effect + + + + + + + + + + + + + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + characteristic of part of + + + + + + + + + true + + + + + + + + A relationship that holds via some environmental process + evolutionarily related to + + + + + + + + A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) + ecologically related to + + + + + + + + + + RO:0002322 + adapted_for + uberon + confers_advantage_in + confers_advantage_in + confers advantage in + + + + + + + + A mereological relationship or a topological relationship + mereotopologically related to + + + + + + + + A relationship that holds between entities participating in some developmental process (GO:0032502) + developmentally related to + + + + + + + + + + + + + + + + + + enables + + + + + + + + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. + RO:0002328 + uberon + 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. + RO:0002329 + uberon + part_of_structure_that_is_capable_of + part_of_structure_that_is_capable_of + part of structure that is capable of + + + + + + + + + true + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + involved in + + + + + + + + + + inverse of enables + enabled by + + + + + + + + + + + + inverse of regulates + regulated by + + + + + + + + + inverse of negatively regulates + negatively regulated by + + + + + + + + + inverse of positively regulates + positively regulated by @@ -1450,11 +3424,12 @@ + is member of is a mereological relation between a item and a collection. RO:0002350 uberon member_of member_of - member of + member of @@ -1463,11 +3438,43 @@ + + has member is a mereological relation between a collection and an item. RO:0002351 uberon has_member has_member - has member + has member + + + + + + + + + + inverse of has input + RO:0002352 + uberon + input_of + input_of + input of + + + + + + + + + + inverse of has output + RO:0002353 + uberon + output_of + output_of + output of @@ -1475,27 +3482,76 @@ + + + a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a RO:0002371 uberon attaches_to attaches_to - attaches_to + attached to + + + + + + + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. + 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 + + + + + + + We need to import uberon muscle into RO to use as a stricter domain constraint + + + + + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. + + + + + + + + + + + + + A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. + in branching relationship with + + + + + + x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. RO:0002376 uberon drains into tributary_of tributary_of - tributary_of + tributary of @@ -1506,31 +3562,79 @@ + + + + + + + + + + + x spatially_coextensive_with y if and inly if x and y have the same location + spatially coextensive with + + + + + + + + + + + + x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve RO:0002380 uberon branching_part_of 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). + 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 + x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y. RO:0002385 uberon has_potential_to_developmentally_contribute_to has_potential_to_developmentally_contribute_to - has potential to developmentally contribute to + has potential to developmentally contribute to + + + + + + + + + x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y + has potential to developmentally induce @@ -1538,19 +3642,214 @@ - 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 + x has the potential to develop into y iff x develops into y or if x is capable of developing into y. RO:0002387 uberon has_potential_to_develop_into has_potential_to_develop_into - has potential to develop into + has potential to develop into + + + + + + + + + x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y + x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y. + RO:0002388 + uberon + has_potential_to_directly_develop_into + has_potential_to_directly_develop_into + has potential to directly develop into + + + + + + + + + + + inverse of upstream of + causally downstream of + + + + + + + + + + + immediately causally downstream of + + + + + + + + This relation groups causal relations between material entities and causal relations between processes + 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 + 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. + 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. + causally upstream of or within + + + + + + + + + + inverse of causally upstream of or within + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + 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 + involved in or involved in regulation of + + + + + + + + + + + + + + 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. + is active in + + + + + + + + true + + + + + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + GOC:cjm + GOC:dos + + + p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. RO:0002433 uberon contributes_to_morphology_of @@ -1560,14 +3859,104 @@ + + + + + + + A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + interacts with + + + + + + + + + + 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. + molecularly interacts with + + + + + + + + + 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. + 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. + 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. + directly positively regulates activity of + + + + - x composed_primarily_of y iff: more than half of the mass of x is made from parts of y + + + x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. + x composed_primarily_of y iff: more than half of the mass of x is made from parts of y. RO:0002473 uberon - RO:0002473 composed_primarily_of composed_primarily_of composed primarily of @@ -1575,19 +3964,54 @@ + + + + + + + + + + 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. + has part that occurs in + + + + + + + + + true + + + + + + + + + + relation between physical entity and a process or stage + + + + + Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. + x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). RO:0002488 begins_to_exist_during uberon - RO:0002488 existence_starts_during existence_starts_during existence starts during @@ -1606,6 +4030,7 @@ Relation between continuant and occurrent, such that c comes into existence at the start of p. + x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). RO:0002489 uberon existence_starts_with @@ -1621,11 +4046,22 @@ + + + + + x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) + existence overlaps + + + + + x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) RO:0002491 uberon existence_starts_and_ends_during @@ -1638,16 +4074,17 @@ + Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. + x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). RO:0002492 ceases_to_exist_during uberon - RO:0002492 existence_ends_during existence_ends_during existence ends during @@ -1666,6 +4103,7 @@ Relation between continuant and occurrent, such that c ceases to exist at the end of p. + x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). RO:0002493 uberon existence_ends_with @@ -1686,6 +4124,7 @@ + x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships RO:0002494 transforms from uberon @@ -1706,7 +4145,9 @@ + + x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t RO:0002495 direct_transformation_of immediately transforms from @@ -1734,10 +4175,15 @@ + + + + + @@ -1746,6 +4192,11 @@ + + + + + x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). RO:0002496 uberon existence_starts_during_or_after @@ -1758,10 +4209,15 @@ + + + + + @@ -1770,6 +4226,11 @@ + + + + + x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. RO:0002497 uberon existence_ends_during_or_before @@ -1779,13 +4240,60 @@ + + + + + + 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. + causal relation between processes + + + + + + + + depends on + + + + + + + + + + + causal relation between entities + + + + + + + + + A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. RO:0002551 uberon @@ -1795,6 +4303,12 @@ has_skeleton has skeleton + + + + + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. + @@ -1804,10 +4318,56 @@ + + + + + + causally influenced by + + + + + + + + + + + + + + + + + + + + + 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). + causally influences + + + + + + + + + + + A relation that holds between elements of a musculoskeletal system or its analogs. + biomechanically related to + + + + + + inverse of branching part of RO:0002569 uberon has_branching_part @@ -1817,10 +4377,28 @@ + + + + + + x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. + RO:0002571 + uberon + lumen_of + lumen_of + lumen of + + + + + + + s is luminal space of x iff s is lumen_of x and s is an immaterial entity RO:0002572 uberon luminal_space_of @@ -1834,6 +4412,9 @@ + + + inverse of has skeleton RO:0002576 uberon skeleton_of @@ -1843,67 +4424,292 @@ - + - - RO:0003000 - uberon - produces - produces - produces + + + + 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. + directly regulates - + - - RO:0003001 - uberon - produced_by - produced_by - produced_by + + + + + + + + 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 + has part structure that is capable of - + - - - - - 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 + + + + + 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. + causal relation between material entity and a process - - - - 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 + + + + + + + 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 + + + + + + + + + + + + + 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(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 + + + + + + + + + + + + + + + + + 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. + RO:0003000 + uberon + produces + produces + produces + + + + + + + + + + a produced_by b iff some process that occurs_in b has_output a. + RO:0003001 + uberon + 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. + enables subfunction + + + + + + + + + + + + + acts upstream of or within, positive effect + + + + + + + + + + + + + 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 + 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 + acts upstream of, negative effect + + + + + + + + + causally upstream of or within, negative effect + + + + + + + + + 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. + regulates activity of + + + + + + + + + + + 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 @@ -1954,6 +4760,18 @@ + + + + + + uberon + extends_fibers_into + extends_fibers_into + + + + @@ -1966,6 +4784,27 @@ + + + + + + + + + + + + + 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 + + + + @@ -2015,6 +4854,18 @@ + + + + c site_of p if c is the bearer of a disposition that is realized by a process that has p as part. + uberon + capable_of_has_part + site_of + site_of + + + + @@ -2026,6 +4877,17 @@ + + + + Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. + uberon + synapsed_by + synapsed by + + + + @@ -2102,3989 +4964,75563 @@ - + - - - 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 + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity - - - 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 + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + + + + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + - + - - - - - - - - - - - - - - - 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 + + + continuant + Continuant + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + continuant - - - 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]. - + + + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + - - - UMLS:C0225344 - ncithesaurus:Submucosa + + + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + - - - organ submucosa - FMA:85391 + + + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + - - - region of submucosa - FMA:85392 + + + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + - - - submucosa of organ - FMA:85391 + + + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + - - - submucosa of region of organ - FMA:85392 + + + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + - - - submucous layer - BTO:0002107 + + + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + - - - tela submucosa - BTO:0002107 + + + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + + + + + + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + - + - - - - - - - - - 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 + + + occurrent + + + + + + + + + + ic + IndependentContinuant + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + independent continuant - - - - 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 + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + - - - Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000142 - TAO - ZFIN:curator + + + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + - - - 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 + + + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + - - - 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) - + + + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + - - - (...) 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) + + + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + - - - PNS - + + + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + + + + + + + + s-region + SpatialRegion + BFO 2 Reference: Spatial regions do not participate in processes. + Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. + A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) + All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) + (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] + (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] + + spatial region + - - - UMLS:C0206417 - BIRNLEX:1111 + + + Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. + + per discussion with Barry Smith - - - UMLS:C0206417 - ncithesaurus:Peripheral_Nervous_System + + + A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) + - - - UMLS:C1305921 - BIRNLEX:1111 + + + All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) + - - - pars peripherica - - FMA:9903 - FMA:TA - + + + (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] + - - - systema nervosum periphericum - - FMA:9903 - FMA:TA - + + + (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] + - + - - - - - - - - - - - - - - - - - - - - - - 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 + + + process + + + + + + + + + + disposition + Disposition + an atom of element X has the disposition to decay to an atom of element Y + certain people have a predisposition to colon cancer + children are innately disposed to categorize objects in certain ways. + the cell wall is disposed to filter chemicals in endocytosis and exocytosis + BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) + (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + + disposition - - - (...) 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) + + + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + - - - skin - MA:0000151 + + + If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) + - - - - FMA + + + (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] + - - - Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. - - + + + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + - + - - - 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 + + + realizable + RealizableEntity + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + realizable entity - - - - CARO + + + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + - - - A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. - CARO:0000010 + + + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + - - - anatomical boundary - CARO:0000010 + + + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + + + + + + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + - + - - - - - - - - - - - - - - - + + + quality + + + + + + + + + sdc + SpecificallyDependentContinuant + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + specifically dependent continuant + + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + + + + + + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + per discussion with Barry Smith + + + + + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + + + + + + + + + role + Role + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + the priest role + the role of a boundary to demarcate two neighboring administrative territories + the role of a building in serving as a military target + the role of a stone in marking a property boundary + the role of subject in a clinical trial + the student role + BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + role + + + + + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + + + + + + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + + + + + + + + + object + object + + + + + + + + + function + Function + the function of a hammer to drive in nails + the function of a heart pacemaker to regulate the beating of a heart through electricity + the function of amylase in saliva to break down starch into sugar + BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. + A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) + (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] + + function + + + + + A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) + + + + + + (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] + + + + + + + + + + material entity + material entity + + + + + + + + + immaterial + ImmaterialEntity + BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 + + immaterial entity + + + + + + + + + anatomical entity + + + + + + + + + connected anatomical structure + + + + + + + + + + material anatomical entity + + + + + + + + + + + + + + + + + + + + + + + + + + + biological entity + + + + + + + + + electron + + + + + + + + + + + water + + + + + + + + + + polypeptide + + + + + + + + + + hyaluronic acid + + + + + + + + + + + + + + + protein polypeptide chain + + + + + + + + + + + + + + + + peptide + + + + + + + + + glycan + + + + + + + + + + glycoprotein + + + + + + + + + glycosaminoglycan + + + + + + + + + acyl group + + + + + + + + + + aminoglycan + + + + + + + + + carbamoyl group + + + + + + + + + molecular entity + + + + + + + + + chemical entity + + + + + + + + + biological role + + + + + + + + + + + + + + + group + + + + + + + + + + + + + + + + + hydroxides + + + + + + + + + inorganic molecular entity + + + + + + + + + + nitrogen atom + + + + + + + + + nonmetal atom + + + + + + + + + organic sulfate + + + + + + + + + + oxygen atom + + + + + + + + + + + + + + + oxygen molecular entity + + + + + + + + + + sulfuric ester + + + + + + + + + sulfates + + + + + + + + + + sulfur atom + + + + + + + + + + + + + + + sulfur molecular entity + + + + + + + + + univalent carboacyl group + + + + + + + + + + carbon atom + + + + + + + + + amide + + + + + + + + + fundamental particle + + + + + + + + + oxoacid derivative + + + + + + + + + + inorganic hydride + + + + + + + + + inorganic group + + + + + + + + + organic group + + + + + + + + + + + + + + + + + + + + + atom + + + + + + + + + + + + + + + atomic nucleus + + + + + + + + + + nucleon + + + + + + + + + primary amide + + + + + + + + + heteroorganic entity + + + + + + + + + food + + + + + + + + + pnictogen + + + + + + + + + + + + + + + pnictogen molecular entity + + + + + + + + + chalcogen + + + + + + + + + + + + + + + chalcogen molecular entity + + + + + + + + + carbon group element atom + + + + + + + + + main group element atom + + + + + + + + + + sulfur oxoacid derivative + + + + + + + + + s-block element atom + + + + + + + + + p-block element atom + + + + + + + + + + + + + + + main group molecular entity + + + + + + + + + + + + + + + carbon group molecular entity + + + + + + + + + + + + + + + hydrogen molecular entity + + + + + + + + + + + + + + + s-block molecular entity + + + + + + + + + + + + + + + p-block molecular entity + + + + + + + + + + hydrides + + + + + + + + + oxygen hydride + + + + + + + + + + biomacromolecule + + + + + + + + + information biomacromolecule + + + + + + + + + proteinogenic amino-acid residue + + + + + + + + + amino-acid residue + + + + + + + + + alpha-amino-acid residue + + + + + + + + + conjugated protein + + + + + + + + + macromolecule + + + + + + + + + + organonitrogen compound + + + + + + + + + ester + + + + + + + + + + sulfated glycosaminoglycan + + + + + + + + + + + carbohydrate sulfate + + + + + + + + + + + + + + + protein + + + + + + + + + + lepton + + + + + + + + + + baryon + + + + + + + + + fermion + + + + + + + + + subatomic particle + + + + + + + + + composite particle + + + + + + + + + hadron + + + + + + + + + nuclear particle + + + + + + + + + + + + + + + polyatomic entity + + + + + + + + + + chalcogen hydride + + + + + + + + + + organochalcogen compound + + + + + + + + + + organooxygen compound + + + + + + + + + mononuclear parent hydride + + + + + + + + + mucopolysaccharide + + + + + + + + + heteroatomic molecular entity + + + + + + + + + + + + + + + + + carboxamide + + + + + + + + + sulfuric acid derivative + + + + + + + + + carboacyl group + + + + + + + + + hydroxy group + + + + + + + + + + + hydrogen atom + + + + + + + + + organic amino compound + + + + + + + + + + + + + + + organic molecular entity + + + + + + + + role + + + + + + + + + + + + + + + nitrogen molecular entity + + + + + + + + + physiological role + + + + + + + + + + inorganic hydroxy compound + + + + + + + + + carbohydrate derivative + + + + + + + + + + + polysaccharide derivative + + + + + + + + + exopolysaccharide + + + + + + + + + carbohydrates and carbohydrate derivatives + + + + + + + + + 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 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 + CL:0000003 + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any fibroblast that is deriived from the neural crest. + cell + CL:0000005 + fibroblast neural crest derived + + + + + + + + + + neuronal receptor cell (sensu Animalia) + cell + CL:0000006 + neuronal receptor cell + + + + + + + + + A cell found in the embryo before the formation of all the gem layers is complete. + cell + CL:0000007 + early embryonic cell (metazoa) + + + + + + + + + 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 + CL:0000008 + migratory cranial 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. + cell + CL:0000011 + migratory trunk neural crest cell + + + + + + + + + Female germ cell is a germ cell that supports female gamete production. + MA:0000388 + VHOG:0001530 + ncithesaurus:Egg + cell + CL:0000021 + female germ cell + + + + + + + + + + A female germ cell that has entered meiosis. + BTO:0000964 + CALOHA:TS-0711 + FBbt:00004886 + FMA:18644 + WBbt:0006797 + cell + oogonium + CL:0000023 + oocyte + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A smooth muscle cell derived from the neural crest. + cell + CL:0000027 + smooth muscle cell neural crest derived + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuron neural crest derived + cell + CL:0000029 + neural crest derived neuron + + + + + + + + + + + + + + + FBbt:00005145 + cell + CL:0000030 + glioblast + + + + + + + + + + A cell that will develop into a neuron often after a migration phase. + CL:0000337 + BTO:0000930 + FMA:70563 + neuroblast + cell + CL:0000031 + neuroblast (sensu Vertebrata) + + + + + + + + + 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 + CL:0000034 + 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 + CL:0000037 + 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 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 + CL:0000038 + erythroid progenitor cell + + + + + + + + + + A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. + cell + CL:0000039 + + Originally this term had some plant germ line cell children. + germ line 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 + CL:0000048 + multi fate stem cell + + + + + + + + + + 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) + CL:0000049 + 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 + + + + + + + + + + + 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 + CL:0000050 + 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 + + + + + + + + + A stem cell from which all cells of the body can form. + FMA:84790 + totipotential stem cell + cell + CL:0000052 + totipotent stem cell + + + + + + + + + A precursor cell with a limited number of potential fates. + BTO:0000125 + FMA:84782 + blast cell + cell + CL:0000055 + define using PATO mulit-potent or oligopotent? + non-terminally differentiated cell + + + + + + + + + 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 + CL:0000056 + myoblast + + + + + + + + + + + + + + + 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 + CL:0000057 + These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. + 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 + CL:0000058 + chondroblast + + + + + + + + + A cell that has a filiform extrusion of the cell surface. + VHOG:0001532 + XAO:0000031 + cell + CL:0000064 + ciliated 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. + BTO:0000414 + CALOHA:TS-2026 + CARO:0000077 + FBbt:00000124 + FMA:66768 + WBbt:0003672 + epitheliocyte + cell + CL:0000066 + epithelial cell + + + + + + + + + + An epithelial cell that has a cilia. + FMA:70605 + cell + CL:0000067 + ciliated epithelial cell + + + + + + + + + + + + + + + + An endothelial cell that lines the vasculature. + cuboidal endothelial cell of vascular tree + cell + CL:0000071 + blood vessel endothelial 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. + cell + CL:0000075 + columnar/cuboidal epithelial cell + + + + + + + + + CALOHA:TS-1249 + cell + CL:0000076 + squamous epithelial cell + + + + + + + + + + + A flattened epithelial cell of mesenchymal origin that lines the serous cavity. + FMA:66773 + mesotheliocyte + cell + CL:0000077 + mesothelial cell + + + + + + + + + A cell found predominately in the blood. + FMA:62844 + cell + CL:0000081 + blood cell + + + + + + + + + + + + + + + cell + CL:0000095 + neuron associated 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. + neuroepithelial cell + BTO:0004301 + cell + CL:0000098 + The term "neuroepithelial cell" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710). + sensory epithelial cell + + + + + + + + + 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 + CL:0000099 + interneuron + + + + + + + + + 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 + CL:0000100 + motor neuron + + + + + + + + + Any neuron having a sensory function; an afferent neuron conveying sensory impulses. + BTO:0001037 + FBbt:00005124 + FMA:84649 + WBbt:0005759 + cell + CL:0000101 + sensory neuron + + + + + + + + + + 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 + CL:0000115 + 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 + + + + + + + + + + + + + + + cell + CL:0000117 + CNS neuron (sensu Vertebrata) + + + + + + + + + + + + + + + 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 + CL:0000125 + glial cell + + + + + + + + + Ectoderm destined to be nervous tissue. + neurectoderm cell + cell + CL:0000133 + neurectodermal cell + + + + + + + + + + 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 + CL:0000134 + 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 + + + + + + + + + + + + + + + + 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 + CL:0000136 + fat cell + + + + + + + + + + + + + + + + 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 + CL:0000138 + chondrocyte + + + + + + + + + A pigment cell is a cell that contains pigment granules. + VHOG:0001678 + chromatocyte + chromatophore + cell + CL:0000147 + pigment cell + + + + + + + + + pigment cell + cell + CL:0000149 + visual pigment cell + + + + + + + + + + + A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules. + CALOHA:TS-2085 + FMA:86494 + cell + CL:0000150 + glandular epithelial cell + + + + + + + + + A cell that specializes in controlled release of one or more substances. + BTO:0003659 + FMA:86916 + cell + CL:0000151 + secretory cell + + + + + + + + + + A cell that secretes glycosaminoglycans. + GAG secreting cell + hyaluronic acid secreting cell + cell + CL:0000153 + glycosaminoglycan secreting cell + + + + + + + + + cell + CL:0000159 + seromucus secreting cell + + + + + + + + + A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions. + FMA:83809 + endocrinocyte + cell + CL:0000163 + endocrine cell + + + + + + + + + + An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas. + BTO:0003865 + FMA:62930 + cell + CL:0000164 + enteroendocrine cell + + + + + + + + + cell + CL:0000167 + peptide hormone secreting cell + + + + + + + + + A cell that secretes glucagon. + FMA:84045 + glucagon-secreting cell + cell + CL:0000170 + glucagon secreting cell + + + + + + + + + cell + CL:0000172 + somatostatin secreting cell + + + + + + + + + cell + CL:0000174 + steroid hormone secreting cell + + + + + + + + + A cell whose primary function is to shorten. + cell + CL:0000183 + contractile cell + + + + + + + + + + + + + + + + + + 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 + CL:0000187 + muscle cell + + + + + + + + + A somatic cell located in skeletal muscle. + BTO:0004392 + CALOHA:TS-2158 + FMA:9727 + skeletal muscle cell + cell + CL:0000188 + cell of skeletal muscle + + + + + + + + + + + + + + + + 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 + CL:0000192 + smooth muscle cell + + + + + + + + + A cell that is capable of detection of a stimulus involved in sensory perception. + receptor cell + cell + CL:0000197 + sensory receptor 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. + cell + CL:0000206 + chemoreceptor cell + + + + + + + + + + + BTO:0004185 + FMA:67860 + Schultze's cell + odorant receptor cell + olfactory receptor neuron + olfactory sensory neuron + cell + CL:0000207 + olfactory 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 + CL:0000209 + taste receptor cell + + + + + + + + + A cell specialized to detect and transduce light. + BTO:0001060 + CALOHA:TS-0868 + FBbt:00004211 + FMA:86740 + cell + CL:0000210 + photoreceptor cell + + + + + + + + + A cell whose function is determined by the generation or the reception of an electric signal. + cell + CL:0000211 + electrically active 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. + boundary cell + cell + CL:0000213 + lining cell + + + + + + + + + + + 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 + CL:0000214 + synovial cell + + + + + + + + + A cell whose primary function is to prevent the transport of stuff across compartments. + cell + CL:0000215 + barrier cell + + + + + + + + + A cell that moves by its own activities. + cell + CL:0000219 + motile cell + + + + + + + + + A cell of the outer of the three germ layers of the embryo. + FMA:72549 + ectoderm cell + cell + CL:0000221 + ectodermal cell + + + + + + + + + A cell of the middle germ layer of the embryo. + FMA:72554 + mesoblast + mesoderm cell + cell + CL:0000222 + mesodermal cell + + + + + + + + + A cell of the inner of the three germ layers of the embryo. + FMA:72555 + endoderm cell + cell + CL:0000223 + endodermal cell + + + + + + + + + A cell with more than one nucleus. + AEO:0000203 + WBbt:0008074 + syncitium + syncytial cell + syncytium + cell + CL:0000228 + multinucleate cell + + + + + + + + + + + + + + + + + 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 + CL:0000232 + erythrocyte + + + + + + + + + cell + CL:0000255 + eukaryotic cell + + + + + + + + + cell + CL:0000287 + eye photoreceptor cell + + + + + + + + + A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism. + cell + CL:0000293 + structural cell + + + + + + + + + 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 + CL:0000313 + serous secreting cell + + + + + + + + + BTO:0003689 + mucous cell + cell + CL:0000319 + mucus secreting cell + + + + + + + + + A cell that is specialised to accumulate a particular substance(s). + cell + CL:0000325 + + stuff accumulating cell + + + + + + + + + + cell + CL:0000327 + extracellular matrix secreting cell + + + + + + + + + cell + CL:0000329 + oxygen accumulating 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. + FMA:86667 + cell + CL:0000333 + migratory neural crest cell + + + + + + + + + A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors. + cell + CL:0000335 + mesenchyme condensation cell + + + + + + + + + + + + + + + A cell of the sclera of the eye. + cell + CL:0000347 + scleral cell + + + + + + + + + + cell + CL:0000349 + extraembryonic 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 + CL:0000351 + trophoblast cell + + + + + + + + + A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. + cell + CL:0000352 + epiblast cell + + + + + + + + + An undifferentiated cell produced by early cleavages of the fertilized egg (zygote). + BTO:0001473 + FMA:72551 + blastomere + cell + CL:0000353 + blastoderm 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 + CL:0000355 + 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 + + + + + + + + + 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 + CL:0000362 + epidermal cell + + + + + + + + + + Diploid cell produced by the fusion of sperm cell nucleus and egg cell. + zygote + BTO:0000854 + EHDAA2:0004546 + FMA:72395 + cell + CL:0000365 + animal zygote + + + + + + + + + A cell whose function is determined by its response to an electric signal. + cell + CL:0000393 + electrically responsive cell + + + + + + + + + + + cell + CL:0000402 + CNS interneuron + + + + + + + + + A cell that initiates an electrical signal and passes that signal to another cell. + cell + CL:0000404 + electrically signaling cell + + + + + + + + + cell + CL:0000447 + carbohydrate secreting 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. + BTO:0002064 + FMA:83624 + cell + CL:0000499 + stromal cell + + + + + + + + + + A precursor cell destined to differentiate into cardiac muscle cell. + CL:0000714 + FMA:84797 + cardiac muscle progenitor cell + cardiomyocyte progenitor cell + cell + CL:0000513 + cardiac muscle myoblast + + + + + + + + + A precursor cell destined to differentiate into smooth muscle myocytes. + FMA:84798 + myoblast, smooth muscle + cell + satellite cell + CL:0000514 + smooth muscle myoblast + + + + + + + + + + + + + + + + A myoblast that differentiates into skeletal muscle fibers. + FMA:84799 + skeletal myoblast + cell + CL:0000515 + skeletal muscle myoblast + + + + + + + + + A neuron which conveys sensory information centrally from the periphery. + FMA:87653 + input neuron + cell + CL:0000526 + afferent neuron + + + + + + + + + A neuron which sends impulses peripherally to activate muscles or secretory cells. + output neuron + cell + CL:0000527 + efferent neuron + + + + + + + + + cell + CL:0000530 + primary neuron + + + + + + + + + + + + + + + + + + cell + CL:0000531 + primary sensory 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. + + BTO:0000938 + CALOHA:TS-0683 + FBbt:00005106 + FMA:54527 + VHOG:0001483 + WBbt:0003679 + nerve cell + cell + CL:0000540 + These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. + neuron + neuron + + + + + + + + + + + + + + + + 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 + CL:0000547 + proerythroblast + + + + + + + + + cell + CL:0000548 + + 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 + CL:0000549 + basophilic erythroblast + + + + + + + + + + + + + + + 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 + CL:0000550 + polychromatophilic erythroblast + + + + + + + + + + + + + + + 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 + CL:0000552 + orthochromatic erythroblast + + + + + + + + + + + + + + + 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 + CL:0000558 + reticulocyte + + + + + + + + + + + + + + + + A mesenchymal stem cell capable of developing into blood vessel endothelium. + angioblast + chondroplast + cell + CL:0000566 + These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. + angioblastic mesenchymal 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. + BTO:0001036 + CALOHA:TS-0866 + FMA:67748 + cell + CL:0000573 + retinal cone cell + + + + + + + + + The reproductive cell in multicellular organisms. + BTO:0000535 + VHOG:0001534 + WBbt:0006796 + cell + CL:0000586 + germ cell + + + + + + + + + A steroid hormone secreting cell that secretes androgen. + cell + CL:0000593 + androgen secreting 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. + BTO:0001024 + CALOHA:TS-0870 + FMA:67747 + cell + CL:0000604 + retinal rod cell + + + + + + + + + A cell whose primary function is to support other cell types. + BTO:0002315 + cell + CL:0000630 + supportive cell + + + + + + + + + An extracellular matrix secreting cell that secretes collagen. + cell + CL:0000667 + collagen secreting cell + + + + + + + + + + + + + + + + A non-terminally differentiated cell that is capable of developing into a muscle cell. + cell + CL:0000680 + muscle precursor cell + + + + + + + + + + A cell that stores and secretes pancreatic polypeptide hormone. + FMA:62938 + FMA:83409 + type F enteroendocrine cell + cell + CL:0000696 + PP cell + + + + + + + + + + + + + + + + + + + + + + + + + + + Epithelial cells derived from neural plate and neural crest. + neuroepithelial cell + BTO:0004301 + FMA:70557 + cell + CL:0000710 + The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098). + neurecto-epithelial cell + + + + + + + + + + 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 + CL:0000723 + somatic stem cell + + + + + + + + + + Muscle cell which has as its direct parts myofilaments organized into sarcomeres. + BTO:0002916 + CALOHA:TS-2157 + FMA:86936 + cell + CL:0000737 + striated muscle 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. + BTO:0001800 + FMA:67765 + RGC + gangliocyte + ganglion cell of retina + cell + CL:0000740 + retinal ganglion 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. + FMA:83808 + cardiocyte + BTO:0001539 + CALOHA:TS-0115 + FMA:14067 + cardiac muscle fiber + cardiac myocyte + cardiomyocyte + heart muscle cell + cell + CL:0000746 + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage. + BTO:0001441 + CALOHA:TS-0647 + cell + CL:0000763 + myeloid cell + + + + + + + + + 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 + CL:0000764 + Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. + erythroid lineage cell + + + + + + + + + + + + + + + + A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers. + BTO:0001571 + CALOHA:TS-0289 + FMA:83504 + normoblast + cell + CL:0000765 + erythroblast + + + + + + + + + + + + + + + + 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 + CL:0000837 + Markers differ between mouse and human. + hematopoietic multipotent progenitor cell + + + + + + + + + + A progenitor cell restricted to the myeloid lineage. + myeloid progenitor cell + BTO:0004730 + CALOHA:TS-2099 + FMA:70339 + cell + CL:0000839 + Note that this is a class of cell types, not an identified single cell type. + myeloid lineage restricted progenitor cell + + + + + + + + + + A cell of a hematopoietic lineage. + BTO:0000574 + CALOHA:TS-2017 + FMA:70366 + FMA:83598 + haematopoietic cell + haemopoietic cell + hemopoietic cell + cell + CL:0000988 + hematopoietic cell + + + + + + + + + A connective tissue cell found in bone. + adiehl + 2011-11-16T04:28:16Z + cell + CL:0001035 + bone cell + + + + + + + + + + + + + + + + A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. + tmeehan + 2010-01-06T03:43:20Z + cell + CL:0002031 + hematopoietic lineage restricted 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. + tmeehan + 2010-01-06T03:43:27Z + cell + CL:0002032 + 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 + + + + + + + + + + An enteroendocrine cell that produces glucagon. + tmeehan + 2010-09-10T10:48:54Z + FMA:62939 + cell + CL:0002067 + type A enteroendocrine cell + + + + + + + + + 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 + CL:0002068 + Purkinje 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. + tmeehan + 2010-06-29T11:41:37Z + pacemaker cell + BTO:0004190 + FMA:67101 + P cell + cardiac pacemaker cell + myocytus nodalis + cell + CL:0002072 + nodal 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. + tmeehan + 2010-06-29T02:39:32Z + FMA:67142 + cell + CL:0002073 + transitional myocyte + + + + + + + + + + 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 + CL:0002074 + myocardial endocrine cell + + + + + + + + + + + + + + + + An epithelial cell derived from endoderm. + tmeehan + 2010-06-29T03:38:14Z + FMA:69075 + cell + CL:0002076 + endo-epithelial cell + + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelial cell derived from ectoderm. + tmeehan + 2010-06-29T03:38:22Z + FMA:69074 + cell + CL:0002077 + ecto-epithelial cell + + + + + + + + + + + + + + + + + + + + + + + + + + + Epithelial cell derived from mesoderm or mesenchyme. + tmeehan + 2010-06-29T03:49:14Z + FMA:69076 + epithelial mesenchymal cell + cell + CL:0002078 + meso-epithelial cell + + + + + + + + + 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 + CL:0002086 + specialized cardiac myocyte + + + + + + + + + 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 + CL:0002092 + MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. + bone marrow cell + + + + + + + + + + A cell in the hilum of the ovary that produces androgens. + tmeehan + 2010-08-23T11:18:18Z + FMA:18710 + hilar cell of ovary + cell + CL:0002095 + hilus cell of ovary + + + + + + + + + A stomal cell of the ovary + tmeehan + 2010-08-23T12:10:31Z + FMA:72299 + ovarian stromal cell + cell + CL:0002132 + stromal cell of ovary + + + + + + + + + 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 + CL:0002139 + These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. + endothelial cell of vascular tree + + + + + + + + + Epithelial cells derived from general body ectoderm and ectoderm placodes. + tmeehan + 2010-08-26T08:31:08Z + FMA:70556 + cell + CL:0002159 + general ecto-epithelial cell + + + + + + + + + + A fibroblast in the bone marrow. + tmeehan + 2010-09-07T02:25:18Z + FMA:84377 + cell + CL:0002240 + marrow fibroblast + + + + + + + + + A cell containing at least one nucleus. + tmeehan + 2010-09-07T03:32:33Z + FMA:67513 + cell + CL:0002242 + nucleate cell + + + + + + + + + + A cell that is part of the nervous system. + tmeehan + 2010-09-15T01:34:57Z + CALOHA:TS-2040 + FMA:70333 + cell + CL:0002319 + neural cell + + + + + + + + + + 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 + CL:0002320 + connective tissue cell + + + + + + + + + A cell of the embryo. + tmeehan + 2010-09-15T03:39:21Z + CALOHA:TS-0263 + FMA:82840 + FMA:82841 + WBbt:0007028 + cell + CL:0002321 + embryonic cell (metazoa) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A fat cell derived from a neural crest cell. + tmeehan + 2010-09-20T02:25:25Z + cell + CL:0002333 + neural crest derived fat 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). + tmeehan + 2010-09-24T09:44:42Z + BTO:0001268 + FMA:72300 + WBbt:0008378 + cell + CL:0002371 + + somatic cell + + + + + + + + + + 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 + CL:0002372 + myotube + + + + + + + + + + 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 + CL:0002494 + 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 + + + + + + + + + + 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 + CL:0002503 + adventitial cell + + + + + + + + + + An endothelial progenitor cell that participates in angiogenesis during development. + tmeehan + 2011-02-28T04:20:39Z + cell + CL:0002546 + See CL:0002619. + embryonic blood vessel endothelial progenitor cell + + + + + + + + + + + + + + + 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 + CL:0002672 + retinal progenitor cell + + + + + + + + + + + + + + + + A neuroblast derived from a neural crest cell. + tmeehan + 2011-08-22T09:24:15Z + cell + CL:0002676 + neural crest derived neuroblast + + + + + + + + + A CNS interneuron located in the spinal cord. + cell + CL:0005000 + Is_a interneuron, part_of UBERON:0002240. + spinal cord interneuron + + + + + + + + + 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 + CL:0007001 + 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 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 + CL:0007004 + premigratory neural crest cell + + + + + + + + + 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 + CL:0007009 + prechondroblast + + + + + + + + + Any muscle cell in which the fibers are not organised into sarcomeres. + CL:0008000 + non-striated muscle cell + + + + + + + + + Any hematopoietic cell that is a precursor of some other hematopoietic cell type. + CL:0008001 + hematopoietic precursor cell + + + + + + + + + + + + + + + + A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. + CL:0008002 + skeletal muscle fiber + + + + + + + + + A muscle cell that is part of some visceral muscle + CL:0008007 + visceral muscle cell + + + + + + + + + + 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 + CL:0008019 + mesenchymal cell + + + + + + + + + camera type eye photoreceptor cell + CL:0010009 + camera-type eye photoreceptor cell + + + + + + + + + A zygote in a plant or an animal. + CL:0010017 + zygote + + + + + + + + + + cell + CL:0010021 + cardiac myoblast + + + + + + + + + + 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 + CL:0011012 + neural crest 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. + http://orcid.org/0000-0001-5208-3432 + CL:0011026 + progenitor cell + + + + + + + + + A cell that, by division or terminal differentiation, can give rise to other cell types. + CL:0011115 + 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 + + + + + + + + + trophectoderm cell + cell + CL:1000274 + trophectodermal cell + + + + + + + + + A fibroblast that is part of the areolar connective tissue. + FMA:261279 + cell + CL:1000303 + fibroblast of areolar connective tissue + + + + + + + + + + A fibroblast that is part of the tunica adventitia of artery. + FMA:261285 + cell + CL:1000306 + fibroblast of tunica adventitia of artery + + + + + + + + + + A fat cell that is part of the epicardial fat. + FMA:261293 + adipocyte of epicardial fat + epicardial fat cell + cell + CL:1000309 + epicardial adipocyte + + + + + + + + + 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 + CL:1000409 + myocyte of sinoatrial node + + + + + + + + + + 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 + CL:1000410 + myocyte of atrioventricular node + + + + + + + + + Any native cell that is part of a cardiac septum. + TermGenie + 2014-06-24T23:17:07Z + cell + CL:2000022 + cardiac septum cell + + + + + + + + + Any neuron that is part of a central nervous system. + TermGenie + 2014-06-25T01:17:43Z + cell + CL:2000029 + central nervous system neuron + + + + + + + + + biome + + + + + + + + + terrestrial biome + + + + + + + + + environmental system + + + + + + + + + ecosystem + + + + + + + + + reproduction + + + + + + + + + response to acid chemical + + + + + + + + + skeletal system development + + + + + + + + + ossification + + + + + + + + + + + + + + + angiogenesis + + + + + + + + + + + + + + + blood vessel development + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + branching involved in blood vessel 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behavior + + + + + + + + + chewing + + + + + + + + + feeding behavior + + + + + + + + + liquid consumption + + + + + + + + + food consumption + + + + + + + + + sensation behavior + + + + + + + + + behavior process + + + + + + + + + vestibular behavior + + + + + + + + + somatic sensation related behavior + + + + + + + + + kinesthetic behavior + + + + + + + + + motor coordination + + + + + + + + + limb coordination + + + + + + + + + gross motor coordination + + + + + + + + + posture + + + + + + + + + body posture + + + + + + + + + limb posture + + + + + + + + + gait + + + + + + + + + involuntary movement behavior + + + + + + + + + reflexive behavior + + + + + + + + + cranial nerve related reflex + + + + + + + + + pupillary light reflex + + + + + + + + + tail movement + + + + + + + + + personal grooming + + + + + + + + + swallowing + + + + + + + + + cognitive behavior + + + + + + + + + jaw movement + + + + + + + + + perception behavior by means + + + + + + + + + regulation of behavior + + + + + + + + + consumption behavior + + + + + + + + + regulation of consumption behavior + + + + + + + + + regulation of feeding behavior + + + + + + + + + root + + + + + + + + + Viruses + + + + + + + + + + + + + + + Teleostomi + + + + + + + + + + + + + + + Euteleostomi + + + + + + + + + cellular organisms + + + + + + + + + + + + + + + Dipnotetrapodomorpha + + + + + + + + + + Bacteria + + + + + + + + + Archaea + + + + + + + + + + + + + + + + Eukaryota + + + + + + + + + + + + + + + Tetrapoda + + + + + + + + + + + + + + + Amniota + + + + + + + + + + + + + + + Theria <mammals> + + + + + + + + + + + + + + + Opisthokonta + + + + + + + + + + + + + + + Metazoa + + + + + + + + + + + + + + + Bilateria + + + + + + + + + + + + + + + Deuterostomia + + + + + + + + + + + + + + + Mammalia + + + + + + + + + + + + + + + Eumetazoa + + + + + + + + + + + + + + + Chordata + + + + + + + + + + + + + + + Vertebrata <vertebrates> + + + + + + + + + + + + + + + Gnathostomata <vertebrates> + + + + + + + + + + + + + + + Sarcopterygii + + + + + + + + + + + + + + + Craniata <chordates> + + + + + + + + + + + + + + + + + + + organism + + + + + + + + + quality + + + + + + + + + + color + + + + + + + + + composition + + + + + + + + + morphology + + + + + + + + + shape + + + + + + + + + qualitative + + + + + + + + + deviation (from_normal) + + + + + + + + + size + + + + + + + + + mass + + + + + + + + + closure + + + + + + + + + structure + + + + + + + + + temperature + + + + + + + + + texture + + + + + + + + + branched + + + + + + + + + flat + + + + + + + + + closed + + + + + + + + + opacity + + + + + + + + + opaque + + + + + + + + + transparent + + + + + + + + + viscosity + + + + + + + + + viscous + + + + + + + + + physical quality + + + + + + + + + elasticity + + + + + + + + + elastic + + + + + + + + + + physical object quality + + + + + + + + + electromagnetic (EM) radiation quality + + + + + + + + + optical quality + + + + + + + + + + decreased temperature + + + + + + + + + quality of a gas + + + + + + + + + quality of a liquid + + + + + + + + + + increased mass + + + + + + + + + contractility + + + + + + + + + curvature + + + + + + + + + contractile + + + + + + + + + radiation quality + + + + + + + + + invaginated + + + + + + + + + concave + + + + + + + + + cylindrical + + + + + + + + + saccular + + + + + + + + + cellularity + + + + + + + + + multicellular + + + + + + + + + organismal quality + + + + + + + + + concavity + + + + + + + + + convex 3-D shape + + + + + + + + + branchiness + + + + + + + + + structure, cavities + + + + + + + + + dendritic + + + + + + + + + hollow + + + + + + + + + laminar + + + + + + + + + quality of a substance + + + + + + + + + flattened + + + + + + + + + grooved + + + + + + + + + 3-D shape + + + + + + + + + + tubular + + + + + + + + + increased quality + + + + + + + + + decreased quality + + + + + + + + + + decreased object quality + + + + + + + + + + increased object quality + + + + + + + + + acinar + + + + + + + + + collagenous + + + + + + + + + distensible + + + + + + + + + distensibility + + + + + + + + + protein + + + + + + + + + fibroblast growth factor 8 + + + + + + + + + lactotransferrin + + + + + + + + + sonic hedgehog protein + + + + + + + + + amino acid chain + + + + + + + + + system + + + + + + + + + + An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. + uberon + UBERON:0000000 + + processual entity + + + + + An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. + span:ProcessualEntity + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + FBbt:00005157 + chemosensory sensory organ + uberon + UBERON:0000005 + + + chemosensory organ + + + + + chemosensory sensory organ + FBbt:00005157 + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions. + + + + BTO:0002330 + FMA:62517 + NCIT:C32918 + UMLS:C1179187 + lamina propria mucosa + lamina propria mucosae + uberon + tunica propria + UBERON:0000030 + + lamina propria + GI:Organization.svg + + + + + A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions. + + + + + + UMLS:C1179187 + ncithesaurus:Lamina_Propria + + + + + tunica propria + BTO:0002330 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A lamina propria that is part of a respiratory airway. + + EMAPA:35877 + FMA:265157 + MA:0001858 + NCIT:C49305 + UMLS:C1710457 + lamina propria mucosa of trachea + lamina propria mucosa of windpipe + lamina propria mucosae of trachea + lamina propria mucosae of windpipe + lamina propria of windpipe + trachea lamina propria + trachea lamina propria mucosa + trachea lamina propria mucosae + tracheal lamina propria + windpipe lamina propria + windpipe lamina propria mucosa + windpipe lamina propria mucosae + uberon + UBERON:0000031 + lamina propria of trachea + + + + + + + + + + + true + + + + + + A lamina propria that is part of a respiratory airway. + OBOL:automatic + + + + + UMLS:C1710457 + ncithesaurus:Trachea_Lamina_Propria + + + + + lamina propria mucosa of trachea + OBOL:automatic + + + + + lamina propria mucosa of windpipe + OBOL:automatic + + + + + lamina propria mucosae of trachea + OBOL:automatic + + + + + lamina propria mucosae of windpipe + OBOL:automatic + + + + + lamina propria of windpipe + OBOL:automatic + + + + + trachea lamina propria mucosa + OBOL:automatic + + + + + trachea lamina propria mucosae + OBOL:automatic + + + + + windpipe lamina propria + OBOL:automatic + + + + + windpipe lamina propria mucosa + OBOL:automatic + + + + + windpipe lamina propria mucosae + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + The head is the anterior-most division of the body [GO]. + Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] + Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] + Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] + + + + AAO:0010335 + AEO:0000106 + BILA:0000115 + BIRNLEX:1230 + BTO:0000282 + CALOHA:TS-0436 + EFO:0000964 + EHDAA2:0003106 + EMAPA:31858 + FBbt:00000004 + FMA:7154 + GAID:61 + HAO:0000397 + MA:0000023 + MAT:0000294 + MESH:D006257 + MIAA:0000294 + NCIT:C12419 + OpenCyc:Mx4rEOLm4rgPEdmAAAACs6hRjg + OpenCyc:Mx4rvVi6YJwpEbGdrcN5Y29ycA + SPD:0000016 + TAO:0001114 + TGMA:0000002 + UMLS:C0018670 + VHOG:0001644 + WBbt:0005739 + XAO:0003024 + ZFA:0001114 + galen:Head + head (volume) + adult head + uberon + cephalic area + UBERON:0000033 + + + + + head + + + + + The head is the anterior-most division of the body [GO]. + + GO:0060322 + + + + + Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] + 2012-06-20 + AAO:0010335 + AAO + AAO:BJB + + + + + Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] + 2012-08-14 + TAO:0001114 + TAO + ZFIN:curator + + + + + Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] + 2012-09-17 + VHOG:0001644 + VHOG + + ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82 + + + + + UMLS:C0018670 + BIRNLEX:1230 + + + + + UMLS:C0018670 + ncithesaurus:Head + + + + + head (volume) + FMA:7154 + + + + + cephalic area + SPD:0000016 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. + A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] + a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] + in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. + + + + + FMA:9581 + GAID:19 + MESH:D012704 + NCIT:C13169 + TAO:0005425 + UMLS:C0036760 + ZFA:0005425 + tunica serosa + wall of serous sac + uberon + serosa + UBERON:0000042 + + + serous membrane + http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png + http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png + + + + + + + + + + + Wikipedia + + + + + 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 + + + + + + + + + + + AEO + + + + + + + + + + + AEO + + + + + Dense regular connective tissue that connects muscle to bone[VSAO]. + + + GO_REF:0000034 + VSAO:0000073 + + + + + Dense regular connective tissue that connects muscle to bone.[VSAO] + 2012-08-14 + VSAO:0000073 + VSAO + PSPUB:0000170 + + + + + Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG] + 2012-09-17 + VHOG:0001286 + VHOG + + DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002) + + + + + in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis + FMA + + + + + UMLS:C0039508 + ncithesaurus:Tendon + + + + + sinew + + + + + + tendo + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A biological tissue mass, most commonly a mass of nerve cell bodies. + TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system. + A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures + Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO] + Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO] + Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302]. + Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG] + ganglionic + + + + AAO:0010426 + AEO:0000135 + BAMS:G + BTO:0000497 + CALOHA:TS-0397 + EFO:0000899 + EHDAA2:0003135 + EHDAA:2897 + EHDAA:4662 + EHDAA:5621 + EHDAA:918 + EMAPA:32846 + EV:0100372 + FBbt:00005137 + FMA:5884 + MA:0002406 + MAT:0000207 + MAT:0000343 + MESH:D005724 + MIAA:0000207 + MIAA:0000343 + NCIT:C12719 + NLXANAT:100302 + TAO:0000190 + TGMA:0001016 + UMLS:C0017067 + VHOG:0000156 + WBbt:0005189 + XAO:0000209 + ZFA:0000190 + uberon + ganglia + neural ganglion + UBERON:0000045 + + + + + ganglion + + + + + + + + + + + + + + + + + EHDAA2 + + + + + + + + + + + Bgee:AN + + + + + A biological tissue mass, most commonly a mass of nerve cell bodies. + + + + + + + A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures + + + + + + Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO] + 2012-06-20 + AAO:0010426 + AAO + AAO:EJS + + + + + Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO] + 2012-08-14 + TAO:0000190 + TAO + ZFIN:curator + + + + + Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302]. + NLXANAT:100302 + + + + + Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG] + 2012-09-17 + VHOG:0000156 + VHOG + + DOI:10.1016/j.ydbio.2005.02.021 Mazet F, Hutt JA, Milloz J, Millard J, Graham A, Shimeld SM, Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Developmental Biology (2005) + + + + + UMLS:C0017067 + ncithesaurus:Ganglion + + + + + neural ganglion + BTO:0000497 + + + + + + + + + An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. + + TGMA:0000729 + uberon + UBERON:0000047 + + + simple eye + + + + + An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. + + + + + + + + + + + + + + + + A tubular structure that contains, conveys body fluid, such as blood or lymph. + uberon + UBERON:0000055 + + + vessel + + + + + A tubular structure that contains, conveys body fluid, such as blood or lymph. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. + Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO] + The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] + The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] + ureteral + ureteric + in humans, consists of adventitial, muscular and mucoa layers + + + + AAO:0010254 + BTO:0001409 + CALOHA:TS-1084 + EFO:0000930 + EHDAA2:0002139 + EHDAA:9341 + EMAPA:17950 + EV:0100097 + FMA:9704 + GAID:438 + MA:0000378 + MAT:0000120 + MESH:D014513 + MIAA:0000120 + NCIT:C12416 + OpenCyc:Mx4rvhmm6JwpEbGdrcN5Y29ycA + UMLS:C0041951 + VHOG:0000605 + XAO:0000144 + galen:Ureter + uberon + metanephric duct + UBERON:0000056 + + + + + + ureter + Urinary:system.svg + + + + + + + + + + + MA:0000378 + + + + + + + + + + + FMA + + + + + + + + + + + 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]. + + + + + + + Wikipedia + + + + + Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. + GO:0048513 + + + + + UMLS:C0178784 + ncithesaurus:Organ + + + + + element + + + + + + + + + + A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. + FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction + Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. + Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. + FMA:86140 + uberon + organ region with fixed fiat boundary + organ segment + segment of organ + UBERON:0000063 + + organ subunit + + + + + A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. + + + + + + Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. + FMA:86140 + 3 + + + + + Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. + FMA:86140 + 1 + + + + + organ region with fixed fiat boundary + FMA:86140 + + + + + organ segment + FMA:86140 + + + + + segment of organ + FMA:86140 + + + + + + + + + + + + + + + A multicellular structure that is a part of an organ. + currently defined in a very broad sense, may be replaced by more specific classes in the future + + + AAO:0011124 + BIRNLEX:16 + EFO:0000635 + FMA:82472 + cardinal organ part + uberon + regional part of organ + UBERON:0000064 + + + + organ part + + + + + A multicellular structure that is a part of an organ. + + + + + + cardinal organ part + FMA:82472 + + + + + regional part of organ + BIRNLEX:16 + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts. + + EHDAA2:0001606 + EHDAA:1568 + EHDAA:2219 + EMAPA:16737 + FMA:265130 + OpenCyc:Mx4rvvM--pwpEbGdrcN5Y29ycA + VHOG:0000393 + uberon + UBERON:0000065 + respiratory tract + + + + + + + + + + + NCBIBook:NBK10107 + + + + + Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts. + + + + + + + + + + + + + + + + + + + + + + + + + + + + The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. + adult stage + BTO:0001043 + BilaDO:0000004 + EFO:0001272 + FBdv:00005369 + WBls:0000041 + XtroDO:0000084 + fully formed animal stage + juvenile-adult stage + uberon + UBERON:0000066 + + fully formed stage + https://github.com/obophenotype/uberon/issues/566 + + + + + The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A life cycle stage that starts with fertilization and ends with the fully formed embryo. + + BilaDO:0000002 + EV:0300001 + FBdv:00005289 + FMA:72652 + HsapDv:0000002 + MmusDv:0000002 + OGES:000000 + OGES:000022 + WBls:0000003 + WBls:0000092 + WBls:0000102 + XAO:1000012 + embryonic stage + uberon + embryogenesis + UBERON:0000068 + embryo stage + + + + + A life cycle stage that starts with fertilization and ends with the fully formed embryo. + + + + + + + + + + + + + + + + + + + + + + End of the life of an organism. + ncit:Death is an outcome + XAO:0000437 + XtroDO:0000085 + uberon + death + UBERON:0000071 + death stage + + + + + End of the life of an organism. + XAO:0000437 + + + + + ncit:Death is an outcome + ncit + + + + + + + + + + + + + + + + + + + + + + + + + + + An section of a respiratory tract. + MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole + EMAPA:16737 + FMA:45660 + MA:0000434 + uberon + respiratory tract + subdivision of respiratory tract + UBERON:0000072 + + proximo-distal subdivision of respiratory tract + + + + + An section of a respiratory tract. + + + + + + MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole + MA + + + + + respiratory tract + MA:0000434 + + + + + + + + + + + + + + + + + + + + + + + + + + + Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. + Melissa Haendel + 2009-06-18T09:00:04Z + + + BIRNLEX:1157 + NCIT:C13040 + UMLS:C1518256 + part of nervous system + uberon + UBERON:0000073 + + + regional part of nervous system + + + + + Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. + BIRNLEX:1157 + + + + + UMLS:C1518256 + ncithesaurus:Nervous_System_Part + + + + + part of nervous system + BIRNLEX:1157 + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. + UBERON:0010322 + + + FMA:85544 + NCIT:C34076 + UMLS:C1519343 + galen:ComplexSkeletalStructure + skeletal system subdivision + uberon + skeletal system part + UBERON:0000075 + + subdivision of skeletal system + + + + + + cjm + + + + + Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. + + UBERONREF:0000003 + + + + + UMLS:C1519343 + ncithesaurus:Skeletal_System_Part + + + + + skeletal system subdivision + FMA:85544 + + + + + + + + + + + + + + + + + + + + + + + The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. + merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) + (or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis + + + EHDAA2:0001968 + EHDAA:1494 + EHDAA:350 + EHDAA:4784 + EHDAA:4790 + EHDAA:4796 + EHDAA:7860 + EMAPA:16096 + FMA:87656 + NCIT:C34309 + UMLS:C1515087 + surface (external) ectoderm + surface ectoderm + uberon + UBERON:0000076 + + external ectoderm + http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. + MGI:anna + MP:0012532 + + + + + UMLS:C1515087 + ncithesaurus:Surface_Ectoderm + + + + + surface ectoderm + MP:0012532 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical structure that develops from the endoderm and the mesoderm. + Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple + uberon + UBERON:0000077 + + mixed endoderm/mesoderm-derived structure + + + + + An anatomical structure that develops from the endoderm and the mesoderm. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical structure that develops from the ectoderm, mesoderm and endoderm. + Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple + uberon + UBERON:0000078 + + mixed ectoderm/mesoderm/endoderm-derived structure + + + + + An anatomical structure that develops from the ectoderm, mesoderm and endoderm. + + + + + + + + + + + + + + + + + The 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 + + + + + + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + + + + + + + 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 connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin. + it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces + + EMAPA:35521 + FMA:27533 + MA:0001782 + connective tissue of lung + pulmonary interstitium + uberon + lung interstitial tissue + lung interstitium + pulmonary connective tissue + pulmonary interstitial tissue + UBERON:0000114 + + lung connective tissue + + + + + The connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin. + + ISBN:0-683-40008-8 + MGI:anna + MP:0002276 + + + + + connective tissue of lung + OBOL:automatic + + + + + pulmonary interstitium + FMA:27533 + + + + + lung interstitial tissue + MA:0001782 + + + + + pulmonary connective tissue + EMAPA:35521 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The epithelial layer of the lung. + A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469] + BTO:0001653 + EMAPA:32860 + MA:0001783 + epithelial tissue of lung + epithelium of lung + lung epithelial tissue + uberon + pulmonary epithelium + UBERON:0000115 + + lung epithelium + + + + + The epithelial layer of the lung. + MP:0006382 + + + + + epithelial tissue of lung + OBOL:automatic + + + + + epithelium of lung + OBOL:automatic + + + + + lung epithelial tissue + OBOL:automatic + + + + + pulmonary epithelium + BTO:0001653 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. + in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class) + EMAPA:37946 + FMA:12224 + segment of tracheobronchial tree + respiratory conducting tube + segment of tracheobronchial tree + tracheobronchial tree segment + uberon + airway + UBERON:0000117 + respiratory tube + + + + + A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. + + GO:0030323 + + + + + in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class) + GO + + + + + EMAPA:37946 + MA:th + + + + + segment of tracheobronchial tree + FMA:12224 + + + + + respiratory conducting tube + MP:0004391 + + + + + segment of tracheobronchial tree + FMA:12224 + + + + + tracheobronchial tree segment + FMA:12224 + + + + + + + + + + + + + + + + + + + + + + + + + + + + Structure derived from foregut that becomes a lung[GO]. + clarify successors - include bronchi? + + + + + BTO:0001643 + EHDAA2:0004089 + NCIT:C34260 + NCIT:C34282 + UMLS:C1514420 + UMLS:C1514897 + uberon + gemma pulmonalis + gemma respiratoria + lung bud + primary lung bud + respiratory diverticulum + UBERON:0000118 + + lung bud + http://upload.wikimedia.org/wikipedia/commons/7/71/Gray948.png + + + + + + GO:0060441 + + + + + + + + + + + EHDAA2 + + + + + Structure derived from foregut that becomes a lung[GO]. + + GO:0060431 + + + + + UMLS:C1514420 + ncithesaurus:Primary_Bronchial_Bud + + + + + UMLS:C1514897 + ncithesaurus:Respiratory_Diverticulum + + + + + gemma pulmonalis + + + + + + + gemma respiratoria + + + + + + + lung bud + + + + + + primary lung bud + GO:0060572 + + + + + respiratory diverticulum + + + + + + + + + + + + + + + + + + + + + + + A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. + UBERON:0005163 + CARO:0001001 + FBbt:00005099 + NLX:147821 + funiculus + nerve fiber bundle + neural fiber bundle + uberon + UBERON:0000122 + neuron projection bundle + + + + + A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. + CARO:0001001 + FBC:DOS + FBbt:00005099 + + + + + nerve fiber bundle + FBbt:00005099 + + + + + + + + + + + + + + + + + + + + + + + + + + + A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO). + Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021]. + Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate. + nucleus + + AEO:0000136 + FMA:83686 + NCIT:C13197 + NLX:28443 + nervous system nucleus + neuraxis nucleus + neuronal nucleus + nucleus of CNS + uberon + nucleus of neuraxis + UBERON:0000125 + + neural nucleus + + + + + + + + + + + CUMBO + + + + + + + + + + + we limit this structure by definition to chordate and vertebrate nervous systems + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + EHDAA2 + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + CL:tm + + + + + + + + + + + + + + + + + + + + + + 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. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath. + TODO - add layer relations. 'tendon sheath' GAT in FMA. + + + + BTO:0000051 + FMA:45087 + FMA:76715 + NCIT:C96299 + UMLS:C0224856 + synovial tendon sheath + uberon + vagina tendinis + UBERON:0000304 + tendon sheath + + + + + A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath. + + + + + + UMLS:C0224856 + ncithesaurus:Tendon_Sheath + + + + + synovial tendon sheath + FMA:45087 + + + + + vagina tendinis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. + TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula + UBERON:0007011 + + BILA:0000059 + BTO:0000128 + GAID:1294 + MESH:A16.254.270.274 + OGEM:000006 + OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg + blastula embryo + uberon + blastosphere + UBERON:0000307 + + blastula + http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png + + + + + Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. + + + + + + blastula embryo + BILA:0000059 + + + + + blastosphere + + + + + + + + + + The external portion of an animal body derived from ectoderm and mesoderm layers that encloses the body cavity. + defined generically to encompass both vertebrates and invertebrates + the BTO class refers to earthworms. + + BTO:0000139 + EMAPA:32761 + FMA:10427 + galen:BodyWall + wall fo trunk + trunk wall + wall of trunk + uberon + UBERON:0000309 + + body wall + + + + + The external portion of an animal body derived from ectoderm and mesoderm layers that encloses the body cavity. + MP:0003385 + + + + + the BTO class refers to earthworms. + BTO + + + + + wall fo trunk + FMA:10427 + + + + + trunk wall + FMA:10427 + + + + + wall of trunk + FMA:10427 + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + 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 red vascular substance consisting of connective tissue and blood vessels, containing primitive blood cells, macrophages, megakaryocytes, and fat cells. Red marrow is found in the cavities of many bones. It manufactures and releases leukocytes and erythrocytes into the bloodstream. + + + BTO:0001160 + FMA:74595 + medulla ossium rubra + parenchymal red marrow + red marrow + uberon + parenchyma of none marrow marrow + UBERON:0000361 + red bone marrow + + + + + The red vascular substance consisting of connective tissue and blood vessels, containing primitive blood cells, macrophages, megakaryocytes, and fat cells. Red marrow is found in the cavities of many bones. It manufactures and releases leukocytes and erythrocytes into the bloodstream. + + + + + + medulla ossium rubra + BTO:0001160 + + + + + + parenchymal red marrow + + + + + + red marrow + BTO:0001160 + + + + + parenchyma of none marrow marrow + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + A mucosa that is part of a respiratory airway. + + BTO:0001390 + FMA:7471 + mucosa of organ of trachea + mucosa of organ of windpipe + mucosa of trachea + mucosa of windpipe + mucous membrane of trachea + mucous membrane of windpipe + organ mucosa of trachea + organ mucosa of windpipe + trachea mucosa + trachea mucosa of organ + trachea mucous membrane + trachea organ mucosa + tracheal mucous membrane + tunica mucosa (tracheae) + tunica mucosa tracheae + windpipe mucosa + windpipe mucosa of organ + windpipe mucous membrane + windpipe organ mucosa + uberon + UBERON:0000379 + tracheal mucosa + + + + + A mucosa that is part of a respiratory airway. + OBOL:automatic + + + + + mucosa of organ of trachea + OBOL:automatic + + + + + mucosa of organ of windpipe + OBOL:automatic + + + + + mucosa of trachea + OBOL:automatic + + + + + mucosa of windpipe + OBOL:automatic + + + + + mucous membrane of trachea + FMA:7471 + + + + + mucous membrane of trachea + OBOL:automatic + + + + + mucous membrane of windpipe + OBOL:automatic + + + + + organ mucosa of trachea + OBOL:automatic + + + + + organ mucosa of windpipe + OBOL:automatic + + + + + trachea mucosa + OBOL:automatic + + + + + trachea mucosa of organ + OBOL:automatic + + + + + trachea mucous membrane + OBOL:automatic + + + + + trachea organ mucosa + OBOL:automatic + + + + + tracheal mucous membrane + FMA:7471 + + + + + tunica mucosa (tracheae) + FMA:7471 + + + + + tunica mucosa tracheae + FMA:7471 + FMA:TA + + + + + + windpipe mucosa + OBOL:automatic + + + + + windpipe mucosa of organ + OBOL:automatic + + + + + windpipe mucous membrane + OBOL:automatic + + + + + windpipe organ mucosa + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. + consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 + + Anatomical system that consists of the muscles of the body.[VSAO] + we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA + AAO:0000307 + BILA:0000088 + BTO:0001369 + BTO:0001485 + EFO:0000801 + EMAPA:35578 + FBbt:00005069 + FMA:72954 + MA:0002888 + MAT:0000025 + MIAA:0000025 + VSAO:0000033 + XAO:0004042 + muscle system + muscle system of body + muscular system + musculature system + set of all muscles + set of muscles of body + vertebrate muscular system + uberon + muskelsystem + UBERON:0000383 + + + musculature of body + + + + + The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. + VSAO:0000033 + + + + + Anatomical system that consists of the muscles of the body.[VSAO] + 2012-08-14 + VSAO:0000033 + VSAO + VSAO:curator + + + + + we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA + MA + + + + + muscular system + FMA:72954 + + + + + musculature system + BILA:0000088 + + + + + set of all muscles + FMA:72954 + + + + + set of muscles of body + FMA:72954 + + + + + vertebrate muscular system + BTO:0001369 + + + + + muskelsystem + BTO:0001485 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tissue that surrounds the lens nucleus. + + BTO:0001632 + CALOHA:TS-0542 + FMA:58970 + MESH:A09.371.509.225 + cortex of lens + uberon + UBERON:0000389 + lens cortex + + + + + Tissue that surrounds the lens nucleus. + + + + + + cortex of lens + FMA:58970 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The core of the crystalline lens, surrounded by the cortex. + + BTO:0001633 + FMA:58971 + MESH:A09.371.509.670 + nucleus of lens + uberon + UBERON:0000390 + lens nucleus + + + + + The core of the crystalline lens, surrounded by the cortex. + BTO:0001633 + + + + + nucleus of lens + FMA:58971 + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 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 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 + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + 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 + + + + Editor note: surface epithelium may contain non-epithelial cells, such as melanocytes, lymphocytes and dendritic cells, within the sheet of epithelial cells. Do we consider these part of the epithelium, or located-in it? + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + Wikipedia + + + + + + + + + + + absent in lampreys and hagfishes + ISBN:0073040584 + + + + + + + + + + + ISBN:0486692132 + + + + + 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 + + + + + + Wikipedia + + + + + + Wikipedia + + + + + + ZFA + + + + + + Wikipedia + + + + + 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 + + + + + + + + + + + MA-modified + + + + + 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 + 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 + + + + + + cardium + EMAPA:16105 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + + + + + + + + + + + + + + + + + + + + + + + + + + + The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted]. + + + + + BAMS:cern + FMA:5859 + NCIT:C32299 + NLXANAT:20090207 + UMLS:C0228815 + cervical nerve + cervical nerve tree + cervical spinal nerve + nervus cervicalis + uberon + UBERON:0000962 + + Innervates: sternohyoid muscle, sternothyroid muscle, omohyoid muscle[WP] + nerve of cervical vertebra + http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray795.png + + + + + The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted]. + + + + + + UMLS:C0228815 + ncithesaurus:Cervical_Nerve + + + + + cervical nerve + FMA:5859 + + + + + nervus cervicalis + FMA:5859 + FMA:TA + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure. + corneal + Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water + + + + AAO:0010344 + BTO:0000286 + CALOHA:TS-0171 + EFO:0000377 + EHDAA2:0000316 + EHDAA:10199 + EMAPA:17161 + EV:0100341 + FMA:58238 + GAID:892 + MA:0000266 + MESH:D003315 + NCIT:C12342 + OpenCyc:Mx4rvViBa5wpEbGdrcN5Y29ycA + TAO:0000640 + UMLS:C0010031 + VHOG:0000164 + XAO:0000180 + ZFA:0000640 + cornea of camera-type eye + uberon + corneas + tunica cornea + UBERON:0000964 + + + + + cornea + http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg + + + + + + + + + + + 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 + + + + + + + + + + + FMA + + + + + + + + + + + FMA + + + + + + + + + + + FMA + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + Wikipedia + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + AEO + + + + + 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 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 + + + + + + FMA + MA + + + + + 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 + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + 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 + 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 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 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + EHDAA2-abduced + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx). + Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO] + we deliberately merge the MA classes as we believe them equivalent + UBERON:0006070 + caudal vertebra + + + + EMAPA:18374 + FMA:12527 + MA:0000310 + MA:0001420 + NCIT:C32334 + OpenCyc:Mx4rv9IEzZwpEbGdrcN5Y29ycA + TAO:0000326 + UMLS:C0223616 + XAO:0003079 + ZFA:0000326 + galen:CoccygealVertebra + caudal vertebrae + caudal vertebral bone + caudal vertebral bone element + coccygeal segment + coccygeal vertebra + fused tail vertebra + uberon + coccygea + tail vertebra + UBERON:0001095 + + + + Taxon notes In zebrafish, Vertebra bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae + caudal vertebra + + + + + Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx). + + + + + + Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO] + 2012-08-14 + TAO:0000326 + TAO + ZFIN:curator + + + + + we deliberately merge the MA classes as we believe them equivalent + MA + + + + + caudal vertebra + FMA:12527 + + + + + + UMLS:C0223616 + ncithesaurus:Coccygeal_Vertebra + + + + + caudal vertebrae + + + + + + coccygeal vertebra + FMA:12527 + + + + + fused tail vertebra + + + + + + coccygea + MA:0001420 + + + + + tail vertebra + MA:0000310 + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical wall that is part of a esophagus [Automatically generated definition]. + EMAPA:35326 + FMA:12611 + MA:0002691 + anatomical wall of esophagus + anatomical wall of gullet + anatomical wall of oesophagus + esophageal wall + esophagus anatomical wall + esophagus wall + gullet anatomical wall + gullet wall + oesophagus anatomical wall + oesophagus wall + wall of gullet + wall of oesophagus + uberon + UBERON:0001096 + wall of esophagus + + + + + An anatomical wall that is part of a esophagus [Automatically generated definition]. + OBOL:automatic + + + + + anatomical wall of esophagus + OBOL:automatic + + + + + anatomical wall of gullet + OBOL:automatic + + + + + anatomical wall of oesophagus + OBOL:automatic + + + + + esophagus anatomical wall + OBOL:automatic + + + + + gullet anatomical wall + OBOL:automatic + + + + + gullet wall + OBOL:automatic + + + + + oesophagus anatomical wall + OBOL:automatic + + + + + oesophagus wall + OBOL:automatic + + + + + wall of gullet + OBOL:automatic + + + + + wall of oesophagus + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control. + + The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO]. + The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG] + phrenic + The existence of some membrane separating the pharynx from the stomach can be traced widely among the chordates. Thus amphioxus possesses an atrium by which water exits the pharynx, which has been argued (and disputed) to be homologous to structures in ascidians and hagfishes.[3] + The urochordate epicardium separates digestive organs from the pharynx and heart, but the anus returns to the upper compartment to discharge wastes through an outgoing siphon (Thoracic_diaphragm#Comparative_anatomy_and_evolution) + barrier between thoracic and abdominal cavities; stop gastric contents from refluxing into the oesophagus + breathing control + originate from the cervical somites, likely C3-C5[PMID:23586979] + + + + BTO:0000341 + CALOHA:TS-0198 + EFO:0000937 + EHDAA2:0003495 + EMAPA:17701 + EV:0100376 + FMA:13295 + GAID:158 + MA:0001904 + MAT:0000502 + MESH:D003964 + NCIT:C12702 + OpenCyc:Mx4rvVivz5wpEbGdrcN5Y29ycA + UMLS:C0011980 + VHOG:0000713 + diaphragm muscle + diaphragm of thorax + thoracic diaphragm + uberon + midriff + phren + UBERON:0001103 + + + + + diaphragm + + + + + + + + + + + + + + + + + + + + + + definitional + + + + + A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control. + MP:0002279 + + + + + + + + + + + The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO]. + GO:0060539 + + + + + The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG] + 2012-09-17 + VHOG:0000713 + VHOG + + ISBN:978-0471384618 Colbert EH, Evolution of the vertebrates: a history of the backboned animals through time (2001) p.278 + + + + + UMLS:C0011980 + ncithesaurus:Diaphragm + + + + + diaphragm muscle + BTO:0000341 + + + + + midriff + BTO:0000341 + + + + + phren + BTO:0000341 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + FMA + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal. + Some references do not consider the caecum to be part of the colon. + 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 + + + + + A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal. + + + + ZFIN:curator + + + + + Some references do not consider the caecum to be part of the colon. + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + 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 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 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 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + dorsal aorta in Kardong + Wikipedia + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 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 mucosa that is part of a large intestine [Automatically generated definition]. + + CALOHA:TS-2106 + EMAPA:35467 + FMA:14969 + MA:0002688 + NCIT:C32926 + UMLS:C0734203 + large intestinal mucosa + large intestine mucosa + large intestine mucosa of organ + large intestine mucous membrane + large intestine organ mucosa + mucosa of organ of large intestine + mucous membrane of large intestine + organ mucosa of large intestine + tunica mucosa intestini crassi + uberon + UBERON:0001207 + mucosa of large intestine + + + + + A mucosa that is part of a large intestine [Automatically generated definition]. + OBOL:automatic + + + + + UMLS:C0734203 + ncithesaurus:Large_Intestinal_Mucosa + + + + + large intestine mucosa of organ + OBOL:automatic + + + + + large intestine mucous membrane + OBOL:automatic + + + + + large intestine organ mucosa + OBOL:automatic + + + + + mucosa of organ of large intestine + OBOL:automatic + + + + + organ mucosa of large intestine + OBOL:automatic + + + + + tunica mucosa intestini crassi + FMA:14969 + FMA:TA + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A submucosa that is part of a large intestine [Automatically generated definition]. + + BTO:0002111 + EMAPA:37560 + FMA:14970 + MA:0002690 + NCIT:C32930 + UMLS:C0734204 + large intestinal submucosa + large intestine submucosa + tela submucosa intestini crassi + uberon + submucous layer of large intestine + UBERON:0001208 + submucosa of large intestine + + + + + A submucosa that is part of a large intestine [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37560 + MA:th + + + + + UMLS:C0734204 + ncithesaurus:Large_Intestinal_Submucosa + + + + + tela submucosa intestini crassi + FMA:14970 + FMA:TA + + + + + + submucous layer of large intestine + BTO:0002111 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A serous membrane that is part of a large intestine [Automatically generated definition]. + TODO - check serosa/peritoneum + + EMAPA:37557 + FMA:14975 + MA:0001546 + NCIT:C32929 + UMLS:C1517727 + large intestinal serosa + large intestine serosa + large intestine serous membrane + serous coat of large intestine + serous membrane of large intestine + tunica serosa intestini crassi + visceral peritoneum of large intestine + uberon + UBERON:0001209 + serosa of large intestine + + + + + A serous membrane that is part of a large intestine [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37557 + MA:th + + + + + UMLS:C1517727 + ncithesaurus:Large_Intestinal_Serosal_Surface + + + + + large intestine serous membrane + OBOL:automatic + + + + + serous membrane of large intestine + OBOL:automatic + + + + + tunica serosa intestini crassi + FMA:14975 + FMA:TA + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + BGEE:Ann + GOTAX:0010073 + + + + + + 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 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 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 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 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 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + FMA:24218 + XAO:0000040 + head subdivision + uberon + head region + region of head + UBERON:0001444 + + subdivision of head + + + + + + + + + + + + + + + + + + + + + A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). + Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. + The area that extends from the median ocellus to the oral foramen[HAO]. + facial + The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) + + + + BTO:0003369 + CALOHA:TS-2216 + EMAPA:32763 + FMA:24728 + GAID:64 + HAO:0000316 + MA:0002473 + MESH:D005145 + NCIT:C13071 + OpenCyc:Mx4rvVi5GZwpEbGdrcN5Y29ycA + UMLS:C0015450 + galen:Face + uberon + facia/facies + visage + UBERON:0001456 + + + face + http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg + + + + + A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). + + + + + + Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. + FMA:24728 + + + + + The area that extends from the median ocellus to the oral foramen[HAO]. + + HAO:0000316 + NCBITaxon:7399 + + + + + The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) + vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf + + + + + UMLS:C0015450 + ncithesaurus:Face + + + + + facia/facies + + + + + + + visage + BTO:0003369 + + + + + + + + + + + + + + + + + + + + + + + + + + A zone of skin that is part of a lip [Automatically generated definition]. + + + EMAPA:37643 + FMA:24764 + MA:0001579 + NCIT:C12291 + UMLS:C0222101 + lip skin + lip zone of skin + zone of skin of lip + uberon + skin of lips + UBERON:0001458 + skin of lip + + + + + A zone of skin that is part of a lip [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37643 + MA:th + + + + + UMLS:C0222101 + ncithesaurus:Skin_of_the_Lip + + + + + lip zone of skin + OBOL:automatic + + + + + zone of skin of lip + OBOL:automatic + + + + + skin of lips + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + 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 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + Wikipedia + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 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]. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + 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 branch of the external carotid artery that supplies structures of the face. [WP,unvetted]. + + + + EMAPA:19213 + FMA:49549 + MA:0001950 + NCIT:C32578 + OpenCyc:Mx4rwCt95ZwpEbGdrcN5Y29ycA + UMLS:C0226109 + uberon + arteria maxillaris externa + external maxillary artery + UBERON:0001612 + + facial artery + http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png + + + + + A branch of the external carotid artery that supplies structures of the face. [WP,unvetted]. + + + + + + UMLS:C0226109 + ncithesaurus:Facial_Artery + + + + + arteria maxillaris externa + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted]. + ...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries + + + + EHDAA2:0001069 + EHDAA:7357 + EMAPA:17311 + FMA:49675 + GAID:498 + MA:0001919 + MESH:D008438 + NCIT:C34205 + OpenCyc:Mx4rwDDJ45wpEbGdrcN5Y29ycA + UMLS:C0024949 + uberon + arteria maxillaris + internal maxillary artery + UBERON:0001616 + + maxillary artery + http://upload.wikimedia.org/wikipedia/commons/3/39/Gray510.png + + + + + An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted]. + + + + + + ...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries + + + + + + UMLS:C0024949 + ncithesaurus:Maxillary_Artery + + + + + arteria maxillaris + + + + + + + + + + + + + + + + + + + + + + + + + The ophthalmic artery is a branch of the internal carotid artery which supplies branches to supply the eye and other structures in the orbit. It enters the orbit together with the Optic nerve through the Optic foramen/canal. [WP,modified]. + Part of internal carotid which carries blood via branches to the eye, the eye muscles, and eyelids.[AAO] + relationship loss: part_of internal carotid (AAO:0010219)[AAO] + + + + AAO:0010497 + EHDAA2:0001300 + EHDAA:7363 + EMAPA:17007 + FMA:49868 + GAID:503 + MA:0002011 + MESH:D009880 + NCIT:C33216 + OpenCyc:Mx4rvcCxpJwpEbGdrcN5Y29ycA + UMLS:C0029078 + XAO:0000368 + uberon + arteria ophthalmica + opthalmic artery + UBERON:0001619 + + ophthalmic artery + http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png + + + + + The ophthalmic artery is a branch of the internal carotid artery which supplies branches to supply the eye and other structures in the orbit. It enters the orbit together with the Optic nerve through the Optic foramen/canal. [WP,modified]. + + + + + + Part of internal carotid which carries blood via branches to the eye, the eye muscles, and eyelids.[AAO] + 2012-06-20 + AAO:0010497 + AAO + AAO:BJB + + + + + relationship loss: part_of internal carotid (AAO:0010219)[AAO] + 2012-06-20 + AAO:0010497 + AAO + + + + + UMLS:C0029078 + ncithesaurus:Opthalmic_Artery + + + + + arteria ophthalmica + + + + + + + opthalmic artery + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The lacrimal artery arises close to the optic foramen, and is one of the largest branches derived from the ophthalmic artery: not infrequently it is given off before the artery enters the orbit. It accompanies the lacrimal nerve along the upper border of the Lateral Rectus, supplies the lacrimal gland. [WP,unvetted]. + + + + EMAPA:37094 + FMA:49927 + MA:0001988 + NCIT:C52948 + UMLS:C0226171 + uberon + a. lacrimalis + UBERON:0001622 + + lacrimal artery + http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png + + + + + + + + + + + FMA + + + + + The lacrimal artery arises close to the optic foramen, and is one of the largest branches derived from the ophthalmic artery: not infrequently it is given off before the artery enters the orbit. It accompanies the lacrimal nerve along the upper border of the Lateral Rectus, supplies the lacrimal gland. [WP,unvetted]. + + + + + + EMAPA:37094 + MA:th + + + + + UMLS:C0226171 + ncithesaurus:Lacrimal_Artery + + + + + a. lacrimalis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 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 + + + + + + + + + + + sensory + Wikipedia + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 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 + + + + + + + + + + + FMA + + + + + + + + + + + + + + + + basi paired exo and supra occipital bones + MA-modified + + + + + + + + + + + + + + + + interparietal (postparietal) + + + + + + + + + + + WP + + + + + + + + + + + + + + + + The bone at the lower, posterior part of the skull. + ISBN:0-683-40008-8 + MP:0005269 + + + + + formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII + + + + + + fusion of basi-, exo- and supra-occipitals (and maybe tabular) + Kardong + + + + + UMLS:C0028784 + ncithesaurus:Occipital_Bone + + + + + occipital complex + + + + + + os occipitale + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous. + In many mammals, as in humans, the petrosal, ectotympanic and squamosal bones synostose to form the temporal bone + styloid process + fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic) + The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP]. + Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA + + + + EHDAA:6035 + EMAPA:17682 + FMA:52737 + GAID:232 + MA:0001476 + MESH:D013701 + NCIT:C12797 + OpenCyc:Mx4rvbkAk5wpEbGdrcN5Y29ycA + UMLS:C0039484 + VHOG:0000800 + uberon + os temporale + UBERON:0001678 + + + temporal bone + http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg + + + + + + FMA + + + + + + + + + + + + + + + + petrosal + + + + + + + + + + + + + + + + squamosal plus angular + temporal series + + + + + + + + + + + + + + + + styloid process + + + + + The large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous. + ISBN:0-683-40008-8 + MP:0005272 + + + + + fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic) + chond. + + + + + The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP]. + [WP] + + + + + Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA + FMA + + + + + UMLS:C0039484 + ncithesaurus:Temporal_Bone + + + + + os temporale + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Subdivision of skeleton which includes upper and lower jaw skeletons. + TODO - move ZFA:0001227 (it is the entire jaw skeleton). + Skeletal and cartilage elements of the first pharyngeal arch.[TAO] + There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983). + in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates + + + + AAO:0000988 + BTO:0001749 + EMAPA:35455 + FMA:54396 + GAID:214 + MA:0001905 + MESH:D007568 + NCIT:C48821 + OpenCyc:Mx4rvVjjEZwpEbGdrcN5Y29ycA + TAO:0001227 + UMLS:C0022359 + ZFA:0001227 + galen:Jaw + jaw + jaw cartilage + mandibular arch skeleton + uberon + anterior splanchnocranium + jaws + mandibular arch + oral jaw skeleton + pharyngeal arch 1 skeleton + visceral arch 1 + UBERON:0001708 + + + + jaw skeleton + + + + + + + + + + + cjm + + + + + + + + + + + + + + + + Subdivision of skeleton which includes upper and lower jaw skeletons. + + + + + + + Skeletal and cartilage elements of the first pharyngeal arch.[TAO] + 2012-08-14 + TAO:0001227 + TAO + ZFIN:curator + + + + + in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates + FMA + + + + + UMLS:C0022359 + ncithesaurus:Jaw + + + + + jaw + MA:0001905 + + + + + jaw cartilage + ZFA:0001227 + + + + + mandibular arch skeleton + ZFA:0001227 + + + + + mandibular arch + TAO:0001227 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]. + Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO] + Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] + Note isa/partof difference MA/FMA + + + AAO:0000272 + EFO:0003660 + EHDAA2:0001018 + EHDAA:7995 + EMAPA:17906 + FMA:59398 + MESH:D008334 + VHOG:0000453 + ncithesaurus:Lower_Jaw + mandibular part of mouth + uberon + lower part of mouth + mandibular series + UBERON:0001710 + + + + See notes for jaw w.r.t skeletal element vs subdivision of head + lower jaw region + http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png + + + + + + + + + + + + + + + + Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]. + + + + + + Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO] + 2012-06-20 + AAO:0000272 + AAO + AAO:LAP + + + + + Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] + 2012-09-17 + VHOG:0000453 + VHOG + + DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) + + + + + Note isa/partof difference MA/FMA + MA + + + + + mandibular part of mouth + FMA:59398 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The groups of nerve cell bodies associated with the twelve cranial nerves. + Ganglion which is located in the head.[TAO] + UBERON:0003213 + UBERON:0026601 + + + BIRNLEX:2597 + BTO:0000106 + EFO:0000902 + EMAPA:16659 + FMA:54502 + MA:0000213 + MA:0000214 + MAT:0000200 + MIAA:0000200 + TAO:0000013 + VHOG:0000076 + XAO:0000027 + ZFA:0000013 + cranial ganglion + cranial ganglion part of peripheral nervous system + cranial ganglion/nerve + cranial nerve ganglion + cranial neural ganglion + cranial neural tree organ ganglion + ganglion of cranial nerve + ganglion of cranial neural tree organ + uberon + cranial ganglia + head ganglion + presumptive cranial ganglia + UBERON:0001714 + + + + + cranial ganglion + + + + + The groups of nerve cell bodies associated with the twelve cranial nerves. + + ISBN:0-683-40008-8 + MGI:csmith + MP:0001081 + + + + + Ganglion which is located in the head.[TAO] + 2012-08-14 + TAO:0000013 + TAO + ZFIN:curator + + + + + cranial ganglion part of peripheral nervous system + BIRNLEX:2597 + + + + + cranial neural tree organ ganglion + OBOL:automatic + + + + + ganglion of cranial nerve + FMA:54502 + + + + + ganglion of cranial neural tree organ + OBOL:automatic + + + + + presumptive cranial ganglia + ZFA:0000013 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + cjm + + + + + + + + + + + ZFA + + + + + + + + + + + NIF + + + + + + + + + + + FMA + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An 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 + + + + + + + + + + + XAO + + + + + An anatomical space that is enclosed by a pharynx. + OBOL:automatic + + + + + cavitas pharyngealis + + + + + + cavitas pharyngis + BTO:0002097 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + FMA + + + + + + + + + + + + + + + + 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 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 + + + + + + + + + + + FMA + MA + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + sensory + Wikipedia + + + + + + + + + + + motor + Wikipedia + + + + + Cranial nerve that branches into the lateral (to body sense organs) and the intestino-accessorial (to the skin, muscles of shoulder, hyoid, larynx, gut, lungs, and heart). + + ISBN:0471209627 + + + + + Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[AAO] + 2012-06-20 + AAO:0010475 + AAO + AAO:EJS + + + + + We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] + 2012-09-17 + VHOG:0000737 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625 + + + + + 10n + BIRNLEX:801 + NIFSTD:NeuroNames_abbrevSource + + + + + + EMAPA:37797 + MA:th + + + + + UMLS:C0042276 + BIRNLEX:801 + + + + + UMLS:C0042276 + ncithesaurus:Vagus_Nerve + + + + + UMLS:C1305910 + BIRNLEX:801 + + + + + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=702 + BIRNLEX:801 + + + + + nervus vagus [x] + FMA:5731 + FMA:TA + + + + + + vagus X nerve + MA:0001106 + + + + + nerve X + NeuroNames:702 + + + + + nervus vagus + + + + + + + nervus vagus + BTO:0003472 + + + + + pneuomgastric nerve + BTO:0003472 + + + + + vagus nerve or its root + BAMS:10n + + + + + + + + + + + + + + + + + + + + + The space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens. + The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG] + space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball + + + + BTO:0002084 + EHDAA2:0000129 + EHDAA:9033 + EMAPA:18231 + FMA:58078 + GAID:889 + MA:0000262 + MESH:D000867 + NCIT:C12667 + UMLS:C0003151 + VHOG:0001431 + anterior chamber + anterior chamber of eye + camera anterior + eye anterior chamber + uberon + camera anterior bulbi + camera anterior bulbi oculi + camera oculi anterior + UBERON:0001766 + + anterior chamber of eyeball + http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg + + + + + + FMA + + + + + The space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens. + MESH:A09.371.060.067 + MP:0005205 + + + + + The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG] + 2012-09-17 + VHOG:0001431 + VHOG + + + + + + + space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball + EHDAA2 + + + + + UMLS:C0003151 + ncithesaurus:Anterior_Chamber_of_the_Eye + + + + + anterior chamber + HP:0000593 + MP:0010709 + + + + + camera anterior bulbi + BTO:0002084 + + + + + camera anterior bulbi oculi + + + + + + + camera oculi anterior + BTO:0002084 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]. + TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus + + uveal + + + + CALOHA:TS-2228 + EMAPA:35901 + FMA:58103 + GAID:912 + MA:0002480 + MESH:D014602 + NCIT:C12811 + UMLS:C0042160 + tunica vasculosa of eyeball + uvea + uveal tract + uberon + pars iridica retinae + tunica vasculatis oculi + tunica vasculosa bulbi + vascular layer of eyeball + UBERON:0001768 + + + uvea + http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png + + + + + + FMA + + + + + The pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]. + + MP:0005197 + + + + + + + + + + + UMLS:C0042160 + ncithesaurus:Uvea + + + + + tunica vasculosa of eyeball + FMA:58103 + + + + + uvea + FMA:58103 + + + + + uveal tract + FMA:58103 + + + + + pars iridica retinae + + + + + + tunica vasculatis oculi + + + + + + tunica vasculosa bulbi + + + + + + + vascular layer of eyeball + FMA:58103 + + + + + + + + + + + + + + + + + + + + + + + + + + + + The adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye. + The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] + The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] + iridial + The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019] + + + + AAO:0010347 + BTO:0000653 + CALOHA:TS-0491 + EFO:0004245 + EMAPA:19154 + EV:0100345 + FMA:58235 + GAID:917 + MA:0000273 + MESH:D007498 + NCIT:C12737 + OpenCyc:Mx4rvVjbppwpEbGdrcN5Y29ycA + TAO:0001238 + UMLS:C0022077 + VHOG:0000101 + XAO:0000185 + ZFA:0001238 + uberon + anterior uvea + irides + irises + UBERON:0001769 + + + + + iris + + + + + + + + + + + XAO + + + + + The adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye. + ISBN:0-683-40008-8 + MP:0001322 + + + + + The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] + 2012-09-17 + VHOG:0000101 + VHOG + + + + + + The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] + 2012-09-17 + VHOG:0000101 + VHOG + + DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) + + + + + UMLS:C0022077 + ncithesaurus:Iris + + + + + irides + + + + + + irises + VHOG:0000101 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The smooth stratified squamous epithelium that covers the outer surface of the cornea. + Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO] + In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei + In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals + + + + BTO:0000287 + CALOHA:TS-0173 + EFO:0001917 + EHDAA2:0000319 + EMAPA:17162 + FMA:58263 + GAID:895 + MA:0001243 + MESH:D019573 + NCIT:C12928 + TAO:0002187 + UMLS:C0459875 + ZFA:0001683 + anterior corneal epithelium + cornea epithelial tissue + cornea epithelium + epithelial tissue of cornea + epithelium anterius (cornea) + epithelium anterius corneae + epithelium corneæ anterior layer + epithelium of cornea + external epithelium of cornea + uberon + anterior endothelium of cornea + e. anterius corneae + endothelium anterius corneae + endothelium camerae anterioris bulbi + endothelium corneale + epithelium posterius corneae + UBERON:0001772 + + + + + corneal epithelium + http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png + + + + + + + + + + + ISBN:0781772214 + + + + + The smooth stratified squamous epithelium that covers the outer surface of the cornea. + MESH:A09.371.060.217.325 + MGI:smb + MP:0006000 + + + + + Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO] + 2012-08-14 + TAO:0002187 + TAO + ZFIN:ZDB-PUB-061010-3 + + + + + UMLS:C0459875 + ncithesaurus:Corneal_Epithelium + + + + + cornea epithelial tissue + OBOL:automatic + + + + + cornea epithelium + OBOL:automatic + + + + + epithelial tissue of cornea + OBOL:automatic + + + + + epithelium anterius corneae + FMA:58263 + FMA:TA + + + + + + anterior endothelium of cornea + BTO:0000287 + + + + + e. anterius corneae + + + + + + + endothelium anterius corneae + BTO:0000287 + + + + + endothelium camerae anterioris bulbi + BTO:0000287 + + + + + endothelium corneale + BTO:0000287 + + + + + epithelium posterius corneae + BTO:0000287 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]. + The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]. + The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG] + scleral + in fish, reptiles and monotremes the connective tissue of the sclera is skeletal + continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe. + Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson]. + Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709]. + + + + AAO:0010354 + BTO:0001606 + EMAPA:19027 + EV:0100342 + FMA:58269 + GAID:911 + MA:0000280 + MESH:D012590 + NCIT:C12784 + OpenCyc:Mx4rv7yR55wpEbGdrcN5Y29ycA + UMLS:C0036410 + VHOG:0001274 + XAO:0000183 + ZFA:0005563 + uberon + scleral capsule + UBERON:0001773 + + + + Disease notes: implicated in rheumatoid arthritis. + sclera + http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg + + + + + + + + + + + FMA + + + + + + + + + + + ZFA + + + + + + + + + + + ISBN:0781772214 + + + + + + + + + + + cjm + ISBN:0781772214 + Wikipedia + + + + + 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 + + + + + + + + + + + MP + + + + + + + + + + + Wikipedia + + + + + A double layer covering the ciliary body that produces aqueous humor. + + + + + + UMLS:C0459736 + ncithesaurus:Ciliary_Epithelium + + + + + ciliary body epithelium + FMA:58464 + + + + + epithelium of ciliary body + FMA:58464 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The delicate vascular connective tissue that lies between the anterior surface of the iris and the pars iridica retinae. + + + EMAPA:35451 + FMA:58526 + MA:0002777 + ZFA:0005569 + iridial stroma + stroma of iris + uberon + UBERON:0001779 + + + + iris stroma + http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png + + + + + The delicate vascular connective tissue that lies between the anterior surface of the iris and the pars iridica retinae. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified]. + Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG] + + + + + AAO:0011101 + BAMS:spin + BTO:0000870 + EHDAA2:0001898 + EMAPA:16989 + FMA:5858 + GAID:841 + MA:0000233 + MESH:D013127 + NCIT:C12792 + OpenCyc:Mx4rwK_iFJwpEbGdrcN5Y29ycA + UMLS:C0037941 + VHOG:0000824 + XAO:0003101 + backbone nerve + nerve of backbone + nerve of spinal column + nerve of spine + nerve of vertebral column + spinal column nerve + spinal nerve tree + spine nerve + vertebral column nerve + uberon + nervi spinales + spinal nerves + UBERON:0001780 + + + spinal nerve + Spinal:nerve.svg + + + + + The any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified]. + MESH:A08.800.800.720 + MP:0001077 + + + + + Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG] + 2012-09-17 + VHOG:0000824 + VHOG + + + + + + + UMLS:C0037941 + ncithesaurus:Spinal_Nerve + + + + + backbone nerve + OBOL:automatic + + + + + nerve of backbone + OBOL:automatic + + + + + nerve of spinal column + OBOL:automatic + + + + + nerve of spine + OBOL:automatic + + + + + nerve of vertebral column + OBOL:automatic + + + + + spinal column nerve + OBOL:automatic + + + + + spine nerve + OBOL:automatic + + + + + vertebral column nerve + OBOL:automatic + + + + + nervi spinales + + + + + + + spinal nerves + BAMS:spin + + + + + + + + + + + + + + + + + + + + + + Any of the layers that make up the retina[MP]. + MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers + + + AAO:0010353 + EMAPA:35742 + FMA:58617 + MA:0001319 + NCIT:C49328 + UMLS:C0459649 + XAO:0000266 + retina layer + retina neuronal layer + retinal layer + retinal neuronal layer + uberon + UBERON:0001781 + + + layer of retina + + + + + Any of the layers that make up the retina[MP]. + MP:0003727 + + + + + MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers + MA + + + + + UMLS:C0459649 + ncithesaurus:Retina_Layer + + + + + retina neuronal layer + MP:0006069 + + + + + retinal neuronal layer + MP:0006069 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord. + classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN. + Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO] + We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG] + See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6 + + + + + + AAO:0000108 + BAMS:cran + BIRNLEX:1623 + BTO:0001104 + EHDAA2:0000323 + EMAPA:17264 + FMA:5865 + GAID:802 + HBA:9299 + MA:0000215 + MBA:967 + MESH:D003391 + NCIT:C12700 + OpenCyc:Mx4rvWvJVpwpEbGdrcN5Y29ycA + TAO:0000641 + UMLS:C0010268 + UMLS:C1269897 + VHOG:0000279 + XAO:0000429 + XAO:0003089 + ZFA:0000641 + cranial neural tree organ + uberon + cranial nerves + nervus cranialis + UBERON:0001785 + + + + cranial nerve + http://upload.wikimedia.org/wikipedia/commons/1/18/Brain_human_normal_inferior_view_with_labels_en-2.svg + http://upload.wikimedia.org/wikipedia/commons/8/84/Brain_human_normal_inferior_view_with_labels_en.svg + + + + + Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord. + + + + + + Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO] + 2012-08-14 + TAO:0000641 + TAO + ZFIN:curator + + + + + We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG] + 2012-09-17 + VHOG:0000279 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 + + + + + UMLS:C0010268 + BIRNLEX:1623 + + + + + UMLS:C0010268 + ncithesaurus:Cranial_Nerve + + + + + UMLS:C1269897 + BIRNLEX:1623 + + + + + nervus cranialis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A thick watery refractive medium that fills the space between the lens and the cornea[WP]. + The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG] + (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] + FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa. + + + + EHDAA2:0000139 + EHDAA:10196 + EMAPA:18232 + ENVO:02000024 + FMA:58819 + GAID:890 + MA:0001236 + MESH:D001082 + NCIT:C13190 + OpenCyc:Mx4rvdGd-5wpEbGdrcN5Y29ycA + UMLS:C0003662 + VHOG:0000548 + ZFA:0005564 + aqueous humor + aqueous humour + humor aquosus + uberon + UBERON:0001796 + + + + aqueous humor of eyeball + http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg + + + + + + + + + + + FMA def states A and P + located_in in EHDAA2 + VHOG + + + + + A thick watery refractive medium that fills the space between the lens and the cornea[WP]. + + + + + + The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG] + 2012-09-17 + VHOG:0000548 + VHOG + + + + + + + (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] + 2012-09-17 + VHOG:0000548 + VHOG + + DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 + + + + + FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa. + FMA + + + + + UMLS:C0003662 + ncithesaurus:Aqueous_Humor + + + + + aqueous humour + EHDAA2:0000139 + + + + + humor aquosus + FMA:58819 + FMA:TA + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + Wikipedia + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Aqueous substance secreted by the lacrimal gland. + + + BTO:0001499 + CALOHA:TS-1016 + EMAPA:36537 + ENVO:02000034 + FMA:59756 + GAID:1173 + MA:0002508 + MESH:D013666 + NCIT:C33739 + UMLS:C0039409 + galen:Tear + galen:Tears + lacrimal fluid + lacrimal gland secretion + lacrimal secretion + tear + tears + uberon + tear fluid + UBERON:0001827 + + secretion of lacrimal gland + + + + + Aqueous substance secreted by the lacrimal gland. + + + + + + + UMLS:C0039409 + ncithesaurus:Tear + + + + + tear + FMA:59756 + + + + + tears + + + + + + tear fluid + BTO:0001499 + + + + + + + + + + + + + + + + + + + + + + + + + + + One of the 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 nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. + A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. [TFD][VHOG] + + + + BAMS:phn + BTO:0001063 + EHDAA:4677 + EMAPA:17813 + FMA:6191 + GAID:848 + MA:0001170 + MESH:D010791 + NCIT:C52813 + OpenCyc:Mx4rvtmdUJwpEbGdrcN5Y29ycA + UMLS:C0031774 + VHOG:0000728 + uberon + diaphragmatic nerve + nervus phrenicus + phrenic + UBERON:0001884 + + + phrenic nerve + http://upload.wikimedia.org/wikipedia/commons/3/3c/Gray806.png + + + + + A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. + VHOG:0000728 + + + + + A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. [TFD][VHOG] + 2012-09-17 + VHOG:0000728 + VHOG + + + + + + + UMLS:C0031774 + ncithesaurus:Phrenic_Nerve + + + + + diaphragmatic nerve + BTO:0001063 + + + + + nervus phrenicus + + + + + + + nervus phrenicus + BTO:0001063 + + + + + phrenic + BTO:0001063 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of a capillary [Automatically generated definition]. + + BTO:0004954 + CALOHA:TS-0112 + EMAPA:36292 + FMA:62114 + MA:0000711 + NCIT:C49215 + UMLS:C0006904 + blood capillary endothelium + capillary endothelium + capillary vessel endothelium + endothelium of blood capillary + endothelium of capillary vessel + uberon + UBERON:0001915 + endothelium of capillary + + + + + An endothelium that is part of a capillary [Automatically generated definition]. + OBOL:automatic + + + + + UMLS:C0006904 + ncithesaurus:Capillary_Endothelium + + + + + blood capillary endothelium + OBOL:automatic + + + + + capillary vessel endothelium + OBOL:automatic + + + + + endothelium of blood capillary + OBOL:automatic + + + + + endothelium of capillary vessel + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of an arteriole [Automatically generated definition]. + + EMAPA:36286 + FMA:62115 + MA:0000705 + NCIT:C49192 + UMLS:C1179024 + arteriole endothelium + uberon + UBERON:0001916 + endothelium of arteriole + + + + + An endothelium that is part of an arteriole [Automatically generated definition]. + OBOL:automatic + + + + + UMLS:C1179024 + ncithesaurus:Arteriole_Endothelium + + + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of an artery [Automatically generated definition]. + The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO] + Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] + + AAO:0011013 + BTO:0004757 + EMAPA:35148 + FMA:62116 + MA:0000707 + NCIT:C49194 + UMLS:C1179025 + VHOG:0001215 + XAO:0000357 + arterial endothelium + artery endothelium + uberon + UBERON:0001917 + endothelium of artery + + + + + An endothelium that is part of an artery [Automatically generated definition]. + OBOL:automatic + + + + + The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO] + 2012-06-20 + AAO:0011013 + AAO + XAO:curator + + + + + Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] + 2012-09-17 + VHOG:0001215 + VHOG + + ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 + + + + + UMLS:C1179025 + ncithesaurus:Artery_Endothelium + + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of a venule [Automatically generated definition]. + + EMAPA:36290 + FMA:62117 + MA:0000716 + NCIT:C49319 + UMLS:C1179026 + venule endothelium + uberon + UBERON:0001918 + endothelium of venule + + + + + An endothelium that is part of a venule [Automatically generated definition]. + OBOL:automatic + + + + + UMLS:C1179026 + ncithesaurus:Venule_Endothelium + + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of a vein [Automatically generated definition]. + Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] + + AAO:0011110 + BTO:0004756 + EMAPA:36288 + FMA:62118 + MA:0000712 + NCIT:C49317 + UMLS:C1179027 + VHOG:0001216 + XAO:0000358 + vein endothelium + venous endothelium + uberon + veinous endothelium + UBERON:0001919 + endothelium of vein + + + + + An endothelium that is part of a vein [Automatically generated definition]. + OBOL:automatic + + + + + Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] + 2012-09-17 + VHOG:0001216 + VHOG + + ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 + + + + + UMLS:C1179027 + ncithesaurus:Vein_Endothelium + + + + + veinous endothelium + VHOG:0001216 + + + + + + + + + + + + + + + + + + + + + + + + + + + Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. + Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] + MTg + tegmentum + + + + + BAMS:MTg + BIRNLEX:1200 + BTO:0003388 + DHBA:12195 + EFO:0000921 + EHDAA2:0004475 + EMAPA:18215 + FMA:62393 + HBA:9002 + MA:0000212 + MAT:0000452 + TAO:0000160 + UMLS:C0039441 + VHOG:0001367 + XAO:0004271 + ZFA:0000160 + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491 + tegmentum mesencephali + tegmentum of midbrain + uberon + mesencephalic tegmentum + tegmentum mesencephalicum + UBERON:0001943 + + + + + 'tegmentum' is used generically for the ventral part of the brainstem (ISBN:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum + midbrain tegmentum + http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png + + + + + + + + + + + ZFA + + + + + Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. + + FMA:FMA + ISBN:0471888893 + + + + + Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] + 2012-09-17 + VHOG:0001367 + VHOG + + DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005) + + + + + MTg + BIRNLEX:1200 + NIFSTD:NeuroNames_abbrevSource + + + + + + tegmentum + ISBN:0471888893 + + + + + UMLS:C0039441 + BIRNLEX:1200 + + + + + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491 + BIRNLEX:1200 + + + + + tegmentum mesencephali + + + + + + + mesencephalic tegmentum + VHOG:0001367 + + + + + tegmentum mesencephalicum + NeuroNames:491 + + + + + + + + + + + + + + + + + + + + + + + + + + + + A multi-tissue structure that is part of a spinal cord. + + + BIRNLEX:1496 + NCIT:C33969 + UMLS:C1268166 + uberon + spinal cord part + UBERON:0001948 + + regional part of spinal cord + + + + + A multi-tissue structure that is part of a spinal cord. + OBOL:automatic + + + + + UMLS:C1268166 + ncithesaurus:Spinal_Cord_Part + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + AEO + + + + + + + + + + + EHDAA2 + + + + + + + + + + + GO:0072360 + + + + + A vessel through which blood circulates in the body. + + BTO:0001102 + + + + + Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] + 2012-09-17 + VHOG:0001250 + VHOG + + + + + + Any of the vessels through which blood circulates in the body.[AAO] + 2012-06-20 + AAO:0011004 + AAO + AAO:EJS + + + + + The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] + 2012-09-17 + VHOG:0001250 + VHOG + + DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) + + + + + FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX + FMA + + + + + vascular element + EMAPA:35993 + + + + + UMLS:C0005847 + ncithesaurus:Blood_Vessel + + + + + region of vascular tree organ + FMA:50722 + + + + + vascular tree organ region + FMA:50722 + + + + + vas sanguineum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any of the smallest blood vessels connecting arterioles with venules. + not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element + Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] + The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] + capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs + + + AAO:0010252 + BTO:0002045 + CALOHA:TS-2006 + EFO:0001906 + EMAPA:35198 + EV:0100035 + FMA:63194 + MA:0000065 + MESH:A07.231.432.410 + NCIT:C12685 + NLXANAT:090902 + OpenCyc:Mx4rvWEU-5wpEbGdrcN5Y29ycA + TAO:0005250 + UMLS:C0935624 + VHOG:0001253 + XAO:0000116 + ZFA:0005250 + blood capillary + capillary vessel + uberon + UBERON:0001982 + + + + + capillary + http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg + + + + + + FMA + MA + XAO + + + + + + ZFA + + + + + Any of the smallest blood vessels connecting arterioles with venules. + + + ISBN:0073040584 + + + + + Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] + 2012-06-20 + AAO:0010252 + AAO + AAO:BJB + + + + + The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] + 2012-09-17 + VHOG:0001253 + VHOG + + DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) + + + + + UMLS:C0935624 + ncithesaurus:Capillary + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP]. + + + + CALOHA:TS-0172 + EMAPA:35935 + FMA:63882 + GAID:891 + MA:0001242 + MESH:D004728 + NCIT:C12707 + TAO:0002186 + UMLS:C0014259 + ZFA:0001687 + cornea endothelium + endothelium of cornea + uberon + epithelium posterius corneae + UBERON:0001985 + + + + corneal endothelium + http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png + + + + + + + + + + + WP + + + + + 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 + + + + + + + + + + + UBERON:0001985 + FMA-inferred + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + piece of shit + portion of excrement + portion of faeces + portion of fecal material + portion of fecal matter + portion of feces + portionem cacas + stool + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 cranial nerve that originates from neurons in the medulla and in the cervical spinal cord. + + A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris. + Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] + Small motor nerve which innervates a single pectoral suspensory muscle, the m. cucullaris.[AAO] + Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG] + In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve + FMA has distinct cranial and spinal parts - WP says 'Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2] + + + + + + AAO:0010476 + BAMS:11n + BAMS:XIn + BIRNLEX:812 + EHDAA2:0000106 + EHDAA:2855 + EMAPA:17265 + FMA:6720 + FMA:80284 + GAID:825 + HBA:9340 + MA:0001088 + MBA:717 + MESH:D000055 + NCIT:C32041 + OpenCyc:Mx4rwTEwI5wpEbGdrcN5Y29ycA + UMLS:C0000905 + UMLS:C1305777 + VHOG:0000699 + XAO:0004214 + Willis' nerve + accessory XI + accessory XI nerve + accessory nerve + accessory nerve [XI] + cervical accessory nerve + cranial nerve XI + eleventh cranial nerve + nervus accessorius [XI] + pars spinalis nervus accessorius + radix spinalis nervus accessorius + spinal accessory nerve + spinal accessory nerve tree + spinal part of accessory nerve + uberon + CN-XI + accessory spinal nerve + UBERON:0002019 + + + accessory XI nerve + http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png + + + + + A cranial nerve that originates from neurons in the medulla and in the cervical spinal cord. + + BIRNLEX:812 + + + + + + http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7 + VHOG + Wikipedia + + + + + A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris. + ISBN:080184780X + XAO:0004214 + + + + + Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] + 2012-09-17 + VHOG:0000699 + VHOG + + + + + + Small motor nerve which innervates a single pectoral suspensory muscle, the m. cucullaris.[AAO] + 2012-06-20 + AAO:0010476 + AAO + AAO:EJS + + + + + Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG] + 2012-09-17 + VHOG:0000699 + VHOG + + + + + + + In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve + GO + + + + + FMA has distinct cranial and spinal parts - WP says 'Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2] + FMA + + + + + UMLS:C0000905 + BIRNLEX:812 + + + + + UMLS:C0000905 + ncithesaurus:Accessory_Nerve + + + + + UMLS:C1305777 + BIRNLEX:812 + + + + + accessory XI + EHDAA2:0000106 + + + + + cranial nerve XI + BIRNLEX:812 + + + + + eleventh cranial nerve + BIRNLEX:812 + + + + + nervus accessorius [XI] + FMA:6720 + FMA:TA + + + + + + pars spinalis nervus accessorius + FMA:6720 + FMA:TA + + + + + + radix spinalis nervus accessorius + FMA:6720 + FMA:TA + + + + + + spinal accessory nerve + FMA:6720 + + + + + CN-XI + VHOG:0000699 + + + + + accessory spinal nerve + BAMS:XIn + + + + + + + + + + + + + + + + + + + + + A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. + Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] + + + + AEO:0001012 + EHDAA2:0003136 + EHDAA2_RETIRED:0004658 + EMAPA:37596 + FMA:67242 + HBA:4006 + MA:0001112 + NCIT:C32695 + OpenCyc:Mx4rwDdKMpwpEbGdrcN5Y29ycA + TAO:0002197 + UMLS:C0018220 + VHOG:0001768 + ZFA:0001681 + gray matter + gray matter of neuraxis + grey matter + grey matter of neuraxis + grey substance + neuronal grey matter + substantia grisea + uberon + gray mater + grisea + UBERON:0002020 + + + + gray matter + Spinal:nerve.svg + + + + + A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. + + + + + + + Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] + 2012-08-14 + TAO:0002197 + TAO + ZFIN:curator + + + + + EMAPA:37596 + MA:th + + + + + UMLS:C0018220 + ncithesaurus:Gray_Matter + + + + + gray matter of neuraxis + FMA:67242 + + + + + neuronal grey matter + AEO:0001012 + + + + + substantia grisea + FMA:67242 + FMA:TA + + + + + + gray mater + ZFA:0001681 + + + + + grisea + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. + + Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] + The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO] + relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] + Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] + rhombencephalic + in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps + + + + + + AAO:0010150 + BAMS:HB + BIRNLEX:942 + BTO:0000672 + CALOHA:TS-0457 + DHBA:10653 + DMBA:16808 + EFO:0000923 + EHDAA2:0000746 + EHDAA:3514 + EHDAA:6487 + EMAPA:16916 + FMA:67687 + MA:0000195 + MAT:0000107 + MBA:1065 + MESH:D012249 + MIAA:0000107 + NCIT:C40336 + TAO:0000029 + UMLS:C0035507 + UMLS:C1522180 + VHOG:0000070 + XAO:0000015 + ZFA:0000029 + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540 + uberon + rhombencephalon + UBERON:0002028 + + + + + hindbrain + http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg + + + + + + + + + + + ZFA + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + 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. + + + + + + + BGEE:fb + + + + + + + BGEE:fb + + + + + + 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 artery that supplies the diaphragm. + In humans this includes the superior and inferior phrenic arteries + + EMAPA:37108 + FMA:69330 + MA:0002019 + NCIT:C33320 + UMLS:C1181536 + uberon + UBERON:0002057 + + phrenic artery + + + + + An artery that supplies the diaphragm. + + + + + + EMAPA:37108 + MA:th + + + + + UMLS:C1181536 + ncithesaurus:Phrenic_Artery + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The 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 + + + + + + GO + + + + + + + + + + + ZFA + + + + + + + + + + + ZFA + + + + + + + + + + + + Wikipedia + + + + + 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 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 + + + + + + + + + + + FMA + + + + + + + + + + + + + + + + + + + + + + definitional + + + + + The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. + + ZFIN:curator + + + + + A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO] + 2012-08-14 + TAO:0001119 + TAO + ZFIN:curator + + + + + When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG] + 2012-09-17 + VHOG:0000108 + VHOG + + ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1 + + + + + UMLS:C0011646 + ncithesaurus:Dermis + + + + + corium + + + + + + + corium + BTO:0000294 + + + + + cutis + BTO:0000294 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. + A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO] + A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544]. + hypodermal + subcutaneous + subcutaneus + BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument. + + + BTO:0001314 + CALOHA:TS-2366 + EMAPA:37505 + FMA:70544 + NCIT:C33645 + TAO:0001136 + UMLS:C0278403 + ZFA:0001136 + hypoderm + vertebrate hypodermis + uberon + sub-tegumental tissue + subcutaneous tissue + subcutis + subtegumental tissue + superficial fascia + tela subcutanea + UBERON:0002072 + + + + hypodermis + http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg + + + + + + FMA + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + 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 + + + + + splanchnic tissue + BTO:0001491 + + + + + visceral tissue + BTO:0001491 + + + + + + + + + + + + + + + + + + + + + + + + + + + A cardiac atrium that is in the left side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve. + Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA] + The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] + https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern + + + + AAO:0010248 + BTO:0001703 + EHDAA2:0000290 + EMAPA:17321 + FMA:7096 + MA:0000075 + NCIT:C12868 + OpenCyc:Mx4runNcs6fqEdudWQACs5b6Bw + OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rDJ89oqgPEdudWQACs5b6Bw + UMLS:C0225844 + VHOG:0000328 + XAO:0003192 + galen:RightAtrium + cardiac right atrium + heart right atrium + right atrium + right atrium of heart + right cardiac atrium + uberon + atrium dextrum + UBERON:0002078 + + + right cardiac atrium + http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg + + + + + A cardiac atrium that is in the left side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve. + + + + + + + Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA] + FMA:7096 + + + + + The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] + 2012-09-17 + VHOG:0000328 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 + + + + + UMLS:C0225844 + ncithesaurus:Right_Atrium + + + + + heart right atrium + MA:0000075 + + + + + right atrium + VHOG:0000328 + + + + + atrium dextrum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve. + Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA] + The chamber of the heart that receives blood from the lungs[XAO:EJS]. + The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] + https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern + + + + AAO:0010247 + BTO:0001702 + EHDAA2:0000275 + EMAPA:17315 + FMA:7097 + MA:0000074 + NCIT:C12869 + OpenCyc:Mx4rkJN1AagEEdudWQACs5b6Bw + OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rDJ89oqgPEdudWQACs5b6Bw + UMLS:C0225860 + VHOG:0000369 + XAO:0003191 + galen:LeftAtrium + atrium sinistrum + cardiac left atrium + heart left atrium + left atrium + left atrium of heart + left cardiac atrium + uberon + UBERON:0002079 + + + left cardiac atrium + http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg + + + + + A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve. + + + + + + + Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA] + FMA:7097 + + + + + The chamber of the heart that receives blood from the lungs[XAO:EJS]. + XAO:EJS + + + + + The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] + 2012-09-17 + VHOG:0000369 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 + + + + + UMLS:C0225860 + ncithesaurus:Left_Atrium + + + + + atrium sinistrum + + + + + + + heart left atrium + MA:0000074 + + + + + left atrium + VHOG:0000369 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A cardiac ventricle that is in the right side of the heart. + The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG] + https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern + In mammals continuous with the pulmonary arteries + + + + BTO:0001630 + CALOHA:TS-0443 + EHDAA2:0000196 + EMAPA:17340 + FMA:7098 + MA:0000093 + NCIT:C12870 + OpenCyc:Mx4rRMlc0KgNEdudWQACs5b6Bw + OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjj1pwpEbGdrcN5Y29ycA + UMLS:C0225883 + VHOG:0000717 + galen:RightVentricle + cardiac right ventricle + right ventricle + right ventricle of heart + uberon + right cardiac ventricle + ventriculus dexter + UBERON:0002080 + + + heart right ventricle + http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg + + + + + + + + + + + + + + + + + + + + + + cjm + + + + + A cardiac ventricle that is in the right side of the heart. + + + + + + The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG] + 2012-09-17 + VHOG:0000717 + VHOG + + + + + + UMLS:C0225883 + ncithesaurus:Right_Ventricle + + + + + right ventricle + FMA:7098 + + + + + right cardiac ventricle + EMAPA:17340 + + + + + ventriculus dexter + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Cardiac chamber in which blood enters the heart. + One of four heart chambers.[TAO] + One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO] + In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] + + + + AAO:0010246 + BTO:0000903 + CALOHA:TS-0437 + EFO:0000277 + EHDAA2:0000154 + EHDAA:1265 + EMAPA:16688 + EV:0100019 + FMA:7099 + GAID:555 + MA:0000073 + MAT:0000496 + MESH:D006325 + NCIT:C12728 + TAO:0000471 + UMLS:C0018792 + VHOG:0000175 + ZFA:0000471 + galen:Atrium + atria + atrium + atrium of heart + cardiac atria + heart atrium + uberon + atrial tissue + UBERON:0002081 + + + + + cardiac atrium + + + + + Cardiac chamber in which blood enters the heart. + + + + + + + One of four heart chambers.[TAO] + 2012-08-14 + TAO:0000471 + TAO + ZFIN:curator + + + + + One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO] + 2012-06-20 + AAO:0010246 + AAO + AAO:BJB + + + + + In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] + 2012-09-17 + VHOG:0000175 + VHOG + + ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428 + + + + + UMLS:C0018792 + ncithesaurus:Cardiac_Atrium + + + + + atria + + + + + + atrium + ZFA:0000471 + + + + + cardiac atria + + + + + + atrial tissue + BTO:0000903 + + + + + + + + + + + + + + + + + + + + + + + + + + + Cardiac chamber through which blood leaves the heart. + A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO] + One of four heart chambers.[TAO] + In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG] + ventricle + + + + AAO:0010249 + BTO:0000862 + CALOHA:TS-0444 + EFO:0000317 + EHDAA2:0004164 + EHDAA:1912 + EMAPA:17331 + EV:0100020 + FMA:7100 + GAID:568 + MA:0000091 + MAT:0000497 + MESH:D006352 + NCIT:C12730 + OpenCyc:Mx4rvVjj1pwpEbGdrcN5Y29ycA + TAO:0000009 + UMLS:C0018827 + VHOG:0000435 + XAO:0003193 + ZFA:0000009 + galen:Ventricle + heart ventricle + lower chamber of heart + ventricle of heart + uberon + UBERON:0002082 + + + + + cardiac ventricle + + + + + + + + + + + Bgee:AN + + + + + Cardiac chamber through which blood leaves the heart. + + + + + + + A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO] + 2012-06-20 + AAO:0010249 + AAO + AAO:BJB + + + + + One of four heart chambers.[TAO] + 2012-08-14 + TAO:0000009 + TAO + ZFIN:curator + + + + + In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG] + 2012-09-17 + VHOG:0000435 + VHOG + + ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428 + + + + + UMLS:C0018827 + ncithesaurus:Cardiac_Ventricle + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A cardiac ventricle that is in the left side of the heart. + Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] + The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG] + https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern + In mammals continuous with aorta + + + + BTO:0001629 + CALOHA:TS-0439 + EHDAA2:0002178 + EMAPA:17337 + FMA:7101 + MA:0000092 + NCIT:C12871 + OpenCyc:Mx4rtW8v46gEEdudWQACs5b6Bw + OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjj1pwpEbGdrcN5Y29ycA + UMLS:C0225897 + VHOG:0000718 + galen:LeftVentricle + cardiac left ventricle + left cardiac ventricle + left ventricle + left ventricle of heart + uberon + ventriculus sinister cordis + UBERON:0002084 + + + heart left ventricle + http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg + + + + + + + + + + + GO + + + + + A cardiac ventricle that is in the left side of the heart. + + + + + + Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] + 2012-09-17 + VHOG:0000718 + VHOG + + + + + + The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG] + 2012-09-17 + VHOG:0000718 + VHOG + + DOI:10.1126/science.1190181 Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010) + + + + + UMLS:C0225897 + ncithesaurus:Left_Ventricle + + + + + left ventricle + FMA:7101 + + + + + ventriculus sinister cordis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A cardiac septum that divides the left and right atria of the heart. + The partition separating the right and left atria of the heart. [TFD][VHOG] + The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] + + + + EHDAA2:0000838 + EHDAA:1896 + EMAPA:17011 + FMA:7108 + MA:0000084 + NCIT:C32818 + OpenCyc:Mx4rpd49nLYEEduAAAACs2IKfQ + OpenCyc:Mx4rwGvku5wpEbGdrcN5Y29ycA + UMLS:C0225836 + VHOG:0000385 + galen:InteratrialSeptum + atrial septum + atrium septum + interatrial septal wall + uberon + UBERON:0002085 + + + interatrial septum + http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png + + + + + A cardiac septum that divides the left and right atria of the heart. + + + + + + The partition separating the right and left atria of the heart. [TFD][VHOG] + 2012-09-17 + VHOG:0000385 + VHOG + + + + + + + The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] + 2012-09-17 + VHOG:0000385 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 + + + + + UMLS:C0225836 + ncithesaurus:Interatrial_Septum + + + + + + + + + + + + + + + + + + + + + + + + + + + + The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. + Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] + The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] + The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] + The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] + axial skeleton + AAO:0000034 + EFO:0000942 + EHDAA2:0000161 + EHDAA:5049 + EMAPA:17214 + EMAPA:37721 + FMA:71221 + MA:0002986 + MAT:0000148 + MIAA:0000148 + TAO:0000317 + VHOG:0000317 + VSAO:0000093 + XAO:0003073 + ZFA:0000317 + post-cranial axial skeleton + uberon + UBERON:0002090 + + + + + previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed. + postcranial axial skeleton + http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton + + + + + The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. + + + ZFA:0000317 + + + + + Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] + 2012-08-14 + VSAO:0000093 + VSAO + PSPUB:0000170 + + + + + The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] + 2012-06-20 + AAO:0000034 + AAO + AAO:LAP + + + + + The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] + 2012-08-14 + TAO:0000317 + TAO + ZFIN:curator + + + + + The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] + 2012-09-17 + VHOG:0000317 + VHOG + + DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011) + + + + + axial skeleton + + FMA:71221 + + + + + EMAPA:37721 + MA:th + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. + Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] + Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] + The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO] + ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. + + + + AAO:0000747 + EFO:0000951 + EMAPA:32729 + FMA:71222 + MA:0000290 + MAT:0000278 + MIAA:0000278 + NCIT:C49477 + UMLS:C0222646 + VHOG:0001666 + VSAO:0000076 + XAO:0003166 + appendicular skeleton + entire appendicular skeleton + paired fin skeleton + uberon + skeleton appendiculare + UBERON:0002091 + + + + + appendicular skeleton + https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton + http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg + + + + + Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. + + + UBERONREF:0000003 + + + + + Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] + 2012-08-14 + VSAO:0000076 + VSAO + + PSPUB:0000170 + + + + + Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] + 2012-08-14 + TAO:0000027 + TAO + TAO:wd + + + + + The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO] + 2012-06-20 + AAO:0000747 + AAO + AAO:LAP + + + + + ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. + FMA + + + + + UMLS:C0222646 + ncithesaurus:Appendicular_Skeleton + + + + + entire appendicular skeleton + + + + + + paired fin skeleton + + + + + + skeleton appendiculare + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + MA:0000085 + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + 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 + + + + + + + + + + + extends to stem tetrapods such as Eusthenopteron + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + FMA + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + GO + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + 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 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 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 + + + + + + + + + + + NIFSTD + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of adipose tissue that is part of the hypodermis, beneath the dermis. + the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156] + UBERON:0008875 + panniculus adiposus + BTO:0004042 + EMAPA:35829 + FMA:74315 + MA:0000473 + fatty layer of subcutaneous tissue + hypodermis fat layer + panniculus adiposus (tela subcutanea) + panniculus adiposus telae subcutaneae + subcutaneous fat layer + uberon + fatty layer of superficial fascia + subcutaneous fat + UBERON:0002190 + + subcutaneous adipose tissue + + + + + A portion of adipose tissue that is part of the hypodermis, beneath the dermis. + + + + + + the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156] + MP:0011156 + + + + + panniculus adiposus + MP:0011156 + + + + + fatty layer of subcutaneous tissue + FMA:74315 + + + + + hypodermis fat layer + MP:0011156 + + + + + panniculus adiposus (tela subcutanea) + FMA:74315 + FMA:TA + + + + + + panniculus adiposus telae subcutaneae + FMA:74315 + FMA:TA + + + + + + subcutaneous fat layer + MP:0011156 + + + + + fatty layer of superficial fascia + FMA:74315 + + + + + subcutaneous fat + BTO:0004042 + + + + + + + + + + + + + + + Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs. + CALOHA:TS-2018 + EHDAA2:0004615 + EMAPA:18765 + FMA:74562 + MA:0000013 + hematolymphoid system + lymphomyeloid complex + uberon + haemolymphoid system + UBERON:0002193 + hemolymphoid system + + + + + + MA + + + + + Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + 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 + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Vasculature that is part of the eye region. + not part of the eye in ZFA. Note this changed to a blood vessel in ZFA + + FMA:74743 + TAO:0007057 + ZFA:0007057 + eye vascular network + ocular blood vessel + ocular vasculature + vascular network of eye + uberon + eye vasculature + optic vasculature + UBERON:0002203 + + + vasculature of eye + + + + + + + + + + + ISBN:0781772214 + + + + + Vasculature that is part of the eye region. + + OBOL:automatic + + + + + not part of the eye in ZFA. Note this changed to a blood vessel in ZFA + ZFA + + + + + eye vascular network + OBOL:automatic + + + + + ocular blood vessel + ZFA:0007057 + + + + + vascular network of eye + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical system that consists of the muscular and skeletal systems. + Anatomical system that provides locomotion and physical support to the organism.[AAO] + There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] + musculoskeletal + + + + + AAO:0010546 + CALOHA:TS-1311 + EMAPA:32714 + EV:0100139 + FMA:7482 + GAID:98 + MA:0002418 + MESH:D009141 + NCIT:C12754 + OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g + UMLS:C0026860 + VHOG:0001275 + VSAO:0000031 + XAO:0000168 + musculo-skeletal system + uberon + UBERON:0002204 + + musculoskeletal system + + + + + + + + + + + check ctenophore + + + + + Anatomical system that consists of the muscular and skeletal systems. + + VSAO:0000031 + VSAO:curator + + + + + Anatomical system that provides locomotion and physical support to the organism.[AAO] + 2012-06-20 + AAO:0010546 + AAO + AAO:EJS + + + + + There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] + 2012-09-17 + VHOG:0001275 + VHOG + + DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009) + + + + + UMLS:C0026860 + ncithesaurus:Musculoskeletal_System + + + + + + + + + + + + + + + + + + + + + + + + + + + Nonsynovial joint in which the articulating bones or cartilages are connected by 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + ZFA + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ. + An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint + fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint + AAO:0010180 + BTO:0001772 + FBbt:00005158 + FMA:77659 + VHOG:0000287 + XAO:0000273 + olfactory organ + olfactory sense organ + olfactory sensory organ + main olfactory organ + primary olfactory organ + uberon + olfactory neuroepithelium + organ olfactus + organum olfactorium + UBERON:0002268 + + olfactory organ + + + + + An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ. + UBERON:cjm + + + + + olfactory organ + BTO:0001772 + + + + + olfactory sensory organ + FBbt:00005158 + + + + + olfactory neuroepithelium + BTO:0001772 + + + + + organ olfactus + BTO:0001772 + + + + + organum olfactorium + BTO:0001772 + + + + + + + + + + + + + + + A composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ). + this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation. + It is essential for governing some of the basic functions of higher organisms, and is one of the phylogenetically oldest portions of the brain. + FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure + + + + BAMS:RET + EMAPA:35188 + FMA:77719 + MA:0003185 + MESH:D012154 + NLX:143558 + brain stem reticular formation + brainstem reticular formation + reticular formation (classical) + reticular formation of the brainstem + uberon + UBERON:0002275 + + reticular formation + http://upload.wikimedia.org/wikipedia/commons/9/9b/Gray701.png + + + + + A composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ). + NeuroNames:1223 + + + + + FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure + FMA + + + + + brain stem reticular formation + NeuroNames:1223 + + + + + brainstem reticular formation + MA:0003185 + + + + + brainstem reticular formation + NeuroNames:1223 + + + + + reticular formation (classical) + NeuroNames:1223 + + + + + reticular formation of the brainstem + NeuroNames:1223 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + ZFA + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A neural nucleus that is part of the brain. + + + EMAPA:35185 + FMA:83840 + MA:0000811 + NCIT:C49346 + UMLS:C1706993 + ZFA:0005575 + brain nucleus + uberon + brain nuclei + UBERON:0002308 + nucleus of brain + + + + + A neural nucleus that is part of the brain. + + + + + + UMLS:C1706993 + ncithesaurus:Brain_Nucleus + + + + + brain nuclei + ZFA:0005575 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue. + + + + BAMS:Scgrey + DHBA:146035048 + EMAPA:35792 + FMA:256580 + MA:0000002 + NCIT:C32696 + NLXANAT:100204 + UMLS:C0475853 + gray matter of spinal cord + gray substance of spinal cord + grey matter of spinal cord + grey substance of spinal cord + spinal cord gray matter + spinal cord grey matter + spinal cord grey substance + substantia grisea medullae spinalis + uberon + UBERON:0002315 + + gray matter of spinal cord + + + + + The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue. + MP:0008503 + + + + + UMLS:C0475853 + ncithesaurus:Gray_Matter_of_the_Spinal_Cord + + + + + gray matter of spinal cord + OBOL:automatic + + + + + gray substance of spinal cord + FMA:256580 + + + + + spinal cord gray matter + OBOL:automatic + + + + + spinal cord grey substance + OBOL:automatic + + + + + substantia grisea medullae spinalis + FMA:256580 + FMA:TA + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. + check the FMA placement here; ncit placement of body cavity here probably not correct + Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. + The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. + In mammals it forms the peritoneal, pleural, and pericardial cavities + UBERON:0000169 + body cavity + + + AEO:0000186 + BTO:0001707 + EHDAA2:0000267 + FBbt:00005060 + FMA:85006 + NCIT:C25444 + RETIRED_EHDAA2:0003186 + TAO:0001438 + UMLS:C0333343 + ZFA:0001438 + galen:BodyCavity + coelomic cavity + coelomic cavity lumen + main body cavity + space of body compartment + ventral body cavity + uberon + celom + coelom + coelome + hemocoel + UBERON:0002323 + + + coelemic cavity lumen + + + + + + + + + + + definitional + + + + + The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. + BTO:0001707 + + + + + Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. + 2012-09-12 + ZFA:0001438 + ZFA + ZFIN:curator + + + + + The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. + 2012-09-12 + BTO:0001707 + BTO + BTO + + + + + body cavity + BTO:0001707 + + + + + UMLS:C0333343 + ncithesaurus:Cavity + + + + + coelomic cavity + EHDAA2:0000267 + + + + + coelomic cavity lumen + EHDAA2:0000267 + + + + + space of body compartment + FMA:85006 + + + + + ventral body cavity + NCBITaxon:7742 + + + + + celom + BTO:0001707 + + + + + coelome + BTO:0001707 + + + + + hemocoel + FBbt:00005060 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any muscle organ that is part of a back [Automatically generated definition]. + EMAPA:35161 + FMA:85216 + MA:0000496 + back muscle + back muscle organ + muscle organ of back + uberon + UBERON:0002324 + muscle of back + + + + + + + + + + + prolog + + + + + Any muscle organ that is part of a back [Automatically generated definition]. + OBOL:automatic + + + + + back muscle organ + OBOL:automatic + + + + + muscle organ of back + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The urethra is a renal system organ that carries urine from the bladder to outside the body. The epithelium is the tubular, planar layer of cells through which the urine passes.. + + EMAPA:31518 + FMA:85275 + MA:0001686 + NCIT:C49309 + UMLS:C1710584 + epithelial tissue of urethra + urethra epithelial tissue + urethra epithelium + uberon + urethral epithelium + urethral plate + urethral seam + UBERON:0002325 + epithelium of urethra + + + + + + GO + + + + + The urethra is a renal system organ that carries urine from the bladder to outside the body. The epithelium is the tubular, planar layer of cells through which the urine passes.. + GO:0061071 + + + + + UMLS:C1710584 + ncithesaurus:Urethra_Epithelium + + + + + epithelial tissue of urethra + OBOL:automatic + + + + + urethra epithelial tissue + OBOL:automatic + + + + + urethral plate + EMAPA:31518 + + + + + urethral seam + EMAPA:31518 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A lamina propria that is part of a urethra [Automatically generated definition]. + EMAPA:37785 + FMA:85276 + MA:0001689 + lamina propria mucosa of urethra + lamina propria mucosae of urethra + urethra lamina propria + urethra lamina propria mucosa + urethra lamina propria mucosae + uberon + urethral lamina propria + UBERON:0002326 + lamina propria of urethra + + + + + A lamina propria that is part of a urethra [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37785 + MA:th + + + + + lamina propria mucosa of urethra + OBOL:automatic + + + + + lamina propria mucosae of urethra + OBOL:automatic + + + + + urethra lamina propria mucosa + OBOL:automatic + + + + + urethra lamina propria mucosae + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + GOTAX:0000352 + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells + ISBN:0073040584 + + + + + + + + + + + BTO + + + + + + + + + + + + + + + + + + + + + + pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + ZFA + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + FMA + + + + + + + + + + + FMA + + + + + + + + + + + FMA + + + + + + + + + + + FMA + + + + + + + + + + + FMA + + + + + + + + + + + FMA + + + + + The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO]. + GO:0003161 + + + + + The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG] + 2012-09-17 + VHOG:0001271 + VHOG + + DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003) + + + + + cardiac conducting system + VHOG:0001271 + + + + + cardiac impulse conducting system + GO:0003161 + + + + + complexus stimulans cordis + FMA:9476 + FMA:TA + + + + + + heart conduction system + GO:0003161 + + + + + impulse conducting system + MA:0000094 + + + + + systema conducente cordis + FMA:9476 + FMA:TA + + + + + + + + + + + + + + + + + + + + + + The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs. + pelvic + MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs + + + + BTO:0001006 + CALOHA:TS-2227 + EFO:0002805 + EMAPA:35931 + EV:0100012 + FMA:9578 + GAID:87 + MA:0000030 + MESH:A01.673 + NCIT:C12767 + OpenCyc:Mx4rvVjiTJwpEbGdrcN5Y29ycA + UMLS:C0030797 + galen:Pelvis + lesser pelvis + pelvic region + pelvis + pelvis region + true pelvis + uberon + UBERON:0002355 + + + + pelvic region of trunk + + + + + The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs. + + + + + + + + MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs + MA + + + + + UMLS:C0030797 + ncithesaurus:Pelvis + + + + + lesser pelvis + FMA:9578 + + + + + pelvis + FMA:9578 + MA:0000030 + + + + + true pelvis + FMA:9578 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Serous membrane which is divided into parietal and visceral serous pericardium. + + + EMAPA:19030 + FMA:9582 + MA:0002739 + serous portion of pericardium + uberon + pericardium serosum + UBERON:0002357 + + serous pericardium + + + + + + + + + + + FMA + + + + + + + + + + + FMA + + + + + Serous membrane which is divided into parietal and visceral serous pericardium. + + + + + + + serous portion of pericardium + FMA:9582 + + + + + pericardium serosum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any skeletal muscle that is part of the head region. + UBERON:0003899 + + AAO:0000107 + BTO:0000021 + EFO:0003524 + EHDAA2:0000322 + EMAPA:18172 + FMA:9616 + MA:0000578 + ZFA:0001652 + cephalic muscle + cephalic musculature + head muscle + head muscle organ + muscle of head + muscle organ of adult head + muscle organ of head + musculus caput + adult head muscle organ + uberon + cranial muscle + head muscles + UBERON:0002376 + + + + defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984) + cranial muscle + + + + + + + + + + + + + + + + + + + + + + EHDAA2-abduced + + + + + Any skeletal muscle that is part of the head region. + + + + + + cephalic muscle + ZFA:0001652 + + + + + head muscle + MA:0000578 + + + + + head muscle organ + OBOL:automatic + + + + + muscle of head + FMA:9616 + + + + + muscle organ of adult head + OBOL:automatic + + + + + muscle organ of head + OBOL:automatic + + + + + adult head muscle organ + OBOL:automatic + + + + + cranial muscle + ZFA:0001652 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any muscle that is part of the cervical (neck) region. + + EMAPA:36050 + FMA:9617 + GAID:149 + MA:0000587 + MESH:D009334 + NCIT:C33163 + UMLS:C0027532 + muscle organ of neck + muscle organ of neck (volume) + neck (volume) muscle organ + neck muscle + neck muscle organ + uberon + UBERON:0002377 + + + muscle of neck + + + + + + + + + + + prolog + + + + + Any muscle that is part of the cervical (neck) region. + + + + + + UMLS:C0027532 + ncithesaurus:Neck_Muscle + + + + + muscle organ of neck + OBOL:automatic + + + + + muscle organ of neck (volume) + OBOL:automatic + + + + + neck (volume) muscle organ + OBOL:automatic + + + + + neck muscle organ + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis. + + + + BTO:0001261 + EMAPA:35103 + FMA:9620 + GAID:89 + MA:0000520 + MESH:D000009 + NCIT:C32040 + OpenCyc:Mx4rvlygNJwpEbGdrcN5Y29ycA + UMLS:C0000739 + abdomen muscle + abdomen muscle organ + abdominal muscle + abdominal wall muscle + muscle organ of abdomen + uberon + abdominal wall musculature + UBERON:0002378 + + + muscle of abdomen + + + + + + + + + + + prolog + + + + + Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis. + + + + + + UMLS:C0000739 + ncithesaurus:Abdominal_Muscle + + + + + abdomen muscle organ + OBOL:automatic + + + + + muscle organ of abdomen + OBOL:automatic + + + + + abdominal wall musculature + EMAPA:35103 + + + + + + + + + + + + + + + + + + + + + Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. + One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] + Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] + Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] + MA also has set of connective tissues + + + + + AAO:0000098 + BTO:0000421 + CALOHA:TS-2009 + EFO:0000952 + EMAPA:35251 + FMA:9640 + GAID:100 + MA:0000011 + MAT:0000301 + MESH:D003238 + MIAA:0000301 + NCIT:C12374 + OpenCyc:Mx4rv-aBgZwpEbGdrcN5Y29ycA + TAO:0001641 + UMLS:C0009780 + VSAO:0000017 + XAO:0001017 + ZFA:0001632 + galen:ConnectiveTissue + portion of connective tissue + textus connectivus + uberon + Bindegewebe + UBERON:0002384 + + + + connective tissue + + + + + Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. + + + GO_REF:0000034 + PSPUB:0000170 + VSAO:0000017 + + + + + One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] + 2012-06-20 + AAO:0000098 + AAO + AAO:LAP + + + + + Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] + 2012-08-14 + TAO:0001641 + TAO + TAO:wd + + + + + Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] + 2012-08-14 + VSAO:0000017 + VSAO + GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 + PSPUB:0000170 + + + + + MA also has set of connective tissues + MA + + + + + UMLS:C0009780 + ncithesaurus:Connective_Tissue + + + + + portion of connective tissue + FMA:9640 + + + + + Bindegewebe + BTO:0000421 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. + One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] + + + + AAO:0000306 + AEO:0000122 + CALOHA:TS-0642 + EHDAA2:0003122 + EMAPA:32715 + FMA:9641 + MA:0002437 + MESH:D009132 + NCIT:C12435 + UMLS:C2328219 + galen:MuscleTissue + muscular tissue + portion of muscle tissue + textus muscularis + uberon + UBERON:0002385 + + Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach. + muscle tissue + + + + + Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. + + + GO:0060537 + + + + + One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] + 2012-06-20 + AAO:0000306 + AAO + AAO:LAP + + + + + UMLS:C2328219 + ncithesaurus:Muscle_Tissue + + + + + muscular tissue + + + + + + portion of muscle tissue + FMA:9641 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 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 + + + + + + Wikipedia + + + + + 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 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + MP + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]. + Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO] + [In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO] + + EMAPA:36615 + TAO:0001644 + ZFA:0001635 + uberon + intramembranous bones + membrane bone + UBERON:0002514 + intramembranous bone + + + + + + VSAO + + + + + Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]. + + + GO:0001957 + + + + + Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO] + 2012-08-14 + TAO:0001644 + TAO + TAO:wd + + + + + [In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO] + 2012-09-06 + TAO:0001644 + TAO + Curator + + + + + intramembranous bones + ZFA:0001635 + + + + + + membrane bone + AEO:0000085 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + An organ that functions as a secretory or excretory organ. + glandular + UBERON:MIAA_0000021 + + + + AAO:0000212 + AEO:0000096 + BTO:0000522 + EFO:0000797 + EHDAA2:0003096 + EHDAA:2161 + EHDAA:4475 + EHDAA:6522 + EMAPA:18425 + FBbt:00100317 + FMA:7146 + FMA:86294 + HAO:0000375 + MA:0003038 + MAT:0000021 + MIAA:0000021 + NCIT:C13319 + OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA + UMLS:C1285092 + WikipediaCategory:Glands + galen:Gland + glandular organ + uberon + Druese + glandula + UBERON:0002530 + + + + gland + http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png + + + + + An organ that functions as a secretory or excretory organ. + MGI:csmith + MP:0002163 + + + + + UMLS:C1285092 + ncithesaurus:Gland + + + + + glandular organ + + + + + + Druese + BTO:0000522 + + + + + glandula + + + + + + + glandula + BTO:0000522 + + + + + + + + + + + + + + + In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]. + MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class + In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] + + BTO:0004593 + FMA:296704 + MAT:0000067 + MIAA:0000067 + VHOG:0000243 + epiblast + uberon + blastocyst + ectoblast + epiblastus + primitive ectoderm + UBERON:0002532 + + + + + epiblast (generic) + http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png + + + + + In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]. + + ZFIN:curator + + + + + In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] + 2012-09-17 + VHOG:0000243 + VHOG + + DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009) + + + + + epiblast + VHOG:0000243 + + + + + ectoblast + MP:0003886 + + + + + epiblastus + + + + + + + primitive ectoderm + VHOG:0000243 + + + + + + + + + + + + + + + + + + + + + + + + + + + The rapidly proliferating mass of cells at the caudal extremity of the embryo; remnant of the primitive node. + See notes from https://github.com/obophenotype/uberon/wiki/The-neural-crest + Rapidly proliferating mass of cells at the caudal extremity of the embryo. Its formation is reflected in a caudal carving of the posterior portion of the archenteric canal at NF stage 22. With its further outgrowth, the postanal gut primordium becomes stretched. Its lumen is in broad communication with the hindgut at NF stage 25.[AAO] + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (5) a larva or embryo with a postanal tail.[well established][VHOG] + AAO:0011104 + BTO:0001445 + EFO:0002748 + EHDAA2:0001976 + EHDAA:1595 + EMAPA:16580 + MAT:0000070 + MIAA:0000070 + TAO:0000077 + VHOG:0000201 + XAO:0000107 + ZFA:0000077 + tail bud + tailbud + uberon + end bud + tail bud mesenchyme + UBERON:0002533 + + + + + post-anal tail bud + + + + + The rapidly proliferating mass of cells at the caudal extremity of the embryo; remnant of the primitive node. + BTO:0001445 + + + + + Rapidly proliferating mass of cells at the caudal extremity of the embryo. Its formation is reflected in a caudal carving of the posterior portion of the archenteric canal at NF stage 22. With its further outgrowth, the postanal gut primordium becomes stretched. Its lumen is in broad communication with the hindgut at NF stage 25.[AAO] + 2012-06-20 + AAO:0011104 + AAO + ISBN:0815318960 + OMD:tail+bud + + + + + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (5) a larva or embryo with a postanal tail.[well established][VHOG] + 2012-09-17 + VHOG:0000201 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 + + + + + tail bud + ZFA:0000077 + + + + + end bud + BTO:0001445 + + + + + tail bud mesenchyme + ZFA:0000077 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches. + One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] + A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG] + Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering + + + + AAO:0010359 + BTO:0001785 + EFO:0000959 + EHDAA:571 + EMAPA:16117 + FMA:293015 + GAID:1292 + MAT:0000242 + MESH:A16.254.160 + MIAA:0000242 + NCIT:C34249 + TAO:0001306 + UMLS:C0080322 + VHOG:0000155 + XAO:0000096 + ZFA:0001306 + pharyngeal arches + branchial arch + uberon + arcus pharyngei + visceral arch + UBERON:0002539 + + + + + pharyngeal arch + http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png + + + + + + EHDAA2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches. + + + ZFA:yb + + + + + One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] + 2012-06-20 + AAO:0010359 + AAO + NLM:branchial+arch + + + + + A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG] + 2012-09-17 + VHOG:0000155 + VHOG + + DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) + + + + + UMLS:C0080322 + ncithesaurus:Pharyngeal_Arch + + + + + pharyngeal arches + + + + + + branchial arch + BTO:0001785 + MP:0002884 + + + + + arcus pharyngei + + + + + + + + + + + + + + + + + + + + + + + Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. + Do not merge with neurogenic placode + Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons + The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass + ectodermal placode + placode + AAO:0010466 + EFO:0001650 + FMA:293966 + MAT:0000369 + MIAA:0000369 + XAO:0000305 + ectodermal cranial placode + uberon + cranial placodes + UBERON:0002546 + + cranial placode + + + + + + cjm + + + + + + + + + + + + + + + + + Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. + + + + + + + + + + Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons + + + + + + ectodermal placode + + FMA:293966 + + + + + + placode + + + + + + ectodermal cranial placode + UBERON:cjm + + + + + cranial placodes + XAO:0000305 + + + + + + + + + + + + + + + + Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. + cavity + BIRNLEX:1011 + EMAPA:37442 + FMA:67552 + MA:0002447 + NCIT:C34007 + galen:Cavity + uberon + UBERON:0002553 + + anatomical cavity + + + + + Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. + FMA:67552 + + + + + EMAPA:37442 + MA:th + + + + + + + + + + BIRNLEX:1019 + FMA:12237 + cavity of organ + uberon + UBERON:0002558 + + organ cavity + + + + + cavity of organ + FMA:12237 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The cavity that is enclosed by the central nervous system. In vertebrates this is the cavity that includes as parts ventricular cavities and the central canal of the spinal cord that develops from the lumen of the neura tube. + + BIRNLEX:1029 + FMA:75007 + cavity of neuraxis + cavity of ventricular system of neuraxis + neuraxis cavity + neuraxis lumen + uberon + UBERON:0002561 + lumen of central nervous system + + + + + The cavity that is enclosed by the central nervous system. In vertebrates this is the cavity that includes as parts ventricular cavities and the central canal of the spinal cord that develops from the lumen of the neura tube. + + + + + + + + + + + + cavity of neuraxis + FMA:75007 + + + + + cavity of ventricular system of neuraxis + FMA:75007 + + + + + neuraxis cavity + FMA:75007 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. + + + BIRNLEX:1167 + FMA:55676 + NCIT:C13031 + UMLS:C0445620 + anatomical structure of brain + biological structure of brain + brain anatomical structure + brain biological structure + brain part + neuraxis segment + neuroanatomical region + segment of brain + uberon + UBERON:0002616 + + regional part of brain + + + + + Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. + BIRNLEX:1167 + + + + + UMLS:C0445620 + ncithesaurus:Brain_Part + + + + + anatomical structure of brain + OBOL:automatic + + + + + biological structure of brain + OBOL:automatic + + + + + brain anatomical structure + OBOL:automatic + + + + + brain biological structure + OBOL:automatic + + + + + neuraxis segment + FMA:55676 + + + + + segment of brain + BIRNLEX:1167 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A spinal cord segment that adjacent_to a cervical region. + + + + + BIRNLEX:1499 + FMA:71166 + MA:0003081 + NCIT:C12892 + UMLS:C0581619 + UMLS:C1278837 + cervical segment of spinal cord + cervical segments of spinal cord [1-8] + cervical spinal cord + pars cervicalis medullae spinalis + segmenta cervicalia medullae spinalis [1-8 + uberon + UBERON:0002726 + cervical spinal cord + + + + + A spinal cord segment that adjacent_to a cervical region. + OBOL:automatic + + + + + UMLS:C0581619 + BIRNLEX:1499 + + + + + UMLS:C0581619 + ncithesaurus:Cervical_Spinal_Cord + + + + + UMLS:C1278837 + BIRNLEX:1499 + + + + + cervical segment of spinal cord + FMA:71166 + + + + + cervical segments of spinal cord [1-8] + FMA:71166 + + + + + cervical spinal cord + FMA:71166 + + + + + pars cervicalis medullae spinalis + FMA:71166 + FMA:TA + + + + + + segmenta cervicalia medullae spinalis [1-8 + FMA:71166 + FMA:TA + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A 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 + + + + + + FMA + + + + + A nucleus of brain that is part of a trigeminal nuclear complex. + OBOL:automatic + + + + + massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA. + GO + https://github.com/obophenotype/mouse-anatomy-ontology/issues/58 + + + + + UMLS:C0040999 + ncithesaurus:Trigeminal_Nucleus + + + + + nucleus of trigeminal nuclear complex + FMA:71247 + + + + + trigeminal V nucleus + MA:0001028 + + + + + trigeminal nuclear complex nucleus + FMA:71247 + + + + + trigeminal nucleus + FMA:71248 + + + + + nucleus mesencephalicus nervi trigemini + BTO:0001074 + + + + + nucleus mesencephalicus trigeminalis + BTO:0001074 + + + + + nucleus tractus mesencephali nervi trigeminalis + BTO:0001074 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A sensory epithelium that is part of a gustatory system. + + FMA:62412 + uberon + UBERON:0002926 + gustatory epithelium + + + + + + + + + + + NIFSTD + + + + + A sensory epithelium that is part of a gustatory system. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133). + involved in the initiation of REM sleep [Wikipedia:Pontine_tegmentum] + + + + + BAMS:PTg + BIRNLEX:923 + DHBA:12416 + FMA:71108 + HBA:9135 + UMLS:C0228426 + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=557 + dorsal pons + dorsal portion of pons + tegmental portion of pons + tegmentum of pons + tegmentum pontis + uberon + pars dorsalis pontis + pars posterior pontis + tegmentum pontis + UBERON:0003023 + + pontine tegmentum + Brainstem:Abducens.png + + + + + Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133). + BIRNLEX:923 + + + + + UMLS:C0228426 + BIRNLEX:923 + + + + + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=557 + BIRNLEX:923 + + + + + dorsal portion of pons + FMA:71108 + + + + + tegmental portion of pons + FMA:71108 + + + + + tegmentum of pons + FMA:71108 + + + + + tegmentum pontis + FMA:71108 + FMA:TA + + + + + + pars dorsalis pontis + NeuroNames:557 + + + + + + pars posterior pontis + NeuroNames:557 + + + + + + tegmentum pontis + + + + + + + + + + + + + + + + + A wall, dividing a cavity or structure into smaller ones[WP]. + septal + + AAO:0011127 + FMA:86461 + OpenCyc:Mx4rrqot_on_EdaAAAACs0uFOQ + septa + uberon + UBERON:0003037 + + general anatomical term in FMA + septum + + + + + A wall, dividing a cavity or structure into smaller ones[WP]. + + + + + + septa + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The thoracic nerves are the spinal nerves emerging from the thoracic vertebrae. [WP,unvetted]. + + + + + BIRNLEX:966 + FMA:71167 + MA:0003082 + NCIT:C12894 + UMLS:C0581620 + pars thoracica medullae spinalis + segmenta thoracica medullae spinalis [1-12] + thoracic region of spinal cord + thoracic segment of spinal cord + thoracic segments of spinal cord [1-12] + thoracic spinal cord + uberon + UBERON:0003038 + + thoracic spinal cord + http://upload.wikimedia.org/wikipedia/commons/6/68/Gray820.png + + + + + The thoracic nerves are the spinal nerves emerging from the thoracic vertebrae. [WP,unvetted]. + + + + + + UMLS:C0581620 + BIRNLEX:966 + + + + + UMLS:C0581620 + ncithesaurus:Thoracic_Spinal_Cord + + + + + pars thoracica medullae spinalis + FMA:71167 + FMA:TA + + + + + + segmenta thoracica medullae spinalis [1-12] + FMA:71167 + FMA:TA + + + + + + thoracic region of spinal cord + FMA:71167 + + + + + thoracic segment of spinal cord + FMA:71167 + + + + + thoracic segments of spinal cord [1-12] + FMA:71167 + + + + + thoracic spinal cord + FMA:71167 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + 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 + + + + + + + + + + + ISBN:0073040584 + + + + + + + + + + + ISBN:0073040584 + + + + + 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 + + + + + + + + + + + + + + + + + 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 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 + + + + + + + + + + + + + + + + + + + + + - - + + - 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 + 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 - camera-type eye plus associated structures - eyes - orbital part of face - orbital region - UBERON:0000019 + eye cup + eyecup + ocular cup + ophtalmic cup + UBERON:0003072 - - camera-type eye + optic cup - + - - + + - definitional + ZFA - - - An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid. - - GO:0043010 + + + + + + + + + ZFA - - - A cavitated compound organ that transduces light waves into neural signals.[TAO] - 2012-08-14 - TAO:0000107 - TAO - TAO:wd + + + 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 - + - 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] + (...) 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:0000275 + VHOG:0000167 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 + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - + - UMLS:C1280202 - BIRNLEX:1169 - - - - - regio orbitalis - FMA:54448 - FMA:TA - + UMLS:C0231109 + ncithesaurus:Optic_Cup - + - eyes - TAO:0000107 - + eyecup + BTO:0005351 - + - orbital part of face - FMA:54448 + ocular cup + VHOG:0000167 - + - orbital region - FMA:54448 + ophtalmic cup + BTO:0005351 - + - - + + + + + + + + + + + + + + + + + - + - 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 + + + + + + + + + + + + + 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 - Sinnesorgan - sensor - UBERON:0000020 + lens placodes + placoda lentis + UBERON:0003073 + + - sense organ - http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png + + lens placode + http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png - - - An organ that is capable of transducing sensory stimulus to the nervous system. - - - - - - - UMLS:C0935626 - ncithesaurus:Organ_of_the_Special_Sense + + + + NCBIBook:NBK53175 - - - organ of sense organ system - OBOL:accepted + + + + + + + + + ZFA - - - organ of sensory organ system - OBOL:accepted + + + A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]. + + ZFIN:curator - - - organ of sensory system - OBOL:accepted + + + Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0000122 + TAO + ZFIN:curator - - - sense organ system organ - 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:0000166 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - - - sensory organ system organ - OBOL:automatic + + + 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 - - - sensory system organ - OBOL:accepted + + + UMLS:C1517770 + ncithesaurus:Lens_Placodes - - - sensillum - WBbt:0006929 + + + lens placodes + ZFA:0000122 + - + - Sinnesorgan - BTO:0000202 + placoda lentis + + - + - - + + + - - + + - 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 + + + + + + + + + + + + + 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 - appendages - extremitaet - extremity - limbs/digits/tail - UBERON:0000026 - + Leydig's duct + archinephric duct + ductus mesonephricus; ductus Wolffi + renal duct + UBERON:0003074 - appendage + + mesonephric duct + http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + + + + GO + + + + + + + + + + + EHDAA2 + + + - Major subdivision of an organism that protrudes from the body[DOS, CARO]. - CARO:DOS + 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 - + - 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 + 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 - + - Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. - GO:0048736 + 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 + - - - EMAPA:37283 - MA:th + + + (...) 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:C0598782 - ncithesaurus:Appendage + UMLS:C0043204 + ncithesaurus:Mesonephric_Duct + + + + + Wolffian duct + + GOC:yaf + ZFA:0000546 - + - appendages - XAO:0000218 - + Leydig's duct + - + - extremitaet - BTO:0001492 + archinephric duct + + VHOG:0000082 - + - limbs/digits/tail - MP:0000001 + ductus mesonephricus; ductus Wolffi + + - + - - + + + + + + - - + + - - + + - - + + - 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 + + + + + + + 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 - tunica propria - UBERON:0000030 + lamina neuralis + presumptive central nervous system + UBERON:0003075 + - lamina propria - GI:Organization.svg + + neural plate + Neural:Crest.png - - - 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. - + + + + GO - - - UMLS:C1179187 - ncithesaurus:Lamina_Propria + + + + + + + + + GOTAX:0000352 - - - tunica propria - BTO:0002330 - - - - - - - - - + + + - - + + - - 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 - + + Wikipedia + - - - The head is the anterior-most division of the body [GO]. - - GO:0060322 + + + + + + + + + Bgee:AN - - - 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 + + + 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 - + - Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] + 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:0001114 + TAO:0000132 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] + (...) 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:0001644 + VHOG:0000068 VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82 + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - + - UMLS:C0018670 - BIRNLEX:1230 + UMLS:C0920623 + ncithesaurus:Neural_Plate - - - UMLS:C0018670 - ncithesaurus:Head + + + 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 + - - - head (volume) - FMA:7154 + + + + lexical - - - cephalic area - SPD:0000016 + + + (...) 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 - + - - - + + + + - + - - + + - - + + - 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 + + + + + + + + + + + + + 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 - serosa - UBERON:0000042 + mesoderma paraxiale + UBERON:0003077 + - 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 + paraxial mesoderm + http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + + + + EHDAA2 + + + + + + + + + + + Bgee:AN + + + - multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. - - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. + + GO:0048339 - + - A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] - 2012-08-14 - TAO:0005425 - TAO - + 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 - - - 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] - + + + 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) - + - 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 + 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:C0036760 - ncithesaurus:Serosa + UMLS:C1284009 + ncithesaurus:Paraxial_Mesoderm - + - tunica serosa - FMA:9581 - + paraxial mesenchyme + + + ZFA:0000255 - + - wall of serous sac - FMA:9581 + somitic mesoderm + ISBN:9780878932504 - + - serosa - - - - - - - - - - An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. - - TGMA:0000729 - uberon - UBERON:0000047 - - - simple eye - - - - - An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. - - - - - - - - - - - - - - - - A tubular structure that contains, conveys body fluid, such as blood or lymph. - uberon - UBERON:0000055 - - - vessel - - - - - A tubular structure that contains, conveys body fluid, such as blood or lymph. - + mesoderma paraxiale + + - - - - - - - - - - - - - - - - - - - + + + + - - + + - - + + - - + + - - - - - 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 + + + + + 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 - - - - - ureter - Urinary:system.svg + epibranchial placode - + + + + NCBIBook:NBK53175 + ZFA + + + - - + + - GO + ZFA - - - Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. - - GO:0090189 + + + + + + + + + EHDAA2-abduced - - - 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 + + + 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 - + - 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] + 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:0000605 + VHOG:0000117 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] + 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:0000605 + VHOG:0000117 VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 + DOI:10.1046/j.1469-7580.2001.19910133.x Graham A, The development and evolution of the pharyngeal arches. J Anat (2001) - - - UMLS:C0041951 - ncithesaurus:Ureter + + + 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 + + + + - metanephric duct - ISBN:0073040584 - VHOG:0000605 + 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 + + + + + + + + + + + - - + + - - + + - - + + - 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 + + + + + + + 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 - UBERON:0000057 - - - + lateral plate + lateral plate mesenchyme + mesoderma laminae lateralis + UBERON:0003081 - urethra - Female:anatomy.png + lateral plate mesoderm + http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + + + + EHDAA2 + + + - - + + - pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra - Wikipedia + EHDAA2 + VHOG - + - + - Wikipedia + EHDAA2 + XAO - + - 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 + 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 - - - UMLS:C0041967 - ncithesaurus:Urethra + + + 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 - - - - - - - - - - - - - - - - - - - - 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. - - + + + 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 tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. - ZFA:0005171 + + + 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:C0687028 - ncithesaurus:Duct + UMLS:C1517749 + ncithesaurus:Lateral_Mesoderm - + + + LPM + ZFA:0000121 + + + + + + lateral mesoderm + GO:0048368 + + + - ducts - XAO:0004000 - + lateral plate mesenchyme + EHDAA2:0000919 + + + + + mesoderma laminae lateralis + + - + - - - + + + - - + + - - + + - + - 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 - - - + 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 - large intestine + + + myotome + http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - - cjm + + AEO - - - A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. - - ISBN:0073040584 + + + + + + + + + WP + ZFA - - - 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 + + + + + + + + + EHDAA2-abduced - - - UMLS:C0021851 - ncithesaurus:Large_Intestine + + + A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells. + AEO:0001018 - - - 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 - + + + Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0001056 + TAO + ZFIN:curator + - - - Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. - FMA:82482 + + + 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) - - - in FMA, serosa is a wall - FMA + + + UMLS:C1513802 + ncithesaurus:Myotome_Region - + - wall of organ - FMA:82482 + myomeres + TAO:0001056 + - + - organ wall - FMA:82482 + myotomus + + - + - - + + + - - + + - - + + - 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 + 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 - + + + + + + + + + ZFA + + + - 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 + 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 + + + - connected biological structure - CARO:0000003 + TNC + XAO:0000319 + - + - - + + + - + - - + + - - + + - - 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 + + + + + + + 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 - anatomical unit - body organ - element - UBERON:0000062 - - organ + cardiac field + fused heart primordium + UBERON:0003084 + + heart primordium - - - Anatomical structure that performs a specific function or group of functions [WP]. - + + + + Obol - - - 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 + + + + + + + + + ZFA - - - UMLS:C0178784 - ncithesaurus:Organ + + + + + + + + + ZFA - - - element - + + + + + + + + + XAO - - - - - - - - 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. - + 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 - + - 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 + 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 - + - 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 + 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 - - - organ region with fixed fiat boundary - FMA:86140 + + + relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] + 2012-08-14 + TAO:0000028 + TAO - - - organ segment - FMA:86140 + + + UMLS:C1514450 + ncithesaurus:Primordium_of_the_Heart - + - segment of organ - FMA:86140 + cardiac field + ZFA:0000028 - + - - + + + + + + + + + + + + + + + + + + + - + - 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 - - - - - - - - - + - - + + - - - - - 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 + + + + + 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 - fully formed stage - https://github.com/obophenotype/uberon/issues/566 + + caudal artery - + - The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. - + 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 - + - - + + + - - + + - - + + - - 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 + 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 - embryogenesis - UBERON:0000068 - embryo stage + sclerotomus + UBERON:0003089 + + + + sclerotome + http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + + + + EHDAA2 + + + + + + EHDAA2 + + + + + + + + + + + VHOG:0000680 + + + + + + + + + + + ZFA + + + - A life cycle stage that starts with fertilization and ends with the fully formed embryo. - + 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 + + - + - - + + + + - - + + - End of the life of an organism. - ncit:Death is an outcome - XAO:0000437 - XtroDO:0000085 + + + + + + + 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 - death - UBERON:0000071 - death stage + crista neuralis cranialis + head crest + head neural crest + UBERON:0003099 + + + + cranial neural crest - + - End of the life of an organism. - XAO:0000437 + 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 - - - ncit:Death is an outcome - ncit + + + 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 + + - + - - - - - - - - - - - - - - - - - - - - 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 + + + 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 - + - Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. - BIRNLEX:1157 + Gonochoristic organism that can produce female gametes. + CARO:0000028 - - - UMLS:C1518256 - ncithesaurus:Nervous_System_Part + + + female human body + FMA:67812 + - - - part of nervous system - BIRNLEX:1157 + + + female + TAO:0000303 - + - - + + + - + - - + + + + + + + - 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 + 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 - UBERON:0000076 - - external ectoderm - http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png + surface feature + surface region + surface structures + UBERON:0003102 + + surface structure - - - - EHDAA2 - - - - - - - - - - - EHDAA2 - - - + - The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. - MGI:anna - MP:0012532 + Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. + + - - - UMLS:C1515087 - ncithesaurus:Surface_Ectoderm + + + Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA] + 2012-08-14 + TAO:0000292 + TAO + ZFIN:curator - + - surface ectoderm - MP:0012532 + anatomical surface feature + EHDAA2:0003010 + + + + + surface structures + ZFA:0000292 + - + - - - - - - - - - - - - - - - - - - - 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 + + + + + + + + + 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 - UBERON:0000077 - - mixed endoderm/mesoderm-derived structure + organ + UBERON:0003103 + + + compound organ - + - An anatomical structure that develops from the endoderm and the mesoderm. - + 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 - + - + - - - - - - - - - + - - + + - - - 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 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 + + + + + + + + + + + + + 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 - amphibian adult kidney - corpus Wolffi - middle kidney - opisthonephros - opisto nephros - opistonephros - UBERON:0000080 - - + mesenchyma + UBERON:0003104 + - mesonephros - http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png + mesenchyme + http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg - + - 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 + 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 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 - + + + + A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0000393 + TAO + ZFIN:curator - + - Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO] + 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:0010384 + AAO:0010427 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 + AAO:EJS - + - 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 + UMLS:C0162415 + ncithesaurus:Mesenchyme - + - opistonephros - + mesenchyma + + - + - - - - - - - - - - - - - - - + + - - + + - - + + - - + + - 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 + 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 - definite kidney - definitive kidney - hind kidney - metanephric kidney - UBERON:0000081 - - - metanephros + dermal bone cranium + dermal part of skull + dermal skull bones + roofing bones of the skull + skull exoskeleton + UBERON:0003113 + dermatocranium - + - - + + - definitional + ZFA - - - - - - - - - GO + + + Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified]. + + ZFA:0000863 - - - - - - - - - ISBN:9780878932504 + + + + ISBN:0073040584 - + + + 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 + + + - 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 + The third branchial arch contributes to the development of the hyoid bone, stylopharyngeus muscle, inferior parathyroid gland, and thymus. + MP:0006339 - + - 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 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 - + - 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] + 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:0000039 + VHOG:0000298 VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 + 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:C0231049 - ncithesaurus:Metanephros + + + in XAO, called branchial arch 1 and df VP3 + XAO - + - metanephron - BTO:0001543 + first gill arch + ZFA:0001606 + - + + + gill arch 1 + ZFA:0001606 + + + + - definite kidney - BTO:0001543 + 3rd arch + EHDAA2:0000069 - + - definitive kidney - BTO:0001543 + 3rd visceral arch + VHOG:0000298 - + - hind kidney - BTO:0001543 + branchial arch 1 + AAO:0010365 + ZFA:0001606 + - + - metanephric kidney - VHOG:0000039 + first branchial arch + ZFA:0001606 + - + - - - - - - - - - - - - - - - - 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 + + + 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 - + - A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]. - + 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 - + - 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 - - + 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 - + - 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] + 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:0000500 + VHOG:0000299 VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639 + 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 + + + + - renal tubules - VHOG:0000500 - + 4th arch + EHDAA2:0000086 - + - tubuli mesonephrici - - + branchial arch 2 + AAO:0010366 + ZFA:0001607 + + + + + + fourth visceral arch + VHOG:0000299 + + + + + second branchial arch + ZFA:0001607 + - + - - - - - - - - - - - - - - - - - - - - - - - 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 + + + 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 - ureteric bud + pharyngeal arch 6 - - - - EHDAA2 - - - - - - - - - - - EHDAA2 - - - - - - - - - - - ISBN:9780878932504 - - - + - An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP] - - MP:0010979 + The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles. + MP:0006347 - + - 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] + 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:0000541 + 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) - - - 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 + + + 6th arch + EHDAA2:0004075 - - - 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 + + + gill arch 4 + ZFA:0001609 - - - UMLS:C1284058 - ncithesaurus:Metanephric_Diverticulum + + + visceral arch 6 + ZFA:0001609 - + - diverticulum - BTO:0001646 + 6th pharyngeal arch + VHOG:0001205 - + - diverticulum metanephricum - - + 6th visceral arch + VHOG:0001205 - + - gemma ureterica - - + branchial arch 4 + AAO:0010368 + ZFA:0001609 + - + - metanephric bud - BTO:0001646 + fourth branchial arch + - + - metanephric diverticulum - + sixth pharyngeal arch + VHOG:0001205 - + - ureteric diverticulum - VHOG:0000541 + sixth visceral arch + XAO:0000453 - + - - + + + + + + + + + + + + + - - + + - 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 + 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 - - - - - - - - - FMA-def + + + The vessels formed within the first pair of branchial arches in embryogenesis. + MP:0010355 - - - 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 + + + 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 - - - - - - - - - - - - - - - - - - - - - - - - - - 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. - + + + 1st arch artery + EMAPA:16685 - - - - - - - - - - - - - - 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. - + + + 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 - + - - + + + + + + + + + + + + + - + - - - - - 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 - + + + + + 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 - + - A stage at which the organism is a single cell produced by means of sexual reproduction. - + The vessels formed within the third pair of branchial arches in embryogenesis. + MP:0006356 - - - 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 + + + 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 + + + - fertilized egg stage - BTO:0000854 + 3rd arch artery + EHDAA2:0000070 - + + + AA3 + ZFA:0005007 + + + + + aortic arch 3 + ZFA:0005007 + + + + + carotid arch + + + + + + third aortic arch + XAO:0000344 + + + - one-cell stage - VHOG:0000745 + 3rd aortic arch artery + EMAPA:16687 - + - zygote - VHOG:0000745 + 3rd branchial arch artery + EMAPA:16687 - + - zygotum - - + 3rd pharyngeal arch artery + EMAPA:16687 - + - - + + + + + + + + + + + + + - - - - - - - + - 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 + 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 - UBERON:0000107 - - cleavage stage + 4th aortic arch artery + 4th branchial arch artery + 4th pharyngeal arch artery + systemic arch + UBERON:0003121 + + + proximal right subclavian + pharyngeal arch artery 4 - + - 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 + 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 - + - - + + + + + + + + + + + + + - - - - - - - + - 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 + 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 - UBERON:0000108 - - blastula stage - http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png + 6th aortic arch artery + 6th branchial arch artery + 6th pharyngeal arch artery + pulmonary arch + UBERON:0003123 + + + pharyngeal arch artery 6 - + - 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. - + 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 - + - - + + - - - - - - - + - 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 + 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 - gastrula stage + + + + cranium - + - - - - - - - BILS + + FMA-inferred - + - 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 + Upper portion of the skull that excludes the mandible (when present in the organism). + + - - - blastocystis trilaminaris stage - + + + 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 - - - trilaminar blastocyst stage - + + + The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton + WP - - - trilaminar blastoderm stage - + + + bones of cranium + FMA:71325 - - - trilaminar disk stage - + + + ossa cranii + FMA:71325 + FMA:TA + - - - trilaminar germ stage - + + + set of bones of cranium + FMA:71325 - + - trilaminar stage - + calvarium + BTO:0001328 - + - - + + + - + - - + + - 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. - - - - - - - - - - - + + - + 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 - UBERON:0000153 - anterior region of body + cranial skeleton + skeletal system of head + UBERON:0003129 + + + skull - - - - lexical + + + + FMA - - - - - - - - uberon - UBERON:0000154 - posterior region of body - - - - - lexical + + + 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 - + - - + + + + + + + + + + + + + + - - + + - 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 + + + + + + + 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 - UBERON:0000158 - membranous layer + genitalia + UBERON:0003133 + + + + reproductive organ - - - 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 + + + An organ involved in reproduction. + UBERON:xp - - - membranous organ component - FMA:82500 + + + GO uses genitalia for the singular organ + GO + + + + + EMAPA:37731 + MA:th + + + + + UMLS:C0017420 + ncithesaurus:Genitalia + + + + + genitalia + - + - - - + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - - - - - - - - - + - 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 + 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 - anal pad - anus - canalis analis - cloaca - cloacal chamber - mesenteron - pars analis recti - UBERON:0000159 + UBERON:0003134 + - - anal canal - https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png + female reproductive organ - - - - - - - - - Wikipathways:WP2062 + + + A female organ involved in reproduction. + UBERON:xp - - - The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus. - + + + female organism reproductive organ + OBOL:automatic - - - UMLS:C0227411 - ncithesaurus:Anal_Canal + + + female organism reproductive structure + OBOL:automatic - - - canalis analis - - + + + female organism reproductive system organ + OBOL:automatic - - - canalis analis - BTO:0001978 + + + female organism sex organ + OBOL:automatic - - - pars analis recti - BTO:0001978 + + + 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 - + - - + + + + + + + + + + + + + - + - - + + - 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 + 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 - intestinal tract - UBERON:0000160 - - - - - intestine + UBERON:0003212 + gustatory organ - - - - cjm + + + Any sense organ that functions in (some) detection of chemical stimulus involved in sensory perception of taste (GO:0050912). + FBC:auto_generated_definition - - - 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 + + + gustatory organ system organ + OBOL:automatic + + + + + gustatory system organ + OBOL:automatic + + + + + organ of gustatory organ system + OBOL:automatic - - - 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 + + + organ of gustatory system + OBOL:automatic - - - 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 - + + + organ of taste system + OBOL:automatic - - - UMLS:C0021853 - ncithesaurus:Intestine + + + taste system organ + OBOL:automatic - + - - - 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 + + + + + + + + + + + + + + + + + + + + + Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO]. uberon - UBERON:0000161 - orifice + UBERON:0003218 + ovary septum - + - 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 + Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO]. + GO:0080126 - + - - + + + + + + + + + + + + + + + + + - + - - + + - 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 - + + + + + + + + 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 + - + - - + + - AAO + ISBN:9780878932504 - + - 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. + 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 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] + 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:0001186 + VHOG:0000540 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] + 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:0001186 + VHOG:0000540 VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572 + ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.462 - - - hindgut endoderm and proctodeal ectoderm. - WP + + + metanephric blastema + - - - UMLS:C0008987 - ncithesaurus:Cloaca + + + metanephric mesoderm + - - - cloacal chamber - AAO:0000095 + + + metanephrogenic mesenchyme + EHDAA:5021 - - - vent - XAO:0000244 + + + metanephros associated mesenchyme + RETIRED_EHDAA2:0001139 - + - - + + + + + + + + + + + + + + - + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + - + - - + + - - + + - 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 + 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 - cloaca - UBERON:0000163 - - embryonic cloaca + UBERON:0003257 + yolk sac endoderm - + - + + EHDAA2 + + + + + The portion of the yolk sac that is derived from endoderm and lines the yolk sac. + UBERON:cjm + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - EHDAA2 + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - EHDAA2 - + + + + + + + + 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 + - + - 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 + An endoderm that is part of a midgut [Automatically generated definition]. + OBOL:automatic - - - cloaca - + + + midgut endoderm + OBOL:automatic - + - - + + + + + + + + + + + + + + + + + + + - + - - - - - - - + - 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 + An endoderm that is part of a hindgut [Automatically generated definition]. + TODO - check + EHDAA:979 + RETIRED_EHDAA2:0000781 + hindgut endoderm uberon - UBERON:0000164 - - primitive urogenital sinus - http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png + UBERON:0003260 + endoderm of hindgut - - - - - - - - - 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 + An endoderm that is part of a hindgut [Automatically generated definition]. + OBOL:automatic - - - 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 + + + hindgut endoderm + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - urogenital sinus - MP:0010116 + + + A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition]. + OBOL:automatic - - - UMLS:C0231057 - ncithesaurus:Urogenital_Sinus + + + eye skeletal muscle + OBOL:automatic - + - UGS - MP:0010116 + eye skeletal muscle tissue + OBOL:automatic - + - fetal UGS - + skeletal muscle tissue of eye + OBOL:automatic - - - sinus urogenitalis - + + + eye skeletal muscle group + EHDAA2:0000486 - + - + - + - - + + - + + + - + + + + + + + @@ -6093,92 +80529,55 @@ - + - - - - - - - - + + - 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 + 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 - 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 - - + mandibles + mandibular series + UBERON:0003278 - - - mouth - https://github.com/obophenotype/uberon/issues/661 - http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg + skeleton of lower jaw - + - - the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts + + + + + + + EHDAA2 - + @@ -6186,748 +80585,952 @@ - + - exceptions in some taxa + VHOG-modified - + - 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). - - + 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. + - + - Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] - 2012-06-20 - AAO:0010355 - AAO - AAO:BJB + The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO] + 2012-08-14 + TAO:0001273 + TAO + ZFIN:curator - + - 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] + 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:0000812 + VHOG:0000428 VHOG - DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008) + 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 - + - 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 + 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 - - - regio oralis - BTO:0004698 - - - - - regio oralis - FMA:49184 - FMA:TA - + + + lower jaw + MA:0001906 - - - cavital oralis - - + + + lower jaw + ZFA:0001273 - - - cavitas oris - BTO:0001090 + + + mandible + ZFA:0001273 - - - cavum oris - BTO:0001090 + + + lower jaw skeleton + AAO:0000274 - + - mouth cavity - BTO:0001090 + mandibles + TAO:0001273 + - + - oral region - EHDAA2:0001326 + mandibular series + ZFA:0001273 + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - oral vestibule - BTO:0001090 + + + A gland that is part of a foregut [Automatically generated definition]. + OBOL:automatic - - - rima oris - BTO:0001090 + + + 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 + - - - stomatodaeum - VHOG:0000812 + + + + + + + + + BTO - - - trophic apparatus - + + + Racemose mucous glands beneath the mucous membrane of the pharynx. + - - - vestibule of mouth - BTO:0001090 + + + pharynx gland + EHDAA2:0001461 - + - vestibulum oris - BTO:0001090 + glandulae pharyngeae + BTO:0004849 - + - - + + + + + + + + + + + + + - + - 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 + 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 - mouth - oral part of face - UBERON:0000166 - - - oral opening + UBERON:0003297 + gland of integumental system - - - - 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) + A gland that is part of a integumental system [Automatically generated definition]. + OBOL:automatic - + - oral fissure - FMA:59806 + integumental gland + - + - oral orifice - FMA:59806 + integumental system gland + - - - mouth - + + + integumentary gland + - + - + - + - - + + - + + + + - + - - + + - - + + - 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 + 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 - bucca - UBERON:0000167 - - - - oral cavity + mesenchyme blood island + UBERON:0003304 + mesoderm blood island - - - 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 + + + + EHDAA2 - - - 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 + + + + + + + + + EHDAA2 - - - The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG] - 2012-09-17 - VHOG:0000188 - VHOG - - + + + + + + + + + EHDAA2 - - - 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 + + + A blood island that is part of a mesoderm. + OBOL:automatic - - - UMLS:C0226896 - ncithesaurus:Oral_Cavity + + + in EHDAA2, gives rise to blood and dorsal aorta + EHDAA2 - + - buccal cavity - FMA:20292 - ISBN:0073040584 + mesoderm blood islands + EHDAA2:0003241 + + + + + + mesenchyme blood island + OBOL:automatic - + - + - + - - + + - + + - + - - + + - A section dividing a colon along a proximal-distal axis. - FMA:222905 + 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 - segment of colon - UBERON:0000168 - - proximal-distal subdivision of colon + UBERON:0003314 + eye mesenchyme - + - - 4 - cjm + + + + + + + EHDAA2 - + - A section dividing a colon along a proximal-distal axis. - + Mesenchyme that is part of a developing camera-type eye. + OBOL:automatic - - - segment of colon - FMA:222905 + + + mesenchyme of eye + OBOL:automatic - + - - - A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity - UBERON:0000324 - UBERON:0007550 - AEO:0000184 - BTO:0000491 - EHDAA2_RETIRED:0003184 - ENVO:02000022 - FMA:9674 - galen:Excretion - excreted substance - portion of excreted substance - waste substance + + + + + + + + + + + + + + + + + + + + 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 - excretion - UBERON:0000174 - excreta + UBERON:0003315 + mesenchyme of ovary - + - 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 + Mesenchyme that is part of a developing ovary [Automatically generated definition]. + OBOL:automatic - + - portion of excreted substance - FMA:9674 + female reproductive system gonad mesenchyme + OBOL:automatic - + - waste substance - AEO:0000184 + female reproductive system gonada mesenchyme + OBOL:automatic - - - excretion - BTO:0000491 + + + 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 + + + + + + + + + + + + + + + + + + + + - - + + - - - - - - - + - 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 + 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 - whole blood - UBERON:0000178 - - - - - blood + 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 + + + + + + + + + + + + + + + + + + + + + - - + + - - Bgee:AN + + 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 - - - A fluid that is composed of blood plasma and erythrocytes. - - - - FMA:9670 + + + anal canal submucosa + OBOL:automatic - - - 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 + + + anal canal viewed anatomically submucosa + OBOL:automatic - - - 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 + + + anal region submucosa + OBOL:automatic - - - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - 2012-06-20 - AAO:0000046 - AAO + + + anatomical anal canal submucosa + OBOL:automatic - - - 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) + + + submucosa of anal canal viewed anatomically + OBOL:automatic - - - UMLS:C0005767 - ncithesaurus:Blood + + + submucosa of anal region + OBOL:automatic - - - whole blood - BTO:0000089 + + + submucosa of anatomical anal canal + OBOL:automatic - + - + - + - + - + - + - Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. - cjm - 2009-04-08T04:38:19Z - CARO:0000081 + The submucous layer of the wall of the rectum. + + BTO:0002114 + EMAPA:27083 + FMA:15034 + rectal submucosa + rectum submucosa + tela submucosa recti uberon - blood or blood analog - circulating fluid - UBERON:0000179 - haemolymphatic fluid + UBERON:0003330 + submucosa of rectum - + - Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. - + The submucous layer of the wall of the rectum. + BTO:0002114 + + + + + rectal submucosa + FMA:15034 + + + + + rectum submucosa + OBOL:automatic + + + + + tela submucosa recti + BTO:0002114 + - + - + - + - - + + - - - - - - - + - - + + - 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 + 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 - blastosphere - UBERON:0000307 - - blastula - http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png + UBERON:0003331 + submucosa of colon - + - 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. - + A submucosa that is part of a colon [Automatically generated definition]. + OBOL:automatic - + - blastula embryo - BILA:0000059 + colon submucosa + OBOL:automatic - - - blastosphere - + + + colonic submucosa + FMA:14985 + + + + + large bowel submucosa + OBOL:automatic + + + + + submucosa of large bowel + OBOL:automatic - + - - - 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 + + + + + + + + + + + + + + + + + + + + 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:0000309 - - body wall + UBERON:0003334 + serosa of rectum - + - The external portion of an animal body derived from ectoderm and mesoderm layers that encloses the body cavity. - MP:0003385 + A serous membrane that is part of a rectum [Automatically generated definition]. + OBOL:automatic - - - the BTO class refers to earthworms. - BTO + + + rectal serosa + FMA:15039 - + - wall fo trunk - FMA:10427 + rectum serosa + OBOL:automatic - - - trunk wall - FMA:10427 + + + rectum serous membrane + OBOL:automatic - - - wall of trunk - FMA:10427 + + + serous membrane of rectum + OBOL:automatic + + + + + visceral peritoneum of rectum + FMA:15039 - + - + - + @@ -6935,7771 +81538,6778 @@ - + - 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 + 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:0000317 - - colonic mucosa + UBERON:0003335 + serosa of colon - + - 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. - + A serous membrane that is part of a colon [Automatically generated definition]. + OBOL:automatic - + - colon mucosa - FMA:14984 + colon serosa + OBOL:automatic - + - colon mucous membrane + colon serous membrane OBOL:automatic - + - colonic mucous membrane - FMA:14984 + colonic serosa + FMA:14990 - + - large bowel mucosa + large bowel serosa OBOL:automatic - + - mucosa of colon - FMA:14984 + large bowel serous membrane + OBOL:automatic - + - mucosa of large bowel + 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 + - + - + - + - + - + - + - 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 + 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 - wall of alimentary tract - UBERON:0000328 - gut wall + UBERON:0003338 + + ganglion of peripheral nervous system - + - The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity). - + 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 + + + - wall of gut - FMA:45653 + peripheral nervous system ganglion + OBOL:automatic - + - + - + - + - + + - + - 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 + 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 - glandulae intestinales - UBERON:0000333 - - intestinal gland + UBERON:0003342 + mucosa of anal canal - + - A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm]. - - - - - - bowel mucosa gland + A mucosa that is part of an anal canal [Automatically generated definition]. OBOL:automatic - - - bowel mucosa of organ gland - OBOL:automatic + + + UMLS:C0227414 + ncithesaurus:Anal_Mucosa - + - bowel mucous membrane gland + anal canal mucosa OBOL:automatic - + - bowel organ mucosa gland + anal canal mucosa of organ OBOL:automatic - + - gland of bowel mucosa + anal canal mucous membrane OBOL:automatic - + - gland of bowel mucosa of organ + anal canal organ mucosa OBOL:automatic - + - gland of bowel mucous membrane + anal canal viewed anatomically mucosa OBOL:automatic - + - gland of bowel organ mucosa + anal canal viewed anatomically mucosa of organ OBOL:automatic - + - gland of intestinal mucosa + anal canal viewed anatomically mucous membrane OBOL:automatic - + - gland of intestine mucosa + anal canal viewed anatomically organ mucosa OBOL:automatic - + - gland of intestine mucosa of organ - OBOL:automatic + anal mucosa + FMA:74654 - + - gland of intestine mucous membrane - OBOL:automatic + anal mucous membrane + FMA:74654 - + - gland of intestine organ mucosa + anal region mucosa OBOL:automatic - + - gland of mucosa of bowel + anal region mucosa of organ OBOL:automatic - + - gland of mucosa of intestine + anal region mucous membrane OBOL:automatic - + - gland of mucosa of organ of bowel + anal region organ mucosa OBOL:automatic - + - gland of mucosa of organ of intestine + anatomical anal canal mucosa OBOL:automatic - + - gland of mucous membrane of bowel + anatomical anal canal mucosa of organ OBOL:automatic - + - gland of mucous membrane of intestine + anatomical anal canal mucous membrane OBOL:automatic - + - gland of organ mucosa of bowel + anatomical anal canal organ mucosa OBOL:automatic - + - gland of organ mucosa of intestine + mucosa of anal canal viewed anatomically OBOL:automatic - + - glandula intestinalis - FMA:15052 + mucosa of anal region + OBOL:automatic - + - intestinal mucosa gland + mucosa of anatomical anal canal OBOL:automatic - + - intestine mucosa gland + mucosa of organ of anal canal OBOL:automatic - + - intestine mucosa of organ gland + mucosa of organ of anal canal viewed anatomically OBOL:automatic - + - intestine mucous membrane gland + mucosa of organ of anal region OBOL:automatic - + - intestine organ mucosa gland + mucosa of organ of anatomical anal canal OBOL:automatic - + - mucosa of bowel gland + mucous membrane of anal canal OBOL:automatic - + - mucosa of intestine gland + mucous membrane of anal canal viewed anatomically OBOL:automatic - + - mucosa of organ of bowel gland + mucous membrane of anal region OBOL:automatic - + - mucosa of organ of intestine gland + mucous membrane of anatomical anal canal OBOL:automatic - + - mucous membrane of bowel gland + organ mucosa of anal canal OBOL:automatic - + - mucous membrane of intestine gland + organ mucosa of anal canal viewed anatomically OBOL:automatic - + - organ mucosa of bowel gland + organ mucosa of anal region OBOL:automatic - + - organ mucosa of intestine gland + organ mucosa of anatomical anal canal 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 + 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 - 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 + UBERON:0003343 + mucosa of oral region - + - 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] - + A mucosa that is part of a oral opening [Automatically generated definition]. + OBOL:automatic - - - 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 + + + mucosa of oral opening + OBOL:automatic - - - UMLS:C0026724 - ncithesaurus:Mucosa + + + mucosa of oral part of face + OBOL:automatic - + - mucosa of organ - FMA:85355 + mucosa of organ of oral opening + OBOL:automatic - + - mucosa of organ part - FMA:85358 + mucosa of organ of oral part of face + OBOL:automatic - + - mucosal region - FMA:85358 + mucosa of organ of oral region + OBOL:automatic - + - mucous membrane - FMA:85355 + mucosa of organ of subdivision of mouth + OBOL:automatic - + - organ mucosa - FMA:85355 + mucosa of subdivision of mouth + OBOL:automatic - - - region of mucosa - FMA:85358 + + + mucous membrane of oral opening + OBOL:automatic - - - tunica mucosa - - + + + mucous membrane of oral part of face + OBOL:automatic - - - tunica mucosa - BTO:0000886 + + + mucous membrane of oral region + OBOL:automatic - - - - - - - - - - - - - - - - - - - - - - - - - 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]. + + + mucous membrane of subdivision of mouth OBOL:automatic - + - mucosa of organ of pharynx + oral opening mucosa OBOL:automatic - + - mucosa of pharynx + oral opening mucosa of organ OBOL:automatic - + - mucous membrane of pharynx - FMA:55031 + oral opening mucous membrane + OBOL:automatic - + - mucous membrane of pharynx + 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 pharynx + organ mucosa of oral region OBOL:automatic - + - pharynx mucosa + organ mucosa of subdivision of mouth OBOL:automatic - + - pharynx mucosa of organ + subdivision of mouth mucosa OBOL:automatic - + - pharynx mucous membrane + subdivision of mouth mucosa of organ OBOL:automatic - + - pharynx organ mucosa + subdivision of mouth mucous membrane OBOL:automatic - + - tunica mucosa pharyngea - FMA:55031 - FMA:TA - - - - - - mucous membrane of the pharynx - BTO:0001047 + subdivision of mouth organ mucosa + OBOL:automatic - + - + - + - - + + - + - - - - - - - + - The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. - consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 - Anatomical system that consists of the muscles of the body.[VSAO] - we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA - AAO:0000307 - BILA:0000088 - BTO:0001369 - BTO:0001485 - EFO:0000801 - EMAPA:35578 - FBbt:00005069 - FMA:72954 - MA:0002888 - MAT:0000025 - MIAA:0000025 - VSAO:0000033 - XAO:0004042 - muscle system - muscle system of body - muscular system - musculature system - set of all muscles - set of muscles of body - vertebrate muscular system + 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 - muskelsystem - UBERON:0000383 - - - musculature of body + UBERON:0003346 + mucosa of rectum - + - The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. - VSAO:0000033 + A mucosa that is part of a rectum [Automatically generated definition]. + OBOL:automatic - - - Anatomical system that consists of the muscles of the body.[VSAO] - 2012-08-14 - VSAO:0000033 - VSAO - VSAO:curator + + + mucosa of organ of rectum + OBOL:automatic - - - we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA - MA + + + mucous membrane of rectum + OBOL:automatic - + - muscular system - FMA:72954 + organ mucosa of rectum + OBOL:automatic - + - musculature system - BILA:0000088 + rectal mucosa + FMA:15033 - + - set of all muscles - FMA:72954 + rectal mucous membrane + FMA:15033 - + - set of muscles of body - FMA:72954 + rectum mucosa + OBOL:automatic - + - vertebrate muscular system - BTO:0001369 + rectum mucosa of organ + OBOL:automatic - - - muskelsystem - BTO:0001485 + + + rectum mucous membrane + OBOL:automatic + + + + + rectum organ mucosa + OBOL:automatic - + - + - + - - + + - - - + - - - - - - - - - - - - - + - Tissue that surrounds the lens nucleus - - BTO:0001632 - CALOHA:TS-0542 - FMA:58970 - MESH:A09.371.509.225 - cortex of lens + A layer of epithelial cells on the surface of the mucosa. + BTO:0003752 uberon - UBERON:0000389 - lens cortex + lamina epithelialis mucosa + lamina epithelialis mucosae + UBERON:0003350 + lies on top of lamina propria + epithelium of mucosa - + - Tissue that surrounds the lens nucleus - + A layer of epithelial cells on the surface of the mucosa. + BTO:0003752 - - - cortex of lens - FMA:58970 + + + lamina epithelialis mucosa + BTO:0003752 + + + + + lamina epithelialis mucosae + BTO:0003752 - + - + - + - - + + - - - + + + - + - - - - - - - + - The core of the crystalline lens, surrounded by the cortex. - - BTO:0001633 - FMA:58971 - MESH:A09.371.509.670 - nucleus of lens + 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:0000390 - lens nucleus + UBERON:0003351 + + pharyngeal epithelium - + + + + + + + + + ZFA + + + + + + + + + + + ZFA + + + - The core of the crystalline lens, surrounded by the cortex. - BTO:0001633 + 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 + + + - nucleus of lens - FMA:58971 + 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 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 + 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:0000397 - - colonic epithelium + UBERON:0003352 + epithelium of midgut - - - 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 + + + + + + + + + BTO - - - colon epithelial tissue + + + An epithelium that is part of a midgut. OBOL:automatic - - - colon epithelium - FMA:17302 - - - + - colon epithelium + epithelial tissue of midgut OBOL:automatic - + - epithelial tissue of colon + midgut epithelial tissue OBOL:automatic - + - epithelial tissue of large bowel - OBOL:automatic + midgut epithelium + BTO:0005053 - + - epithelium of colon + 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 + - - - epithelium of large bowel + + + An epithelium that is part of a hindgut [Automatically generated definition]. OBOL:automatic - + - large bowel epithelial tissue + epithelial tissue of hindgut OBOL:automatic - + - large bowel epithelium + hindgut epithelial tissue OBOL:automatic - + - posterior intestine epithelium - ZFA:0005128 + hindgut epithelium + OBOL:automatic - + - - - - - - - - + + + + + + + + + + + + + + - - + + - 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 + 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:0000409 - - - serous gland - http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png + UBERON:0003354 + epithelium of rectum - + - A gland in which the principal secretory cells are serous secreting cells. - - + An epithelium that is part of a rectum [Automatically generated definition]. + OBOL:automatic - - - glands that secrete watery albuminous material that often contains enzymes[MP:0008052]. - MP:0008052 + + + epithelial tissue of rectum + OBOL:automatic - - - EMAPA:37950 - MA:th + + + rectal epithelium + FMA:17510 + + + + + rectum epithelial tissue + OBOL:automatic + + + + + rectum epithelium + OBOL:automatic - + - - + + + + + + + + + + + + + - - + + - 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 + 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 - muciparous gland - mucous secreting gland - mucus gland - mucus-secreting gland - UBERON:0000414 - - mucous gland - http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png + UBERON:0003364 + epithelium of right lung - + - 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 + An epithelium that is part of a right lung [Automatically generated definition]. + OBOL:automatic - - - EMAPA:37913 - MA:th + + + epithelial tissue of right lung + OBOL:automatic - + - glandula mucosa - - + right lung epithelial tissue + OBOL:automatic - - - muciparous gland - BTO:0001979 + + + right lung epithelium + OBOL:automatic - + - + - + - + - + - + - An anatomical wall that is part of an artery [Automatically generated definition]. - BTO:0002009 - FMA:14155 - galen:ArterialWall - arterial wall - wall of artery + 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:0000415 - artery wall + UBERON:0003365 + epithelium of left lung - + - An anatomical wall that is part of an artery [Automatically generated definition]. + An epithelium that is part of a left lung [Automatically generated definition]. OBOL:automatic - + - arterial wall - FMA:14155 + epithelial tissue of left lung + OBOL:automatic - + - wall of artery - FMA:14155 + left lung epithelial tissue + OBOL:automatic + + + + + left lung epithelium + OBOL:automatic - + - + - + - - + + - + + + - - + + - 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 + + + + + + + + + + + + + + + + + + + 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 - exocrine gland fluid - exocrine gland fluid or secretion - exocrine gland secretion - external secretion - UBERON:0000456 - secretion of exocrine gland + leg ectoderm + UBERON:0003371 + pelvic appendage bud ectoderm - + + + + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + - A portion of organism substance that is produced by exocrine glands. - + An unilaminar epithelium that surrounds a pelvic appendage bud. + OBOL:automatic - - - 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 + + + hindlimb ectoderm + VHOG:0001048 - - - secretion - FMA:9675 + + + hindlimb bud ectoderm + EMAPA:16780 + - - - UMLS:C1516992 - ncithesaurus:Exocrine_Gland_Fluid_or_Secretion + + + hindlimb bud ectoderm + - - - bodily secretion - MESH:D012634 + + + hindlimb ectoderm + VHOG:0001048 + - - - exocrine gland fluid/secretion - MA:0002504 + + + lower limb bud ectoderm + EHDAA2:0001034 + - + + + pelvic fin bud ectoderm + + + + - external secretion - BTO:0002977 + leg ectoderm + 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 + + + + + + + + + + + + + + + + + + + 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 - UBERON:0000463 - - - organism substance + arm ectoderm + UBERON:0003372 + pectoral appendage bud ectoderm - + - + - this relationship may be too strong and may be weakened in future + EHDAA2 - + + + + + + + + + EHDAA2 + + + - 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. - + An unilaminar epithelium that surrounds a pectoral appendage bud. + OBOL:automatic - - - body fluid or substance - MA:0002450 + + + forelimb bud ectoderm + EMAPA:16407 + - - - body substance - FMA:9669 + + + forelimb bud ectoderm + - - - organism substance - CARO:0000004 + + + forelimb ectoderm + VHOG:0001047 + - - - portion of body substance - FMA:9669 + + + pectoral fin bud ectoderm + - - - portion of organism substance - ZFA:0001487 + + + upper limb bud ectoderm + EHDAA2:0002134 + + + + + + wing ectoderm + Geisha:syn + NCBITaxon:8782 + + + + + + arm ectoderm + OBOL:automatic - + - - + + + + + + + + + + + + + - - + + - - 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 + + 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 - anatomical spaces - UBERON:0000464 - - anatomical space + UBERON:0003379 + cardiac muscle of right atrium - + - 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. - + A portion of cardiac muscle tissue that is part of a right atrium [Automatically generated definition]. + OBOL:automatic - - - UMLS:C0524461 - ncithesaurus:Lumen_Space + + + cardiac muscle of cardiac right atrium + OBOL:automatic - - - anatomical spaces - ZFA:0001643 - + + + cardiac muscle of heart right atrium + OBOL:automatic - - - - - - - - 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. - + + + cardiac muscle tissue of heart right atrium + OBOL:automatic - - - - - - - - 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. - + + + cardiac muscle tissue of right atrium + OBOL:automatic - + - immaterial physical anatomical entity - FMA:67112 + 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 - + - - + + + + + + + + + + + + + - - - - - - - - - - - - - + - 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 + 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 - anatomical systems - UBERON:0000467 - - - - anatomical system - + UBERON:0003380 + cardiac muscle of left atrium - + - 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 + A portion of cardiac muscle tissue that is part of a left atrium [Automatically generated definition]. + OBOL:automatic - - - UMLS:C0460002 - ncithesaurus:Organ_System + + + cardiac left atrium cardiac muscle + OBOL:automatic - + - body system - BIRNLEX:14 + cardiac left atrium cardiac muscle tissue + OBOL:automatic - + - connected anatomical system - CARO:0000011 + cardiac muscle of cardiac left atrium + OBOL:automatic - - - anatomical systems - ZFA:0001439 - + + + cardiac muscle of heart left atrium + OBOL:automatic - - - - - - - - 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 + + + cardiac muscle of left atrium of heart + OBOL:automatic - - - organism - FBbt:00000001 - VHOG:0000671 - WBbt:0007833 + + + left atrium heart muscle + EHDAA2:0004154 - + - multi-cellular organism - CARO:0000012 + left atrium myocardium + VHOG:0001225 - - - animal - BTO:0000042 + + + textus muscularis of myocardium of cardiac left atrium + OBOL:automatic - - - Koerper - BTO:0001489 + + + textus muscularis of myocardium of heart left atrium + OBOL:automatic - - - body - AEO:0000103 - BIRNLEX:18 - FMA:256135 - NCIT:C13041 + + + textus muscularis of myocardium of left atrium + OBOL:automatic - - - whole body - BTO:0001489 + + + textus muscularis of myocardium of left atrium of heart + OBOL:automatic - - - whole organism - FBbt:00000001 + + + 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 + + + + + + + + + + + - + - - - + + + + - - - - - - - + + - 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 + 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 - body part - body region - cardinal body part - UBERON:0000475 - - - - - organism subdivision + left ventricle cardiac muscle + UBERON:0003382 + cardiac muscle of left ventricle - - - - 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 + A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition]. + OBOL:automatic - + - anatomic region - MA:0002433 + cardiac muscle tissue of left ventricle + FMA:83453 - - - body region - FMA:7153 + + + left ventricular cardiac muscle tissue + GO:0003220 - + - cardinal body part - FMA:7153 + left ventricle cardiac muscle + VHOG:0001234 - + - - - - 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 + + + + + + + + + + + + + + + + + + + + + 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 - acellular anatomical structures - UBERON:0000476 - - acellular anatomical structure + interventricular septum muscle + UBERON:0003383 + cardiac muscle tissue of interventricular septum - - - - CARO + + + A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition]. + OBOL:automatic - - - Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. - + + + 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 + + + - acellular anatomical structures - ZFA:0000382 - + interventricular septum muscle + - + - - - 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 + + + + + + + + + + + + + + + + + + + + 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:0000477 - - anatomical cluster + UBERON:0003384 + skeletal muscle tissue of pharynx - + - Anatomical group that has its parts adjacent to one another. - + 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 - + - + - + - + - + + - + - - + + - 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 + 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 - extraembryonic structures - extraembryonic tissue - UBERON:0000478 + UBERON:0003386 - - - see also conceptus extraembryonic component in EHDAA2. - extraembryonic structure + smooth muscle of eye - + - 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 + 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 - - - extraembryonic structures - ZFA:0000020 - + + + ocular smooth muscle + MA:0001268 - + - - + + + + + + + + + + + + + - + - 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 + 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:0000479 - - - tissue + UBERON:0003388 + mesothelium of pericardial cavity - - - - CARO + + + A mesothelium that is part of a pericardium [Automatically generated definition]. + OBOL:automatic - - - 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 + + + cavity of pericardial sac meso-epithelium + OBOL:automatic - - - UMLS:C0040300 - ncithesaurus:Tissue + + + cavity of pericardial sac mesothelium + OBOL:automatic - + - portion of tissue - CARO:0000043 + meso-epithelium of cavity of pericardial sac + OBOL:automatic - - - simple tissue - AEO:0000043 + + + 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 - + - - + + + + + + + + + + + + + + - - + + - 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 + A mesothelium that is part of a diaphragm [Automatically generated definition]. + EMAPA:18429 + diaphragm meso-epithelium + diaphragm mesothelium + meso-epithelium of diaphragm + meso-epithelium of thoracic diaphragm + mesothelium of thoracic diaphragm + thoracic diaphragm meso-epithelium + thoracic diaphragm mesothelium uberon - multi-tissue structures - UBERON:0000481 - - multi-tissue structure + UBERON:0003389 + mesothelium of diaphragm - - - - CARO + + + A mesothelium that is part of a diaphragm [Automatically generated definition]. + OBOL:automatic - - - 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 + + + diaphragm meso-epithelium + OBOL:automatic - - - multi-tissue structures - ZFA:0001488 - + + + diaphragm mesothelium + OBOL:automatic + + + + + meso-epithelium of diaphragm + OBOL:automatic + + + + + meso-epithelium of thoracic diaphragm + OBOL:automatic + + + + + mesothelium of thoracic diaphragm + OBOL:automatic + + + + + thoracic diaphragm meso-epithelium + OBOL:automatic + + + + + thoracic diaphragm mesothelium + OBOL:automatic - + - + - - - - + + + + + + + - + - - + + - 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 + 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 - UBERON:0000483 - - - - epithelium - Tkanka:nablonkowa.png + pleura + UBERON:0003390 + mesothelium of pleural cavity - + - 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]. - - + A mesothelium that is part of a pleural cavity [Automatically generated definition]. + OBOL:automatic - - - 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 + + + meso-epithelium of pleural cavity + OBOL:automatic - - - UMLS:C0014609 - ncithesaurus:Epithelium + + + mesothelium of pleura + FMA:18148 - + - portion of epithelium - FMA:9639 + pleural cavity meso-epithelium + OBOL:automatic - - - - - - - - - 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. - - + + + pleural cavity mesothelium + OBOL:automatic - - - UMLS:C0836134 - ncithesaurus:Simple_Cuboidal_Epithelium + + + pleural mesothelium + EMAPA:16775 - + - simple cuboidal epithelia - ZFA:0001497 - + pleura + EMAPA:16775 - + - - - - 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 + + + + + + + + + + + + + + + + + + + + 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 - + - 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 + A cartilage element that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic - - - columnar epithlium - AEO:0000068 + + + apparatus respiratorius cartilage + OBOL:automatic - - - UMLS:C0836135 - ncithesaurus:Simple_Columnar_Epithelium + + + cartilage of apparatus respiratorius + OBOL:automatic - - - simple columnar epithelia - ZFA:0001496 - + + + respiratory system cartilage + OBOL:automatic - + - - - 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 + + + + + + + + + + + + + + + + + + + + + + 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 - laminated epithelium - UBERON:0000486 - - - multilaminar epithelium + UBERON:0003408 + gland of digestive tract - + - 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 + A gland that is part of a digestive tract [Automatically generated definition]. + OBOL:automatic - - - Epithelium that consists of more than one layer of epithelial cells.[CARO] - 2012-06-20 - CARO:0000069 - CARO - - FMA:45562 + + + digestive tract gland + OBOL:automatic - - - UMLS:C0682575 - ncithesaurus:Stratified_Epithelium + + + gland of digestive tract + OBOL:automatic - - - laminated epithelium - BTO:0002074 + + + gland of lower gastrointestinal tract + OBOL:automatic + + + + + gut gland + MA:0003202 + + + + + lower gastrointestinal tract gland + OBOL:automatic - + - - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - simple squamous epithelia - UBERON:0000487 - - - simple squamous epithelium - Illu:epithelium.jpg + UBERON:0003412 + pelvic appendage bud mesenchyme - + - Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA] - - - FMA:45565 + Mesenchyme that is part of a pelvic appendage bud. + OBOL:automatic - + - Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] - 2012-06-20 - CARO:0000070 - CARO - - FMA:45565 + Mesoderm part of pelvic fin bud.[TAO] + 2012-08-14 + TAO:0001386 + TAO + ZFIN:curator - - - UMLS:C0836133 - ncithesaurus:Simple_Squamous_Epithelium + + + leg mesenchyme + OBOL:automatic - - - simple squamous epithelia - ZFA:0001498 - + + + lower limb bud mesenchyme + EHDAA2:0001035 + + + + + hindlimb bud mesenchyme + EMAPA:16781 + + + + + + mesoderm pelvic fin bud + ZFA:0001386 + + + + + + pelvic fin bud mesenchyme + - + - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - atypical epithelia - UBERON:0000488 - - atypical epithelium + UBERON:0003413 + pectoral appendage bud mesenchyme - + - Epithelium that consists of epithelial cells not arranged in one ore more layers. - + Mesenchyme that is part of a pectoral appendage bud. + OBOL:automatic - - - atypical epithelia - ZFA:0001493 - + + + 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 - + - + - + - - + + - + + - - + + - 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 + 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 - cavitated compound organs - UBERON:0000489 - - - cavitated compound organ + UBERON:0003426 + + dermis adipose tissue - + - Compound organ that contains one or more macroscopic anatomical spaces. - + An adipose tissue that is part of a dermis [Automatically generated definition]. + OBOL:automatic - + - cavitated organ - FMA:55671 + adipose tissue of dermis + OBOL:automatic - - - cavitated compound organs - ZFA:0001490 - + + + dermis fat tissue + OBOL:automatic + + + + + dermis fatty tissue + OBOL:automatic + + + + + fat tissue of dermis + OBOL:automatic + + + + + fatty tissue of dermis + OBOL:automatic - + - - - 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 + + + + + + + + + + + + + + + + + + + + A nerve that is part of an abdomen [Automatically generated definition]. + MA:0000521 + nerve of abdomen + uberon + UBERON:0003429 + abdomen nerve - + - Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA] - - FMA:45561 + A nerve that is part of an abdomen [Automatically generated definition]. + OBOL:automatic - - - Epithelium that consists of a single layer of epithelial cells.[CARO] - 2012-06-20 - CARO:0000073 - CARO - - FMA:45561 + + + 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 - + - UMLS:C0682574 - ncithesaurus:Simple_Epithelium + EMAPA:37263 + MA:th - + - simple epithelium - FMA:45561 + neck (volume) nerve + OBOL:automatic - - - unilaminar epithelia - ZFA:0001495 - + + + nerve of neck + OBOL:automatic + + + + + nerve of neck (volume) + OBOL:automatic - + - - - + + + + + + + + + + + + + + - - + + - 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 + 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:0000912 - mucus + UBERON:0003438 + iris nerve - + - 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. - + Any nerve that innervates the iris. + UBERON:cjm - - - UMLS:C0026727 - ncithesaurus:Mucus + + + nerve of iris + OBOL:automatic - + - + - + - - + + - - + - - + + - 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 + 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 - anterior subdivision of trunk - upper body - upper trunk - UBERON:0000915 - - thoracic segment of trunk + trunk nerve + UBERON:0003439 + + + nerve of trunk region - - - - FMA - - - + - Subdivision of trunk that lies between the head and the abdomen. + A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk). - + + + EMAPA:37264 + MA:th + + + - thorax - MA:0000022 + nerve of torso + OBOL:automatic - + + + nerve of trunk + OBOL:automatic + + + + + torso nerve + OBOL:automatic + + + - upper trunk - FMA:259209 + trunk nerve + MA:0000515 - + - - + + + + + + + + + + + + + - + - 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 + A nerve that is part of a limb [Automatically generated definition]. + + EMAPA:37291 + MA:0000693 + nerve of limb uberon - adult abdomen - belly - celiac region - UBERON:0000916 - - - - abdomen + UBERON:0003440 + limb nerve - - - - - - - - - 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. - + A nerve that is part of a limb [Automatically generated definition]. + OBOL:automatic - - - abdominopelvic region - FMA:9577 + + + EMAPA:37291 + MA:th - + - abdominopelvis - FMA:9577 + nerve of limb + OBOL:automatic - + - + - + - - - - - - + + - - - - - - - + - - + + - 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 + 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 - developing organism - developmental tissue - UBERON:0000922 - - - - - embryo - https://github.com/obophenotype/uberon/issues/503 - Wrinkledfrog:embryos.jpg + UBERON:0003441 + forelimb nerve - + - 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 + A nerve that is part of a forelimb [Automatically generated definition]. + OBOL:automatic - - - Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo - ZFA + + + EMAPA:37334 + MA:th - - - UMLS:C0013935 - ncithesaurus:Embryo + + + fore limb nerve + OBOL:automatic - + - embryonic organism - BILA:0000056 + nerve of fore limb + OBOL:automatic - - - developing organism - BILA:0000056 + + + nerve of forelimb + OBOL:automatic + + + + + nerve of superior member + OBOL:automatic + + + + + nerve of upper extremity + OBOL:automatic + + + + + wing nerve + NCBITaxon:8782 + OBOL:automatic + - + - - - 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 + + + + + + + + + + + + + + + + + + + + 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 - 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 + UBERON:0003442 + hindlimb nerve - + - 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. - - + A nerve that is part of a hindlimb [Automatically generated definition]. + OBOL:automatic - - - 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 + + + EMAPA:37342 + MA:th - - - embryonic tissue - FMA:69069 + + + hind limb nerve + OBOL:automatic - - - UMLS:C0920502 - ncithesaurus:Embryonic_Tissue + + + nerve of hind limb + OBOL:automatic - - - UMLS:C1708239 - ncithesaurus:Germinal_Layer + + + nerve of hindlimb + OBOL:automatic - + - germinal layer - ncithesaurus:Germinal_Layer + nerve of inferior member + OBOL:automatic - - - primary germ layer - GO:0001704 - ZFA:0001122 + + + nerve of lower extremity + OBOL:automatic - + - - - - - - - - + + + + + + + + + + + + + - - + + - 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 + 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:0000924 - - - - - ectoderm - http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png + UBERON:0003443 + thoracic cavity nerve - - - - - - - - - Bgee:AN + + + 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 - - - Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. - + + + chest cavity nerve + OBOL:automatic - - - 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 + + + nerve of cavity of chest + OBOL:automatic - - - 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 + + + nerve of cavity of thorax + OBOL:automatic - - - UMLS:C0013574 - ncithesaurus:Ectoderm + + + nerve of chest cavity + OBOL:automatic - + - embryonic ectoderm - VHOG:0000153 + nerve of pectoral cavity + OBOL:automatic + + + + + nerve of thoracic cavity + OBOL:automatic + + + + + pectoral cavity nerve + OBOL:automatic - + - - - - - - - - + + + + + + + + + + + + + - - + + - 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 + A nerve that is part of a pelvis [Automatically generated definition]. + EMAPA:37269 + MA:0000542 + nerve of pelvis 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 + UBERON:0003444 + pelvis nerve - - - - - - - - - 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 + A nerve that is part of a pelvis [Automatically generated definition]. + OBOL:automatic - + - UMLS:C0014144 - ncithesaurus:Endoderm + EMAPA:37269 + MA:th - - - entoderm - - + + + nerve of pelvis + OBOL:automatic - + - - - - - - - - + + + + + + + + + + + + + - - + + - 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 + 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 - embryonic mesoderm - entire mesoderm - mesodermal mantle - UBERON:0000926 - + craniofacial bone + UBERON:0003457 - - - mesoderm - http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png + Different sources vary regarding which bones are craniofacial; e.g. hyoid bone + head bone - - - - sometimes not considered primary + + + A bone that is part of a head [Automatically generated definition]. + OBOL:automatic - - - - - - - - - Bgee:AN + + + adult head bone + OBOL:automatic - - - The middle germ layer of the embryo, between the endoderm and ectoderm. - + + + adult head bone organ + OBOL:automatic - - - Primary germ layer that is the middle of the embryonic germ layers.[AAO] - 2012-06-20 - AAO:0000304 - AAO - AAO:EJS + + + bone of adult head + OBOL:automatic - - - 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 + + + bone of head + OBOL:automatic - - - 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 - + + + bone organ of adult head + OBOL:automatic - - - UMLS:C0025485 - ncithesaurus:Mesoderm + + + bone organ of head + OBOL:automatic - - - embryonic mesoderm - VHOG:0000152 + + + head bone organ + OBOL:automatic - + - entire mesoderm - - + craniofacial bone + - + - - - - - - - - + + + + + + + + + + + + + - + - 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 + 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 - mouth pit - oral ectoderm - oral pit - UBERON:0000930 - - - - - stomodeum - http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png + UBERON:0003458 + neck bone - + - 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 + A bone that is part of a neck [Automatically generated definition]. + OBOL:automatic - - - stomodeal-hypophyseal primordium - XAO:0000269 + + + EMAPA:37246 + MA:th - - - UMLS:C1514977 - ncithesaurus:Stomodeum + + + bone of neck + OBOL:automatic - + - mouth primordium - XAO:0000269 + bone of neck (volume) + OBOL:automatic - + - primitive oral cavity - + bone organ of neck + OBOL:automatic - + - stomatodeum - + bone organ of neck (volume) + OBOL:automatic - - - mouth pit - EMAPA:16263 + + + neck (volume) bone + OBOL:automatic - - - oral ectoderm - ZFA:0001290 - ZFIN:ZDB-PUB-100726-23 + + + neck (volume) bone organ + OBOL:automatic - - - oral pit - EMAPA:16263 + + + neck bone organ + OBOL:automatic - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 + + + + + + + + + + + + + + + + + + + + + + + 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 - anal pit - anus porus - UBERON:0000931 - - proctodeum - https://github.com/obophenotype/uberon/issues/685 + bone of viscerocranium + viscerocranium bone + UBERON:0003462 + + facial bone - - - - EHDAA2 - - - + - - + + - EHDAA2 + MA - + - Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract. - - - ZFA:0000066 + A bone that is part of a facial skeleton [Automatically generated definition]. + OBOL:automatic - - - 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 + + + UMLS:C0015455 + ncithesaurus:Facial_Bone - - - 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 + + + bone of facial skeleton + OBOL:automatic - - - UMLS:C0231054 - ncithesaurus:Proctodeum + + + facial bone + EMAPA:19019 - - - amnioproctodeal invagination - FBbt:00000123 + + + facial skeleton bone + OBOL:automatic - + - anal pit - VHOG:0000139 + bone of viscerocranium + OBOL:automatic - + - anus porus - XAO:0001019 + viscerocranium bone + OBOL:automatic - + - + - + - - + + - - - - + + - - - - - - - - - - - - - - - - - - - + - 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 + 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 - 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 + UBERON:0003463 + trunk bone - - - - - - - - - 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 + A bone that is part of a trunk [Automatically generated definition]. + OBOL:automatic - - - 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 + + + bone of torso + OBOL:automatic - - - 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 + + + bone of trunk + OBOL:automatic - - - UMLS:C0018787 - ncithesaurus:Heart + + + bone organ of torso + OBOL:automatic - + - chambered heart - + bone organ of trunk + OBOL:automatic - - - branchial heart - + + + torso bone + OBOL:automatic - - - Herz@de - BTO:0000562 + + + torso bone organ + OBOL:automatic - - - cardium - EMAPA:16105 + + + trunk bone organ + OBOL:automatic - + - - - + + + + + + + + + + + + + + + - + - - + + - - - - - - - - - - - - - - - - - - - + - 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 + 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 - encephalon - suprasegmental levels of nervous system - suprasegmental structures - synganglion - the brain - UBERON:0000955 - + UBERON:0003464 - - - - - brain + hindlimb bone - - - - 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]. - - + 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). + - - - 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 + + + the MA class is actually bone of pelvic complex; in contrast the NCIT class excludes ilium etc + MA - - - 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 + + + UMLS:C0448188 + ncithesaurus:Bone_of_the_Lower_Extremity - - - 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) - + + + bone of hind limb + 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 (...) (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 + + + bone of hindlimb + OBOL:automatic - - - UMLS:C0006104 - BIRNLEX:796 + + + bone of inferior member + OBOL:automatic - - - UMLS:C0006104 - ncithesaurus:Brain + + + bone of lower extremity + OBOL:automatic - - - UMLS:C1269537 - BIRNLEX:796 + + + bone organ of hind limb + OBOL:automatic - - - http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 - BIRNLEX:796 + + + bone organ of hindlimb + OBOL:automatic - - - encephalon - BTO:0000142 + + + bone organ of lower extremity + OBOL:automatic - - - suprasegmental levels of nervous system - NeuroNames:21 + + + hind limb bone + OBOL:automatic - - - suprasegmental structures - NeuroNames:21 + + + hind limb bone organ + OBOL:automatic - - - the brain - NeuroNames:21 + + + hindlimb bone organ + OBOL:automatic - + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - + + - - + + - 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 + The ureteral branches of renal artery are small branches which supply the ureter. + ureteric artery + + + EMAPA:37676 + FMA:70491 + MA:0002074 uberon - corneas - tunica cornea - UBERON:0000964 - - - - - cornea - http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg + UBERON:0003468 + ureteric segment of renal artery - - - - XAO - - - - - - - - - - - MA - - - + - + - MA + FMA - + - - + + - FMA-isa + FMA - - - - - - - - - definitional + + + The ureteral branches of renal artery are small branches which supply the ureter. + - - - 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 + + + ureteric artery + MA:0002074 - + - UMLS:C0010031 - ncithesaurus:Cornea + 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 + - - - cornea of camera-type eye - GO:0061303 + + + An artery that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic - - - corneas - ZFA:0000640 - + + + EMAPA:37569 + MA:th - + - - - + + + + + + + + + + + + + + + + - + - - + + - - + + - - + + - 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 + The inferior 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 - 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 + UBERON:0003471 + artery of lower lip - - - Transparent part of camera-type eye that helps to refract light to be focused on the retina. - - + + + + + + + + + FMA - - - 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) + + + The inferior 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. + - + - UMLS:C0023317 - ncithesaurus:Crystalline_Lens + EMAPA:37429 + MA:th - + - camera-type eye lens - GO:0002088 + arteria labialis inferior + + - + - eye lens - + inferior labial artery + FMA:49567 - + - lens - + inferior labial branch of facial artery + FMA:49567 - + - lens crystallina - - - - - - crystalline lens - BTO:0000723 - - - - - lenses - ZFA:0000035 - + ramus labialis inferior (arteria facialis) + FMA:TA - - - ocular lens - BTO:0000723 + + + ramus labialis inferior arteriae facialis + + - + - - - - - - - - - - - - - - - + + + + + + + + + + + + + + - - + + - 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 - + 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 + - - - UMLS:C1278894 - BIRNLEX:1153 + + + An artery that is part of a thoracic cavity[cjm]. + - - - retina of camera-type eye - GO:0060041 + + + in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity + MA - - - Netzhaut - BTO:0001175 + + + EMAPA:37241 + MA:th - + - retinas - ZFA:0000152 - + thoracic artery + MESH:A07.231.114.891 - + - - + + + + + + + + + + + + + + - + - 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 + A vein that is part of a ureter [Automatically generated definition]. + EMAPA:37679 + MA:0002250 + ureter vein + vein of ureter uberon - light-detecting organ - visual apparatus - UBERON:0000970 - - - - - - eye + UBERON:0003475 + ureteric vein - - - visual apparatus - EV:0100336 + + + A vein that is part of a ureter [Automatically generated definition]. + OBOL:automatic - - - An organ that detects light. - + + + EMAPA:37679 + MA:th + + + + + ureter vein + OBOL:automatic + + + + + vein of ureter + OBOL:automatic - + - - + + + + + + + + + + + + + - - - - - - - + - - + + - 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 + 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 - collum - neck (volume) - UBERON:0000974 - - - - neck - Female:neck.jpg + UBERON:0003476 + respiratory system venous blood vessel - + - An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. - + A vein that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic - - - - ISBN:9780674021839 + + + EMAPA:37584 + MA:th - - - UMLS:C0027530 - ncithesaurus:Neck + + + apparatus respiratorius vein + OBOL:automatic - - - collum - - + + + respiratory system vein + OBOL:automatic - - - neck (volume) - FMA:7155 + + + vein of apparatus respiratorius + OBOL:automatic + + + + + vein of respiratory system + OBOL:automatic - + - + - - - - + + + + + + + - + - - + + - - + + - - 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 + 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 - articular joint - joints - UBERON:0000982 - - - - - - skeletal joint + venae labiales inferiores + UBERON:0003478 + vein of lower lip + http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png - - - 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 + + + + + + + + + FMA - - - 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 + + + The inferior labial vein is the vein receiving blood from the lower lip. + - - - articulation - VSAO:0000101 + + + EMAPA:37202 + MA:th - - - joint - FMA:7490 - VSAO:0000101 + + + inferior labial vein + FMA:52541 - - - UMLS:C0022417 - ncithesaurus:Joint + + + lower lip vein + OBOL:automatic - - - articular joint - BTO:0001686 + + + vena labialis inferior + - + - joints - ZFA:0001596 - + venae labiales inferiores + + - + - - - - - - - - + + + + + + + + + + + + + + - - + + - - - - - - - - - - - - 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 + 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 - 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 + UBERON:0003479 + thoracic cavity vein - + - Anatomical system that has as its parts the organs concerned with reproduction. - + A vein that is part of a thoracic cavity [Automatically generated definition]. + OBOL:automatic - - - Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO] - 2012-06-20 - AAO:0010258 - AAO - AAO:BJB + + + EMAPA:37242 + MA:th + + + + + cavity of chest vein + OBOL:automatic - - - 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) + + + cavity of thorax vein + OBOL:automatic - - - UMLS:C1261210 - ncithesaurus:Reproductive_System + + + chest cavity vein + OBOL:automatic - - - Geschlechtsorgan - BTO:0000081 + + + pectoral cavity vein + OBOL:automatic - - - animal reproductive system - BTO:0000081 + + + vein of cavity of chest + OBOL:automatic - - - genitalia - + + + vein of cavity of thorax + OBOL:automatic - - - organa genitalia - BTO:0000081 + + + vein of chest cavity + OBOL:automatic - - - reproductive tissue - BTO:0000081 + + + vein of pectoral cavity + OBOL:automatic - - - systemata genitalia - - + + + vein of thoracic cavity + OBOL:automatic - + - - + + + + + + + + + + + + + + - - + + - 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 + 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 - gonads - UBERON:0000991 - - - - - - gonad + caudal vein + UBERON:0003481 + tail vein - + - 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 + A vein that is part of a tail [Automatically generated definition]. + + OBOL:automatic - - - The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO] - 2012-08-14 - TAO:0000413 - TAO - ZFIN:curator + + + EMAPA:37761 + MA:th - - - 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) + + + post-vent region vein + OBOL:automatic - - - FMA xref is a 'general anatomical term' - FMA + + + vein of post-vent region + OBOL:automatic - - - UMLS:C0018067 - ncithesaurus:Gonad + + + vein of tail + OBOL:automatic - + - gonads - ZFA:0000413 - + caudal vein + - + - + - + - + - - + + - + - - + + - - + + - 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 + 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:0001003 - - - - - skin epidermis + UBERON:0003489 + respiratory system capillary endothelium - - - 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 - + + true + + - + - Functional system which consists of structures involved in respiration. - - + An endothelium of capillary that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic - - - 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 + + + EMAPA:37575 + MA:th - - - 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 + + + apparatus respiratorius blood capillary endothelium + OBOL:automatic - - - UMLS:C0035237 - ncithesaurus:Respiratory_System + + + apparatus respiratorius capillary endothelium + OBOL:automatic - - - Atmungssystem - BTO:0000203 + + + apparatus respiratorius capillary vessel endothelium + OBOL:automatic - - - apparatus respiratorius - BTO:0000203 + + + apparatus respiratorius endothelium of blood capillary + OBOL:automatic - - - systema respiratorium - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - + + + apparatus respiratorius endothelium of capillary + OBOL:automatic + - - - 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 + + + apparatus respiratorius endothelium of capillary vessel + OBOL:automatic - - - 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 + + + blood capillary endothelium of apparatus respiratorius + OBOL:automatic - - - 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 + + + blood capillary endothelium of respiratory system + OBOL:automatic - - - - - - - - - - - - - - - - - - - - - - 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 + + + capillary endothelium of apparatus respiratorius + OBOL:automatic - - - An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] - 2012-06-20 - AAO:0010257 - AAO - AAO:BJB + + + capillary endothelium of respiratory system + OBOL:automatic - - - 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 + + + capillary vessel endothelium of apparatus respiratorius + OBOL:automatic - - - In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels - GO + + + capillary vessel endothelium of respiratory system + OBOL:automatic - - - 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 - + + + endothelium of blood capillary of apparatus respiratorius + OBOL:automatic - - - UMLS:C1508753 - ncithesaurus:Urinary_System + + + endothelium of blood capillary of respiratory system + OBOL:automatic - + - renal system - GO:0001977 + endothelium of capillary of apparatus respiratorius + OBOL:automatic - + - systema urinaria - FMA:7159 + endothelium of capillary of respiratory system + OBOL:automatic - + - systema urinarium - BTO:0003092 + endothelium of capillary vessel of apparatus respiratorius + OBOL:automatic - - - renal or urinary system - EHDAA:5901 + + + 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 - + - - + + + + + + + + + + + + + + - - + + - - - - - - - - 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 + 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 - systema cardiovasculare - UBERON:0001009 - - circulatory system - http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg + UBERON:0003494 + respiratory system venule - + - 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]. - + A venule that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic - - - - WBbt coelomocyte currently classified as circulating cell + + + EMAPA:37587 + MA:th - - - 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 + + + apparatus respiratorius venule + OBOL:automatic - - - 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 + + + venule of apparatus respiratorius + OBOL:automatic - - - systema cardiovasculare - - + + + venule of respiratory system + OBOL:automatic - + - - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + An arteriole that is part of a respiratory system [Automatically generated definition]. + EMAPA:37568 + MA:0001803 uberon - adipose - bodyfat - fatty depot - UBERON:0001013 - - - - - adipose tissue + UBERON:0003495 + respiratory system arteriole - + - - FMA + + + + + + + true + - + - 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 + An arteriole that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic - - - 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) + + + 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 + - - - in FMA this is dense irregular connective tissue - FMA + + + + + + + + + true + - - - UMLS:C0001527 - ncithesaurus:Adipose_Tissue + + + A blood vessel that is part of a head [Automatically generated definition]. + OBOL:automatic - + - fat - MA:0000009 + adult head blood vessel + OBOL:automatic - - - adipose - BTO:0001487 + + + blood vessel of adult head + OBOL:automatic - - - bodyfat - BTO:0001487 + + + blood vessel of head + OBOL:automatic - + - - + + + + + + + + + + + + + - - - - - - - + - 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 + A blood vessel that is part of an abdomen [Automatically generated definition]. + MA:0000518 + blood vessel of abdomen uberon - muscle system - muscles - musculature system - UBERON:0001015 - - - - - musculature - http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png + UBERON:0003497 + abdomen blood vessel + UBERON:0012254 - + - 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 - + A blood vessel that is part of an abdomen [Automatically generated definition]. + OBOL:automatic - + - set of muscles - FMA:32558 + blood vessel of abdomen + OBOL:automatic - - - set of skeletal muscles - MA:0000165 + + + UBERON:0012254 + abdominal aorta artery - + - - - - - - - - + + + + + + + + + + + + + + - - + + - - + + - - - - - - - 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 + A blood vessel that is part of a heart [Automatically generated definition]. + EMAPA:35397 + MA:0002483 + blood vessel of heart uberon - systema nervosum - UBERON:0001016 - - + cardiac blood vessel + UBERON:0003498 - - - 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 + heart blood vessel - - - - - - - - - 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 + A blood vessel that is part of a heart [Automatically generated definition]. + OBOL:automatic - + - neurological system - GO:0050877 - - - - - nerve net - + blood vessel of heart + OBOL:automatic - + - systema nervosum - - + cardiac blood vessel + EMAPA:35397 - + - + + + + + + + + + + + + + - - - - - - - - + - - + + - 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 + A blood vessel that is part of a brain [Automatically generated definition]. + EMAPA:35182 + MA:0002769 + blood vessel of brain uberon - neuraxis - UBERON:0001017 - - + UBERON:0003499 - - - central nervous system + brain blood vessel - - - - FBbt - cjm + + + A blood vessel that is part of a brain [Automatically generated definition]. + OBOL:automatic - - - + + + blood vessel of brain + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + - - + + - - Bgee:AN - + + 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 + - + - 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 + A blood vessel that is part of a cornea [Automatically generated definition]. + + - - - CNS - + + + + - + - systema nervosum centrale - FMA:55675 - FMA:TA - - - - - - cerebrospinal axis - FMA:55675 - - - - - neuraxis - FMA:55675 + blood vessel of cornea + OBOL:automatic + + + + + cornea blood vessel + OBOL:automatic - + - - + + + + + + + + + + + + + + - + - - - - - - - + + - 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 + + + + + + + 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 - organa sensuum - sensory organ system - set of sense organs - UBERON:0001032 - - - - sensory system - http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png + UBERON:0003501 + + retina blood vessel - + - 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) + A blood vessel that is part of a retina [Automatically generated definition]. + OBOL:automatic - + - organa sensuum - FMA:75259 - FMA:TA - + blood vessel of inner layer of eyeball + OBOL:automatic - + - sense organs - FMA:75259 + blood vessel of retina + OBOL:automatic - + - sense organs set - FMA:75259 + blood vessel of tunica interna of eyeball + OBOL:automatic - + - sensory systems - TAO:0000282 - + inner layer of eyeball blood vessel + OBOL:automatic - - - organa sensuum - - + + + retinal blood vessel + OBOL:automatic - - - set of sense organs - FMA:75259 + + + tunica interna of eyeball blood vessel + OBOL:automatic - + - - - 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 + + + + + + + + + + + + + + + + + + + + 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 - praeenteron - proenteron - UBERON:0001041 - - - - foregut - http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png + UBERON:0003502 + neck blood vessel - + - 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 + A blood vessel that is part of a neck [Automatically generated definition]. + OBOL:automatic - - - 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 + + + EMAPA:37236 + MA:th - - - UMLS:C0231051 - ncithesaurus:Foregut + + + blood vessel of neck + OBOL:automatic - - - praeenteron - - + + + blood vessel of neck (volume) + OBOL:automatic - - - proenteron - - + + + neck (volume) blood vessel + OBOL:automatic - + - - + + + + + + + + + + + + + - - - - - - - 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 + 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:0001042 - - - - - Consider generalizing to deuterostome pharynx - chordate pharynx + UBERON:0003504 + respiratory system blood vessel - - - - - - - - - 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 - + A blood vessel that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic - - - 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 + + + apparatus respiratorius blood vessel + OBOL:automatic - - - 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 + + + blood vessel of apparatus respiratorius + OBOL:automatic - - - (...) 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 + + + blood vessel of respiratory system + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme - MA + + + A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A blood vessel that is part of a iris [Automatically generated definition]. + EMAPA:37387 + MA:0001290 + ZFA:0005568 + blood vessel of iris + uberon + UBERON:0003511 + + iris blood vessel + - - - pharynx - FMA:46688 - + + + A blood vessel that is part of a iris [Automatically generated definition]. + OBOL:automatic - + - UMLS:C0031354 - ncithesaurus:Pharynx + EMAPA:37387 + MA:th + + + + + blood vessel of iris + OBOL:automatic - + - - + + + + + + + + + + + + + + + - - + + - 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 + + + + + + + A blood vessel that is part of a lung [Automatically generated definition]. + EMAPA:32867 + MA:0002457 + blood vessel of lung uberon - mesenteron - UBERON:0001045 - - + pulmonary vascular element + UBERON:0003512 - - midgut - http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg + lung blood vessel - + - 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 + A blood vessel that is part of a lung [Automatically generated definition]. + OBOL:automatic - - - UMLS:C0231052 - ncithesaurus:Midgut + + + blood vessel of lung + OBOL:automatic - + - mesenteron - - + pulmonary vascular element + EMAPA:32867 - + - - - - - - - - + + + + + + + + + + + + + - - + + - 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 + 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 - metenteron - UBERON:0001046 - - - - hindgut - http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png + UBERON:0003513 + trunk blood vessel - - - - - - - - - Wikipedia + + + A blood vessel that is part of a trunk [Automatically generated definition]. + OBOL:automatic - - - The caudalmost subdivision of a digestive tract. - + + + EMAPA:37237 + MA:th - - - the caudal portion of the primitive digestive tube of the embryo - MP:0008786 + + + blood vessel of torso + OBOL:automatic - - - 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 + + + blood vessel of trunk + OBOL:automatic - - - in FMA this class has no children. In MA it has a single child hindgut epithelium - FMA + + + 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 + - - - UMLS:C0231053 - ncithesaurus:Hindgut + + + A blood vessel that is part of a limb [Automatically generated definition]. + OBOL:automatic - - - metenteron - - + + + blood vessel of limb + OBOL:automatic - + - - + + + + + + + + + + + + + + - + - 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 + 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 - bud - future organ - placode - primordia - rudiment - UBERON:0001048 - - - - primordium + UBERON:0003515 + forelimb blood vessel - - - - 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 + A blood vessel that is part of a forelimb [Automatically generated definition]. + OBOL:automatic - + - UMLS:C0678727 - ncithesaurus:Primordium + EMAPA:37292 + MA:th - - - placode - FBbt:00005495 + + + anteriormost limb blood vessel + OBOL:automatic - - - primordia - XAO:0003043 - + + + 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 + - + - - - - - + + + + + + + + + + + + + - - + + - 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 + 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 - neural primordium - presumptive central nervous system - tubus neuralis - UBERON:0001049 - - - - neural tube - http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png + UBERON:0003516 + hindlimb blood vessel - - - - 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 + A blood vessel that is part of a hindlimb [Automatically generated definition]. + OBOL:automatic - - - The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] - 2012-09-17 - VHOG:0000307 - VHOG - - + + + EMAPA:37298 + MA:th - - - (...) 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 + + + blood vessel of hind limb + OBOL:automatic - - - 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 + + + blood vessel of hindlimb + OBOL:automatic - - - UMLS:C0231024 - ncithesaurus:Neural_Tube + + + blood vessel of lower extremity + OBOL:automatic - - - tubus neuralis - - + + + 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 + + + + + + + + + + + + + + + + + + + - - + + - 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 + 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 - intestinum rectum - rectal sac - terminal portion of large intestine - UBERON:0001052 - - - - rectum - http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif + UBERON:0003519 + thoracic cavity blood vessel - - - - 4 - cjm + + + A blood vessel that is part of a thoracic cavity [Automatically generated definition]. + OBOL:automatic - - - - - - - - - MA + + + EMAPA:37240 + MA:th - - - - - - - - - EHDAA2 + + + blood vessel of cavity of chest + OBOL:automatic - - - - - - - - - ISBN:0073040584 + + + blood vessel of cavity of thorax + OBOL:automatic - - - the terminal portion of the intestinal tube, terminating with the anus - - ISBN:0-683-40008-8 - MP:0000492 + + + blood vessel of chest cavity + OBOL:automatic - - - 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 - + + + blood vessel of pectoral cavity + OBOL:automatic - - - UMLS:C0034896 - ncithesaurus:Rectum + + + blood vessel of thoracic cavity + OBOL:automatic - - - intestinum rectum - BTO:0001158 + + + cavity of chest blood vessel + OBOL:automatic - - - - - - - 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 + + + cavity of thorax blood vessel + OBOL:automatic - - - UMLS:C1515976 - ncithesaurus:Anatomic_Structure_System_or_Substance + + + chest cavity blood vessel + OBOL:automatic + + + + + pectoral cavity blood vessel + OBOL:automatic - + - + - + - + - + - + - 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 + A blood vessel that is part of a pelvis [Automatically generated definition]. + EMAPA:37244 + MA:0000531 + blood vessel of pelvis uberon - UBERON:0001068 - - skin of back + UBERON:0003520 + pelvis blood vessel - - - - MA - - - - - - - - - - - MA - - - + - A zone of skin that is part of a back [Automatically generated definition]. - OBOL:automatic - - - - - back zone of skin + A blood vessel that is part of a pelvis [Automatically generated definition]. OBOL:automatic - - - skin, dorsal region - + + + EMAPA:37244 + MA:th - + - zone of skin of back + blood vessel of pelvis OBOL:automatic - + - + - + - + - + - + - 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 + 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:0001071 - - The transverse cervical artery splits into two branches, a superficial one and a deep one[WP] - superficial cervical artery + UBERON:0003524 + tail blood vessel - + - 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. - + A blood vessel that is part of a tail [Automatically generated definition]. + OBOL:automatic - - - EMAPA:37117 - MA:th + + + blood vessel of post-vent region + OBOL:automatic - - - UMLS:C0226271 - ncithesaurus:Superficial_Cervical_Artery + + + blood vessel of tail + OBOL:automatic - + - superficial branch of transverse cervical artery - + post-vent region blood vessel + OBOL:automatic - + - + - + - - + + - + + - - + + - - 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 + 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 - caudal vena cava - postcava - vena cava inferior - UBERON:0001072 - - - posterior vena cava - http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png + UBERON:0003526 + respiratory system capillary - - - - lexical + + + A capillary that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic - - - A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart. - - + + + EMAPA:37574 + MA:th - - - 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 + + + apparatus respiratorius blood capillary + OBOL:automatic - - - 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 + + + apparatus respiratorius capillary + OBOL:automatic + + + + + apparatus respiratorius capillary vessel + OBOL:automatic - - - UMLS:C0042458 - ncithesaurus:Inferior_Vena_Cava + + + blood capillary of apparatus respiratorius + OBOL:automatic - + - inferior caval vein - + blood capillary of respiratory system + OBOL:automatic - + - inferior vena cava - + capillary of apparatus respiratorius + OBOL:automatic - + - posterior vena cava - + capillary of respiratory system + OBOL:automatic - - - caudal vena cava - VHOG:0001194 + + + capillary vessel of apparatus respiratorius + OBOL:automatic - - - vena cava inferior - - + + + capillary vessel of respiratory system + OBOL:automatic - - - vena cava inferior - BTO:0002682 + + + respiratory system blood capillary + OBOL:automatic + + + + + respiratory system capillary vessel + OBOL:automatic - + - + - + - - + + - - + + - - - - - - - - - - - - - - - - - - - + - - + + - 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 + 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 - cavitas pericardiaca - UBERON:0001074 + UBERON:0003527 - - - pericardial cavity + kidney capillary - - - - MA - - - + - - - - FMA - - - - - - - - + - Wikipedia + - + - A potential space between the visceral and parietal layers of the pericardium. - - - - - - - + A capillary that is part of a kidney [Automatically generated definition]. + OBOL:automatic - - - Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO] - 2012-08-14 - TAO:0002220 - TAO - ZFIN:curator + + + blood capillary of kidney + OBOL:automatic - - - 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 + + + capillary of kidney + OBOL:automatic - - - 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 + + + capillary vessel of kidney + OBOL:automatic - - - UMLS:C0225972 - ncithesaurus:Pericardial_Cavity + + + kidney blood capillary + OBOL:automatic - + - pericardial space - + kidney capillary vessel + OBOL:automatic - - - cavitas pericardiaca - - + + + renal capillary + OBOL:automatic - + - + - + - + - - - + - - - - - - - + - 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 + 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 - ventricle endocardial tissue - UBERON:0001081 - - - endocardium of ventricle + UBERON:0003528 + brain gray matter - - - - - - - - - + + + A gray matter that is part of a brain [Automatically generated definition]. + OBOL:automatic - - - Endocardium that is part of the cardiac ventricle. - ZFIN:curator + + + UMLS:C1707348 + ncithesaurus:Cerebral_Gray_Matter - + - cardiac ventricle endocardium + brain grey matter + MA:0000810 + + + + + brain grey substance OBOL:automatic - + - endocardium of cardiac ventricle + gray matter of brain OBOL:automatic - + - endocardium of heart ventricle + grey matter of brain OBOL:automatic - + - endocardium of lower chamber of heart + grey substance of brain + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + - endocardium of ventricle of heart + anteriormost limb skin OBOL:automatic - + - heart ventricle endocardium + fore limb skin OBOL:automatic - + - lower chamber of heart endocardium + skin of fore limb OBOL:automatic - + - ventricle of heart endocardium + skin of forelimb OBOL:automatic - - - ventricle endocardial tissue - VHOG:0000607 + + + skin of upper limb + FMA:23101 + + + + + upper limb skin + FMA:23101 + + + + + wing skin + NCBITaxon:8782 + OBOL:automatic + - + - + - + - + - + - + - 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 + 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:0001082 - - epicardium of ventricle + UBERON:0003532 + hindlimb skin - + - An epicardial layer that lines a cardiac ventricle - + A zone of skin that is part of a hindlimb [Automatically generated definition]. + OBOL:automatic - - - 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 + + + UMLS:C0222268 + ncithesaurus:Skin_of_the_Lower_Limb_and_Hip - + - cardiac ventricle epicardium + 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 + - + - + - + - + - + - - - - - - - + - 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 + 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 - ventricle cardiac muscle - UBERON:0001083 - + UBERON:0003534 - - myocardium of ventricle + tail skin - - - - - - - - - - - - + - Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer. - ZFIN:curator + A zone of skin that is part of a tail [Automatically generated definition]. + OBOL:automatic - - - 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 + + + post-vent region skin + OBOL:automatic - - - 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 + + + skin of post-vent region + OBOL:automatic - - - ventricle cardiac muscle - VHOG:0000604 + + + skin of tail + OBOL:automatic - + - + - + @@ -14707,26612 +88317,25482 @@ - + + - 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 + + + + + + + + + + + + + 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:0001084 - skin of head + UBERON:0003566 + head connective tissue - + - A zone of skin that is part of a head [Automatically generated definition]. + A portion of connective tissue that is part of a head [Automatically generated definition]. OBOL:automatic - - - UMLS:C0205029 - ncithesaurus:Head_Skin + + + adult head connective tissue + OBOL:automatic - + - adult head zone of skin + adult head portion of connective tissue OBOL:automatic - + - head zone of skin + adult head textus connectivus OBOL:automatic - + - zone of skin of adult head + connective tissue of adult head OBOL:automatic - + - zone of skin of head + 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 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 + 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:0001085 - skin of trunk + UBERON:0003567 + abdomen connective tissue - + - A zone of skin that is part of a trunk [Automatically generated definition]. + A portion of connective tissue that is part of an abdomen [Automatically generated definition]. OBOL:automatic - - - EMAPA:37278 - MA:th - - - - - UMLS:C0205031 - ncithesaurus:Skin_of_the_Trunk + + + abdomen portion of connective tissue + OBOL:automatic - + - torso zone of skin + abdomen textus connectivus OBOL:automatic - + - trunk zone of skin + connective tissue of abdomen OBOL:automatic - + - zone of skin of torso + portion of connective tissue of abdomen OBOL:automatic - + - zone of skin of trunk + textus connectivus of abdomen OBOL:automatic - + - + - + - - + + - + - - + + - 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 + 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:0001088 - - - - urine + UBERON:0003568 + neck connective tissue - + - Excretion that is the output of a kidney - - + A portion of connective tissue that is part of a neck [Automatically generated definition]. + OBOL:automatic - + - UMLS:C0042036 - ncithesaurus:Urine + EMAPA:37250 + MA:th - - - - - - - - - - - - - - - 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 + + + connective tissue of neck + OBOL:automatic - - - Joint fluid is a transudate of plasma that is actively secreted by synovial cells. - + + + connective tissue of neck (volume) + OBOL:automatic - - - 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 + + + neck (volume) connective tissue + OBOL:automatic - - - UMLS:C0039097 - ncithesaurus:Synovial_Fluid + + + neck (volume) portion of connective tissue + OBOL:automatic - + - joint fluid - + 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 - + - - - - - - - - - - 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 - + + 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 + - + - Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]. - ZFA:0005280 + A portion of connective tissue that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic - + - cardiac muscle muscle tissue + apparatus respiratorius connective tissue OBOL:automatic - + - cardiac muscle textus muscularis + apparatus respiratorius portion of connective tissue OBOL:automatic - + - heart muscle muscle tissue + apparatus respiratorius textus connectivus OBOL:automatic - + - heart muscle textus muscularis + connective tissue of apparatus respiratorius OBOL:automatic - + - heart myocardium muscle tissue + connective tissue of respiratory system OBOL:automatic - + - heart myocardium textus muscularis + portion of connective tissue of apparatus respiratorius OBOL:automatic - + - muscle of heart muscle tissue + portion of connective tissue of respiratory system OBOL:automatic - + - muscle of heart textus muscularis + respiratory system portion of connective tissue OBOL:automatic - + - muscle tissue of cardiac muscle + respiratory system textus connectivus OBOL:automatic - + - muscle tissue of heart muscle + textus connectivus of apparatus respiratorius OBOL:automatic - + - muscle tissue of heart myocardium + textus connectivus of respiratory system + 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 + + + - muscle tissue of muscle of heart + connective tissue of lower respiratory tract OBOL:automatic - + - muscle tissue of myocardium + lower respiratory tract portion of connective tissue OBOL:automatic - + - myocardium muscle tissue + lower respiratory tract textus connectivus OBOL:automatic - + - myocardium textus muscularis + portion of connective tissue of lower respiratory tract OBOL:automatic - + - textus muscularis of cardiac muscle + textus connectivus of lower respiratory tract + 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 + + + - textus muscularis of heart muscle + connective tissue of larynx OBOL:automatic - + - textus muscularis of heart myocardium + larynx portion of connective tissue OBOL:automatic - + - textus muscularis of muscle of heart + larynx textus connectivus OBOL:automatic - + - textus muscularis of myocardium + portion of connective tissue of larynx OBOL:automatic - + + + textus connectivus of larynx + OBOL:automatic + + + - cardiac musculature - BILA:0000134 + laryngeal connective tissue + EMAPA:35471 - + - - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - textus muscularis levis; textus muscularis nonstriatus - UBERON:0001135 - + UBERON:0003585 - - - smooth muscle tissue - Glatte:Muskelzellen.jpg + dermis connective tissue - - - 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) + + + A portion of connective tissue that is part of a dermis [Automatically generated definition]. + OBOL:automatic - - - UMLS:C1267092 - ncithesaurus:Smooth_Muscle_Tissue + + + connective tissue of dermis + OBOL:automatic - + - textus muscularis nonstriatus - FMA:14070 - FMA:TA - + dermis portion of connective tissue + OBOL:automatic - - - visceral muscle - + + + dermis textus connectivus + OBOL:automatic - - - visceral muscle tissue - + + + portion of connective tissue of dermis + OBOL:automatic - - - textus muscularis levis; textus muscularis nonstriatus - - + + + textus connectivus of dermis + OBOL:automatic - + - + - + - - - - - + - - + - + - 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 + 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:0001136 - - mesothelium - http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg + UBERON:0003586 + trunk connective tissue - + - 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 + A portion of connective tissue that is part of a trunk [Automatically generated definition]. + OBOL:automatic - + - UMLS:C0086610 - ncithesaurus:Mesothelium + 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 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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:0001137 - - - dorsum - http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG + UBERON:0003587 + limb connective tissue - + - 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 + A portion of connective tissue that is part of a limb [Automatically generated definition]. + OBOL:automatic - + - UMLS:C0004600 - ncithesaurus:Back + EMAPA:37313 + MA:th - + - back - FMA:14181 + connective tissue of limb + OBOL:automatic - + - back of body proper - FMA:14181 + 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 - + - + - + - - + + - + - + - - + + - - + + - 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 + 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 - venae renales - UBERON:0001140 - - - renal vein - http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png + UBERON:0003588 + forelimb connective tissue - + - 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 + A portion of connective tissue that is part of a forelimb [Automatically generated definition]. + OBOL:automatic - - - 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]. - + + + EMAPA:37314 + MA:th - - - in EHDAA2, the renal vein is part of the kidney - EHDAA2 + + + connective tissue of anteriormost limb + OBOL:automatic - - - UMLS:C0035092 - ncithesaurus:Renal_Vein + + + connective tissue of fore limb + OBOL:automatic - + - kidney vein + connective tissue of forelimb OBOL:automatic - + - vein of kidney + connective tissue of superior member OBOL:automatic - - - venae renales - - + + + connective tissue of upper extremity + OBOL:automatic + + + + + wing connective tissue + NCBITaxon:8782 + OBOL:automatic + - + - - + + + + + + + + + + + + + - + - - + + - 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 + + + + + + + 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 - hindgut - UBERON:0001155 - - - - - colon + UBERON:0003589 + hindlimb connective tissue - - - - 3 - cjm + + + A portion of connective tissue that is part of a hindlimb [Automatically generated definition]. + OBOL:automatic - - - - - - - - - FMA + + + EMAPA:37322 + MA:th - - - Last portion of the large intestine before it becomes the rectum. - - - ZFIN:curator + + + connective tissue of hind limb + OBOL:automatic - - - 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 + + + connective tissue of hindlimb + OBOL:automatic - - - 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 + + + connective tissue of inferior member + 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:0000648 - VHOG - - ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 + + + connective tissue of lower extremity + OBOL:automatic - - - UMLS:C0009368 - ncithesaurus:Colon + + + hind limb connective tissue + OBOL:automatic - + - - - - - - - - + + + + + + + + + + + + + - - + + - 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 + 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 - colon sigmoideum - pelvic colon - sigmoid colon - sigmoid flexure - UBERON:0001159 - - - sigmoid colon - http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg + UBERON:0003593 + thoracic cavity connective tissue - - - - FMA + + + 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 - - - - - - - - - Wikipedia + + + connective tissue of pectoral cavity + OBOL:automatic - - - 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. - + + + connective tissue of thoracic cavity + OBOL:automatic - - - UMLS:C0227391 - ncithesaurus:Sigmoid_Colon + + + pectoral cavity connective tissue + OBOL:automatic - - - UMLS:C0682612 - ncithesaurus:Sigmoid_Flexure + + + pectoral cavity portion of connective tissue + OBOL:automatic - - - colon sigmoideum - - + + + pectoral cavity textus connectivus + 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]. + + + portion of connective tissue of cavity of chest OBOL:automatic - + - anatomical wall of large intestine + portion of connective tissue of cavity of thorax OBOL:automatic - + - large intestine anatomical wall + portion of connective tissue of chest cavity OBOL:automatic - - - - - - - - - - - - - - - - - - - - - - - - - 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]. + + + portion of connective tissue of pectoral cavity OBOL:automatic - - - UMLS:C0734203 - ncithesaurus:Large_Intestinal_Mucosa + + + portion of connective tissue of thoracic cavity + OBOL:automatic - + - large intestine mucosa of organ + textus connectivus of cavity of chest OBOL:automatic - + - large intestine mucous membrane + textus connectivus of cavity of thorax OBOL:automatic - + - large intestine organ mucosa + textus connectivus of chest cavity OBOL:automatic - + - mucosa of organ of large intestine + textus connectivus of pectoral cavity OBOL:automatic - + - organ mucosa of large intestine + textus connectivus of thoracic cavity OBOL:automatic - + - tunica mucosa intestini crassi - FMA:14969 - FMA:TA - + thoracic cavity portion of connective tissue + OBOL:automatic + + + + + thoracic cavity textus connectivus + OBOL:automatic - + - + - + - + - + - + - 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 + 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 - submucous layer of large intestine - UBERON:0001208 - submucosa of large intestine + UBERON:0003594 + pelvis connective tissue - - - A submucosa that is part of a large intestine [Automatically generated definition]. + + + pelvis portion of connective tissue OBOL:automatic - - - EMAPA:37560 - MA:th + + + pelvis textus connectivus + OBOL:automatic - - - UMLS:C0734204 - ncithesaurus:Large_Intestinal_Submucosa + + + portion of connective tissue of pelvis + OBOL:automatic - + - tela submucosa intestini crassi - FMA:14970 - FMA:TA - + textus connectivus of pelvis + OBOL:automatic - - - submucous layer of large intestine - BTO:0002111 + + + 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 - + - + - + - + - + + - + - 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 + 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:0001209 - serosa of large intestine + UBERON:0003599 + tail connective tissue - + - A serous membrane that is part of a large intestine [Automatically generated definition]. + A portion of connective tissue that is part of a tail [Automatically generated definition]. OBOL:automatic - - - EMAPA:37557 - MA:th - - - - - UMLS:C1517727 - ncithesaurus:Large_Intestinal_Serosal_Surface + + + connective tissue of post-vent region + OBOL:automatic - + - large intestine serous membrane + connective tissue of tail OBOL:automatic - + - serous membrane of large intestine + portion of connective tissue of post-vent region OBOL:automatic - + - tunica serosa intestini crassi - FMA:14975 - FMA:TA - + portion of connective tissue of tail + OBOL:automatic - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 + + + post-vent region connective tissue + OBOL:automatic - - - 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]. - + + + post-vent region portion of connective tissue + OBOL:automatic - - - UMLS:C0226754 - ncithesaurus:Inferior_Mesenteric_Vein + + + post-vent region textus connectivus + OBOL:automatic - - - lower mesenteric vein - BTO:0002782 + + + tail portion of connective tissue + OBOL:automatic - - - vena mesenterica inferior - - + + + tail textus connectivus + OBOL:automatic - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 + + + + textus connectivus of post-vent region + OBOL:automatic - - - + + + textus connectivus of tail + OBOL:automatic + + + + + + + + + + + + + + + + + + + + - - + + - - FMA - + + 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 funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP]. - MP:0004194 + A cartilage that is part of a neck [Automatically generated definition]. + OBOL:automatic - + - UMLS:C0227666 - ncithesaurus:Renal_Pelvis + EMAPA:37251 + MA:th - - - p. renallis - - + + + cartilage of neck + OBOL:automatic - - - pyelum - MP:0004194 + + + cartilage of neck (volume) + OBOL:automatic + + + + + neck (volume) cartilage + 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 + 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:0001242 - - - intestinal mucosa + UBERON:0003603 + lower respiratory tract cartilage - + - Mucosal layer that lines the intestine. - UBERON:cjm + A cartilage that is part of a lower respiratory tract [Automatically generated definition]. + OBOL:automatic - + - UMLS:C0021839 - ncithesaurus:Intestinal_Mucosa + EMAPA:37547 + MA:th - + + + UMLS:C1708759 + ncithesaurus:Lower_Respiratory_Tract_Cartilage + + + - bowel mucosa + cartilage of lower respiratory tract OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - bowel mucosa of organ + + + A skin gland that is part of a camera-type eye [Automatically generated definition]. OBOL:automatic - + + + EMAPA:37530 + MA:th + + + - bowel mucous membrane + camera-type eye skin gland OBOL:automatic - + - bowel organ mucosa + camera-type eye skin glands OBOL:automatic - + - intestine mucosa of organ + camera-type eye skin glands set OBOL:automatic - + - intestine mucous membrane + skin gland of camera-type eye OBOL:automatic - + - intestine organ mucosa + skin gland of vertebrate eye OBOL:automatic - + - mucosa of bowel + skin glands of camera-type eye OBOL:automatic - + - mucosa of organ of bowel + skin glands of vertebrate eye OBOL:automatic - + - mucosa of organ of intestine + skin glands set of camera-type eye OBOL:automatic - + - mucous membrane of bowel + skin glands set of vertebrate eye OBOL:automatic - + - mucous membrane of intestine + vertebrate eye skin gland OBOL:automatic - + - organ mucosa of bowel + vertebrate eye skin glands OBOL:automatic - + - organ mucosa of intestine + vertebrate eye skin glands set 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 + 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:0001243 - serosa of intestine + UBERON:0003609 + + aorta elastic tissue - + - A serous membrane that is part of a wall of intestine [Automatically generated definition]. + 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 - - - EMAPA:37619 - MA:th + + + adult aorta elastic tissue + OBOL:automatic - + - anatomical wall of bowel serosa + adult aorta textus connectivus elasticus OBOL:automatic - + - anatomical wall of bowel serous membrane + aorta elastic connective tissue OBOL:automatic - + - anatomical wall of intestine serosa + aorta elastic lamina + MP:0009862 + + + + + aorta elastic laminae + MP:0009862 + + + + + + aorta textus connectivus elasticus OBOL:automatic - + - anatomical wall of intestine serous membrane + dorsal aorta elastic connective tissue OBOL:automatic - + - bowel anatomical wall serosa + dorsal aorta elastic tissue OBOL:automatic - + - bowel anatomical wall serous membrane + dorsal aorta textus connectivus elasticus OBOL:automatic - + - bowel wall serosa + elastic connective tissue of adult aorta OBOL:automatic - + - bowel wall serous membrane + elastic connective tissue of aorta OBOL:automatic - + - intestinal wall serosa + elastic connective tissue of dorsal aorta OBOL:automatic - + - intestinal wall serous membrane + elastic connective tissue of trunk of aortic tree OBOL:automatic - + - intestine anatomical wall serosa + elastic tissue of adult aorta OBOL:automatic - + - intestine anatomical wall serous membrane + elastic tissue of aorta OBOL:automatic - + - intestine wall serosa + 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 + + + - intestine wall serous membrane + apparatus respiratorius elastic connective tissue OBOL:automatic - + - serosa of anatomical wall of bowel + apparatus respiratorius elastic tissue OBOL:automatic - + - serosa of anatomical wall of intestine + apparatus respiratorius textus connectivus elasticus OBOL:automatic - + - serosa of bowel anatomical wall + elastic connective tissue of apparatus respiratorius OBOL:automatic - + - serosa of bowel wall + elastic connective tissue of respiratory system OBOL:automatic - + - serosa of intestinal wall + elastic tissue of apparatus respiratorius OBOL:automatic - + - serosa of intestine anatomical wall + elastic tissue of respiratory system OBOL:automatic - + - serosa of intestine wall + respiratory system elastic connective tissue OBOL:automatic - + - serosa of wall of bowel + respiratory system textus connectivus elasticus OBOL:automatic - + - serosa of wall of intestine + textus connectivus elasticus of apparatus respiratorius OBOL:automatic - + - serous membrane of anatomical wall of bowel + 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 + - - - serous membrane of anatomical wall of intestine + + + An elastic tissue that is part of a circulatory system [Automatically generated definition]. OBOL:automatic - + - serous membrane of bowel anatomical wall + cardiovascular system elastic connective tissue OBOL:automatic - + - serous membrane of bowel wall + cardiovascular system textus connectivus elasticus OBOL:automatic - + - serous membrane of intestinal wall + circulatory system elastic connective tissue OBOL:automatic - + - serous membrane of intestine anatomical wall + circulatory system elastic tissue OBOL:automatic - + - serous membrane of intestine wall + circulatory system textus connectivus elasticus OBOL:automatic - + - serous membrane of wall of bowel + elastic connective tissue of cardiovascular system OBOL:automatic - + - serous membrane of wall of intestine + elastic connective tissue of circulatory system OBOL:automatic - + - wall of bowel serosa + elastic tissue of cardiovascular system OBOL:automatic - + - wall of bowel serous membrane + elastic tissue of circulatory system OBOL:automatic - + - wall of intestine serosa + textus connectivus elasticus of cardiovascular system OBOL:automatic - + - wall of intestine serous membrane + textus connectivus elasticus of circulatory system 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 + 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 - proctodeum - UBERON:0001245 + UBERON:0003614 - - anus - http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg - http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif + blood vessel elastic tissue - + - 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 + Elastic tissue layer that lines a blood vessel layer. + + - - - UMLS:C0003461 - ncithesaurus:Anus + + + elastic lamina + MP:0006083 - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - + + + elastic laminae + MP:0006083 + - - - An adventitia that is part of a ureter. + + + blood vessel elastic connective tissue OBOL:automatic - + - tunica adventitia (ureter) - FMA:15892 - FMA:TA - + blood vessel textus connectivus elasticus + OBOL:automatic - + - tunica adventitia ureteris - FMA:15892 - FMA:TA - + 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 - + - + - + - + - - + + - + - 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 + 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:0001253 - lamina propria of ureter + UBERON:0003615 + lung elastic tissue - - - - - - - - - true - + + + Elastic tissue that is part of a lung [Automatically generated definition]. + OBOL:automatic - - - A lamina propria that is part of a ureter [Automatically generated definition]. + + + elastic connective tissue of lung OBOL:automatic - + - lamina propria mucosa of ureter + elastic tissue of lung OBOL:automatic - + - lamina propria mucosae of ureter + lung elastic connective tissue OBOL:automatic - + - ureter lamina propria mucosa + lung textus connectivus elasticus OBOL:automatic - + - ureter lamina propria mucosae + textus connectivus elasticus of lung OBOL:automatic + + + + pulmonary elastic fiber + + - + - - - - + + + + + + + + + + + + + - + - - + + - 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 - - - + + + + + + + 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 - - urinary bladder - Urinary:system.svg + aorta tunica media - - - - 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 - + The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers. + MP:0009873 - - - 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 + + + adult aorta tunica media + OBOL:automatic - - - 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 + + + dorsal aorta tunica media + OBOL:automatic - - - - bladder - EHDAA2:0000174 + + + + trunk of aortic tree tunica media + OBOL:automatic - - - UMLS:C0005682 - ncithesaurus:Bladder + + + tunica media of adult aorta + OBOL:automatic - + - vesica urinaria - - + tunica media of aorta + OBOL:automatic - - - urocyst - + + + tunica media of dorsal aorta + OBOL:automatic - - - vesica - BTO:0001418 + + + tunica media of trunk of aortic tree + OBOL:automatic - + - + - + - + - - + + - + - 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 + + + + + + + + + + + + + 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 - wall of urinary bladder + aorta tunica intima - + - An anatomical wall that lines the insider of a urinary bladder. - + The innermost layer of the aorta, containing the endothelium and an inner elastic membrane. + MP:0009872 - - - UMLS:C0458421 - ncithesaurus:Bladder_Wall + + + adult aorta tunica intima + OBOL:automatic - + - anatomical wall of bladder + dorsal aorta tunica intima OBOL:automatic - + - anatomical wall of urinary bladder + trunk of aortic tree tunica intima OBOL:automatic - + - bladder anatomical wall + tunica intima of adult aorta OBOL:automatic - + - bladder wall + tunica intima of aorta OBOL:automatic - + - urinary bladder anatomical wall + tunica intima of dorsal aorta OBOL:automatic - + - wall of bladder + 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 + + + + + + + + + + + + + + + + + + + + - - + + - 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 + An arterial blood vessel that is part of a kidney [Automatically generated definition]. + EMAPA:31436 + MA:0002578 uberon - UBERON:0001259 - + kidney arterial system + UBERON:0003644 - mucosa of urinary bladder + kidney arterial blood vessel - + - the mucous membrane lining the urinary bladder - MGI:anna - MP:0011766 + An arterial blood vessel that is part of a kidney [Automatically generated definition]. + OBOL:automatic - - - UMLS:C0227691 - ncithesaurus:Bladder_Mucosa + + + kidney arterial system + EMAPA:31436 + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - bladder mucous membrane - OBOL:automatic + + + Any joint that is part of a (free) limb. + - + - bladder organ mucosa + joint of limb skeletal system OBOL:automatic - + - mucosa of bladder - OBOL:automatic + skeletal limb joint + GO:0036023 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - - - tunica mucosa (vesica urinaria) - FMA:15928 - FMA:TA - + + + + + + + + + https://purl.obolibrary.org/obo/uberon/tracker/324 - + + + Any muscle organ that is part of a limb [Automatically generated definition]. + OBOL:automatic + + + - tunica mucosa vesicae - FMA:15928 - FMA:TA - + limb muscle organ + OBOL:accepted - + - tunica mucosa vesicae urinariae - MP:MP + limb skeletal muscle + OBOL:exploratory - + - urinary bladder mucous membrane - OBOL:automatic + muscle organ of limb + OBOL:accepted - + - + - + - + - + + - + - 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 + + + + + + + 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 - UBERON:0001260 - serosa of urinary bladder + arm muscle system + musculature of arm + musculature of the arm + UBERON:0003662 + forelimb muscle - + - + - + prolog - + - A serous membrane that is part of a urinary bladder [Automatically generated definition]. + Any muscle organ that is part of a forelimb. OBOL:automatic - + + + FMA and MA class actually refer to muscles of entire pectoral complex + FMA + + + - bladder serous membrane + fore limb muscle organ OBOL:automatic - + - serous membrane of bladder + forelimb muscle organ OBOL:automatic - + - serous membrane of urinary bladder - OBOL:automatic + free upper limb muscle + FMA:37348 - + - tunica serosa (vesica urinaria) - FMA:15932 - FMA:TA - + muscle of free upper limb + FMA:37348 - + - tunica serosa vesicae - FMA:15932 - FMA:TA - + muscle of upper limb + FMA:9621 - + - urinary bladder serous membrane + 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 + - + - + - + - + - - + + - + - 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 + + + + + + + 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:0001261 - lamina propria of urinary bladder + UBERON:0003663 + + hindlimb muscle - + + + + + + + + + prolog + + + - A lamina propria that is part of a urinary bladder [Automatically generated definition]. + Any muscle organ that is part of a hindlimb [Automatically generated definition]. OBOL:automatic - - - UMLS:C1706967 - ncithesaurus:Bladder_Lamina_Propria + + + free lower limb muscle + FMA:37368 - + - bladder lamina propria + hind limb muscle organ OBOL:automatic - + - bladder lamina propria mucosa + hindlimb muscle organ OBOL:automatic - + - bladder lamina propria mucosae + inferior member muscle organ OBOL:automatic - + - lamina propria mucosa of bladder + lower extremity muscle organ OBOL:automatic - + - lamina propria mucosa of urinary bladder - OBOL:automatic + lower limb skeletal muscle + - + - lamina propria mucosae of bladder - OBOL:automatic + muscle of free lower limb + FMA:37368 - + - lamina propria mucosae of urinary bladder + muscle of posterior limb + + + + + + muscle organ of hind limb OBOL:automatic - + - lamina propria of bladder + muscle organ of hindlimb OBOL:automatic - + - urinary bladder lamina propria mucosa + muscle organ of inferior member OBOL:automatic - + - urinary bladder lamina propria mucosae + muscle organ of lower extremity 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 + + + + + + + + + + + + + + + + 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 - bowel wall - UBERON:0001262 - wall of intestine + UBERON:0003665 + post-anal tail muscle - + - An anatomical wall that is part of a intestine [Automatically generated definition]. + A muscle organ that attaches to a tail vertebra [Automatically generated definition]. OBOL:automatic - - - UMLS:C1708548 - ncithesaurus:Intestinal_Wall_Tissue + + + the BTO class may possibly refer to an invertebrate structure + BTO - - - anatomical wall of bowel - OBOL:automatic + + + EMAPA:37759 + MA:th - + - anatomical wall of intestine + muscle organ of post-vent region OBOL:automatic - + - bowel anatomical wall + muscle organ of tail OBOL:automatic - + - bowel wall + post-vent region muscle organ OBOL:automatic - + - intestine anatomical wall - OBOL:automatic + tail muscle + MA:0000699 - + - wall of bowel + tail muscle organ OBOL:automatic - - - - bowel wall - MA:0001525 - - + - + - + - + + + + + - - + + - + - + - - + + - - + + - - 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 + 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 - girdle - pelvic - pelvic girdle - UBERON:0001271 - - - pelvic girdle region + cavitas abdominis + UBERON:0003684 + + abdominal cavity + http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg - + - 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 + The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity). + UBERON:cjm - - - 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 - + + + in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity + FMA - + - EMAPA:37862 - MA:th + UMLS:C0230168 + ncithesaurus:Abdominal_Cavity - - - UMLS:C0684083 - ncithesaurus:Pelvic_Girdle + + + cavity of abdominal compartment + FMA:12266 - + + + cavity of compartment of abdomen + FMA:12266 + + + + + space of abdominal compartment + FMA:12266 + + + - pelvic girdle - + cavitas abdominis + + + + + + + cavitas abdominis + GAID:17 - + - + - + - - + + - - - - + - - + + - - + + - 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 + 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 - intestine epithelium - UBERON:0001277 + UBERON:0003687 - - intestinal epithelium + Design pattern notes: check whether this fits the foramen design pattern + foramen magnum + http://upload.wikimedia.org/wikipedia/commons/3/39/Gray130.png - + - Epithelial layer that lines the intestine. - UBERON:cjm + 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]. + - + - 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] + Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO] 2012-08-14 - TAO:0005124 + TAO:0002045 TAO - ZFIN:curator + TAO:wd - + - UMLS:C0226890 - ncithesaurus:Intestinal_Epithelium + EMAPA:37868 + MA:th - - - bowel epithelial tissue - OBOL:automatic + + + UMLS:C0016519 + ncithesaurus:Foramen_Magnum + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - bowel epithelium - OBOL:automatic + + + 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 - - - epithelial tissue of bowel - OBOL:automatic + + + EMAPA:37064 + MA:th - - - epithelial tissue of intestine - OBOL:automatic + + + UMLS:C0836916 + ncithesaurus:Abdominal_Wall - + - epithelium of bowel - OBOL:automatic + paries abdominalis + - + - epithelium of intestine - OBOL:automatic + wall of abdomen + FMA:259054 - + - intestine epithelial tissue - OBOL:automatic + wall of abdomen proper + FMA:10429 - - - villous epithelium - ZFA:0005124 + + + abdominal wall proper + FMA:10429 + + + + + layers of the abdominal wall + + + + + + paries abdominalis + + - + - - - - - - - - - - - - - - - - - - - - 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 + + + 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 - UBERON:0001278 - epithelium of large intestine + 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 - + - An epithelium that is part of a large intestine [Automatically generated definition]. - OBOL:automatic + A vein arising from the splenic trabecular vein in the hilum of the spleen that drains into the portal vein. + ncithesaurus:Splenic_Vein - - - epithelial tissue of large intestine - OBOL:automatic + + + EMAPA:37226 + MA:th - + + + UMLS:C0038001 + ncithesaurus:Splenic_Vein + + + - large intestine epithelial tissue - OBOL:automatic + vena splenica + FMA:14331 + FMA:TA + + + + + + lienal vein + + MA:0002164 + + + + + vena lienalis + + - + - - + + + + + + + + + + + + + + + + + + - - + + - 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 + + + + + + + + + + + + + + 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 - hypogastric vein - v. hypogastrica - v. iliaca interna - UBERON:0001317 - - internal iliac vein - http://upload.wikimedia.org/wikipedia/commons/c/cb/Internaliliacv.png + UBERON:0003714 + neural tissue - - - - MA + + + Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. + FMA:9642 - - - 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]. - + + + 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 - - - EMAPA:37148 - MA:th + + + FMA definition includes vasculature + FMA - + - UMLS:C0226764 - ncithesaurus:Internal_Iliac_Vein + UMLS:C0027757 + ncithesaurus:Nervous_Tissue - - - hypogastric vein - - MA:0002139 + + + nerve tissue + FMA:9642 - - - v. hypogastrica - - + + + nervous tissue + FMA:9642 - - - v. iliaca interna - - + + + portion of neural tissue + FMA:9642 - + - + - + - - + + - - + + - + - - + + - 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 - + + + + + + + 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 - - urethral gland + splanchnic nerve - - - - 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 + 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:37784 + EMAPA:37959 MA:th - - - gland of urethra - OBOL:automatic + + + splanchnic nerves + BAMS:spn + + + + + visceral nerve + - + - - + + + - - - - - - - + + - - + + - 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 + + + + + + + + + + + + + + + + + + + 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 - 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 + inferior laryngeal nerve + ramus recurrens + UBERON:0003716 + recurrent laryngeal nerve - + - - + + - cjm + Wikipedia - + - The anus and surrounding regions. Encompasses both internal and external regions, where present - + 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. + - - - 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 + + + Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754]. + AAO:0010754 - - - UMLS:C0230120 - ncithesaurus:Anal_Region + + + recurrent nerve + + + + + + nervus laryngeus recurrens + + + + + + + vagus X nerve recurrent laryngeal branch + VHOG:0001347 + + + + + inferior laryngeal nerve + GAID:804 + + + + + ramus recurrens + AAO:0010754 - + - + - + - - + + - + - - + + - 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 + 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 - UBERON:0001415 - skin of pelvis + nervi thoracici + pectoral nerve + UBERON:0003726 + thoracic nerve - + - A zone of skin that is part of a pelvis [Automatically generated definition]. - OBOL:automatic + 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]. + + + + - EMAPA:37282 - MA:th + UMLS:C1285089 + ncithesaurus:Intercostal_Nerve - + - pelvis zone of skin - OBOL:automatic + anterior ramus of thoracic nerve + FMA:6028 - + - zone of skin of pelvis - OBOL:automatic + 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 + + - + - + - + - + - + + - + - 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 + + + + + + + + + + + + + + + + + + + + + + + + + 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 - UBERON:0001416 - + buccal mucosa + mucosal lining of mouth + oral mucosa + tunica mucosa oris + UBERON:0003729 - skin of abdomen + mouth mucosa - + - A zone of skin that is part of an abdomen [Automatically generated definition]. - OBOL:automatic + 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:C0222166 - ncithesaurus:Abdominal_Skin + UMLS:C0026639 + ncithesaurus:Oral_Mucosa - + - abdomen zone of skin - OBOL:automatic + mouth mucosa + FMA:59660 - + - skin of abdomen proper - FMA:22988 + mouth mucous membrane + OBOL:accepted - + - zone of skin of abdomen - OBOL:automatic + 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 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) + 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 - UBERON:0001417 - skin of neck + upper body nerve + UBERON:0003824 + nerve of thoracic segment - + - A zone of skin that is part of a neck [Automatically generated definition]. + A nerve that is part of a thorax [Automatically generated definition]. OBOL:automatic - + - EMAPA:37277 + EMAPA:37265 MA:th - - - UMLS:C0205030 - ncithesaurus:Neck_Skin - - - - - neck (volume) zone of skin - OBOL:automatic - - - + - neck zone of skin + nerve of thorax OBOL:automatic - - - zone of skin of neck - OBOL:automatic + + + thoracic segment nerve + MA:0000562 - + - zone of skin of neck (volume) + thorax nerve OBOL:automatic + + + + upper body nerve + MA:0000562 + - + - + - + - + - + - + - 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 + A nerve that is part of an abdominal segment of trunk [Automatically generated definition]. + EMAPA:37061 + MA:0000528 + abdominal segment nerve uberon - upper body skin - UBERON:0001418 - skin of thorax + UBERON:0003825 + nerve of abdominal segment - + - A zone of skin that is part of a thorax [Automatically generated definition]. + A nerve that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic - + - EMAPA:37765 + EMAPA:37061 MA:th - - - thorax zone of skin - OBOL:automatic - - - + - zone of skin of thorax - OBOL:automatic + abdominal segment nerve + MA:0000528 - + - + - + - + - + + - + - 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 + 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 - UBERON:0001419 - - skin of limb + upper body bone + UBERON:0003827 + thoracic segment bone - + - A zone of skin that is part of a limb [Automatically generated definition]. + A bone that is part of a thorax [Automatically generated definition]. OBOL:automatic - + - UMLS:C1282135 - ncithesaurus:Skin_of_the_Extremity + EMAPA:37247 + MA:th - + - limb zone of skin + bone of thorax OBOL:automatic - + - zone of skin of limb + bone organ of thorax OBOL:automatic + + + + thorax bone + OBOL:automatic + + + + + thorax bone organ + OBOL:automatic + + + + + upper body bone + MA:0000559 + - + - + - + - + - - + + - - - - - - - - - - - - - + - - 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 + 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 - pectoral girdle - pectoral region - UBERON:0001421 - - - - pectoral girdle region + UBERON:0003828 + abdominal segment bone - + - 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 + A bone that is part of an abdominal segment of trunk [Automatically generated definition]. + OBOL:automatic - + - EMAPA:37856 + EMAPA:37058 MA:th - + - cingulum membri superioris - FMA:23217 - FMA:TA - + abdominal segment of trunk bone + OBOL:automatic - - - cingulum membri superioris - FMA:TA + + + abdominal segment of trunk bone organ + OBOL:automatic - - - shoulder girdle - FMA:23217 + + + bone of abdominal segment of trunk + OBOL:automatic - - - upper limb girdle - FMA:23217 + + + bone organ of abdominal segment of trunk + OBOL:automatic - + - + - - - - - + - - + + - + + - - - - - - - - - - - - - - - - - - - + - - - - - - - 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 + Any muscle tissue that is part of the urethra. + EMAPA:37787 + MA:0002649 uberon - Skelettsystem - UBERON:0001434 - - - - - skeletal system - https://github.com/obophenotype/uberon/wiki/The-skeletal-system + urethral muscle layer + UBERON:0003829 + urethra muscle tissue - + - 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 + Any muscle tissue that is part of the urethra. + UBERON:cjm - + - UMLS:C0037253 - ncithesaurus:Skeletal_System - - - - - set of all bones and joints - + EMAPA:37787 + MA:th - + - Skelettsystem - BTO:0001486 + urethral muscle layer + MA:0002649 - + - + - + - - + + - - + + - + - - - - - - - - - - - - - + - 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 + Any muscle organ that is part of a thorax [Automatically generated definition]. + MA:0000561 + muscle organ of thorax + thorax muscle organ uberon - UBERON:0001440 - forelimb skeleton + upper body muscle + UBERON:0003830 + thoracic segment muscle - + - + - FMA + prolog - + - 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 + Any muscle organ that is part of a thorax [Automatically generated definition]. + OBOL:automatic - - - 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 + + + muscle organ of thorax + OBOL:automatic - + - forelimb skeleton - VHOG:0001256 + thorax muscle organ + OBOL:automatic - - - free upper limb skeleton - FMA:24142 + + + 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 + - - - ossa membri superioris - FMA:24139 - FMA:TA - + + + Any muscle organ that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic - + - skeleton of free upper limb - FMA:24142 + apparatus respiratorius muscle organ + OBOL:automatic - + - skeleton of upper limb - FMA:24139 + muscle organ of apparatus respiratorius + OBOL:automatic - + - upper limb skeleton - EHDAA2:0002222 + muscle organ of respiratory system + OBOL:automatic - - - wing skeleton - NCBITaxon:8782 + + + respiratory system muscle organ 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 + 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:0001441 - - TOOD - find a home for: FMA:24140 - hindlimb skeleton + UBERON:0003832 + esophagus muscle - + - + - FMA + MA - + - Subdivision of skeleton consisting of all skeletal elements in an hindlimb region. - + Any muscle organ that is part of a esophagus [Automatically generated definition]. + OBOL:automatic - - - Skeletal structure of the paired, posterior appendages.[AAO] - 2012-06-20 - AAO:0000217 - AAO - AAO:LAP + + + esophagus muscle organ + OBOL:automatic - - - 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 + + + gullet muscle organ + OBOL:automatic - - - 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 + + + muscle organ of esophagus + OBOL:automatic - + - free lower limb skeleton - FMA:24144 + muscle organ of gullet + OBOL:automatic - + - hind limb skeleton - XAO:0003062 + muscle organ of oesophagus + OBOL:automatic - + - hind-limb skeleton - VSAO:0000152 + 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 + + + - hindlimb skeleton - VHOG:0001255 + abdominal segment of trunk muscle organ + OBOL:automatic - + - ossa membri inferioris - FMA:24140 - FMA:TA - + 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 + + + - skeleton of free lower limb - FMA:24144 + blood vessel of thorax + OBOL:automatic - + - skeleton of lower limb - FMA:24140 + thorax blood vessel + OBOL:automatic + + + + + upper body blood vessel + MA:0000558 - + - - + + + + + + + + + + + + + - + - - FMA:24218 - XAO:0000040 - head subdivision + 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 - head region - region of head - UBERON:0001444 - - subdivision of head + 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 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 + 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 - facia/facies - visage - UBERON:0001456 - - - face - http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg + upper body connective tissue + UBERON:0003837 + thoracic segment connective tissue - + - 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). - + A portion of connective tissue that is part of a thorax [Automatically generated definition]. + OBOL:automatic - - - Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. - FMA:24728 + + + EMAPA:37253 + MA:th - - - The area that extends from the median ocellus to the oral foramen[HAO]. - - HAO:0000316 - NCBITaxon:7399 + + + connective tissue of thorax + OBOL:automatic - - - 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 + + + portion of connective tissue of thorax + OBOL:automatic - - - UMLS:C0015450 - ncithesaurus:Face + + + textus connectivus of thorax + OBOL:automatic - - - facia/facies - - + + + thorax connective tissue + OBOL:automatic - + + + thorax portion of connective tissue + OBOL:automatic + + + + + thorax textus connectivus + OBOL:automatic + + + - visage - BTO:0003369 + upper body connective tissue + MA:0000560 - + - + - + - + - + - + - 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 + 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 - skin of lips - UBERON:0001458 - skin of lip + UBERON:0003838 + abdominal segment connective tissue - + - A zone of skin that is part of a lip [Automatically generated definition]. + A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic - + - EMAPA:37643 + EMAPA:37059 MA:th - - - UMLS:C0222101 - ncithesaurus:Skin_of_the_Lip + + + abdominal segment of trunk connective tissue + OBOL:automatic - + - lip zone of skin + abdominal segment of trunk portion of connective tissue OBOL:automatic - + - zone of skin of lip + abdominal segment of trunk textus connectivus OBOL:automatic - - - skin of lips - + + + 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 - + - + - + - - + + - + - - + + - - - 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 + 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 - bone - bones - UBERON:0001474 - - - + UBERON:0003839 - - - bone element + forelimb joint - - - - - - - - - VSAO-modified + + + A limb joint that is part of a forelimb [Automatically generated definition]. + OBOL:automatic - - - Skeletal element that is composed of bone tissue. - - - GO_REF:0000034 - PSPUB:0000170 - VSAO:0000057 + + + anteriormost limb joint of limb + OBOL:automatic - - - 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 + + + anteriormost limb limb joint + OBOL:automatic - - - 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 + + + fore limb joint of limb + OBOL:automatic - - - Skeletal element that is composed of bone tissue.[VSAO] - 2012-08-14 - VSAO:0000057 - VSAO - PSPUB:0000170 + + + fore limb limb joint + OBOL:automatic - - - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - 2012-06-20 - AAO:0000047 - AAO + + + forelimb joint of limb + OBOL:automatic - - - 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) + + + forelimb limb joint + OBOL:automatic - - - UMLS:C0262950 - ncithesaurus:Bone + + + joint of free upper limb + - + - bone organ - FMA:5018 + joint of limb of anteriormost limb + OBOL:automatic - - - bone - AEO:0000082 - BTO:0000140 - MA:0001459 - VHOG:0001190 + + + joint of limb of fore limb + OBOL:automatic - - - bones - ZFA:0001514 - + + + 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 + - + - + - - - - - + - - + + - - - - - - - + - - + + - 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 + 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 - 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 + UBERON:0003840 + + hindlimb joint - + - An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]. - + A limb joint that is part of a hindlimb [Automatically generated definition]. + OBOL:automatic - - - check ncita - ncit + + + hind limb joint of limb + OBOL:automatic - - - EMAPA:37621 - MA:th + + + hind limb limb joint + OBOL:automatic - - - UMLS:C0206207 - ncithesaurus:Joint_Capsule + + + 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 - + - capsula articularis - FMA:34836 - FMA:TA - + lower extremity joint of limb + OBOL:automatic - - - capsulae articulares - - + + + lower extremity limb joint + 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 + 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 - digestive canal - gut tube - UBERON:0001555 - - - digestive tract + central lumen + neural lumen + neurocoel + UBERON:0003842 + neural tube lumen - - - - - - - - - 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 + An anatomical space that surrounded_by a neural tube. + OBOL:automatic - + - 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] + (...) 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:0000309 + VHOG:0001119 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 + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - - - 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 + + + cavity of neural tube + - - - UMLS:C0017189 - ncithesaurus:Gastrointestinal_Tract + + + lumen of neural tube + - + - enteric tract - ZFA:0000112 + neural tube neural lumen + EHDAA2:0001269 - + - digestive canal - BTO:0000058 + neural lumen + EHDAA:2889 - - - - - - - - - - - - - - - - - - - - - - - - - - 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 + + + neurocoel + VHOG:0001119 - + - + - + - - + + - + + - - + + - 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 + + + + + + + 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 - cranial vena cava - precava - vena cava superior - vena maxima - UBERON:0001585 - - - anterior vena cava - http://upload.wikimedia.org/wikipedia/commons/b/b4/Venenwinkel.png + UBERON:0003848 + gonadal vein + http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.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 + 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]. + - + - superior caval vein - + gonad vein + OBOL:automatic - + - superior vena cava - FMA:4720 - - - - - cranial vena cava - VHOG:0001195 - - - - - vena cava superior - - + gonada vein + OBOL:automatic - - - vena cava superior - BTO:0002683 + + + vein of gonad + OBOL:automatic - - - vena maxima - - + + + vein of gonada + OBOL:automatic - + - - - - - - - - + + + + + + + + + + + + + + - - + + - 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 + 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 - vena jugularis interna - UBERON:0001586 - - internal jugular vein - http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray562.png + UBERON:0003849 + + + mesencephalic neural crest - - - One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted]. - + + + + ZFA - - - 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 + + + A neural crest that has_potential_to_developmentally_contribute_to a midbrain. + OBOL:automatic - - - UMLS:C0226550 - ncithesaurus:Internal_Jugular_Vein + + + 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 - + - internal jugular - EHDAA2:0000877 + mesencephalic neural crest + ZFA:0000935 - - - vena jugularis interna - - + + + neural crest midbrain + ZFA:0000935 - + - - - - + + + + + + + + + + + + + + - - + + - 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 + 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 - Bowman`s muscles - ciliaris - musculus ciliaris - UBERON:0001605 - - - ciliary muscle - http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png + rhombomere neural crest + UBERON:0003852 + + rhombencephalon neural crest - - - - MA - - - - - - FMA - - - + - - - - - - - FMA + + ZFA - + - 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]. - + A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. + OBOL:automatic - - - UMLS:C0559230 - ncithesaurus:Ciliary_Muscle + + + Cranial neural crest that is part of the hindbrain.[TAO] + 2012-08-14 + TAO:0007063 + TAO + ZFIN:curator - - - musculus ciliarus - BTO:0000654 + + + 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 - - - Bowman`s muscles - BTO:0000654 + + + neural crest hindbrain + ZFA:0007063 - - - ciliaris - + + + rhombencephalic neural crest + ZFA:0007063 - + - musculus ciliaris - - + rhombomere neural crest + EMAPA:35747 - + - + - + - - + + - + - - + + - . - 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 + 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 - UBERON:0001606 - - muscle of iris + spinal neural crest + UBERON:0003853 + spinal cord neural crest - - - - FMA + + + 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 - + - iris muscle organ - OBOL:automatic + neural crest spinal cord + VHOG:0001006 - - - muscle organ of iris - OBOL:automatic + + + spinal neural crest + VHOG:0001006 - + - + - + - - + + - - - - - - - - + - - + + - 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 + 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:0001630 - - - - - muscle organ + UBERON:0003854 + spinal cord neural plate - + + + + + + + + + ZFA + + + - 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 + A neural plate that develops_from a future spinal cord. + OBOL:automatic - + - Portion of tissue composed of contractile fibers.[TAO] - 2012-08-14 - TAO:0005145 - TAO - ZFIN:curator + Neural plate that is part of the spinal cord. [Bgee_curator][VHOG] + 2012-09-17 + VHOG:0000439 + VHOG + - + - 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] + (...) 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:0001245 + VHOG:0000439 VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75 - - - - - muscle - ZFA:0005145 + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - - - EMAPA:37474 - MA:th + + + neural plate of spinal cord + OBOL:automatic - + - - + + + + + + + + + + + + + + + - - + + - 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 + 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 - arterial system - arterial vessel - UBERON:0001637 - + UBERON:0003855 - - - artery + gonad mesenchyme - + - 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 + Mesenchyme that is part of a developing gonad [Automatically generated definition]. + OBOL:automatic - - - 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) + + + gonada mesenchyme + OBOL:automatic - - - UMLS:C0003842 - ncithesaurus:Artery + + + mesenchyme of gonad + OBOL:automatic - + - arteries - TAO:0000005 - + mesenchyme of gonada + OBOL:automatic - + - + - + - - + + - - - - - - - + - - + + - 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 + 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 - vascular element - vena - venae - UBERON:0001638 - - - - - vein - http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg + UBERON:0003859 + forelimb mesenchyme - + - Any of the tubular branching vessels that carry blood from the capillaries toward the heart. - + Mesenchyme that is part of a developing forelimb [Automatically generated definition]. + OBOL:automatic - - - 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 + + + 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 - - - 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) + + + mesenchyme of upper extremity + OBOL:automatic - - - UMLS:C0042449 - ncithesaurus:Vein + + + superior member mesenchyme + OBOL:automatic - - - vascular element - EMAPA:th + + + upper extremity mesenchyme + OBOL:automatic - - - vena - - + + + wing mesenchyme + Geisha:syn + NCBITaxon:8782 + - - - venae - VHOG:0001743 - + + + wing mesenchyme + NCBITaxon:8782 + OBOL:automatic + - + - - - - - - - - - - + + + + + + + + + + + + + - - - - - - - + - 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 + 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 - anterior facial vein - vena facialis anterior - UBERON:0001653 - - facial vein - http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png + UBERON:0003860 + hindlimb mesenchyme - - - - - - - - - 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]. - + Mesenchyme that is part of a developing hindlimb [Automatically generated definition]. + OBOL:automatic - - - 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 + + + hind limb mesenchyme + OBOL:automatic - - - MA and NCITA also has 'anterior facial vein' - MA + + + inferior member mesenchyme + OBOL:automatic - - - UMLS:C0226532 - ncithesaurus:Facial_Vein + + + lower extremity mesenchyme + OBOL:automatic - + - face vein + mesenchyme of hind limb OBOL:automatic - + - vein of face + mesenchyme of hindlimb OBOL:automatic - - - anterior facial vein - - + + + mesenchyme of inferior member + OBOL:automatic - - - vena facialis anterior - - + + + mesenchyme of lower extremity + OBOL:automatic - + - - - + + + + + + + + + + + + + - - + + - - - - + 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 + + + + + + + + + + + - - + + - + + + + + + + + + - - - - - - - + + - - + + - - + + - 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 + An anatomical cavity that has the potential to develop into a coelemic cavity lumen. uberon - occipital complex - occipital squama - os occipitale - UBERON:0001676 - - - occipital bone - http://upload.wikimedia.org/wikipedia/commons/2/27/Gray194.png + body cavity precursor + UBERON:0003886 + + + future coelemic cavity lumen - - - - FMA + + + An anatomical cavity that has the potential to develop into a coelemic cavity lumen. + OBOL:automatic - - - - + + + + + + + + + - - - - FMA - - - - - - - - - - - - - + - - basi paired exo and supra occipital bones - MA-modified - - - - - + + - - - - - - - + + - - interparietal (postparietal) - + + 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 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 - + 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 - - - fusion of basi-, exo- and supra-occipitals (and maybe tabular) - Kardong + + + (...) 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:C0028784 - ncithesaurus:Occipital_Bone - - - - - occipital complex - + UMLS:C1512940 + ncithesaurus:Intraembryonic_Coelom - - - os occipitale - - + + + somatic coelom + - + - - - - - - - - - - - - - - + + - - + + - - + + - 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 + Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma. + stromal + + FMA:81494 + NCIT:C67387 + UMLS:C0927195 uberon - brain case - brain pan - braincase - UBERON:0001703 - - - - neurocranium + stromal connective tissue + UBERON:0003891 + + stroma - - - - 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 + Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma. + + + + + + UMLS:C0927195 + ncithesaurus:Stroma_Connective_Tissue - + - + - + - - + + + + + + - - + + - + - + - - + + + + + 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 + + + + + + + + + + + - + - + + + + + + + + - - + + - 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 + + + + + + + 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 - anterior splanchnocranium - jaws - mandibular arch - oral jaw skeleton - pharyngeal arch 1 skeleton - visceral arch 1 - UBERON:0001708 - - - - jaw skeleton + UBERON:0003898 + skeletal muscle tissue of trunk - + - + - cjm + - + - Subdivision of skeleton which includes upper and lower jaw skeletons. - - + A portion of skeletal muscle tissue in the trunk. + - - - Skeletal and cartilage elements of the first pharyngeal arch.[TAO] - 2012-08-14 - TAO:0001227 - TAO - ZFIN:curator + + + skeletal muscle of torso + OBOL:automatic - - - 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 + + + skeletal muscle tissue of torso + OBOL:automatic - - - UMLS:C0022359 - ncithesaurus:Jaw + + + skeletal muscle tissue of trunk + OBOL:automatic - + - jaw - MA:0001905 + torso skeletal muscle + OBOL:automatic - + - jaw cartilage - ZFA:0001227 + torso skeletal muscle tissue + OBOL:automatic - + - mandibular arch skeleton - ZFA:0001227 + trunk skeletal muscle + OBOL:automatic - - - mandibular arch - TAO:0001227 + + + trunk skeletal muscle tissue + OBOL:automatic - + - + - + - - + + - - + + - - + + + + + + + + - + - - + + - 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 + + + + + + + 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 - lower part of mouth - mandibular series - UBERON:0001710 - - + neural retinal epithelium + UBERON:0003902 + - 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 + retinal neural layer - + - - + + - + Bgee:AN - + - 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 + The part of the retina that contains neurons and photoreceptor cells[GO]. + GO:0003407 - + - 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] + (...) 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:0000453 + VHOG:0000535 VHOG - DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) + 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-inconsistent + + + + + + 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 + + + - Note isa/partof difference MA/FMA - MA + some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined). + FMA - + - mandibular part of mouth - FMA:59398 + sinusoidal blood vessel endothelium + ZFA:0005261 + + + + + sinusoidal capillary + - + - + - + - - + + - - - - - - - + + - - + + + 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 + + + + + + + + + + + + + + + + + + + + - - + + - 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 + Any endothelium that has the quality of being cylindrical [Automatically generated definition]. uberon - cavitas pharyngealis - cavitas pharyngis - UBERON:0001731 - cavity of pharynx + UBERON:0003915 + endothelial tube - - - - - - - - - XAO - - - + - A anatomical space that is enclosed by a pharynx. + Any endothelium that has the quality of being cylindrical [Automatically generated definition]. OBOL:automatic - - - - cavitas pharyngealis - - - - - - cavitas pharyngis - BTO:0002097 - - + - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + - - + + - 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 + Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO]. + check this + mesenchyme of kidney uberon - lacrimal drainage system - nasolacrimal drainage system - nasolacrimal system - UBERON:0001750 + UBERON:0003918 - - lacrimal apparatus - http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png + kidney mesenchyme - - - - - - - - - MA + + + Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO]. + GO:0072074 - - - - + + + + + + + + + + + + + + + + + + + - - - - HPO:pr - - - - - - - - + - - ISBN:0781772214 - + + 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 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 + A blood vessel that carries blood from the capillaries toward the heart. + - + - apparatus lacrimalis - - + segment of venous tree organ + FMA:86188 - + - lacrymal system - MGI:anna - - - - - lacrimal drainage system - - - - - - nasolacrimal drainage system - - - - - - nasolacrimal system - HPO:pr + venous tree organ segment + FMA:86188 - + - - + + + + + + + + + + + + + - - - - - - - + - 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 + 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 - 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 + UBERON:0003928 + digestive system duct - - - - 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 + A duct that is part of a digestive system [Automatically generated definition]. + OBOL:automatic - + - anterior chamber - HP:0000593 - MP:0010709 - - - - - camera anterior bulbi - BTO:0002084 + duct of digestive system + OBOL:automatic - - - camera anterior bulbi oculi - - + + + duct of gastrointestinal system + OBOL:automatic - - - camera oculi anterior - BTO:0002084 + + + gastrointestinal system duct + OBOL:automatic - + - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - + - 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 + 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 - 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 + alimentary tract epithelium + UBERON:0003929 + digestive tract epithelium - - - - 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 + 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:C0042160 - ncithesaurus:Uvea + UMLS:C0836205 + ncithesaurus:Gut_Epithelium - + - tunica vasculosa of eyeball - FMA:58103 + digestive tract epithelial tissue + OBOL:automatic - + - uvea - FMA:58103 + epithelial tissue of digestive tract + OBOL:automatic - + - uveal tract - FMA:58103 + epithelial tissue of gut + OBOL:automatic - - - pars iridica retinae - + + + epithelium of digestive tract + OBOL:automatic - - - tunica vasculatis oculi - + + + epithelium of gut + OBOL:automatic - - - tunica vasculosa bulbi - - + + + gastrodermis + BGEE:ANN + NCBITaxon:6073 + - + + + gut epithelial tissue + OBOL:automatic + + + + + gut epithelium + EHDAA2:0004567 + MA:0003201 + ZFA:0005123 + + + - vascular layer of eyeball - FMA:58103 + alimentary tract epithelium + OBOL:automatic - + - - - + + + + + + + + + + + + + - - - - - - - - - - - - - + - 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 + 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 - anterior uvea - irides - irises - UBERON:0001769 + UBERON:0003932 - - - - iris + 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 + + + + + + + + + + + + + + + + + + + + - - + + - - XAO - + + 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 + - + - 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 + A cartilage element that is part of the cranial skeleton. + + ZFA:0001458 - + - 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) + Cartilage which is part of the cranium.[TAO] + 2012-08-14 + TAO:0001458 + TAO + ZFIN:curator - - - UMLS:C0022077 - ncithesaurus:Iris + + + cartilage of cranium + OBOL:automatic - - - irides - + + + cranium cartilage + OBOL:automatic - + - irises - VHOG:0000101 + cranial cartilages + ZFA:0001458 - + - + - + - - + + - - + + - - - - - - - - - - - - - - - - - - - + - 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 + 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 - anterior endothelium of cornea - e. anterius corneae - endothelium anterius corneae - endothelium camerae anterioris bulbi - endothelium corneale - epithelium posterius corneae - UBERON:0001772 - + UBERON:0003937 + - - - corneal epithelium - http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png + reproductive gland - - - - - - - - - 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 + Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. + MP:0000653 - - - 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 + + + genitalia gland + OBOL:automatic - - - UMLS:C0459875 - ncithesaurus:Corneal_Epithelium + + + gland of genitalia + MP:0000653 - + - cornea epithelial tissue + gland of reproductive system OBOL:automatic - + - cornea epithelium - OBOL:automatic + reproductive gland + MA:0001751 - + - epithelial tissue of cornea + reproductive system gland OBOL:automatic - + - epithelium anterius corneae - FMA:58263 - FMA:TA - - - - - - anterior endothelium of cornea - BTO:0000287 + 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 + - - - e. anterius corneae - - + + + The sensory system for the sense of touch and pain. + NLXANAT:090818 - - - endothelium anterius corneae - BTO:0000287 + + + The neural tissue involved in the transmission of sensory signals + MP:0000959 - - - endothelium camerae anterioris bulbi - BTO:0000287 + + + MP defines this in a may more appropriate to somatosensory cortex + MP - - - endothelium corneale - BTO:0000287 + + + EMAPA:37954 + MA:th - - - epithelium posterius corneae - BTO:0000287 + + + somatosensory system + NLXANAT:090818 - + - - + + + + + + + + + + + + + - + - - + + - + - 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 + + The anterior segment of the lamellated connective tissue layer of the cornea. + anterior stroma + EMAPA:37414 + cornea anterior stroma uberon - scleral capsule - UBERON:0001773 + UBERON:0003952 - - - Disease notes: implicated in rheumatoid arthritis. - sclera - http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg + anterior stroma of cornea - - - - - - - - - FMA - - - - - - - - - - - ISBN:0781772214 + + + + lexical - + - Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]. - - ZFIN:ZDB-PUB-050701-15 + The anterior segment of the lamellated connective tissue layer of the cornea. + MP:0003093 - - - 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]. - + + + anterior stroma + MP:0003093 - - - 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 - - + + + EMAPA:37414 + MA:th - - - UMLS:C0036410 - ncithesaurus:Sclera + + + cornea anterior stroma + MP:0003093 - + - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - + - - + + - + - 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 + The posterior segment of the lamellated connective tissue layer of the cornea. + posterior stroma + EMAPA:37415 + cornea posterior stroma uberon - anterior uvea - ciliary bodies - corpus ciliare - UBERON:0001775 + UBERON:0003953 - - - ciliary body - http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg + posterior stroma of cornea - - - - - - - - - ISBN:0781772214 + + + + lexical - + - 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 posterior segment of the lamellated connective tissue layer of the cornea. + MP:0003094 - - - 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) + + + posterior stroma + MP:0003094 - + - UMLS:C0008779 - ncithesaurus:Ciliary_Body - - - - - ciliary bodies - VHOG:0000102 - - - - - - corpus ciliare - + EMAPA:37415 + MA:th - - - corpus ciliare - - + + + cornea posterior stroma + MP:0003094 - - - - - - - - - - - - - - - - - - - - + + + + + + + - + - - - - - - - - - - - - - - - + + + + + - - + + - + - - 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 + 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 - chorioid - choroidea - optic choroid - UBERON:0001776 + UBERON:0003967 - - - optic choroid - http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg + cutaneous elastic tissue - - - - - - - - - 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 + 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 - + - UMLS:C0008520 - ncithesaurus:Choroid + EMAPA:37841 + MA:th - - - choroid - MA:0000263 + + + cutaneous elastic fiber + MP:0008418 - - - choroid coat - + + + dermal elastic fiber + MP:0008418 + + + + + + + + + + + + + + + + + + + + + + + + + + The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina. + + BTO:0003099 + FMA:45654 + female internal genitalia + internal female genital organ + internal genitalia of female reproductive system + uberon + organa genitalia feminina interna + UBERON:0003975 + + + TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 + internal female genitalia + - - - choroidea - + + + The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina. + MP:0009209 - + - eye choroid - VHOG:0001568 + female internal genitalia + FMA:45654 - + - posterior uvea - + internal female genital organ + BTO:0003099 - - - chorioid - BTO:0001829 + + + internal genitalia of female reproductive system + OBOL:automatic - + - choroidea - - + 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 + - - - optic choroid - ZFA:0005229 + + + anatomical valve + FMA:67611 - + - + - + - - + + + + + + - - + - - + + - - + + - 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 + The connection between the embryo proper and extraembryonic tissues. uberon - UBERON:0001778 - ciliary epithelium + 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 + + + - - FMA + + AEO - + - - + + - MA + AEO-text - + - - + + - Wikipedia + EHDAA2-abduced - + - A double layer covering the ciliary body that produces aqueous humor. - + A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. + AEO:0001017 + AEO:JB - + - UMLS:C0459736 - ncithesaurus:Ciliary_Epithelium + UMLS:C0180383 + ncithesaurus:Dermatome - + - ciliary body epithelium - FMA:58464 + cutis plate + - + - epithelium of ciliary body - FMA:58464 + dermatomal mesenchyme + + + + + + mesenchyma dermatomiale + + - + - - + + + + - + - - + + - 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 + + + + + + + + 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:0001781 + UBERON:0004022 - - layer of retina + germinal neuroepithelium - - - Any of the layers that make up the retina[MP]. - MP:0003727 + + + + NCBIBook:NBK10047 - - - 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 + + + 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 - - - UMLS:C0459649 - ncithesaurus:Retina_Layer + + + germinal neuroepithelial layer + - + - retina neuronal layer - MP:0006069 + germinal neuroepithelium + NCBIBook:NBK10047 - + - retinal neuronal layer - MP:0006069 + original neural tube + NCBIBook:NBK10047 - + - - - + + + + - + - - + + - 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 + + + + + + + + + + + + + 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:0001796 + UBERON:0004060 - - - aqueous humor of eyeball - http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg + neural tube ventricular layer - + + + + NCBIBook:NBK10047 + + + - - + + - FMA def states A and P - located_in in EHDAA2 - VHOG + NCBIBook:NBK10047 - + - A thick watery refractive medium that fills the space between the lens and the cornea[WP]. - + The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium. + + MP:0009689 - + - 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 - - + The layer of undifferentiated, proliferating cells that line the neural tube lumen + MP:0009689 - - - (...) 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 + + + ependymal layer + NCBIBook:NBK10047 - - - 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 + + + neural tube ependymal layer + NCBIBook:NBK10047 - - - UMLS:C0003662 - ncithesaurus:Aqueous_Humor + + + neural tube ventricular germinal zone + NCBIBook:NBK10047 - + - aqueous humour - EHDAA2:0000139 + neural tube ventricular zone + MP:0009689 - - - humor aquosus - FMA:58819 - FMA:TA - + + + neural tube ependymal zone + MP:0009689 - + - - - + + + + - + - - + + - - + + - - 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) + + + + + + + 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 - segmentum anterius bulbi oculi - UBERON:0001801 + future brain marginal layer + UBERON:0004061 - - anterior segment of eyeball - http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png + neural tube mantle layer - + - - - - - - - FMA + + NCBIBook:NBK10047 - + - - + + - cjm - - - - - - lexical + by division + NCBIBook:NBK10047 - + - 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 + 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 - + - anterior segment eye - ZFA:0005566 + neural tube intermediate zone + + MP:0009690 - + - segmentum anterius bulbi oculi - - + future brain marginal layer + EMAPA:35360 - + - - - + + + - + - - + + - - + + - 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) + 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 - segmentum posterius bulbi oculi - UBERON:0001802 + brain marginal zone + UBERON:0004062 - - posterior segment of eyeball - http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg + neural tube marginal layer - - - - - - - - - FMA - - - + - - + + - cjm - - - - - - lexical + forms from axons - + - 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 + The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter. + + MP:0009691 - + - posterior segment eye - ZFA:0005567 - - - - - segmentum posterius bulbi oculi - - + neural tube marginal zone + MP:0009691 - + - - - - - - - - - - - - - - + + + + - + + + + + + + + + + + + + + + + + + + - + - 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 + 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 + - - epithelium of lens + neural tube basal plate - - - A layer of epithelial cells that is part of the eye. - + + + + + + + + + Shh + Swenson - - - epithelial tissue of eye lens - OBOL:automatic + + + 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 - - - epithelial tissue of lens - OBOL:automatic + + + UMLS:C1511061 + ncithesaurus:Basal_Plate - + - epithelium lentis - FMA:58871 - FMA:TA - + basal plate of neural tube + - - - epithelium of eye lens - OBOL:automatic + + + spinal cord basal plate + MP:0009693 + + + + + + + + + + + + + + + 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 + - - - eye lens epithelial tissue - OBOL:automatic + + + Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart. + + - - - eye lens epithelium - OBOL:automatic + + + UMLS:C0042460 + ncithesaurus:Vena_Cava - - - lens epithelial tissue - OBOL:automatic + + + venae cavae + + - + - - - - - - - - - - - - - - - + + - - - - - - - - - - - - - + - 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 + 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 - UBERON:0001804 + ocular and peri-ocular region + ocular region + orbital content + orbital part of eye + UBERON:0004088 - - - capsule of lens - http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png + orbital region - - - - - - - - - EHDAA2 - - - + - the elastic, clear, membrane-like structure, that is outer most layer of the lens - - MGI:smb - MP:0003236 + 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. + - - - 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 - + + + in HP covers eyelid, eyebrow. + HP:0000284 - - - (...) 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 + + + content of orbital part of eye + FMA:260119 - - - FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular - FMA + + + eye region + - - - UMLS:C0229232 - ncithesaurus:Lens_Capsule + + + orbital part of face + - - - capsula lentis - + + + orbital content + FMA:260119 + + + + + orbital part of eye + FMA:72951 - + - + - + - - + + + + + + - - - - - + - - - - + + + + + 2 + + + + + 2 + + + + - - + + - - + + - 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 + 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 - glandula praeorbitalis - preorbital gland - tear gland - UBERON:0001817 - - - - - lacrimal gland - http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png + opening + ostia + ostium + UBERON:0004111 + anatomical conduit - + - 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]. - + Any tube, opening or passage that connects two distinct anatomical spaces. - - - 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 - + + + FMA has both conduit and conduit space. In EHDAA2 this is a surface feature + FMA - - - glandula praeorbitalis - - NCBITaxon:91561 - + + + foramen + EHDAA2:0003080 - - - preorbital gland - - NCBITaxon:91561 - + + + foramina + + - + - tear gland - BTO:0000044 + ostia + - + - + - + - - + + - + - - + + - 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 + 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 - tear fluid - UBERON:0001827 - - secretion of lacrimal gland + UBERON:0004118 + + vasculature of iris - + - Aqueous substance secreted by the lacrimal gland. - - - - - - - UMLS:C0039409 - ncithesaurus:Tear + A vasculature that is part of a iris [Automatically generated definition]. + OBOL:automatic - + - tear - FMA:59756 + iris blood vessels + ZFA:0005568 - + - tears - + iris vascular network + OBOL:automatic - - - tear fluid - BTO:0001499 + + + 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. + + + + + + + + + + + + + + + + + + + + + - - + + - 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 + An anatomical structure that develops (entirely or partially) from the mesoderm. + Grouping term for query purposes + FBbt:00025998 + mesodermal derivative 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 + UBERON:0004120 + + mesoderm-derived structure - - - - ZFA + + + An anatomical structure that develops (entirely or partially) from the mesoderm. + - - - - - - - - - BTO - FMA-implicit - VHOG - ZFA + + + mesodermal derivative + FBbt:00025998 - - - - + + + + + + + + + + + + + + + + + + + + - - + + - - cjm - + + 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 + - + - 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 + An anatomical structure that develops (entirely or partially) from the ectoderm. + - - - labia oris - - + + + ectodermal deriviative + FBbt:00025990 - + - + - + - - + + + + + + - - + + - - + + + + + + + + - - + + - 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 + 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 - labium inferius oris - UBERON:0001835 + GU tract + UG tract + Urogenitalsystem + genito-urinary system + genitourinary tract + urogenital tract + UBERON:0004122 + - - - lower lip - http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg + genitourinary system - + - Lip that covers the lower portion of the mouth.[TAO]. - - TAO:0002060 + Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. + VHOG:0000286 - + - Lip that covers the lower portion of the mouth.[TAO] - 2012-08-14 - TAO:0002060 - TAO - TAO:wd + 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:C0458583 - ncithesaurus:Lower_Lip + UMLS:C0042066 + ncithesaurus:Genitourinary_System - - - lower jaw lip - + + + Urogenitalsystem + BTO:0003091 - + - labium inferius oris - - + genito-urinary system + FMA:280610 + + + + + urogenital tract + BTO:0003091 - + - - - + + + + - - + + - - + + - - + + - - + + - 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 + 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 - mesencephalon - UBERON:0001891 - + evagination + eye vesicle + ocular vesicle + optic vesicles + UBERON:0004128 - - midbrain - http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG + 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 - + - - + + - definitional + ZFA - + - - + + - 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 + GO-def - - - Middle part of the brain composed of the optic tectum and penducular region.[AAO] - 2012-06-20 - AAO:0010149 - AAO - AAO:BJB + + + + + + + + + ZFA - - - 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 + + + 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 - + - 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] + (...) 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:0000069 + VHOG:0000165 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 - + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - + - UMLS:C0025462 - BIRNLEX:1667 + UMLS:C0231106 + ncithesaurus:Optic_Vesicle - - - UMLS:C0025462 - ncithesaurus:Mesencephalon + + + eye vesicle + XAO:0000228 - - - http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462 - BIRNLEX:1667 + + + ocular vesicle + VHOG:0000165 - + - mesencephalon - - + optic vesicles + ZFA:0000050 + - + - - - - - - - - - - - - - + + + - + - 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 + salivary nucleus uberon - future rhombencephalon - rhombomeres - UBERON:0001892 - - - - - rhombomere + UBERON:0004133 + salivatory nucleus - - - 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 - + salivary nucleus + GO:0021751 - + - - - - + + + - + - - + + - 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 + 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 - 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 - + cardiac crescent + cardiogenic crescent + heart rudiment + UBERON:0004139 + + cardiogenic plate + - - - 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 - + + + The first recognizable structure derived from the heart field. + GO:0003142 - + - 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] + (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:0000181 + VHOG:0000975 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) + 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) - - - medulla - ABA:MY + + + myocardial plate + EHDAA2:0000215 - - - UMLS:C0025148 - BIRNLEX:957 + + + cardiac crescent + EMAPA:16106 - - - UMLS:C0025148 - ncithesaurus:Medulla_Oblongata + + + 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 - - - UMLS:C1269575 - BIRNLEX:957 + + + + + + + + + BGEE:ann - - - http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698 - BIRNLEX:957 + + + 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 + + + - bulbus - FMA:62004 - FMA:TA - + first heart field + XAO:0004185 - + + + primary heart field + + XAO:0004185 + + + - medulla oblonzata - - + FHF + XAO:0004185 + - + - metepencephalon - FMA:62004 + PHF + XAO:0004185 + + + + + + heart field + XAO:0004185 - + - - - - - - - - - - - - - + + + + - + - 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 + + + + + + + + + + + + + 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:0001915 - endothelium of capillary + UBERON:0004141 + + + + heart tube - - - An endothelium that is part of a capillary [Automatically generated definition]. - OBOL:automatic + + + + + + + + + ZFA-modified - - - UMLS:C0006904 - ncithesaurus:Capillary_Endothelium + + + An epithelial tube that will give rise to the mature heart. + GO:0003143 + GOC:mtg_heart - - - blood capillary endothelium - OBOL:automatic + + + 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 - + - capillary vessel endothelium - OBOL:automatic + embryonic heart tube + GO:0003143 - + - endothelium of blood capillary - OBOL:automatic + endocardial heart tube + MP:0012700 - + - endothelium of capillary vessel - OBOL:automatic + endocardial tube + XAO:0000337 - + - + - + - + - - + - + - An endothelium that is part of an arteriole [Automatically generated definition]. - - EMAPA:36286 - FMA:62115 - MA:0000705 - NCIT:C49192 - UMLS:C1179024 - arteriole endothelium + The outflow tract septum is a partition in the outflow tract. + XAO:0004141 uberon - UBERON:0001916 - endothelium of arteriole + UBERON:0004142 + outflow tract septum - + - An endothelium that is part of an arteriole [Automatically generated definition]. - OBOL:automatic - - - - - UMLS:C1179024 - ncithesaurus:Arteriole_Endothelium + The outflow tract septum is a partition in the outflow tract. + GO:0003148 - + - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + - 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 + 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 - + - 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 + The outflow tract is the portion of the heart through which blood flows into the arteries. + GO:0003151 - - - 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 + + + cardiac outflow tract + - - - UMLS:C1179025 - ncithesaurus:Artery_Endothelium + + + arterial (outflow) pole + - + - + - + - + + + + + - - + + + - + - An endothelium that is part of a venule [Automatically generated definition]. - - EMAPA:36290 - FMA:62117 - MA:0000716 - NCIT:C49319 - UMLS:C1179026 - venule endothelium + + + + + + + + + + + + + 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 - UBERON:0001918 - endothelium of venule + coronary vein + UBERON:0004148 + + cardiac vein - + + + + FMA + + + - An endothelium that is part of a venule [Automatically generated definition]. - OBOL:automatic + Vein of heart that drains the myocardium. + - + - UMLS:C1179026 - ncithesaurus:Venule_Endothelium + EMAPA:37137 + MA:th + + + + + UMLS:C0226654 + ncithesaurus:Cardiac_Vein + + + + + UMLS:C0226737 + ncithesaurus:Coronary_Vein + + + + + cardiac vein + FMA:12846 - - - - - - - - - - - - - - - - - - - - - - - - - - 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 + + + coronary vein + ZFA:0005814 - - - 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 + + + heart vein + OBOL:automatic - - - UMLS:C1179027 - ncithesaurus:Vein_Endothelium + + + vein of heart + OBOL:automatic - + - veinous endothelium - VHOG:0001216 + 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 + + + + + + + + - + - - + + - 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 + 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 - 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 + UBERON:0004160 + proepicardium - + - - + + + + + todo check other taxa + + + + + + + + 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 + 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 - - - 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] + + + 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:0001367 + VHOG:0000019 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 + + + 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 - - - UMLS:C0039441 - BIRNLEX:1200 + + + in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum + EHDAA2 - + - http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491 - BIRNLEX:1200 + UMLS:C0231004 + ncithesaurus:Septum_Transversum - + - tegmentum mesencephali - - + transverse septum + + + + + + + + + The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals. + FMA:45652 + internal genitalia + internal genitals + uberon + internal reproductive organ + internal sex organ + UBERON:0004175 + + + TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 + internal genitalia + - - - mesencephalic tegmentum - VHOG:0001367 + + + 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 + - - - tegmentum mesencephalicum - NeuroNames:491 - + + + The external genitalia are the outer sex organs, such as the penis or vulva in mammals. + GO:0035261 - + - + - + - + - - + + - + - A multi-tissue structure that is part of a spinal cord. - - - BIRNLEX:1496 - NCIT:C33969 - UMLS:C1268166 + 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 - spinal cord part - UBERON:0001948 - - regional part of spinal cord + UBERON:0004177 + + + hemopoietic organ - + - A multi-tissue structure that is part of a spinal cord. - OBOL:automatic + 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 + + + - UMLS:C1268166 - ncithesaurus:Spinal_Cord_Part + EMAPA:37665 + MA:th - - - - - - - - - - - - - - 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. - + + + haematological system organ + OBOL:automatic - - - plasma - MA:0002501 + + + haemopoietic system organ + OBOL:automatic - - - portion of plasma - FMA:62970 + + + hematopoietic system organ + OBOL:automatic - - - UMLS:C0032105 - ncithesaurus:Plasma + + + organ of haematological system + OBOL:automatic - - - - - - - - - - - - - - - - - - - - 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 + + + organ of haemopoietic system + OBOL:automatic - - - 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 + + + organ of hematopoietic system + OBOL:automatic + + + + + organ of organa haemopoietica + OBOL:automatic + + + + + organa haemopoietica organ + OBOL:automatic - - - UMLS:C0042520 - ncithesaurus:Venule + + + lymph organ + MA:0000747 - - - venula - - + + + lymphoid organ + BTO:0004605 + FMA:7143 - + - + - - - - - + - - + + - - - - - - - - - - - - - + + - - + + - 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 + 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 - arteriola - UBERON:0001980 + UBERON:0004178 + - - - arteriole - Illu:capillary.jpg + aorta smooth muscle tissue - - - - MA - - - + - The smallest division of the artery located between the muscular arteries and the capillaries[GO]. - GO:0014830 + The nonstriated, involuntary muscle tissue located in the wall of the aorta. + MGI:csmith + MP:0009865 - - - 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 + + + UMLS:C1706825 + ncithesaurus:Aorta_Smooth_Muscle_Tissue - - - Small, terminal branch of an artery which generally connects to capillaries.[AAO] - 2012-06-20 - AAO:0010253 - AAO - AAO:BJB + + + aorta non-striated muscle + OBOL:automatic - - - UMLS:C0003847 - ncithesaurus:Arteriole + + + aorta smooth muscle + OBOL:automatic - - - arteriola - - + + + aortic smooth muscle + BTO:0001685 - + - - - + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - + - + + 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 + + + + + + + + + + + + + + + + + + + - - + + - 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 + A nerve that is part of a back [Automatically generated definition]. + EMAPA:37268 + MA:0000497 + nerve of back uberon - vas sanguineum - UBERON:0001981 - - - - - blood vessel - http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg + UBERON:0004215 + back nerve - - - - - - - - - EHDAA2 + + + A nerve that is part of a back [Automatically generated definition]. + OBOL:automatic - - - - - - - - - GO:0072360 + + + EMAPA:37268 + MA:th - - - A vessel through which blood circulates in the body. - - BTO:0001102 + + + nerve of back + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] - 2012-09-17 - VHOG:0001250 - VHOG - + + + A portion of smooth muscle tissue that is part of a urethra [Automatically generated definition]. + OBOL:automatic - - - Any of the vessels through which blood circulates in the body.[AAO] - 2012-06-20 - AAO:0011004 - AAO - AAO:EJS + + + muscle layer of urethra + FMA:76909 - - - 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) + + + muscular coat of urethra + FMA:76909 - - - FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX - FMA + + + muscular layer of urethra + FMA:76909 - - - vascular element - EMAPA:35993 + + + smooth muscle of urethra + OBOL:automatic - - - UMLS:C0005847 - ncithesaurus:Blood_Vessel + + + smooth muscle tissue of urethra + OBOL:automatic - + - region of vascular tree organ - FMA:50722 + tunica muscularis urethrae + FMA:TA + - + - vascular tree organ region - FMA:50722 + urethra smooth muscle tissue + OBOL:automatic - + - vas sanguineum - - + urethral smooth muscle + MA:0001691 - + - + - - - - - + - - + + - - + - - + + - - + + - 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 + + + + + + + + + + + + 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:0001982 - - - - - capillary - http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg + UBERON:0004220 + large intestine smooth muscle - + - - FMA + + + + + + MA - XAO - - - - ZFA + + + + + + + + + + + + + + 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 - - - Any of the smallest blood vessels connecting arterioles with venules. - - - ISBN:0073040584 + + + large intestine smooth muscle tissue + OBOL:automatic - - - Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] - 2012-06-20 - AAO:0010252 - AAO - AAO:BJB + + + non-striated muscle of large intestine + OBOL:automatic - - - 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) + + + smooth muscle of large intestine + OBOL:automatic - - - UMLS:C0935624 - ncithesaurus:Capillary + + + smooth muscle tissue 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 + 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 - epithelium posterius corneae - UBERON:0001985 + intestinal muscularis + intestinal smooth muscle + UBERON:0004221 - - - corneal endothelium - http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png + intestine smooth muscle - + + + + + + + + + + + + + + consider merging + + + - 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]. - + 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:C0014259 - ncithesaurus:Corneal_Endothelium + UMLS:C1708547 + ncithesaurus:Intestinal_Smooth_Muscle_Tissue - + - cornea endothelium + bowel involuntary muscle OBOL:automatic - + - endothelium of cornea + bowel non-striated muscle 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 + + + bowel smooth muscle + OBOL:automatic - - - 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 + + + bowel smooth muscle tissue + OBOL:automatic - - - UMLS:C0014257 - ncithesaurus:Endothelium + + + intestine involuntary muscle + OBOL:automatic - - - - - - - - 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] - - + + + intestine non-striated muscle + OBOL:automatic - - - Excretion in semisolid state processed by the intestine.[FMA] - FMA:64183 + + + intestine smooth muscle tissue + OBOL:automatic - - - UMLS:C0015733 - ncithesaurus:Feces + + + involuntary muscle of bowel + OBOL:automatic - + - piece of shit - + involuntary muscle of intestine + OBOL:automatic - + - portionem cacas - + non-striated muscle of bowel + OBOL:automatic - - - cow dung - + + + non-striated muscle of intestine + OBOL:automatic - - - cow pat - + + + smooth muscle of bowel + OBOL:automatic - - - fewmet - + + + smooth muscle of intestine + OBOL:automatic - - - frass - + + + smooth muscle tissue of bowel + OBOL:automatic - - - guano - + + + smooth muscle tissue of intestine + OBOL:automatic - - - spraint - + + + intestinal muscularis + EMAPA:35441 - + - excrement - BTO:0000440 + intestinal smooth muscle + BTO:0000643 - + - + - + - - + + - - + - - - - - - - + - - + + - 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 + 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 - UBERON:0002015 - - - kidney capsule - Illu:kidney.jpg + gastric muscle + gastric smooth muscle + stomach muscle + UBERON:0004222 + stomach smooth muscle - + - 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 + A portion of smooth muscle tissue that is part of a stomach [Automatically generated definition]. + OBOL:automatic - - - UMLS:C0227637 - ncithesaurus:Renal_Capsule + + + involuntary muscle of stomach + OBOL:automatic - + - capsula fibrosa renis - FMA:66610 - FMA:TA - + involuntary muscle of ventriculus + OBOL:automatic - + - fibrous capsule of kidney - FMA:66610 + non-striated muscle of stomach + OBOL:automatic - + - renal capsule - GO:0072127 + non-striated muscle of ventriculus + OBOL:automatic - - - - - - - - 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. - - + + + smooth muscle of stomach + OBOL:automatic - - - Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] - 2012-08-14 - TAO:0002197 - TAO - ZFIN:curator + + + 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 - - - EMAPA:37596 - MA:th + + + stomach non-striated muscle + OBOL:automatic - - - UMLS:C0018220 - ncithesaurus:Gray_Matter + + + stomach smooth muscle tissue + OBOL:automatic - + - gray matter of neuraxis - FMA:67242 + ventriculus involuntary muscle + OBOL:automatic - + - neuronal grey matter - AEO:0001012 + ventriculus non-striated muscle + OBOL:automatic - + - substantia grisea - FMA:67242 - FMA:TA - + ventriculus smooth muscle + OBOL:automatic - + + + ventriculus smooth muscle tissue + OBOL:automatic + + + - gray mater - ZFA:0001681 + gastric muscle + BTO:0001818 - + - grisea - + gastric smooth muscle + MA:0001627 + + + + + stomach muscle + BTO:0001818 - + - - - - - - - + + + + + - + - - - - - - - - - - - - - - - + + + + - - + + - 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 + 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 - rhombencephalon - UBERON:0002028 - - - - - hindbrain - http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg + airway smooth muscle + airway smooth muscle cell + UBERON:0004225 + respiratory system smooth muscle - - - - - - - - - - - - - - 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 + A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic - - - UMLS:C0035507 - BIRNLEX:942 + + + respiratory smooth muscle + BTO:0001660 - - - UMLS:C0035507 - ncithesaurus:Hind-Brain + + + smooth muscle of respiratory system + OBOL:automatic - - - UMLS:C1522180 - BIRNLEX:942 + + + airway smooth muscle + BTO:0001660 - - - http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540 - BIRNLEX:942 + + + airway smooth muscle cell + BTO:0001660 - + - - - 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 + + + + + + + + + + + + + + + + + + + + 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:0002036 - - - striated muscle tissue + UBERON:0004226 + gastrointestinal system smooth muscle - + - 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 + A portion of smooth muscle tissue that is part of a digestive system [Automatically generated definition]. + OBOL:automatic - - - UMLS:C1331262 - ncithesaurus:Striated_Muscle_Tissue + + + 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 + + + + + + + + + + + + + + + + + + + - - + + - 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 + 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 - UBERON:0002049 - - - - vasculature - http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg + smooth muscle layer of bladder + UBERON:0004228 + urinary bladder smooth muscle - - - - FMA + + + 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 - - - 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 + + + smooth muscle of urinary bladder + OBOL:automatic - + - vascular network - FMA:69050 + 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 - + - + - + - + - + - + - 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 + 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 - developing structure - embryonale Struktur - embryonic structures - UBERON:0002050 - - - - embryonic structure + UBERON:0004231 + anal region smooth muscle - + - 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 + A portion of smooth muscle tissue that is part of an anal region [Automatically generated definition]. + OBOL:automatic - + - UMLS:C0013948 - ncithesaurus:Embryonic_Structure + EMAPA:37394 + MA:th - + - developing embryonic structure - FBbt:00004208 + anal part of perineum involuntary muscle + OBOL:automatic - + - embryonic anatomical structure - RETIRED_EHDAA2:0003169 - - - - - embryonale Struktur - BTO:0000174 - - - - - embryonic structures - ZFA:0001105 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 + anal part of perineum non-striated muscle + OBOL:automatic - - - - - - - - - definitional + + + anal part of perineum smooth muscle + OBOL:automatic - - - 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 + + + anal part of perineum smooth muscle tissue + OBOL:automatic - - - 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 + + + anal region involuntary muscle + OBOL:automatic - - - 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 + + + anal region non-striated muscle + OBOL:automatic - - - UMLS:C0011646 - ncithesaurus:Dermis + + + anal region smooth muscle tissue + OBOL:automatic - - - corium - - + + + anal triangle involuntary muscle + OBOL:automatic - - - corium - BTO:0000294 + + + anal triangle non-striated muscle + OBOL:automatic - - - cutis - BTO:0000294 + + + anal triangle smooth muscle + OBOL:automatic - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 + + + anal triangle smooth muscle tissue + OBOL:automatic - - - - - - - - - FMA-modified + + + involuntary muscle of anal part of perineum + OBOL:automatic - - - 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]. - + + + involuntary muscle of anal region + OBOL:automatic - - - 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 + + + involuntary muscle of anal triangle + OBOL:automatic - - - 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 + + + non-striated muscle of anal part of perineum + OBOL:automatic - - - 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 + + + non-striated muscle of anal region + OBOL:automatic - - - EMAPA:37505 - MA:th + + + non-striated muscle of anal triangle + OBOL:automatic - - - UMLS:C0278403 - ncithesaurus:Subcutis + + + smooth muscle of anal part of perineum + OBOL:automatic - - - sub-tegumental tissue - BTO:0004525 + + + smooth muscle of anal region + OBOL:automatic - - - subcutaneous tissue - + + + smooth muscle of anal triangle + OBOL:automatic - - - subtegumental tissue - BTO:0004525 + + + smooth muscle tissue of anal part of perineum + OBOL:automatic - - - superficial fascia - + + + smooth muscle tissue of anal region + OBOL:automatic - - - tela subcutanea - - + + + smooth muscle tissue of anal triangle + OBOL:automatic - + - + - + - - + + - + + - - + + - 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 + 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 - Organsystem@de - splanchnic tissue - viscera - visceral tissue - UBERON:0002075 - - - - - viscus + UBERON:0004233 + lower respiratory tract smooth muscle - + - 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 + A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition]. + OBOL:automatic - - - general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. - FMA + + + involuntary muscle of lower respiratory tract + OBOL:automatic - - - UMLS:C0042779 - ncithesaurus:Viscera + + + lower respiratory tract involuntary muscle + OBOL:automatic - + - visceral organ - RETIRED_EHDAA2:0002201 + lower respiratory tract non-striated muscle + OBOL:automatic - + - visceral organ system - MA:0000019 + lower respiratory tract smooth muscle tissue + OBOL:automatic - - - Organsystem@de - BTO:0001491 + + + non-striated muscle of lower respiratory tract + OBOL:automatic - - - splanchnic tissue - BTO:0001491 + + + smooth muscle of lower respiratory tract + OBOL:automatic - - - visceral tissue - BTO:0001491 + + + smooth muscle tissue of lower respiratory tract + OBOL:automatic - + - - - - - - - - + + + + + + + + + + + + + - - + + - - + + - 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 + 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 - atrial tissue - UBERON:0002081 - - - - - cardiac atrium + UBERON:0004234 + iris smooth muscle - + + + + MA + + + - Cardiac chamber in which blood enters the heart. - - + A portion of smooth muscle tissue that is part of a iris [Automatically generated definition]. + OBOL:automatic - - - One of four heart chambers.[TAO] - 2012-08-14 - TAO:0000471 - TAO - ZFIN:curator + + + involuntary muscle of iris + OBOL:automatic - - - 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 + + + iridial smooth muscle + - - - 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 + + + iris involuntary muscle + OBOL:automatic - - - UMLS:C0018792 - ncithesaurus:Cardiac_Atrium + + + iris non-striated muscle + OBOL:automatic - + - atria - + iris smooth muscle tissue + OBOL:automatic - + - atrium - ZFA:0000471 + non-striated muscle of iris + OBOL:automatic - + - cardiac atria - + smooth muscle of iris + OBOL:automatic - - - atrial tissue - BTO:0000903 + + + smooth muscle tissue of iris + OBOL:automatic - + - - - - - - - - - - - - - - + + + + + + + + + + + + + + - - + + - 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 + A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition]. + EMAPA:36287 + FMA:312251 + MA:0000706 uberon - UBERON:0002082 - - - - - cardiac ventricle + UBERON:0004236 + arteriole smooth muscle - - - - - - - - - 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 portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition]. + OBOL:automatic - + - - - - - - - - + + + + + + + + + + + + + - - - - - - - + - 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 + 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:0002090 - + UBERON:0004237 - - - 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 + blood vessel smooth muscle - + - 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 + Smooth muscle found within, and composing the majority of the wall of blood vessels. + - - - Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] - 2012-08-14 - VSAO:0000093 - VSAO - PSPUB:0000170 + + + UMLS:C1519956 + ncithesaurus:Vascular_Smooth_Muscle_Tissue - - - 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 + + + blood vessel involuntary muscle + OBOL:automatic - - - 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 + + + blood vessel non-striated muscle + OBOL:automatic - - - 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) + + + blood vessel smooth muscle tissue + OBOL:automatic - - - axial skeleton - - FMA:71221 + + + involuntary muscle of blood vessel + OBOL:automatic - - - EMAPA:37721 - MA:th + + + 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 - + - - - - - - - - - - - - + + + + + - + - - - + + + + - - + + - 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 + 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 - 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 + UBERON:0004246 + outflow tract smooth muscle - + - Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. - - - UBERONREF:0000003 + A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition]. + OBOL:automatic - - - Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] - 2012-08-14 - VSAO:0000076 - VSAO - - PSPUB:0000170 + + + EMAPA:37708 + MA:th - - - Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] - 2012-08-14 - TAO:0000027 - TAO - TAO:wd + + + involuntary muscle of outflow tract + OBOL:automatic - - - 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 + + + non-striated muscle of outflow tract + OBOL:automatic - - - 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 + + + outflow tract involuntary muscle + OBOL:automatic - - - UMLS:C0222646 - ncithesaurus:Appendicular_Skeleton + + + outflow tract non-striated muscle + OBOL:automatic - + - entire appendicular skeleton - + outflow tract smooth muscle tissue + OBOL:automatic - - - paired fin skeleton - + + + smooth muscle of outflow tract + OBOL:automatic - - - skeleton appendiculare - - + + + 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 + + + + + + + + + + + + + + + + + + + + - - + + - - + + - 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 + 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 - entire integument - integument - integumental organ - pelt - skin - UBERON:0002097 - - - - - skin of body - http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg + UBERON:0004253 + skin muscle - - - - - - - - - Wikipathways:WP2062 - - - + - The organ covering the body that consists of the dermis and epidermis. - UBERON:cjm + Any muscle organ that is part of a skin of body [Automatically generated definition]. + OBOL:automatic - + - MA uses the term skin to refer to what is called here: zone of skin - FMA + in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only + MA - - - UMLS:C1123023 - ncithesaurus:Skin + + + integumental system muscle + MA:0003139 + + + + + muscle of integumental system + EMAPA:18187 + + + + + muscle organ of skin + OBOL:automatic + + + + + skin muscle organ + 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 + + + + + + + + + + + + + + + + + + + - - + + - 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 + 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 - spiral septa - UBERON:0002099 - - - cardiac septum + UBERON:0004265 + outflow tract myocardium - - - The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles. - MESH:A07.541.459 + + + 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 - - - in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this - GO + + + myocardium of outflow tract + OBOL:automatic - - - UMLS:C0018819 - ncithesaurus:Heart_Septum + + + outflow tract cardiac muscle + OBOL:automatic - + - cardiac septa - + outflow tract heart muscle + OBOL:automatic - + - heart septa - + outflow tract heart myocardium + OBOL:automatic - - - spiral septa - XAO:0004141 - + + + outflow tract muscle of heart + OBOL:automatic - + - - + + + + + + + + + + + + + - + - 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 + A portion of connective tissue that is part of a back [Automatically generated definition]. + EMAPA:37256 + MA:0000495 uberon - Rumpf - UBERON:0002100 - - - - - trunk + mesenchyne of back + UBERON:0004267 + back connective tissue - + - 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 + A portion of connective tissue that is part of a back [Automatically generated definition]. + OBOL:automatic - + - UMLS:C0460005 - ncithesaurus:Trunk - - - - - trunk region - XAO:0000054 + EMAPA:37256 + MA:th - + - Rumpf - BTO:0001493 + mesenchyne of back + OBOL:automatic - + - + - + - - + + - - - - - - - - - - - - - + + - - + + - 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 + A pericardium that is part of a outflow tract [Automatically generated definition]. + EMAPA:37707 + MA:0000491 + pericardium of outflow tract uberon - extremities - extremity - UBERON:0002101 - - - - limb + UBERON:0004271 + outflow tract pericardium - - - - 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 + A pericardium that is part of a outflow tract [Automatically generated definition]. + OBOL:automatic - + - UMLS:C0015385 - ncithesaurus:Limb - - - - - free limb - FMA:24875 + EMAPA:37707 + MA:th - + - limb sensu Vertebrata - MAT:0000090 - - - - - flipper - - - - - - extremities - + pericardium of outflow tract + 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 + + + + + + + + - - + + - - + + - 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 + + 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 - foreleg - UBERON:0002102 + UBERON:0004288 - forelimb + skeleton + https://github.com/obophenotype/uberon/wiki/The-skeletal-system - + - 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 + Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. + VSAO:0000026 - + - Upper limb, which connects the manus with the pectoral girdle.[AAO] + 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:0000205 + AAO:0010572 AAO - AAO:LAP + 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 - - - 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 + + + 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 + - - - UMLS:C1140618 - ncithesaurus:Upper_Extremity + + + + + + + + + ZFA - - - free part of upper limb - FMA:24878 + + + 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 - - - free upper limb - FMA:24878 - UBERONREF:0000003 + + + 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 - + - membrum superius - FMA:7183 - FMA:TA - + heart cone + GO:0003313 - - - pectoral flipper - + + + rudimentary heart + ZFA:0000115 - + - - - - - - - - - - - - - - + + + - + - - + + - - + + - 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 + 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 - free part of lower limb - lower extremity - membrum inferius - pelvic appendage - UBERON:0002103 - - - - hindlimb - http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray1239.png + 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 - + - 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 + Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart. + + GO:0003204 - + - free lower limb - FMA:24879 - UBERONREF:0000003 + cardiac fibrous skeleton + EMAPA:36645 - + - hind-limb - VSAO:0000150 + heart fibrous skeleton + GO:0003204 - + - membrum inferius - FMA:7184 - FMA:TA - + skeleton of heart + FMA:9496 - + - free part of lower limb - FMA:24879 + anulus fibrosus dexter cordis + + - + - membrum inferius - + anulus fibrosus sinister cordis + - - - - - - - - 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 + + + trigona fibrosa + + - - - The sensory system used for balance and hearing.[AAO] - 2012-06-20 - AAO:0000631 - AAO - AAO:EJS + + + trigonum fibrosum dextrum cordis + + - - - EMAPA:37985 - MA:th + + + trigonum fibrosum sinistrum cordis + + - + - + - + + - - + - 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 + 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 - arterial smooth muscle cell - UBERON:0002111 - artery smooth muscle tissue + UBERON:0004297 + respiratory system blood vessel smooth muscle - + - A portion of smooth muscle tissue that is part of an artery [Automatically generated definition]. + A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. OBOL:automatic - + - UMLS:C1706851 - ncithesaurus:Artery_Smooth_Muscle_Tissue - - - - - arterial smooth muscle - BTO:0000087 + EMAPA:37573 + MA:th - + - smooth muscle of artery - FMA:72024 - - - - - arterial smooth muscle cell - BTO:0000087 + smooth muscle tissue of blood vessel of respiratory system + 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 + 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:0002113 - - - + UBERON:0004341 + - - - kidney + primitive streak + http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png - + - - - - - - - FMA + + EHDAA2 - + - - + + - definitional + EHDAA2 - + - A paired organ of the urinary tract which has the production of urine as its primary function. - - + 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 - - - 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 + + + (...) 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:C0022646 - ncithesaurus:Kidney + UMLS:C0033153 + ncithesaurus:Primitive_Streak - - - reniculate kidney - - + + + primitive streak - blastopore - germ ring + VHOG:0001202 - + - - - - + + + - - + + - - + + - - - - 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 + + + + 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 - + - - GO + + EHDAA2 - + - - + + - OG + EHDAA2 - + - + - ZFA + EHDAA2 - + - 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 + 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 - + - 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] + 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:0000037 + VHOG:0000979 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] + (...) 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:0000037 + VHOG:0000979 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 + ISBN:978-0721676685 Romer AS, Parsons TS, Vertebrate body (1977) p.105-106 - - - pronephron - BTO:0001541 + + + BTO has this has part of the trophoblast + BTO - + - - - + + + - - + + - - + + - - + + - 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 + + + + + + + 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 - heart endocardial tissue - UBERON:0002165 - + gemmae membrorum + UBERON:0004347 - - - 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 + developmentally_induced_by Fgf10, capable of initiating limb forming interactions between endoderm and mesoderm + limb bud - + - - + + - Bgee:AN + ISBN:9780878932504 - + - 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 + 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 - + - Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO] + Early outgrowth of presumptive limb.[AAO] 2012-06-20 - AAO:0010408 + AAO:0010375 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 + AAO:EJS - + - UMLS:C0014124 - ncithesaurus:Endocardium + UMLS:C0282505 + ncithesaurus:Limb_Bud - + - endocardial lining - EMAPA:32686 + limb buds + - + - endocardial tissue - EMAPA:17868 + limbbud + GO:0060174 - + - heart endocardial tissue - VHOG:0000084 + 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 + + + + + + + + + - + - - + + - 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 + + + + + + + + + + + + + + + + + + + + + + + + + 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 - atrium endocardial tissue - UBERON:0002166 + AER + crista ectodermalis apicalis + UBERON:0004356 - - endocardium of atrium + apical ectodermal ridge + http://upload.wikimedia.org/wikipedia/commons/5/56/Limbbuddiagram.jpg - + - Endocardium that is part of the atrium. - ZFIN:curator - - - - - Cardiac atria endocardium - OBOL:automatic - - - - - atrium of heart endocardium - OBOL:automatic + 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 - - - cardiac atrium endocardium - OBOL:automatic + + + 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 - - - endocardium of Cardiac atria - OBOL:automatic + + + Proliferative region that is part of the developing fin fold or fin.[TAO] + 2012-08-14 + TAO:0002146 + TAO + ZFIN:curator - - - endocardium of atrium of heart - OBOL:automatic + + + relationship loss: subclass proliferative region (TAO:0000098)[TAO] + 2012-08-14 + TAO:0002146 + TAO - - - endocardium of cardiac atrium - OBOL:automatic + + + The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold + - - - endocardium of heart atrium - OBOL:automatic + + + UMLS:C1516037 + ncithesaurus:Apical_Ectodermal_Ridge - + - heart atrium endocardium - OBOL:automatic + apical epidermal ridge + XAO:0004121 - + - atrium endocardial tissue - VHOG:0000606 + AER + MP:0001676 + + + + + crista ectodermalis apicalis + + - + - - - - - - - - - - - - - - + + + - + - - + + - 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 + + + + + + + + + + + + + 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 - fatty layer of superficial fascia - subcutaneous fat - UBERON:0002190 + 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 - subcutaneous adipose tissue + + + pharyngeal arch 1 + http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png - + - A portion of adipose tissue that is part of the hypodermis, beneath the dermis. + The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries. - + - the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156] - MP:0011156 + 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 - - - panniculus adiposus - MP:0011156 + + + 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 - - - fatty layer of subcutaneous tissue - FMA:74315 + + + 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) - - - hypodermis fat layer - MP:0011156 + + + UMLS:C1517197 + ncithesaurus:First_Pharyngeal_Arch - + - panniculus adiposus (tela subcutanea) - FMA:74315 - FMA:TA - + branchial arch 1 + - + - panniculus adiposus telae subcutaneae - FMA:74315 - FMA:TA - + first branchial arch + - + - subcutaneous fat layer - MP:0011156 + first visceral arch + - - - fatty layer of superficial fascia - FMA:74315 + + + visceral arch 1 + - + - subcutaneous fat - BTO:0004042 + 1st arch + EHDAA2:0000006 - - - - - - - - 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 + + + 1st visceral arch + VHOG:0000296 - - - Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs. - + + + arcus pharyngeus primus + + - + - - + + + + + + - + - - + + - - + + - - + + - 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 + + + + + + + + + + + + + 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 + - integument + pharyngeal arch artery + http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png - + - - FMA + + ZFA - + - + - FMA + ZFA - - - The dermis, epidermis and hypodermis. - + + + + + + + + + abduced from EHDAA2 - - - Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO] - 2012-06-20 - AAO:0000239 - AAO - AAO:EJS + + + 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 - + - Surface structure that is the outer protective covering of the body.[VSAO] - 2012-08-14 - VSAO:0000029 - VSAO - PSPUB:0000170 + Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG] + 2012-09-17 + VHOG:0000122 + VHOG + + - - - 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 + + + 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 - + - EMAPA:37504 - MA:th + UMLS:C0003489 + ncithesaurus:Aortic_Arch - + - integumentum commune - FMA:74657 - FMA:TA - + PAA + MP:0002672 + - + - the integument - FMA:74657 + aortic arch + ZFA:0005004 - - - Hautsystem@de - BTO:0000634 + + + aortic arches + ZFA:0005004 + - - - dermal system - BTO:0000634 + + + branchial aortic arches + ZFIN:ZDB-PUB-080512-6 + - - - dermoid system - BTO:0000634 + + + branchial arch artery + EMAPA:16684 - - - tegument - BTO:0000634 + + + embryonic aortic arch artery + EMAPA:16684 + MP:0002672 - - - - - - - - - - - - - - - - - - - - - - - - - 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 + + + pharyngeal arch artery + MP:0002672 - - - adult head vascular network - OBOL:automatic + + + a. arcuum pharyngeorum + + - - - adult head vasculature - OBOL:automatic + + + aortic arch artery + EMAPA:16684 - - - head vascular network - OBOL:automatic + + + arteriae arcuum pharyngeorum + + - - - vascular network of adult head - OBOL:automatic + + + branchial aortic arches + ZFA:0005004 + ZFIN:ZDB-PUB-080512-6 + - - - vascular network of head - OBOL:automatic + + + 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 + - - - vasculature of adult head - OBOL:automatic + + + Blood vessel that is connected to the yolk sac. + - + - + - + - + + + + + + + + + - + + - + - 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 + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - vasculature of trunk + 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 vasculature that is part of a trunk [Automatically generated definition]. - OBOL:automatic + 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 + + ZFIN:ZDB-PUB-061010-3 + + + + + UMLS:C0011665 + ncithesaurus:Descemet_s_Membrane + + + - torso vascular network - OBOL:automatic + Descemet's posterior elastic lamina + FMA:58309 - + - torso vasculature - OBOL:automatic + lamina limitans posterior + FMA:58309 - + - trunk vascular network - OBOL:automatic + lamina limitans posterior corneae + FMA:58309 + FMA:TA + - + - vascular network of torso - OBOL:automatic + posterior limiting lamina + MA:0001246 - + - vascular network of trunk - OBOL:automatic + posterior limiting lamina of cornea + FMA:58309 - + - vasculature of torso - OBOL:automatic + posterior limiting membrane + ZFA:0001686 - + - + - + - + + + + + - - + + + - + - - + + - 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 + + + + + + + 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 - eye vasculature - optic vasculature - UBERON:0002203 + Reichert's membrane + anterior limiting membrane + UBERON:0004370 - vasculature of eye + anterior limiting lamina of cornea - - - - - - - - - ISBN:0781772214 + + + + lexical - + - Vasculature that is part of the eye region. - - OBOL:automatic + 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 - - - not part of the eye in ZFA. Note this changed to a blood vessel in ZFA - ZFA + + + 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 + + + - eye vascular network - OBOL:automatic + Bowman's anterior elastic lamina + FMA:58273 - + - ocular blood vessel - ZFA:0007057 + Bowman's layer + FMA:58273 - + - vascular network of eye - OBOL:automatic + 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 - + - - - - - - - - - - - - - - + + + + + + + + + + + + + - - + + - - + + - - - - - 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 + Vascular network that is connected to the yolk sac. + uberon - UBERON:0002204 - - musculoskeletal system + omphalomesenteric system + vitelline bloos vessel system + vitelline system + UBERON:0004374 + + vitelline vasculature - - - - - - - - - check ctenophore - - - + - Anatomical system that consists of the muscular and skeletal systems. - - VSAO:0000031 - VSAO:curator + Vascular network that is connected to the yolk sac. + - - - Anatomical system that provides locomotion and physical support to the organism.[AAO] - 2012-06-20 - AAO:0010546 - AAO - AAO:EJS + + + omphalomesenteric system + - - - 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) + + + vitelline bloos vessel system + - - - UMLS:C0026860 - ncithesaurus:Musculoskeletal_System + + + vitelline system + - + - + - + - - + + - + + - - + + - 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 + + + + + + + A bone that is part of an appendage [Automatically generated definition]. + appendage bone + bone of appendage + bone of free segment of appendicular skeleton uberon - junctura cartilaginea - UBERON:0002213 - - - cartilaginous joint + UBERON:0004375 + + bone of free limb or fin - - - - 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 - - + A bone that is part of an appendage [Automatically generated definition]. + OBOL:automatic - + - + - + - - + + - + + - - + + - - 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 + + + + + + + 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 - diarthrodial joints - UBERON:0002217 - - - - synovial joint + UBERON:0004381 + skeleton of limb - + - 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 + The collection of all skeletal elements in an individual limb. + - + - 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] + Skeletal subdivision that is part of the limb.[VSAO] 2012-08-14 - TAO:0005153 - TAO - ZFIN:Curator + 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 + + + - diarthroses - ZFA:0005153 - + free limb skeleton + VSAO:0000300 - - - diarthrodial joints - ZFA:0005153 - + + + limb skeleton + EHDAA2:0002221 - + - + - - - - - + - - + + - - - - - - - - - - - - - + + + + + + + + + - - + + - 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 + 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 - UBERON:0002224 + presacral vertebra + UBERON:0004451 - - 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 + trunk or cervical vertebra - + - The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. - - UBERON:cjm + A vertebra in the trunk or cervical region. Includes all cervical, thoracic and lumbar vertebrae, but excludes caudal vertebra. + UBERONREF:0000006 - - - UMLS:C0230139 - ncithesaurus:Thoracic_Cavity + + + it's not clear if the XAO class belongs here or below + XAO - - - cavitas thoracis - - + + + EMAPA:37722 + MA:th - - - space of thoracic compartment - FMA:7565 + + + presacral vertebra + MA:0002869 - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - + - - + + - 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 + An embryo at the neurula stage. + UBERON:0007013 + + BILA:0000061 + BTO:0001766 + NCIT:C34229 + UMLS:C1518306 + neurula 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 + UBERON:0004455 + neurula embryo - - - - - - - - - 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 + An embryo at the neurula stage. + - + - 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 + UMLS:C1518306 + ncithesaurus:Neurula - - - spinal medulla - BTO:0001279 + + + neurula + BTO:0001766 - + - - + + + - + - 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 + + + + + + + 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 - calvarium - neurocranium - UBERON:0002241 - - chondrocranium + UBERON:0004456 + + entire sense organ system - + - 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 + Sum of all sensory systems in an organism. + - - - neurocranium - MA:0000317 - + + + sense organ system + FMA:78499 - + - - - + + + + + + + + + + + + + + + + + + - - + + - - + + - - + + - - + + - 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 + 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 - 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 + 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 - + - 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 + Any collection of skeletal muscles that is part of a head [Automatically generated definition]. + OBOL:automatic - + - brain stem - ABA:BS + head musculature + FMA:71287 - + - truncus encephali - - - - - - - accessory medullary lamina of pallidum - NeuroNames:236 - - - - - lamella pallidi incompleta - NeuroNames:236 - - - - - - lamina medullaris accessoria - NeuroNames:236 - + muscle group of head + FMA:71287 - - - lamina medullaris incompleta pallidi - NeuroNames:236 - + + + muscles of head + FMA:71287 - - - lamina pallidi incompleta - NeuroNames:236 + + + musculi capitis + FMA:71287 + FMA:TA - - - truncus encephalicus - BTO:0000146 - + + + set of muscles of head + FMA:71287 - + - + - + - + - + - - - - - - - + - 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 + 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 - atrium cardiac muscle - UBERON:0002302 - - - - myocardium of atrium + body wall muscles + UBERON:0004462 + musculature of body wall - + - the atrial part of middle layer of the heart, comprised of involuntary muscle - ISBN:0-683-40008-8 - MP:0010493 + Any collection of muscles that is part of a body wall [Automatically generated definition]. + OBOL:automatic - - - 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 + + + EMAPA:37853 + MA:th - + - atrial myocardium - ZFA:0001374 - - - - - atrium cardiac muscle - VHOG:0000602 + body wall musculature + FMA:86931 - + - + - + - + - + - - - - - - - + - 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 + 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:0002315 + UBERON:0004464 - gray matter of spinal cord + musculature of thorax - + - 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 + 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 + + + - UMLS:C0475853 - ncithesaurus:Gray_Matter_of_the_Spinal_Cord + EMAPA:37260 + MA:th - + - gray matter of spinal cord - OBOL:automatic + muscle group of thorax + FMA:71293 - + - gray substance of spinal cord - FMA:256580 + muscles of thorax + FMA:71293 - + - spinal cord gray matter - OBOL:automatic + musculi thoracis + FMA:71293 + FMA:TA + - + - spinal cord grey substance - OBOL:automatic + set of muscles of thorax + FMA:71293 - + - substantia grisea medullae spinalis - FMA:256580 - FMA:TA - + thoracic musculature + FMA:71293 - + - - + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - + - 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 + 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 - celom - coelom - coelome - hemocoel - UBERON:0002323 - - - coelemic cavity lumen + UBERON:0004465 + + musculature of neck - - - - - - - - - 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 + Any collection of muscles that is part of a neck [Automatically generated definition]. + OBOL:automatic - + - coelomic cavity - EHDAA2:0000267 + cervical muscles + AAO:0000091 - + - coelomic cavity lumen - EHDAA2:0000267 + muscle group of neck + FMA:71290 - + - space of body compartment - FMA:85006 + muscles of neck + FMA:71290 - - - ventral body cavity - NCBITaxon:7742 + + + musculi cervicis + FMA:71290 + FMA:TA + - - - celom - BTO:0001707 + + + musculi colli + FMA:71290 + FMA:TA + - - - coelome - BTO:0001707 + + + neck musculature + FMA:71290 - - - hemocoel - FBbt:00005060 + + + set of muscles of neck + FMA:71290 - + - + - + - - + + - - - - - + + - + - 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 + + + + + + + FMA:33061 + muscle group of vertebral column uberon - urethral epithelium - urethral plate - urethral seam - UBERON:0002325 - epithelium of urethra + UBERON:0004468 + set of muscles of vertebral column - - - - 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 + muscle group of vertebral column + FMA:33061 - + - + - + - + - - + - + - 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 + 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 - urethral lamina propria - UBERON:0002326 - lamina propria of urethra + UBERON:0004469 + musculature of back - + - A lamina propria that is part of a urethra [Automatically generated definition]. + Any collection of muscles that is part of a back [Automatically generated definition]. OBOL:automatic - - - EMAPA:37785 - MA:th - - - + - lamina propria mucosa of urethra - OBOL:automatic + muscle group of back + FMA:71291 - + - lamina propria mucosae of urethra - OBOL:automatic + muscles of back + FMA:71291 - + - urethra lamina propria mucosa - OBOL:automatic + musculi dorsi + FMA:71291 + FMA:TA + - + - urethra lamina propria mucosae - OBOL:automatic + set of muscles of back + FMA:71291 - + - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - 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 + 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 - notochorda - UBERON:0002328 + muscular system of pelvis + set of muscles of pelvis + UBERON:0004470 - - - 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 + musculature of pelvic girdle - - - - 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 + Any collection of muscles that is part of a pelvic girdle [Automatically generated definition]. + OBOL:automatic - - - Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] - 2012-08-14 - VSAO:0000032 - VSAO - PSPUB:0000170 + + + we merge two FMA classes here + FMA - - - 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 + + + muscle group of pelvic girdle + FMA:50205 - - - 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 + + + muscle group of pelvis + FMA:50248 - - - relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] - 2012-06-20 - AAO:0000327 - AAO + + + pelvic girdle muscle system + EHDAA2:0001429 - - - (...) 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 + + + pelvic girdle muscles + AAO:0000427 - - - UMLS:C0028439 - ncithesaurus:Notochord + + + pelvic girdle musculature + FMA:50205 - + - notocord - ZFA:0000135 + set of muscles of pelvic girdle + FMA:50205 - + - notochorda - - + muscular system of pelvis + FMA:50248 + + + + + set of muscles of pelvis + FMA:50248 - + - - - + + + + + + + + + + + + + - - + + - 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 + 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 - epimere - epimere mesoderm - epithelial somite - somites - somitic mesoderm - somitus - UBERON:0002329 + UBERON:0004471 - - - 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 + musculature of pectoral girdle - - - - 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. - - + A subdivision of the musculature of the body in the pectoral girdle region. Includes pectoral and shoulder muscles. + - - - Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] - 2012-06-20 - AAO:0010569 - AAO - AAO:EJS + + + EMAPA:37857 + MA:th - - - 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 + + + muscle group of pectoral girdle + FMA:33519 - - - relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] - 2012-08-14 - TAO:0000155 - TAO + + + pectoral girdle muscles + AAO:0000423 - - - relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] - 2012-08-14 - TAO:0000155 - TAO + + + pectoral girdle musculature + FMA:33519 - - - relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] - 2012-06-20 - AAO:0010569 - AAO + + + 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 + - - - (...) 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) + + + Any collection of muscles that is part of a face. + OBOL:automatic - - - mesodermal cluster - GO:0001756 + + + entire facial musculature + - - - UMLS:C0376449 - ncithesaurus:Somite + + + facial muscles + FMA:71288 - - - epimere - ISBN:0073040584 + + + muscle group of face + FMA:71288 - - - epithelial somite - + + + musculi faciei + FMA:71288 + FMA:TA + - + - somites - + set of facial muscles + FMA:71288 - + - somitus - - + set of muscles of face + FMA:71288 - + - - - - - - - - + + + + + + + + + + + + + + - - + + - - - - 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 + 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:0002330 - - - exocrine system + UBERON:0004478 + musculature of larynx - + - 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]. - + The collection of muscles that are part of the larynx. + - - - UMLS:C1516995 - ncithesaurus:Exocrine_System + + + laryngeal muscles + FMA:46616 - + - exocrine glandular system - EHDAA2:0002225 + laryngeal muscles set + FMA:46616 + + + + + muscle group of larynx + FMA:46616 + + + + + set of laryngeal muscles + FMA:46616 + + + + + set of muscles of larynx + FMA:264611 - + - - - - + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - + - 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 + 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 - crista neuralis - neural crest material - UBERON:0002342 + muscular system of trunk + UBERON:0004479 + - - - 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 + musculature of trunk - - - - - - - - - - XAO + + + Any collection of muscles that is part of a trunk [Automatically generated definition]. + OBOL:automatic - - - - - - - - - BTO + + + 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 + - + - 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) + Any collection of muscles that is part of a limb [Automatically generated definition]. + OBOL:automatic - - - UMLS:C0027789 - ncithesaurus:Neural_Crest + + + limb muscle system + EHDAA2:0000995 - + - NC - XAO:0000048 - + limb musculature + FMA:50188 - - - crista neuralis - - + + + muscle group of limb + FMA:50188 - - - neural crest material - VHOG:0000057 + + + set of muscles of limb + FMA:50188 - + - + - + - + + - + - 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 + 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:0002343 + UBERON:0004481 - - abdomen musculature + musculature of upper limb - + - Set of all muscles in abdomen. + Any collection of muscles that is part of a forelimb [Automatically generated definition]. OBOL:automatic - + - muscle group of abdomen - FMA:71294 + free upper limb musculature + FMA:50396 - + - muscles of abdomen - FMA:71294 + muscle group of free upper limb + FMA:50396 - + - musculature of abdominal wall - FMA:86917 + musculature of free upper limb + FMA:50396 - + - set of muscles of abdomen - FMA:71294 + set of muscles of free upper limb + FMA:50396 - + - - - - 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 + + + + + + + + + + + + + + + + + + + + + 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 - epithelium tubi neuralis; neuroectoderma - neuaral ectoderm - presumptive central nervous system - ventral neurogenic region - UBERON:0002346 - - - neurectoderm + UBERON:0004482 + + musculature of lower limb - + - Embryonic ectoderm that gives rise to nervous tissue. - + Any collection of muscles that is part of a hindlimb [Automatically generated definition]. + OBOL:automatic - - - (...) 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) + + + free lower limb musculature + FMA:50399 - - - UMLS:C1518271 - ncithesaurus:Neuroectoderm + + + muscle group of free lower limb + FMA:50399 - - - epithelium tubi neuralis; neuroectoderma - - + + + musculature of free lower limb + FMA:50399 - - - ventral neurogenic region - VHOG:0000150 + + + set of muscles of free lower limb + FMA:50399 - + - - - + + + + + + + + + + + + + - + - - - - - - - - - - - - - + - 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 + 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 - pericardium visceral mesothelium - UBERON:0002348 - - - - epicardium + atrial myocardium + UBERON:0004490 + cardiac muscle tissue of atrium - - - - - - - - - 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 + A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition]. + OBOL:automatic - - - 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 + + + in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging. + GO - - - UMLS:C0225968 - ncithesaurus:Epicardium + + + atrial cardiac muscle tissue + GO:0055009 - + - visceral serous pericardium of heart - FMA:9461 + atrial heart muscle + GO:0055009 - + - visceral serous pericardium proper - FMA:9461 + cardiac atrium muscle + GO:0055009 - + - pericardium visceral mesothelium - EMAPA:16589 + atrial myocardium + GO:0055009 + GOC:mtg_heart - + - + - + - - + + - - - + - - - - - - - - - - - - - + - 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 + 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 - cardiac muscle - heart muscle - UBERON:0002349 - - - - - myocardium - http://upload.wikimedia.org/wikipedia/commons/6/6e/Glanzstreifen.jpg + UBERON:0004491 + cardiac muscle tissue of interatrial septum - + - 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 + A portion of cardiac muscle tissue that is part of a interatrial septum [Automatically generated definition]. + OBOL:automatic - + - muscle of heart - FMA:9462 + interatrial septum cardiac muscle tissue + - - - cardiac muscle - ZFA:0001319 + + + interatrial septum heart muscle + - - - heart muscle - FMA:9462 + + + interatrial septum muscle + - - - heart muscle - ZFA:0001319 + + + interatrial septum myocardium + - + - - - + + + + + + + + + + + + + - - + + - 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 + 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 - central conduction system - UBERON:0002350 - - - - conducting system of heart + UBERON:0004492 + cardiac muscle tissue of cardiac septum - - - - 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) + A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition]. + OBOL:automatic - + - cardiac conducting system - VHOG:0001271 + cardiac septum cardiac muscle tissue + - + - cardiac impulse conducting system - GO:0003161 + cardiac septum heart muscle + - + - complexus stimulans cordis - FMA:9476 - FMA:TA - + cardiac septum muscle + - + - heart conduction system - GO:0003161 + 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 + - - - impulse conducting system - MA:0000094 + + + + + + + + + MA - - - systema conducente cordis - FMA:9476 - FMA:TA - + + + A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]. + OBOL:automatic - + - - + + + + + + + + + + + + + + + + + + + + + A portion of skeletal muscle tissue that is part of a diaphragm [Automatically generated definition]. + FMA:261898 + uberon + UBERON:0004495 + skeletal muscle tissue of diaphragm + + + + + A portion of skeletal muscle tissue that is part of a diaphragm [Automatically generated definition]. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + - + - - + + - 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 + A muscle that is attached to a vertebra of the vertebral column. + FMA:22594 + vertebral column muscle uberon - UBERON:0002355 - - - - pelvic region of trunk + UBERON:0004518 + muscle of vertebral column - + - 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 + A muscle that is attached to a vertebra of the vertebral column. + - + - lesser pelvis - FMA:9578 + vertebral column muscle + FMA:22594 + + + + + + + + + + + + + + + + + + + + + + + + + + A vasculature that is part of a muscle organ [Automatically generated definition]. + FMA:87123 + muscular organ vasculature + uberon + UBERON:0004521 + vasculature of muscle organ + - - - pelvis - FMA:9578 - MA:0000030 + + + A vasculature that is part of a muscle organ [Automatically generated definition]. + OBOL:automatic - + - true pelvis - FMA:9578 + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - + - - + + - Serous membrane which is divided into parietal and visceral serous pericardium. - - - EMAPA:19030 - FMA:9582 - MA:0002739 - serous portion of pericardium + 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 - pericardium serosum - UBERON:0002357 + CV system + Herz und Gefaesssystem + UBERON:0004535 + + - serous pericardium + + cardiovascular system - - - - - - - - - FMA + + + Anatomical system that has as its parts the heart and blood vessels. + BTO:0000088 - - - - - - - - - FMA + + + 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 - - - Serous membrane which is divided into parietal and visceral serous pericardium. - - + + + UMLS:C0007226 + ncithesaurus:Cardiovascular_System - - - serous portion of pericardium - FMA:9582 + + + CV system + BTO:0000088 - + - pericardium serosum - - + Herz und Gefaesssystem + BTO:0000088 - + - - - + + + + + + + + + + + + + + - - - - - - - + - + - 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 + A vascular network consisting of blood vessels. + TAO:0001079 + ZFA:0001079 + blood vascular network + set of blood vessels uberon - pericardium fibrosum - UBERON:0002359 - - - fibrous pericardium + blood system + blood vessel system + blood vessels + UBERON:0004537 + blood vasculature - - - - FMA + + + A vascular network consisting of blood vessels. + - - - - - - - - - FMA + + + blood vessels + TAO:0001079 - - - - + + + + + + + + + + + + + + + + + + + - - + + - - WP - + + 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 + - + - 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 + A kidney that is part of a left side of organism [Automatically generated definition]. + OBOL:automatic - - - pericardium fibrosum - - + + + UMLS:C0227614 + ncithesaurus:Left_Kidney - + - + - + - - + + - - - - - - - + - - + + - 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 - + 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 - - exocrine gland + right kidney - + - 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 - + A kidney that is part of a right side of organism [Automatically generated definition]. + OBOL:automatic - + - UMLS:C0015282 - ncithesaurus:Exocrine_Gland - - - - - ducted gland - AEO:0000097 - - - - - glandula exocrina - - + UMLS:C0227613 + ncithesaurus:Right_Kidney - + - - - 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 + + + + + + + + + + + + + + + + + + + + + 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 - - - connective tissue + left eye - - - Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. - - - GO_REF:0000034 - PSPUB:0000170 - VSAO:0000017 + + + An eye that is part of a left side of organism [Automatically generated definition]. + OBOL:automatic - - - 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 + + + EMAPA:37362 + MA:th - - - 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 + + + left eyeball + FMA:12515 - - - 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 + + + left orbital part of face + FMA:54450 - - - MA also has set of connective tissues - MA + + + 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 + + + - UMLS:C0009780 - ncithesaurus:Connective_Tissue + EMAPA:37363 + MA:th - + - portion of connective tissue - FMA:9640 + right eyeball + FMA:12514 - - - Bindegewebe - BTO:0000421 + + + right orbital part of face + FMA:54449 + + + + + right orbital region + FMA:54449 - + - - - + + - + - - 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 + 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: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 + UBERON:0004571 + + systemic arterial system - - - 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 + + + + MA-inferred - - - muscular tissue - + + + 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. + + - + - portion of muscle tissue - FMA:9641 + systemic arterial circulatory system + FMA:45623 - + - - - + + + - + - - + + - - - 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 + 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 - Blutbildungssystem - haematopoietic system - hematological system - hematolymphoid system - hemopoietic system - UBERON:0002390 - + UBERON:0004572 - - - hematopoietic system + arterial system - + - - - - - - - FMA + + MA - + - - + + - definitional + EHDAA2 - + - 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 + The part of the cardiovascular system consisting of all arteries. + - + - Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] + 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:0001624 + VHOG:0000273 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 + 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) - + - + - - - - - + - - + + - - + - - - - - - - - - - - - - - - - - - - + - a double-walled sac containing the heart and the roots of the great vessels. - - FMA:9868 - RETIRED_EHDAA2:0001443 - TAO:0000054 + 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 - pericardium - UBERON:0002406 - - - pericardial sac - http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png + UBERON:0004573 + + systemic artery - - - - - - - - - FMA + + + 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. + + - - - a double-walled sac containing the heart and the roots of the great vessels. - - + + + EMAPA:37126 + MA:th + + + + + systemic arterial subtree + FMA:66464 - + - - + + - - - - - - - - - - - - - - - - - - - + - 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 + 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:0002407 - - - - - pericardium - http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png + UBERON:0004581 + systemic venous system - - - - - - - - - MA + + + The part of the venous system that drains the general body tissues[Kardong]. + + ISBN:0073040584 - - - The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium. - - + + + 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] + - + - Peritoneum that surrounds the heart.[AAO] - 2012-06-20 - AAO:0010817 - AAO - AAO:JMG + 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 - - - 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 + + + 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) - - - 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 + + + 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 - - - we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium - FMA + + + 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:C0031050 - ncithesaurus:Pericardium + UMLS:C1267406 + ncithesaurus:Venous_System - + - + - + - + - + - + - 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 + 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 - pericardial sac - UBERON:0002408 + UBERON:0004638 - - parietal serous pericardium - http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png + + blood vessel endothelium - + - Parietal serous membrane which is part of the pericardium and forms the outer layer of the pericardial sac. - + An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart. + - + - UMLS:C0225969 - ncithesaurus:Parietal_Pericardium - - - - - lamina parietalis pericardii - FMA:9870 - FMA:TA - - - - - - parietal pericardium - VHOG:0000537 - - - - - pericardial sac - - + UMLS:C1706972 + ncithesaurus:Blood_Vessel_Endothelium - + - + - + - - + + - - + - - + + - - + + - Transudate contained in the pericardial cavity.[FMA] - - BTO:0001016 - FMA:9887 - MA:0002530 + 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:0002409 - - pericardial fluid + UBERON:0004663 + + aorta wall - - - - FMA + + + An anatomical wall that is part of an aorta, enclosing the luminal space. + - - - Transudate contained in the pericardial cavity.[FMA] - - FMA:9887 + + + aortic wall + FMA:14156 + + + + + wall of aorta + FMA:14156 - + - - - - - - - - + + + + + + + + + + + + + - - + + - - + + - - + + - - 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 + 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 - body surface - dermal system - external covering of organism - integumentum commune - organism surface - surface - UBERON:0002416 - - + UBERON:0004664 - integumental system + aorta tunica adventitia - + - 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 + The outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers. + ISBN:0-683-40008-8 + MP:0009871 - + - 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 - + tunica adventitia of aorta + FMA:14283 - + - - + + + + + + + + + + + + + + + - - + + - - 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 - + + + + + + + + + + + + + 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 - - - 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 + interventricular septum membranous part - - - - + + + + + + + + + Wikipedia - + - 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 + The membranous portion of the wall between the two lower chambers of the heart. + MP:0008823 - + - 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 + The membranous septum is the upper part of ventricular septum[GO:0003149]. + GO:0003149 - - - 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 + + + membranous septum + GO:0003149 - - - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - 2012-06-20 - AAO:0000060 - AAO + + + ventricle membranous septum + VT:0000018 - - - 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) + + + ventricular membranous septum + MP:0008823 - - - UMLS:C0007301 - ncithesaurus:Cartilage + + + cardiac ventricular membranous septum + - + - cartilage tissue - FMA:37377 + membranous interventricular septum + FMA:7135 - + - chondrogenic tissue - VSAO:0000040 + membranous part interventricular septum + VHOG:0000927 - - - cartilages - VHOG:0001207 + + + membranous part of interventricular septum + FMA:7135 - - - portion of cartilage tissue - FMA:37377 + + + membranous portion of interventricular septum + FMA:7135 - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 + + + pars membranacea (septi interventricularis) + FMA:7135 - + - glandulae cutis - FMA:71878 + pars membranacea septi interventricularis + FMA:7135 FMA:TA - - - set of skin glands - FMA:71878 - - - - - skin glands - - - - + - skin glands set - + membranous interventricular septum + MA:0002939 - + - + - + - + - - + - + - - - - - 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 + + + + + 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 - - - - - - - - - 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 muscular portion of the wall between the two lower chambers of the heart. + + - + - 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 muscular septum is the lower part of the ventricular septum[GO] + GO:0003150 - - - the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme - + + + muscular septum + GO:0003150 - - - UMLS:C1709332 - ncithesaurus:Oral_Cavity_Epithelium + + + cardiac ventricular muscular septum + - + - epithelium of mucosa of mouth - FMA:265152 + muscular interventricular septum + FMA:7134 - + - epithelium of oral mucosa - FMA:265152 + 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 - + - + - + - - + + - + - + - - + + - - + + + + + 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 + + + + + + + + + + + + - - + + - 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 + 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 - epicardium - pericardium visceral mesothelium - UBERON:0002425 - - - visceral serous pericardium + 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 - + - - + + - cjm + GO + Wikipedia - + - - + + - FMA + Wikipedia - + - Visceral serous membrane which is continuous with the parietal serous pericardium and is attached to the myocardium[FMA]. - + The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane. + + NLXANAT:20090205 - + + + UMLS:C0034671 + ncithesaurus:Raphe_Nuclei + + + - lamina visceralis pericardii serosi - + nuclei raphes + FMA:84017 + FMA:TA - + - visceral pericardium - VHOG:0000538 + raphe nuclei + FMA:84017 - + + + raphe nuclei + NLXANAT:20090205 + + + + + raphe nuclei set + FMA:84017 + + + - epicardium - MA:0000484 + nuclei raphes + + - + - pericardium visceral mesothelium - EMAPA:16589 + 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 + + + + + + + + + - + - + - - - + - - + + - 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 + A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]. + EMAPA:36503 + MA:0000704 uberon - UBERON:0002428 - - - limb bone + UBERON:0004695 + arterial system smooth muscle - + - 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 + A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]. OBOL:automatic - - - - free limb bone - - UBERONREF:0000003 - - + - + - + - + - - + - + - 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 + + + + + + + A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]. + EMAPA:36613 + MA:0000715 uberon - set of choroid blood vessels - UBERON:0002443 - - cannot find singular in FMA, using Set class - choroidal blood vessel + UBERON:0004696 + venous system smooth muscle - + - 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 + A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]. OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of a vena cava [Automatically generated definition]. + + EMAPA:37800 + MA:0000713 + NCIT:C49318 + UMLS:C1710623 + uberon + UBERON:0004698 + vena cava endothelium + - - - blood vessel of posterior uvea + + + An endothelium that is part of a vena cava [Automatically generated definition]. OBOL:automatic - - - choroid blood vessel - OBOL:automatic + + + EMAPA:37800 + MA:th - - - choroid coat blood vessel - OBOL:automatic + + + 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 + - - - choroidea blood vessel + + + An endothelium that is part of a outflow tract [Automatically generated definition]. OBOL:automatic - - - posterior uvea blood vessel - 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 + - - - vasa sanguinea choroideae - FMA:76550 - FMA:TA - + + + An endothelium that is part of an arterial system [Automatically generated definition]. + OBOL:automatic - - - set of choroid blood vessels - FMA:76550 + + + UMLS:C1706849 + ncithesaurus:Arterial_System_Endothelium - + - + - + - - + + - + - - - - - - - - - - - - - + - A tributary of the iliac vein that drains the urinary bladder. - - - - EMAPA:37205 - MA:0002263 - venae vesicales - vesical veins - vesical veins set + An endothelium that is part of a venous system [Automatically generated definition]. + + EMAPA:35907 + MA:0000714 + NCIT:C49320 + UMLS:C1710626 uberon - UBERON:0002460 - - vesical vein - http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png + UBERON:0004701 + venous system endothelium - + - A tributary of the iliac vein that drains the urinary bladder. - - UBERON:cjm + An endothelium that is part of a venous system [Automatically generated definition]. + OBOL:automatic - + - EMAPA:37205 - MA:th - - - - - venae vesicales - FMA:70911 - FMA:TA - - - - - - vesical veins - + UMLS:C1710626 + ncithesaurus:Venous_System_Endothelium - + - + - + - - + + - + + - - + + - 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 + + + + + + + A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]. + EMAPA:35732 + MA:0001805 uberon - intestinal juice - UBERON:0002466 - - - intestine secretion + UBERON:0004702 + respiratory system blood vessel endothelium - + - 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. - + A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + + + + + + + + + + + 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 + - - - UMLS:C0021849 - ncithesaurus:Intestinal_Secretion + + + 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 - - - intestinal secretion - FMA:62974 + + + 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 - - - succus entericus - + + + UMLS:C1284055 + ncithesaurus:Bulbus_Cordis - - - intestinal juice - BTO:0000644 + + + primitive right ventricle endocardium + EHDAA2:0000197 + JB:def - + - - + + + + + + + + + + + + + + - + - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - bone - portion of bone tissue - UBERON:0002481 - - - bone tissue + UBERON:0004708 + + paired limb/fin - + - + VSAO - - - - + + + + + + + + + VSAO - + + + + + + + + + definitional + + + - 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 + An appendage that is part of an appendage girdle complex. + + UBERON:cjm - - - 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 + + + girdle-associated appendage + - - - UMLS:C0391978 - ncithesaurus:Bone_Tissue + + + limb or fin + - + - osteogenic tissue - VSAO:curator + limb/fin + - - - mineralized bone tissue - XAO:0004040 + + + pectoral or pelvic appendage + - - - bone - MESH:A02.835.232 + + + pelvic/pectoral appendage + - - - portion of bone tissue - FMA:224804 + + + jointed paired lateral appendage + + + + + + paired appendage + VSAO:0000067 - + - + - + - + - - + - + - - + + - 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 + + + + + + + + + + + + + + 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 - iris pigmented epithelium - UBERON:0002506 - - iris epithelium + UBERON:0004709 + + pelvic appendage - - - - 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 + definitional - - - epithelium pigmentosum (iris) - FMA:58517 + + + + lexical - - - epithelium pigmentosum iridis - FMA:58517 - FMA:TA - + + + 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 - + - iris epithelial tissue - OBOL:automatic + hindlimb/pelvic fin + - + - iris epithelium - FMA:58517 + pelvic appendage + VSAO:0000126 - + - pigmented epithelium of iris - FMA:58517 + pelvic limb/fin + - - - - iris pigmented epithelium - MA:0002826 + + + + posterior paired appendage + VSAO:0000126 - + - + - + - - + + - - + + + + + + + + + + + + + - + - - + + - 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 + 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 - 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 + UBERON:0004710 + + pectoral appendage - - - - VSAO - - - + - + - VSAO + definitional - + + + + lexical + + + - Replacement bone that forms within cartilage. - - - GO:0001958 - GO_REF:0000034 - VSAO:0000145 + 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 - - - 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 + + + 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) - - - some structures, e.g. in ZFA are both intramembrane and endochondral - ZFA + + + anterior limb/fin + - + - ossified chondrogenic bone - VSAO:0000145 + anterior paired appendage + VSAO:0000148 - - - cartilaginous bone - BTO:0002157 + + + forelimb - pectoral fin + VHOG:0001753 - - - endochondral bones - ZFA:0001591 - + + + forelimb or pectoral fin + - - - - - - - - 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. - + + + forelimb/pectoral fin + - + - textus connectivus elasticus - + pectoral limb/fin + - + - - - - - - - - + + + - - + + - - + + - 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 + 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 - tunica media vasorum - UBERON:0002522 - - May be composed of smooth muscle and elastic tissue - tunica media - Illu:artery.jpg + jugular + vena jugularis + UBERON:0004711 + jugular vein + http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray558.png - - - - MA - - - - - - - - - - - cjm - - - - - - - - - - - cjm - - - + - The middle layer of an artery or vein. [WP,unvetted]. - + The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava. + - + - UMLS:C0162867 - ncithesaurus:Tunica_Media - - - - - tunica media vasorum - - + UMLS:C0022427 + ncithesaurus:Jugular_Vein - + - tunica media vasorum - BTO:0002011 + vena jugularis + BTO:0001744 - + - - + + + - + - - + + - - + + - 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 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 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 - + 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:C0162864 - ncithesaurus:Tunica_Intima - - - - - Bichat's tunic - BTO:0002012 - - - - - intima - BTO:0002012 - - - - - tunica intima vasorum - BTO:0002012 + UMLS:C1516779 + ncithesaurus:Conceptus - + - - + + + + + + + + + + + + + + - - + + - 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 + 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 - Druese - glandula - UBERON:0002530 - + neural metamere + neural segment + UBERON:0004731 - - gland - http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png + neuromere - + - an organ that functions as a secretory or excretory organ - MGI:csmith - MP:0002163 + 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). + + - - - UMLS:C1285092 - ncithesaurus:Gland + + + A metameric segment of the central nervous system.[ZFA] + 2012-08-14 + TAO:0001328 + TAO + ZFIN:curator - + - glandular organ + neural tube metameric segment - - - Druese - BTO:0000522 + + + 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 + - - - glandula - - + + + Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres. + + FBbt:00005140 - + - glandula - BTO:0000522 + neuromere + FBbt:00005140 - + - - - 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 + + + + + + + + + + + + + + + + + + + + + + An organ subunit that is part of a hindbrain [Automatically generated definition]. + FMA:61998 + hindbrain segment + segment of hindbrain uberon - blastocyst - ectoblast - epiblastus - primitive ectoderm - UBERON:0002532 - - - - - epiblast (generic) - http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png + UBERON:0004733 + + segmental subdivision of hindbrain - + - 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) + An organ subunit that is part of a hindbrain [Automatically generated definition]. + OBOL:automatic - + - epiblast - VHOG:0000243 - - - - - ectoblast - MP:0003886 - - - - - epiblastus - - + hindbrain segment + FMA:61998 - - - primitive ectoderm - VHOG:0000243 + + + segment of hindbrain + FMA:61998 - + - - - - - - - - - - + + + + + + + + + + + + + + - - + + - - + + - 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 + 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 - arcus pharyngei - visceral arch - UBERON:0002539 - + blastocystis trilaminaris + tri-laminar disc + tri-laminar disk + trilaminar blastocyst + trilaminar blastoderm + trilaminar disc + trilaminar disk + trilaminar germ + UBERON:0004734 - - - pharyngeal arch - http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png + gastrula - - - - 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 + Organism at the gastrula stage. + + - - - 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 + + + We explicitly merge the NCITA terms here + NCIT - - - 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:C0017199 + ncithesaurus:Gastrula - + - UMLS:C0080322 - ncithesaurus:Pharyngeal_Arch + UMLS:C1284022 + ncithesaurus:Trilaminar_Embryonic_Disc - + - pharyngeal arches - - - - - - branchial arch - BTO:0001785 - MP:0002884 + gastrula embryo + BILA:0000060 - + - arcus pharyngei - - + blastocystis trilaminaris + - - - - - - - - - - - - - - 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 + + + tri-laminar disc + - - - 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. - - - + + + tri-laminar disk - - - - 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 - + + + trilaminar blastocyst + - - - ectodermal placode - - FMA:293966 - + + + trilaminar blastoderm + - - - placode - + + + trilaminar disc + - - - ectodermal cranial placode - UBERON:cjm + + + trilaminar disk + - + - cranial placodes - XAO:0000305 - + trilaminar germ + - + - - + + + - - + + - 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 + + + + + + + + + + + + + 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:0002553 - - anatomical cavity + 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 + + + + + + + + + + + 2012-08-14 + VSAO:0000015 + VSAO + + + - 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 + 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:37442 + EMAPA:37744 MA:th - + - + - + - - + + + + + + - + + - - + + - - + + - 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 + Dermis-derived entity that is made of skeletal tissue. + dermal element uberon - UBERON:0002616 - - regional part of brain + UBERON:0004756 + dermal skeletal element - + - 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 + Dermis-derived entity that is made of skeletal tissue. + + - + - segment of brain - BIRNLEX:1167 + dermal element + VSAO:curator - + - - + + + + + + + + + + + + + + - - + + - A wall, dividing a cavity or structure into smaller ones[WP]. - septal - - AAO:0011127 - FMA:86461 - OpenCyc:Mx4rrqot_on_EdaAAAACs0uFOQ - septa + 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 - UBERON:0003037 - - general anatomical term in FMA - septum + anal gland + anal sac + gland of anus + rectal gland + UBERON:0004760 + + gland of anal canal - + - A wall, dividing a cavity or structure into smaller ones[WP]. - + A gland that is part of an anal canal [Automatically generated definition]. + + OBOL:automatic - + + + UMLS:C0162322 + ncithesaurus:Anal_Gland + + + - septa - + gland of anal canal + OBOL:automatic + + + + + anal sac + + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + - - - - - - + - - - - - - - + + - - - - - - - + - 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 + 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 - isthmic organizer territory - isthmo-cerebellar region - isthmus - isthmus/MHB - UBERON:0003052 - - - - midbrain-hindbrain boundary + cartilaginous skull + chondocranium + embryonic chondocranium + neurocranium + UBERON:0004761 + cartilaginous neurocranium - - - - ZFA - - - - + - - - - - - - ZFA + + FMA - + - - + + - ZFA + PMC1571569 - + - 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 + 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]. + - - - 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) + + + 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 - - - isthmic organizer territory - XAO:0000016 + + + UMLS:C1516496 + ncithesaurus:Chondrocranium - + - isthmo-cerebellar region - VHOG:0000649 + chondocranium + - + - isthmus/MHB - Geisha:syn - NCBITaxon:8782 + neurocranium + - + - - - + + + + + + + + + + + + + - + - + - 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 + + + + + + + Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]. + note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes) + + MA:0002837 uberon - EVL - epidermis epithelial layer - epidermis outer layer - epitrichium - periderm - UBERON:0003055 - - - periderm + UBERON:0004764 + intramembranous bone tissue - - - - EHDAA2 + + + Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]. + + GO:0001957 - - - + + + note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes) + MA + + + + + + + + + - + - - EHDAA2 - + + 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 + - + - - + + - ZFA + VSAO - + - 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 + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. + - + - 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] + Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] 2012-08-14 - TAO:0001185 - TAO - ZFIN:curator + VSAO:0000128 + VSAO + PSPUB:0000170 - - - relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO] + + + Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] 2012-08-14 - TAO:0001185 + TAO:0001890 TAO - - - - - UMLS:C1518973 - ncithesaurus:Periderm - - - - - skin periderm - EHDAA2:0001846 - - - - - EVL - ZFA:0001185 - - - - - epitrichium - MP:0013530 + TAO:VSAO_workshop - + - - - - - - - - - + + + + + + + + + + + + + - - + + - 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 + A bone that is part of a cranium. + here cranium = skull - mandible + + cranium bone uberon - anterior neural plate - UBERON:0003056 - pre-chordal neural plate + UBERON:0004766 + cranial bone - + - The portion of neural plate anterior to the mid-hindbrain junction. - XB:curator + A bone that is part of a cranium. + UBERON: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:0001200 - VHOG - - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 + + + cranium bone + UBERON:automatic - + - - + + + + + + + + + + + + + - + - - + + - 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 + + + + + + + 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 - posterior neural plate - UBERON:0003057 - chordal neural plate + UBERON:0004768 + + bone of lower jaw - - - 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 + + + Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular. + - + - + - - - - - + - - + + - + - + - - + + - - + + - - + + - 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 + + + + + + + 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 - PSM - presumptive somite mesoderm - somitogenic mesoderm - somitomeric mesoderm - unsegmented mesenchyme - UBERON:0003059 - - - presomitic mesoderm + set of all joints + set of joints of body + UBERON:0004770 + articular system - + - - + + - Bgee:AN + FMA - + - 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) + Anatomical system that consists of all the joints of the body. + VSAO:0000181 - + - unsegmented paraxial mesoderm - + joint system + FMA:23878 - - - somitomeric mesoderm - GO:0002075 + + + set of all joints of body + FMA:23878 - + - unsegmented mesenchyme - VHOG:0000559 + set of joints of body + FMA:23878 - + - - - + + + + + + + + + + + + + - - - - - - - + - - + + - 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 + 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 - 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 + UBERON:0004777 + respiratory system submucosa - - - - 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 + A submucosa that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic - + - UMLS:C1283945 - ncithesaurus:Pronephric_Duct + EMAPA:37578 + MA:th - - - archinephric duct - VHOG:0000082 + + + apparatus respiratorius submucosa + OBOL:automatic - - - ductus pronephricus - - + + + submucosa of apparatus respiratorius + OBOL:automatic - - - pronephric ducts - ZFA:0000150 - + + + submucosa of respiratory system + OBOL:automatic - + - - - - - - - - + + + + + + + + + + + + + + - - + + - 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 + A submucosa that is part of a larynx [Automatically generated definition]. + + EMAPA:35474 + FMA:321584 + MA:0002728 + submucosa of larynx uberon - VBI - caudal hematopoietic tissue - posterior ICM - posterior blood island - ventral blood island - UBERON:0003061 - - - - - blood island + laryngeal submucosa + UBERON:0004778 + larynx submucosa - + - 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 + A submucosa that is part of a larynx [Automatically generated definition]. + OBOL:automatic - - - UMLS:C1511224 - ncithesaurus:Blood_Island + + + submucosa of larynx + OBOL:automatic - - - blood islands - + + + laryngeal submucosa + EMAPA:35474 - + - - + + + + + + + + + + + + + - + - - + + - - + + - 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 + 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:0003063 - - - - prechordal plate + UBERON:0004779 + respiratory system lamina propria - + - + - ZFA + true + - - - - - - - - - PMID:16313393 + + + A lamina propria that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic - - - 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 + + + EMAPA:37576 + MA:th - - - 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 + + + apparatus respiratorius lamina propria + OBOL:automatic - - - 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 - + + + apparatus respiratorius lamina propria mucosa + OBOL:automatic - - - 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) + + + lamina propria mucosa of apparatus respiratorius + OBOL:automatic - - - head mesenchyme - XAO:0000079 + + + lamina propria mucosa of respiratory system + OBOL:automatic - - - head mesoderm - XAO:0000079 + + + lamina propria of apparatus respiratorius + OBOL:automatic + + + + + lamina propria of respiratory system + OBOL:automatic + + + + + respiratory system lamina propria mucosa + OBOL:automatic - + - - + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - - - + - 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 + A lamina propria that is part of a gastrointestinal system. + + MA:0001899 + NCIT:C49299 + UMLS:C1708197 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 + UBERON:0004780 + gastrointestinal system lamina propria - + - + - AAO + true + - - - - - - - - - EMAPA + + + A lamina propria that is part of a gastrointestinal system. + OBOL:automatic - - - + + + UMLS:C1708197 + ncithesaurus:Gastrointestinal_Tract_Lamina_Propria + + + + + + + + + + + + + + + + + + + + - - + + - - XAO - + + 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 + - + - The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads. - - GOC:curators + A serous membrane that is part of a digestive system [Automatically generated definition]. + OBOL:automatic - - - Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO] - 2012-06-20 - AAO:0010575 - AAO - AAO:EJS + + + EMAPA:37592 + MA:th - - - (...)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 + + + digestive system serosa + OBOL:automatic - - - 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 + + + digestive system serous membrane + OBOL:automatic - - - UMLS:C1284010 - ncithesaurus:Intermediate_Mesoderm + + + gastrointestinal system serous membrane + OBOL:automatic - - - intermediate mesenchyme - + + + serosa of digestive system + OBOL:automatic - - - intermediate plate - EMAPA:16178 + + + serosa of gastrointestinal system + OBOL:automatic - - - intermediate plate mesoderm - + + + serous membrane of digestive system + OBOL:automatic - - - mesenchyma intermedium - - + + + serous membrane of gastrointestinal system + OBOL:automatic - + - - + + + + + + + + + + + + + - - - - - - - + - 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 + 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 - chordamesoderm - UBERON:0003068 - - - axial mesoderm - http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png + wall of ventricle + UBERON:0004784 + + heart ventricle wall - + - The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. - - GO:0048318 + An anatomical wall that is part of a cardiac ventricle [Automatically generated definition]. + OBOL:automatic - - - 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 - + + + 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 + + + - chordamesoderm - + wall of ventricle + MA:0002791 - + - + - + - - + + - - - - - + - - - - - - - - - - - - - + - 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 + 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 - eye anlage - eye field - optic field - optic placodes - UBERON:0003071 - - eye primordium + laryngeal mucous membrane + respiratory mucosa + respiratory tract mucosa + UBERON:0004785 + + respiratory system mucosa - - - - 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 + The mucous membrane lining the respiratory tract. + MESH:A04.760 + MGI:cwg + MP:0002277 - - - 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 + + + EMAPA:37577 + MA:th - + - eye placode + apparatus respiratorius mucosa OBOL:automatic - + - optic placode - GO:0046619 + apparatus respiratorius mucosa of organ + OBOL:automatic - + - optic placode of camera-type eye - - GO:0046619 + apparatus respiratorius mucous membrane + OBOL:automatic - - - eye anlage - XAO:0000227 + + + mucosa of apparatus respiratorius + OBOL:automatic - - - optic placodes - + + + mucosa of organ of apparatus respiratorius + OBOL:automatic - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 + + + mucosa of organ of respiratory system + OBOL:automatic - - - - - - - - - ZFA + + + mucosa of respiratory system + OBOL:automatic - - - 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 + + + mucous membrane of apparatus respiratorius + 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.[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 + + + mucous membrane of respiratory system + OBOL:automatic - - - UMLS:C0231109 - ncithesaurus:Optic_Cup + + + respiratory system mucosa of organ + OBOL:automatic - - - eyecup - BTO:0005351 + + + respiratory system mucous membrane + OBOL:automatic - + - ocular cup - VHOG:0000167 + laryngeal mucous membrane + EMAPA:18334 - + - ophtalmic cup - BTO:0005351 + respiratory mucosa + BTO:0000973 - + - + - + - - + + - - - - + + - - + + - - + + - 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 + + + + + + + + + + + + + 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 - 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 + UBERON:0004786 + The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468 + gastrointestinal system mucosa - + - - 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 + + + + + + + + + BTO-modified + + + + + A mucosa that is part of a gastrointestinal system. + OBOL:automatic - - - 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 - + + + digestive tract mucosa + - - - (...) 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 + + + gut mucosa + BTO:0000546 - - - UMLS:C0043204 - ncithesaurus:Mesonephric_Duct + + + gut mucuous membrane + - + - Wolffian duct - - GOC:yaf - ZFA:0000546 + mucosa of gut + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A mucous gland that is part of a larynx [Automatically generated definition]. + EMAPA:37631 + MA:0001767 + mucous gland of larynx + uberon + UBERON:0004789 + larynx mucous gland + - - - Leydig's duct - + + + A mucous gland that is part of a larynx [Automatically generated definition]. + OBOL:automatic - - - archinephric duct - - VHOG:0000082 + + + EMAPA:37631 + MA:th - - - ductus mesonephricus; ductus Wolffi - - + + + mucous gland of larynx + OBOL:automatic - + - - - - + + + + + + + + + + + + + + + - - + + - - + + - - + + - 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 + 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 - lamina neuralis - presumptive central nervous system - UBERON:0003075 - - - - neural plate - Neural:Crest.png + UBERON:0004790 + + skin mucous gland - - - - - - - - - Wikipedia + + + 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 + + + + + + + + + + + + + + + + + + + + + - - + + - - Bgee:AN - + + 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 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 + A secretion that is part of a esophagus [Automatically generated definition]. + OBOL:automatic - - - 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 + + + UMLS:C0227179 + ncithesaurus:Esophagus_Secretion - - - (...) 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 + + + esophageal secretion + FMA:79662 - - - UMLS:C0920623 - ncithesaurus:Neural_Plate + + + gullet secretion + OBOL:automatic - - - lamina neuralis - - + + + oesophagus secretion + OBOL:automatic + + + + + secretion of esophagus + OBOL:automatic + + + + + secretion of gullet + OBOL:automatic + + + + + secretion of oesophagus + 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] - AAO:0011082 - TAO:0007037 - VHOG:0001383 - XAO:0000250 - ZFA:0007037 + Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. + EMAPA:36296 + MA:0002854 uberon - UBERON:0003076 - posterior neural tube + UBERON:0004797 + blood vessel layer + Blood:vessels.svg - - - - 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 + + + Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. + - + - - - - + + + + + + + + + + + + + + + - - + + - - + + - - + + + 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 + + + + + + + + + + + + + + + + + + + - - + + - 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 + 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 - mesoderma paraxiale - UBERON:0003077 - - - - paraxial mesoderm - http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png + UBERON:0004807 + + respiratory system epithelium - - - - EHDAA2 + + + 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 + + + + + + + + + + + + + + + + + + + + - - + + - - Bgee:AN - + + 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 + - + - The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO] - - GO:0048339 + An epithelium that is part of a digestive system [Automatically generated definition]. + OBOL:automatic - - - 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 + + + digestive system epithelial tissue + OBOL:automatic - - - 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) + + + digestive system epithelium + OBOL:automatic - - - 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 + + + epithelial tissue of digestive system + OBOL:automatic - - - UMLS:C1284009 - ncithesaurus:Paraxial_Mesoderm + + + epithelial tissue of gastrointestinal system + OBOL:automatic - + - paraxial mesenchyme - - - ZFA:0000255 + epithelium of digestive system + OBOL:automatic - + - somitic mesoderm - ISBN:9780878932504 + epithelium of gastrointestinal system + OBOL:automatic - - - mesoderma paraxiale - - + + + gastrointestinal system epithelial tissue + OBOL:automatic - + - - + + + + + + + + + + + + + - - - - - - - + - 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 + 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:0003080 - anterior neural tube + UBERON:0004815 + lower respiratory tract epithelium - - - - lexical + + + An epithelium that is part of a lower respiratory tract [Automatically generated definition]. + 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:0001384 - VHOG - - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 + + + 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 - + - - - - - + + + + + + + + + + + + + - + - - - - - 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 + + + + + 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 - - lateral plate mesoderm - http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png + larynx epithelium - - - - 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 + An epithelium that is part of a larynx [Automatically generated definition]. + OBOL:automatic - + - UMLS:C1517749 - ncithesaurus:Lateral_Mesoderm + UMLS:C0751258 + ncithesaurus:Laryngeal_Epithelium - + - LPM - ZFA:0000121 - + epithelial tissue of larynx + OBOL:automatic - + - lateral mesoderm - GO:0048368 + epithelium of larynx + OBOL:automatic - - - lateral plate mesenchyme - EHDAA2:0000919 + + + laryngeal epithelium + OBOL:automatic - - - mesoderma laminae lateralis - - + + + larynx epithelial tissue + OBOL:automatic - + - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - + - 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 + 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 - cardiac field - fused heart primordium - UBERON:0003084 - - heart primordium + UBERON:0004817 + lacrimal gland epithelium - - - - 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 + An epithelium that is part of a lacrimal gland [Automatically generated definition]. + OBOL:automatic - - - relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] - 2012-08-14 - TAO:0000028 - TAO + + + epithelial tissue of lacrimal gland + OBOL:automatic - - - UMLS:C1514450 - ncithesaurus:Primordium_of_the_Heart + + + epithelium of lacrimal gland + OBOL:automatic - - - cardiac field - ZFA:0000028 + + + lacrimal gland epithelial tissue + OBOL:automatic - + - - - + + + + + + + + + + + + + + - - + + - 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 + + + + + + + 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 - sclerotomus - UBERON:0003089 + renal epithelium + UBERON:0004819 - - - sclerotome - http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png + kidney epithelium - - - - EHDAA2 + + + The cellular avascular layer of the kidney luminar surfaces. + MGI:csmith + MP:0004967 + + + + + epithelial tissue of kidney + OBOL:automatic + + + + + epithelium of kidney + OBOL:automatic - - - - EHDAA2 + + + kidney epithelial tissue + OBOL:automatic - - - + + + renal epithelium + EMAPA:35457 + + + + + + + + + + + + + + + + + + + + - - + + - - ZFA - + + + + + + + + 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 + - + - 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 + A portion of skeletal muscle tissue that is part of a urethra [Automatically generated definition]. + OBOL:automatic - - - Skeletogenic portion of somites.[AAO] - 2012-06-20 - AAO:0010571 - AAO - AAO:EJS + + + EMAPA:37788 + MA:th - - - 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) + + + skeletal muscle of urethra + OBOL:automatic - - - part_of somite in XAO - XAO + + + skeletal muscle tissue of urethra + OBOL:automatic - - - UMLS:C0183176 - ncithesaurus:Sclerotome + + + urethra skeletal muscle tissue + OBOL:automatic - - - sclerotomes - TAO:0001080 - + + + urethra skeletal muscle + MA:0001690 - + - sclerotomus - - + urethral skeletal muscle + MA:0001690 - + - - - - + + + + + + + + + + + + + - + - 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 + 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 - crista neuralis cranialis - head crest - head neural crest - UBERON:0003099 - - - - cranial neural crest + UBERON:0004830 + respiratory system skeletal muscle - + - 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 + A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic - - - 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 + + + EMAPA:37583 + MA:th - - - Neural crest that is part of the head.[TAO] - 2012-08-14 - TAO:0001194 - TAO - ZFIN:curator + + + respiratory system skeletal muscle tissue + 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:0000063 - VHOG - - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 + + + skeletal muscle of apparatus respiratorius + OBOL:automatic - + - CNC - XAO:0001001 - + skeletal muscle of respiratory system + OBOL:automatic - + - cephalic neural crest - EMAPA:16091 + skeletal muscle tissue of apparatus respiratorius + OBOL:automatic - - - crista neuralis cranialis - - + + + skeletal muscle tissue of respiratory system + OBOL:automatic - + - - - - - - - - - - - - + + + + + - + - + + + + + + + + - - + + - 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 + 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 - surface feature - surface region - surface structures - UBERON:0003102 - - surface structure + UBERON:0004831 + Most muscle tissue lining the digestive tract is smooth, but part of the externa of the esophagus is skeletal + esophagus skeletal muscle - + - 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 + A portion of skeletal muscle tissue that is part of a esophagus [Automatically generated definition]. + OBOL:automatic - + - anatomical surface feature - EHDAA2:0003010 + esophagus skeletal muscle tissue + OBOL:automatic - - - surface structures - ZFA:0000292 - + + + skeletal muscle of esophagus + OBOL:automatic - + - - - 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 + + + + + + + + + + + + + + + + + + + + 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 - organ - UBERON:0003103 - - - compound organ + UBERON:0004832 + anal region skeletal muscle - + - 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 + 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 - + - - - 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 + + + + + + + + + + + + + + + + + + + + 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 - mesenchyma - UBERON:0003104 - - - - mesenchyme - http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg + UBERON:0004833 + lip skeletal muscle - + - 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 portion of skeletal muscle tissue that is part of a lip [Automatically generated definition]. + OBOL:automatic - - - A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000393 - TAO - ZFIN:curator + + + EMAPA:37642 + MA:th - - - 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 + + + lip skeletal muscle tissue + OBOL:automatic - - - UMLS:C0162415 - ncithesaurus:Mesenchyme + + + skeletal muscle of lip + OBOL:automatic - - - mesenchyma - - + + + skeletal muscle tissue of lip + 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 + + + + + + + + + - - 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 + An endothelium of artery that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic - - - Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO] - 2012-08-14 - TAO:0000863 - TAO - ZFIN:curator + + + EMAPA:37566 + MA:th - - - Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO] - 2012-06-20 - AAO:0010154 - AAO - AAO:BJB + + + apparatus respiratorius arterial endothelium + OBOL:automatic - + - dendrocranium - TAO:0000863 + apparatus respiratorius artery endothelium + OBOL:automatic - + - exocranium - UBERONREF:0000007 + apparatus respiratorius endothelium of artery + OBOL:automatic - - - dermal skull roof - - + + + arterial endothelium of apparatus respiratorius + OBOL:automatic - - - roof of skull - + + + arterial endothelium of respiratory system + OBOL:automatic - - - skull roof - - + + + artery endothelium of apparatus respiratorius + OBOL:automatic - - - dermal bone cranium - ZFA:0000863 + + + artery endothelium of respiratory system + OBOL:automatic - - - roofing bones of the skull - + + + 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 - + - - + + + + + + + + + + + + + + - + - 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 + + + + + + + + + + + + + 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 - calvarium - epicranial plate - skeletal system of head - UBERON:0003128 - - - - - cranium + UBERON:0004849 + respiratory system venous endothelium - + - - FMA-inferred + + + + + + + - + - Upper portion of the skull that excludes the mandible (when present in the organism). - - + An endothelium of vein that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic - - - 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 + + + EMAPA:37585 + MA:th - - - The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton - WP + + + apparatus respiratorius endothelium of vein + OBOL:automatic - + - bones of cranium - FMA:71325 + apparatus respiratorius vein endothelium + OBOL:automatic - + - ossa cranii - FMA:71325 - FMA:TA - + apparatus respiratorius venous endothelium + OBOL:automatic - + - set of bones of cranium - FMA:71325 + endothelium of vein of apparatus respiratorius + OBOL:automatic - - - calvarium - BTO:0001328 + + + 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 - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - + - 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 + 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 - cranial skeleton - skeletal system of head - UBERON:0003129 + aortic endothelium + UBERON:0004851 + - - skull + aorta endothelium - - - - FMA + + + 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 - - - Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]. - - - + + + UMLS:C1706824 + ncithesaurus:Aorta_Endothelium - - - 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 + + + adult aorta endothelium + OBOL:automatic - - - 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 + + + endothelium of adult aorta + OBOL:automatic - - - UMLS:C0037303 - ncithesaurus:Skull + + + endothelium of aorta + OBOL:automatic - - - - - - - - - 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 + + + endothelium of trunk of aortic tree + OBOL:automatic - - - GO uses genitalia for the singular organ - GO + + + endothelium of trunk of systemic arterial tree + OBOL:automatic - - - EMAPA:37731 - MA:th + + + trunk of aortic tree endothelium + OBOL:automatic - - - UMLS:C0017420 - ncithesaurus:Genitalia + + + trunk of systemic arterial tree endothelium + OBOL:automatic - + - genitalia - + aortic endothelium + BTO:0000394 - + - + - + - - + + - - - - - - - - - - - - - - - - + - - + + - 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 + 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 - 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 + endothelia + vascular endothelia + UBERON:0004852 + + cardiovascular system endothelium - - - - - - - - - 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 - - + An endothelium that is part of the cardiovascular system. + - + - 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] + 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:0000540 + VHOG:0001217 VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.462 - - - - - metanephric blastema - + ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 - - - metanephric mesoderm - + + + UMLS:C0014261 + ncithesaurus:Vascular_Endothelium - - - metanephrogenic mesenchyme - EHDAA:5021 + + + endothelia + ZFA:0001639 + - - - metanephros associated mesenchyme - RETIRED_EHDAA2:0001139 + + + vascular endothelia + XAO:0000356 + - + - + - + - - + + - - + - - + + - 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 + 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 - UBERON:0003236 - epithelium of lower jaw + skeletal muscle interstitial tissue + skeletal muscle interstitum + UBERON:0004857 + skeletal muscle connective tissue - + - An epithelium that is part of a lower jaw [Automatically generated definition]. + A connective tissue that surrounds a skeletal muscle tissue. OBOL:automatic - + + + EMAPA:37743 + MA:th + + + - epithelial tissue of lower jaw + connective tissue of skeletal muscle OBOL:automatic - + - epithelial tissue of ventral mandibular arch + connective tissue of skeletal muscle tissue OBOL:automatic - + - epithelium of ventral mandibular arch + portion of connective tissue of skeletal muscle OBOL:automatic - + - lower jaw epithelial tissue + portion of connective tissue of skeletal muscle tissue OBOL:automatic - + - lower jaw epithelium + skeletal muscle portion of connective tissue OBOL:automatic - + - ventral mandibular arch epithelial tissue + skeletal muscle textus connectivus OBOL:automatic - + - ventral mandibular arch epithelium + 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 + - + - + - + - - - - - + - - - - An endoderm that is part of a foregut [Automatically generated definition]. - TODO - check - EHDAA2:0004568 - EHDAA:524 - foregut endoderm + + + + + + + + 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:0003258 - endoderm of foregut + UBERON:0004859 + + Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands + eye gland - + - An endoderm that is part of a foregut [Automatically generated definition]. - OBOL:automatic + 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. + - + - foregut endoderm + eye-associated gland + + + + + + gland of eye 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 + + + + + + + + + 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:0003259 - endoderm of midgut + UBERON:0004864 + + vasculature of retina - + - An endoderm that is part of a midgut [Automatically generated definition]. + A vasculature that is part of a retina [Automatically generated definition]. OBOL:automatic - + + + + + + michaelerice + + + - midgut endoderm + 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 + + - + - - - - - + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - - - - - - An endoderm that is part of a hindgut [Automatically generated definition]. - TODO - check - EHDAA:979 - RETIRED_EHDAA2:0000781 - hindgut endoderm + + + + 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 - UBERON:0003260 - endoderm of hindgut + chorda nephrogenica + UBERON:0004875 + part_of or develops_from urogenital ridge? + nephrogenic cord - + - An endoderm that is part of a hindgut [Automatically generated definition]. - OBOL:automatic + A portion of the urogenital ridge which is the source of much of the urinary system[WP]. + - - - hindgut endoderm - OBOL:automatic + + + UMLS:C1283944 + ncithesaurus:Nephrogenic_Cord + + + + + chorda nephrogenica + + - + - - - - - - - - - - - - - - + + - + - + - - - - - - - + + - - + + - 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 + + + + + + + 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 - mandibles - mandibular series - UBERON:0003278 + urogenital ridge + UBERON:0004876 - skeleton of lower jaw + urogenital fold - + - + 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 + Wikipedia - - - lower jaw - ZFA:0001273 + + + + + + + + + EHDAA2 - - - mandible - ZFA:0001273 + + + 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 - + - lower jaw skeleton - AAO:0000274 + urethral fold + EMAPA:30888 - - - mandibles - TAO:0001273 - + + + urogenital fold + EHDAA2:0004022 + MP:0011835 - + - mandibular series - ZFA:0001273 + urogenital ridge + MP:0011835 + - + - - - - - - - - - - - - - + + + - + - A gland that is part of a foregut [Automatically generated definition]. - EHDAA2:0000567 - EHDAA:950 - EMAPA:16557 - VHOG:0000650 - foregut gland + + + + + + + + + + + + + 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:0003294 - gland of foregut + UBERON:0004880 + + + chordamesoderm - + - A gland that is part of a foregut [Automatically generated definition]. - OBOL:automatic + The central region of trunk mesoderm. This tissue forms the notochord. + - + + + Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. + ZFIN:ZDB-PUB-961014-576 + + + - foregut gland - OBOL:automatic + axial chorda mesoderm + ZFA:0000091 + + + + + dorsal mesoderm + + + + + + presumptive notochord + ZFA:0000091 - + - + - + - + - - + + - + - Racemose mucous glands beneath the mucous membrane of the pharynx. - BTO:0004849 - EHDAA2:0001461 - EHDAA:2967 - FMA:55075 - pharynx gland + + + + + + + The mass of tissue made up of mesenchymal cells in the lung. + EMAPA:32866 + lung-associated mesenchyme + mesenchyme of lung + pulmonary mesenchyme uberon - glandulae pharyngeae - UBERON:0003295 - - pharyngeal gland + UBERON:0004883 + + lung mesenchyme - - - - - - - - - BTO + + + The mass of tissue made up of mesenchymal cells in the lung. + GO:0060484 - - - Racemose mucous glands beneath the mucous membrane of the pharynx. - + + + lung-associated mesenchyme + GO:0060484 - + - pharynx gland - EHDAA2:0001461 + mesenchyme of lung + OBOL:automatic - - - glandulae pharyngeae - BTO:0004849 + + + pulmonary mesenchyme + GO:0060484 - + - + - + - + - + + + + - + - 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 + + + + + + + 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:0003297 - gland of integumental system + UBERON:0004902 + urogenital sinus epithelium - + + + + + + + + + + + + + + + EHDAA2 + + + - A gland that is part of a integumental system [Automatically generated definition]. - OBOL:automatic + 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. + - - - integumental gland - + + + we follow EHDAA2 in dividing the UGS into epithelium and lumen + EHDAA2 - + - integumental system gland - + UGE + - + - integumentary gland - + epithelium of urogenital sinus + OBOL:automatic - + - + - + - - + + + + + + - - - - + - + - + - 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 + + + + + + + + + + + + + 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 - mesenchyme blood island - UBERON:0003304 - mesoderm blood island + UBERON:0004904 + + + for the vertebrate-specific structure, see UBERON:0000941 (cranial nerve II) + neuron projection bundle connecting eye with brain - - - - EHDAA2 + + + 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 + + + + + + + + + - + - - 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 - - + + Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. + FBbt:00005811 + joint + uberon + UBERON:0004905 + + articulation + - - - mesenchyme blood island - OBOL:automatic + + + Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. + - + - + - + - + + + + + - - + + - + - + - 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 + A portion of the gut that is derived from ectoderm. + ectodermal gut + gut ectoderm uberon - UBERON:0003314 - eye mesenchyme + UBERON:0004906 + ectodermal part of digestive tract - - - - - - - - - EHDAA2 - - - + - Mesenchyme that is part of a developing camera-type eye. - OBOL:automatic + A portion of the gut that is derived from ectoderm. + GO:0007439 - + - mesenchyme of eye - OBOL:automatic + gut ectoderm + EMAPA:32930 - + - - - - - - - - - - - - - - + + - + - + - 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 + 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:0003324 - mesenchyme of lower jaw + 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 + + + + + + + + + - + - - EHDAA2 - + + 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 + - + - Mesenchyme that is part of a developing lower jaw [Automatically generated definition]. - OBOL:automatic - - - - - lower jaw mesenchyme - OBOL:automatic + The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum. + - - - mesenchyme of ventral mandibular arch - OBOL:automatic + + + 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 - - - ventral mandibular arch mesenchyme - OBOL:automatic + + + UMLS:C0226874 + ncithesaurus:Upper_Gastrointestinal_Tract - + - + - + - + - - + + + - + - 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 + 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 - UBERON:0003329 - submucosa of anal canal + gonadal sheath + UBERON:0004909 + epithelium of gonad - + - A submucosa that is part of an anal canal [Automatically generated definition]. + An epithelium surrounding a gonad. OBOL:automatic - - - anal canal submucosa - OBOL:automatic + + + UMLS:C1517534 + ncithesaurus:Germinal_Epithelium - + - anal canal viewed anatomically submucosa + gonad epithelium OBOL:automatic - + - anal region submucosa + gonadal epithelium OBOL:automatic - - - anatomical anal canal submucosa - OBOL:automatic + + + gonadal sheath + FBbt:00004859 + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - submucosa of anal canal viewed anatomically + + + An epithelium surrounding an ovary. OBOL:automatic - + - submucosa of anal region + ovarian epithelium OBOL:automatic - + - submucosa of anatomical anal canal + ovary epithelium OBOL:automatic + + + + ovarian sheath + FBbt:00004896 + + - + - + - + - - + + - + + - + - The submucous layer of the wall of the rectum. - - BTO:0002114 - EMAPA:27083 - FMA:15034 - rectal submucosa - rectum submucosa - tela submucosa recti + + + + + + + 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 - UBERON:0003330 - submucosa of rectum + alimentary system subdivision + intestinal tract + segment of intestinal tract + subdivision of alimentary system + UBERON:0004921 + + subdivision of digestive tract - + - The submucous layer of the wall of the rectum. - BTO:0002114 + A proximal-distal subdivision of the digestive tract. + - - - rectal submucosa - FMA:15034 + + + alimentary system subdivision + FMA:71131 - - - rectum submucosa - OBOL:automatic + + + 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 + - - - tela submucosa recti - BTO:0002114 - + + + A part of a wall of an organ that forms a layer. + - + - + - + - + + - + - 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 + The tissue underlying the tunica mucosa of the pharynx. + + BTO:0002113 + FMA:75144 + pharyngeal submucosa + pharynx submucosa + tela submucosa pharyngea + tela submucosa pharyngis uberon - UBERON:0003331 - submucosa of colon + pharyngobasilar fascia + submucous coat of pharynx + submucous layer of pharynx + UBERON:0004924 + submucosa of pharynx - + - A submucosa that is part of a colon [Automatically generated definition]. - OBOL:automatic + The tissue underlying the tunica mucosa of the pharynx. + BTO:0002113 - + - colon submucosa - OBOL:automatic + pharyngeal submucosa + FMA:75144 - + - colonic submucosa - FMA:14985 + pharynx submucosa + OBOL:automatic - + - large bowel submucosa - OBOL:automatic + tela submucosa pharyngea + FMA:75144 + FMA:TA + - + - submucosa of large bowel - OBOL:automatic + tela submucosa pharyngis + BTO:0002113 + + + + + + submucous coat of pharynx + BTO:0002113 + + + + + submucous layer of pharynx + BTO:0002113 - + - + - + - + - + - + - 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 + A submucosa that is part of a sigmoid colon [Automatically generated definition]. + FMA:15027 + sigmoid colon submucosa 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 - + UBERON:0004932 + submucosa of sigmoid colon + - - - serous membrane of rectum + + + A submucosa that is part of a sigmoid colon [Automatically generated definition]. OBOL:automatic - + - visceral peritoneum of rectum - FMA:15039 + sigmoid colon submucosa + OBOL:automatic - + - + - + - + - + + - + - 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 + + + + + + + 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 - UBERON:0003335 - serosa of colon + submucous layer of urinary bladder + UBERON:0004943 + submucosa of urinary bladder - - - A serous membrane that is part of a colon [Automatically generated definition]. - OBOL:automatic + + + + + + + + + - - - colon serosa - OBOL:automatic + + + The submucous layer of the wall of the urinary bladder. + BTO:0002117 - + - colon serous membrane + bladder submucosa OBOL:automatic - - - colonic serosa - FMA:14990 - - - + - large bowel serosa + submucosa of bladder OBOL:automatic - + - large bowel serous membrane - OBOL:automatic + tela submucosa (vesica urinaria) + FMA:15929 + FMA:TA + - + - serosa of large bowel - OBOL:automatic + tela submucosa vesicae + FMA:15929 + FMA:TA + - + - serous membrane of colon - OBOL:automatic + tela submucosa vesicae urinariae + BTO:0002117 - + - serous membrane of large bowel + urinary bladder submucosa OBOL:automatic - - - visceral peritoneum of colon - FMA:14990 + + + submucous layer of urinary bladder + BTO:0002117 - + - + - + - - + + - + - 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 + + + + + + + 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:0003342 - mucosa of anal canal + UBERON:0004980 + mucosa of ureter - + + + + + + + + + + + + - A mucosa that is part of an anal canal [Automatically generated definition]. + A mucosa that is part of a ureter [Automatically generated definition]. OBOL:automatic - - - UMLS:C0227414 - ncithesaurus:Anal_Mucosa + + + mucosa of organ of ureter + OBOL:automatic - + - anal canal mucosa - OBOL:automatic + mucosal layer of ureter + FMA:15894 - + - anal canal mucosa of organ + mucous membrane of ureter OBOL:automatic - + - anal canal mucous membrane + organ mucosa of ureter OBOL:automatic - + - anal canal organ mucosa - OBOL:automatic + tunica mucosa (ureter) + FMA:15894 - + - anal canal viewed anatomically mucosa - OBOL:automatic + tunica mucosa ureteris + FMA:15894 + FMA:TA + - + - anal canal viewed anatomically mucosa of organ + ureter mucosa OBOL:automatic - + - anal canal viewed anatomically mucous membrane + ureter mucosa of organ OBOL:automatic - + - anal canal viewed anatomically organ mucosa + ureter mucous membrane OBOL:automatic - + - anal mucosa - FMA:74654 + ureter organ mucosa + OBOL:automatic - + - anal mucous membrane - FMA:74654 + ureteral mucosa + FMA:15894 - + - anal region mucosa + ureteric mucosa + FMA:15894 + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - anal region mucosa of organ + mucosa of organ of sigmoid colon OBOL:automatic - + - anal region mucous membrane + mucous membrane of sigmoid colon OBOL:automatic - + - anal region organ mucosa + organ mucosa of sigmoid colon OBOL:automatic - + - anatomical anal canal mucosa + sigmoid colon mucosa OBOL:automatic - + - anatomical anal canal mucosa of organ + sigmoid colon mucosa of organ OBOL:automatic - + - anatomical anal canal mucous membrane + sigmoid colon mucous membrane OBOL:automatic - + - anatomical anal canal organ mucosa + sigmoid colon organ mucosa 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 anal canal viewed anatomically + mucosa of organ of right ureter OBOL:automatic - + - mucosa of anal region + mucous membrane of right ureter OBOL:automatic - + - mucosa of anatomical anal canal + organ mucosa of right ureter OBOL:automatic - + - mucosa of organ of anal canal + right ureter mucosa OBOL:automatic - + - mucosa of organ of anal canal viewed anatomically + right ureter mucosa of organ OBOL:automatic - + - mucosa of organ of anal region + right ureter mucous membrane OBOL:automatic - + - mucosa of organ of anatomical anal canal + right ureter organ mucosa OBOL:automatic - + - mucous membrane of anal canal + 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 - + - mucous membrane of anal canal viewed anatomically + left ureter mucosa OBOL:automatic - + - mucous membrane of anal region + left ureter mucosa of organ OBOL:automatic - + - mucous membrane of anatomical anal canal + left ureter mucous membrane OBOL:automatic - + - organ mucosa of anal canal + left ureter organ mucosa OBOL:automatic - + - organ mucosa of anal canal viewed anatomically + left ureteral mucosa + FMA:17807 + + + + + mucosa of organ of left ureter OBOL:automatic - + - organ mucosa of anal region + mucous membrane of left ureter OBOL:automatic - + - organ mucosa of anatomical anal canal + organ mucosa of left ureter 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 + 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:0003343 - mucosa of oral region + UBERON:0005006 + mucosa of renal pelvis - + - 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 + A mucosa that is part of a renal pelvis [Automatically generated definition]. OBOL:automatic - + - mucosa of subdivision of mouth + kidney pelvis mucosa OBOL:automatic - + - mucous membrane of oral opening + kidney pelvis mucosa of organ OBOL:automatic - + - mucous membrane of oral part of face + kidney pelvis mucous membrane OBOL:automatic - + - mucous membrane of oral region + kidney pelvis organ mucosa OBOL:automatic - + - mucous membrane of subdivision of mouth + mucosa of kidney pelvis OBOL:automatic - + - oral opening mucosa + mucosa of organ of kidney pelvis OBOL:automatic - + - oral opening mucosa of organ + mucosa of organ of pelvis of ureter OBOL:automatic - + - oral opening mucous membrane + mucosa of organ of renal pelvis OBOL:automatic - + - oral opening organ mucosa + mucosa of pelvis of ureter OBOL:automatic - + - oral part of face mucosa + mucous membrane of kidney pelvis OBOL:automatic - + - oral part of face mucosa of organ + mucous membrane of pelvis of ureter OBOL:automatic - + - oral part of face mucous membrane + mucous membrane of renal pelvis OBOL:automatic - + - oral part of face organ mucosa + organ mucosa of kidney pelvis OBOL:automatic - + - oral region mucosa + organ mucosa of pelvis of ureter OBOL:automatic - + - oral region mucosa of organ + organ mucosa of renal pelvis OBOL:automatic - + - oral region mucous membrane + pelvis of ureter mucosa OBOL:automatic - + - oral region organ mucosa + pelvis of ureter mucosa of organ OBOL:automatic - + - organ mucosa of oral opening + pelvis of ureter mucous membrane OBOL:automatic - + - organ mucosa of oral part of face + pelvis of ureter organ mucosa OBOL:automatic - + - organ mucosa of oral region - OBOL:automatic + renal pelvic mucosa + FMA:17931 - + - organ mucosa of subdivision of mouth + renal pelvis mucosa OBOL:automatic - + - subdivision of mouth mucosa + renal pelvis mucosa of organ OBOL:automatic - + - subdivision of mouth mucosa of organ + renal pelvis mucous membrane OBOL:automatic - + - subdivision of mouth mucous membrane + renal pelvis organ mucosa OBOL:automatic - + - subdivision of mouth organ mucosa - OBOL:automatic + tunica mucosa pelvis renalis + FMA:17931 + FMA:TA + - + - + - + - + - + - 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 + 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:0003346 - mucosa of rectum + UBERON:0005014 + mucosa of female urethra - + - A mucosa that is part of a rectum [Automatically generated definition]. + A mucosa that is part of a female urethra [Automatically generated definition]. OBOL:automatic - + - mucosa of organ of rectum + female urethra mucosa OBOL:automatic - + - mucous membrane of rectum + female urethra mucosa of organ OBOL:automatic - + - organ mucosa of rectum + female urethra mucous membrane OBOL:automatic - - - rectal mucosa - FMA:15033 - - - - - rectal mucous membrane - FMA:15033 - - - + - rectum mucosa + female urethra organ mucosa OBOL:automatic - + - rectum mucosa of organ + mucosa of organ of female urethra OBOL:automatic - + - rectum mucous membrane + mucous membrane of female urethra OBOL:automatic - + - rectum organ mucosa + organ mucosa of female urethra 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 + 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:0003351 - - pharyngeal epithelium + UBERON:0005032 + mucosa of lower lip - - - - - - - - - ZFA - - - - - - - - - - - ZFA - - - + - An epithelium that is part of a pharynx [Automatically generated definition]. + A mucosa that is part of a lower lip [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 + + + UMLS:C0226939 + ncithesaurus:Mucosa_of_the_Lower_Lip - + - epithelial tissue of pharynx - OBOL:automatic + lower labial mucosa + UBERON:cjm - + - epithelium of pharynx + lower lip mucosa OBOL:automatic - + - pharynx epithelial tissue + lower lip mucosa of organ 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. + lower lip mucous membrane OBOL:automatic - + - epithelial tissue of midgut + lower lip organ mucosa OBOL:automatic - + - midgut epithelial tissue + mucosa of organ of lower lip OBOL:automatic - + - midgut epithelium - BTO:0005053 + mucous membrane of lower lip + OBOL:automatic - + - midgut epithelium + organ mucosa of lower lip 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 + + 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 - UBERON:0003353 - epithelium of hindgut + organa genitalia feminina externa + UBERON:0005056 + + + TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 + external female genitalia - + - An epithelium that is part of a hindgut [Automatically generated definition]. + An external genitalia that is part of a female reproductive system [Automatically generated definition]. OBOL:automatic - + - epithelial tissue of hindgut - OBOL:automatic + external female genital organ + BTO:0003100 - + - hindgut epithelial tissue + external genitalia of female reproductive system OBOL:automatic - + - hindgut epithelium - OBOL:automatic + female external genitalia + FMA:45649 + + + + + organa genitalia feminina externa + BTO:0003100 - + - + - + - + - - + - + - 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 + An organ that is part of a immune system [Automatically generated definition]. + immune system organ 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 - + UBERON:0005057 + + + immune organ + - - - rectum epithelium + + + An organ that is part of a immune system [Automatically generated definition]. OBOL:automatic - + - + - + - - + + - - - - - - - - - + - - - - - - - - - - - - - + - An unilaminar epithelium that surrounds a pelvic appendage bud. - UBERON:0005232 - EHDAA2:0001034 - EMAPA:16780 - VHOG:0001048 - hindlimb ectoderm - hindlimb bud ectoderm - hindlimb ectoderm - lower limb bud ectoderm - pelvic fin bud ectoderm + 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 - leg ectoderm - UBERON:0003371 - pelvic appendage bud ectoderm + haemolymphoid system gland + UBERON:0005058 + + hemolymphoid system gland - - - - - - - - - EHDAA2 - - - - - - - - - - - EHDAA2 - - - + - An unilaminar epithelium that surrounds a pelvic appendage bud. + A gland that is part of a hemolymphoid system [Automatically generated definition]. OBOL:automatic - - - hindlimb ectoderm - VHOG:0001048 - - - - - hindlimb bud ectoderm - EMAPA:16780 - + + + hemopoietic or lymphoid organ + GO:0048534 - - - hindlimb bud ectoderm - + + + hemopoietic or lymphoid gland + - - - hindlimb ectoderm - VHOG:0001048 - + + + 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 + - - - lower limb bud ectoderm - EHDAA2:0001034 - + + + The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. + + + GO:0001842 - - - pelvic fin bud ectoderm - + + + 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]. + - - - leg ectoderm - OBOL:automatic + + + 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 + + + + + + + + - - + + - + - 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 + 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 - arm ectoderm - UBERON:0003372 - pectoral appendage bud ectoderm + neural tube rod + UBERON:0005068 + + neural rod - - - - - - - - - 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 - + 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 - - - wing ectoderm - Geisha:syn - NCBITaxon:8782 - + + + 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 - + - arm ectoderm - OBOL:automatic + neural tube rod + GO:0014027 - + - + - + - - + + + + + + - + - + - - + + - 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 + + + + + + + An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord. + hindbrain-spinal cord boundary region uberon - UBERON:0003386 - - smooth muscle of eye + UBERON:0005076 + hindbrain-spinal cord boundary - + - 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 + An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord. + OBOL:automatic - + - + - + - - + + - + - - + + - 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 + The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]. uberon - UBERON:0003388 - mesothelium of pericardial cavity + UBERON:0005080 + metanephric ureteric bud - + - 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 + The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]. + GO:0035502 - + - + - + - - + + - + - - + + - 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 + 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:0003406 - cartilage of respiratory system + UBERON:0005081 + ureter ureteric bud - + - 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 + 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 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 + A hole in a tube[GO]. + AEO:0000078 + EHDAA2:0004618 + RETIRED_EHDAA2:0003078 uberon - UBERON:0003408 - gland of digestive tract + UBERON:0005082 + tube lumen - + - A gland that is part of a digestive tract [Automatically generated definition]. - OBOL:automatic + 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 + - - - digestive tract gland - OBOL:automatic + + + An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]. + GO:0060788 - - - gland of digestive tract - OBOL:automatic + + + in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures + GO + - - - gland of lower gastrointestinal tract - OBOL:automatic + + + epithelial placode + AEO:0000112 + + + + + + + + + + + + + + + + + + + + + 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 + - - - gut gland - MA:0003202 + + + Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. + GO:0061061 - + - lower gastrointestinal tract gland - OBOL:automatic + musculus + FMA:30316 - + - - - - - - - - - - - - - + + + - + - - + + - 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 + 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:0003412 - pelvic appendage bud mesenchyme + UBERON:0005092 + right horn of sinus venosus - - - 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 + + + + FMA - - - leg mesenchyme - OBOL:automatic + + + 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 - + - lower limb bud mesenchyme - EHDAA2:0001035 - - - - - hindlimb bud mesenchyme - EMAPA:16781 - + sinus venosus right horn + VHOG:0000489 + + + + + + + + + + + + + + + + + + + + + class added for consistency with GO - consider merging with kidney mesenchyme. + uberon + kidney anlage + UBERON:0005095 + kidney rudiment + - - - mesoderm pelvic fin bud - ZFA:0001386 - + + + + + + + + + GO - - - pelvic fin bud mesenchyme - + + + kidney anlage + GOC:mtg_kidney_jan10 - + - + - + - + - + + - - - - - - - + - 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 + An epithelium that is part of a mesonephros [Automatically generated definition]. uberon - UBERON:0003413 - pectoral appendage bud mesenchyme + UBERON:0005103 + mesonephric epithelium - + - 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 + An epithelium that is part of a mesonephros [Automatically generated definition]. 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 + + + + + + + + + + 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:0003426 - - dermis adipose tissue + UBERON:0005106 + metanephric tubule - + - 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 + A metanephric tubule is an epithelial tube that is part of the metanephros[GO]. + GO:0072173 - - - fatty tissue of dermis - OBOL:automatic + + + 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 - + - + - + - + - + + - + - 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 - + An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO]. + uberon + UBERON:0005108 + metanephric epithelium + - - - craniofacial bone - + + + An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO]. + GO:0072207 - + - + - + - + - + - + - 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 + Any smooth muscle tissue that is part of a metanephros. uberon - UBERON:0003458 - neck bone + UBERON:0005109 + metanephric smooth muscle tissue - + - 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 + Any smooth muscle tissue that is part of a metanephros. + + GO:0072208 - + - + - + - + - - + + - + - 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 + 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 - bone of viscerocranium - viscerocranium bone - UBERON:0003462 - - facial bone + UBERON:0005137 + metanephric capsule - - - - - - - - - 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 + The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage[GO]. + GO:0072213 + + + + + + + + A bud is a protrusion that forms from an epithelial sheet by localized folding. + BTO:0001639 + uberon + UBERON:0005153 + epithelial bud + - - - viscerocranium bone - OBOL:automatic + + + A bud is a protrusion that forms from an epithelial sheet by localized folding. + GO:0060572 - + - + - + - + - - - 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 + + + + + + + + Any anatomical structure that is part of the reproductive system. + reproductive system element + reproductive system structure uberon - UBERON:0003463 - trunk bone + UBERON:0005156 + + reproductive structure - + - 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 + Any anatomical structure that is part of the reproductive system. + + + + + + + + + An epithelial sheet bent on a linear axis. + uberon + UBERON:0005157 + epithelial fold + - - - trunk bone organ - OBOL:automatic + + + An epithelial sheet bent on a linear axis. + GO:0060571 - + - + - + - + - - - + + - - + + - 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 + 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:0003464 - - hindlimb bone + UBERON:0005158 + parenchyma of central nervous system - + - 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 + The functional tissue of the central nervous system consisting of neurons and glial cells. + + CL:tm - + - bone of hindlimb + CNS parenchyma OBOL:automatic - + - bone of inferior member + central nervous system parenchyma OBOL:automatic - + - bone of lower extremity + 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 + - - - bone organ of hind limb - OBOL:automatic + + + + FMA - - - bone organ of hindlimb - 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. + CARO:0001000 - - - bone organ of lower extremity - OBOL:automatic + + + 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 - + - hind limb bone - OBOL:automatic + multi-cell-component structure + CARO:0001000 - + - hind limb bone organ - OBOL:automatic + multi-cell-part structure + CARO:0001000 - - - hindlimb bone organ - OBOL:automatic + + + cell part cluster + FMA:83115 - + - + - + - - - - - - - - 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 - - - - - - - - - - - - - - + - - - 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 + + + + + + + + An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. + + MA:0000522 + abdomen organ 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 - + UBERON:0005172 + + abdomen element + - - - EMAPA:37241 - MA:th + + + An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. + - - - thoracic artery - MESH:A07.231.114.891 + + + abdomen organ + MA:0000522 - + - + - + - + - - + - + - A vein that is part of a ureter [Automatically generated definition]. - EMAPA:37679 - MA:0002250 - ureter vein - vein of ureter + 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:0003475 - ureteric vein + UBERON:0005173 + + abdominal segment element - + - A vein that is part of a ureter [Automatically generated definition]. - OBOL:automatic + 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:37679 + EMAPA:37062 MA:th - - - ureter vein - OBOL:automatic - - - + - vein of ureter - OBOL:automatic + abdominal segment organ + MA:0000529 - + - + - + - - + + - + - - + + - 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 + 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:0003476 - respiratory system venous blood vessel + UBERON:0005174 + + dorsal region element - + - A vein that is part of a respiratory system [Automatically generated definition]. - OBOL:automatic + An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back. + - + - EMAPA:37584 + EMAPA:37274 MA:th - - - apparatus respiratorius vein - OBOL:automatic - - - - - respiratory system vein - OBOL:automatic - - - - - vein of apparatus respiratorius - OBOL:automatic - - - + - vein of respiratory system - OBOL:automatic + back organ + MA:0001901 - + - + - + - - + + - + - - + + - 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 + 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 - venae labiales inferiores - UBERON:0003478 - vein of lower lip - http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png + UBERON:0005177 + + + trunk region element - + - The inferior labial vein is the vein receiving blood from the lower lip. - + 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:37202 + EMAPA:37270 MA:th - - - inferior labial vein - FMA:52541 - - - - - lower lip vein - OBOL:automatic - - - + - vena labialis inferior - - - - - - venae labiales inferiores - - + trunk organ + MA:0000516 - + - + - + @@ -41320,15309 +113800,16794 @@ - - - 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 + + + + + + + + + + + + + + + An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. + EMAPA:37273 + MA:0000557 + thoracic cavity organ uberon - UBERON:0003479 - thoracic cavity vein + UBERON:0005178 + + + thoracic cavity element - + - A vein that is part of a thoracic cavity [Automatically generated definition]. - OBOL:automatic + An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. + - + - EMAPA:37242 + EMAPA:37273 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 + thoracic cavity organ + MA:0000557 - + - + - + - + - - + - + - 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 + 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:0003489 - respiratory system capillary endothelium + UBERON:0005179 + + + + pelvic region element - - - - - - - - - true - - - - + - An endothelium of capillary that is part of a respiratory system [Automatically generated definition]. - OBOL:automatic + An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis. + - + - EMAPA:37575 + EMAPA:37275 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 + 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 + - - - endothelium of capillary of respiratory system - OBOL:automatic + + + An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. + - - - endothelium of capillary vessel of apparatus respiratorius - OBOL:automatic + + + EMAPA:37271 + MA:th - - - endothelium of capillary vessel of respiratory system - OBOL:automatic + + + upper body organ + MA:0000563 + + + + + + + + + + + + + + + + + + + + + + + + + + A vein that is part of a thorax [Automatically generated definition]. + + + EMAPA:37197 + MA:0002235 + NCIT:C53142 + UMLS:C0226629 + uberon + UBERON:0005194 + thoracic vein + - - - respiratory system blood capillary endothelium + + + A vein that is part of a thorax [Automatically generated definition]. OBOL:automatic - - - respiratory system capillary vessel endothelium - OBOL:automatic + + + EMAPA:37197 + MA:th - - - respiratory system endothelium of blood capillary - OBOL:automatic + + + UMLS:C0226629 + ncithesaurus:Thoracic_Vein + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - respiratory system endothelium of capillary + + + A gland that is part of a larynx submucosa [Automatically generated definition]. OBOL:automatic - - - respiratory system endothelium of capillary vessel - OBOL:automatic + + + laryngeal submucosa gland + EMAPA:35475 - + - + - + - + - - - 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 + + + + + + + + + A valve that is part of a right atrium [Automatically generated definition]. + EHDAA2:0000302 + EMAPA:17327 + MA:0001871 + valve of right atrium uberon - UBERON:0003494 - respiratory system venule + right atrium valves + superior vena cava valve + UBERON:0005208 + right atrium valve - + - A venule that is part of a respiratory system [Automatically generated definition]. + A valve that is part of a right atrium [Automatically generated definition]. OBOL:automatic - - - EMAPA:37587 - MA:th - - - + - apparatus respiratorius venule - OBOL:automatic + valve of right atrium + EMAPA:17327 - - - venule of apparatus respiratorius - OBOL:automatic + + + right atrium valves + EHDAA2:0000302 + - - - venule of respiratory system - OBOL:automatic + + + superior vena cava valve + EMAPA:17327 - + - + - + - + - - + - + - An arteriole that is part of a respiratory system [Automatically generated definition]. - EMAPA:37568 - MA:0001803 + + + + + + + An external ectoderm that is part of a optic eminence [Automatically generated definition]. + EMAPA:16539 + RETIRED_EHDAA2:0001311 + VHOG:0000520 uberon - UBERON:0003495 - respiratory system arteriole + UBERON:0005216 + optic eminence surface ectoderm - + - + true - + - An arteriole that is part of a respiratory system [Automatically generated definition]. + An external ectoderm that is part of a optic eminence [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 + An ectoderm that is part of a optic eminence [Automatically generated definition]. + EHDAA:940 + EMAPA:16539 + RETIRED_EHDAA2:0001309 + VHOG:0001105 uberon - UBERON:0003496 - head blood vessel + 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 + + + + + + + + + + + + + + + + + + + + - + - - true - - + + 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 + - + - A blood vessel that is part of a head [Automatically generated definition]. + An endocardium that is part of a interventricular septum [Automatically generated definition]. OBOL:automatic - + - adult head blood vessel + 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 - - - blood vessel of adult head + + + 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 + + + - blood vessel of head - OBOL:automatic + metanephros pelvis + VHOG:0000945 - + - + - + - + - + + - + - A blood vessel that is part of an abdomen [Automatically generated definition]. - MA:0000518 - blood vessel of abdomen + A gland that is part of a stomodeum. + check this + VHOG:0000658 + stomatodaeum gland uberon - UBERON:0003497 - abdomen blood vessel - UBERON:0012254 + UBERON:0005250 + + stomatodeum gland - + - A blood vessel that is part of an abdomen [Automatically generated definition]. + A gland that is part of a stomodeum. OBOL:automatic - + - blood vessel of abdomen + 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 - - - UBERON:0012254 - abdominal aorta artery + + + 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 - + - + - + - + - - + + - + - A blood vessel that is part of a heart [Automatically generated definition]. - EMAPA:35397 - MA:0002483 - blood vessel of heart + + + + + + + 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 - cardiac blood vessel - UBERON:0003498 + cranial mesenchyme + desmocranium + UBERON:0005253 + - heart blood vessel + + head mesenchyme - + + + + + + + + + EHDAA2 + + + - A blood vessel that is part of a heart [Automatically generated definition]. - OBOL:automatic + 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 - + - blood vessel of heart - OBOL:automatic + cephalic mesenchyme + MP:0011260 - + - cardiac blood vessel - EMAPA:35397 + cranial mesenchyme + MGI:anna + + + + + desmocranium + FMA:76622 + - + - + - + - + + + + + - - + + - + - A blood vessel that is part of a brain [Automatically generated definition]. - EMAPA:35182 - MA:0002769 - blood vessel of brain + + + + + + + + + + + + + Mesenchyme that is part of a developing trunk. + EFO:0003485 + EHDAA2:0002092 + EHDAA:377 + EMAPA:16177 + TAO:0000081 + VHOG:0000281 + ZFA:0000081 uberon - UBERON:0003499 - - brain blood vessel + trunk and cervical mesenchyme + UBERON:0005256 + + + trunk mesenchyme - + + + + + + + + + EHDAA2 + + + - A blood vessel that is part of a brain [Automatically generated definition]. + Mesenchyme that is part of a developing trunk. OBOL:automatic - - - blood vessel of brain - OBOL:automatic + + + trunk and cervical mesenchyme + EHDAA2:0002092 - + - - - - - - - - - - - - - - + + - + - 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 + + + + + + + + + + + + + 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 - UBERON:0003500 - corneal blood vessel + myelencephalon (medulla oblongata) + UBERON:0005290 + + myelencephalon + http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + + + + + + + + + definitional + + + - A blood vessel that is part of a cornea [Automatically generated definition]. - - + 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 + + - - - blood vessel of cornea - OBOL:automatic + + + 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 - - - cornea blood vessel - OBOL:automatic + + + myelencephalon (medulla oblongata) + DHBA:10662 - + - + - + - + - - + - + - - + + - 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 + A portion of tissue that is part of an embryo. + CALOHA:TS-2100 + portion of embryonic tissue uberon - UBERON:0003501 + developing tissue + UBERON:0005291 - retina blood vessel + + embryonic tissue - + - 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 + A portion of tissue that is part of an embryo. OBOL:automatic - + - tunica interna of eyeball blood vessel + portion of embryonic tissue 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 + 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:0003502 - neck blood vessel + UBERON:0005292 + + extraembryonic tissue - + - 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 + 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. + - + - + - + - + - + - + - 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 + The endothelial lining of the endocardium. + FMA:83596 + endocardium endothelium + endothelium of endocardium uberon - UBERON:0003504 - respiratory system blood vessel + UBERON:0005316 + endocardial endothelium - + - A blood vessel that is part of a respiratory system [Automatically generated definition]. - OBOL:automatic - - - - - apparatus respiratorius blood vessel - OBOL:automatic + The endothelial lining of the endocardium. + UBERON:cjm - + - blood vessel of apparatus respiratorius - OBOL:automatic + endocardium endothelium + FMA:83596 - + - blood vessel of respiratory system - OBOL:automatic + endothelium of endocardium + FMA:83596 - + - + - + - + - + + - + - A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. - EMAPA:35144 - MA:0000061 + An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO]. + BTO:0000137 + pulmonary artery endothelial tube uberon - UBERON:0003509 - - only in MA - supertype of artery, arteriole, aorta. - arterial blood vessel + UBERON:0005317 + pulmonary artery endothelium - + - A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. - + An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO]. + GO:0061155 + + + + + pulmonary artery endothelial tube + GO:0061155 - + - + - + - + - - + - + - 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 + UBERON:0005321 + mesonephric smooth muscle tissue - - - - 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 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 - + 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 + - - - torso blood vessel - OBOL:automatic + + + Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros[GO]. + GO:0061219 - + - + - + - + - + + - + - A blood vessel that is part of a limb [Automatically generated definition]. - EMAPA:36598 - MA:0000687 - blood vessel of limb + A lamina propria that is part of a mucosa of oral region. + EMAPA:26947 + lamina propria of oral mucosa uberon - UBERON:0003514 - limb blood vessel + UBERON:0005334 + oral lamina propria - + - A blood vessel that is part of a limb [Automatically generated definition]. - OBOL:automatic - - - - - blood vessel of limb + A lamina propria that is part of a mucosa of oral region. 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 + 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:0003515 - forelimb blood vessel + UBERON:0005337 + outflow tract of ventricle - + - 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 + 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]. + - + - blood vessel of upper extremity - OBOL:automatic + heart ventricle outflow tract + MP:0010224 - + - fore limb blood vessel - OBOL:automatic - - - - - wing blood vessel - NCBITaxon:8782 - OBOL:automatic - + ventricular outflow tract + - + - + - + - + - + - + - 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 + An outflow tract that is part of a aorta. + merge with LVOT? + EHDAA2:0001353 + EMAPA:17329 + MA:0000101 + VHOG:0001394 uberon - UBERON:0003516 - hindlimb blood vessel + UBERON:0005338 + outflow tract aortic component - + - 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 + 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 + + + + + + + - + - - + + - + - - + + - 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 + 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 - UBERON:0003517 + vagus X + UBERON:0005362 - - kidney blood vessel + vagus X ganglion - + + + + ZFA + + + - A blood vessel that is part of a kidney [Automatically generated definition]. - OBOL:automatic + The group of sensory neuron cell bodies associated with the vagus nerve. + ISBN:0-683-40008-8 + MP:0001100 - + + + gX + ZFA:0007067 + + + - blood vessel of kidney - OBOL:automatic + ganglion of vagus nerve + FMA:53472 - + - renal blood vessel - OBOL:automatic + right glossopharyngeal ganglion + FMA:53472 + + + + + vagal ganglion + ZFA:0007067 + + + + + vagus neural ganglion + FMA:53472 + + + + + vagus X + EMAPA:16798 - + - + - + - - + + + + + + - + + - - + + - 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 + + + + + + + + + + + + + An array of photoreceptors and any supporting cells found in an eye. + FBbt:00004200 + light-sensitive tissue uberon - UBERON:0003519 - thoracic cavity blood vessel + UBERON:0005388 + photoreceptor array - + - A blood vessel that is part of a thoracic cavity [Automatically generated definition]. - OBOL:automatic - - - - - EMAPA:37240 - MA:th + 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 + - - - blood vessel of cavity of chest - OBOL:automatic + + + A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array. + + + + + + + + + One of: the common carotid artery, or its branches, the external and internal carotid arteries. + This is a generic grouping class that is the superclass of the trunks/branches of the common carotid artery. Note that AOs vary widely in how they divide up and generalize arteries + Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO] + + + + + AAO:0010217 + BTO:0000168 + CALOHA:TS-0116 + EFO:0000818 + EHDAA:6385 + EMAPA:18609 + EV:0100379 + FMA:70504 + GAID:478 + MA:0001925 + MAT:0000501 + MESH:D002339 + NCIT:C12687 + OpenCyc:Mx4rvg7rcJwpEbGdrcN5Y29ycA + TAO:0000097 + UMLS:C0007272 + VHOG:0000266 + ZFA:0000097 + galen:CarotidArtery + carotid + carotid artery + subdivision of common carotid artery + uberon + common carotid arterial subdivision + UBERON:0005396 + + + + + carotid artery segment + - - - blood vessel of cavity of thorax - OBOL:automatic + + + + FMA - - - blood vessel of chest cavity - OBOL:automatic + + + One of: the common carotid artery, or its branches, the external and internal carotid arteries. + + - - - blood vessel of pectoral cavity - OBOL:automatic + + + 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 - - - blood vessel of thoracic cavity - OBOL:automatic + + + UMLS:C0007272 + ncithesaurus:Carotid_Artery - + - cavity of chest blood vessel - OBOL:automatic + carotid + AAO:0010217 - + - cavity of thorax blood vessel - OBOL:automatic + carotid artery + MA:0001925 - + - chest cavity blood vessel - OBOL:automatic + subdivision of common carotid artery + FMA:70504 - - - pectoral cavity blood vessel - OBOL:automatic + + + common carotid arterial subdivision + FMA:70504 - + - + - + - + - + - + - A blood vessel that is part of a pelvis [Automatically generated definition]. - EMAPA:37244 - MA:0000531 - blood vessel of pelvis + + + + + + + A sex gland that is part of a female reproductive system. + BTO:0000254 + MA:0000383 uberon - UBERON:0003520 - pelvis blood vessel + UBERON:0005398 + + + female reproductive gland - + - A blood vessel that is part of a pelvis [Automatically generated definition]. - OBOL:automatic - - - - - EMAPA:37244 - MA:th - - - - - blood vessel of pelvis + A sex gland that is part of a female reproductive system. 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 + + + + + + + + + + + + + + + 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 - UBERON:0003526 - respiratory system capillary + 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 - + - A capillary that is part of a respiratory system [Automatically generated definition]. - OBOL:automatic + The part of the digestive system that excludes the hepatobiliary system. + - - - EMAPA:37574 - MA:th + + + The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System]. + ncithesaurus:Gastrointestinal_System - - - apparatus respiratorius blood capillary - OBOL:automatic + + + 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 - - - apparatus respiratorius capillary - OBOL:automatic + + + 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 - - - apparatus respiratorius capillary vessel - OBOL:automatic + + + UMLS:C0012240 + ncithesaurus:Gastrointestinal_System - - - blood capillary of apparatus respiratorius - OBOL:automatic + + + GI tract + GAID:294 - - - blood capillary of respiratory system - OBOL:automatic + + + alimentary system + MA:0000323 - - - capillary of apparatus respiratorius - OBOL:automatic + + + alimentary tract + MA:0000323 - - - capillary of respiratory system - OBOL:automatic + + + gastro-intestinal system + FMA:71132 - - - capillary vessel of apparatus respiratorius - OBOL:automatic + + + gastroenterological system + UBERON:cjm - - - capillary vessel of respiratory system - OBOL:automatic + + + gastrointestinal (GI) tract + GAID:294 - - - respiratory system blood capillary - OBOL:automatic + + + gastrointestinal system + FMA:71132 - - - respiratory system capillary vessel - OBOL:automatic + + + gastrointestinal tract + FMA:71132 + - + - + - + - - + + - - - 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 + + + + + + + + + + + + + + + + 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 - UBERON:0003527 + arm bud + UBERON:0005417 - kidney capillary + 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 - - - A capillary that is part of a kidney [Automatically generated definition]. - OBOL:automatic - - - - - blood capillary of kidney - OBOL:automatic - - - - - capillary of kidney - OBOL:automatic + + + + lexical - - - capillary vessel of kidney - OBOL:automatic + + + A limb bud that develops into a forelimb. + - + - kidney blood capillary - OBOL:automatic + limb bud - forelimb + MIAA:0000065 - + - kidney capillary vessel - OBOL:automatic + upper limb bud + RETIRED_EHDAA2:0003198 - - - renal capillary + + + wing bud + NCBITaxon:8782 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 + + + + + + + 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 - UBERON:0003528 - brain gray matter + leg bud + limb bud - hindlimb + UBERON:0005418 + + Genes: Tbx4 specifies hindlimbs. Wnt8c restricts Fgf10 in chick. + hindlimb bud - - - 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 + + + + lexical - - - gray matter of brain - OBOL:automatic + + + A limb bud that develops into a hindlimb. + - - - grey matter of brain - OBOL:automatic + + + 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 - + - grey substance of brain - OBOL:automatic + hind limb bud + XAO:0003066 - + - + - + - - + + - + - + - 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 + + + + + + + + + + + + + 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 - UBERON:0003531 - forelimb skin + 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 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 + A limb bud that develops into a forelimb or pectoral fin. OBOL:automatic - - - skin of fore limb - OBOL:automatic + + + Fin bud that develops into the pectoral fin.[TAO] + 2012-08-14 + TAO:0000141 + TAO + ZFIN:curator - - - skin of forelimb - OBOL:automatic + + + 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) - + - skin of upper limb - FMA:23101 + forelimb - pectoral fin bud + VHOG:0001754 - - - upper limb skin - FMA:23101 + + + pectoral fin bud + TAO:0000141 - - - wing skin - NCBITaxon:8782 - OBOL:automatic - + + + pectoral fin buds + TAO:0000141 + - + - + - + - + + + + + - + - + - 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 + + + + + + + + + + + + + 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 - UBERON:0003532 - hindlimb skin + 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 zone of skin that is part of a hindlimb [Automatically generated definition]. + A limb bud that develops into a hindlimb or pelvic fin. OBOL:automatic - - - UMLS:C0222268 - ncithesaurus:Skin_of_the_Lower_Limb_and_Hip - - - - - hind limb skin - OBOL:automatic + + + + - - - lower limb skin - FMA:23102 + + + Fin bud that develops into the pelvic fin.[TAO] + 2012-08-14 + TAO:0001384 + TAO + ZFIN:curator - - - skin of hind limb - OBOL:automatic + + + 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 - + - skin of hindlimb - OBOL:automatic + hindlimb/pelvic fin bud + VHOG:0001260 - - - skin of lower extremity - OBOL:automatic + + + pelvic fin bud + TAO:0001384 - - - skin of lower limb - FMA:23102 + + + pelvic fin buds + ZFA:0001384 + - + - + - + - + - + - + - - - - - - - + - 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 + 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 - UBERON:0003566 - head connective tissue + aer pectoral fin + apical ectodermal ridge pectoral fin + apical fold pectoral fin + UBERON:0005421 + + + pectoral appendage apical ectodermal ridge - + + + + + + + + + EHDAA2 + + + - A portion of connective tissue that is part of a head [Automatically generated definition]. + An apical ectodermal ridge that is part of a pectoral appendage bud. OBOL:automatic - - - adult head connective tissue - OBOL:automatic + + + An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG] + 2012-09-17 + VHOG:0001064 + VHOG + + - - - adult head portion of connective tissue - OBOL:automatic + + + Apical ectodermal ridge that is part of the pectoral fin bud.[TAO] + 2012-08-14 + TAO:0000085 + TAO + ZFIN:curator - - - adult head textus connectivus - OBOL:automatic + + + 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 + + - - - connective tissue of adult head - OBOL:automatic + + + AER forelimb + VHOG:0001064 - - - connective tissue of head - OBOL:automatic + + + apical ectodermal ridge forelimb + VHOG:0001064 - - - head portion of connective tissue - OBOL:automatic + + + apical ectodermal ridge pectoral fin bud + ZFA:0000085 - - - head textus connectivus - OBOL:automatic + + + upper limb bud apical ectodermal ridge + EHDAA2:0000138 - - - portion of connective tissue of adult head - OBOL:automatic + + + wing AER + Giesha:syn + - - - portion of connective tissue of head - OBOL:automatic + + + wing apical ectodermal ridge + - - - textus connectivus of adult head - OBOL:automatic + + + aer pectoral fin + TAO:0000085 - - - textus connectivus of head - OBOL:automatic + + + apical ectodermal ridge pectoral fin + TAO:0000085 + + + + + apical fold pectoral fin + TAO:0000085 - + - + - + - + - + - + - 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 + + + + + + + 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 - UBERON:0003567 - abdomen connective tissue + AER hindlimb + apical ectodermal ridge pelvic fin bud + leg AER + UBERON:0005422 + + + pelvic appendage apical ectodermal ridge - + + + + + + + + + EHDAA2 + + + - A portion of connective tissue that is part of an abdomen [Automatically generated definition]. + An apical ectodermal ridge that is part of a pelvic appendage bud. OBOL:automatic - - - abdomen portion of connective tissue - OBOL:automatic + + + An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG] + 2012-09-17 + VHOG:0001066 + VHOG + + - - - abdomen textus connectivus - OBOL:automatic + + + Apical ectodermal ridge that is part of the pelvic fin bud.[TAO] + 2012-08-14 + TAO:0001385 + TAO + ZIFIN:curator - - - connective tissue of abdomen - OBOL:automatic + + + 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 + + - - - portion of connective tissue of abdomen - OBOL:automatic + + + apical ectodermal ridge hind limb + VHOG:0001066 - - - textus connectivus of abdomen - OBOL:automatic + + + 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 + + + + + + + - + - - + + - + + - + - 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) + + + + + + + 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 - UBERON:0003568 - neck connective tissue + future NR + future neural epithelium + future neural layer + presumptive retina + UBERON:0005425 + + presumptive neural retina - + - A portion of connective tissue that is part of a neck [Automatically generated definition]. - OBOL:automatic + Portion of tissue that is the inner layer of the optic cup and will become the neural retina. + ZFIN:curator - - - EMAPA:37250 - MA:th + + + (...) 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 - + - connective tissue of neck - OBOL:automatic + inner layer optic cup + ZFA:0001071 - + - connective tissue of neck (volume) - OBOL:automatic + optic cup inner layer + EHDAA2:0001304 - + - neck (volume) connective tissue - OBOL:automatic + presumptive retinas + ZFA:0001071 + - - - neck (volume) portion of connective tissue - OBOL:automatic + + + 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 + + - - - neck (volume) textus connectivus - 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:0001163 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - - - neck portion of connective tissue - OBOL:automatic + + + 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 - - - neck textus connectivus - OBOL:automatic + + + hollow lens vesicle + - - - portion of connective tissue of neck - OBOL:automatic + + + solid lens vesicle + ZFA:0001679 + - - - portion of connective tissue of neck (volume) - OBOL:automatic + + + immature lens + ZFA:0001679 - - - textus connectivus of neck - OBOL:automatic + + + lens mass + ZFA:0001679 + ZFIN:ZDB-PUB-091023-49 - - - textus connectivus of neck (volume) - OBOL:automatic + + + presumptive lens + ZFA:0001679 - + - - - - - - - - - - - - - + + + + + - + - 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 + + + + + + + Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. + TAO:0002188 + ZFA:0001688 uberon - UBERON:0003570 - respiratory system connective tissue + UBERON:0005427 + corneal primordium - - - 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 + + + + ZFA - - - apparatus respiratorius textus connectivus - OBOL:automatic + + + + Obol - - - connective tissue of apparatus respiratorius - OBOL:automatic + + + + + + + + + ZFA - - - connective tissue of respiratory system - OBOL:automatic + + + 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 + - - - portion of connective tissue of apparatus respiratorius - OBOL:automatic + + + Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA]. + ZFIN:curator - - - portion of connective tissue of respiratory system - OBOL:automatic + + + 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 - - - respiratory system portion of connective tissue - 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:0001208 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 - - - respiratory system textus connectivus - OBOL:automatic + + + 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 - + - textus connectivus of apparatus respiratorius - OBOL:automatic + VNC + XAO:0004191 + - - - textus connectivus of respiratory system - OBOL:automatic + + + post-otic neural crest + ZFA:0000818 - + - - - - - - - - - - - - - - + + + + + - + + + + + + + - + - 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 + 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:0003585 + UBERON:0005432 - dermis connective tissue + aortic sac - + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + - A portion of connective tissue that is part of a dermis [Automatically generated definition]. - OBOL:automatic + 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]. + + + + - connective tissue of dermis - OBOL:automatic + saccus aorticus + + + + + + + + + + + + + + + + + + + + + + FMA:24219 + cervical region + neck subdivision + region of neck + subdivision of neck + uberon + UBERON:0005434 + cervical region + - + - dermis portion of connective tissue - OBOL:automatic + cervical region + FMA:24219 - + - dermis textus connectivus - OBOL:automatic + neck subdivision + FMA:24219 - + - portion of connective tissue of dermis - OBOL:automatic + region of neck + FMA:24219 - + - textus connectivus of dermis - OBOL:automatic + subdivision of neck + FMA:24219 - + - + - + - + + + + + - + - + - 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 + + + + + + + + + + + + + + + + + + + + + + + + + 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 - UBERON:0003586 - trunk connective tissue + foramen jugulare + UBERON:0005456 + jugular foramen + http://upload.wikimedia.org/wikipedia/commons/f/fa/Foramenjugulare.PNG - + - 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 + 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. + - - - textus connectivus of trunk - OBOL:automatic + + + 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 - - - torso connective tissue - OBOL:automatic + + + 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 + + - - - torso portion of connective tissue - OBOL:automatic + + + relationship loss: subclass braincase and otic capsule opening (AAO:0000051)[AAO] + 2012-06-20 + AAO:0000249 + AAO - - - torso textus connectivus - OBOL:automatic + + + UMLS:C0222712 + ncithesaurus:Jugular_Foramen - + - trunk portion of connective tissue - OBOL:automatic + Posterior lacerate foramen + FMA:56432 - - - trunk textus connectivus - OBOL:automatic + + + foramen jugulare + - + - + - + - - + + - - - - - - - + + - - + + + 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 + + + + + + + + + + + + + + + + + + + + - - + + - 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 + 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:0003587 - limb connective tissue + UBERON:0005472 + right vitelline vein - + - 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 + A vitelline vein that is in the right side of a multicellular organism. OBOL:automatic - - - - limb textus connectivus - OBOL:automatic + + + + + + + + + + + + + + + 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 - - - portion of connective tissue of limb - OBOL:automatic + + + 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]. + + - + - textus connectivus of limb - OBOL:automatic + neural tube lateral wall sulcus limitans + EHDAA2:0001265 - + - + - + - - + + - + + - - - - - - - + - - - - - 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 + + + + + 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 - + - A portion of connective tissue that is part of a forelimb [Automatically generated definition]. - OBOL:automatic + 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 + + + - EMAPA:37314 - MA:th + UMLS:C0231091 + ncithesaurus:Vitelline_Vein - + - connective tissue of anteriormost limb - OBOL:automatic + embryonic vitelline vein + VHOG:0000401 - + - connective tissue of fore limb - OBOL:automatic + vascular vitelline network + XAO:0004147 - + - connective tissue of forelimb - OBOL:automatic + vena vitellina + + - - - connective tissue of superior member - OBOL:automatic + + + omphalomesenteric vein + EMAPA:16244 - - - connective tissue of upper extremity - OBOL:automatic + + + 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 + - - - wing connective tissue - NCBITaxon:8782 - OBOL:automatic - + + + 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 + + + + + + + + + - - - - - - - + - 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 + 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 - - - A portion of connective tissue that is part of a hindlimb [Automatically generated definition]. - OBOL:automatic + + + + ZFA - - - EMAPA:37322 - MA:th + + + + + + + + + - - - connective tissue of hind limb - OBOL:automatic + + + 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) - + - connective tissue of hindlimb - OBOL:automatic + non neural ectoderm + ZFA:0001178 - - - connective tissue of inferior member - OBOL:automatic + + + epidermal ectoderm + - - - connective tissue of lower extremity - OBOL:automatic + + + 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 + + + - hind limb connective tissue - OBOL:automatic + primitive heart tube + EMAPA:16215 + + + + + early primitive heart tube + EMAPA:16208 - + - + - + - - + + - + - - + + - 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 + A neural tube lateral wall that is part of a rhombomere. + EMAPA:32819 + EMAPA:35364 uberon - UBERON:0003593 - thoracic cavity connective tissue + future hindbrain lateral wall + UBERON:0005501 + rhombomere lateral wall - + - 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 + A neural tube lateral wall that is part of a rhombomere. OBOL:automatic - - - chest cavity portion of connective tissue - OBOL:automatic + + + future hindbrain lateral wall + EMAPA:35364 + + + + + + + + + + + + + + + + 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 + - - - chest cavity textus connectivus - OBOL:automatic + + + + ZFA - - - connective tissue of cavity of chest - OBOL:automatic + + + + EHDAA2 - - - connective tissue of cavity of thorax - OBOL:automatic + + + + + + + + + EHDAA2 - - - connective tissue of chest cavity - OBOL:automatic + + + Cranial neural crest which gives rise to the trigeminal ganglion. + ZFA:0000080 - - - connective tissue of pectoral cavity - 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: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 + - - - connective tissue of thoracic cavity - OBOL:automatic + + + + Obol - - - pectoral cavity connective tissue - OBOL:automatic + + + + + + + + + ZFA - - - pectoral cavity portion of connective tissue - OBOL:automatic + + + Portion of tissue that gives rise to the immature gonad. + ZFA:0001262 - - - pectoral cavity textus connectivus - OBOL:automatic + + + Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO] + 2012-08-14 + TAO:0001262 + TAO + ZFIN:curator - + - portion of connective tissue of cavity of chest - OBOL:automatic + future gonad + - + - portion of connective tissue of cavity of thorax - OBOL:automatic + gonadal primordium + ZFA:0001262 - + - portion of connective tissue of chest cavity - OBOL:automatic + primitive gonad + - + - portion of connective tissue of pectoral cavity - OBOL:automatic + undifferentiated gonad + ZFA:0001262 - - - portion of connective tissue of thoracic cavity - OBOL:automatic + + + immature gonad + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - textus connectivus of cavity of chest - OBOL:automatic + + + + + + + + + EHDAA2 - - - textus connectivus of cavity of thorax - OBOL:automatic + + + + + + + + + EHDAA2 - - - textus connectivus of chest cavity - OBOL:automatic + + + Somite located in the head region, caudal to the otic vesicle. + - - - textus connectivus of pectoral cavity - OBOL:automatic + + + 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) + - - - textus connectivus of thoracic cavity - OBOL:automatic + + + EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter + EHDAA2 - + - thoracic cavity portion of connective tissue - OBOL:automatic + occipital somite + + XAO:0000313 - - - thoracic cavity textus connectivus - OBOL:automatic + + + cranial somite + XAO:0000313 - + - - - - - - - - - - - - - + + + - + - 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 + + + + + + + + + + + + + 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. + AAO:0011059 + EFO:0002578 + EMAPA:36007 + XAO:0001002 uberon - UBERON:0003594 - pelvis connective tissue + lateral diverticula + lung diverticulum + lung endoderm + UBERON:0005597 + + lung primordium - - - A portion of connective tissue that is part of a pelvis [Automatically generated definition]. - OBOL:automatic - - - - - EMAPA:37257 - MA:th + + + + XAO - - - connective tissue of pelvis - OBOL:automatic + + + + + + + + + XAO - - - pelvis portion of connective tissue - OBOL:automatic + + + 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 - - - pelvis textus connectivus - OBOL:automatic + + + lateral diverticula + XAO:0001002 - - - portion of connective tissue of pelvis - OBOL:automatic + + + lung diverticulum + AAO:3010717 - - - textus connectivus of pelvis - OBOL:automatic + + + lung endoderm + EFO:0002578 - + - + - + - + - + - + - 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 + A somite that is part of a trunk. + AAO:0010385 + EHDAA2:0003438 + EMAPA:16184 + XAO:0000314 uberon - UBERON:0003601 - neck cartilage + UBERON:0005598 + trunk somite - + - A cartilage that is part of a neck [Automatically generated definition]. + A somite that is part of a trunk. OBOL:automatic + + + + + + + + + + + + + + + + + + + + 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:37251 + EMAPA:37151 MA:th - - - cartilage of neck - OBOL:automatic + + + 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 + - - - cartilage of neck (volume) - OBOL:automatic + + + 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 - - - neck (volume) cartilage - OBOL:automatic + + + Contributes to the arch of aorta in humans + - + - + - + - + + + + + - - - + - + - 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 + + + + + + + + + + + + + + + + + + + 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 - UBERON:0003605 - - eye skin gland + anterior epithelium of lens vesicle + anterior surface of lens + UBERON:0005614 + lens anterior epithelium - - - 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 + + + + + + + + + FMA-inferred - - - skin glands of vertebrate eye - OBOL:automatic + + + A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex. + - - - skin glands set of camera-type eye - OBOL:automatic + + + UMLS:C1182652 + ncithesaurus:Subcapsular_Epithelium_of_the_Lens - + - skin glands set of vertebrate eye - OBOL:automatic + lens subcapsular epithelium + - + - vertebrate eye skin gland - OBOL:automatic + subcapsular lens epithelium + FMA:70612 - - - vertebrate eye skin glands - OBOL:automatic + + + anterior epithelium of lens vesicle + EMAPA:17304 - - - vertebrate eye skin glands set - OBOL:automatic + + + anterior surface of lens + FMA:58889 - + - + - + - - + + - - - + - + - 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 + + + + + + + + + + + + + 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:0003610 - - heart elastic tissue + UBERON:0005616 + mesenteric artery - - - 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 + + + + + + + + + Wikipedia - - - heart textus connectivus elasticus - OBOL:automatic + + + Arteries which arise from the abdominal aorta and distribute to most of the intestines. + + MESH:A07.231.114.565 - - - textus connectivus elasticus of heart - OBOL:automatic + + + UMLS:C0025465 + ncithesaurus:Mesenteric_Artery - + - + - + - - + + - - + - + - 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 + + + + + + + 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 - UBERON:0003611 - respiratory system elastic tissue + intestinal vein + UBERON:0005617 + mesenteric vein - + - An elastic tissue that is part of a respiratory system [Automatically generated definition]. - OBOL:automatic + A vein that returns blood from the intestines. + + MESH:A07.231.908.670.385 - + - 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 + UMLS:C0025473 + ncithesaurus:Mesenteric_Vein - - - elastic tissue of respiratory system - OBOL:automatic + + + 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 + - - - respiratory system elastic connective tissue - OBOL:automatic + + + 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 - - - respiratory system textus connectivus elasticus - OBOL:automatic + + + Normally regresses in humans + + + + + + + + + + + + + + + + + + + + + + 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 + - - - textus connectivus elasticus of apparatus respiratorius - OBOL:automatic + + + Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo. + ISBN:0073040584 - - - textus connectivus elasticus of respiratory system - OBOL:automatic + + + EHDAA2 is a mereological sum. + EHDAA2 - + - + - + - + - + - + - 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 + An epithelium that is part of a anterior chamber of eyeball. + EHDAA2:0000130 uberon - UBERON:0003613 - cardiovascular system elastic tissue + UBERON:0005638 + anterior chamber epithelium - + - 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 + An epithelium that is part of a anterior chamber of eyeball. 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 + An epithelium that is part of a lens vesicle. + EHDAA2:0000987 + EMAPA:17165 + VHOG:0000532 uberon - UBERON:0003614 - - blood vessel elastic tissue + UBERON:0005656 + lens vesicle epithelium - + - Elastic tissue layer that lines a blood vessel layer. - - - - - - - elastic lamina - MP:0006083 - - - - - elastic laminae - MP:0006083 - - - - - - blood vessel elastic connective tissue + An epithelium that is part of a lens vesicle. OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - blood vessel textus connectivus elasticus + + + An ectoderm that is part of a pharyngeal arch 3. OBOL:automatic - - - elastic connective tissue of blood vessel - 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) - + - elastic tissue of blood vessel - OBOL:automatic + 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 + - - - textus connectivus elasticus of blood vessel + + + An ectoderm that is part of a pharyngeal arch 4. OBOL:automatic - - - vascular elastic lamina - - - - - - vascular elastic laminae - - + + + 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) - + - vascular elastic tissue - MP:0006083 + 4th pharyngeal arch ectoderm + VHOG:0001095 - + - + - + - + - - - An arterial blood vessel that is part of a respiratory system [Automatically generated definition]. - EMAPA:37565 - MA:0001800 + + + + + + + + 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:0003643 - respiratory system arterial blood vessel + UBERON:0005665 + 3rd arch endoderm - + - An arterial blood vessel that is part of a respiratory system [Automatically generated definition]. + An endoderm that is part of a pharyngeal arch 3. OBOL:automatic - - - EMAPA:37565 - MA:th + + + 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 arterial blood vessel that is part of a kidney [Automatically generated definition]. - EMAPA:31436 - MA:0002578 + + + + + + + + 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 - kidney arterial system - UBERON:0003644 - - kidney arterial blood vessel + UBERON:0005666 + 4th arch endoderm - + - An arterial blood vessel that is part of a kidney [Automatically generated definition]. + An endoderm that is part of a pharyngeal arch 4. OBOL:automatic - - - kidney arterial system - EMAPA:31436 + + + 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 - + - + - + - - + + - + - - + + - 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 + 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:0003657 - - Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses - limb joint + UBERON:0005669 + peritoneal cavity mesothelium - + - Any joint that is part of a (free) limb. - + 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 + + + + - joint of limb skeletal system - OBOL:automatic + mesothelium of peritoneal component + EMAPA:16139 - + - skeletal limb joint - GO:0036023 + 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 + + + + + + + + + + + + + + + + + + + + + - - - - - - - + - 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 + An endothelium that is part of a left lung. + EHDAA2:0000961 uberon - cavitas abdominis - UBERON:0003684 - - abdominal cavity - http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg + UBERON:0005673 + left lung endothelium - + - 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 + An endothelium that is part of a left lung. + 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 + 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:0003687 - - - Design pattern notes: check whether this fits the foramen design pattern - foramen magnum - http://upload.wikimedia.org/wikipedia/commons/3/39/Gray130.png + UBERON:0005688 + lens vesicle cavity - + - 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]. - + An anatomical cavity that is part of a lens vesicle. + OBOL:automatic - - - Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO] - 2012-08-14 - TAO:0002045 - TAO - TAO:wd + + + (...) 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 - - - EMAPA:37868 - MA:th + + + lens cavity + EHDAA2:0000986 - - - UMLS:C0016519 - ncithesaurus:Foramen_Magnum + + + cavity of lens vesicle + EMAPA:17164 - + - + - + - + - + - + - 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 + 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 - 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 + 3rd branchial arch mesenchyme + pharyngeal arch 3 mesenchyme + UBERON:0005690 + 3rd arch mesenchyme - + - 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 - + Mesenchyme that is part of a pharyngeal arch 3. + OBOL:automatic - - - wall of abdomen - FMA:259054 + + + 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) - + - wall of abdomen proper - FMA:10429 - - - - - abdominal wall proper - FMA:10429 - - - - - layers of the abdominal wall - - - - - - paries abdominalis - - + 3rd pharyngeal arch mesenchyme + VHOG:0001083 - + - - - 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 + + + + + + + + + + + + + + + + + + + + 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 - 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 + 4th branchial arch mesenchyme + pharyngeal arch 4 mesenchyme + UBERON:0005691 + 4th arch mesenchyme - + - 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 + Mesenchyme that is part of a pharyngeal arch 4. + OBOL:automatic - - - UMLS:C0038001 - ncithesaurus:Splenic_Vein + + + 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) - + - vena splenica - FMA:14331 - FMA:TA - - - - - - lienal vein - - MA:0002164 + 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 + - - - vena lienalis - - + + + Mesenchyme that is part of a optic eminence. + OBOL:automatic - + - - + + + + + + + + + + + + + + + - + - - 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 + A venous system that is part of a hindbrain. + EHDAA2:0000776 + EMAPA:18632 + VHOG:0001322 uberon - UBERON:0003714 - neural tissue + rhombencephalon venous system + UBERON:0005720 + hindbrain venous system - + - 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 + A venous system that is part of a hindbrain. + OBOL:automatic - - - portion of neural tissue - FMA:9642 + + + rhombencephalon venous system + VHOG:0001322 - + - + - + - - + + - + + + - - - - - - - + - - + + - - + + - - + + - 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 + 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 - buccal mucosa - mucosal lining of mouth - oral mucosa - tunica mucosa oris - UBERON:0003729 - - mouth mucosa + 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 - - - 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 + + + + + + + + + ZFA - - - mucous membrane of mouth - FMA:59660 + + + + + + + + + Bgee:AN - - - oral part of viscerocranial mucosa - FMA:59660 + + + A mesoderm that has the potential to develop into a pronephros. + OBOL:automatic - - - tunica mucosa oris - FMA:59660 - FMA:TA - + + + 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 - + - buccal mucosa - GAID:951 + pronephric anlage + XAO:0000264 - + - mucosal lining of mouth - MA:0002794 + pronephric bulge + XAO:0000264 - + - oral mucosa - GAID:951 + pronephric mesenchyme + XAO:0000264 - + - tunica mucosa oris - - + pronephric primordium + XAO:0000264 - + - + - + - - + + - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + A sensory system that is capable of olfaction (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 - upper body bone - UBERON:0003827 - thoracic segment bone + UBERON:0005725 + + + + olfactory system - + - 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 + A sensory system that is capable of olfaction (the sensory perception of smell). + - - - thorax bone - OBOL:automatic + + + 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]. + - - - thorax bone organ - OBOL:automatic + + + The sensory system used for olfaction (the sense of smell).[AAO] + 2012-06-20 + AAO:0000978 + AAO + AAO:EJS - - - upper body bone - MA:0000559 + + + UMLS:C0228065 + ncithesaurus:Olfactory_System - + - + - + - - + + - - - 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 + + + + + + + + BILA:0000139 uberon - UBERON:0003828 - abdominal segment bone + UBERON:0005726 + + chemosensory system + + + + + + + + + + + + + + + + + + + + + + + + + + + + + EHDAA2:0000474 + EMAPA:31862 + EMAPA:31863 + FMA:296719 + VHOG:0000616 + extra-embryonic mesoderm + extraembryonic mesenchyme + uberon + UBERON:0005728 + extraembryonic mesoderm - - - A bone that is part of an abdominal segment of trunk [Automatically generated definition]. - OBOL:automatic - - - - - EMAPA:37058 - MA:th + + + + EHDAA2 - - - abdominal segment of trunk bone - OBOL:automatic + + + + + + + + + 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 + - - - abdominal segment of trunk bone organ + + + A limb/fin field that has the potential to develop into a pectoral appendage bud mesenchyme. OBOL:automatic - - - bone of abdominal segment of trunk - OBOL:automatic + + + Embryonic region that develops into the pectoral fin bud.[TAO] + 2012-08-14 + TAO:0001453 + TAO + ZFIN:curator - - - bone organ of abdominal segment of trunk - OBOL:automatic + + + pectoral fin field + ZFA:0001453 + - + - + - + - - + + - - + + - - + + - Any muscle tissue that is part of the urethra. - EMAPA:37787 - MA:0002649 + 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 - urethral muscle layer - UBERON:0003829 - urethra muscle tissue + UBERON:0005730 + pelvic appendage field - + - Any muscle tissue that is part of the urethra. - UBERON:cjm + A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme. + OBOL:automatic - - - EMAPA:37787 - MA:th + + + Embryonic region that develops into the pelvic fin bud.[TAO] + 2012-08-14 + TAO:0001454 + TAO + ZFIN:curator - - - urethral muscle layer - MA:0002649 + + + pelvic fin field + ZFA:0001454 + - + - + - + - - + + - + + + + - + - 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 + + + + + + + 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:0003831 - respiratory system muscle + UBERON:0005732 + + paired limb/fin field - - - 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 + + + + + + + + + ISBN:9780878932504 + ZFA-inferred - - - respiratory system muscle organ - OBOL:automatic + + + A ring of cells capable of forming a limb or paired fin[Gilbert,modified]. + ISBN:9780878932504 - + - + - + - - + + - + - - + + - A blood vessel that is part of a thorax [Automatically generated definition]. - EMAPA:37238 - MA:0000558 - blood vessel of thorax - thorax blood vessel + A ring of cells capable of forming a limb. + limb field of lateral plate mesoderm uberon - upper body blood vessel - UBERON:0003834 - thoracic segment blood vessel + 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 blood vessel that is part of a thorax [Automatically generated definition]. - OBOL:automatic + 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)]. + + + + - EMAPA:37238 - MA:th + UMLS:C0225342 + ncithesaurus:Tunica_Adventitia - + - blood vessel of thorax - OBOL:automatic + adventitia externa + - + - thorax blood vessel - OBOL:automatic + tunica adventitia + - + + + tunica adventitia of vessel + + + + - upper body blood vessel - MA:0000558 + external coat + + + + + + tunica adventitia vasorum + + + + + + + tunica externa vasorum + + - + - + - + - + - + + - + - 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 + + + + + + + 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:0003835 - abdominal segment blood vessel + UBERON:0005740 + tunica intima of artery - + - A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition]. + A tunica intima that is part of a artery. OBOL:automatic - - - EMAPA:37057 - MA:th - - - + - abdominal segment of trunk blood vessel - OBOL:automatic + arterial intima + EV:0100028 - + - blood vessel of abdominal segment of trunk - OBOL:automatic + tunica interna (intima)(arteriae) + FMA:14272 - + - - - - - - - - - - - - - + + - - + + - 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 + + + + + + + An outermost connective tissue covering of an organ, vessel, or other structure[WP]. + + + BTO:0002010 + FMA:45635 + tunica advetitia + tunica externa uberon - UBERON:0003836 - abdominal segment skin + UBERON:0005742 + + adventitia + http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg - + - A skin of body that is part of an abdominal segment of trunk [Automatically generated definition]. - OBOL:automatic - - - - - EMAPA:37063 - MA:th + An outermost connective tissue covering of an organ, vessel, or other structure[WP]. + - - - abdominal segment of trunk skin - OBOL:automatic + + + tunica advetitia + - - - skin of abdominal segment of trunk - OBOL:automatic + + + tunica externa + FMA:45635 - + - + - + - + - + - + - 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 + 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 uberon - upper body connective tissue - UBERON:0003837 - thoracic segment connective tissue + UBERON:0005744 + + bone foramen + http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png - + - 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 + Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves. + TAO:curator - - - thorax textus connectivus - OBOL:automatic + + + 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 - - - upper body connective tissue - MA:0000560 + + + foramen + ZFA:0005386 - + - - - - - - - - - - - - - + + + - + - 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 + + + + + + + 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:0003838 - abdominal segment connective tissue + UBERON:0005753 + caudal part of nephrogenic cord - + - 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 + The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm. + - + - abdominal segment of trunk portion of connective tissue + caudal portion of nephrogenic cord OBOL:automatic - + - abdominal segment of trunk textus connectivus + caudal region of nephrogenic cord OBOL:automatic - + - connective tissue of abdominal segment of trunk + rear part of nephrogenic cord OBOL:automatic - + - portion of connective tissue of abdominal segment of trunk - 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 + - - - textus connectivus of abdominal segment of trunk - OBOL:automatic + + + The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros. + - + - + - + - - + + - + - + - 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 + + + + + + + An acellular anatomical structure that is the bounding layer of a anatomical structure. + FMA:63871 uberon - UBERON:0003839 - - forelimb joint + UBERON:0005764 + acellular membrane - + - 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 + An 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 + - - - forelimb limb joint - OBOL:automatic + + + + FMA - - - joint of free upper limb + + + 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. + - - - 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 + + + UMLS:C0004799 + ncithesaurus:Basement_Membrane - + - upper extremity joint of limb - OBOL:automatic + basement membrane of connective tissue + FMA:63872 - + - upper extremity limb joint - OBOL:automatic + membrana basalis + + - - - wing joint - NCBITaxon:8782 - OBOL:automatic - + + + basement membrane + FMA:63872 - + - - - - - - - - - - - - - + + - + - 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 + + + + + + + + + + + + + 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 - UBERON:0003840 - - hindlimb joint + nephric cord + UBERON:0005792 + nephric ridge - + - A limb joint that is part of a hindlimb [Automatically generated definition]. - OBOL:automatic + 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. + - - - hind limb joint of limb - OBOL:automatic + + + nephric cord + VHOG:0001240 + + + + + + + + + + + + + + + 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 + - - - hind limb limb joint - OBOL:automatic + + + 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 - - - hindlimb joint of limb - OBOL:automatic + + + UMLS:C0506947 + ncithesaurus:Aortic_Segment - - - hindlimb limb joint - OBOL:automatic + + + aortic segment + FMA:13087 - - - inferior member joint of limb - OBOL:automatic + + + segment of aorta + FMA:13087 - - - - inferior member limb joint - OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - - - joint of free lower limb - + + + 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]. + - - - joint of limb of hind limb - OBOL:automatic + + + 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 - - - joint of limb of hindlimb - OBOL:automatic + + + 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 - - - joint of limb of inferior member - OBOL:automatic + + + relationship loss: part_of axial vasculature (TAO:0001073)[TAO] + 2012-08-14 + TAO:0000014 + TAO - - - joint of limb of lower extremity - OBOL:automatic + + + 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 - + - joint of lower limb - + DA + ZFA:0000014 - + - limb joint of hind limb - OBOL:automatic + aorta dorsalis + XAO:0000051 + - - - limb joint of hindlimb - OBOL:automatic + + + aortae dorsales + + - - - limb joint of inferior member - OBOL:automatic + + + dorsal aorta root + VHOG:0000264 - - - limb joint of lower extremity - OBOL:automatic + + + dorsal aortae + + - - - lower extremity joint of limb - OBOL:automatic + + + dorsal aortic root + VHOG:0000264 - - - lower extremity limb joint - OBOL:automatic + + + dorsal aortæ + + - + - - - - - - - - - - - - - + + - - - - - - - + - 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 + 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 - central lumen - neural lumen - neurocoel - UBERON:0003842 - neural tube lumen + spinal neuromeres + UBERON:0005844 + spinal cord segment - - - 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 - + axial part of spinal cord + BIRNLEX:2665 - + - lumen of neural tube - + axial regional part of spinal cord + BIRNLEX:2665 - + - neural tube neural lumen - EHDAA2:0001269 - - - - - neural lumen - EHDAA:2889 + segment of spinal cord + FMA:62420 - + - neurocoel - VHOG:0001119 + spinal neuromeres + TAO:0001332 + - + - + - + - - + + - + - - + + - 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 + 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 - UBERON:0003848 - gonadal vein - http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png + 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 - + - 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]. - + A spinal cord segment that adjacent_to a caudal region. + OBOL:automatic - + - gonad vein - OBOL:automatic + coccygeal segment of spinal cord + FMA:256635 - + - gonada vein - OBOL:automatic + coccygeal segments of spinal cord [1-3] + FMA:256635 - + - vein of gonad - OBOL:automatic + pars coccygea medullae spinalis + FMA:256635 + FMA:TA + - + - vein of gonada - OBOL:automatic + segmenta coccygea medullae spinalis [1-3] + FMA:256635 + FMA:TA + + + + + + segmenta coccygea + NeuroNames:1656 + - + - - - - - - - - - - - - - - + + + - - + + - 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 + A delimited region of dense mesenchyme within looser mesenchyme. + AEO:0000148 + EHDAA2_RETIRED:0003148 + EHDAA:8979 + mesenchyme condensation uberon - UBERON:0003849 - - - mesencephalic neural crest + UBERON:0005856 + developing mesenchymal condensation - + - - ZFA + + AEO - - - A neural crest that has_potential_to_developmentally_contribute_to a midbrain. - OBOL:automatic + + + + cjm - - - 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 + + + + + + + + + AEO-modified-relation - - - mesencephalic neural crest - ZFA:0000935 + + + A delimited region of dense mesenchyme within looser mesenchyme. + AEO:0000148 - + - neural crest midbrain - ZFA:0000935 + mesenchyme condensation + EMAPA:25351 - + - - - - - - - - - - - - - - + + - - + + - 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 + + + + + + + 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 - rhombomere neural crest - UBERON:0003852 - - rhombencephalon neural crest + UBERON:0005863 + cartilaginous condensation - + - - ZFA + + AEO - - - A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. - OBOL:automatic + + + + + + + + + AEO - - - Cranial neural crest that is part of the hindbrain.[TAO] - 2012-08-14 - TAO:0007063 - TAO - ZFIN:curator + + + Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes. + GO: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 + + + isa cell condensation in VSAO; has_part chondroblast in AEO + VSAO - + - neural crest hindbrain - ZFA:0007063 + cartilage condensation + EMAPA:25353 - + - rhombencephalic neural crest - ZFA:0007063 + cartilagenous condensation + EHDAA2:0003147 - - - rhombomere neural crest - EMAPA:35747 + + + chondrogenic condensation + VSAO:0000092 - + - + - + - - + + - + - - + + - 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:0008714 + AEO:0000149 + EHDAA2_RETIRED:0003149 + pre muscle mass + premuscle mass uberon - spinal neural crest - UBERON:0003853 - spinal cord neural crest + UBERON:0005865 + pre-muscle condensation - - - 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 + + + + + + + + + AEO - + - - - - - - - - - - - - - + + + - - + + - 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 + + + + + + + + + + + + + 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:0003854 - spinal cord neural plate + UBERON:0005866 + pre-cartilage condensation - + + + + AEO + + + - - + + - ZFA + AEO - + - A neural plate that develops_from a future spinal cord. - OBOL:automatic + A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts. + AEO:0000150 + AEO:JB - + - 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 + A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage. + - + - - - - - - - - - - - - - - + + + - + - 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 + + + + + + + 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 - UBERON:0003855 + mandibular process + mandibular swelling + prominentia mandibularis + UBERON:0005867 - gonad mesenchyme + mandibular prominence - + - Mesenchyme that is part of a developing gonad [Automatically generated definition]. - OBOL:automatic + 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 - - - gonada mesenchyme - OBOL:automatic + + + UMLS:C1512982 + ncithesaurus:Mandibular_Prominence - - - mesenchyme of gonad - OBOL:automatic + + + mandibular process + - - - mesenchyme of gonada - OBOL:automatic + + + mandibular swelling + + + + + + prominentia mandibularis + + - + - - - - - - - - - - - - - + + - + - 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 + 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 - UBERON:0003859 - forelimb mesenchyme + back of head + UBERON:0005902 + occipital region - + - 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 + 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 - - - mesenchyme of forelimb - OBOL:automatic + + + 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 - - - mesenchyme of superior member - OBOL:automatic + + + 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 - + - mesenchyme of upper extremity - OBOL:automatic + basicranial region + ZFA:0001414 - + - superior member mesenchyme - OBOL:automatic + occipital part of head + FMA:49187 - + - upper extremity mesenchyme - OBOL:automatic + occipital region of head + FMA:49187 - - - wing mesenchyme - Geisha:syn - NCBITaxon:8782 - + + + back of head + FMA:49187 + + + + + + + + + + + + + + + + + + + + + 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 + - - - wing mesenchyme - NCBITaxon:8782 - OBOL:automatic - + + + 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 - + - + - + - - + + - + + - - + + - 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 + 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:0003860 - hindlimb mesenchyme + UBERON:0005911 + endo-epithelium - + - Mesenchyme that is part of a developing hindlimb [Automatically generated definition]. - OBOL:automatic - - - - - hind limb mesenchyme - OBOL:automatic + 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 + - - - inferior member mesenchyme - OBOL:automatic + + + + FMA - + - lower extremity mesenchyme - OBOL:automatic + bone organ zone + FMA:10483 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - mesenchyme of hind limb - OBOL:automatic + + + Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. + + + + FMA:71221 + VSAO:0000056 - - - mesenchyme of hindlimb - OBOL:automatic + + + Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] + 2012-08-14 + VSAO:0000056 + VSAO + PSPUB:0000170 - - - mesenchyme of inferior member - OBOL:automatic + + + UMLS:C0222645 + ncithesaurus:Axial_Skeleton - - - mesenchyme of lower extremity - OBOL:automatic + + + skeleton axiale + + - + - + - + - - + + - - - - - - - - - - - - - - - - + + + + - - + + - - + + - An anatomical cavity that has the potential to develop into a coelemic cavity lumen. + An outflow tract that is part of a cardiac atrium. + FMA:14141 + outflow part of atrium uberon - body cavity precursor - UBERON:0003886 - - - future coelemic cavity lumen + UBERON:0005946 + outflow tract of atrium - + - An anatomical cavity that has the potential to develop into a coelemic cavity lumen. + An outflow tract that is part of a cardiac atrium. OBOL:automatic + + + + outflow part of atrium + FMA:14141 + - + - - + + + + + + + + + + + + + - + - - + + - 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 - - - + + + + + + + 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 + + + - + - 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 + Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk. + MP:0010428 - - - (...) 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 + + + infundibulum + - + - UMLS:C1512940 - ncithesaurus:Intraembryonic_Coelom + EMAPA:37926 + MA:th - + + + UMLS:C1881209 + ncithesaurus:Infundibulum + + + - somatic coelom - + 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 - + - + - + - - + + - - - - - - - - - - - - - + - - + + - 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 + 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 - neural retinal epithelium - UBERON:0003902 + UBERON:0005956 - - retinal neural layer + outflow part of left ventricle - - - - - - - - - Bgee:AN + + + Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta. + MP:0010429 - - - The part of the retina that contains neurons and photoreceptor cells[GO]. - GO:0003407 + + + EMAPA:37925 + MA:th - - - (...) 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 + + + LVOT + MP:0010429 + - - - UMLS:C1518263 - ncithesaurus:Neural_Retina + + + Sibson vestibule + MP:0010429 - + - neural layer of retina - FMA:58628 + aortic vestibule + FMA:9473 - + - neural retina - XAO:0003216 - ZFA:0000046 + aortic vestibule + MP:0010429 - + - neuroretina - ZFA:0000046 + heart left ventricle outflow tract + MP:0010429 - + - stratum nervosum (retina) - FMA:58628 + left ventricular outflow + FMA:9473 - + - stratum nervosum retinae - FMA:58628 - FMA:TA - + left ventricular outflow tract + HP:0011103 - - - neural retinal epithelium - MA:000027 + + + outflow tract of left ventricle + FMA:9473 + + + + + vestibulum aortae + FMA:9473 + FMA:TA + - + - - - - 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 + + + + + + + + + + + + + + + + + + + + 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:0003914 - epithelial tube + UBERON:0005965 + outflow part of right atrium - + - 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 + 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 - + - - - - Any endothelium that has the quality of being cylindrical [Automatically generated definition]. + + + + + + + + + + + + + + + + + + + + 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:0003915 - endothelial tube + UBERON:0005966 + outflow part of left atrium - + - Any endothelium that has the quality of being cylindrical [Automatically generated definition]. + 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 + - + - + - + - - + + - + + - - + + - Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO]. - check this - mesenchyme of kidney + + + + + + + The laminar structure of the heart. uberon - UBERON:0003918 + UBERON:0005983 + - kidney mesenchyme + heart layer - + - Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO]. - GO:0072074 + The laminar structure of the heart. + MP:0010545 - + - + - + - + - + + - + - 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 + + + + + + + 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:0003920 - Compare to: vein - venous blood vessel + UBERON:0005985 + + coronary 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 + Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation. + MP:0010551 - + - + - + - - + + + + + + - + + - - + + - 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 + + + + + + + + + + + + + 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:0003928 - digestive system duct + UBERON:0005989 + + atrioventricular septum - - - A duct that is part of a digestive system [Automatically generated definition]. - OBOL:automatic + + + + + + + + + + Wikipedia - - - duct of digestive system - OBOL:automatic + + + 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 - - - duct of gastrointestinal system - OBOL:automatic + + + EMAPA:37431 + MA:th - + - gastrointestinal system duct - OBOL:automatic + membranous atrioventricular septum + FMA:7136 - + - + - + - - + + - + + + - + - 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 + + + + + + + + + + + + + The paired arteries that carry blood to the yolk sac from the dorsal aorta. + + EHDAA2:0002208 + EMAPA:16207 uberon - alimentary tract epithelium - UBERON:0003929 - digestive tract epithelium + 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 - + - An epithelium that lines the lumen of the digestive tract. + Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. + - + - Epithelium lining the lumen of the gut.[TAO] - 2012-08-14 - TAO:0005123 - TAO - ZFIN:curator + 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 - + - 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 + EMAPA:37883 + MA:th - - - gastrodermis - BGEE:ANN - NCBITaxon:6073 - + + + body hair or bristle + GO:GO - - - gut epithelial tissue - OBOL:automatic + + + adnexae cutis + + - - - gut epithelium - EHDAA2:0004567 - MA:0003201 - ZFA:0005123 + + + skin adnexa + - + - alimentary tract epithelium - OBOL:automatic + skin appendage + - + - + - + + + + + + + + + + + + + + + + + + + + + + uberon + UBERON:0006056 + posterior surface of head + + + + + + + + + + + - + - + - + - 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 + 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 - UBERON:0003932 - - cartilage element of chondrocranium + tail bone + tail vertebra + UBERON:0006068 + + bone of tail - + - A cartilage element of chondrocranium. Example: neurocranial trabecula. - - - - - - cartilage of chondrocranium - OBOL:accepted + A bone that is part of a post-anal tail. + OBOL:automatic - - - cartilaginous element of chondrocranium - OBOL:accepted + + + 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 - - - chondrocranium cartilage - ZFA:0001461 + + + tail bone + MA:0000696 - - - neurocranium cartilage - ZFA:0001461 + + + tail vertebra + - + - - - - - - - - - - - - - + + + - + - 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 + + + + + + + + + + + + + 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 - cranial cartilages - UBERON:0003933 - cranial cartilage + post-anal caudal region + post-anal tail region + postsacral region + tail region + UBERON:0006071 + caudal region - + - A cartilage element that is part of the cranial skeleton. - - ZFA:0001458 + 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. + - - - Cartilage which is part of the cranium.[TAO] - 2012-08-14 - TAO:0001458 - TAO - ZFIN:curator + + + 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 - - - cartilage of cranium - OBOL:automatic + + + post-anal caudal region + - - - cranium cartilage - OBOL:automatic + + + post-anal tail region + - + - cranial cartilages - ZFA:0001458 - + postsacral region + AAO:0000082 + + + + + tail region + AAO:0000082 - + - + - + - - + + - - - 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 - + + + + + + + + + + + + + + + + + + + + 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 - reproductive gland + cervical region of vertebral column - + + + + + + + + + FMA + + + - Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. - MP:0000653 + That portion of the spine comprising the cervical vertebrae. The neck area of the spine. + - - - genitalia gland - OBOL:automatic + + + 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 + + + - gland of genitalia - MP:0000653 + axial skeleton cervical region + MA:0003154 - + - gland of reproductive system - OBOL:automatic + cervical skeleton + EHDAA2:0000238 - + - reproductive gland - MA:0001751 + cervical spinal column + FMA:24138 - + - reproductive system gland - OBOL:automatic + cervical spine + FMA:24138 - + - sex gland - MP:0000653 + cervical vertebral column + FMA:24138 + + + + + skeletal system of neck + FMA:24138 - + - + - + - - + + - - + - + - - + + - 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 + + + + + + + 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 - cutaneous elastic tissue + thoracic region of vertebral column - + + + + + + + + + FMA + + + - 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 + 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 + + + - EMAPA:37841 - MA:th + UMLS:C0581269 + ncithesaurus:Thoracic_Spine - - - cutaneous elastic fiber - MP:0008418 + + + axial skeleton thoracic region + MA:0003155 - - - dermal elastic fiber - MP:0008418 + + + columna vertebralis thoracicus + FMA:9140 - - - - - - - - valvular - EHDAA2:0004046 - EHDAA:1892 - EHDAA:4406 - FMA:67611 - OpenCyc:Mx4rvqiwE5wpEbGdrcN5Y29ycA - galen:Valve - anatomical valve - uberon - UBERON:0003978 - - valve - - + - anatomical valve - FMA:67611 + thoracic spine + FMA:9140 + + + + + thoracic vertebral column + FMA:9140 - + - + - - - - - + - - + + - + - - + + - - + + - 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 + 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 - epimere mesoderm - mesenchyma dermatomiale - UBERON:0004016 - - dermatome - http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png + caudal region + postsacral region + tail region + UBERON:0006076 + caudal region of vertebral column - - - - AEO + + + Subdivision of vertebral column that corresponds to the caudal subdivision of the body, containing the caudal vertebrae. + UBERONREF:0000006 - - - - - - - - - EHDAA2-abduced + + + 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 - - - A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. - AEO:0001017 - AEO:JB + + + in AAO, this is posterior to the caudal-sacral region + AAO - - - UMLS:C0180383 - ncithesaurus:Dermatome + + + axial skeleton tail region + MA:0003158 - + - cutis plate - + caudal skeleton + UBERONREF:0000006 - + - dermatomal mesenchyme - + caudal vertebrae series + - + - mesenchyma dermatomiale - - + caudal region + AAO:0000082 + + + + + postsacral region + AAO:0000082 + + + + + tail region + AAO:0000082 - + - - - - + + + + + + + + + + + + + + - + - - + + - - + + - 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 + 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 - UBERON:0004022 - - germinal neuroepithelium + vertebral region + vertebral subdivision + UBERON:0006077 + + subdivision of vertebral column - + - - NCBIBook:NBK10047 + + + + + + + FMA - + - 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 + A collection of all skeletal elements in some subdivision of the vertebral column. + - + - germinal neuroepithelial layer - + subdivision of vertebral skeleton + - + - germinal neuroepithelium - NCBIBook:NBK10047 + vertebral column subdivision + FMA:16201 + + + + + + + + + + + + + + + + + + + + + + + + + + The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue. + uberon + UBERON:0006170 + mesonephric capsule + - - - original neural tube - NCBIBook:NBK10047 + + + 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 - + - - - - + + + + + + + + + + + + + + + + + + - + - + - + - - - - - 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 + + + + + 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 + - neural tube ventricular layer + aortico-pulmonary spiral septum + http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray470.png - + - - NCBIBook:NBK10047 + + + + + + + EMAPA - + - - + + - NCBIBook:NBK10047 + + Wikipedia - + - 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 + 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 - - - ependymal layer - NCBIBook:NBK10047 + + + aortico-pulmonary septum + - + - neural tube ependymal layer - NCBIBook:NBK10047 + aorticopulmonary septum + - + - neural tube ventricular germinal zone - NCBIBook:NBK10047 + septum aorticopulmonale + + - - - neural tube ventricular zone - MP:0009689 + + + aortic septum + - - - neural tube ependymal zone - MP:0009689 + + + spiral septum + - + - - - - + + + - + - - + + - - + + + + + + + - - + + + + + + + - 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 + + + + + + + + + + + + + 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 - future brain marginal layer - UBERON:0004061 + oral membrane + oral plate + oropharyngeal membrane + pharyngeal membrane + UBERON:0006211 + - neural tube mantle layer + buccopharyngeal membrane + http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png - - - - NCBIBook:NBK10047 - - - + - - + + - by division - NCBIBook:NBK10047 + EHDAA2 - + - 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 + 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 - - - neural tube intermediate zone - - MP:0009690 + + + oral membrane + MP:0012521 - + - future brain marginal layer - EMAPA:35360 + oral plate + MP:0012521 + + + + + oropharyngeal membrane + + + + + + pharyngeal membrane + MP:0012521 + - + - - + + + - + - + - - + + - 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 + + + + + + + + + + + + + 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 - brain marginal zone - UBERON:0004062 + membrana cloacalis + UBERON:0006217 + - neural tube marginal layer + cloacal membrane + http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png - + - + - forms from axons + Wikipedia - + - The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter - - MP:0009691 + 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 - - - neural tube marginal zone - MP:0009691 + + + 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 + + - + - - - - 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 + + + + + + + + + + EHDAA:1267 + EMAPA:16342 + RETIRED_EHDAA2:0000268 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 + UBERON:0006218 + + common atrial chamber + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - 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 + An anatomical junctions that overlaps the foregut and midgut. + OBOL:automatic - - - venae cavae - - + + + 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 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 + + + + + + + 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 - ocular and peri-ocular region - ocular region - orbital content - orbital part of eye - UBERON:0004088 - - orbital region + embryonic brain + UBERON:0006238 + + + + + future brain - + - 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 + The embryonic precursor of the brain. + NLX:94995 - - - content of orbital part of eye - FMA:260119 + + + The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) + - + - eye region - + brain rudiment + TAO:0000146 - + - orbital part of face - + presumptive brain + ZFA:0000146 - - - orbital content - FMA:260119 + + + encephalon + NLX:94995 - + - orbital part of eye - FMA:72951 + embryonic brain + BTO:0004726 - + - + - - - - - + - - + + - + + + - - - - - 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 + A tendon that has the potential to develop into a central tendon. + The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. + EHDAA2:0000593 + EHDAA:4118 + EMAPA:25035 uberon - opening - ostia - ostium - UBERON:0004111 - anatomical conduit + cranial derivative of septum transversum + cranial part of septum transversum + UBERON:0006239 + + future central tendon - - - Any tube, opening or passage that connects two distinct anatomical spaces. - + + + + + + + + + EHDAA2 - - - FMA has both conduit and conduit space. In EHDAA2 this is a surface feature - FMA + + + + + + + + + mesenchyme + cranial part + Wikipedia - - - foramen - EHDAA2:0003080 + + + A tendon that has the potential to develop into a central tendon. + OBOL:automatic - - - foramina - - + + + cranial derivative of septum transversum + - + - ostia - + cranial part of septum transversum + - + - - - - - - - - - - - - - + + - + - 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 + + + + + + + + + + + + + + + + + + + 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:0004118 - - vasculature of iris + UBERON:0006241 + + + future spinal cord - - - A vasculature that is part of a iris [Automatically generated definition]. - OBOL:automatic + + + + + + + + + EHDAA2 - + - iris blood vessels - ZFA:0005568 + presumptive spinal cord + ZFA:0000417 - + - iris vascular network - OBOL:automatic + presumptive spinal cord neural keel + TAO:0000417 - + - vascular network of iris - OBOL:automatic + presumptive spinal cord neural plate + TAO:0000417 + + + + + presumptive spinal cord neural rod + TAO:0000417 - + - + - + - - + + + + + + + + + + + + + + + + - + + - - + + - An anatomical structure that develops (entirely or partially) from the endoderm. - Grouping term for query purposes + + + + + + + + + + + + + + + + + + + + + + + An anatomical junctions that overlaps the mouth and foregut. + EHDAA:534 + EMAPA:16258 + RETIRED_EHDAA2:0001205 + VHOG:0000592 uberon - UBERON:0004119 - - endoderm-derived structure + UBERON:0006264 + + mouth-foregut junction - + - An anatomical structure that develops (entirely or partially) from the endoderm. - + An anatomical junctions that overlaps the mouth and foregut. + OBOL:automatic - + - - - - - - - - - - - - - + + + + + + + + + + + - + - An anatomical structure that develops (entirely or partially) from the mesoderm. - Grouping term for query purposes - FBbt:00025998 - mesodermal derivative + 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:0004120 - - mesoderm-derived structure + UBERON:0006267 + + notochordal plate - + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + - An anatomical structure that develops (entirely or partially) from the mesoderm. - + 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 - - - mesodermal derivative - FBbt:00025998 + + + 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 - + - - - - - - - - - - - - - + + + + + + + + + - An anatomical structure that develops (entirely or partially) from the ectoderm. - Grouping term for query purposes - FBbt:00025990 - ectodermal deriviative + 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 - UBERON:0004121 - - ectoderm-derived structure + 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 + + + - An anatomical structure that develops (entirely or partially) from the ectoderm. - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. + - - - ectodermal deriviative - FBbt:00025990 + + + UMLS:C1518430 + ncithesaurus:Notochordal_Process - + - + - + - - + + - - + + - + + + + + + + + + + + + + + - - + + - - + + - - + + - 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 + 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 - GU tract - UG tract - Urogenitalsystem - genito-urinary system - genitourinary tract - urogenital tract - UBERON:0004122 - - - genitourinary system + pleuroperitoneal channel + UBERON:0006279 + + pleuroperitoneal canal - - - Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. - VHOG:0000286 + + + + EHDAA2 - - - 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 + + + + + + + + + EHDAA2 - - - relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO] - 2012-06-20 - AAO:0000624 - AAO + + + Each of the canals that links the peritoneal cavity and the caudal part of a pleural cavity. + ISBN:0124020607 + VHOG:0001505 - - - 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] + + + Each of the canal that links the peritoneal cavity and the caudal part of a pleural cavity. [ISBN:0124020607][VHOG] 2012-09-17 - VHOG:0000286 + VHOG:0001505 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 + pleuroperitoneal channel + VHOG:0001505 - + - - - + + - + - - + + - - + + - - + + - 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 + 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 - 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 + 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 - - - - - - - - - GO-def - - - + - - + + - ZFA + EMAPA - + - 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 + Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle. + ZFA:0001719 - - - (...) 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 + + + presumptive cardiac ventricle heart tube + ZFA:0001719 - - - UMLS:C0231106 - ncithesaurus:Optic_Vesicle + + + primitive ventricle + EHDAA2:0001531 - - - eye vesicle - XAO:0000228 + + + primitive ventricle of heart + EMAPA:16350 - - - ocular vesicle - VHOG:0000165 + + + primordial cardiac ventricle + FMA:71006 - - - optic vesicles - ZFA:0000050 - + + + primordial ventricle + FMA:71006 - + - - + + + + + + + + - + - 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 - + + 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 + - + - - + + - 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 + EHDAA2 - + - primary heart field - - XAO:0004185 - - - - - FHF - XAO:0004185 - - - - - - PHF - XAO:0004185 - + trigeminal V preganglion + EMAPA:16663 - + - heart field - XAO:0004185 + trigeminal preganglion + EMAPA:16663 - + - - - - + + + + + + + + + + + + + + + + + + - - + + - - + + - 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 + 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 - UBERON:0004141 - - - - heart tube + chamber of eye + UBERON:0006311 + chamber of eyeball - - - - - - - - - ZFA-modified + + + A segment of the eyeball that is filled with refractive media. + - - - An epithelial tube that will give rise to the mature heart. - GO:0003143 - GOC:mtg_heart + + + EMAPA:37529 + MA:th - - - 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 + + + UMLS:C0459556 + ncithesaurus:Chamber_of_the_Eye - + - embryonic heart tube - GO:0003143 + eye chamber + MA:0002459 - + - endocardial heart tube - MP:0012700 + 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 + - - - endocardial tube - XAO:0000337 + + + Body substance in a liquid or semi-solid state in the eyeball which serves to refract light. + - + - + - - - - - + - - + + - - - + - - + + - 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 + 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 - coronary vein - UBERON:0004148 + UBERON:0006314 - cardiac vein + bodily fluid - - - - FMA - - - + - Vein of heart that drains the myocardium - + 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:37137 + EMAPA:37441 MA:th - - - UMLS:C0226654 - ncithesaurus:Cardiac_Vein - - - - - UMLS:C0226737 - ncithesaurus:Coronary_Vein - - - - - cardiac vein - FMA:12846 - - - - - coronary vein - ZFA:0005814 - - - + - heart vein - OBOL:automatic + 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 + - - - vein of heart + + + A nucleus of brain that is part of a brainstem. OBOL:automatic - + - coronary vein - + brain stem nucleus + EMAPA:32790 - + - - - + + + + + + + + + + 2 + + + + + 2 + + + + + + + + - - + + - A cardiac chamber surrounds an enclosed cavity within the heart - - FMA:7095 - OpenCyc:Mx4rmexpjPdAEduAAAAOpmP6tw - chamber of heart - heart chamber + An artery that connects two larger arteries. + + EMAPA:18598 + MA:0001938 + NCIT:C52851 + UMLS:C1707451 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 + UBERON:0006347 + Grouping for anterior and posterior + communicating artery - + - A cardiac chamber surrounds an enclosed cavity within the heart - GO:0003205 + An artery that connects two larger arteries. + ncithesaurus:Communicating_Artery + + + + + UMLS:C1707451 + ncithesaurus:Communicating_Artery - + - - - - - - - - + + + + + + + + + + + + + - - + + - 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 + inferred from artery + EMAPA:18646 + MA:0002227 uberon - UBERON:0004160 - proepicardium + UBERON:0006355 + superior vesical vein - + - - - - - - - todo check other taxa + + true + MA - - - - + + + + + + + + + + + + + + + + + + + - - + + - - ZFA - + + 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 + - + - 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 + A portion of organism substance that secreted_by a zone of skin. + OBOL:automatic - + - proepicardial organ - ZFIN:ZDB-PUB-080218-16 + skin fluid/secretion + MA:0002537 - + - - - - - - - - + + + + + + + + + + + + + - - + + - 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 + A portion of organism substance that is secreted by a female reproductive gland. + MA:0002510 + female reproductive system fluid/secretion uberon - UBERON:0004161 - - septum transversum + female reproductive system fluid + female reproductive system secretion + UBERON:0006537 + female reproductive gland secretion - + - 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 - - + A portion of organism substance that is secreted by a female reproductive gland. + UBERON:cjm - - - 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 + + + 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 + - - - in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum - EHDAA2 + + + A portion of organism substance that secreted_by a respiratory system. + OBOL:automatic - + - UMLS:C0231004 - ncithesaurus:Septum_Transversum + UMLS:C1514899 + ncithesaurus:Respiratory_System_Fluid_or_Secretion + + + + + + + + + + + + + + + + + + + + + + + + + + + A vasculature that is part of a kidney. + EMAPA:28457 + TAO:0005305 + ZFA:0005305 + uberon + UBERON:0006544 + + kidney vasculature + - - - transverse septum - + + + A vasculature that is part of a kidney. + OBOL:automatic - + - - - The external genitalia are the outer sex organs, such as the penis or vulva in mammals - - FMA:45643 - external genitalia + + + + + + + + + + + + + + + + + + + + + A tube in the kidney that collect and transport urine. + in ZFA this is defined as part of mesonephros + TAO:0005289 + ZFA:0005289 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 + UBERON:0006553 + renal duct - + - The external genitalia are the outer sex organs, such as the penis or vulva in mammals - GO:0035261 + 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 - + - + - + - + - - + - + - 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 + A tube that is part of a excretory system. uberon - UBERON:0004177 - - - hemopoietic organ + UBERON:0006555 + excretory tube - + - 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 + A tube that is part of a excretory system. OBOL:automatic + + + + + + + + + + + + + + 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 + - - - lymph organ - MA:0000747 - - - - - lymphoid organ - BTO:0004605 - FMA:7143 + + + The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. + GO:0060465 - + - + - + - - - - - + - - - A portions of the gut that is derived from endoderm. - EMAPA:32930 - endodermal gut - gut endoderm + + + + + + + + Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA]. + FMA:85030 uberon - UBERON:0004185 - endodermal part of digestive tract + UBERON:0006563 + tunica media of pulmonary trunk - + - A portions of the gut that is derived from endoderm. - GO:0061031 - - - - - gut endoderm - EMAPA:32930 + Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA]. + FMA:85030 + FMA:FMA - + - + - + - + - + - + - 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 + + + + + + + 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 - urethral smooth muscle - UBERON:0004219 - urethra smooth muscle layer + distal urethral opening of female + urethral opening of clitoral urethra + UBERON:0006565 + female urethral meatus - + - A portion of smooth muscle tissue that is part of a urethra [Automatically generated definition]. + A urethral meatus that is part of a female urethra[Automatically generated definition]. + OBOL:automatic - - - muscle layer of urethra - FMA:76909 - - - - - muscular coat of urethra - FMA:76909 + + + 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. + - + - muscular layer of urethra - FMA:76909 + external orifice of female urethra + FMA:85266 - + - smooth muscle of urethra - OBOL:automatic + external urethral orifice (female) + FMA:85266 - + - smooth muscle tissue of urethra - OBOL:automatic + female urethral meatus + FMA:85266 - + - tunica muscularis urethrae + ostium urethrae externum (urethra feminina) + FMA:85266 FMA:TA - + - urethra smooth muscle tissue - OBOL:automatic + urethral meatus of clitoral urethra + EMAPA:36453 - + - urethral smooth muscle - MA:0001691 + distal urethral opening of female + EMAPA:36453 + + + + + urethral opening of clitoral urethra + EMAPA:36453 - + - + - + - + - + - + - - - - - - - + + - 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 + 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:0004220 - large intestine smooth muscle + UBERON:0006566 + left ventricle myocardium - - - - - - - - - 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 + A myocardium that is part of a left ventricle of a heart. + - - - non-striated muscle of large intestine - OBOL:automatic + + + Myocardium of ventricle which is continuous with the tunica media of aorta. + FMA:9558 - + - smooth muscle of large intestine - OBOL:automatic + left ventricular myocardium + FMA:9558 - + - smooth muscle tissue of large intestine - OBOL:automatic + myocardium of left ventricle + FMA:9558 - + - + - + - + - + - + - - - - - - - - - - - - - + + - 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 + 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 - intestinal muscularis - intestinal smooth muscle - UBERON:0004221 + UBERON:0006567 - intestine smooth muscle + right ventricle myocardium - - - - - - - - - - - - - - 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 + A myocardium that is part of a right ventricle of a heart. + - - - intestine involuntary muscle - OBOL:automatic + + + Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk. + FMA:9535 - + - intestine non-striated muscle - OBOL:automatic + myocardium of right ventricle + FMA:9535 - + - intestine smooth muscle tissue - OBOL:automatic + right ventricular myocardium + FMA:9535 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - involuntary muscle of bowel - 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:. + - - - involuntary muscle of intestine - OBOL:automatic + + + FMA also has FMA:29321 but it's not clear how this differs + FMA - - - non-striated muscle of bowel - OBOL:automatic + + + UMLS:C0821671 + ncithesaurus:Pectinate_Line - + - non-striated muscle of intestine - OBOL:automatic + linea pectinata canalis analis + FMA:75383 + FMA:TA + - + - smooth muscle of bowel - OBOL:automatic + pectinate line of anal canal + FMA:75383 - - - smooth muscle of intestine - OBOL:automatic + + + Hilton's 'white line' + EMAPA:19159 - - - smooth muscle tissue of bowel - OBOL:automatic + + + dentate line + - - - smooth muscle tissue of intestine - OBOL:automatic + + + linea anocutanea + + - + - intestinal muscularis - EMAPA:35441 + recto-anal junction + - + - intestinal smooth muscle - BTO:0000643 + site of anal membrane + EMAPA:19159 - + - + - + - + - + + - + - 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 + + + + + + + An organ that is part of a vestibular system. + + BIRNLEX:2519 + UMLS:C0682674 + balance organ uberon - airway smooth muscle - airway smooth muscle cell - UBERON:0004225 - respiratory system smooth muscle + UBERON:0006585 + vestibular organ - - - A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition]. - OBOL:automatic - - - - - respiratory smooth muscle - BTO:0001660 + + + + + + + + + NIFSTD - - - smooth muscle of respiratory system + + + An organ that is part of a vestibular system. OBOL:automatic - - - airway smooth muscle - BTO:0001660 + + + UMLS:C0682674 + BIRNLEX:2519 - - - airway smooth muscle cell - BTO:0001660 + + + balance organ + - + - + - + - + + + + + - + - + - 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 + + + + + + + + + + + + + Presumptive structure of the blastula that will develop into endoderm. + AAO:0000471 + EFO:0003437 + TAO:0000416 + ZFA:0000416 uberon - UBERON:0004226 - gastrointestinal system smooth muscle + UBERON:0006595 + + presumptive endoderm - + - 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 + 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 + + + + + + + + + + + - + + + + + - + + - + - - + + - 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 + 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 - pelvic smooth muscle - UBERON:0004227 - - kidney pelvis smooth muscle + UBERON:0006598 + presumptive structure - + - the smooth muscle tissue surrounding the urothelium of the kidney pelvis - MGI:csmith - MP:0011335 - - - - - kidney pelvis smooth muscle - EMAPA:28120 + Portion of embryonic tissue determined by fate mapping to become a structure. + GOC:CVS + GOC:YMB + ZFA:0001116 - + - renal pelvis smooth muscle - EMAPA:28120 + presumptive structures + ZFA:0001116 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Presumptive structure of the blastula that will develop into ectoderm. + AAO:0000470 + EFO:0003466 + TAO:0001376 + XAO:0004132 + ZFA:0001376 + uberon + presumptive epidermis + UBERON:0006601 + + presumptive ectoderm + - - - smooth muscle tissue of renal pelvis - FMA:262022 + + + Presumptive structure of the blastula that will develop into ectoderm. + - + - pelvic smooth muscle - EMAPA:28120 + presumptive epidermis + ZFA:0001376 - + - + - + - + + + + + - + - + - 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 + + + + + + + + + + + + + Presumptive structure of the blastula that will develop into mesoderm. + AAO:0000476 + EFO:0003467 + TAO:0001377 + ZFA:0001377 uberon - smooth muscle layer of bladder - UBERON:0004228 - urinary bladder smooth muscle + UBERON:0006603 + + presumptive mesoderm - + - 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 + Presumptive structure of the blastula that will develop into mesoderm. + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - bladder smooth muscle tissue - OBOL:automatic + + + + FMA - - - involuntary muscle of bladder - OBOL:automatic + + + 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. + - - - involuntary muscle of urinary bladder - OBOL:automatic + + + 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 - - - non-striated muscle of bladder - OBOL:automatic + + + UMLS:C0225358 + ncithesaurus:Muscle_Layer - + - non-striated muscle of urinary bladder + muscular layer OBOL:automatic - + - smooth muscle of bladder - OBOL:automatic + muscularis layer + FMA:45634 - + - smooth muscle of urinary bladder - OBOL:automatic + tunica muscularis + BTO:0004838 + - - - smooth muscle tissue of bladder - OBOL:automatic + + + muscular coat + - - - smooth muscle tissue of urinary bladder - OBOL:automatic + + + muscularis externa + BTO:0004838 - - - urinary bladder involuntary muscle - OBOL:automatic + + + muscularis propria + - - - urinary bladder muscle - MA:0001697 + + + transverse muscular fibers + - - - urinary bladder non-striated muscle - OBOL:automatic + + + tunica externa + BTO:0004838 - - - urinary bladder smooth muscle tissue - OBOL:automatic + + + tunica muscularis + - + - + - + - - + + - + - + - 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 + + + + + + + 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 - UBERON:0004231 - anal region smooth muscle + canalis caroticus + UBERON:0006668 + carotid canal + http://upload.wikimedia.org/wikipedia/commons/4/4c/Gray141.png - + - 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 + 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]. + - - - non-striated muscle of anal part of perineum - OBOL:automatic + + + canalis caroticus + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers. + In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG] + + + + EMAPA:17702 + FMA:58279 + NCIT:C34119 + UMLS:C0230162 + VHOG:0001399 + central tendon + centrum tendineum + centrum tendineum diaphragmatis + uberon + UBERON:0006670 + + central tendon of diaphragm + - - - non-striated muscle of anal region - OBOL:automatic + + + + + + + + + VHOG - - - non-striated muscle of anal triangle - OBOL:automatic + + + + + + + + + definitional - - - smooth muscle of anal part of perineum - OBOL:automatic + + + The three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers. + MGI:csmith + MP:0012061 - - - smooth muscle of anal region - OBOL:automatic + + + In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG] + 2012-09-17 + VHOG:0001399 + VHOG + + - - - smooth muscle of anal triangle - OBOL:automatic + + + UMLS:C0230162 + ncithesaurus:Central_Tendon_of_the_Diaphragm - + - smooth muscle tissue of anal part of perineum - OBOL:automatic + central tendon + FMA:58279 - + - smooth muscle tissue of anal region - OBOL:automatic + centrum tendineum + FMA:58279 - + - smooth muscle tissue of anal triangle - OBOL:automatic + centrum tendineum diaphragmatis + FMA:58279 + FMA:TA + - + - + - + - + - + + - + - 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 + A valve that is part of a vein. + FMA:68095 + valve of vein uberon - UBERON:0004234 - iris smooth muscle + UBERON:0006675 + venous valve - - - - MA - - - + - A portion of smooth muscle tissue that is part of a iris [Automatically generated definition]. - OBOL:automatic - - - - - involuntary muscle of iris + A valve that is part of a vein. OBOL:automatic - - - iridial smooth muscle - - - - + - iris involuntary muscle - 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 + - - - iris non-striated muscle + + + An anatomical boundary that adjacent_to a epithelium. OBOL:automatic - + - iris smooth muscle tissue - OBOL:automatic + epithelium surface + FMA:70997 + + + + + + + + + + + + + + + + + + + + + + + + + A vein that is part of a vertebral column. + + + EMAPA:18255 + FMA:76735 + MA:0002108 + vena spinalis + uberon + spinal branch + UBERON:0006686 + spinal vein + - - - non-striated muscle of iris + + + A vein that is part of a vertebral column. OBOL:automatic - + - smooth muscle of iris - OBOL:automatic + vena spinalis + FMA:76735 + FMA:TA + - - - smooth muscle tissue of iris - OBOL:automatic + + + spinal branch + FMA:76735 - + - + - + - - + + + + + + - - + + - + - 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 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 portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition]. - OBOL:automatic + 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 + - + - + - + - - + + + + + + - + + - + - 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 + + + + + + + + + + + + + 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 - UBERON:0004237 + limbus corneae + UBERON:0006761 + - blood vessel smooth muscle + + 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 - + - smooth muscle found within, and composing the majority of the wall of blood vessels. - + 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 - + - UMLS:C1519956 - ncithesaurus:Vascular_Smooth_Muscle_Tissue + EMAPA:37835 + MA:th - + - blood vessel involuntary muscle - OBOL:automatic + corneal limbus + FMA:58342 - + - blood vessel non-striated muscle - OBOL:automatic + corneal limbus + GAID:896 - + - blood vessel smooth muscle tissue - OBOL:automatic + corneal-scleral limbus + - + - involuntary muscle of blood vessel - OBOL:automatic + corneoscleral junction + GAID:896 - + - non-striated muscle of blood vessel - OBOL:automatic + limbus corneae + + - + - smooth muscle of blood vessel - OBOL:automatic + sclerocorneal junction + FMA:58342 - + - smooth muscle tissue of blood vessel - OBOL:automatic + sclerocorneal limbus + GAID:896 - - - vascular smooth muscle - ZFA:0005321 + + + limbus corneae + + - + - + - + - - + + - - - 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 + + + + + + + + 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 - back bone - bone of back - dorsal region bone - UBERON:0004247 - - bone of dorsum + UBERON:0006799 + glandular epithelium - + - A bone that is part of the dorsal region of an animal. + An epithelium that is composed primarily of secretory cells. - + - EMAPA:37248 - MA:th - - - - - back bone - MA:0000494 + UMLS:C0682578 + ncithesaurus:Glandular_Epithelium - - - bone of back - OBOL:automatic - - - - - dorsal region bone - + + + UMLS:C1708242 + ncithesaurus:Glandular_Epithelial_Tissue - + - - - - - - - - - - - - - + + + - + - - + + - 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 + + + + + + + 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 - UBERON:0004253 - skin muscle + areolar tissue + loose connective tissue + UBERON:0006815 + areolar connective tissue - + + + + FMA + + + + + + + + + + + FMA + + + - Any muscle organ that is part of a skin of body [Automatically generated definition]. - OBOL:automatic + 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 - - - in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only - MA + + + 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 - - - integumental system muscle - MA:0003139 + + + relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] + 2012-06-20 + AAO:0000027 + AAO - - - muscle of integumental system - EMAPA:18187 + + + cushions body organs + AAO - + - muscle organ of skin - OBOL:automatic + loose areolar connective tissue + FMA:63897 - - - skin muscle organ - OBOL:automatic + + + loose connective tissue + AAO:0000027 - + - + - + - - + + - + + - + - A blood vessel that is part of a back [Automatically generated definition]. - EMAPA:37243 - MA:0000493 - blood vessel of back + + + + + + + + + + + + + A subdivision of a the reproductive tract in a female organism that is the site of embryo development. + uterus + FBbt:00004924 + TADS:0000421 + WBbt:0006760 uberon - UBERON:0004258 - back blood vessel + UBERON:0006834 + + uterus or analog - + - A blood vessel that is part of a back [Automatically generated definition]. - OBOL:automatic - - - - - EMAPA:37243 - MA:th + A subdivision of a the reproductive tract in a female organism that is the site of embryo development. + - - - blood vessel of back - OBOL:automatic + + + uterus + FBbt:00004924 + - + - + - + - - + + - + - - + + - A portion of connective tissue that is part of a back [Automatically generated definition]. - EMAPA:37256 - MA:0000495 + A furrow or an incomplete tube. + AEO:0000161 + EHDAA2_RETIRED:0003161 uberon - mesenchyne of back - UBERON:0004267 - back connective tissue + groove + UBERON:0006846 + + surface groove - + - A portion of connective tissue that is part of a back [Automatically generated definition]. - OBOL:automatic - - - - - EMAPA:37256 - MA:th + A furrow or an incomplete tube. + + AEO:0000161 + AEO:JB - + - mesenchyne of back - OBOL:automatic + groove + AEO:0000161 - + - + - + - + - - + + - + - - + + - A muscle that is part of the eye region. - AAO:0000156 - EMAPA:35335 - MA:0000271 - OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycB4rvYA8cJwpEbGdrcN5Y29ycA + 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 - UBERON:0004277 - - eye muscle + ureteral smooth muscle layer + UBERON:0006855 + muscular coat of ureter - + - + - MA + FMA - + - A muscle that is part of the eye region. + 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 + - + - - + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + - - - - - - - + - - 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 + A vasculature that is part of a organ. + FMA:74612 + organ vasculature + set of blood vessels of organ uberon - UBERON:0004288 - - - - skeleton - https://github.com/obophenotype/uberon/wiki/The-skeletal-system + UBERON:0006876 + + vasculature of organ - + - Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. - VSAO:0000026 + A vasculature that is part of a organ. + OBOL:automatic - - - 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 + + + organ vasculature + FMA:74612 + + + + + set of blood vessels of organ + FMA:74612 - + - - - + + + + + + + + + + + + + + - + - 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 + + + + + + + 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 - dermamyotome - dermomyotomes - UBERON:0004290 - dermomyotome + cranial mesoderm + head mesoderm + UBERON:0006904 + + + head mesenchyme from mesoderm - + - - AEO + + ZFA - + - - AEO + + + + + + + EHDAA2 - + - + EHDAA2 - ZFA + XAO - + - 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. - + A head mesenchyme that develops_from a mesoderm. + OBOL:automatic - - - 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) + + + head mesenchyme from head mesoderm + EHDAA2:0001118 - - - UMLS:C1511786 - ncithesaurus:Dermomyotome + + + mesenchyme derived from head mesoderm + EHDAA:1057 - + - dermamyotome - VHOG:0000676 + cranial mesoderm + UBERON:0005280 - + - dermomyotomes - VHOG:0000676 - + head mesoderm + AAO:0011051 + UBERON:0005280 - + - - + + + + + + + + + + + + + + - - + + - 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 + 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:0004291 - heart rudiment + UBERON:0006905 + mandibular process mesenchyme - + - 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 + Mesenchyme that is part of a mandibular prominence. + OBOL:automatic - + - heart cone - GO:0003313 + mesenchyme of mandibular process + EMAPA:17357 - + - rudimentary heart - ZFA:0000115 + mesenchyme of mandibular prominence + - + - - - + + + + + + + + + + + + + + - - - - - - - + - - + + - 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 + 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 - 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 + UBERON:0006909 + lumen of digestive tract - + - Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart. - - GO:0003204 + An anatomical space that surrounded_by a digestive tract. + OBOL:automatic - + - cardiac fibrous skeleton - EMAPA:36645 + digestive tract lumen + - + - heart fibrous skeleton - GO:0003204 + gut cavity + BTO:0000349 - + - skeleton of heart - FMA:9496 + gut lumen + FMA:45677 - - - anulus fibrosus dexter cordis - - + + + lumen of alimentary tract + - - - anulus fibrosus sinister cordis - - + + + lumen of digestive tract + - - - trigona fibrosa - - + + + 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 + - - - trigonum fibrosum dextrum cordis - - + + + An epithelium that is part of a lip. + OBOL:automatic - - - trigonum fibrosum sinistrum cordis - - + + + 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 - + - + - + - - + + - - + - - + + - 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 + 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:0004297 - respiratory system blood vessel smooth muscle + UBERON:0006914 + squamous epithelium - + - A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. - OBOL:automatic + 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 - + - EMAPA:37573 - MA:th - - - - - smooth muscle tissue of blood vessel of respiratory system - OBOL:automatic + UMLS:C0221909 + ncithesaurus:Squamous_Epithelium - + - - - - - - - - - + + + + + + + + + + + + + + - - + + - 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 + 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:0004341 - + UBERON:0006915 - primitive streak - http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png + stratified squamous epithelium - - - - 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 + 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:C0033153 - ncithesaurus:Primitive_Streak + UMLS:C0836131 + ncithesaurus:Stratified_Squamous_Epithelium - + - primitive streak - blastopore - germ ring - VHOG:0001202 + epithelium stratificatum squamosum + FMA:45563 - + - - - - - - - - - - - - - - + + + + + + + + + + + + + + - - + + - 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 + 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 - gemmae membrorum - UBERON:0004347 + esophageal squamous epithelium + squamous epithelium of esophagus + squamous oesophageal epithelium + UBERON:0006920 - developmentally_induced_by Fgf10, capable of initiating limb forming interactions between endoderm and mesoderm - limb bud + esophagus squamous epithelium - - - - - - - - - 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 + A squamous epithelium that is part of a esophagus. + OBOL:automatic - - - Early outgrowth of presumptive limb.[AAO] - 2012-06-20 - AAO:0010375 - AAO - AAO:EJS + + + 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:C0282505 - ncithesaurus:Limb_Bud + UMLS:C1707950 + ncithesaurus:Esophageal_Squamous_Epithelium - - - limb buds - + + + esophageal squamous epithelium + OBOL:automatic - - - limbbud - GO:0060174 + + + squamous epithelium of esophagus + OBOL:automatic - + - gemmae membrorum - - + squamous oesophageal epithelium + MA:0001567 - + - - + + + + + + + + + + + + + + - - + + - The embryonic structure that gives rise to the corneal ectoderm - EHDAA:938 - EMAPA:16322 - RETIRED_EHDAA2:0001308 - VHOG:0001296 + A squamous epithelium that is part of a stomach. + EMAPA:35824 + MA:0001611 uberon - UBERON:0004348 + UBERON:0006921 - optic eminence + stomach squamous epithelium - + - The embryonic structure that gives rise to the corneal ectoderm - MP:0006305 + A squamous epithelium that is part of a stomach. + OBOL:automatic - + - - + + + + + + + + + + + + + + - + - + - - + + - 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 + 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 - AER - crista ectodermalis apicalis - UBERON:0004356 + gastric gland epithelium + UBERON:0006924 - apical ectodermal ridge - http://upload.wikimedia.org/wikipedia/commons/5/56/Limbbuddiagram.jpg + stomach glandular epithelium - - - 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 + + + + FMA - - - apical epidermal ridge - XAO:0004121 + + + A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands. + ISBN:0073040584 - - - AER - MP:0001676 + + + epithelium of gastric gland + FMA:63458 - + - crista ectodermalis apicalis - - + gastric gland epithelium + FMA:63458 - + - - - - - - - - - - - - - - - + + + + + + + + + + + + + + - - + + - 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 + 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: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 + UBERON:0006929 + glandular columnar epithelium - + - 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 + Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA]. + FMA:64800 - - - paired limb/fin bud - VHOG:0001258 + + + UMLS:C0225337 + ncithesaurus:Columnar_Epithelium - + - - - 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 + + + + + + + + + + + + + + + + + + + + + FMA:66809 uberon - 1st arch - 1st visceral arch - arcus pharyngeus primus - UBERON:0004362 - - - - pharyngeal arch 1 - http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png + UBERON:0006930 + glandular cuboidal epithelium - - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + 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. + - - - arcus pharyngeus primus - - + + + stomach glandular region glandular mucous membrane + EMAPA:27167 - + - + - - - - - + - - + + - - + + - + - - + + - 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 + 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 - Reichert's membrane - anterior limiting membrane - UBERON:0004370 - - - anterior limiting lamina of cornea + neuroepithelium + UBERON:0006934 + sensory epithelium - + - 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 + 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 - - - 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 + + + note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical + FMA - - - UMLS:C0229127 - ncithesaurus:Bowman_s_Membrane + + + neuroepithelium + BTO:0000314 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - Bowman's anterior elastic lamina - FMA:58273 + + + + + + + + + FMA - - - Bowman's layer - FMA:58273 + + + 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. + - - - Bowman's membrane - FMA:58273 + + + UMLS:C0737271 + ncithesaurus:Stroma_of_the_Ovarian_Cortex - + - anterior elastic lamina - ZFA:0001684 + interstitial tissue of ovary + FMA:18626 - + - anterior limiting lamina - MA:0001240 + ovarian stroma + FMA:18626 - + - anterior limiting lamina of cornea - FMA:58273 + ovary stroma + MA:0002991 - + - lamina limitans anterior (cornea) - FMA:58273 + stroma of the ovary + - + - lamina limitans anterior corneae - FMA:58273 - FMA:TA - - - - - - Reichert's membrane - - + stroma ovarica + FMA:18626 - + - anterior limiting membrane - ZFA:0001684 + stroma ovarii + + - + - - - - - - - - - - - - - - + + + - + - A bone that is part of an appendage [Automatically generated definition]. - appendage bone - bone of appendage - bone of free segment of appendicular skeleton + + + + + + + + + + + + + + + + + + + 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:0004375 - - bone of free limb or fin + UBERON:0006965 + + vascular cord - + - A bone that is part of an appendage [Automatically generated definition]. - OBOL:automatic + 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 - + - + - + - - + + - - + + - - + + - 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 + + + + + + + A capillary that is part of the coronary system. + ZFA:0005813 + heart capillary uberon - UBERON:0004381 - skeleton of limb + UBERON:0006966 + coronary capillary - + + + + + + + + + ZFA + + + - The collection of all skeletal elements in an individual limb. - + A capillary that is part of the coronary system. + - - - 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 + + + 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 + - - - EHDAA2 considers hip and shoulder joints part of limb skeleton. - EHDAA2 + + + + via morphological boundary in CARO - - - free limb skeleton - VSAO:0000300 + + + 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 - - - limb skeleton - EHDAA2:0002221 + + + UMLS:C1515977 + ncithesaurus:Anatomic_Surface - + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - + - - + + - An embryo at the neurula stage. - UBERON:0007013 - - BILA:0000061 - BTO:0001766 - NCIT:C34229 - UMLS:C1518306 - neurula + 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 - UBERON:0004455 - neurula embryo + cardiac mesoderm + cardiogenic mesoderm + cardiogenic region + heart primordia + UBERON:0007005 + + + cardiogenic splanchnic mesoderm - + - An embryo at the neurula stage. - + 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 - - - UMLS:C1518306 - ncithesaurus:Neurula + + + cardiogenic splanchnopleure + EHDAA2:0000214 - - - neurula - BTO:0001766 + + + cardiac mesoderm + XAO:0000235 + + + + + cardiogenic mesoderm + + + + + + cardiogenic region + + + + + + heart primordia + XAO:0000235 - + - - - - - - + + + + + - - + + - + + + + + + + + + + + + - - + + - 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 + Organism at the cleavage stage. + BILA:0000058 uberon - UBERON:0004456 - - entire sense organ system + UBERON:0007010 + cleaving embryo - + - Sum of all sensory systems in an organism. - - - - - - sense organ system - FMA:78499 + Organism at the cleavage stage. + OBOL:automatic - + - + - - - - - + - - + + - + - - + + - - + + - - + + - - + + - 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 + 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 - 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 + embryonic digestive tube + primordial digestive tube + primordial gut + UBERON:0007026 + presumptive gut - - - 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 - + + + 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 - - - set of muscles of head - FMA:71287 + + + UMLS:C1514442 + ncithesaurus:Primordial_Gut - + - + - + - - + + - + + + + + + + + BILA:0000142 + uberon + UBERON:0007037 + mechanosensory system + + + + + + + + - + - 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 + Cranial neural crest that migrates into the mandibular arch. + TAO:0007064 + XAO:0000024 + ZFA:0007064 uberon - body wall muscles - UBERON:0004462 - musculature of body wall + UBERON:0007098 + mandibular neural crest - - - Any collection of muscles that is part of a body wall [Automatically generated definition]. - OBOL:automatic + + + + ZFA - - - EMAPA:37853 - MA:th + + + + + + + + + ZFA - - - body wall musculature - FMA:86931 + + + Cranial neural crest that migrates into the mandibular arch. + ZFA:0007064 - + - + - + - - + + - + - - + + - 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 + + + + + + + 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 - UBERON:0004464 - - musculature of thorax + adult heart + UBERON:0007100 + + Gene notes: Bmp, Nkx, Gata + primary circulatory organ - - - 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 + + + + + + + + + GO uses blood circulation generically to include the haemolymphatic fluid of arthropods - - - muscles of thorax - FMA:71293 + + + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. + GO:0007507 - - - musculi thoracis - FMA:71293 - FMA:TA - + + + dorsal tube + - - - set of muscles of thorax - FMA:71293 + + + heart + GO:0007507 - - - thoracic musculature - FMA:71293 + + + adult heart + FBbt:00003154 - + - + - + - + - + + - + - 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 + Ganglion which is located in the trunk. + EFO:0000901 + MAT:0000344 + MIAA:0000344 + TAO:0001573 + ZFA:0001573 + body ganglion + trunk ganglia uberon - UBERON:0004465 - - musculature of neck + UBERON:0007134 + + trunk ganglion - + - 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 + Ganglion which is located in the trunk. + ZFIN:curator - + - muscles of neck - FMA:71290 + body ganglion + MAT:0000344 - + - musculi cervicis - FMA:71290 - FMA:TA - + 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 + - - - musculi colli - FMA:71290 - FMA:TA - + + + 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 - - - neck musculature - FMA:71290 + + + 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 - - - set of muscles of neck - FMA:71290 + + + presumptive central nervous system + ZFA:0000131 - + - - - - - - - - - - - - - + + + - + - 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 + + + + + + + + + + + + + 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 - UBERON:0004469 - musculature of back + embryonic tail + UBERON:0007144 + embryonic post-anal tail - + - Any collection of muscles that is part of a back [Automatically generated definition]. - OBOL:automatic - - - - - muscle group of back - FMA:71291 + An embryonic structure that will either develop into a post-anal tail or recede into a vestigial remnant of the tail. + - + - muscles of back - FMA:71291 + embryo tail + FMA:85540 - + - musculi dorsi - FMA:71291 - FMA:TA - + tail of embryo + FMA:85540 - - - set of muscles of back - FMA:71291 + + + embryonic tail + FMA:85540 - + - + - + - - + + - - + + - + - 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 + + + + + + + An anatomical cavity that surrounded_by a midgut. + EMAPA:18377 + FMA:54366 + midgut lumen uberon - muscular system of pelvis - set of muscles of pelvis - UBERON:0004470 - - musculature of pelvic girdle + UBERON:0007147 + lumen of midgut - + - Any collection of muscles that is part of a pelvic girdle [Automatically generated definition]. + An anatomical cavity that surrounded_by a midgut. 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 + midgut lumen + FMA:54366 - + - + - + - - + + - + + - + - 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 + + + + + + + An anatomical cavity that surrounded_by a hindgut. + EMAPA:18396 + FMA:54367 + hindgut lumen uberon - UBERON:0004471 - - musculature of pectoral girdle + UBERON:0007148 + lumen of hindgut - + - 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 + An anatomical cavity that surrounded_by a hindgut. + OBOL:automatic - + - set of muscles of pectoral girdle - FMA:33519 + hindgut lumen + FMA:54367 - + - + - + - - + + - + + - + - 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 + + + + + + + An anatomical cavity that surrounded_by a anal canal. + EMAPA:18836 + FMA:17357 + anal canal lumen uberon - set of facial muscles - set of muscles of face - UBERON:0004473 - - musculature of face + UBERON:0007158 + lumen of anal canal - + - Any collection of muscles that is part of a face. + An anatomical cavity that surrounded_by a anal canal. 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 + anal canal lumen + FMA:17357 - + - + - + - - + + - + + - + - 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 + + + + + + + An anatomical cavity that surrounded_by a colon. + + EMAPA:18945 + FMA:18374 + colon lumen uberon - muscular system of trunk - UBERON:0004479 - - - musculature of trunk + colonic lumen + UBERON:0007159 + lumen of colon - + - Any collection of muscles that is part of a trunk [Automatically generated definition]. + An anatomical cavity that surrounded_by a colon. OBOL:automatic - - - muscle group of trunk - FMA:50187 - - - + - set of muscles of trunk - FMA:50187 + colon lumen + FMA:18374 - + - muscular system of trunk - FMA:50187 + colonic lumen + FMA:18374 - + - + - + - + - + - + - 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 + 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:0004480 - - musculature of limb + UBERON:0007177 + lamina propria of mucosa of colon - + - Any collection of muscles that is part of a limb [Automatically generated definition]. + A lamina propria that is part of a colonic mucosa. OBOL:automatic - + - limb muscle system - EHDAA2:0000995 + colonic lamina propria + FMA:15657 - + - limb musculature - FMA:50188 + lamina propria mucosae of colon + FMA:15657 - + - muscle group of limb - FMA:50188 + lamina propria of colonic mucosa + FMA:15657 - + - set of muscles of limb - FMA:50188 + lamina propria of colonic mucous membrane + FMA:15657 - + - + - + - + - - + - + - 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 + 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:0004481 - - musculature of upper limb + UBERON:0007188 + mesothelium of serous pericardium - + - Any collection of muscles that is part of a forelimb [Automatically generated definition]. + A mesothelium that is part of a serous pericardium. OBOL:automatic - - - free upper limb musculature - FMA:50396 - - - + - muscle group of free upper limb - FMA:50396 + mesothelium of pericardium + FMA:18149 - + - musculature of free upper limb - FMA:50396 + pericardial mesothelium + FMA:18149 - + - set of muscles of free upper limb - FMA:50396 + serous pericardium mesothelium + FMA:18149 - + - + - + - + - - + + - + - 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 + + + + + + + + + + + + + + + + + + + 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:0004482 - - musculature of lower limb + UBERON:0007195 + stroma of bone marrow - + - Any collection of muscles that is part of a hindlimb [Automatically generated definition]. - OBOL:automatic + 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. + - + - free lower limb musculature - FMA:50399 + bone marrow stroma + FMA:21426 + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - muscle group of free lower limb - FMA:50399 + + + + ZFA - - - musculature of free lower limb - FMA:50399 + + + Mesenchyme that develops_from a cranial neural crest. + OBOL:automatic - + - set of muscles of free lower limb - FMA:50399 + head mesenchyme from neural crest + EHDAA2:0000735 - + - + - + - - + + - + + - - + + - 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 + 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 - atrial myocardium - UBERON:0004490 - cardiac muscle tissue of atrium + UBERON:0007214 + + mesenchyme derived from trunk neural crest - + - A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition]. + Mesenchyme that develops_from a trunk neural crest. OBOL:automatic - - - in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging. - GO + + + trunk mesenchyme from neural crest + EHDAA2:0002093 + + + + + + + + + + + + + + + + + + + + + + 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 - - - atrial cardiac muscle tissue - GO:0055009 + + + 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) - + - atrial heart muscle - GO:0055009 + ventral pharyngeal arch 1 + VHOG:0000510 - - - cardiac atrium muscle - GO:0055009 + + + ventral mandibular arch + VHOG:0000510 - + - atrial myocardium - GO:0055009 - GOC:mtg_heart + ventral visceral arch 1 + VHOG:0000510 - + - + - + - + - + - + - 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 + + + + + + + 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:0004492 - cardiac muscle tissue of cardiac septum + UBERON:0007239 + tunica media of artery - + - A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition]. + A tunica media that is part of a artery. OBOL:automatic - - - cardiac septum cardiac muscle tissue - - - - - - cardiac septum heart muscle - + + + UMLS:C1710627 + ncithesaurus:Venous_System_Smooth_Muscle_Tissue - + - cardiac septum muscle - + arterial media + EV:0100029 - + - cardiac septum myocardium - + tunica media (arteriae) + FMA:14273 - + - + - + - + - + - + - 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 + + + + + + + + + + + + + A tunica adventitia that is part of a artery. + + EMAPA:36295 + EV:0100030 + FMA:14274 + arterial adventitia + tunica externa (adventitia)(arteriae) uberon - UBERON:0004493 - - cardiac muscle tissue of myocardium + UBERON:0007240 + tunica adventitia of artery - + - - + + - MA + FMA - + - A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]. + A tunica adventitia that is part of a artery. OBOL:automatic + + + + arterial adventitia + EV:0100030 + + + + + tunica externa (adventitia)(arteriae) + FMA:14274 + - + - + - + - + - - + - + - A vasculature that is part of a muscle organ [Automatically generated definition]. - FMA:87123 - muscular organ vasculature + A tunica adventitia that is part of a vein. + + EMAPA:36310 + EV:0100034 + FMA:14355 + tunica externa (adventitia)(venae) + venous adventitia uberon - UBERON:0004521 - vasculature of muscle organ + UBERON:0007241 + tunica adventitia of vein - + - A vasculature that is part of a muscle organ [Automatically generated definition]. + A tunica adventitia that is part of a vein. OBOL:automatic - + - muscular organ vasculature - FMA:87123 + tunica externa (adventitia)(venae) + FMA:14355 + + + + + venous adventitia + EV:0100034 - + - + - + - + - + + - + - A vasculature that is part of a musculoskeletal system [Automatically generated definition]. - FMA:239607 + A tunica intima that is part of a vein. + + EMAPA:36308 + EV:0100032 + FMA:14353 + tunica interna (intima)(venae) + venous intima uberon - UBERON:0004522 - vasculature of musculoskeletal system + UBERON:0007242 + tunica intima of vein - + - A vasculature that is part of a musculoskeletal system [Automatically generated definition]. + A tunica intima that is part of a vein. OBOL:automatic + + + + tunica interna (intima)(venae) + FMA:14353 + + + + + venous intima + EV:0100032 + - + - + - + - - - - - - - - - + - + - - - - - - - - - - - - - + - 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 + A tunica media that is part of a vein. + + EMAPA:36309 + EV:0100033 + FMA:14354 + tunica media (venae) + venous media uberon - CV system - Herz und Gefaesssystem - UBERON:0004535 - - - - - cardiovascular system + UBERON:0007243 + tunica media of vein - + - 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 + A tunica media that is part of a vein. + OBOL:automatic - - - CV system - BTO:0000088 + + + tunica media (venae) + FMA:14354 - - - Herz und Gefaesssystem - BTO:0000088 + + + venous media + EV:0100033 - + - + - + - + - + - - - - 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 - - - - - - - - - - - - + - 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 + Gray matter of the central nervous system which is a collection of clustered nuclei. + FMA:256381 + FMA:84059 uberon - UBERON:0004572 - - arterial system + cluster of neural nuclei + neural nuclei + nuclear complex + UBERON:0007245 + nuclear complex of neuraxis - - - - 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) + Gray matter of the central nervous system which is a collection of clustered nuclei. + - + - - + + + + + + + + + + + + + + - + - 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 + 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:0004581 - systemic venous system + UBERON:0007247 + + + nucleus of superior olivary complex - + - 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) + 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. + - + - systemic venous circulatory system - FMA:45626 + superior olivary complex nucleus + FMA:72246 - + - - + + + + + + + + + + + + + + - - + + - 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 + 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:0004582 - venous system + UBERON:0007269 + + pectoral appendage musculature - - - - 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. - + Any collection of muscles that is part of a pectoral appendage. + OBOL:automatic - - - 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) + + + pectoral fin muscle + ZFA:0000563 - - - UMLS:C1267406 - ncithesaurus:Venous_System + + + pectoral fin musculature + ZFA:0000563 + - + - + - + - + - + + - + - 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 + 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:0004638 - - - blood vessel endothelium + UBERON:0007270 + pelvic appendage musculature - + - An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart - + Any collection of muscles that is part of a pelvic appendage. + OBOL:automatic - - - UMLS:C1706972 - ncithesaurus:Blood_Vessel_Endothelium + + + Musculature that is part of the pelvic fin.[TAO] + 2012-08-14 + TAO:0000258 + TAO + TAO:curator + + + + + pelvic fin musculature + ZFA:0000258 + - + - - - 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 + + + + + + + + + + + + + + + + + + + + Any collection of muscles that is part of an appendage. + currently defined by location rather than attachment + TAO:0000207 + ZFA:0000207 + fin musculature uberon - truncus costocervicalis - UBERON:0004688 - costo-cervical trunk - http://upload.wikimedia.org/wikipedia/commons/b/b3/Costocervical_trunk_with_branches.png + UBERON:0007271 + appendage musculature - + - 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 + Any collection of muscles that is part of an appendage. + OBOL:automatic - - - truncus costocervicalis - - + + + fin musculature + ZFA:0000207 + - + - + - + - - + + - + - + - A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]. - EMAPA:36503 - MA:0000704 + + + + + + + + + + + + + Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle. + VSAO:0005000 uberon - UBERON:0004695 - arterial system smooth muscle + cheiropterygium + UBERON:0007272 + pectoral appendage skeleton - + + + + + + + + + VSAO + + + - A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]. - OBOL:automatic + Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle. + VSAO:0005000 + VSAO:NI + + + + + cheiropterygium + VSAO:0005000 + VSAO:NI - + - + - + - - + + - + - + - A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]. - EMAPA:36613 - MA:0000715 + + + + + + + + + + + + + The collection of all skeletal elements in a pelvic appendage region. uberon - UBERON:0004696 - venous system smooth muscle + UBERON:0007273 + pelvic appendage skeleton - + + + + + + + + + VSAO + + + - A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]. - OBOL:automatic + The collection of all skeletal elements in a pelvic appendage region. + - + - + - + - - + + - + - + - An endothelium that is part of a vena cava [Automatically generated definition]. - - EMAPA:37800 - MA:0000713 - NCIT:C49318 - UMLS:C1710623 + + + + + + + + + + + + + + + + + + + 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 - UBERON:0004698 - vena cava endothelium + embryonic rhombencephalon + future hindbrain + rhombencephalon + UBERON:0007277 + + presumptive hindbrain - + + + + + + + + + XAO-abduced + + + + + + + + + + + cjm + + + - An endothelium that is part of a vena cava [Automatically generated definition]. - OBOL:automatic + 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. + - - - EMAPA:37800 - MA:th + + + 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 - - - UMLS:C1710623 - ncithesaurus:Vena_Cava_Endothelium + + + presumptive rhombencephalon + ZFA:0000569 + + + + + embryonic rhombencephalon + CALOHA:TS-2118 + + + + + future hindbrain + + + + + + rhombencephalon + EHDAA2:0001630 - + - + - + - - + + - + - + - An endothelium that is part of an arterial system [Automatically generated definition]. - - EMAPA:35145 - MA:0000703 - NCIT:C49329 - UMLS:C1706849 + + + + + + + Portion of tissue that is part of the heart tube and will become the sinus venosus. + TAO:0002234 + ZFA:0001722 uberon - UBERON:0004700 - arterial system endothelium + UBERON:0007278 + presumptive sinus venosus - - - An endothelium that is part of an arterial system [Automatically generated definition]. - OBOL:automatic + + + + + + + + + ZFA - - - UMLS:C1706849 - ncithesaurus:Arterial_System_Endothelium + + + Portion of tissue that is part of the heart tube and will become the sinus venosus. + ZFA:0001722 - + - + - + - - + + - + - + - An endothelium that is part of a venous system [Automatically generated definition]. - - EMAPA:35907 - MA:0000714 - NCIT:C49320 - UMLS:C1710626 + + + + + + + + + + + + + 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:0004701 - venous system endothelium + UBERON:0007280 + presumptive endocardium - + - An endothelium that is part of a venous system [Automatically generated definition]. + A presumptive structure that has the potential to develop into a endocardium. OBOL:automatic - - - UMLS:C1710626 - ncithesaurus:Venous_System_Endothelium + + + Portion of tissue that is part of the heart tube and will become the endocardium.[TAO] + 2012-08-14 + TAO:0002233 + TAO + ZFIN:curator - + - + - + - - + + - - + - + - A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]. - EMAPA:35732 - MA:0001805 + + + + + + + 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:0004702 - respiratory system blood vessel endothelium + UBERON:0007281 + + presumptive midbrain hindbrain boundary - + + + + + + + + + ZFA + + + - A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]. - OBOL:automatic + Embryonic structure that gives rise to the midbrain hindbrain boundary. + ZFA:0001187 + + + + + presumptive MHB + + + + + + presumptive midbrain-hindbrain boundary + ZFA:0001187 - + - + - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - + - - + + - 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 + A presumptive structure that has the potential to develop into a presomitic mesoderm. + EFO:0003421 + TAO:0000053 + ZFA:0000053 uberon - UBERON:0004708 - - paired limb/fin + presumptive segmental plates + UBERON:0007282 + + presumptive segmental plate - - - - VSAO - - - - - - - - - - - VSAO - - - + - + - definitional + https://github.com/obophenotype/uberon/wiki/The-neural-crest + EDHAA2 - + - 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 - + A presumptive structure that has the potential to develop into a presomitic mesoderm. + OBOL:automatic - - - paired appendage - VSAO:0000067 + + + presumptive segmental plates + ZFA:0000053 + - + - + - + - - + + - + - - - - - - - + - + - - + + - - 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 + 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:0004709 - - pelvic appendage + UBERON:0007284 + + presumptive neural plate - - - - - - - - - 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 - + A presumptive structure that has the potential to develop into a neural plate. + OBOL:automatic - - - pelvic appendage - VSAO:0000126 + + + Region of the gastrula which gives rise to the neural plate.[TAO] + 2012-08-14 + TAO:0000063 + TAO + ZFIN:curator - + - pelvic limb/fin - + prospective neuroectoderm + ZFA:0000063 - + - posterior paired appendage - VSAO:0000126 + prospective vegetal ectoderm + ZFA:0000063 - + - + - + - + + + + + - + - - - - - - - - - - - - - + - - + + - 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 + 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:0004710 - - pectoral appendage + UBERON:0007285 + + presumptive paraxial mesoderm - - + + - - - - + + + + + + + + + + + + + - 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 + The part of the blastula that has the potential to develop into a paraxial mesoderm. + + UBERON:cjm - + - forelimb or pectoral fin - + future paraxial mesenchyme + UBERON:cjm + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - forelimb/pectoral fin - + + + A presumptive structure that has the potential to develop into a pronephric mesoderm. + OBOL:automatic - + - pectoral limb/fin - + nephron primordium + ZFA:0001070 - + - - - + + + + + + + + + + + + + - - + + - 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 + A blood vessel that is part of a pectoral appendage. + TAO:0005301 + ZFA:0005301 + pectoral fin blood vessel uberon - jugular - vena jugularis - UBERON:0004711 - jugular vein - http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray558.png + UBERON:0007300 + pectoral appendage blood vessel - + - 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 + A blood vessel that is part of a pectoral appendage. + OBOL:automatic - - - vena jugularis - BTO:0001744 + + + pectoral fin blood vessel + ZFA:0005301 + - + - - - - - - - - - - - - - - + + + + + + + + + + + + + - - + + - - + + - 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 + A blood vessel that is part of a limb/fin. + TAO:0005299 + ZFA:0005299 + fin blood vessel + limb blood vessel uberon - UBERON:0004716 - conceptus + UBERON:0007301 + appendage blood vessel - + - 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 + A blood vessel that is part of a limb/fin. + OBOL:automatic - - - UMLS:C1516779 - ncithesaurus:Conceptus + + + fin blood vessel + ZFA:0005299 + + + + + + limb blood vessel + - + - + - + - + - - + + - + - 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 + A vasculature that is part of a pectoral appendage. + TAO:0005096 + ZFA:0005096 + pectoral fin vasculature uberon - neural metamere - neural segment - UBERON:0004731 - - neuromere + UBERON:0007302 + pectoral appendage vasculature - + - 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 - + A vasculature that is part of a pectoral appendage. + OBOL:automatic - - - neuromeres - TAO:0001328 - + + + pectoral fin vasculature + ZFA:0005096 + - + - + - + - + - + + - + - 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 + A vasculature that is part of a chordate pharynx. + TAO:0005003 + ZFA:0005003 + branchial vasculature uberon - neuromere - UBERON:0004732 - - segmental subdivision of nervous system + UBERON:0007303 + pharyngeal vasculature - + - Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres. - - FBbt:00005140 + A vasculature that is part of a chordate pharynx. + OBOL:automatic - - - neuromere - FBbt:00005140 + + + branchial vasculature + ZFA:0005003 - + - + - + - + - - - + - + - An organ subunit that is part of a hindbrain [Automatically generated definition]. - FMA:61998 - hindbrain segment - segment of hindbrain + A vasculature that is part of a limb/fin. + TAO:0005095 + ZFA:0005095 + fin vasculature uberon - UBERON:0004733 - - segmental subdivision of hindbrain + UBERON:0007304 + appendage vasculature - + - An organ subunit that is part of a hindbrain [Automatically generated definition]. + A vasculature that is part of a limb/fin. OBOL:automatic - - - hindbrain segment - FMA:61998 - - - - - segment of hindbrain - FMA:61998 + + + fin vasculature + ZFA:0005095 + - + - + - + - - + + + + + + - + + - - + + - - + + - 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 + + + + + + + + + + + + + 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 - blastocystis trilaminaris - tri-laminar disc - tri-laminar disk - trilaminar blastocyst - trilaminar blastoderm - trilaminar disc - trilaminar disk - trilaminar germ - UBERON:0004734 - - gastrula + hypoderm + hypodermis + UBERON:0007376 + + outer epithelium - - - Organism at the gastrula stage. - - - - - - - We explicitly merge the NCITA terms here - NCIT - - - - - UMLS:C0017199 - ncithesaurus:Gastrula + + + + + + + + + - - - UMLS:C1284022 - ncithesaurus:Trilaminar_Embryonic_Disc + + + 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 - + - gastrula embryo - BILA:0000060 - - - - - blastocystis trilaminaris - - - - - - tri-laminar disc - - - - - - tri-laminar disk - - - - - - trilaminar blastocyst - - - - - - trilaminar blastoderm - - - - - - trilaminar disc - + epidermis + GO:0008544 - + - trilaminar disk - + hypoderm + BTO:0000313 + - + - trilaminar germ - + hypodermis + GO:0008544 + WBbt:0005733 + - + - - + + + + - + - 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 + + + + + + + + + + + + + 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: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 + UBERON:0007383 + + enveloping layer of ectoderm - - - - 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 + Outermost layer of cells surrounding the embryo. + - + - 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] + 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 - 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 + TAO:0000086 + TAO + ZFIN:curator - - - EMAPA:37744 - MA:th + + + 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 - + - + - - - - - + - - + + - - - + - - + + - - + + - dermis-derived entity that is made of skeletal tissue. - dermal element + 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:0004756 - dermal skeletal element + UBERON:0007389 + + paired limb/fin cartilage - + - dermis-derived entity that is made of skeletal tissue. + A cartilage tissue that is part of a paired limb or fin. - - - - dermal element - VSAO:curator + + + Cartilage which is part of one of the paired fins.[TAO] + 2012-08-14 + TAO:0001543 + TAO + ZFIN: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 + + + + + + + + + + + + + A cartilage tissue that is part of a pectoral appendage. + Cartilage which is part of the pectoral fin.[TAO] + TAO:0000257 + ZFA:0000257 uberon - anal gland - anal sac - gland of anus - rectal gland - UBERON:0004760 - - gland of anal canal + pectoral fin cartilage + UBERON:0007390 + pectoral appendage cartilage tissue - + - A gland that is part of an anal canal [Automatically generated definition]. - + A cartilage tissue that is part of a pectoral appendage. OBOL:automatic - - - UMLS:C0162322 - ncithesaurus:Anal_Gland - - - - - gland of anal canal - OBOL:automatic + + + Cartilage which is part of the pectoral fin.[TAO] + 2012-08-14 + TAO:0000257 + TAO + ZFIN:curator - + - anal sac - - + pectoral fin cartilage + TAO:0000257 - + - - + + + + + + + + + + + + + + - - + + - - + + - 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 - + + 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 + - + - 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 + A cartilage tissue that is part of a pelvic appendage. + OBOL:automatic - - - chondocranium - + + + Cartilage which is part of the pelvic fin.[TAO] + 2012-08-14 + TAO:0001459 + TAO + ZFIN:curator - + - neurocranium - + pelvic fin cartilage + TAO:0001459 - + - - + + + + + + + + + + + + + + + + + + - - + + + + + + + - 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 + 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:0004765 - - - skeletal element + UBERON:0007414 + nucleus of midbrain tegmentum - - - - - - - - - VSAO - - - + - Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. - + A nucleus of brain that spans a midbrain tegmentum. + OBOL:automatic - - - 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 + + + tegmental nuclei + - - - 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 + + + tegmental nucleus + ZFA:0005577 - + - + - + - - + + - + - + - A bone that is part of a cranium. - here cranium = skull - mandible - - cranium bone + + + + + + + + + + + + + The space within an epithelial sphere. + EHDAA2:0003079 + AEO:0000079 + cavity of vesicle uberon - UBERON:0004766 - cranial bone + UBERON:0007473 + lumen of epithelial sac - + - A bone that is part of a cranium. - UBERON:automatic + The space within an epithelial sphere. + AEO:JB - + - cranium bone - UBERON:automatic + cavity of vesicle + AEO:0000079 - + - + - + - - + + - + - - + + - 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 + A tissue whose predominant feature is extracellular matrix which may or may not be highly hydrated or calcified. + EHDAA2:0003081 + AEO:0000081 + EHDAA2:0003081 uberon - UBERON:0004768 - - bone of lower jaw + UBERON:0007475 + matrix-based tissue - + - Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular - + A tissue whose predominant feature is extracellular matrix which may or may not be highly hydrated or calcified. + AEO:JB - + - + - + - - + + - - - - - - - + + - - + + + 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 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 + + + + + + + + + - - + + - 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 + Mesenchyme with little extracellular matrix. + EHDAA2:0003146 + AEO:0000146 + EHDAA2:0003146 uberon - set of all joints - set of joints of body - UBERON:0004770 - articular system + UBERON:0007524 + dense mesenchyme tissue - + + + + AEO + + + - - + + - FMA + AEO - + - 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 + Mesenchyme with little extracellular matrix. + AEO:JB - + - + - + - - + + - + - - + + - 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 + Mesenchymal cells that are migrating. + this class will be an important part of the NC reorganization + EHDAA2:0003152 + AEO:0000152 + EHDAA2:0003152 uberon - UBERON:0004777 - respiratory system submucosa + UBERON:0007530 + migrating mesenchyme population - + - 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 + Mesenchymal cells that are migrating. + AEO:JB - + - + - + - - + + - - - - - - - + + - - + + - 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 + 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:0004779 - respiratory system lamina propria + UBERON:0007592 + ciliated columnar epithelium - + - - - - - - - true - + + FMA - + - 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 + Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]. + FMA:64798 - + - + - + - - + + - + - - + + - A lamina propria that is part of a gastrointestinal system. - - MA:0001899 - NCIT:C49299 - UMLS:C1708197 + Epithelium bearing vibratile cilia on the free surface. uberon - UBERON:0004780 - gastrointestinal system lamina propria + UBERON:0007601 + ciliated epithelium - - - - - - - - - true - - - - + - A lamina propria that is part of a gastrointestinal system. - OBOL:automatic - - - - - UMLS:C1708197 - ncithesaurus:Gastrointestinal_Tract_Lamina_Propria + Epithelium bearing vibratile cilia on the free surface. + - + - + - - + + @@ -56630,6223 +130595,6729 @@ - - + + - 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 + + + + + + + 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 - UBERON:0004782 - gastrointestinal system serosa + synovial tissue + UBERON:0007616 + layer of synovial tissue - - - A serous membrane that is part of a digestive system [Automatically generated definition]. - OBOL:automatic - - - - - EMAPA:37592 - MA:th - - - - - digestive system serosa - OBOL:automatic + + + + + + + + + BTO - - - digestive system serous membrane - OBOL:automatic + + + 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 - + - gastrointestinal system serous membrane - OBOL:automatic + synovium + CALOHA:TS-0998 - - - serosa of digestive system - OBOL:automatic + + + stratum synoviale + FMA:TA - - - serosa of gastrointestinal system - OBOL:automatic + + + synovial layer + FMA:66762 - - - serous membrane of digestive system - OBOL:automatic + + + synovial membrane + FMA:66762 - - - serous membrane of gastrointestinal system - OBOL:automatic + + + synovial tissue + BTO:0001338 - + - + - + - - + + - + - + - 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 + + + + + + + An anatomical cavity that surrounded_by a synovial joint. + FMA:11356 + articular cavity (synovial joint) + cavitas articularis (junctura synovialis) + cavity of synovial joint uberon - wall of ventricle - UBERON:0004784 - - heart ventricle wall + joint cavity + synovial cavity + UBERON:0007617 + synovial cavity of joint - + - 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 + An anatomical cavity that surrounded_by a synovial joint. OBOL:automatic - - - ventricular wall - FMA:13884 - - - + - wall of cardiac ventricle - OBOL:automatic + articular cavity (synovial joint) + FMA:11356 - + - wall of heart ventricle - OBOL:automatic + cavitas articularis (junctura synovialis) + FMA:11356 - + - wall of lower chamber of heart - OBOL:automatic + cavity of synovial joint + FMA:11356 - - - wall of ventricle of heart - OBOL:automatic + + + joint cavity + FMA:11356 - + - wall of ventricle - MA:0002791 + synovial cavity + FMA:11356 - + - + - + - + - + - + - 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 + Epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules. + GAID:907 + MESH:D010857 uberon - laryngeal mucous membrane - respiratory mucosa - respiratory tract mucosa - UBERON:0004785 + eye pigment epithelium + UBERON:0007625 - respiratory system mucosa + pigment epithelium of eye - + - 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 + Epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules. + MP:0005200 - + - respiratory mucosa - BTO:0000973 + 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 + + + + + + + + - + - - + + + + + + + - 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 + + + + + + + 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 - UBERON:0004786 - The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468 - gastrointestinal system mucosa + nuclei trigemini + UBERON:0007641 + trigeminal nuclear complex + http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png - + + + + FMA + + + - - + + + + + + + - BTO-modified + FMA - + - A mucosa that is part of a gastrointestinal system. - OBOL:automatic + The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. There is also a distinct trigeminal motor nucleus that is medial to the chief sensory nucleus[WP]. + - - - digestive tract mucosa - + + + 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 - - - gut mucosa - BTO:0000546 + + + UMLS:C0040999 + BIRNLEX:4096 - + - gut mucuous membrane - + trigeminal nuclei + FMA:71248 - - - mucosa of gut - + + + nuclei trigemini + + - + - - - - - - - - - - - - - - - - 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 + + + + + + 2 + + + + An anatomical structure that connects two structures. + junction + + FMA:5898 + anatomical junction uberon - UBERON:0004790 - - skin mucous gland + UBERON:0007651 + + anatomical junction - - - 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 + + + + FMA - - - skin of body mucous gland - OBOL:automatic + + + An anatomical structure that connects two structures. + - + - + - + - - + + - - + + + - + - Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. - EMAPA:36296 - MA:0002854 + + + + + + + Region of the embryo into the area in which the kidney rudiment will develop. uberon - UBERON:0004797 - blood vessel layer - Blood:vessels.svg + kidney anlage + UBERON:0007687 + kidney field - + - Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. - + 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 - + - - - - - - - - - - - - - + + + - + - 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 + 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 - UBERON:0004807 - - respiratory system epithelium + future organ + organ field + UBERON:0007688 + + anlage - - - An epithelium that is part of a respiratory system [Automatically generated definition]. - OBOL:automatic + + + + FBbt - - - apparatus respiratorius epithelial tissue - OBOL:automatic + + + + AEO + FBbt - - - apparatus respiratorius epithelium - OBOL:automatic + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + EHDAA2 - - - epithelial tissue of apparatus respiratorius - OBOL:automatic + + + + + + + + + cjm - - - epithelial tissue of respiratory system - OBOL:automatic + + + + + + + + + EHDAA2 - + - epithelium of apparatus respiratorius - OBOL:automatic + early pharyngeal arch endoderm + EHDAA2:0001457 - - - epithelium of respiratory system - OBOL:automatic + + + pharyngeal endoderm + ZFA:0001104 - - - respiratory system epithelial tissue - OBOL:automatic + + + pharyngeal region endoderm + EHDAA2:0001456 - + - + - + - + - + + - + - 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 + + + + + + + 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:0004808 - gastrointestinal system epithelium + UBERON:0007691 + gustatory pore + Taste:bud.svg - - - 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 + + + + FMA - - - epithelial tissue of digestive system - OBOL:automatic + + + + + + + + + FMA - - - epithelial tissue of gastrointestinal system - OBOL:automatic + + + 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. + - - - epithelium of digestive system - OBOL:automatic + + + UMLS:C0226971 + ncithesaurus:Taste_Pore - + - epithelium of gastrointestinal system - OBOL:automatic + porus gustatorius + - + - gastrointestinal system epithelial tissue - OBOL:automatic + taste pore + FMA:63589 - + - + - + - + - - + + - + - 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 + A bone that is part of a reproductive organ. + + baculum uberon - UBERON:0004817 - lacrimal gland epithelium + os penis/os clitoris + UBERON:0007719 + bone of reproductive organ - + - An epithelium that is part of a lacrimal gland [Automatically generated definition]. + A bone that is part of a reproductive organ. + OBOL:automatic - - - epithelial tissue of lacrimal gland - OBOL:automatic + + + + Wikipedia + + + + + + + + + + + + + + + + + + + + + + + + + A gland that is part of a epidermis. + FMA:59153 + epidermal gland + gland of epidermis + uberon + UBERON:0007771 + + epidermis gland + - - - epithelium of lacrimal gland + + + A gland that is part of a epidermis. OBOL:automatic - + - lacrimal gland epithelial tissue - OBOL:automatic + gland of epidermis + FMA:59153 - + - + - + - - + + + + + + + + + + - + + - - + + - - + + - 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 + + + + + + + + + + + + + + + + + + + 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 - renal epithelium - UBERON:0004819 - - kidney epithelium + plasma ultrafiltrate + UBERON:0007779 + transudate - + - 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 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 + + + + + + + + + - + - 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 + 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 - UBERON:0004848 - respiratory system arterial endothelium + UBERON:0007798 + + vascular system - + - + - true - + MA - + - An endothelium of artery that is part of a respiratory system [Automatically generated definition]. - OBOL:automatic + 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 + + + - EMAPA:37566 - MA:th + UMLS:C0489903 + ncithesaurus:Vascular_System + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - apparatus respiratorius arterial endothelium - OBOL:automatic + + + 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 - - - apparatus respiratorius artery endothelium - OBOL:automatic + + + abdominal adipose tissue + BTO:0004041 - - - apparatus respiratorius endothelium of artery - OBOL:automatic + + + abdominal fat + BTO:0004041 - - - arterial endothelium of apparatus respiratorius - OBOL:automatic + + + 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 + - - - arterial endothelium of respiratory system - OBOL:automatic + + + + MA - - - artery endothelium of apparatus respiratorius - OBOL:automatic + + + 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. + - - - artery endothelium of respiratory system - OBOL:automatic + + + UMLS:C0460004 + ncithesaurus:Head_and_Neck - - - endothelium of artery of apparatus respiratorius - OBOL:automatic + + + cephalic area + - - - endothelium of artery of respiratory system - OBOL:automatic + + + cephalic part of animal + - - - respiratory system artery endothelium - OBOL:automatic + + + cephalic region + - - - respiratory system endothelium of artery - OBOL:automatic + + + head and neck + FMA:280881 - + - + - + - + - - + - + - 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 + + + + + + + + + + + + + + + + + + + + + + + + + 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 - - - 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 + + + + + + + + + possible exception in hemichordates + cjm - - - respiratory system endothelium of vein - OBOL:automatic + + + A tail that extends from the posterior tip of the organism to the anus, contains muscle and skeleton. + - - - respiratory system vein endothelium - OBOL:automatic + + + Anatomical structure that is the terminal, flexible posterior appendage of the organism.[AAO] + 2012-06-20 + AAO:0010338 + AAO + AAO:EJS - - - vein endothelium of apparatus respiratorius - OBOL:automatic + + + 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 - - - vein endothelium of respiratory system - OBOL:automatic + + + UMLS:C0039259 + ncithesaurus:Tail - - - venous endothelium of apparatus respiratorius - OBOL:automatic + + + post-anal fin tail + + - - - venous endothelium of respiratory system - OBOL:automatic + + + post-vent region + TAO:0001117 - + - + - + - - + + - + + - + - 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 + + + + + + + + + + + + + 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 - endothelia - vascular endothelia - UBERON:0004852 - - cardiovascular system endothelium + fin girdle + fin girdle region + limb girdle + limb girdle region + UBERON:0007823 + appendage girdle region - + - An endothelium that is part of the cardiovascular system. + 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 - - - 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 + + + 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 + - + - UMLS:C0014261 - ncithesaurus:Vascular_Endothelium + EMAPA:37854 + MA:th - + - endothelia - ZFA:0001639 - + fin girdle + - + - vascular endothelia - XAO:0000356 - + fin girdle region + + + + + + limb girdle + + + + + + limb girdle region + - + - + - + - + - + - + - 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 + + + + + + + + + + + + + A bone that is part of a appendage girdle region. + EMAPA:35379 + MA:0000291 + girdle bone uberon - UBERON:0004859 - - Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands - eye gland + UBERON:0007828 + girdle bone/zone - + - 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 - + A bone that is part of a appendage girdle region. + OBOL:automatic - + - gland of eye - OBOL:automatic + girdle bone + MA:0000291 - + - + - + - + - - + + - + - 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 + + + + + + + A bone that is part of a pectoral girdle region. + EMAPA:35669 + MA:0000292 + bone of pectoral girdle uberon - UBERON:0004864 - - vasculature of retina + UBERON:0007829 + + pectoral girdle bone - - - 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 + + + + MA - - - set of blood vessels of retina + + + A bone that is part of a pectoral girdle region. OBOL:automatic - - - - set of retinal blood vessels - FMA:76552 - - - - - vasa sanguinea retinae - FMA:76552 - FMA:TA - - - + - - + + + + + + + + + + + + + + + + + + - + - 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 + + + + + + + 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 - splanchnic mesoderm - UBERON:0004872 + UBERON:0007830 - splanchnic layer of lateral plate mesoderm + + pelvic girdle bone/zone - - - Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. - + + + + MA - - - We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors - BILA + + + A bone element or fused bone that is part of pelvic girdle. + - - - visceral mesoderm - - - BILA:0000044 + + + UMLS:C0030786 + ncithesaurus:Pelvic_Bone - - - splanchnic mesoderm - ISBN:9780878932504 + + + pelvic girdle bone + MA:0000293 - + - - + + + + + + + + + + + + + + + + + - + - - - - - - - + + - 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 + + + + + + + + + + + + + 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 - UBERON:0004874 - somatopleure - http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png + cingulum pectorale + pectoral girdle + scapular girdle + UBERON:0007831 + + + pectoral girdle skeleton + http://upload.wikimedia.org/wikipedia/commons/2/22/Pectoral_girdle_front_diagram.svg - + - + - EHDAA2 + XAO - + - 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]. - + 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. + - - - UMLS:C1519423 - ncithesaurus:Somatopleure + + + 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 - - - - - - - - - - - - - - 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]. - + + + 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:C1283944 - ncithesaurus:Nephrogenic_Cord + UMLS:C0427245 + ncithesaurus:Shoulder_Girdle - + + + skeletal parts of pectoral girdle + + + + + + skeleton of pectoral girdle + + + + - chorda nephrogenica - + cingulum pectorale + + + + + pectoral girdle + VSAO:0000156 + + + + + + scapular girdle + TAO:0000407 + - + - - + + + + + + + + + + + + + + + + + + - + - - + + - + - - + + - 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 + 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 - urogenital ridge - UBERON:0004876 - - urogenital fold + pelvic girdle + UBERON:0007832 + + + pelvic girdle skeleton + http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png - + - - + + - EHDAA2 + - - - - - - - - - Wikipedia + + + 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 - - - - - - - - - EHDAA2 + + + Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO] + 2012-06-20 + AAO:0000426 + AAO + AAO:LAP - - - 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 + + + 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 + + + - urethral fold - EMAPA:30888 + pelvic girdle skeleton + VSAO:0000155 - + - urogenital fold - EHDAA2:0004022 - MP:0011835 + skeletal parts of pelvic girdle + - + + + skeleton of pelvic girdle + + + + - urogenital ridge - MP:0011835 + pelvic girdle + VSAO:0000155 - + - - + + - - + + - 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 + 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 - UBERON:0004880 - - - chordamesoderm + membrane bones + UBERON:0007842 + membrane bone - + + + + VSAO + + + - The central region of trunk mesoderm. This tissue forms the notochord - + Bone element that arises as a result of intramembranous ossification. + + + GO_REF:0000034 + VSAO:0000023 - + - Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. - ZFIN:ZDB-PUB-961014-576 + 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 + - - - axial chorda mesoderm - ZFA:0000091 + + + + VSAO - - - dorsal mesoderm - + + + + + + + + + VSAO - - - presumptive notochord - ZFA:0000091 - - - - - - - - - - - - - - - - - - - - - - + + + - - + + - - 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 - + + VSAO + - + - 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 - + Skeletal element that is composed of cartilage tissue and may be permanent or transient. + + GO_REF:0000034 + PSPUB:0000170 + VSAO:0000000 - + - we follow EHDAA2 in dividing the UGS into epithelium and lumen - EHDAA2 + TAO still mixes tissue and element + TAO - + - UGE - + cartilage organ + FMA:55107 - + - epithelium of urogenital sinus - OBOL:automatic + cartilaginous element + + + + + + chondrogenic element + VSAO:0000000 + + + + + cartilage + VSAO:0000000 - + - - + + + - - + + - Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. - FBbt:00005811 - joint + + + + + + + + + + + + + + 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:0004905 - - articulation + UBERON:0007845 + regular connective tissue - + + + + FMA + + + - Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. - + 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 - + - + - + - - + + - - + + - - - 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 + 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:0004907 - - lower digestive tract + UBERON:0007846 + dense regular connective tissue - - - The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition]. - + + + + FMA - - - MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509 - MA + + + + ncithesaurus - - - 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 + + + 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 - - - gut - GO:0048565 + + + 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 - - - UMLS:C0226875 - ncithesaurus:Lower_Gastrointestinal_Tract + + + 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 - - - - - - - - - - - - - - - - - - - - - - - - - - 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:C0225333 + ncithesaurus:Regular_Dense_Connective_Tissue - - - UMLS:C1517534 - ncithesaurus:Germinal_Epithelium + + + dense fibrous connective tissue + FMA:64781 - + - gonad epithelium - OBOL:automatic + dense regular collagenous connective tissue + FMA:64781 - + - gonadal epithelium - OBOL:automatic + dense regular collagenous tissue + FMA:64781 - - - gonadal sheath - FBbt:00004859 + + + typus regularis (textus connectivus collagenosus compactus) + FMA:64781 - + - + - + - - + + - + - - - - - - - + - 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 + A bone that is part of a craniocervical region. + EMAPA:37245 + MA:0000569 + head or neck bone uberon - alimentary system subdivision - intestinal tract - segment of intestinal tract - subdivision of alimentary system - UBERON:0004921 - - subdivision of digestive tract + cranial bone + UBERON:0007914 + bone of craniocervical region - + + + + MA + + + + + + + + + + + MA + + + - A proximal-distal subdivision of the digestive tract. - + A bone that is part of a craniocervical region. + OBOL:automatic - - - alimentary system subdivision - FMA:71131 + + + EMAPA:37245 + MA:th - - - subdivision of alimentary system - FMA:71131 + + + head or neck bone + MA:0000569 - + - - - - - - - - - A part of a wall of an organ that forms a layer. - FMA:82485 + + + 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 - UBERON:0004923 - - organ component layer + os irregulare + UBERON:0008001 + irregular bone - + + + + FMA + + + - A part of a wall of an organ that forms a layer. - + 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 + + - + - + - + - + - - + - + - The tissue underlying the tunica mucosa of the pharynx. - - BTO:0002113 - FMA:75144 - pharyngeal submucosa - pharynx submucosa - tela submucosa pharyngea - tela submucosa pharyngis + + + + + + + + + + + + + A skeletal joint that is part of a appendage girdle region. + MA:0001505 + girdle joint uberon - pharyngobasilar fascia - submucous coat of pharynx - submucous layer of pharynx - UBERON:0004924 - submucosa of pharynx + UBERON:0008114 + + joint of girdle - - - The tissue underlying the tunica mucosa of the pharynx. - BTO:0002113 - - - - - pharyngeal submucosa - FMA:75144 + + + + MA - - - pharynx submucosa + + + A skeletal joint that is part of a appendage girdle region. 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 + girdle joint + OBOL:automatic - + - + - + - - + + - + + - + + + + + + + - A submucosa that is part of a sigmoid colon [Automatically generated definition]. - FMA:15027 - sigmoid colon submucosa + An anatomical surface that is part of a cartilage element. + FMA:76668 + cartilage surface uberon - UBERON:0004932 - submucosa of sigmoid colon + UBERON:0008115 + surface of cartilage - + - A submucosa that is part of a sigmoid colon [Automatically generated definition]. + An anatomical surface that is part of a cartilage element. OBOL:automatic - + - sigmoid colon submucosa - OBOL:automatic + cartilage surface + FMA:76668 - + - + - + - - + + - - + - - + + - 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 + 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 - submucous layer of urinary bladder - UBERON:0004943 - submucosa of urinary bladder + hollow bone + UBERON:0008193 + pneumatized bone - - - - - - - - - - - - + - 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 - + A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD]. + - + - tela submucosa vesicae urinariae - BTO:0002117 + os pneumaticum + FMA:7478 - + - urinary bladder submucosa - OBOL:automatic - - - - - submucous layer of urinary bladder - BTO:0002117 + pneumatic bone + FMA:7478 - + - + - + - + - - + - + - 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 - - - - - + - + - - - + + 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 + - + - 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 + Any muscle organ that is part of a pectoral girdle region. OBOL:automatic - - - ureter organ mucosa - 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 - + - ureteral mucosa - FMA:15894 + muscle of shoulder girdle + FMA:37347 - + - ureteric mucosa - FMA:15894 + pectoral girdle muscle + FMA:37347 - + - + - + - + + + + + - + + - + - 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 + + + + + + + + + + + + + + + + + + + The part of the ventral body cavity that is within the pelvis. + + + EMAPA:37235 + FMA:9738 + MA:0003089 + space of pelvic compartment uberon - UBERON:0004993 - mucosa of sigmoid colon + cavitas pelvis + UBERON:0008203 + pelvic cavity + http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg - + - 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 + The part of the ventral body cavity that is within the pelvis. + UBERON:cjm - - - sigmoid colon mucosa of organ - OBOL:automatic + + + EMAPA:37235 + MA:th - + - sigmoid colon mucous membrane - OBOL:automatic + space of pelvic compartment + FMA:9738 - - - sigmoid colon organ mucosa - OBOL:automatic + + + cavitas pelvis + + - + - + - + - + - + - + - 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 + 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 - UBERON:0005006 - mucosa of renal pelvis + head muscles + head or neck muscle + UBERON:0008229 + craniocervical region musculature - - - 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 + + + + MA - - - mucosa of organ of renal pelvis - OBOL:automatic + + + + + + + + + MA - - - mucosa of pelvis of ureter - OBOL:automatic + + + Musculature system of the pharyngeal and head regions. + ZFA:0000328 + ZFA:curator - - - mucous membrane of kidney pelvis - OBOL:automatic + + + in MA this is restricted to skeletal muscles + MA - - - mucous membrane of pelvis of ureter - OBOL:automatic + + + EMAPA:37259 + MA:th - + - mucous membrane of renal pelvis - OBOL:automatic + head or neck muscle + MA:0000571 - - - organ mucosa of kidney pelvis - OBOL:automatic + + + head muscles + ZFA:0000328 - - - organ mucosa of pelvis of ureter - OBOL:automatic + + + 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 + - - - organ mucosa of renal pelvis - OBOL:automatic + + + + + + + + + FMA - - - pelvis of ureter mucosa - OBOL:automatic + + + + + + + + + MA - - - pelvis of ureter mucosa of organ - OBOL:automatic + + + + + + + + + FMA - - - pelvis of ureter mucous membrane - OBOL:automatic + + + 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 - - - pelvis of ureter organ mucosa - OBOL:automatic + + + EMAPA:37234 + MA:th - + - renal pelvic mucosa - FMA:17931 + dorsum of thorax + FMA:24217 - + - renal pelvis mucosa - OBOL:automatic + posterior part of thorax + FMA:24217 - + - renal pelvis mucosa of organ - OBOL:automatic + thoracic back + FMA:24217 - + - renal pelvis mucous membrane - OBOL:automatic + thoracic part of back + FMA:24217 - + - renal pelvis organ mucosa - OBOL:automatic + upper back + MA:0000028 - - - tunica mucosa pelvis renalis - FMA:17931 - FMA:TA - + + + back of thorax + FMA:24217 - + - + - + - + - - + + - + - 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 + A muscle of back that is part of a dorsal thoracic segment of trunk. + + EMAPA:37261 + MA:0000508 uberon - UBERON:0005032 - mucosa of lower lip + UBERON:0008243 + upper back muscle - - - 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 + + + + MA - - - mucosa of organ of lower lip - OBOL:automatic + + + + + + + + + MA - - - mucous membrane of lower lip + + + A muscle of back that is part of a dorsal thoracic segment of trunk. OBOL:automatic - - - organ mucosa of lower lip - OBOL:automatic + + + EMAPA:37261 + MA:th - + - + - + - + - + - + - A gland that is part of a hemolymphoid system [Automatically generated definition]. - hemopoietic or lymphoid organ - EMAPA:18766 - MA:0002962 - hemopoietic or lymphoid gland + 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 - haemolymphoid system gland - UBERON:0005058 - - hemolymphoid system gland + cardiac endothelium + UBERON:0008307 + heart endothelium - + - A gland that is part of a hemolymphoid system [Automatically generated definition]. + An endothelium that is part of a heart [Automatically generated definition]. OBOL:automatic - - - hemopoietic or lymphoid organ - GO:0048534 - - - - - hemopoietic or lymphoid gland - - - - + - haemolymphoid system gland - EMAPA:18766 + cardiac endothelium + BTO:0004293 - + - - + + + + + + + + + + + + + + - + - 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 + A vertebral foramen that is part of a cervical vertebra. + + FMA:13480 uberon - UBERON:0005061 - neural groove + UBERON:0008429 + cervical vertebral foramen - + - 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]. - + 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 + - - - UMLS:C0814992 - ncithesaurus:Neural_Groove + + + A vertebral foramen that is part of a thoracic vertebra. + OBOL:automatic - + - - - - - - + + + + + + + + + + + + + + - + - - + + - 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 + 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 - UBERON:0005062 + embryonic epiblast + UBERON:0008780 + - neural fold + 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 - - - One of the two elevated edges of the neural groove[GO,MP]. - - GO:0001842 - MP:0011256 + + + + + + + + + Wikipedia - - - 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]. - + + + 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:C0814993 - ncithesaurus:Neural_Fold + UMLS:C1516906 + ncithesaurus:Epiblast - - - medullary fold - MP:0011256 + + + embryonic epiblast + MP:0003886 - + - - + + + - - + + - 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 + + + + + + + + + + + + + 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 - neural tube rod - UBERON:0005068 - - neural rod + pharyngeal arch complex + pharyngeal arch region + pharyngeal arches and clefts + pharyngeal complex + UBERON:0008814 + pharyngeal arch system - + - 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 + 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 - - - 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 + + + UMLS:C1519038 + ncithesaurus:Pharyngeal_Apparatus - + + + pharyngeal system + GO:0060037 + + + - neural tube rod - GO:0014027 + pharyngeal arch region + EHDAA2:0000187 - + - + - - - - - + - - + + - - + - - - - - - - - - - - - - + - An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord. - hindbrain-spinal cord boundary region + A head that is part of a embryo. + CALOHA:TS-0246 + FBbt:00000155 + FMA:293011 uberon - UBERON:0005076 - hindbrain-spinal cord boundary + UBERON:0008816 + + embryonic head - + - An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord. + A head that is part of a embryo. 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 + + + + + + + + - - The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]. - uberon - UBERON:0005080 - metanephric ureteric bud - + + definitional + - + - The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]. - GO:0035502 + A brain that develops_from a neural tube. + + OBOL:automatic - + - + - + - - + + - + + + - - + + - 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]. + + + + + + + + + + + + + + + + + + + + + + + + + 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:0005081 - ureter ureteric bud + UBERON:0008856 + + stomach muscularis externa - + + + + + + + + + FMA + + + + + + + + + + + MA-abduced + + + - 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 + 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 - + - + - + - - + + - + + + + - - + + - A hole in a tube[GO]. - AEO:0000078 - EHDAA2:0004618 - RETIRED_EHDAA2:0003078 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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:0005082 - tube lumen + UBERON:0008876 + + hypodermis skeletal muscle layer - + + + + + + + + + MP-def + + + - A hole in a tube[GO]. - GO:0060609 + 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 - + - - - + + + - + - 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 + + + + + + + + + + + + + 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 - epithelial placode - UBERON:0005085 - ectodermal placode + UBERON:0008886 + pulmonary vascular system - - - An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO] - GO:0060788 + + + + Obol - - - in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures - GO - + + + + + + + + + FMA - - - epithelial placode - AEO:0000112 + + + The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins. + + ISBN:0073040584 - - - - - - - - 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 + + + Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA] + FMA + FMA:45621 - + - musculus - FMA:30316 + pulmonary circulatory system + FMA:45621 + + + + + pulmonary system + ISBN:0073040584 - + - - + + + - + - . - class added for consistency with GO - consider merging with kidney mesenchyme. + + + + + + + + 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 - kidney anlage - UBERON:0005095 - kidney rudiment + 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 - + - + - GO + - + + + + + + + + + redundant + + Grays + + + - . - GO:0072003 + 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 + + + + - kidney anlage - GOC:mtg_kidney_jan10 + pharyngeal arch + VSAO:0000149 + + + + + + pharyngeal arch skeleton + ZFA:0001216 + + + + + pharyngeal skeleton + ZFA:0001216 + + + + + visceral cranium + + + + + + visceral skeletal system + + + + + + visceral skeleton + UBERONREF:0000007 - + - + - + - + - - + + - + - An epithelium that is part of a mesonephros [Automatically generated definition]. + 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 - UBERON:0005103 - mesonephric epithelium + dermal bones + UBERON:0008907 + dermal bone - + + + + wd + + + + + + VSAO + + + + + + + + + + + VSAO + + + - An epithelium that is part of a mesonephros [Automatically generated definition]. - OBOL:automatic + 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 + - + - + - + - - + + - - - - 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 + + + + + + + + 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 - UBERON:0005106 - metanephric tubule + perichordal bone + UBERON:0008909 + perichordal bone - + + + + not in VSAO + ZFA + + + - A metanephric tubule is an epithelial tube that is part of the metanephros[GO]. - GO:0072173 + Bone element that is adjacent to the notochord. + + GO_REF:0000034 + VSAO:0000307 - - - 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 + + + 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 - + - + - + - + - - + + - + - An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO]. + A parenchyma that is part of a lung. + + EMAPA:35522 + FMA:27360 + MA:0003168 + respiratory portion of lung uberon - UBERON:0005108 - metanephric epithelium + parenchyma of lung + pulmonary parenchyma + UBERON:0008946 + lung parenchyma - + + + + FMA + + + + + + + + + + + FMA + + + - An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO]. - GO:0072207 + 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 - + - - - - - - - - - - - - - + + + - + - Any smooth muscle tissue that is part of a metanephros. + + + + + + + + EHDAA2:0004069 + NCIT:C34283 + UMLS:C1514898 uberon - UBERON:0005109 - metanephric smooth muscle tissue + UBERON:0008947 + respiratory primordium - - - Any smooth muscle tissue that is part of a metanephros. - - GO:0072208 + + + + Obol + + + + + UMLS:C1514898 + ncithesaurus:Respiratory_Primordium - + - + - + - - + + - - + + + - - + + - 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 + + + + + + + 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:0005137 - metanephric capsule + UBERON:0008962 + forelimb bone - + - The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage[GO]. - GO:0072213 + A 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. + - - - - - - - - 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 + + + 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 + - + - + - + - + - + + - + - 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. + The functional tissue of the kidney, consisting of the nephrons. + + BTO:0003604 + FMA:15574 + parenchyma of kidney uberon - UBERON:0005157 - epithelial fold + kidney parenchyma + UBERON:0008987 + renal parenchyma - - - An epithelial sheet bent on a linear axis. - GO:0060571 + + + + FMA - - - - - - - - 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 + The functional tissue of the kidney, consisting of the nephrons. + BTO:0003604 - + - multi-cell-part structure - CARO:0001000 + parenchyma of kidney + FMA:15574 - + - cell part cluster - FMA:83115 + kidney parenchyma + BTO:0003604 - + - + - + - + - + + + - + - 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 + + + + + + + + + + + + + + + + + + + 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 + submocosal esophageal gland + UBERON:0008989 + submucosal esophageal gland + http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg - + - An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. - + 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 + + + - abdomen organ - MA:0000522 + esophageal gland + FMA:9404 + + + + + glandulae oesophageae + + + + + + mucous gland of submucosa of esophagus + FMA:9404 - + - - - - - - - - - - - - - + + + - + - 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 + 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:0005173 - - abdominal segment element + UBERON:0008998 + + vasculature of brain - + - 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. - + System pertaining to blood vessels in the brain. + BTO:0003840 - - - EMAPA:37062 - MA:th + + + cerebrovascular system + BTO:0003840 - + - abdominal segment organ - MA:0000529 + intracerebral vasculature + FMA:61935 - + - + - + - - + + - + - + - 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 + + + + + + + Any portion of tissue that surrounds a urethra. + + BTO:0005081 uberon - UBERON:0005174 - - dorsal region element + UBERON:0009010 + periurethral tissue - + - 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 + Any portion of tissue that surrounds a urethra. + UBERON:cjm - + - + - + - + - + + - + - 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 + A zone of skin that is part of a dorsal thoracic segment of trunk. + + EMAPA:37280 + MA:0000510 uberon - UBERON:0005177 - - - trunk region element + UBERON:0009015 + upper back skin - + + + + MA + + + - 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. - + A zone of skin that is part of a dorsal thoracic segment of trunk. + OBOL:automatic - + - EMAPA:37270 + EMAPA:37280 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 + An artery that supplies blood to the urinary bladder. + + EMAPA:37131 + MA:0002078 + arteria vesicali + vesical arteries uberon - UBERON:0005178 - - - thoracic cavity element + UBERON:0009027 + vesical artery - + - An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. + An artery that supplies blood to the urinary bladder. - + - EMAPA:37273 + EMAPA:37131 MA:th - + - thoracic cavity organ - MA:0000557 + arteria vesicali + + + + + + vesical arteries + - + - + - + - - + + - + - - + + - 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 + 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:0005179 - - - - pelvic region element + UBERON:0009030 + left pulmonary vein - + - An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis. + 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:37275 + EMAPA:37165 MA:th - - - pelvis organ - MA:0000543 + + + UMLS:C0226670 + ncithesaurus:Left_Pulmonary_Vein - + - + - + - - + + - + - - + + - An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. - EMAPA:37271 - MA:0000563 + 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 - upper body organ - UBERON:0005181 - - thoracic segment organ + UBERON:0009032 + right pulmonary vein - + - An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. + 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:37271 + EMAPA:37379 MA:th - - - upper body organ - MA:0000563 + + + UMLS:C0226669 + ncithesaurus:Right_Pulmonary_Vein - + - - - - - - - - - - - - - - - A vein that is part of a thorax [Automatically generated definition]. - - - EMAPA:37197 - MA:0002235 - NCIT:C53142 - UMLS:C0226629 + + + + + + + + + A gonad prior to differentiating into a definitive testis or ovary. + + EHDAA2:0000716 + NCIT:C34192 + UMLS:C1512703 uberon - UBERON:0005194 - thoracic vein + 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 vein that is part of a thorax [Automatically generated definition]. - OBOL:automatic + A gonad prior to differentiating into a definitive testis or ovary. + - + - EMAPA:37197 - MA:th + UMLS:C1512703 + ncithesaurus:Indifferent_Gonad + + + + + + + + + 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 - - - UMLS:C0226629 - ncithesaurus:Thoracic_Vein + + + 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 - + - + - + - - + + - + + - - + + - An external ectoderm that is part of a optic eminence [Automatically generated definition]. - EMAPA:16539 - RETIRED_EHDAA2:0001311 - VHOG:0000520 + Cranial ganglion which develops from an epibranchial placode. + TAO:0001555 + ZFA:0001555 + epibranchial ganglia uberon - UBERON:0005216 - optic eminence surface ectoderm + UBERON:0009127 + Epibranchial ganglia orchestrate the development of the cranial neurogenic crest + epibranchial ganglion - + + + + ZFA + + + - - + + - true - + NCBIBook:NBK53175 - + - An external ectoderm that is part of a optic eminence [Automatically generated definition]. - OBOL:automatic + Cranial ganglion which develops from an epibranchial placode. + + ZFIN:curator + + + + + epibranchial ganglia + ZFA:0001555 + - + - + - + - + - + + + + + + - + - An ectoderm that is part of a optic eminence [Automatically generated definition]. - EHDAA:940 - EMAPA:16539 - RETIRED_EHDAA2:0001309 - VHOG:0001105 + + + + + + + + + + + + + Endocardium that is part of the right atrium. + + EHDAA2:0000274 + FMA:7281 + NCIT:C102339 + VHOG:0001228 + endocardium of right atrium + right atrial endocardium uberon - UBERON:0005234 - optic eminence ectoderm + right atrium endocardial tissue + UBERON:0009129 + right atrium endocardium - + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + - An ectoderm that is part of a optic eminence [Automatically generated definition]. - OBOL:automatic + 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 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 + + + + + + + A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities. + In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] + UBERON:0009146 + + + + EHDAA2:0001483 + EMAPA:17709 + NCIT:C34256 + UMLS:C1283968 + VHOG:0000757 + pleuroperitoneal fold + pleuroperitoneal membranes uberon - UBERON:0005249 - metanephric renal pelvis + UBERON:0009133 + pleuroperitoneal membrane - + + + + EHDAA2 + + + + + + EHDAA2 + + + - A renal pelvis that is part of a metanephros. - OBOL:automatic + A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities. + + - + - 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] + 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:0000945 + VHOG:0000757 VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639 + ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 - + + + UMLS:C1283968 + ncithesaurus:Pleuroperitoneal_Membrane + + + - metanephros pelvis - VHOG:0000945 + pleuroperitoneal fold + VHOG:0000757 + + + + + pleuroperitoneal membranes + EHDAA2:0001483 + - + - + - + - + - + - + - A gland that is part of a stomodeum. - check this - VHOG:0000658 - stomatodaeum gland + + + + + + + A vein that is part of a craniocervical region. + + EHDAA2:0004542 + craniocervical vein + head and neck veins + vein of head and neck uberon - UBERON:0005250 - - stomatodeum gland + UBERON:0009141 + craniocervical region vein - + + + + + + + + + EHDAA2 + + + - A gland that is part of a stomodeum. + A vein that is part of a craniocervical region. OBOL:automatic - + - stomatodaeum gland - VHOG:0000658 + head and neck veins + EHDAA2:0004542 - + - - - - - - - - - - - - - - + + + + - + - - + + - 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 + + + + + + + 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 - cranial mesenchyme - desmocranium - UBERON:0005253 - - - - head mesenchyme + UBERON:0009142 + entire embryonic 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 - + Sum total of mesenchyme in the embryo. + - + - - - - - - - - - - - - - - - - - - - - - - - - + + + - + - Mesenchyme that is part of a developing trunk. - EFO:0003485 - EHDAA2:0002092 - EHDAA:377 - EMAPA:16177 - TAO:0000081 - VHOG:0000281 - ZFA:0000081 + EMAPA:16549 + RETIRED_EHDAA2:0001454 + pharyngeal region uberon - trunk and cervical mesenchyme - UBERON:0005256 - - - trunk mesenchyme + UBERON:0009145 + pharyngeal region of foregut - + - + EHDAA2 - - - Mesenchyme that is part of a developing trunk. - OBOL:automatic - - - - - trunk and cervical mesenchyme - EHDAA2:0002092 + + + pharyngeal region + EMAPA:16549 - + - - - - - - - - + + - - + + - 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 + EHDAA2:0004021 uberon - myelencephalon (medulla oblongata) - UBERON:0005290 - - myelencephalon - http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg + UBERON:0009196 + + indifferent external genitalia - + - - - - - - - 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 + + cjm - + - + - + - + - + + - + - A portion of tissue that is part of an embryo. - CALOHA:TS-2100 - portion of embryonic tissue + The limb epidermis is the outer epithelial layer of the limb, it is a complex stratified squamous epithelium. + EMAPA:32728 uberon - developing tissue - UBERON:0005291 - - - embryonic tissue + UBERON:0009200 + limb epidermis - + - A portion of tissue that is part of an embryo. - OBOL:automatic - - - - - portion of embryonic tissue - OBOL:automatic + 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 - + - + - - - - - - - + + + + - + + + + - + - 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 + A nephric duct is a tube that drains a primitive kidney[GO]. + + EMAPA:16577 uberon - UBERON:0005292 - - extraembryonic tissue + UBERON:0009201 + pronephric duct or mesonephric duct + nephric duct - + + + + EHDAA2 + + + - 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. - + A nephric duct is a tube that drains a primitive kidney[GO]. + GO:0072176 - + - + - + - + - + - + - The endothelial lining of the endocardium. - FMA:83596 - endocardium endothelium - endothelium of endocardium + An ectoderm that is part of a buccopharyngeal membrane. + EHDAA2:0000190 + EMAPA:16260 uberon - UBERON:0005316 - endocardial endothelium + UBERON:0009479 + + ectoderm of buccopharyngeal membrane - + - The endothelial lining of the endocardium. - UBERON:cjm - - - - - endocardium endothelium - FMA:83596 - - - - - endothelium of endocardium - FMA:83596 + 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:0005321 - mesonephric smooth muscle tissue + UBERON:0009480 + + endoderm of buccopharyngeal membrane - + - . - GO:0061214 + An endoderm that is part of a buccopharyngeal membrane. + OBOL:automatic - + - + - + + - - + - Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros[GO]. - AAO:0011062 - EHDAA2:0001132 - EMAPA:16745 - XAO:0000291 + Mesenchyme that is part of a foregut-midgut junction. + EHDAA2:0000570 + EMAPA:16364 uberon - UBERON:0005323 - - mesonephric mesenchyme + UBERON:0009482 + + associated mesenchyme of foregut-midgut junction - + - Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros[GO]. - GO:0061219 + Mesenchyme that is part of a foregut-midgut junction. + OBOL:automatic - + - + - + - + - + + + - + - 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 - - - - - - - - - + - - + + - An array of photoreceptors and any supporting cells found in an eye. - FBbt:00004200 - light-sensitive tissue + 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:0005388 - photoreceptor array + UBERON:0009494 + + pharyngeal arch mesenchymal region - - - An array of photoreceptors and any supporting cells found in an eye. - + + + + EHDAA2 - - - - - - - - - - - - - - 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 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 + + cjm - - - gastroenterological system - UBERON:cjm + + + A portion of mesenchymal tissue associated with an individual pharyngeal arch. + - - - gastrointestinal (GI) tract - GAID:294 + + + 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 - - - gastrointestinal system - FMA:71132 + + + branchial arch mesenchyme + MP:0011262 - - - gastrointestinal tract - FMA:71132 - + + + pharyngeal arch mesenchyme + - + - + - + - - + + - - + + + - - + + - - 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 + + + + + + + + + + + + + An epithelium that is part of a foregut-midgut junction. + EHDAA2:0000573 + EMAPA:16564 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 + UBERON:0009497 + + epithelium of foregut-midgut junction - - - - lexical - - - - - A limb bud that develops into a forelimb. - - - - - - limb bud - forelimb - MIAA:0000065 + + + + + + + + + EHDAA2 - - - upper limb bud - RETIRED_EHDAA2:0003198 + + + + + + + + + EHDAA2 - - - wing bud - NCBITaxon:8782 + + + An epithelium that is part of a foregut-midgut junction. 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 + Mesenchyme that is part of a developing hindgut. + EHDAA2:0000780 + EMAPA:16716 + hindgut associated mesenchyme uberon - leg bud - limb bud - hindlimb - UBERON:0005418 - - Genes: Tbx4 specifies hindlimbs. Wnt8c restricts Fgf10 in chick. - hindlimb bud + UBERON:0009503 + + mesenchyme of hindgut - - - - 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 + Mesenchyme that is part of a developing hindgut. + OBOL:automatic - + - hind limb bud - XAO:0003066 + hindgut associated mesenchyme + EHDAA2:0000780 - + - + - + - - + + + + + + - + + - - - - - - - + - - + + - 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 + An endoderm that is part of a anal region. + EHDAA2:0004020 + EMAPA:17177 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 + UBERON:0009521 + + anal membrane endodermal component - + - A limb bud that develops into a forelimb or pectoral fin. + An endoderm that is part of a anal region. 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 + An endoderm that is part of a foregut-midgut junction. + EHDAA2:0000572 + EMAPA:18403 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 + UBERON:0009550 + + endoderm of foregut-midgut junction - + - A limb bud that develops into a hindlimb or pelvic fin. + An endoderm that is part of a foregut-midgut junction. 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 + A submucosa that is part of a intestine. + FMA:15696 + submucosa of intestine uberon - aer pectoral fin - apical ectodermal ridge pectoral fin - apical fold pectoral fin - UBERON:0005421 - - - pectoral appendage apical ectodermal ridge + UBERON:0009566 + intestinal submucosa - + - - + + - EHDAA2 + FMA - + - An apical ectodermal ridge that is part of a pectoral appendage bud. + A submucosa that is part of a intestine. 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 + + + 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 + - - - 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 - - + + + 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 - - - AER forelimb - VHOG:0001064 + + + 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 - - - apical ectodermal ridge forelimb - VHOG:0001064 + + + thoracolumbar vertebrae set + FMA:72066 - - - apical ectodermal ridge pectoral fin bud - ZFA:0000085 + + + presacral region + AAO:0000612 - - - upper limb bud apical ectodermal ridge - EHDAA2:0000138 + + + thoracolumbar region + AAO:0000612 - - - wing AER - Giesha:syn - + + + trunk region + AAO:0000612 + + + + + + + + + + + + + + + FMA:25054 + region of trunk + trunk subdivision + uberon + UBERON:0009569 + + subdivision of trunk + - - - wing apical ectodermal ridge - + + + region of trunk + FMA:25054 - - - aer pectoral fin - TAO:0000085 + + + 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 + - - - apical ectodermal ridge pectoral fin - TAO:0000085 + + + A sulcus limitans of neural tube that is part of a future spinal cord. + OBOL:automatic - - - apical fold pectoral fin - TAO:0000085 + + + spinal cord lateral wall sulcus limitans + EHDAA2:0001265 - + - + - + - + - + + - + - + - 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 + A sulcus limitans of neural tube that is part of a future medulla oblongata. + EHDAA2:0001100 + EMAPA:17561 uberon - AER hindlimb - apical ectodermal ridge pelvic fin bud - leg AER - UBERON:0005422 - - - pelvic appendage apical ectodermal ridge + UBERON:0009576 + medulla oblongata sulcus limitans - + - + EHDAA2 - + - An apical ectodermal ridge that is part of a pelvic appendage bud. + A sulcus limitans of neural tube that is part of a future medulla oblongata. 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 + + + + + + + + + + + + + + + + + + + + + A sulcus limitans of neural tube that is part of a future metencephalon. + EHDAA2:0001161 + EMAPA:17567 uberon - developing structure - developmental structure - developmental tissue - UBERON:0005423 - developing anatomical structure + UBERON:0009577 + metencephalon sulcus limitans - - - developmental tissue - MIAA:0000019 + + + 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 + + + + + + + + + + + + + + + + + + + - - + + - 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 + EHDAA2:0001172 + EMAPA:16977 + VHOG:0000910 + mantle layer lateral wall midbrain + midbrain lateral wall mantle layer uberon - future NR - future neural epithelium - future neural layer - presumptive retina - UBERON:0005425 - - presumptive neural retina + mantle layer lateral wall mesencephalon + UBERON:0009581 + midbrain mantle layer - - - 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 + mantle layer lateral wall midbrain + VHOG:0000910 - + - presumptive retina - TAO:0001071 + mantle layer lateral wall mesencephalon + VHOG:0000910 - + - - - + + + + + + + + + + + + + - - + + - 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 + EMAPA:17580 + VHOG:0000911 + mantle layer lateral wall spinal cord + spinal cord lateral wall mantle layer uberon - immature lens - lens mass - presumptive lens - UBERON:0005426 - - - lens vesicle + UBERON:0009583 + spinal cord mantle layer - - - Portion of tissue that gives rise to the lens. - - ZFIN:curator + + + 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 + - - - A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG] - 2012-09-17 - VHOG:0001163 - VHOG - - + + + + + + + + + EMAPA - - - (...) 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 + + + Mesenchyme that is part of a 1st arch mandibular component. + OBOL:automatic - - - 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 + + + mesenchymal region of mandibular component of first pharyngeal arch + - - - hollow lens vesicle - + + + 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 + - - - solid lens vesicle - ZFA:0001679 - + + + Mesenchyme that is part of a developing left lung. + OBOL:automatic - - - immature lens - ZFA:0001679 + + + left lung mesenchyme + EMAPA:17654 - - - - lens mass - ZFA:0001679 - ZFIN:ZDB-PUB-091023-49 + + + + + + + + + + + + + + + + + + + + + + + + + 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 - - - presumptive lens - ZFA:0001679 + + + right lung mesenchyme + EMAPA:17662 - + - - - - - + + + + + + + + + + + + + - + - Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. - TAO:0002188 - ZFA:0001688 + + + + + + + A neural plate that develops_from a presumptive midbrain. + TAO:0007019 + ZFA:0007019 uberon - UBERON:0005427 - corneal primordium + UBERON:0009611 + midbrain neural plate - - - + + + + + + + + + + + + + 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 + A neural plate that develops_from a presumptive midbrain. + OBOL:automatic - + - - + + + + + + + + + + + + + + - + - 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 + + + + + + + A neural plate that develops_from a presumptive hindbrain. + TAO:0007022 + ZFA:0007022 uberon - UBERON:0005496 - - neural tube lateral wall + UBERON:0009614 + hindbrain neural plate - - - Portion of tissue on the side of the lumen of the neural tube. - ZFA:0001435 + + + + + + + + + + + + + + ZFA - - - lateral wall neural tube - ZFA:0001435 + + + + + + + + + ZFA + + + + + A neural plate that develops_from a presumptive hindbrain. + OBOL:automatic - + - - - + + - + - + - 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 + + + + + + + TODO - developmental relationships for lines + TAO:0007044 + ZFA:0007044 + MHB neural plate + midbrain-hindbrain boundary neural plate uberon - UBERON:0005498 - - primitive heart tube + UBERON:0009615 + midbrain hindbrain boundary neural plate - + - - + + ZFA - - - Multi-tissue structure that arises from the heart rudiment and will become the heart tube. - ZFA:0000149 + + + + + + + + + https://github.com/obophenotype/uberon/issues/438 + Bgee:AN - + - primitive heart tube - EMAPA:16215 + MHB neural plate + - - - early primitive heart tube - EMAPA:16208 + + + midbrain-hindbrain boundary neural plate + ZFA:0007044 - + - + - + - - + + - + - + - A neural tube lateral wall that is part of a rhombomere. - EMAPA:32819 - EMAPA:35364 + + + + + + + + + + + + + + + + + + + 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 - future hindbrain lateral wall - UBERON:0005501 - rhombomere lateral wall + early midbrain + future midbrain + mesencephalon + UBERON:0009616 + + presumptive midbrain - + + + + + + + + + ZFA + + + + + + + + + + + ZFA + + + - A neural tube lateral wall that is part of a rhombomere. + A presumptive structure that has the potential to develop into a midbrain. OBOL:automatic - + + + presumptive mesencephalon + ZFA:0000148 + + + - future hindbrain lateral wall - EMAPA:35364 + early midbrain + + + + + + future midbrain + + + + + + mesencephalon + EHDAA2:0000615 - + - - + + + - + - - + + - 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 + 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 - immature gonad - UBERON:0005564 - - - - gonad primordium + somitomere + somitomeric mesoderm + UBERON:0009617 + head paraxial mesoderm - - - - Obol - - - + - + - ZFA + EHDAA2 - + - 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 + Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles. + - + - future gonad - + cephalic paraxial mesenchyme + - + - gonadal primordium - ZFA:0001262 + cephalic paraxial mesoderm + - + - primitive gonad - + cranial paraxial mesenchyme + - + - undifferentiated gonad - ZFA:0001262 + cranial paraxial mesoderm + - - - immature gonad - + + + head paraxial mesenchyme + + EHDAA2:0000736 - + - - - - - - - - - - - - - - - + + + - + - - + + - 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 + EHDAA2:0002094 + trunk and cervical paraxial mesenchyme uberon - cranial somite - UBERON:0005594 - head somite + trunk paraxial mesenchyme + UBERON:0009618 + trunk paraxial mesoderm - + - - - - 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 + trunk and cervical paraxial mesenchyme + EHDAA2:0002094 - + - cranial somite - XAO:0000313 + trunk paraxial mesenchyme + - + - + - + @@ -62855,27287 +137326,29288 @@ - + - A somite that is part of a trunk. - AAO:0010385 - EHDAA2:0003438 - EMAPA:16184 - XAO:0000314 + A somite that is part of a tail. + AAO:0010383 + EMAPA:16860 + XAO:0003143 uberon - UBERON:0005598 - trunk somite + UBERON:0009621 + tail somite - + - A somite that is part of a trunk. + A somite that is part of a tail. OBOL:automatic - - - - - - - - - - - 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 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 + + EMAPA:37092 + MA:0001987 + NCIT:C52947 + UMLS:C1708633 + labial artery uberon - anterior epithelium of lens vesicle - anterior surface of lens - UBERON:0005614 - lens anterior epithelium + UBERON:0009657 + artery of lip - - - 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 + EMAPA:37092 + MA:th - - - lens subcapsular epithelium - + + + UMLS:C1708633 + ncithesaurus:Labial_Artery - + - subcapsular lens epithelium - FMA:70612 - - - - - anterior epithelium of lens vesicle - EMAPA:17304 - - - - - anterior surface of lens - FMA:58889 + labial artery + MA:0001987 - + - + - + - - + + - + - - + + - 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 + Nucleus located in the midbrain. + + TAO:0002209 + ZFA:0001665 uberon - intestinal vein - UBERON:0005617 - mesenteric vein + UBERON:0009661 + midbrain nucleus - + - A vein that returns blood from the intestines. - - MESH:A07.231.908.670.385 - - - - - UMLS:C0025473 - ncithesaurus:Mesenteric_Vein - - - - - intestinal vein - + Nucleus located in the midbrain. + ZFIN:curator - + - + - + - + - + - + - An epithelium that is part of a anterior chamber of eyeball. - EHDAA2:0000130 + Nucleus located within the hindbrain. + TAO:0002177 + ZFA:0001658 uberon - UBERON:0005638 - anterior chamber epithelium + UBERON:0009662 + hindbrain nucleus - + - An epithelium that is part of a anterior chamber of eyeball. - OBOL:automatic + Nucleus located within the hindbrain. + ZFIN:curator - + - + - + - - + + - + - + - An epithelium that is part of a lens vesicle. - EHDAA2:0000987 - EMAPA:17165 - VHOG:0000532 + + + + + + + + + + + + + An anatomical space that surrounded_by a embryonic cloaca. + EHDAA2:0004586 uberon - UBERON:0005656 - lens vesicle epithelium + UBERON:0009669 + embryonic cloacal lumen - + - An epithelium that is part of a lens vesicle. + An anatomical space that surrounded_by a embryonic cloaca. OBOL:automatic - + - + - + + - + + + + + + + + + + + + + - + - An anatomical cavity that is part of a lens vesicle. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] - cavity of lens - lens cavity - EHDAA2:0000986 - EMAPA:17164 - VHOG:0000531 - cavity of lens vesicle + An anatomical space that surrounded_by a rectum. + + EHDAA2:0004587 + EMAPA:18388 + FMA:14598 + lumen of rectum uberon - UBERON:0005688 - lens vesicle cavity + UBERON:0009670 + rectal lumen - - - An anatomical cavity that is part of a lens vesicle. - OBOL:automatic + + + + + + + + + cjm - - - (...) 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 + + + + + + + + + EHDAA2 - - - lens cavity - EHDAA2:0000986 + + + An anatomical space that surrounded_by a rectum. + OBOL:automatic - + - cavity of lens vesicle - EMAPA:17164 + lumen of rectum + FMA:14598 - + - + - + - + - - + + + - + - Mesenchyme that is part of a optic eminence. - EHDAA:942 - EMAPA:16324 - RETIRED_EHDAA2:0001310 - VHOG:0001073 + + + + + + + + + + + + + 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 - UBERON:0005702 - optic eminence mesenchyme + endocardial lining of right ventricle + right ventricle endocardial tissue + UBERON:0009712 + endocardium of right ventricle - + + + + + + + + + EHDAA2 + + + + + + + + + + + FMA + + + - Mesenchyme that is part of a optic eminence. - OBOL:automatic + 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 - + - + - + - + - - - + + - + - A venous system that is part of a hindbrain. - EHDAA2:0000776 - EMAPA:18632 - VHOG:0001322 + + + + + + + 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 - rhombencephalon venous system - UBERON:0005720 - hindbrain venous system + endocardial lining of left ventricle + left ventricle endocardial tissue + UBERON:0009713 + endocardium of left ventricle - + + + + + + + + + FMA + + + - A venous system that is part of a hindbrain. - OBOL:automatic + 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 + + + - rhombencephalon venous system - VHOG:0001322 + endocardial lining of left ventricle + EMAPA:17338 + + + + + left ventricle endocardial tissue + VHOG:0001233 - + - + - + - - + + - - - + + - + - - + + + An anatomical cavity that surrounded_by a stomodeum. + lumen of stomatodaeum + lumen of stomodeum + stomatodeal cavity + uberon + UBERON:0009715 + stomodeal lumen + + + + + An anatomical cavity that surrounded_by a stomodeum. + OBOL:automatic + + + + + + + + + + - - + + - - + + - 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 + + + + + + + EHDAA2:0004621 + EMAPA:32754 + FMA:293087 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 + pharyngeal arch endoderm + UBERON:0009722 + entire pharyngeal arch endoderm - + - + - ZFA + EHDAA2 - + - - + + - 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 + EHDAA2 - + - pronephric primordium - XAO:0000264 + pharyngeal arch endoderm + EHDAA2:0004621 - + - - + + + + + + + + + + + + + + - - + + - 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 + 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 - UBERON:0005725 - + limb mesoderm + UBERON:0009749 - - olfactory system + limb mesenchyme - + - 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 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 - - - The sensory system used for olfaction (the sense of smell).[AAO] - 2012-06-20 - AAO:0000978 - AAO - AAO:EJS + + + EMAPA mapping from TH + EMAPA - - - UMLS:C0228065 - ncithesaurus:Olfactory_System + + + limb mesoderm + Geisha:syn + NCBITaxon:8782 - - - - - BILA:0000139 - uberon - UBERON:0005726 - - chemosensory system - - - - - + - + - + - - + + - - + + - - + + - 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 + 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:0005729 - pectoral appendage field + UBERON:0009751 + + cardiac mesenchyme - + - 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 + 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 - - - pectoral fin field - ZFA:0001453 - + + + heart mesenchyme + EMAPA:36438 - + - + - + - - + + - - + + - - + + - 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 + A ganglion that is part of a abdominal segment of trunk. + uberon - UBERON:0005730 - pelvic appendage field + UBERON:0009758 + abdominal ganglion - + - A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme. + A ganglion that is part of a abdominal segment of trunk. 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 + + + + + + + + + + + + + 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:0005732 - - paired limb/fin field + UBERON:0009778 + + pleural sac - + - + - ISBN:9780878932504 - ZFA-inferred + FMA - + + + + + + + + + FMA-abduced-lr + + + - A ring of cells capable of forming a limb or paired fin[Gilbert,modified]. - ISBN:9780878932504 + 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 - + - + - + - - + + + + + + + + + + - + - - + + - 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 + + + + + + + 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 - external coat - tunica adventitia vasorum - tunica externa vasorum - UBERON:0005734 - tunica adventitia of blood vessel - Illu:artery.jpg + acini + UBERON:0009842 + glandular acinus + http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png - - - - 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 - + The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. + - - - tunica adventitia vasorum - - + + + acinus + FMA:55588 - + - tunica externa vasorum - - + acini + + - + - + - + - - + + - - + + - + - A tunica intima that is part of a artery. - - EMAPA:36293 - EV:0100028 - FMA:14272 - galen:IntimaOfArtery - arterial intima - tunica interna (intima)(arteriae) + + + + + + + + + + + + + + + + + + + An anatomical space that surrounded_by a primitive urogenital sinus. + EHDAA2:0002142 uberon - UBERON:0005740 - tunica intima of artery + UBERON:0009844 + urogenital sinus lumen - - - A tunica intima that is part of a artery. - OBOL:automatic - - - - - arterial intima - EV:0100028 + + + + + + + + + EHDAA2 - - - tunica interna (intima)(arteriae) - FMA:14272 + + + An anatomical space that surrounded_by a primitive urogenital sinus. + OBOL:automatic - + - - + + + + + + + + + + + + + - - + + - An outermost connective tissue covering of an organ, vessel, or other structure[WP]. - - - BTO:0002010 - FMA:45635 - tunica advetitia - tunica externa + 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:0005742 - - adventitia - http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg + UBERON:0009845 + urogenital sinus mesenchyme - - - An outermost connective tissue covering of an organ, vessel, or other structure[WP]. - + + + + + + + + + + + + + + - - - tunica advetitia - + + + Mesenchyme that surrounds primitive urogenital sinus. + OBOL:automatic - - - tunica externa - FMA:45635 + + + UGM + + - + - + - + - + - + + + + - + - 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 + + + + + + + + + + + + + An epithelium that is part of a embryonic cloaca. + cloacal epithelium + EHDAA2:0004585 uberon - UBERON:0005744 - - bone foramen - http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png + UBERON:0009846 + embryonic cloacal epithelium - - - Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves. - TAO:curator + + + + EHDAA2 - - - 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 + + + + + + + + + EHDAA2 - - - foramen - ZFA:0005386 + + + + + + + + + EHDAA2 - - - foramens@fr - TAO:0001736 + + + An epithelium that is part of a embryonic cloaca. + OBOL:automatic - - - foramina@fr - TAO:0001736 + + + cloacal epithelium + EHDAA2:0004585 - + - - + + + + + + + + + + + + + + - + - 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 + Branch or outpocketing of the digestive tract. + FBbt:00100316 uberon - UBERON:0005753 - caudal part of nephrogenic cord + diverticulum of gut + intestinal pouch + UBERON:0009854 + digestive tract diverticulum - + - 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 + Branch or outpocketing of the digestive tract. + - - - rear portion of nephrogenic cord - + + + diverticulum of gut + FBbt:00100316 - + - - + + + + + + + + + + + + + - - + + - The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros. + galen:Diverticulum + pouch uberon - UBERON:0005754 - rostral part of nephrogenic cord + diverticulum + UBERON:0009856 + sac - - - - The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros. - - - + - + - + - - + + - + + - - + + - A acellular anatomical structure that is the bounding layer of a anatomical structure. - FMA:63871 + 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:0005764 - acellular membrane + UBERON:0009870 + zone of stomach + http://upload.wikimedia.org/wikipedia/commons/2/29/Regions_of_stomach.svg - + - A acellular anatomical structure that is the bounding layer of a anatomical structure. - OBOL:automatic + 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 - + - - + + + + - + - 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 + EFO:0003704 + TAO:0005041 + ZFA:0005041 + ALPM uberon - basement membrane - UBERON:0005769 - basement membrane of epithelium + UBERON:0009881 + + anterior lateral plate mesoderm - + - - 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 + + ZFA - - - basement membrane of connective tissue - FMA:63872 + + + + + + + + + ZFA - + - membrana basalis - - - - - - - basement membrane - FMA:63872 + ALPM + ZFA:0005041 - + - + + + + - + - - + + - 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 + + + + + + + + + + + + + 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 - nephric cord - UBERON:0005792 - nephric ridge + SHF + UBERON:0009889 + secondary heart field - - - 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 + + + + + + + + + GO:0003129 - - - - - - - - - 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 + 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 condensation - EMAPA:25351 + + + Mesenchyme that is part of a developing face. + OBOL:automatic - + - - + + + + + + + + + + + + + + - + - - + + - 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 + + + + + + + An anatomical wall that is part of a ureter. + + FMA:15888 + ureteral wall uberon - UBERON:0005863 - cartilaginous condensation + UBERON:0009916 + wall of ureter - - - - AEO + + + An anatomical wall that is part of a ureter. + OBOL:automatic - - - + + + ureteral wall + FMA:15888 + + + + + + + + + + + + + + + + + + + + - + - - AEO - + + + + + + + + + + + + + + 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 + - + - 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 + The smooth muscle tissue surrounding the epithelium of the ureter. + MP:0011426 - + - cartilagenous condensation - EHDAA2:0003147 + ureteral smooth muscle + MP:0011426 - + - chondrogenic condensation - VSAO:0000092 + ureteral smooth muscle layer + EMAPA:28844 - + - - - + + + - - - - - - - + - 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 + EHDAA2:0001315 + EHDAA:1122 uberon - UBERON:0005866 - pre-cartilage condensation + UBERON:0009920 + optic neural crest - + - - AEO + + EHDAA2 - + - + - 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. - + EHDAA2 - + - - - - - - - - + + + + + + + + + + + + + - - + + - 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 + 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 - mandibular process - mandibular swelling - prominentia mandibularis - UBERON:0005867 - - mandibular prominence + UBERON:0009953 + post-embryonic organism + https://github.com/obophenotype/uberon/issues/667 - + - 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 + A multicellular organism that existence_starts_with a post-embryonic stage. + OBOL:automatic - - - UMLS:C1512982 - ncithesaurus:Mandibular_Prominence + + + TS28 mouse + MA:0002405 - - - mandibular process - + + + post-hatching organism + - - - mandibular swelling + + + post-natal organism - - - prominentia mandibularis - - + + + postnatal mouse + MA:0002405 - + - - + + + + + + + + + + + + + + + + + + + + + - - + + - 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 + + + + + + + + + + + + + + + + + + + + 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 - - - 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 + + + + cjm - - - basicranial region - ZFA:0001414 + + + Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia. + + - - - occipital part of head - FMA:49187 + + + 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 - + - occipital region of head - FMA:49187 + neurogenic placodes + ZFA:0001309 + - + - back of head - FMA:49187 + placodae neurogenicae + + - + - - + + + + + + + + + + + + + + - - + + - - + + - 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 + + + + + + + An 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:0005906 - See notes for serous membrane - serous sac + UBERON:0009958 + bladder lumen - + + + + + + + + + + + + + + FMA + + + + + + + + + + + FMA + + + + + + + + + + + EHDAA2 + + + - 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 + An 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 - + - + - + - - + + + + + + - - - 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 - - - - - - - - - - + + - - + + - + - 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 + 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 - skeleton axiale - UBERON:0005944 + UBERON:0009972 - - 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 + ureteropelvic junction - - - Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. - - - - FMA:71221 - VSAO:0000056 + + + + + + + + + MP - - - Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] - 2012-08-14 - VSAO:0000056 - VSAO - PSPUB:0000170 + + + The junction between the ureter and the renal pelvis of the kidney. + MP:0011487 - + - UMLS:C0222645 - ncithesaurus:Axial_Skeleton + EMAPA:37782 + MA:th - - - skeleton axiale - - + + + pelviureteric junction + FMA:15898 - + - + - + - - + + + + + + - - + + - + - - + + - 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 + 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:0005985 + UBERON:0009973 - coronary vessel + ureterovesical junction - - - Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation - MP:0010551 - - - - - - - - - + + + - + - - 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. - - + + MP - - - 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 + + + 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:37883 + EMAPA:37783 MA:th - - - body hair or bristle - GO:GO - - - - - adnexae cutis - - - - - - - skin adnexa - - - - - - skin appendage - + + + 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:0006056 - posterior surface of head + 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 mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue. + Mesenchyme that is part of a pharyngeal arch 6. + EHDAA2:0004076 + EMAPA:32765 + FMA:318209 + 6th pharyngeal arch mesenchyme uberon - UBERON:0006170 - mesonephric capsule + 6th branchial arch mesenchyme + pharyngeal arch 6 mesenchyme + UBERON:0010031 + 6th arch mesenchyme - + - 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 + Mesenchyme that is part of a pharyngeal arch 6. + OBOL:automatic - + - - + + + - + - - - - - - - - - - - - + - - - - + 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. + + + + + + + + + + + + - + - - - - - - - - - + + + + - - + + - 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 + Mesenchyme that is part of a pharyngeal arch 1. + EMAPA:16128 + mesenchyme of 1st arch uberon - oral membrane - oral plate - oropharyngeal membrane - pharyngeal membrane - UBERON:0006211 - - - buccopharyngeal membrane - http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png + UBERON:0010042 + 1st arch mesenchyme - - - - - - - - - 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 - + Mesenchyme that is part of a pharyngeal arch 1. + OBOL:automatic - - - pharyngeal membrane - MP:0012521 - + + + mesenchyme of 1st arch + EMAPA:16128 - + - - + + + + - - - - - - - - - - - - - + - - - - - - - + - 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 + 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 - membrana cloacalis - UBERON:0006217 - - - cloacal membrane - http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png + UBERON:0010046 + entire pharyngeal arch associated mesenchyme - + + + + EHDAA2 + + + - - + + - Wikipedia + EHDAA2 - - - 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 + + + + + + + + + cjm - - - 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 - + + + 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 - - - 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) + + + associated mesenchyme of pharyngeal region + EMAPA:16550 - - - UMLS:C0231056 - ncithesaurus:Cloacal_Membrane + + + entire branchial arch associated mesenchyme + - - - membrana cloacalis - - + + + pharyngeal arch associated mesenchyme + EHDAA2:0001459 - + - + - - - - - - - - - - + - - - - - - - + + - + + - - - - - - - - - - - - - - - - - - - - - - - + - 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 + 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 - UBERON:0006235 - - foregut-midgut junction + gland of oral opening + gland of oral region + mouth gland + oral cavity gland + oral region gland + UBERON:0010047 + oral gland - + - An anatomical junctions that overlaps the foregut and midgut. - OBOL:automatic + Gland of the epithelium lining the oral cavity. The most common are the salivary glands. + ISBN:0073040584 - - - 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 + + + Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa + EHDAA2 - + - - + + + 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 + + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + + + - + - 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 + Mesenchyme that has the potential to develop into a dermis. + check development + EHDAA2:0000598 uberon - embryonic brain - UBERON:0006238 - - - - - future brain + UBERON:0010083 + future dermis - - - 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 + + + + + + + + + EHDAA2 - - - presumptive brain - ZFA:0000146 + + + + + + + + + EHDAA2 - - - encephalon - NLX:94995 + + + + + + + + + XAO - - - embryonic brain - BTO:0004726 + + + Mesenchyme that has the potential to develop into a dermis. + OBOL:automatic - + - + + + + + + + + + + + + + - - + + - - + + + + + + + + - + - 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 + A structure that will develop into a diaphragm. + EHDAA2:0000599 uberon - UBERON:0006241 - - - future spinal cord + UBERON:0010084 + future diaphragm - + - - + + 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 structure that will develop into a diaphragm. + - + - + - - - - - - - - - - + - - - - - - - + + - + - + - - + + + + + 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 + + + + + + + + + + + - - + + - + + + + + + + + - - - - - - - + + - An anatomical junctions that overlaps the mouth and foregut. - EHDAA:534 - EMAPA:16258 - RETIRED_EHDAA2:0001205 - VHOG:0000592 + A developing anatomical structure that has the potential to develop into a myelencephalon. + EHDAA2:0000640 uberon - UBERON:0006264 - - mouth-foregut junction + UBERON:0010096 + future myelencephalon - + - An anatomical junctions that overlaps the mouth and foregut. + A developing anatomical structure that has the potential to develop into a myelencephalon. OBOL:automatic - + - - - - - + + + + + + + + + + + + + - - + + - 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 + A gray matter that has the potential to develop into a superior salivatory nucleus. + EHDAA2:0004644 uberon - UBERON:0006267 - - notochordal plate + UBERON:0010125 + future superior salivatory nucleus - - - - EHDAA2 - - - - - - - - - - - EHDAA2 + + + A gray matter that has the potential to develop into a superior salivatory nucleus. + OBOL:automatic + + + + + + + + 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 + - + - 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 + Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers. + - - - 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 - + + + specialized conducting tissue of heart + FMA:83378 - - - UMLS:C1518429 - ncithesaurus:Notochordal_Plate + + + specialized muscle tissue of heart + FMA:83378 - + - - + + + + + + + + + + + + + - - + + - 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 + A mucous secretion that is produced by glands in the epidermis. 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 + epidermal mucus + skin mucous + UBERON:0010152 + skin mucus - - - - - - - - - EHDAA2 - - - + - A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot - + A mucous secretion that is produced by glands in the epidermis. + - - - UMLS:C1518430 - ncithesaurus:Notochordal_Process + + + epidermal mucus + BTO:0005082 - + - - - - - - - - + + + + + + + + + + + + + + - + - - + + - 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 + An anatomical cavity that surrounded_by a blood vessel. + + FMA:312610 + blood vessel lumen 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 + UBERON:0010161 + lumen of blood vessel - - - - - - - - - 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 + An anatomical cavity that surrounded_by a blood vessel. + OBOL:automatic - + - + - - - - - + - - + + - - + - + - - + + - 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 + The distal end of the tail. + EMAPA:37760 + MA:0002848 + XAO:0004057 + tail tip uberon - chamber of eye - UBERON:0006311 - chamber of eyeball + end of tail + UBERON:0010162 + + post-anal tail tip - + + + + + + + + + MA + + + - A segment of the eyeball that is filled with refractive media + The distal end of the tail. - + - EMAPA:37529 + EMAPA:37760 MA:th - - - UMLS:C0459556 - ncithesaurus:Chamber_of_the_Eye - - - - - eye chamber - MA:0002459 - - - + - eyeball chamber - FMA:58071 + tail tip + MA:0002848 - + - chamber of eye - BTO:0002085 + end of tail + MA:0002848 - + - - + + + + + + + + + + + + + - + - Body substance in a liquid or semi-solid state in the eyeball which serves to refract light. - ocular refraction - MA:0001911 + 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:0006312 - ocular refractive media + UBERON:0010187 + female urethral gland - + - Body substance in a liquid or semi-solid state in the eyeball which serves to refract light. - + An urethral gland that is part of a female urethra. + OBOL:automatic + + + + + urethral gland (female) + FMA:21444 - + - - - 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 + + + A roughly circular bulge in a surface. + requires review + AEO:0000205 + EHDAA2:0003250 + FMA:82506 uberon - UBERON:0006314 - - bodily fluid + UBERON:0010188 + protuberance - - - 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 + + + + FMA - - - body fluid - GAID:266 + + + A roughly circular bulge in a surface. + EHDAA2:0003250 - + - + - - - - - - 2 - - - - - 2 - - - - + + + + + - + + - - + + - An artery that connects two larger arteries. - - EMAPA:18598 - MA:0001938 - NCIT:C52851 - UMLS:C1707451 + part_of in EHDAA2. Only child in MA. + EHDAA2:0001762 + EMAPA:17010 + EMAPA:17328 + MA:0001872 uberon - UBERON:0006347 - Grouping for anterior and posterior - communicating artery + 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 + + + - An artery that connects two larger arteries. - ncithesaurus:Communicating_Artery + 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 - - - UMLS:C1707451 - ncithesaurus:Communicating_Artery + + + paired dorsal aortae + EHDAA2:0000410 - + - - - - - - - - - - - - - + + - - + + - inferred from artery - EMAPA:18646 - MA:0002227 + + + + + + + EHDAA2:0004512 uberon - UBERON:0006355 - superior vesical vein + UBERON:0010191 + aortic system - + - - true - MA + + + + + + + Wikipedia - + - + - + - - + + - + - - + + - A portion of organism substance that secreted_by a zone of skin. - MA:0002537 - skin fluid/secretion + + + + + + + + + + + + + One of the laterally paired arteries that supply the gonads. + + gonadal artery uberon - skin fluid - skin substance - UBERON:0006535 - skin secretion + UBERON:0010192 + genital artery - - - A portion of organism substance that secreted_by a zone of skin. - OBOL:automatic + + + + + + + + + Wikipedia - - - skin fluid/secretion - MA:0002537 + + + One of the laterally paired arteries that supply the gonads. + + ISBN:0073040584 - + - - - - - - - - - - - - - - - - - - - - A portion of organism substance that secreted_by a respiratory system. - - EMAPA:36550 - MA:0002533 - NCIT:C13722 - UMLS:C1514899 + + + An anatomical boundary that corresponds to some physical discontinuity. + CARO:0001004 uberon - respiratory system fluid - respiratory system secretion - UBERON:0006538 - respiratory system fluid/secretion + 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 - - - A portion of organism substance that secreted_by a respiratory system. - OBOL:automatic + + + + CARO - - - UMLS:C1514899 - ncithesaurus:Respiratory_System_Fluid_or_Secretion + + + An anatomical boundary that corresponds to some physical discontinuity. + CARO:0001004 - + - + - + - - + + - + - A vasculature that is part of a kidney. - EMAPA:28457 - TAO:0005305 - ZFA:0005305 + 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 - UBERON:0006544 - - kidney vasculature + tail vasculature + UBERON:0010204 + tail vasculature - + - A vasculature that is part of a kidney. + 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 + - + - - - - - - - - - - - - - + + + + - + - A tube in the kidney that collect and transport urine. - in ZFA this is defined as part of mesonephros - TAO:0005289 - ZFA:0005289 + + + + + + + + + + + + + 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:0006553 - renal duct + UBERON:0010212 + laryngeal apparatus - + + + + + + + + + EHDAA2 + + + - A tube in the kidney that collect and transport urine. - ZFIN:ZDB-PUB-071029-9 + 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 - - - in ZFA this is defined as part of mesonephros - ZFA + + + laryngeal cartilage system + EHDAA2:0000904 - + - - - - - - - - - - - - - + + + + - + + + + + + + + + + + + + - A tube that is part of a excretory system. uberon - UBERON:0006555 - excretory tube + UBERON:0010213 + laryngeal pre-cartilage condensation - - - A tube that is part of a excretory system. - OBOL:automatic + + + + + + + + + EHDAA2-abstracted + + + + + + + + + + + EHDAA2-abstracted - + - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + EHDAA2:0004085 uberon - anterior part of foregut - pharyngeal tube - UBERON:0006562 - - - pharynx + UBERON:0010221 + Many sources say: thyroid cartilage from arch 4 other laryngeal cartilage (cricoid/arytenoid) from 6? + laryngeal associated mesenchyme - - - The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. - GO:0060465 + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + + + + + + + Wikipedia + + + + + + + + + + + Wikipedia + + + + + + + + + + + Wikipedia - + - - - - - - - - - - - - - - - - - - + + - - - - - - - + - - + + - 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 + 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 - 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 + UBERON:0010227 + future cardiac atrium - - - 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: - + + + + + + + + + ZFA - - - FMA also has FMA:29321 but it's not clear how this differs - FMA + + + Multi-tissue structure that is part of the heart tube and will become the cardiac atrium. + ZFA:0001718 - - - UMLS:C0821671 - ncithesaurus:Pectinate_Line + + + presumptive atrium heart tube + ZFA:0001718 - + - linea pectinata canalis analis - FMA:75383 - FMA:TA - + primordial atrium + FMA:71005 - + - pectinate line of anal canal - FMA:75383 + 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 - - - Hilton's 'white line' - EMAPA:19159 + + + The core globe-shaped component of the camera-type eye. + UBERON:cjm - - - dentate line - + + + eye globe + VHOG:0001616 - - - linea anocutanea - - + + + eyeball + FMA:12513 - + - recto-anal junction - + eye + - + - site of anal membrane - EMAPA:19159 + globe + HP:0100886 + MIAA:0000283 - + - + - + - + - - + + - + + - + - - + + - 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 + + + + + + + Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme. + EHDAA2:0000037 uberon - UBERON:0006596 - - presumptive blood + UBERON:0010252 + 1st arch mandibular mesenchyme from neural crest + + + + + inferred + + + + + + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme. + OBOL:automatic + - + - + - + - + - - + + - + + + + - - + + - 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 + + + + + + + + + + + + + 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 - UBERON:0006598 - presumptive structure + branchial arch 3 mesenchyme from neural crest + UBERON:0010255 + 3rd arch mesenchyme from neural crest - + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2-inferred + + + - Portion of embryonic tissue determined by fate mapping to become a structure. - GOC:CVS - GOC:YMB - ZFA:0001116 + 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) + + + - presumptive structures - ZFA:0001116 + 3rd pharyngeal arch mesenchyme derived from neural crest + VHOG:0000571 + + + + + mesenchyme derived from neural crest of mesenchyme of 3rd arch + EMAPA:16404 - + - + - + - + - - + + - + + + + - + - - + + - Presumptive structure of the blastula that will develop into ectoderm. - AAO:0000470 - EFO:0003466 - TAO:0001376 - XAO:0004132 - ZFA:0001376 + + + + + + + + + + + + + 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 - presumptive epidermis - UBERON:0006601 - - presumptive ectoderm + branchial arch 4 mesenchyme from neural crest + UBERON:0010256 + 4th arch mesenchyme from neural crest - + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2-inferred + + + - Presumptive structure of the blastula that will develop into ectoderm. - + Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme. + OBOL:automatic - - - presumptive epidermis - ZFA:0001376 + + + 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 - + - + - + - + - - + + - + + + + - + - - + + - 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. - - - - - - - - - - - + + - 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 + + + + + + + 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 - muscular coat - muscularis - muscularis externa - muscularis propria - transverse muscular fibers - tunica externa - tunica muscularis - UBERON:0006660 - muscular coat + branchial arch 6 mesenchyme from neural crest + UBERON:0010257 + 6th arch mesenchyme from neural crest - - - 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 + + + + EHDAA2 - - - muscularis propria - + + + + + + + + + EHDAA2 - - - transverse muscular fibers - + + + + + + + + + EHDAA2 - - - tunica externa - BTO:0004838 + + + + + + + + + EHDAA2-inferred - - - tunica muscularis - + + + Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme. + OBOL:automatic - + - + - + - - + + - - + - + - A valve that is part of a vein. - FMA:68095 - valve of vein + + + + + + + Mesenchyme that develops_from a rhombencephalon neural crest. + EHDAA2:0004423 uberon - UBERON:0006675 - venous valve + UBERON:0010258 + mesenchyme from rhombencephalic neural crest - - - A valve that is part of a vein. - OBOL:automatic + + + + + + + + + EHDAA2 - - - valve of vein - FMA:68095 + + + Mesenchyme that develops_from a rhombencephalon neural crest. + OBOL:automatic - + - + - + - - + + + + + + - + + + - + - - + + - An anatomical boundary that adjacent_to a epithelium. - FMA:70997 - epithelium surface + + + + + + + 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 - UBERON:0006677 - surface of epithelium + branchial arch 1 mesenchyme from neural crest + UBERON:0010259 + 1st arch mesenchyme from neural crest - + + + + + + + + + EHDAA2-inferred + + + - An anatomical boundary that adjacent_to a epithelium. + Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme. OBOL:automatic - + - epithelium surface - FMA:70997 + mesenchyme derived from neural crest of mesenchyme of 1st arch + EMAPA:16129 - + - + - - - - - + - - + + - - + + - + + 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 + + + + + + + + - - + + - - + + - 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 + 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 - limbus corneae - UBERON:0006761 + UBERON:0010285 - - - 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 + midbrain basal plate - - - 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 + + + + EHDAA2 - - - corneal limbus - FMA:58342 + + + + + + + + + EHDAA2 - - - corneal limbus - GAID:896 + + + + + + + + + ZFA - - - corneal-scleral limbus - + + + Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. + ZFA:0000761 - + - corneoscleral junction - GAID:896 + basal plate midbrain + TAO:0000761 - + - limbus corneae - - + 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 + - - - sclerocorneal junction - FMA:58342 + + + + ZFA - - - sclerocorneal limbus - GAID:896 + + + + + + + + + ZFA - - - limbus corneae - - + + + Portion of neural tube that gives rise to the midbrain. + ZFA:0007039 - + - - + + + - + + + uberon + UBERON:0010291 + layer of sclera + + + + + + + + + + + cjm + + + + + + + + + + + + + + + + + + + + + - - + + - 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 + An endothelium that is part of a sclera. uberon - areolar tissue - loose connective tissue - UBERON:0006815 - areolar connective tissue + UBERON:0010294 + scleral endothelium - + - - FMA + + Wikipedia - + - 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 endothelium that is part of a sclera. + OBOL:automatic - + - + - + - + - - + + - + - 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 + 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 - ureteral smooth muscle layer - UBERON:0006855 - muscular coat of ureter + UBERON:0010295 + substantia propria of sclera - + - - - - - - - FMA + + Wikipedia - + - A muscular coat that is part of a ureter. + A stroma that is part of a sclera. OBOL:automatic - - - muscular coat of ureter - FMA:15893 + + + UMLS:C1704397 + ncithesaurus:Substantia_Propria - + - muscular layer of ureter - FMA:15893 + scleral stroma + FMA:58365 - + - muscularis of ureter - FMA:15893 + stroma of sclera + FMA:58365 - + - tunica muscularis (ureter) - FMA:TA - + subsantia propria sclerae + FMA:58365 - + - tunica muscularis ureteris + substantia propria sclerae + FMA:58365 FMA:TA - - - - ureteral smooth muscle layer - EMAPA:28567 - - + - - + + + + + + + + + + + + + + - - + + - - + + - 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 + 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 - rectal part of digestive tract - terminal section of digestive tract - UBERON:0006866 - terminal part of digestive tract + UBERON:0010299 + scleral mesenchyme - + - The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. - - - - - - rectum - FBbt:00005756 + Mesenchyme surrounding the developing optic cup which develops into the sclera. + + - + - + - + - + - + + - + - A vasculature that is part of a organ. - FMA:74612 - organ vasculature - set of blood vessels of organ + An epithelium that is part of a extraembryonic structure. + extra-embryonic epithelium 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 + UBERON:0010303 + extraembryonic epithelium + + + + + An epithelium that is part of a extraembryonic structure. + OBOL:automatic - + - + - + - - + + - - + + - + - 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 + + + + + + + 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 - cranial mesoderm - head mesoderm - UBERON:0006904 - - - head mesenchyme from mesoderm + UBERON:0010312 + immature eye - - - - ZFA - - - + - + - EHDAA2 - XAO + definitional - + - 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 + Developing anatomical structure that develops into the eyeball and associated structures. + ZFA:0001678 - - - head mesoderm - AAO:0011051 - UBERON:0005280 + + + Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO] + 2012-08-14 + TAO:0002201 + TAO + ZFIN:curator - + - + - + - - + + - + - - + + - Mesenchyme that is part of a mandibular prominence. - EHDAA2:0001062 - EHDAA:5861 - EHDAA:5873 - EMAPA:17357 - mesenchyme of mandibular process - mesenchyme of mandibular prominence + An anatomical structure that develops from the neural crest. + Grouping term for query purposes uberon - UBERON:0006905 - mandibular process mesenchyme + UBERON:0010313 + + neural crest-derived structure - + - Mesenchyme that is part of a mandibular prominence. - OBOL:automatic - - - - - mesenchyme of mandibular process - EMAPA:17357 - - - - - mesenchyme of mandibular prominence + An anatomical structure that develops from the neural crest. - + - + - + - - + + - - - - - - - + + - - + + - 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 + An anatomical structure that has some part that develops from the neural crest. + Grouping term for query purposes uberon - UBERON:0006909 - lumen of digestive tract + UBERON:0010314 + + structure with developmental contribution from neural crest - + - 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 + An anatomical structure that has some part that develops from the neural crest. + + + + + + + + + + + + + + + + + uberon + UBERON:0010316 + germ layer / neural crest + - - - lumen of gut - FMA:45677 + + + + GO + ZFA - + - + - + - + - + + - + - 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 + + + + + + + + + + + + + A skeletal element that is part of a orbital region. uberon - UBERON:0006913 - lip epithelium + eye skeleton + ocular skeleton + skeletal element of orbital region + UBERON:0010321 + skeletal element of eye region - - - 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 + + + A skeletal element that is part of a orbital region. + OBOL:automatic - + - - - 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 + + + + + + + + + + + + + + + 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 - UBERON:0006914 - squamous epithelium + cranium + UBERON:0010323 + cranial skeletal system - + - An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. - + Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus. + + GO_REF:0000034 + PSPUB:0000170 + VSAO:0000049 - - - 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 + + + 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 - - - UMLS:C0221909 - ncithesaurus:Squamous_Epithelium + + + 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 + - + - - + + + + + + + + + + + + + - + - 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 + Mesenchyme that is part of a limb bud. uberon - UBERON:0006965 - - vascular cord + UBERON:0010328 + limb bud mesenchyme - + - 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 + Mesenchyme that is part of a limb bud. + OBOL:automatic - + - + - + - + - - - A capillary that is part of the coronary system. - ZFA:0005813 - heart capillary + + + + + + + + + + + + + + Mesenchyme that is part of a limb/fin bud. uberon - UBERON:0006966 - coronary capillary + UBERON:0010329 + paired limb/fin bud mesenchyme - - - A capillary that is part of the coronary system. - + + + + + + + + + EHDAA2-abduced - - - heart capillary - GO:0003248 + + + Mesenchyme that is part of a limb/fin bud. + OBOL:automatic - + - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that is part of a extraembryonic membrane. 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 + UBERON:0010333 + extraembryonic membrane mesenchyme - + - - via morphological boundary in CARO + + + + + + + EHDAA2-abduced - + - 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 + Mesenchyme that is part of a extraembryonic membrane. + OBOL:automatic - + - - - - - - - - - + + + + + + + + + + + + + + + + + + + - + - + - - + + - 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 + Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme. + EHDAA2:0004603 uberon - cardiac mesoderm - cardiogenic mesoderm - cardiogenic region - heart primordia - UBERON:0007005 - - - cardiogenic splanchnic mesoderm + UBERON:0010336 + mandibular process mesenchyme from neural crest - - - 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 + + + + EHDAA2 - - - cardiogenic mesoderm - + + + + + + + + + EHDAA2 - - - cardiogenic region - + + + + + + + + + EHDAA2 - - - heart primordia - XAO:0000235 + + + Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme. + OBOL:automatic - + - + - + - - + + - - + + - + + + - - + + - - + + - Organism at the cleavage stage. - BILA:0000058 + + + + + + + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme. + EHDAA2:0004604 uberon - UBERON:0007010 - cleaving embryo + UBERON:0010337 + mandibular process mesenchyme from head mesenchyme - + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + - Organism at the cleavage stage. + 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 mandibular mesenchyme. + EHDAA2:0000036 + uberon + UBERON:0010339 + 1st arch mandibular mesenchyme from head mesenchyme + + + + + + EHDAA2 + + + + + - - + + - - + + EHDAA2 + + + + + - - + + - - 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 + + EHDAA2 - - - UMLS:C1514442 - ncithesaurus:Primordial_Gut + + + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme. + OBOL:automatic - + - - + + + + + + + + + + + + + + + + + + + + - + - Cranial neural crest that migrates into the mandibular arch. - TAO:0007064 - XAO:0000024 - ZFA:0007064 + + + + + + + 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:0007098 - mandibular neural crest + UBERON:0010341 + 1st arch mesenchyme from head mesenchyme - + - - ZFA + + EHDAA2 - + - + - ZFA + EMAPA - + - Cranial neural crest that migrates into the mandibular arch. - ZFA:0007064 + 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 - + - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - adult heart - UBERON:0007100 - - Gene notes: Bmp, Nkx, Gata - primary circulatory organ + branchial arch 3 mesenchyme from head mesenchyme + UBERON:0010344 + 3rd arch mesenchyme from head mesenchyme - - - A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. - GO:0007507 + + + + EHDAA2 - - - dorsal tube - + + + + + + + + + EHDAA2 - - - heart - GO:0007507 + + + + + + + + + EHDAA2 - - - adult heart - FBbt:00003154 + + + 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 - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + - + - 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 + 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 - presumptive central nervous system - UBERON:0007135 - - neural keel + branchial arch 4 mesenchyme from head mesenchyme + UBERON:0010345 + 4th arch mesenchyme from head mesenchyme - - - 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 + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 - - - 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 + + + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme. + OBOL:automatic - - - presumptive central nervous system - ZFA:0000131 + + + mesenchyme derived from head mesoderm of mesenchyme of 4th arch + EMAPA:16771 - + - + - + - - + + + + + + - + + + + - + - - + + - An anatomical cavity that surrounded_by a midgut. - EMAPA:18377 - FMA:54366 - midgut lumen + 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 - UBERON:0007147 - lumen of midgut + branchial arch 6 mesenchyme from head mesenchyme + UBERON:0010347 + 6th arch mesenchyme from head mesenchyme - - - An anatomical cavity that surrounded_by a midgut. - OBOL:automatic + + + + EHDAA2 - - - midgut lumen - FMA:54366 + + + + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme. + OBOL:automatic - + - + - + - - + + + + + + - + + - + - - + + - An anatomical cavity that surrounded_by a hindgut. - EMAPA:18396 - FMA:54367 - hindgut lumen + 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:0007148 - lumen of hindgut + UBERON:0010359 + Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme + pharyngeal arch mesenchyme from neural crest - + - An anatomical cavity that surrounded_by a hindgut. + Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme. OBOL:automatic - - - - hindgut lumen - FMA:54367 - - + - + - + - - + + + + + + - + + + - + - - + + - An anatomical cavity that surrounded_by a anal canal. - EMAPA:18836 - FMA:17357 - anal canal lumen + 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:0007158 - lumen of anal canal + UBERON:0010360 + Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme + pharyngeal arch mesenchyme from head mesenchyme - + - An anatomical cavity that surrounded_by a anal canal. + 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 + + + + - anal canal lumen - FMA:17357 + 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 + + + + + + + - + - - + + - + + - - + + - - + + - An anatomical cavity that surrounded_by a colon. - - EMAPA:18945 - FMA:18374 - colon lumen + Epithelium composed of cells that develops from the ectoderm[FMA,modified]. + FMA:69064 + ectoderm-derived epithelium uberon - colonic lumen - UBERON:0007159 - lumen of colon + UBERON:0010371 + ecto-epithelium - + - An anatomical cavity that surrounded_by a colon. - OBOL:automatic - - - - - colon lumen - FMA:18374 - - - - - colonic lumen - FMA:18374 + Epithelium composed of cells that develops from the ectoderm[FMA,modified]. + FMA:69064 - + - + - + - + + + + + - + + + - + - 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 + + + + + + + + + + + + + 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:0007177 - lamina propria of mucosa of colon + UBERON:0010377 + mesenchyme from somatopleure - - - A lamina propria that is part of a colonic mucosa. - OBOL:automatic - - - - - colonic lamina propria - FMA:15657 - - - - - lamina propria mucosae of colon - FMA:15657 + + + + EHDAA2 - - - lamina propria of colonic mucosa - FMA:15657 + + + + + + + + + EHDAA2 - - - lamina propria of colonic mucous membrane - FMA:15657 + + + Mesenchyme that develops_from a somatopleure. + OBOL:automatic - + - + - + - + + + + + - + + + - + - A mesothelium that is part of a serous pericardium. - - BTO:0003157 - EMAPA:16133 - FMA:18149 - mesothelium of pericardium - pericardial mesothelium - serous pericardium mesothelium + + + + + + + + + + + + + Mesenchyme that develops_from a splanchnopleure. + EHDAA2:0001122 uberon - UBERON:0007188 - mesothelium of serous pericardium + UBERON:0010378 + mesenchyme from splanchnopleure - - - A mesothelium that is part of a serous pericardium. - OBOL:automatic - - - - - mesothelium of pericardium - FMA:18149 + + + + EHDAA2 - - - - pericardial mesothelium - FMA:18149 + + + + + + + + + + EHDAA2 - - - serous pericardium mesothelium - FMA:18149 + + + Mesenchyme that develops_from a splanchnopleure. + OBOL:automatic - + - + - + - - + + - - + + - - + + - 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 + + + + + + + An organ cavity that is part of a urethra. + + FMA:19709 + urethral lumen uberon - UBERON:0007213 - - - mesenchyme derived from head neural crest + UBERON:0010390 + lumen of urethra - - - - ZFA - - - + - Mesenchyme that develops_from a cranial neural crest. + An organ cavity that is part of a urethra. OBOL:automatic - + - head mesenchyme from neural crest - EHDAA2:0000735 + urethral lumen + FMA:19709 - + - - + + + - + - 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 - + + 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 + - - - 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) + + + 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 - + - ventral pharyngeal arch 1 - VHOG:0000510 - - - - - ventral mandibular arch - VHOG:0000510 - - - - - ventral visceral arch 1 - VHOG:0000510 + eye surface + MA:0002486 - + - + - + - + - + - + - A tunica media that is part of a artery. - - - EMAPA:36294 - EV:0100029 - FMA:14273 - NCIT:C49321 - UMLS:C1710627 - arterial media - tunica media (arteriae) + An orifice that is part of a lower urinary tract. + EMAPA:35965 + MA:0002867 + urethral orifice uberon - UBERON:0007239 - tunica media of artery + UBERON:0010418 + + urethral opening - + - A tunica media that is part of a artery. + An orifice that is part of a lower urinary tract. OBOL:automatic - - - UMLS:C1710627 - ncithesaurus:Venous_System_Smooth_Muscle_Tissue - - - - - arterial media - EV:0100029 - - - + - tunica media (arteriae) - FMA:14273 + urethral orifice + OBOL:automatic - + - - - - - - - - - - - - - + + + - + - A tunica adventitia that is part of a artery. - - EMAPA:36295 - EV:0100030 - FMA:14274 - arterial adventitia - tunica externa (adventitia)(arteriae) + 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 - UBERON:0007240 - tunica adventitia of artery + ciliary process + processus ciliares + UBERON:0010427 + ciliary processes + http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png - + - A tunica adventitia that is part of a artery. - OBOL:automatic + 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. + - + - arterial adventitia - EV:0100030 + ciliary processes + FMA:76551 - + - tunica externa (adventitia)(arteriae) - FMA:14274 + ciliary processes set + FMA:76551 + + + + + processus ciliares + FMA:TA + + + + + + set of ciliary processes + FMA:76551 + + + + + ciliary process + + + + + + processus ciliares + + - + - - - - - - - - - - - - - + + - - + + - A tunica adventitia that is part of a vein. - - EMAPA:36310 - EV:0100034 - FMA:14355 - tunica externa (adventitia)(venae) - venous adventitia + 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 - UBERON:0007241 - tunica adventitia of vein + 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 tunica adventitia that is part of a vein. - OBOL:automatic + 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. + - - - tunica externa (adventitia)(venae) - FMA:14355 + + + UMLS:C0222649 + ncithesaurus:Flat_Bone - - - venous adventitia - EV:0100034 + + + 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 + + + + + + + - + - - + + - - + + - - + + - A tunica intima that is part of a vein. - - EMAPA:36308 - EV:0100032 - FMA:14353 - tunica interna (intima)(venae) - venous intima + 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:0007242 - tunica intima of vein + UBERON:0010499 + pseudostratified ciliated columnar epithelium - + - A tunica intima that is part of a vein. - OBOL:automatic + 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 - - - tunica interna (intima)(venae) - FMA:14353 + + + UMLS:C0506992 + ncithesaurus:Pseudostratified_Columnar_Ciliated_Epithelium - + - venous intima - EV:0100032 + epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) + FMA:13146 - + - - - - - - - - - - - - - + + - + - A tunica media that is part of a vein. - - EMAPA:36309 - EV:0100033 - FMA:14354 - tunica media (venae) - venous media + Skeletal element that forms as a replacement or substitution of another element or tissue. + VSAO:0000135 + XAO:0004016 + ZFA:0005624 uberon - UBERON:0007243 - tunica media of vein + UBERON:0010522 + replacement element - - - A tunica media that is part of a vein. - OBOL:automatic + + + + VSAO - - - tunica media (venae) - FMA:14354 + + + + + + + + + cjm - - - venous media - EV:0100033 + + + Skeletal element that forms as a replacement or substitution of another element or tissue. + + GO_REF:0000034 + PSPUB:0000170 + VSAO:0000135 - + - - - - - - - - - - - - - - + + - - - - - 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 + + + + + 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 - UBERON:0007269 - - pectoral appendage musculature + microcirculatory vessels + UBERON:0010523 + microcirculatory vessel - - - Any collection of muscles that is part of a pectoral appendage. - OBOL:automatic + + + + + + + + + ZFA - - - pectoral fin muscle - ZFA:0000563 + + + 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 - - - pectoral fin musculature - ZFA:0000563 - + + + microcirculatory vessels + TAO:0005251 + - + - + - + - + - - + - + - 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 + An organ cavity that surrounded_by a bone. + FMA:24021 + bone organ cavity uberon - UBERON:0007270 - pelvic appendage musculature + UBERON:0010527 + cavity of bone organ - + - Any collection of muscles that is part of a pelvic appendage. + An organ cavity that surrounded_by a bone. OBOL:automatic - - - Musculature that is part of the pelvic fin.[TAO] - 2012-08-14 - TAO:0000258 - TAO - TAO:curator - - - - - pelvic fin musculature - ZFA:0000258 - + + + bone organ cavity + FMA:24021 - + - - - - - - - - - - - - - + + - + - Any collection of muscles that is part of an appendage. - currently defined by location rather than attachment - TAO:0000207 - ZFA:0000207 - fin musculature + FMA:24028 + air space of bone uberon - UBERON:0007271 - appendage musculature + UBERON:0010528 + pneumatic cavity of bone - - - Any collection of muscles that is part of an appendage. - OBOL:automatic + + + + FMA - - - fin musculature - ZFA:0000207 - + + + air space of bone + FMA:24028 - + - - - - - - - - - - - - - + + + - - + + - - + + - Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle. - VSAO:0005000 + + + + + + + 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 - cheiropterygium - UBERON:0007272 - pectoral appendage skeleton + limb + UBERON:0010707 + + appendage girdle complex - - - - - - - - - VSAO + + + 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). + + - - - Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle. - VSAO:0005000 - VSAO:NI + + + 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 + + + + - cheiropterygium - VSAO:0005000 - VSAO:NI + limb + FMA:7182 + - + - + - + - - + + - + + - - + + - - + + - The collection of all skeletal elements in a pelvic appendage region. + 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 - UBERON:0007273 - pelvic appendage skeleton + upper limb + upper limb and pectoral girdle + upper limb and shoulder + UBERON:0010708 + + pectoral complex - - - - - - - - - VSAO + + + Appendage girdle complex that when present, encompasses the pectoral appendicular skeleton and the pectoral girdle. + VSAO:0000213 - - - The collection of all skeletal elements in a pelvic appendage region. + + + 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 - + - + - + - - + + - - - - - - - - - - - - - + + - - + + - - + + - 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 + 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 - embryonic rhombencephalon - future hindbrain - rhombencephalon - UBERON:0007277 - - presumptive hindbrain + lower limb + lower limb and pelvic girdle + lower limb and pelvis + UBERON:0010709 + + pelvic complex - - - - - - - - - XAO-abduced + + + Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle. + VSAO:0000215 - - - - - - - - - cjm + + + Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO] + 2012-08-14 + VSAO:0000215 + VSAO + VSAO:MAH - - - 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. - + + + 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 - - - 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 + + + EMAPA:37863 + MA:th - + - presumptive rhombencephalon - ZFA:0000569 + pelvic appendage/girdle complex + VSAO:0000215 - + + + pelvic girdle plus pelvic limb or fin + + + + + + pelvic girdle plus posterior limb or fin + + + + - embryonic rhombencephalon - CALOHA:TS-2118 + lower limb + FMA:7184 + - + - future hindbrain + lower limb and pelvic girdle + - + - rhombencephalon - EHDAA2:0001630 + lower limb and pelvis + - + - + - + - - + + - + + - - - - - - - + - - + + - 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 + Skeletal subdivision that is a segment of the limb skeleton. + note the distinction between this and skeleton of limb + VSAO:0005018 uberon - UBERON:0007280 - presumptive endocardium + UBERON:0010712 + limb skeleton subdivision - - - A presumptive structure that has the potential to develop into a endocardium. - OBOL:automatic + + + + + + + + + VSAO - - - Portion of tissue that is part of the heart tube and will become the endocardium.[TAO] - 2012-08-14 - TAO:0002233 - TAO - ZFIN:curator + + + Skeletal subdivision that is a segment of the limb skeleton. + VSAO:0005018 + VSAO:NI - + - + - + - - + + - + + - + - - + + - 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 - + + + + + + + + + + + + + + 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 + - + - Embryonic structure that gives rise to the midbrain hindbrain boundary. - ZFA:0001187 + The subdivision of the skeleton of either the pectoral or pelvic girdle. + - - - presumptive MHB - + + + 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 - - - presumptive midbrain-hindbrain boundary - ZFA:0001187 + + + 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 - + - + - + - - + + - + - - + + - - + + - A presumptive structure that has the potential to develop into a presomitic mesoderm. - EFO:0003421 - TAO:0000053 - ZFA:0000053 + + + + + + + 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 - presumptive segmental plates - UBERON:0007282 - - presumptive segmental plate + bone of extended limb/fin region + limb bone + UBERON:0010740 + + bone of appendage girdle complex - + - - + + - https://github.com/obophenotype/uberon/wiki/The-neural-crest - EDHAA2 + UBERONREF:0000003 - + - A presumptive structure that has the potential to develop into a presomitic mesoderm. - OBOL:automatic + A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle). + + UBERONREF:0000003 - + - presumptive segmental plates - ZFA:0000053 - + bone of extended limb/fin region + + UBERONREF:0000003 + + + + + limb bone + MA:0000688 + UBERONREF:0000003 - + - + - + - - + + - + - - - - - - - + - - + + - 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 + 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 - UBERON:0007284 - - presumptive neural plate + bone of forelimb or pectoral fin or pectoral girdle + forelimb bone + UBERON:0010741 + + bone of pectoral complex - + - A presumptive structure that has the potential to develop into a neural plate. - OBOL:automatic + A bone that is part of a pectoral complex. Examples: scapula, manus phalanx, any carpal bone, any bone of the pectoral fin. + + UBERONREF:0000003 - - - Region of the gastrula which gives rise to the neural plate.[TAO] - 2012-08-14 - TAO:0000063 - TAO - ZFIN:curator + + + note that the MA class includes girdle parts so it belongs here; + MA - - - prospective neuroectoderm - ZFA:0000063 + + + wing bone + UBERONREF:0000003 + - - - prospective vegetal ectoderm - ZFA:0000063 + + + bone of forelimb or pectoral fin or pectoral girdle + + UBERONREF:0000003 + + + + + forelimb bone + MA:0000612 + UBERONREF:0000003 - + - + - + - - - - - + - + - + - - + + - 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 + 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 - UBERON:0007285 - - presumptive paraxial mesoderm + hindlimb bone + UBERON:0010742 + + bone of pelvic complex - - - - - - - - - - - - - - - - - - + + + + MA - + - The part of the blastula that has the potential to develop into a paraxial mesoderm. - - UBERON:cjm + 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 - - - future paraxial mesenchyme - UBERON:cjm + + + the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle + MA + + + + + hindlimb bone + MA:0000660 + UBERONREF:0000003 - + - + - + - - + + - + + - - + + - A presumptive structure that has the potential to develop into a pronephric mesoderm. - EFO:0003619 - TAO:0001070 - ZFA:0001070 - nephron primordium + + + + + + + A skeletal element that is part of a limb and composed of cartilage tissue. uberon - UBERON:0007297 - - presumptive pronephric mesoderm + UBERON:0010881 + limb cartilage element - + - A presumptive structure that has the potential to develop into a pronephric mesoderm. - OBOL:automatic - - - - - nephron primordium - ZFA:0001070 + A skeletal element that is part of a limb and composed of cartilage tissue. + - + - + - + - - + + - + - - + + - A blood vessel that is part of a pectoral appendage. - TAO:0005301 - ZFA:0005301 - pectoral fin blood vessel + A skeletal element that is part of a limb and composed of pre-cartilage tissue. uberon - UBERON:0007300 - pectoral appendage blood vessel + UBERON:0010882 + limb bone pre-cartilage condensation - + - A blood vessel that is part of a pectoral appendage. - OBOL:automatic - - - - - pectoral fin blood vessel - ZFA:0005301 - + A skeletal element that is part of a limb and composed of pre-cartilage tissue. + - + - + - + - - + + - + + - - + + - A blood vessel that is part of a limb/fin. - TAO:0005299 - ZFA:0005299 - fin blood vessel - limb blood vessel + + + + + + + A cartilaginous condensation that has the potential to develop into a forelimb bone. + EMAPA:32626 + forelimb wing cartilaginous condensation + wing cartilaginous condensation uberon - UBERON:0007301 - appendage blood vessel + UBERON:0010883 + + forelimb cartilage element - + - A blood vessel that is part of a limb/fin. + A cartilaginous condensation that has the potential to develop into a forelimb bone. OBOL:automatic - + - fin blood vessel - ZFA:0005299 + forelimb wing cartilaginous condensation + NCBITaxon:8782 + OBOL:automatic - + - limb blood vessel + wing cartilaginous condensation + NCBITaxon:8782 + OBOL:automatic - + - + - + - - + + - + + - - + + - A vasculature that is part of a pectoral appendage. - TAO:0005096 - ZFA:0005096 - pectoral fin vasculature + A pre-cartilage condensation that has the potential to develop into a forelimb bone. + EMAPA:32625 + wing bone pre-cartilage condensation uberon - UBERON:0007302 - pectoral appendage vasculature + UBERON:0010884 + + forelimb bone pre-cartilage condensation - + - A vasculature that is part of a pectoral appendage. + A pre-cartilage condensation that has the potential to develop into a forelimb bone. OBOL:automatic - + - pectoral fin vasculature - ZFA:0005096 + wing bone pre-cartilage condensation + NCBITaxon:8782 + OBOL:automatic - + - + - + - - + + - + + - - + + - A vasculature that is part of a chordate pharynx. - TAO:0005003 - ZFA:0005003 - branchial vasculature + + + + + + + A cartilaginous condensation that has the potential to develop into a hindlimb bone. + EMAPA:32632 + hindlimb cartilage condensation uberon - UBERON:0007303 - pharyngeal vasculature + UBERON:0010885 + hindlimb cartilage element - + - A vasculature that is part of a chordate pharynx. + A cartilaginous condensation that has the potential to develop into a hindlimb bone. OBOL:automatic - + - branchial vasculature - ZFA:0005003 + hindlimb cartilage condensation + EMAPA:32632 - + - + - + - - + + - + + - - + + - A vasculature that is part of a limb/fin. - TAO:0005095 - ZFA:0005095 - fin vasculature + A pre-cartilage condensation that has the potential to develop into a hindlimb bone. + EMAPA:32638 + hindlimb pre-cartilage condensation uberon - UBERON:0007304 - appendage vasculature + UBERON:0010886 + hindlimb pre-cartilage condensation - + - A vasculature that is part of a limb/fin. + A pre-cartilage condensation that has the potential to develop into a hindlimb bone. OBOL:automatic - - - fin vasculature - ZFA:0005095 - + + + hindlimb pre-cartilage condensation + EMAPA:32638 - + - + - - - - - + - - + + - - + - - + + - - + + - 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 + 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 - hypoderm - hypodermis - UBERON:0007376 - - outer epithelium + lower limb muscle + muscle of lower limb + muscle of pelvic girdle and leg + UBERON:0010890 + + pelvic complex muscle - - - 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 + + + + + + + + + prolog - - - hypoderm - BTO:0000313 - + + + Muscles of the pelvic girdle, hindlimb or pelvic fin. + - - - hypodermis - GO:0008544 - WBbt:0005733 - + + + Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO] + 2012-06-20 + AAO:0000218 + AAO + AAO:EJS - - - - - - - - - - - - - - - - - - - - - - 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. - + + + pelvic girdle and hind limb muscles + AAO:0000218 - - - 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 + + + pelvic girdle or hind limb muscle + - - - relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO] - 2012-08-14 - TAO:0000086 - TAO + + + pelvic girdle or posterior limb muscle + - - - EVL - ZFA:0000086 + + + lower limb muscle + FMA:9622 + - - - enveloping layer - ZFIN:ZDB-PUB-961014-576 + + + muscle of lower limb + FMA:9622 + - + - + - + - + - + - + - + - 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 + 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 - UBERON:0007389 - - paired limb/fin cartilage + muscle of pectoral girdle and limb + UBERON:0010891 + pectoral complex muscle - - - 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 - + + prolog + - + - A cartilage tissue that is part of a pectoral appendage. - OBOL:automatic + A muscle of a pectoral girdle, pectoral fin or anterior limb. + - + - Cartilage which is part of the pectoral fin.[TAO] - 2012-08-14 - TAO:0000257 - TAO - ZFIN:curator + Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO] + 2012-06-20 + AAO:0010687 + AAO + AAO:EJS - - - pectoral fin cartilage - TAO:0000257 + + + pectoral girdle and fore limb muscles + AAO:0010687 - - - - - - - - - - - - - - - - - - - - - - - - - - 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 + + + muscle of pectoral girdle and wing + NCBITaxon:8782 + - - - Cartilage which is part of the pelvic fin.[TAO] - 2012-08-14 - TAO:0001459 - TAO - ZFIN:curator + + + muscle of upper limb + FMA:9621 + - - - pelvic fin cartilage - TAO:0001459 + + + upper limb muscle + FMA:9621 + - + - - - - - - - - - - - - - + + - + - - + + - The space within an epithelial sphere. - EHDAA2:0003079 - AEO:0000079 - cavity of vesicle + 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 - UBERON:0007473 - lumen of epithelial sac + subdivision of skeleton (in vivo) + UBERON:0010912 + + subdivision of skeleton - + + + + cjm + + + + + + + + + + + UBERONREF:0000003 + + + + + + + + + + + VSAO + + + - The space within an epithelial sphere. - AEO:JB + 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 + + + - cavity of vesicle - AEO:0000079 + skeletal subdivision + VSAO:0000042 + + + + + subdivision of skeleton (in vivo) + FMA:23879 - + - - - - An epithelial tube that is open at one end only. - AEO:0000115 - EHDAA2:0003115 + + + + + + + + + + + + + + + + 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:0007499 - epithelial sac + UBERON:0010913 + vertebral element - + - - AEO + + + VSAO - - - An epithelial tube that is open at one end only. - AEO:JB - UBERONREF:0000001 + + + + + + + + + VSAO - - - - - - - - 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 + + + + + + + cjm - + - An epithelial tube open at both ends that allows fluid flow. - AEO:JB - UBERONREF:0000001 + Skeletal element that forms around the notochord and is part of the vertebral column. + + + GO_REF:0000034 + VSAO:0000184 - - - - - - - - A closed epithelium with a lumen. - EHDAA2:0003119 - AEO:0000119 - EHDAA2:0003119 - uberon - UBERON:0007503 - epithelial vesicle - - - - - AEO + + + 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) - - - A closed epithelium with a lumen. - AEO:JB + + + vertebra skeletal element + - - - - - - - - Mesenchyme with little extracellular matrix. - EHDAA2:0003146 - AEO:0000146 - EHDAA2:0003146 - uberon - UBERON:0007524 - dense mesenchyme tissue - - - - - AEO + + + vertebra element + - - - Mesenchyme with little extracellular matrix. - AEO:JB + + + vertebra endochondral element + - - - - - - - - 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 + + + vertebral endochondral element + - + - + - + - - + + - + - - + + - - + + - 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 + Any muscle organ that is part of either the head or the neck. + + NCIT:C32716 + UMLS:C0448281 + muscle of head or neck uberon - synovial tissue - UBERON:0007616 - layer of synovial tissue + muscle of head and neck + UBERON:0010959 + craniocervical muscle - + - - + + - BTO + prolog - + - 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 + Any muscle organ that is part of either the head or the neck. + - - - synovial tissue - BTO:0001338 + + + UMLS:C0448281 + ncithesaurus:Head_and_Neck_Muscle - + - + - + - - + + - + + - + - - + + - An anatomical cavity that surrounded_by a synovial joint. - FMA:11356 - articular cavity (synovial joint) - cavitas articularis (junctura synovialis) - cavity of synovial joint + A cartilage element that is part of a splanchnocranium. + EFO:0003689 + TAO:0001460 + ZFA:0001460 + pharyngeal arch cartilages + splanchnocranium cartilage uberon - joint cavity - synovial cavity - UBERON:0007617 - synovial cavity of joint + UBERON:0011004 + + pharyngeal arch cartilage - - - An anatomical cavity that surrounded_by a synovial joint. - OBOL:automatic + + + + ZFA - - - articular cavity (synovial joint) - FMA:11356 + + + + + + + + + ZFA - - - cavitas articularis (junctura synovialis) - FMA:11356 + + + A cartilage element that is part of a splanchnocranium. + OBOL:automatic - + - cavity of synovial joint - FMA:11356 - - - - - joint cavity - FMA:11356 + pharyngeal arch cartilages + ZFA:0001460 + - - - synovial cavity - FMA:11356 + + + splanchnocranium cartilage + ZFA:0001460 - + - + - + - + - + - + - epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules. - GAID:907 - MESH:D010857 + A skeleton of pelvic girdle that is part of a right pelvic girdle region. + FMA:87593 uberon - eye pigment epithelium - UBERON:0007625 - - pigment epithelium of eye + UBERON:0011090 + skeleton of right pelvic girdle - + - epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules. - MP:0005200 + 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 + - - - eye pigment epithelium - MESH:A09.371.670 + + + A skeleton of pelvic girdle that is part of a left pelvic girdle region. + OBOL:automatic - + - - + + + + + + + + + + + + + - - 2 - + + - An anatomical structure that connects two structures - junction - - FMA:5898 - anatomical junction + + + + + + + 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:0007651 - - anatomical junction + UBERON:0011092 + right pelvic girdle region - - - - FMA + + + A pelvic girdle region that is in the right side of a multicellular organism. + OBOL:automatic - - - An anatomical structure that connects two structures - + + + right pelvic girdle + FMA:16582 + - + - + - + - - + + - - - + - - + + + + + + + + - region of the embryo into the area in which the kidney rudiment will develop. + 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 - kidney anlage - UBERON:0007687 - kidney field + UBERON:0011093 + left pelvic girdle region - + - region of the embryo into the area in which the kidney rudiment will develop. - - GO:0072004 - GOC:mtg_kidney_jan10 + A pelvic girdle region that is in the left side of a multicellular organism. + OBOL:automatic - - - kidney anlage - GOC:mtg_kidney_jan10 + + + left pelvic girdle + FMA:16583 + - + - - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - future organ - organ field - UBERON:0007688 - - anlage + UBERON:0011094 + vertebra cartilage element - - - - FBbt + + + 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 - - - - AEO - FBbt + + + + vertebra-like cartilage in hagfish are homologous to gnathostome vertebrae. mesenchymal cells express Pax1/9 and Twist + PMC3157150 - - - 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 + + + This class is a superclass of individual vertebral cartilage condensations. Note that EHDAA2 represents these as condensation groups + EHDAA2 + + + + + vertebral cartilage condensation + VHOG:0000584 - + - - - + + + + + + + + + + + + + - - + + - . - EFO:0003626 - EHDAA2:0001457 - EHDAA:962 - EMAPA:32754 - FMA:293087 - TAO:0001104 - ZFA:0001104 - early pharyngeal arch endoderm + + + + + + + + + + + + + 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 - 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 + UBERON:0011095 + vertebra pre-cartilage condensation - + - - + + - cjm + EHDAA2-abduced - + - . - + 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 - + - early pharyngeal arch endoderm - EHDAA2:0001457 - - - - - pharyngeal endoderm - ZFA:0001104 - - - - - pharyngeal region endoderm - EHDAA2:0001456 + vertebral pre-cartilage condensation + VHOG:0000582 - + - + - + - - + + - - + + - + - A bone that is part of a reproductive organ. - baculum + + + + + + + + + + + + + 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 - os penis/os clitoris - UBERON:0007719 - bone of reproductive organ + UBERON:0011096 + lacrimal nerve - + + + + + + + + + FMA + + + - A bone that is part of a reproductive organ. - - OBOL:automatic + The lacrimal nerve is the smallest of the three branches of the ophthalmic division of the trigeminal nerve. + + + + + + nervus lacrimalis + + - + - + - + - + - + + - + - A gland that is part of a epidermis. - FMA:59153 - epidermal gland - gland of epidermis + + + + + + + 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:0007771 - - epidermis gland + UBERON:0011107 + synovial joint of pelvic girdle - + - A gland that is part of a epidermis. + A synovial joint that is part of a pelvic girdle region. OBOL:automatic - + + + UMLS:C0827002 + ncithesaurus:Joint_of_the_Pelvic_Girdle + + + - gland of epidermis - FMA:59153 + pelvic girdle joint + FMA:35173 - + - - - - - - - - + + + + + + + + + + + + + + - - + + - - + + - 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 + 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 - plasma ultrafiltrate - UBERON:0007779 - transudate + UBERON:0011108 + synovial joint of pectoral girdle - + - Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces - + 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 - + - + - + - - + + - - + - - + + - Any fluid produced by a serous gland. - serous fluid - - serosal fluid - serous gland fluid + + + + + + + A skeletal joint that connects a laryngeal cartilage. + FMA:55100 + joint of larynx + laryngeal articulation uberon - UBERON:0007794 - secretion of serous gland + UBERON:0011120 + laryngeal joint - + + + + FMA + + + - Any fluid produced by a serous gland. - UBERON:cjm + A skeletal joint that connects a laryngeal cartilage. + OBOL:automatic - + - serosal fluid - + joint of larynx + FMA:55100 + + + + + laryngeal articulation + FMA:55100 - + - - + + + 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 + + + + + + + + + - - + + - 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 + + + + + + + + + + + + + Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. + FMA:7483 uberon - Gefaesssystem@de - UBERON:0007798 - - vascular system + UBERON:0011137 + axial skeletal system + http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + - - - - - - - MA + + FMA - + - Anatomical system that consists of all blood and lymph vessels. - + 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 + - - - The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. - ncithesaurus:Vascular_System + + + + FMA - - - in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system - MA + + + + + + + + + cjm - - - UMLS:C0489903 - ncithesaurus:Vascular_System + + + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. + + - - - Gefaesssystem@de - BTO:0001085 + + + axial skeletal system + - + - + - + - + - - - 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 + + + + + + + + + Any synovial joint that is part of a (free) limb. + FMA:258776 + synovial joint of free limb segment uberon - abdominal adipose tissue - abdominal fat - intra-abdominal fat - UBERON:0007808 - - adipose tissue of abdominal region + UBERON:0011139 + Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses. + synovial limb joint - + - 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 + Any synovial joint that is part of a (free) limb. + - - - abdominal adipose tissue - BTO:0004041 + + + synovial joint of free limb segment + FMA:258776 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Subdivision of urinary system which consists of the kidney and the ureters. + + FMA:45658 + NCIT:C61107 + galen:UpperUrinaryTract + uberon + UBERON:0011143 + + upper urinary tract + + + + + + + + + + + FMA - - - abdominal fat - BTO:0004041 + + + + + + + + + FMA-abduced-lr - - - intra-abdominal fat - BTO:0004041 + + + Subdivision of urinary system which consists of the kidney and the ureters. + FMA:45658 - + - - - - - - - - - - - - - - + + + + + + + + + + + + + - - + + - - + + - 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 + 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 - cephalic area - cephalic part of animal - cephalic region - head and neck - head or neck - UBERON:0007811 - - craniocervical region + UBERON:0011148 + submucosal gland - + - - MA + + + + + + + perforates - + - 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. - + Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue. + + BTO:0003751 - + - UMLS:C0460004 - ncithesaurus:Head_and_Neck - - - - - cephalic area - - - - - - cephalic part of animal - - - - - - cephalic region - - - - - - head and neck - FMA:280881 + EMAPA:37970 + MA:th - + - - - - - - - - - - - - - + + + - + - - + + - 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 + Subdivision of skull that consists of the facial bones. + + EHDAA2:0002206 + EHDAA:8361 + EMAPA:18022 + FMA:53673 + MA:0000318 + facial skeleton uberon - fin girdle - fin girdle region - limb girdle - limb girdle region - UBERON:0007823 - appendage girdle region + facial bone + ossa facialia + ossa faciei + viscerocranium + UBERON:0011156 + + facial skeleton + http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg - - - 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 + + + + FMA - - - 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 - + + + + + + + + + FMA - - - EMAPA:37854 - MA:th + + + + + + + + + - + + + Subdivision of skull that consists of the facial bones. + + + + MP:0005274 + + + + + facial skeleton + FMA:53673 + + + - fin girdle - + facial bone + MA:0000318 - + - fin girdle region - + ossa facialia + + - + - limb girdle - + ossa faciei + + - + - limb girdle region - + viscerocranium + MA:0000318 + - + - - - - - - - - - - - - - + + - + - A bone that is part of a appendage girdle region. - EMAPA:35379 - MA:0000291 - girdle bone + The skull can be divided into two: the neurocranium and the facial skeleton. + FMA:54964 + skull subdivision + subdivision of skull uberon - UBERON:0007828 - girdle bone/zone + UBERON:0011158 + + primary subdivision of skull - + + + + FMA + + + - A bone that is part of a appendage girdle region. - OBOL:automatic + The skull can be divided into two: the neurocranium and the facial skeleton. + - + - girdle bone - MA:0000291 + skull subdivision + FMA:54964 + + + + + subdivision of skull + FMA:54964 - + - - - - - - - - - - - - - - + + - + - A bone that is part of a pectoral girdle region. - EMAPA:35669 - MA:0000292 - bone of pectoral girdle uberon - UBERON:0007829 - - pectoral girdle bone + UBERON:0011159 + + primary subdivision of cranial skeletal system - + - - MA - - - - - A bone that is part of a pectoral girdle region. - OBOL:automatic + + FMA - + - + - + - - - - - - + - + - 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 + A bone that is part of a neurocranium [Automatically generated definition]. + + EMAPA:35238 + MA:0001478 + chondrocranium bone uberon - UBERON:0007830 - - - pelvic girdle bone/zone + UBERON:0011164 + neurocranium bone - - - - MA - - - + - A bone element or fused bone that is part of pelvic girdle. - - - - - - UMLS:C0030786 - ncithesaurus:Pelvic_Bone + A bone that is part of a neurocranium [Automatically generated definition]. + OBOL:automatic - + - pelvic girdle bone - MA:0000293 + chondrocranium bone + MA:0001478 - + - + - + - - - - - + - + - + - + - - + + - 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 + 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 - cingulum pectorale - pectoral girdle - scapular girdle - UBERON:0007831 - - - pectoral girdle skeleton - http://upload.wikimedia.org/wikipedia/commons/2/22/Pectoral_girdle_front_diagram.svg + UBERON:0011189 + lamina propria of large intestine - - - 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 + + + + + + + + + FMA - - - Note that the VSAO and many ontologies use the label 'pectoral girdle' to denote the skeletal region specifically. - VSAO + + + A lamina propria that is part of a large intestine. + OBOL:automatic - + - UMLS:C0427245 - ncithesaurus:Shoulder_Girdle + UMLS:C1708644 + ncithesaurus:Large_Intestinal_Lamina_Propria - + - skeletal parts of pectoral girdle - + lamina propria of mucosa of large intestine + FMA:15654 - + - skeleton of pectoral girdle - - - - - - cingulum pectorale - - - - - - - pectoral girdle - VSAO:0000156 - - - - - - scapular girdle - TAO:0000407 + large intestine lamina propria + FMA:15654 - + - + - + - - - - - + - - + - + - - - - - - - - - - - - - + - 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 + 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 - pelvic girdle - UBERON:0007832 - - - pelvic girdle skeleton - http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png + UBERON:0011198 + muscle layer of large intestine - + - - + + - + FMA - + - 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 + A muscle layer that is part of a large intestine. + OBOL:automatic - - - Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO] - 2012-06-20 - AAO:0000426 - AAO - AAO:LAP + + + UMLS:C0734205 + ncithesaurus:Large_Intestinal_Muscular_Coat - - - Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO] - 2012-08-14 - TAO:0000565 - TAO - TAO:wd + + + muscular coat of large intestine + FMA:14971 - - - 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 - + + + muscular layer of large intestine + FMA:14971 - - - 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 + + + muscularis externa of large intestine + FMA:14971 - - - 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 + + + tunica muscularis intestini crassi + FMA:TA + + + + + + + + + + + + + + + + + + + + + + + + + + + A multi cell part structure that is part of a central nervous system. + FMA:83143 + cell part cluster of neuraxis + neuraxis layer + uberon + UBERON:0011215 + + central nervous system cell part cluster + - - - pelvic girdle skeleton - VSAO:0000155 + + + A multi cell part structure that is part of a central nervous system. + OBOL:automatic - + - skeletal parts of pelvic girdle - + cell part cluster of neuraxis + FMA:83143 - + - skeleton of pelvic girdle - + neuraxis layer + FMA:83143 + + + + + + + + + + + + + + + A subdivision of an anatomical system. + + FBbt:00007330 + FMA:67509 + uberon + UBERON:0011216 + + organ system subdivision + + + + + + FBbt - - - pelvic girdle - VSAO:0000155 - + + + + FBbt + + + + + A subdivision of an anatomical system. + - + - - - 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 + + + + + + + + + + + + + + + + + Muscles within the eye (bulbus oculi).[AAO] + AAO:0010038 + EMAPA:18808 + FMA:49150 + intrinsic muscle of eyeball + intrinsic ocular muscle uberon - membrane bones - UBERON:0007842 - membrane bone + UBERON:0011222 + intra-ocular muscle - + - - VSAO + + organ component in FMA - - - Bone element that arises as a result of intramembranous ossification. - - - GO_REF:0000034 - VSAO:0000023 + + + + + + + + + EMAPA - + - 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 + Muscles within the eye (bulbus oculi).[AAO] + 2012-06-20 + AAO:0010038 + AAO + AAO:EJS - - - Intramembranous bone that forms deep in the organism.[TAO] - 2012-08-14 - TAO:0001645 - TAO - TAO:wd + + + 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 - - - membrane bones - ZFA:0001636 - + + + synovium + BTO:0001823 - + - + - + + + + + - + - + - - + + - - + + - + - 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 + FMA:40877 uberon - cartilage - UBERON:0007844 - - - cartilage element + 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 + + + + + + + + + + + + + + + + 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 - - - - VSAO - - - + - - - - - - - VSAO + + FMA - + - - + + - VSAO + FMA - + - 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 + The part of the trunk that is in the dorsum[cjm]. + + UBERONREF:0000006 - + - cartilage organ - FMA:55107 + back of trunk + FMA:25056 - + - cartilaginous element - + dorsum of trunk + FMA:25056 - + - chondrogenic element - VSAO:0000000 - - - - - cartilage - VSAO:0000000 + trunk back + FMA:25056 - + - - - - - - - - - - - - - + + + - + - A bone that is part of a craniocervical region. - EMAPA:37245 - MA:0000569 - head or neck bone + + + + + + + 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 - cranial bone - UBERON:0007914 - bone of craniocervical region + basal cell layer of skin + outer epithelium of body + UBERON:0011272 + embryonic skin basal layer - + - - MA + + EHDAA2 - + - + - MA - - - - - A bone that is part of a craniocervical region. - OBOL:automatic + EHDAA2 - - - EMAPA:37245 - MA:th + + + + + + + + + EHDAA2 - - - head or neck bone - MA:0000569 + + + outer epithelium of body + Wikipathways:WP2062 - + - + - + - + - + + - - - - - - - + - A skeletal joint that is part of a appendage girdle region. - MA:0001505 - girdle joint + 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 - UBERON:0008114 - - joint of girdle + cranial blood vessels + UBERON:0011362 + cranial blood vasculature - - - - MA - - - + - A skeletal joint that is part of a appendage girdle region. + 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 + + + - girdle joint - OBOL:automatic + cranial blood vessel + ZFA:0005297 + + + + + cranial blood vessels + TAO:0005297 + - + - - - - - - - - - - - - - + + - - - - - - - + - A anatomical surface that is part of a cartilage element. - FMA:76668 - cartilage surface + + FMA:54364 + cavity of digestive tract + cavity of gastrointestinal tract + gastrointestinal tract lumen + lumen of gastrointestinal tract uberon - UBERON:0008115 - surface of cartilage + UBERON:0011565 + lumen of gastrointestinal system - - - A anatomical surface that is part of a cartilage element. - OBOL:automatic + + + gastrointestinal tract lumen + FMA:54364 - + - cartilage surface - FMA:76668 + lumen of gastrointestinal tract + FMA:54364 - + - + - - - - - + - + - + + - + - + - - - - 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 + + + + 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 + + + - The part of the ventral body cavity that is within the pelvis. - UBERON:cjm + An anatomical cavity that is part of a esophagus. + OBOL:automatic - - - EMAPA:37235 - MA:th + + + cavity of esophagus + FMA:9398 - + - space of pelvic compartment - FMA:9738 + esophageal cavity + FMA:9398 - - - cavitas pelvis - - + + + esophageal lumen + FMA:9398 + + + + + esophagus lumen + FMA:9398 - + - + - + - - + + - + + - + - 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 - + + 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 + - + - 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 + A tube lumen that is part of a mesonephric duct. + OBOL:automatic - + - head or neck muscle - MA:0000571 - - - - - head muscles - ZFA:0000328 - - - - - head or neck muscle - MA:0000571 + nephric duct lumen + EHDAA2:0001244 - + - + - + - - + + - + + + - + - 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 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 + + + + + + + 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 - pharyngeal arch complex - pharyngeal arch region - pharyngeal arches and clefts - pharyngeal complex - UBERON:0008814 - pharyngeal arch system + UBERON:0011582 + + paired limb/fin skeleton - - - 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 + + + + + + + + + ISBN:9780878932504 - - - UMLS:C1519038 - ncithesaurus:Pharyngeal_Apparatus + + + The collection of all skeletal elements in an individual limb or fin. + - - - pharyngeal system - GO:0060037 + + + 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 - - - - pharyngeal arch region - EHDAA2:0000187 + + + + limb/fin skeleton + VSAO:0000301 - + - - - - - - - - - - - - - - - - - - - - A head that is part of a embryo. - CALOHA:TS-0246 - FBbt:00000155 - FMA:293011 + + + 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:0008816 - - embryonic head + UBERON:0011585 + cell condensation - + + + + VSAO + + + - A head that is part of a embryo. - OBOL:automatic + 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 - + - + - + - - + + - - + + + - + - - + + - A brain that develops_from a neural tube. - a reasoner should automatically classify all the vertebrate ontology brain classes here - vertebrate brain + + + + + + + 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:0008823 - neural tube derived brain - https://github.com/obophenotype/uberon/issues/338 + UBERON:0011595 + jaw region + http://eol.org/collections/11578 - - - - ZFA - - - + - + - FMA + EMAPA + FMA-abduced + ZFA-abduced - + - A brain that develops_from a neural tube. - - OBOL:automatic + 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. + - + - - - + + + - - + + - - + + - - 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 + EHDAA2:0001020 + lower jaw future lip 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 + UBERON:0011596 + future lower lip - + + + + EHDAA2 + + + - - + + - + EHDAA2 - + - - + + - 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 + lower jaw future lip + EHDAA2:0001020 - + - + - + - + + + + + - - + + + - + - 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 + + + + + + + + + + + + + An epithelium that develops_from a ectoderm and is part of a oral epithelium. + EHDAA2:0004137 uberon - dermal bones - UBERON:0008907 - dermal bone + UBERON:0011642 + oral epithelium from ectoderm - - - - wd - - - + - - VSAO + + EHDAA2 - + - - + + - VSAO + EHDAA2 - + - Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]. - - - GO_REF:0000034 - VSAO:0000130 + 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 + - - - Intramembranous bone that forms superficially in the organism.[TAO] - 2012-08-14 - TAO:0001590 - TAO - TAO:wd + + + mandibular muscle + TAO:0000236 - - - dermal bones - ZFA:0001590 + + + 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. + + + + + + + + - + - - + + - + + + - - + + - 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 + 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 - perichordal bone - UBERON:0008909 - perichordal bone + presacral vertebra + UBERON:0011677 + + trunk vertebra - + - - not in VSAO - ZFA + + true - + - 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 + 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 - - - perichordal bones - ZFA:0001629 - + + + presacral vertebra + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - perichordal bone - ZFA:0001629 + + + A cardiovascular system that is part of a conceptus. + OBOL:automatic - + - + - + - - + + - - - + - - + + - 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 + 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:0008962 - forelimb bone + UBERON:0011766 + left recurrent laryngeal nerve + https://upload.wikimedia.org/wikipedia/commons/6/64/Recurrent_laryngeal_nerve.svg - - - 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 + left recurrent laryngeal branch + EMAPA:25350 - - - wing bone - Geisha:syn - NCBITaxon:8782 - + + + left recurrent laryngeal nerve + FMA:14469 - - - wing bone - NCBITaxon:8782 - OBOL:automatic - + + + vagus X nerve left recurrent laryngeal branch + MA:0001107 - + - - - + + + + + + + + + + + + + - - + + - 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 + + EMAPA:17275 + FMA:14468 + MA:0001108 + right recurrent laryngeal branch + right recurrent laryngeal nerve + vagus X nerve right recurrent laryngeal branch uberon - UBERON:0008998 - - vasculature of brain + UBERON:0011767 + right recurrent laryngeal nerve - - - System pertaining to blood vessels in the brain. - BTO:0003840 + + + right recurrent laryngeal branch + EMAPA:17275 - + - cerebrovascular system - BTO:0003840 + right recurrent laryngeal nerve + FMA:14468 - + - intracerebral vasculature - FMA:61935 + vagus X nerve right recurrent laryngeal branch + MA:0001108 - + - + - + - - + + - + + - + - - + + - Any portion of tissue that surrounds a urethra. - - BTO:0005081 + An anatomical space that is part of a bone of lower jaw. + AAO:0000273 uberon - UBERON:0009010 - periurethral tissue + UBERON:0011772 + lower jaw opening - + - Any portion of tissue that surrounds a urethra. - UBERON:cjm + An anatomical space that is part of a bone of lower jaw. + OBOL:automatic - + - + - + - - + + - + + - + - A vein that is part of a craniocervical region. - - EHDAA2:0004542 - craniocervical vein - head and neck veins - vein of head and neck + + + + + + + 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 - UBERON:0009141 - craniocervical region vein + nodosal nucleus + UBERON:0011775 + vagus nerve nucleus - + - A vein that is part of a craniocervical region. + A cranial nerve nucleus that is associated with a vagus nerve. OBOL:automatic - + - head and neck veins - EHDAA2:0004542 + nucleus of vagus nerve + FMA:54573 - - - - - - - - - - - - - - - - - - - - - - - - - - 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 + + + tenth cranial nerve nucleus + FMA:54573 - - - Sum total of mesenchyme in the embryo. - + + + vagal X nucleus + - - - - - - - - - - - - - - EMAPA:16549 - RETIRED_EHDAA2:0001454 - pharyngeal region - uberon - UBERON:0009145 - pharyngeal region of foregut - - - - - - - - - - EHDAA2 + + + vagal nucleus + - + - pharyngeal region - EMAPA:16549 + vagus nucleus + + + + + + nodosal nucleus + - + - - + + + + + + + + + + + + + - + - EHDAA2:0004021 + A neural nucleus that is part of the spinal cord. + FMA:77011 + spinal cord nucleus uberon - UBERON:0009196 - - indifferent external genitalia + UBERON:0011777 + + nucleus of spinal cord - - - - cjm + + + A neural nucleus that is part of the spinal cord. + + + + + + spinal cord nucleus + FMA:77011 - + - + - + - + - - - The limb epidermis is the outer epithelial layer of the limb, it is a complex stratified squamous epithelium. - EMAPA:32728 + + + + + + + + A nerve that is part of a head. uberon - UBERON:0009200 - limb epidermis + cephalic nerve + head nerve + UBERON:0011779 + + nerve of head region - + - 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 nerve that is part of a head. + OBOL:automatic - + - - - - - - - - - - - - - - A nephric duct is a tube that drains a primitive kidney[GO]. - - EMAPA:16577 + + + Ectodermal placode that does not develop into a component of the nervous system. uberon - UBERON:0009201 - pronephric duct or mesonephric duct - nephric duct + UBERON:0011814 + non-neurogenic ectodermal placode - + - - EHDAA2 + + cjm - + - A nephric duct is a tube that drains a primitive kidney[GO]. - GO:0072176 + Ectodermal placode that does not develop into a component of the nervous system. + + - + - + - + - + + + + + + + + + - + + - + - An ectoderm that is part of a buccopharyngeal membrane. - EHDAA2:0000190 - EMAPA:16260 + + + + + + + + + + + + + An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart. + EHDAA2:0004149 + FMA:85125 uberon - UBERON:0009479 - - ectoderm of buccopharyngeal membrane + AV region + AV segment + atrial ventricular junction + atrioventricular junction + atrioventricular segment + UBERON:0011820 + atrioventricular region - + - An ectoderm that is part of a buccopharyngeal membrane. - OBOL:automatic + 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 + + + + + + + - + - - + + + + + + - + + - - + + - An endoderm that is part of a buccopharyngeal membrane. - EHDAA2:0000191 - EMAPA:16261 + + + + + + + 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:0009480 - - endoderm of buccopharyngeal membrane + UBERON:0011822 + dense irregular connective tissue - + + + + FMA + + + - An endoderm that is part of a buccopharyngeal membrane. - OBOL:automatic + 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 - + - + - + - - + + - + - - + + - Mesenchyme that is part of a foregut-midgut junction. - EHDAA2:0000570 - EMAPA:16364 + + 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:0009482 - - associated mesenchyme of foregut-midgut junction + UBERON:0011823 + dense connective tissue - + - Mesenchyme that is part of a foregut-midgut junction. - OBOL:automatic + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 + + + + FMA:75634 uberon - UBERON:0009494 - - pharyngeal arch mesenchymal region + UBERON:0011824 + fibrous connective tissue - + - - EHDAA2 + + 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 + - + - - - - - - - cjm + + FMA - + - A portion of mesenchymal tissue associated with an individual pharyngeal arch. - + 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 - - - 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 + + + UMLS:C1253917 + ncithesaurus:Loose_Connective_Tissue - + - branchial arch mesenchyme - MP:0011262 + textus connectivus collagenosus laxus + FMA:19783 + FMA:TA + - + - pharyngeal arch mesenchyme - + textus connectivus laxus + FMA:19783 + FMA:TA + - + - + - + - + - - - + + + - - - - - - - + - An epithelium that is part of a foregut-midgut junction. - EHDAA2:0000573 - EMAPA:16564 + An acinus that is part of a lacrimal gland. + FMA:85250 + lacrimal gland acinus uberon - UBERON:0009497 - - epithelium of foregut-midgut junction + UBERON:0011857 + acinus of lacrimal gland - - - - - - - - - EHDAA2 - - - + - An epithelium that is part of a foregut-midgut junction. + An acinus that is part of a lacrimal gland. OBOL:automatic + + + + lacrimal gland acinus + FMA:85250 + - + - + - + - + - + - + - Mesenchyme that is part of a developing hindgut. - EHDAA2:0000780 - EMAPA:16716 - hindgut associated mesenchyme + An acinus that is part of a exocrine gland. + exocrine gland acinus uberon - UBERON:0009503 - - mesenchyme of hindgut + UBERON:0011858 + acinus of exocrine gland - + - Mesenchyme that is part of a developing hindgut. + An acinus that is part of a exocrine gland. OBOL:automatic - - - - hindgut associated mesenchyme - EHDAA2:0000780 - - + - - - - - - - - - - - - - - - - - - + + - - + + - An endoderm that is part of a anal region. - EHDAA2:0004020 - EMAPA:17177 + + + + + + + the FMA class specifically refers to ureter + FMA:63212 + MESH:D024022 + NCIT:C32339 + NIF_Subcellular:sao7547390221 uberon - UBERON:0009521 - - anal membrane endodermal component + UBERON:0011860 + collection of collagen fibrils + - - - An endoderm that is part of a anal region. - OBOL:automatic + + + + ZFA + + + + + the FMA class specifically refers to ureter + FMA - + - + - + - + - + + - + - An endoderm that is part of a foregut-midgut junction. - EHDAA2:0000572 - EMAPA:18403 + + + + + + + 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:0009550 - - endoderm of foregut-midgut junction + UBERON:0011861 + + aorta collagen fibril - + - An endoderm that is part of a foregut-midgut junction. - OBOL:automatic + 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 - + - + - + - + - + + - + - 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 - - - - - - - - - - + + - - FMA:25054 - region of trunk - trunk subdivision + 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:0009569 - - subdivision of trunk + UBERON:0011862 + + pulmonary collagen fibril - - - region of trunk - FMA:25054 - - - - - trunk subdivision - FMA:25054 + + + 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 - + - + - + - + - + - + - EHDAA2:0001172 - EMAPA:16977 - VHOG:0000910 - mantle layer lateral wall midbrain - midbrain lateral wall mantle layer + 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 - mantle layer lateral wall mesencephalon - UBERON:0009581 - midbrain mantle layer + UBERON:0011863 + + bone collagen fibril - - - mantle layer lateral wall midbrain - VHOG:0000910 - - - - - mantle layer lateral wall mesencephalon - VHOG:0000910 + + + 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 - + - + - + - + - + - + - EMAPA:17580 - VHOG:0000911 - mantle layer lateral wall spinal cord - spinal cord lateral wall mantle layer + + + + + + + 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:0009583 - spinal cord mantle layer + UBERON:0011864 + + tendon collagen fibril - - - mantle layer lateral wall spinal cord - VHOG:0000911 + + + 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 - + - + - + - + - + + - + - 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 - - + + + + + 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 + - - - mesenchyme of mandibular component - EMAPA:16385 + + + 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 neural plate that develops_from a presumptive midbrain. - TAO:0007019 - ZFA:0007019 + + + + + + + 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:0009611 - midbrain neural plate + UBERON:0011878 + muscle layer of esophagus - - - - - - - - - - - - - - ZFA - - - + - - + + - ZFA + upper part + - + - A neural plate that develops_from a presumptive midbrain. + 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 + + - + - - - - - - - - - - - - - - + + + - + - - + + - A neural plate that develops_from a presumptive hindbrain. - TAO:0007022 - ZFA:0007022 + + + + + + + + + + + + + + + + + + + + + + + + + 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 - UBERON:0009614 - hindbrain neural plate + ciliary body and iris + vasculosa oculi + UBERON:0011892 + + anterior uvea - - - - - - - - - - - - - + + + ZFA - + - + - ZFA + MP - + + + + lexical + + + - A neural plate that develops_from a presumptive hindbrain. - OBOL:automatic + 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 - + - - + + + - + - - + + - - + + - TODO - developmental relationships for lines - TAO:0007044 - ZFA:0007044 - MHB neural plate - midbrain-hindbrain boundary neural plate + 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 - UBERON:0009615 - midbrain hindbrain boundary neural plate + epimysia + UBERON:0011899 + epimysium - + - - - - - - - ZFA + + FMA - + - - + + - https://github.com/obophenotype/uberon/issues/438 - Bgee:AN + FMA - - - MHB neural plate - + + + 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 + + + - midbrain-hindbrain boundary neural plate - ZFA:0007044 + 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 + + + + + + + + + + + + + + + + + + + - - + + - 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 + 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 - early midbrain - future midbrain - mesencephalon - UBERON:0009616 - - presumptive midbrain + glandular stomach + UBERON:0011953 + + stomach glandular region - - - - - - - - - ZFA + + + A region of the stomach that is lined with glandular epithelium. + - - - + + + UMLS:C0227197 + ncithesaurus:Glandular_Stomach + + + + + + + + + - - + + - - ZFA - + + 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 + - - - A presumptive structure that has the potential to develop into a midbrain. - OBOL:automatic + + + + EHDAA2 - - - presumptive mesencephalon - ZFA:0000148 + + + The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. + + + UBERON:cjm - - - early midbrain - + + + + - - - future midbrain - + + + enterocoelom + NCBITaxon:33511 - + - mesencephalon - EHDAA2:0000615 + coelomic cavity + EHDAA2:0004731 - + - - + + + + + + + + + + + + + + - + - 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 + + + + + + + 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 - somitomere - somitomeric mesoderm - UBERON:0009617 - head paraxial mesoderm + UBERON:0012054 + myocoele - + - Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles. - + The cavity within a myotome. + - - - cephalic paraxial mesenchyme - + + + 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 + + + + + + + + + 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 + - - - cephalic paraxial mesoderm - + + + + ZFA - - - cranial paraxial mesenchyme - + + + + ZFA - - - cranial paraxial mesoderm - + + + 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 + + + - head paraxial mesenchyme - - EHDAA2:0000736 + replacement bones + ZFA:0001628 + - + - - + + + - - + + - EHDAA2:0002094 - trunk and cervical paraxial mesenchyme + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical system that consists of the integumental system plus all mucosae and submucosae. + + uberon - trunk paraxial mesenchyme - UBERON:0009618 - trunk paraxial mesoderm + dermatological system + UBERON:0012125 + dermatological-muscosal system - - - trunk and cervical paraxial mesenchyme - EHDAA2:0002094 + + + Anatomical system that consists of the integumental system plus all mucosae and submucosae. + - + - trunk paraxial mesenchyme - + dermatological system + OBI:MC - + - + - + - - + + - + + - - - - - - - + - - + + - An anatomical space that surrounded_by a embryonic cloaca. - EHDAA2:0004586 + A primordium that has the potential to develop into a stomach. + + EFO:0002580 + NCIT:C34305 + UMLS:C1514976 uberon - UBERON:0009669 - embryonic cloacal lumen + stomach endoderm + UBERON:0012172 + + stomach primordium - + - An anatomical space that surrounded_by a embryonic cloaca. + A primordium that has the potential to develop into a stomach. OBOL:automatic + + + + UMLS:C1514976 + ncithesaurus:Stomach_Primordium + + + + + stomach endoderm + EFO:0002580 + - + - + - + - - + + - - - - - - - + - - - - - - - - - - - - - + - An anatomical space that surrounded_by a rectum. - - EHDAA2:0004587 - EMAPA:18388 - FMA:14598 - lumen of rectum + A zone of skin that is part of a craniocervical region. + + EMAPA:37276 + MA:0000574 + NCIT:C12294 + UMLS:C1522650 uberon - UBERON:0009670 - rectal lumen + UBERON:0012180 + head or neck skin - - - - - - - - - cjm - - - - - - - - - - - EHDAA2 - - - + - An anatomical space that surrounded_by a rectum. + A zone of skin that is part of a craniocervical region. OBOL:automatic - - - lumen of rectum - FMA:14598 + + + EMAPA:37276 + MA:th + + + + + UMLS:C1522650 + ncithesaurus:Skin_of_the_Scalp_and_Neck - + - + - + - - + + - + - + - - + + - An anatomical cavity that surrounded_by a stomodeum. - lumen of stomatodaeum - lumen of stomodeum - stomatodeal cavity + The veins that run parallel to the phrenic arteries which include the two superior and two inferior phrenic veins. + + EMAPA:37180 + MA:0002194 + NCIT:C53062 + UMLS:C1709532 uberon - UBERON:0009715 - stomodeal lumen + UBERON:0012193 + phrenic vein - + - An anatomical cavity that surrounded_by a stomodeum. - OBOL:automatic + The veins that run parallel to the phrenic arteries which include the two superior and two inferior phrenic veins. + ncithesaurus:Phrenic_Vein - - - - - - - - - - - - - - - - EHDAA2:0004621 - EMAPA:32754 - FMA:293087 - uberon - pharyngeal arch endoderm - UBERON:0009722 - entire pharyngeal arch endoderm - - - - pharyngeal arch endoderm - EHDAA2:0004621 + + + EMAPA:37180 + MA:th + + + + + UMLS:C1709532 + ncithesaurus:Phrenic_Vein - + - + - + - + - + + + - + - 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 + + + + + + + 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 - limb mesoderm - UBERON:0009749 + blood vessel of bladder + UBERON:0012239 - limb mesenchyme + urinary bladder vasculature - + + + + + + + + + + + + + + EMAPA + + + - 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 + 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 - - - EMAPA mapping from TH - EMAPA + + + blood vessels of bladder + EMAPA:28679 - + - limb mesoderm - Geisha:syn - NCBITaxon:8782 + blood vessel of bladder + EMAPA:28679 - + - + - + - + + + + + + + + + - + - + - 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 + + + + + + + + + + + + + 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 - UBERON:0009751 + urinary meatus + UBERON:0012240 - cardiac mesenchyme + urethral meatus - + - 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 + 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 + + + - heart mesenchyme - EMAPA:36438 + 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 - + - - + + + + + + + + + + + + + + + + + + + + + + - + - 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 + + + + + + + + + + + + + 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 - acini - UBERON:0009842 - glandular acinus - http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png + internal urethral ostium + internal urinary meatus + UBERON:0012242 + + internal urethral orifice - - - The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. - + + + 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 + - - - acinus - FMA:55588 + + + ostium urethrae internum + + - + + + vesicourethral orifice + FMA:85263 + + + - acini - - + internal urethral ostium + MP:0011782 + + + + + internal urinary meatus + MP:0011782 - + - + - + - - + + - + - - - - - - - + - - + + + 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 anatomical space that surrounded_by a primitive urogenital sinus. - EHDAA2:0002142 + 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:0009844 - urogenital sinus lumen + UBERON:0012274 + columnar epithelium - - - - - - - - - EHDAA2 - - - + - An anatomical space that surrounded_by a primitive urogenital sinus. - OBOL:automatic + 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]. + - + - + - + - - + + - + + - - + + - 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 + Epithelium that derives from the mesoderm. [Automatically generated definition]. + FMA:86452 + mesoderm-derived epithelium + mesoepithelium uberon - UBERON:0009845 - urogenital sinus mesenchyme + UBERON:0012275 + meso-epithelium - - - - - - - - - - - - - - - - - + - Mesenchyme that surrounds primitive urogenital sinus. + Epithelium that derives from the mesoderm. [Automatically generated definition]. OBOL:automatic - - - - UGM - - - - + - - - - - - - - - - - - - - - + + - + - - + + - An epithelium that is part of a embryonic cloaca. - cloacal epithelium - EHDAA2:0004585 + + + + + + + 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:0009846 - embryonic cloacal epithelium + 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 - + - An epithelium that is part of a embryonic cloaca. - OBOL:automatic + 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 epithelium - EHDAA2:0004585 + cloacal fold + EHDAA2:0004009 - + - + - + - + - - - Branch or outpocketing of the digestive tract. - FBbt:00100316 + + + + + + + + + A mucosa that is part of a urethra. + + EMAPA:37912 + FMA:76904 + mucous membrane of urethra + tunica mucosa urethrae + urethral mucosa uberon - diverticulum of gut - intestinal pouch - UBERON:0009854 - digestive tract diverticulum + UBERON:0012299 + mucosa of urethra - + - Branch or outpocketing of the digestive tract. - + A mucosa that is part of a urethra. + OBOL:automatic - - - diverticulum of gut - FBbt:00100316 + + + EMAPA:37912 + MA:th + + + + + mucous membrane of urethra + FMA:76904 + + + + + tunica mucosa urethrae + FMA:TA + + + + + urethral mucosa + FMA:76904 - - - - - galen:Diverticulum - pouch - uberon - diverticulum - UBERON:0009856 - sac - - - - - + - - - + + - + - EFO:0003704 - TAO:0005041 - ZFA:0005041 - ALPM - uberon - UBERON:0009881 - - anterior lateral plate mesoderm - - - - - + - + - - ZFA - + + + + + + + + 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 + - - - ALPM - ZFA:0005041 + + + One of five swellings formed during the development of the face. + - + - + - + - + - + + - + - Mesenchyme that is part of a developing face. - EMAPA:35337 - FMA:302884 - face mesenchyme - mesenchyme of face + An artery of the neck. + + EMAPA:37075 + NCIT:C52850 + UMLS:C1707349 uberon - UBERON:0009891 - facial mesenchyme + UBERON:0012320 + cervical artery - + - Mesenchyme that is part of a developing face. - OBOL:automatic + An artery of the neck. + + + + + + EMAPA:37075 + MA:th + + + + + UMLS:C1707349 + ncithesaurus:Cervical_Artery - + - + - + - + - - + - + - - + + - - + + - An anatomical wall that is part of a ureter. - - FMA:15888 - ureteral wall + + + + + + + The deep cervical artery (Profunda cervicalis) is an artery of the neck. + + + FMA:10659 uberon - UBERON:0009916 - wall of ureter + profunda cervicalis + UBERON:0012321 + deep cervical artery - + + + + + + + + + FMA + + + - An anatomical wall that is part of a ureter. - OBOL:automatic + The deep cervical artery (Profunda cervicalis) is an artery of the neck. + - - - ureteral wall - FMA:15888 + + + profunda cervicalis + - + - + - + - + - + + - + - - + + - The smooth muscle tissue surrounding the epithelium of the ureter - EMAPA:28811 - ureteral smooth muscle - ureteral smooth muscle layer + 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:0009919 - - ureter smooth muscle + UBERON:0012360 + bone of jaw - + - The smooth muscle tissue surrounding the epithelium of the ureter - MP:0011426 - - - - - ureteral smooth muscle - MP:0011426 - - - - - ureteral smooth muscle layer - EMAPA:28844 + A bone element that is part of a jaw region. + OBOL:automatic - + - - - - EHDAA2:0001315 - EHDAA:1122 + + + + + + + + + EHDAA2:0004588 uberon - UBERON:0009920 - optic neural crest + UBERON:0012361 + internal anal region - + - + + + + + + EHDAA2 - + - + - + - - + + - + - - + + - A multicellular organism that existence_starts_with a post-embryonic stage. - MA:0002405 - postnatal organism - TS28 mouse - post-hatching organism - post-natal organism - postnatal mouse + + + + + + + A muscle layer that is part of an intestine. + FMA:15697 + intestinal muscularis propria + muscularis externa of intestine uberon - UBERON:0009953 - post-embryonic organism - https://github.com/obophenotype/uberon/issues/667 + smooth muscle of intestine + UBERON:0012367 + muscle layer of intestine - - - A multicellular organism that existence_starts_with a post-embryonic stage. - OBOL:automatic - - - - - TS28 mouse - MA:0002405 + + + + + + + + + FMA - - - post-hatching organism - + + + A muscle layer that is part of an intestine. + OBOL:automatic - - - post-natal organism - + + + intestinal muscularis propria + FMA:15697 - - - postnatal mouse - MA:0002405 + + + muscularis externa of intestine + FMA:15697 - + - + - + - - + + + + + + - + + - - + + - - + + - - + + - 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 + A layer of tissue between the muscularis and serosa. + + + + FMA:45636 + NCIT:C94494 + UMLS:C0225334 uberon - UBERON:0009958 - bladder lumen + UBERON:0012375 + Contains nerves, blood vessels, lymphatics and lymph nodes + subserosa - - - + + + A layer of tissue between the muscularis and serosa. + + + + + + UMLS:C0225334 + ncithesaurus:Subserosa + + + + + + + + - + - + - - FMA - - - - - + + + + - - FMA - + + + + + + + + + + + + + + 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 + - + - - + + - EHDAA2 + FMA - + - A anatomical space that is enclosed by a urinary bladder. + A muscular coat that is part of a urinary bladder. OBOL:automatic - + + + UMLS:C1288327 + ncithesaurus:Bladder_Muscular_Coat + + + - bladder cavity - FMA:15924 + muscle layer of urinary bladder + FMA:15930 - + - cavity of urinary bladder - FMA:15924 + muscular coat of bladder + FMA:15930 - + - lumen of urinary bladder - FMA:15924 + muscular coat of urinary bladder + FMA:15930 - + - urinary bladder lumen - FMA:15924 + muscular layer of bladder + FMA:15930 + + + + + muscular layer of urinary bladder + FMA:15930 + + + + + tunica musculari vesicae + FMA:TA + + + + + tunica muscularis (vesica urinaria) + FMA:TA - + - + - - - - - + - - + + - + + - - - - - - - - - - - - - - - - - - - + - The junction between the ureter and the renal pelvis of the kidney - - EMAPA:37782 - FMA:15898 - MA:0003021 - NCIT:C106203 - pelviureteric junction - pelvoureteric junction + EMAPA:37567 + MA:0001802 uberon - UBERON:0009972 - - ureteropelvic junction + UBERON:0012416 + respiratory system arterial smooth muscle - - - + + + EMAPA:37567 + MA:th + + + + + + + + + + + + + + + + + + + + - + - - MP - + + 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 + - + - The junction between the ureter and the renal pelvis of the kidney - MP:0011487 + A smooth muscle tissue that is part of a respiratory system venous blood vessel. + OBOL:automatic - + - EMAPA:37782 + EMAPA:37586 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 + 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:0009973 - - ureterovesical junction + UBERON:0012429 + hematopoietic tissue - + + + + FMA + + + - + - MP + defitional - + - 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 + Blood-forming tissue, consisting of reticular fibers and cells. + - + - EMAPA:37783 - MA:th + UMLS:C0229619 + ncithesaurus:Hematopoietic_Tissue - + - vesico-ureteral junction - MA:0003020 + haemopoietic tissue + FMA:14073 + + + + + hematopoietic tissue + FMA:14073 + + + + + hemopoietic tissue + FMA:14073 + + + + + textus haemopoieticus + FMA:14073 + + + + + bone marrow tissue + NCBITaxon:9606 - + - - - An anatomical structure that has more than one cell as a part. - CARO:0010000 - FBbt:00100313 - multicellular structure + + + + + + + + + + + + + + + + + + + + + + + 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 - UBERON:0010000 - - multicellular anatomical structure + corneosclera + fibrous tunic + UBERON:0012430 + tunica fibrosa of eyeball - - - - CARO + + + + FMA - + - An anatomical structure that has more than one cell as a part. - CARO:0010000 + 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 + - - - multicellular structure - FBbt:00100313 + + + fibrous tunic + - + - + - + - - + + - + + - + - 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 - - - - - - - - - - - + - - + + - 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 + An 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:0010046 - entire pharyngeal arch associated mesenchyme + UBERON:0012463 + cloacal lumen - - - - 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 + An anatomical space that is enclosed by a cloaca. + OBOL:automatic - - - associated mesenchyme of pharyngeal region - EMAPA:16550 + + + the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/ + ZFA - + - entire branchial arch associated mesenchyme - + cloaca lumen + ZFA:0000330 - + - pharyngeal arch associated mesenchyme - EHDAA2:0001459 + cloacal chamber + ZFA:0000330 - + - + - + - + - - + + - + - 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 - - - - - - - - - An epithelium consisting of cuboidal epithelial cells. - TODO - coordinate with CL, add cuboidal cell - in NCIT this is glandular - - - NCIT:C32415 - UMLS:C0682577 + The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives. + cloacal opening uberon - UBERON:0010077 - cuboidal epithelium + cloacal orifice + vent + UBERON:0012464 + cloacal vent - + - An epithelium consisting of cuboidal epithelial cells. - - - - - - in NCIT this is glandular - NCIT - - - - - UMLS:C0682577 - ncithesaurus:Cuboidal_Epithelium + The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives. + - + - + - + - - + + - + + - - - - - - - - - - - - - + - - + + - Mesenchyme that has the potential to develop into a dermis. - check development - EHDAA2:0000598 + An anatomical space that is enclosed by a terminal part of digestive tract. + includes the cloacal lumen, in species where this is present uberon - UBERON:0010083 - future dermis + UBERON:0012465 + lumen of terminal part of digestive tract - - - - - - - - - EHDAA2 - - - - - - - - - - - EHDAA2 - - - - - - - - - - - XAO - - - + - Mesenchyme that has the potential to develop into a dermis. + An anatomical space that is enclosed by a terminal part of digestive tract. 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 - - - - - - - - - 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 + EHDAA2:0000472 + EMAPA:16054 + VHOG:0000767 uberon - UBERON:0010131 - conducting tissue of heart + extraembryonic cavities + UBERON:0012466 + extraembryonic cavity - - - 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 + + + extraembryonic cavities + EHDAA2:0000472 + - + - + - + - - + + - + - - + + - A mucous secretion that is produced by glands in the epidermis. + An anatomical space with no opening to another space or to the exterior. + AEO:0000222 + closed anatomical space uberon - epidermal mucus - skin mucous - UBERON:0010152 - skin mucus + UBERON:0012467 + enclosed anatomical space - + - A mucous secretion that is produced by glands in the epidermis. - + An anatomical space with no opening to another space or to the exterior. + AEO:0000222 + + + + + + + + + + + + + + EHDAA2:0004589 + uberon + UBERON:0012469 + external anal region + - - - epidermal mucus - BTO:0005082 + + + + + + + + + EHDAA2 - + - + - + - - + + - + + - + - - + + - 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 - - - - - - - - - A roughly circular bulge in a surface. - requires review - AEO:0000205 - EHDAA2:0003250 - FMA:82506 + + + + + + + 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 - UBERON:0010188 - protuberance + 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 - + - A roughly circular bulge in a surface. - EHDAA2:0003250 + 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 - - - - - - - - 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 + + + skeleton of anterior limb/fin and girdle + - - - An anatomical boundary that corresponds to some physical discontinuity. - CARO:0001004 + + + upper limb skeleton + FMA:24139 - + - - + + + + + + + + + + + + + + - + - - + + - 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 + + + + + + + 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 - UBERON:0010227 - future cardiac atrium + 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 - + - + - ZFA + FMA - + - Multi-tissue structure that is part of the heart tube and will become the cardiac atrium. - ZFA:0001718 + The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle. + - - - presumptive atrium heart tube - ZFA:0001718 + + + bones of lower limb + FMA:24140 - - - primordial atrium - FMA:71005 + + + lower limb skeleton + FMA:24140 - - - primordial cardiac atrium - FMA:71005 + + + ossa membri inferioris + FMA:TA + + + + + pelvic complex skeleton + + + + + + set of bones of lower limb + FMA:24140 + + + + + skeleton of posterior limb/fin and girdle + - + - - - + + - + - - + + - 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 + + + + + + + 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 - eyeball of camera-type eye + dorsal part of neck - + + + + FMA + + + - + FMA - + + + + + + + + + FMA + + + + + + + + + + + FMA + + + - The core globe-shaped component of the camera-type eye. - UBERON:cjm + The posterior region of the neck, including the suboccipital region. + MP:0012723 - + + + nape + BTO:0000957 + + + - eye globe - VHOG:0001616 + back of neck + FMA:24189 - + - eyeball - FMA:12513 + neck back + FMA:24189 - - - eye - + + + nucha + FMA:24189 - - - globe - HP:0100886 - MIAA:0000283 + + + 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 - + - + - + - - - - - + - - + - - + + - Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme. - EHDAA2:0000037 + A gland that is part of a cloaca. uberon - UBERON:0010252 - 1st arch mandibular mesenchyme from neural crest + UBERON:0012478 + cloacal gland - - - - inferred - - - + - Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme. + A gland that is part of a cloaca. OBOL:automatic - + - + - + - - + + - + + - - + + - Mesenchyme that develops_from a rhombencephalon neural crest. - EHDAA2:0004423 + 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:0010258 - mesenchyme from rhombencephalic neural crest + UBERON:0012480 + cloacal mucosa - + - Mesenchyme that develops_from a rhombencephalon neural crest. + A mucosa that is part of a cloaca [Automatically generated definition]. 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 - - - - - - - - + + - + - - + + - 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 + 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 - UBERON:0010285 - - midbrain basal plate + cloacal endoderm + UBERON:0012481 + cloacal epithelium - - - - EHDAA2 + + + An epithelium that is part of a cloaca. + - - - - - - - - - EHDAA2 + + + 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 + + + + + + + + + + + + + + + + + + + + - + - - ZFA - + + A submucosa that is part of a cloaca [Automatically generated definition]. + cloaca submucosa + cloacal submucosa + uberon + UBERON:0012482 + submucosa of cloaca + - + - 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 + A submucosa that is part of a cloaca [Automatically generated definition]. + OBOL:automatic - + - - - + + + + + + + + + + + + + - + - 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 + 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:0010286 - midbrain neural tube + UBERON:0012483 + serosa of cloaca - - - + + + A serous membrane that is part of a cloaca [Automatically generated definition]. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + - + - - ZFA - + + A muscular coat that is part of a cloaca. + muscularis externa of cloaca + uberon + smooth muscle of cloaca + UBERON:0012486 + muscle layer of cloaca + - + - Portion of neural tube that gives rise to the midbrain. - ZFA:0007039 + A muscular coat that is part of a cloaca. + OBOL:automatic - + - - - + + + + + + + + + + + + + - + - . - + 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 - UBERON:0010291 - layer of sclera + colon muscularis + UBERON:0012489 + muscle layer of colon - - - - - - - - - cjm + + + 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 - + - + - + - + - - - - An endothelium that is part of a sclera. + + + + + + + + + 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:0010294 - scleral endothelium + UBERON:0012490 + muscle layer of anal canal - - - - Wikipedia - - - + - An endothelium that is part of a sclera. + A muscular coat that is part of a anal canal. OBOL:automatic + + + + anal muscularis propria + FMA:15708 + + + + + muscularis propria of anal canal + FMA:15708 + - + - + - + - - + + - - - - - - - + + - - + + - 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 + An 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:0010299 - scleral mesenchyme + UBERON:0012504 + adventitia of esophagus - + - Mesenchyme surrounding the developing optic cup which develops into the sclera. - - + An 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 - + - + - + - + - - + + - + - An epithelium that is part of a extraembryonic structure. - extra-embryonic epithelium + 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:0010303 - extraembryonic epithelium + UBERON:0013126 + + vein of abdomen - + - An epithelium that is part of a extraembryonic structure. + A vein that is part of a abdomen. OBOL:automatic - + - + - + - - + + - + + + - - + + - - + + - 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 + + + + + + + A vein that drains a lip. + + labial vein of face + lip vein + vena labialis uberon - UBERON:0010312 - immature eye + labial vein + UBERON:0013136 + vein of lip - + - - + + - definitional + FMA - + - Developing anatomical structure that develops into the eyeball and associated structures. - ZFA:0001678 + A vein that drains a lip. + OBOL:automatic - - - Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO] - 2012-08-14 - TAO:0002201 - TAO - ZFIN:curator + + + lip vein + OBOL:automatic + + + + + vena labialis + - + - + - + - - + + - - + - - + + - An anatomical structure that develops from the neural crest. - Grouping term for query purposes + 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:0010313 - - neural crest-derived structure + UBERON:0013140 + systemic vein - + - An anatomical structure that develops from the neural crest. - + 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 - + - + - + - - + + - + - - + + - An anatomical structure that has some part that develops from the neural crest. - Grouping term for query purposes + A gland that is part of a foregut-midgut junction. + EHDAA2:0000574 + EMAPA:17065 + gland of foregut-midgut junction uberon - UBERON:0010314 - - structure with developmental contribution from neural crest + UBERON:0013158 + foregut-midgut junction gland - + - An anatomical structure that has some part that develops from the neural crest. - + A gland that is part of a foregut-midgut junction. + OBOL:automatic + + + + + gland of foregut-midgut junction + EMAPA:17065 - - - - - - - - - - - - uberon - UBERON:0010316 - germ layer / neural crest - - - - - + - + - + - + - - + - + - - + + - A skeletal element that is part of a orbital region. + The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells. + FMA:86279 + acinus of serous gland uberon - eye skeleton - ocular skeleton - skeletal element of orbital region - UBERON:0010321 - skeletal element of eye region + UBERON:0013232 + serous acinus - + - A skeletal element that is part of a orbital region. - OBOL:automatic + The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells. + + - + - - + + + - - + + - 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 + 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 - cranium - UBERON:0010323 - cranial skeletal system + UBERON:0013241 + embryonic urethral groove - - - 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 + + + + + + + + + Wikipedia - - - Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO] - 2012-08-14 - TAO:0000737 - TAO - ZFIN:curator + + + The precursor of the urethra. + - - - cranium - ZFA:0000737 - + + + 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 + + - + - + - + - - + + - + - + - Mesenchyme that is part of a limb bud. + + + + + + + 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 - UBERON:0010328 - limb bud mesenchyme + intracranial cavity + intracranial space + UBERON:0013411 + cranial cavity + http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg - + + + + + + + + + Wikipedia + + + - Mesenchyme that is part of a limb bud. - OBOL:automatic + 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 + - + - + - + - + - + + + - + - Mesenchyme that is part of a limb/fin bud. + A blood vessel endothelium that is part of a lung [Automatically generated definition]. + BTO:0004128 + CALOHA:TS-0573 uberon - UBERON:0010329 - paired limb/fin bud mesenchyme + respiratory endothelium + UBERON:0013479 + lung endothelium - + - Mesenchyme that is part of a limb/fin bud. + A blood vessel endothelium that is part of a lung [Automatically generated definition]. OBOL:automatic + + + + respiratory endothelium + BTO:0004128 + - + - + - - - - - + - - + + - - + + + - - + + - 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 - + + + + + + + + + + + + + + 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 + - + - Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme. + 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 + - + - + - + - - - - - - + + - - + + - - + + - 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 - + + 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 + - + - Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme. + 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 + - + - + - - - - - + - - + + - - - Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme. - EHDAA2:0000036 + + + + + + + + + + + + + + + + + + + + + + + A cervical vertebra endochondral element that is composed primarily of cartilage tissue. + EHDAA2:0000240 + cervical vertebral cartilage condensation group uberon - UBERON:0010339 - 1st arch mandibular mesenchyme from head mesenchyme + UBERON:0013505 + cervical vertebra cartilage element - + - Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme. + A cervical vertebra endochondral element that is composed primarily of cartilage tissue. OBOL:automatic + + + + cervical vertebral cartilage condensation group + EHDAA2:0000240 + - + - + - - - - - + - - + + - - - - 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 + + + + + + + + + A cervical vertebra endochondral element that is composed primarily of a pre-cartilage condensation. uberon - UBERON:0010341 - 1st arch mesenchyme from head mesenchyme + UBERON:0013506 + cervical vertebra pre-cartilage condensation - + - Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme. + A cervical vertebra endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic - - - - mesenchyme derived from head mesoderm of mesenchyme of 1st arch - EMAPA:16130 - - + - + - - - - - + - - + + - - + + + - + - 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 + + + + + + + + + + + + + + + + + + + A thoracic vertebra endochondral element that is composed primarily of cartilage tissue. + EHDAA2:0002014 + thoracic vertebral cartilage condensation group uberon - UBERON:0010359 - Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme - pharyngeal arch mesenchyme from neural crest + UBERON:0013507 + thoracic vertebra cartilage element - + - Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme. + A thoracic vertebra endochondral element that is composed primarily of cartilage tissue. OBOL:automatic + + + + thoracic vertebral cartilage condensation group + EHDAA2:0002014 + - + - + - + - - - - - - + + - - - + + - + - - + + - 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 + A thoracic vertebra endochondral element that is composed primarily of a pre-cartilage condensation. uberon - UBERON:0010360 - Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme - pharyngeal arch mesenchyme from head mesenchyme + UBERON:0013508 + thoracic vertebra pre-cartilage condensation - + - Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme. + A thoracic vertebra endochondral element that is composed primarily of a pre-cartilage condensation. 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 + The space that surrounds an organism. + external to organism + outside of body uberon - UBERON:0010362 - endoskeleton + UBERON:0013514 + space surrounding organism - - - - 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 + The space that surrounds an organism. + - + - - - 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 + UBERON:0013522 + subdivision of tube - - - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - 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 + gastric cavity + UBERON:0013525 + stomach lumen - + - - VSAO + + + + + + + FMA - + - 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 - + The anatomical space that is enclosed by a stomach. + - - - dermal skeletal system - VSAO:curator + + + 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 - - - dermoskeleton - VSAO:curator + + + cavity of stomach + FMA:14585 - + - desmoskeleton - VSAO:curator + gastric cavity + FMA:14585 - + - + - + - - + + - - - Epithelium composed of cells that develops from the ectoderm[FMA,modified]. - FMA:69064 - ectoderm-derived epithelium + + + + + + + + Anatomical space that is an opening in a bone of the skull. + + + FMA:53165 + foramen of skull + cranial conduit + cranial foramen uberon - UBERON:0010371 - ecto-epithelium + foramina of the skull + UBERON:0013685 + foramen of skull - + - Epithelium composed of cells that develops from the ectoderm[FMA,modified]. - FMA:69064 + 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 + - - - - + - + - - + + - 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 + 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:0010377 - mesenchyme from somatopleure + UBERON:0013686 + anatomical conduit space - - - - EHDAA2 - - - + - - - - - - - EHDAA2 + + FMA - + - Mesenchyme that develops_from a somatopleure. - OBOL:automatic + An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]. + + FMA:9338 - + - + - + - - + + - + + - - - - - - - + - An organ cavity that is part of a urethra. - - FMA:19709 - urethral lumen + Vascular endothelium found in blood vessels of the blood-brain-barrier. + BTO:0001852 + BTO:0003248 + CALOHA:TS-0092 uberon - UBERON:0010390 - lumen of urethra + cerebromicrovascular endothelium + UBERON:0013694 + brain endothelium - + - An organ cavity that is part of a urethra. - OBOL:automatic + Vascular endothelium found in blood vessels of the blood-brain-barrier. + CALOHA:TS-0092 - - - urethral lumen - FMA:19709 + + + cerebromicrovascular endothelium + CALOHA:TS-0092 - + - - - + + + + + + + + + + + + + + - - - - - - - + - 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 + Vascular endothelium found in colon blood vessels. + CALOHA:TS-0162 uberon - UBERON:0010409 - - ocular surface region + colon endothelial cell + colon endothelial cells + colonic endothelial cell + colonic endothelium + colorectal endothelial cell + colorectal endothelium + UBERON:0013695 + colon endothelium - + - 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 + Vascular endothelium found in colon blood vessels. + CALOHA:TS-0162 - - - eye surface - MA:0002486 + + + 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 - + - + - + - + + + + + - + + - + - An orifice that is part of a lower urinary tract. - EMAPA:35965 - MA:0002867 - urethral orifice + + + + + + + + + + + + + Musculature of the head and neck, spine, and ribs. + EHDAA2:0000159 + EMAPA:18166 uberon - UBERON:0010418 - - urethral opening + UBERON:0013700 + axial musculature - + - An orifice that is part of a lower urinary tract. - OBOL:automatic - - - - - urethral orifice - OBOL:automatic + Musculature of the head and neck, spine, and ribs. + HP:0003327 - + - - - + + - - + + - 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 + 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 - ciliary process - processus ciliares - UBERON:0010427 - ciliary processes - http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png + UBERON:0013701 + + main body axis - + - 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 + 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 + - - - ciliary processes set - FMA:76551 + + + + AEO - - - processus ciliares - FMA:TA - + + + The region of the organism associated with the visceral organs. + AEO:0000103 - - - set of ciliary processes - FMA:76551 + + + 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 - + - ciliary process - + body + AEO:0000103 - + - processus ciliares - - + whole body + BTO:0001489 - + - - - 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 + + + + + + + + + + + + + + + + + + + + + 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 - 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 + chordal canal + UBERON:0013704 + notochordal canal - - - - 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. - + 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:C0222649 - ncithesaurus:Flat_Bone - - - - - os planum - - + UMLS:C1518428 + ncithesaurus:Notochordal_Canal - + - - + + + + + + + + + + + + + + + + + + - + - 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 - + + Fluid contained within the notochordal canal. + notochord fluid + portion of notochordal fluid + uberon + UBERON:0013727 + Distinct feature of coelocanths + notochordal fluid + - + - Skeletal element that forms as a replacement or substitution of another element or tissue. - - GO_REF:0000034 - PSPUB:0000170 - VSAO:0000135 + Fluid contained within the notochordal canal. + + - + - - + + + + + + + + + + + + + - + - 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 + An organ component layer that is part of a integumental system. + + layer of skin + skin layer uberon - microcirculatory vessels - UBERON:0010523 - microcirculatory vessel + UBERON:0013754 + + integumentary system layer - - - - - - - - - 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 component layer that is part of a integumental system. + OBOL:automatic - + - - - + + + + + + + + + + + + + - - + + - 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 + A blood that is part of a artery. + FMA:83066 + arterial blood + blood in artery + portion of arterial blood uberon - limb - UBERON:0010707 + UBERON:0013755 - appendage girdle complex + arterial blood - + - 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 + A blood that is part of a artery. + OBOL:automatic - - - note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region) - FMA + + + arterial blood + FMA:83066 - - - EMAPA:37858 - MA:th + + + blood in artery + FMA:83066 - + - appendage complex - + 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 + - - - appendage-girdle complex - + + + A blood that is part of a vein. + OBOL:automatic - + - appendage/girdle complex - VSAO:0000214 + blood in vein + FMA:83067 - + - girdle plus limb or fin - + portion of venous blood + FMA:83067 - - - limb - FMA:7182 - + + + 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 + + + + + + + + + + + + + + + + + + + - - + + - 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 + 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 - upper limb - upper limb and pectoral girdle - upper limb and shoulder - UBERON:0010708 + UBERON:0013765 + - pectoral complex + digestive system element - + - 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 + Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. + - + - EMAPA:37860 + 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 + - - - 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 - - + + + Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart. + - - - - upper limb and shoulder - + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - + - + - - + + - + - - + + - - + + - 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 + + + + + + + Muscle that is part of the respiratory system. + this class may be merged with 'respiratory system muscle'; check intercostals uberon - lower limb - lower limb and pelvic girdle - lower limb and pelvis - UBERON:0010709 + UBERON:0014398 - pelvic complex + respiratory muscle - + - 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 + Muscle that is part of the respiratory system. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical space that is enclosed by a sinusoid. + FMA:63133 + lumen of sinusoid + sinusoid lumen + uberon + UBERON:0014399 + sinusoidal space + - - - pelvic appendage/girdle complex - VSAO:0000215 + + + An anatomical space that is enclosed by a sinusoid. + OBOL:automatic - + - pelvic girdle plus pelvic limb or fin - + lumen of sinusoid + FMA:63133 - + - pelvic girdle plus posterior limb or fin - - - - - - lower limb - FMA:7184 - - - - - - lower limb and pelvic girdle - - - - - - - lower limb and pelvis - + sinusoid lumen + FMA:63133 - + - + - + - + - - - - - - - + + - + - Skeletal subdivision that is a segment of the limb skeleton. - note the distinction between this and skeleton of limb - VSAO:0005018 + 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 - UBERON:0010712 - limb skeleton subdivision + kidney venous system + UBERON:0014401 + + renal venous blood vessel - - - - - - - - - VSAO + + + Any member of the network of tubes that return blood from the renal tissues to the systemic circulation. + MGI:csmith - - - Skeletal subdivision that is a segment of the limb skeleton. - VSAO:0005018 - VSAO:NI + + + 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 - + - + - + - - + + + + + + + + + + - + - + - + - - + + - - + + - 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 + 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 - UBERON:0010719 - girdle skeleton + abdominal fat + intra-abdominal adipose tissue + intra-abdominal fat + organ fat + visceral adipose tissue + visceral fat + UBERON:0014454 + visceral abdominal adipose tissue - + - The subdivision of the skeleton of either the pectoral or pelvic girdle. - + Subcutaneous adipose tissue that is located in the peritoneal cavity. + + + CALOHA:paula + MGI:csmith - + - 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 + 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 - - - relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO] - 2012-08-14 - VSAO:0000302 - VSAO + + + abdominal fat + BTO:0004041 - - - 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 + + + 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 + + + + + + + + + + + + + - - + + - A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle). - EMAPA:35494 - MA:0000688 + 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 - bone of extended limb/fin region - limb bone - UBERON:0010740 + UBERON:0014477 - bone of appendage girdle complex + thoracic skeleton - - - - - - - - - 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 + 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. + - UBERONREF:0000003 - - - limb bone - MA:0000688 - UBERONREF:0000003 + + + thoracic skeleton + EHDAA2:0002013 - + - + - + - + - + - + - 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 + A gray matter of spinal cord that is part of a cervical spinal cord. + + + BIRNLEX:1521 + UMLS:C0228610 + cervical spinal cord gray matter uberon - bone of forelimb or pectoral fin or pectoral girdle - forelimb bone - UBERON:0010741 - - bone of pectoral complex + UBERON:0014613 + cervical spinal cord gray matter - + - 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 - + A gray matter of spinal cord that is part of a cervical spinal cord. + OBOL:automatic - - - bone of forelimb or pectoral fin or pectoral girdle - - UBERONREF:0000003 + + + UMLS:C0228610 + BIRNLEX:1521 - - - forelimb bone - MA:0000612 - UBERONREF:0000003 + + + cervical spinal cord gray matter + BIRNLEX:1521 + - + - + - + - + - + - + - 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 + A gray matter of spinal cord that is part of a thoracic spinal cord. + + + BIRNLEX:980 + UMLS:C0228627 + thoracic spinal cord gray matter uberon - hindlimb bone - UBERON:0010742 - - bone of pelvic complex + UBERON:0014636 + thoracic spinal cord gray matter - - - - MA + + + A gray matter of spinal cord that is part of a thoracic spinal cord. + OBOL:automatic - - - 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 + + + UMLS:C0228627 + BIRNLEX:980 - - - the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle - MA + + + thoracic spinal cord gray matter + BIRNLEX:980 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - hindlimb bone - MA:0000660 - UBERONREF:0000003 + + + A unilaminar epithelium that develops_from a ectoderm and is part of a anal region. + OBOL:automatic - + - + - + - - + + - - + + + + + + + + - + - A skeletal element that is part of a limb and composed of cartilage tissue. + + + + + + + An anatomical space that is enclosed by a pleuroperitoneal canal. + EHDAA2:0004736 + EMAPA:25034 + pleuro-peritoneal canal cavity uberon - UBERON:0010881 - limb cartilage element + UBERON:0014704 + pleuroperitoneal canal lumen - + + + + + + + + + EHDAA2 + + + - A skeletal element that is part of a limb and composed of cartilage tissue. - + An anatomical space that is enclosed by a pleuroperitoneal canal. + OBOL:automatic + + + + + pleuro-peritoneal canal cavity + EMAPA:25034 - + - + - + - - + + - + + + + + + + - + - A skeletal element that is part of a limb and composed of pre-cartilage tissue. + 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:0010882 - limb bone pre-cartilage condensation + UBERON:0014717 + mucous acinus - + - A skeletal element that is part of a limb and composed of pre-cartilage tissue. + The secretory unit of a mucous gland. The acinar portion is composed of mucous secreting cells. + - + - - - - - - - - - - - - - - + + + - - + + - A cartilaginous condensation that has the potential to develop into a forelimb bone. - EMAPA:32626 - forelimb wing cartilaginous condensation - wing cartilaginous condensation + + + + + + + + + + + + + + + + + + + + + + + + + The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta. + + + EHDAA2:0000597 + EMAPA:17703 + VHOG:0001546 + crural diaphragm uberon - UBERON:0010883 - - forelimb cartilage element + crura of the diaphragm + crus of the diaphragm + diaphragm crura + diaphragmatic crura + UBERON:0014765 + Classification notes: May be considered an external sphincter[PMID:8224664] + crus of diaphragm - + + + + + + + + + + + + + + + + + + + + + + + - A cartilaginous condensation that has the potential to develop into a forelimb bone. - OBOL:automatic + The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta. + - - - forelimb wing cartilaginous condensation - NCBITaxon:8782 - OBOL:automatic - + + + crural diaphragm + - - - wing cartilaginous condensation - NCBITaxon:8782 - OBOL:automatic - + + + crura of the diaphragm + + + + + + crus of the diaphragm + + + + + + diaphragm crura + + + + + + diaphragmatic crura + - + - + - + - - + + - - - A pre-cartilage condensation that has the potential to develop into a forelimb bone. - EMAPA:32625 - wing bone pre-cartilage condensation + + + + + + + + + A crus of diaphragm that is in_the_right_side_of a diaphragm. + https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern + + FMA:58286 + crus dextrum (Diaphragma) + crus dextrum diaphragmatis + external sphincter of esophagus + right crus of diaphragm + right crus of lumbar part of diaphragm uberon - UBERON:0010884 - - forelimb bone pre-cartilage condensation + UBERON:0014766 + right crus of diaphragm - + - A pre-cartilage condensation that has the potential to develop into a forelimb bone. + A crus of diaphragm that is in_the_right_side_of a diaphragm. OBOL:automatic - - - wing bone pre-cartilage condensation - NCBITaxon:8782 - OBOL:automatic - + + + crus dextrum (Diaphragma) + FMA:58286 + FMA:TA + + + + + + crus dextrum diaphragmatis + FMA:58286 + FMA:TA + + + + + + external sphincter of esophagus + FMA:58286 + + + + + right crus of diaphragm + FMA:58286 + + + + + right crus of lumbar part of diaphragm + FMA:58286 - + - + - + - - + + - - + + - - + + - A cartilaginous condensation that has the potential to develop into a hindlimb bone. - EMAPA:32632 - hindlimb cartilage condensation + A crus of diaphragm that is in_the_left_side_of a diaphragm. + https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern + + FMA:58287 + crus sinistrum (Diaphragma) + crus sinistrum diaphragmatis + left crus of diaphragm + left crus of lumbar part of diaphragm uberon - UBERON:0010885 - hindlimb cartilage element + UBERON:0014767 + left crus of diaphragm - + - A cartilaginous condensation that has the potential to develop into a hindlimb bone. + A crus of diaphragm that is in_the_left_side_of a diaphragm. OBOL:automatic - + - hindlimb cartilage condensation - EMAPA:32632 + crus sinistrum (Diaphragma) + FMA:58287 + FMA:TA + + + + + + crus sinistrum diaphragmatis + FMA:58287 + FMA:TA + + + + + + left crus of diaphragm + FMA:58287 + + + + + left crus of lumbar part of diaphragm + FMA:58287 - + - + - + - - + + - - - A pre-cartilage condensation that has the potential to develop into a hindlimb bone. - EMAPA:32638 - hindlimb pre-cartilage condensation + + + + + + + + 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 - UBERON:0010886 - hindlimb pre-cartilage condensation + future mesencephalon + mesomere group + UBERON:0014776 + midbrain neuromere - + - A pre-cartilage condensation that has the potential to develop into a hindlimb bone. - OBOL:automatic + A neuromere that is part of the presumptive midbrain. + - - - hindlimb pre-cartilage condensation - EMAPA:32638 + + + mesomere group + EHDAA2:0004352 - + - - - - - - - - + + + + + + + + + + + + + - + - 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 + A neuromere that is part of the presumptive spinal cord. + TAO:0001332 + ZFA:0001332 + spinal cord metameric segment + spinal neuromeres uberon - subdivision of skeleton (in vivo) - UBERON:0010912 - - subdivision of skeleton + spinal cord segment + UBERON:0014777 + spinal neuromere - - - - 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 + A neuromere that is part of the presumptive spinal cord. + - + - skeletal subdivision - VSAO:0000042 + spinal neuromeres + TAO:0001332 + - + - subdivision of skeleton (in vivo) - FMA:23879 + spinal cord segment + TAO:0001332 - + - + - + - + - - + + - - - - - - - + - A cartilage element that is part of a splanchnocranium. - EFO:0003689 - TAO:0001460 - ZFA:0001460 - pharyngeal arch cartilages - splanchnocranium cartilage + Any muscle organ that is part of a cloaca. uberon - UBERON:0011004 - - pharyngeal arch cartilage + UBERON:0014783 + cloacal muscle - - - - ZFA - - - - - - - - - - - ZFA - - - + - A cartilage element that is part of a splanchnocranium. + Any muscle organ that is part of a cloaca. OBOL:automatic - - - - pharyngeal arch cartilages - ZFA:0001460 - - - - - - splanchnocranium cartilage - ZFA:0001460 - - + - + - + - + - - + - - - - - - - + - A synovial joint that is part of a pelvic girdle region. - - FMA:35173 - NCIT:C32890 - UMLS:C0827002 - joint of pelvic girdle - pelvic girdle joint + 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:0011107 - synovial joint of pelvic girdle + UBERON:0014792 + musculature of pelvic complex - + - A synovial joint that is part of a pelvic girdle region. + 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 - + - UMLS:C0827002 - ncithesaurus:Joint_of_the_Pelvic_Girdle + EMAPA:37864 + MA:th + + + + + muscles of lower limb + FMA:71297 + + + + + musculature of lower limb + FMA:71297 - - - pelvic girdle joint - FMA:35173 + + + musculi membri inferioris + FMA:TA - + - + - + - + - - + - - - - - - - + - 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 + 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:0011108 - synovial joint of pectoral girdle + UBERON:0014793 + musculature of pectoral complex - + - A synovial joint that is part of a pectoral girdle region. + 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 - - - in FMA, these are part of the bony pectoral girdle - FMA + + + EMAPA:37861 + MA:th - - - pectoral girdle joint - FMA:35243 + + + muscles of upper limb + FMA:71296 - - - - - - - - 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 + + + musculature of upper limb + FMA:71296 - - - 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 + + + musculi membri superioris + FMA:TA - - - solid joint - FMA:7491 + + + set of muscles of upper limb + FMA:71296 + + + + + upper limb musculature + FMA:71296 - + - - + + + + + + + + + + + + + - - + + - - + + - Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. - FMA:7483 + Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin). uberon - UBERON:0011137 - axial skeletal system - http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton + UBERON:0014794 + pectoral appendage muscle - + - - FMA + + + + + + + prolog - + - Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. - + Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin). + OBOL:automatic - + - - + + + + + + + + + + + + + - - + + - 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 + + + + + + + Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin). uberon - UBERON:0011138 - postcranial axial skeletal system - http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton + UBERON:0014795 + pelvic appendage muscle - - - - FMA - - - + - - + + - cjm + prolog - + - Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. - - - - - - - axial skeletal system - + Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin). + OBOL:automatic - + - + - + - - + + + + + + + + + + + + + + - - - Any synovial joint that is part of a (free) limb. - FMA:258776 - synovial joint of free limb segment - uberon - UBERON:0011139 - Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses. - synovial limb joint - - - - - Any synovial joint that is part of a (free) limb. - - - - - - synovial joint of free limb segment - FMA:258776 - - - - - - - - + - + - - + + - - + + - - + + - Subdivision of urinary system which consists of the kidney and the ureters. - - FMA:45658 - NCIT:C61107 - galen:UpperUrinaryTract - uberon - UBERON:0011143 - - upper urinary tract - - - - - - - - - - - FMA - - - - - + - - + + - - FMA-abduced-lr - + + 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 + - + - Subdivision of urinary system which consists of the kidney and the ureters. - FMA:45658 + 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 - + - + - + - - + + - + + - - + + - - + + - Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue. - - BTO:0003751 - EMAPA:37970 + A portion of tissue that will develop into vasculature. + EFO:0003708 + TAO:0005076 + ZFA:0005076 uberon - UBERON:0011148 - submucosal gland + UBERON:0014903 + primordial vasculature - - - - - - - - - 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 + A portion of tissue that will develop into vasculature. + ZFA:0005076 + ZFA:curator - + - - - + + + + + + + + + + + + + + + + + + + + + + + - + - Subdivision of skull that consists of the facial bones. - - EHDAA2:0002206 - EHDAA:8361 - EMAPA:18022 - FMA:53673 - MA:0000318 - facial skeleton + A vertebral endochondral element in the cervical region of the vertebral column. + cervical vertebra skeletal element + cervical vertebra element uberon - facial bone - ossa facialia - ossa faciei - viscerocranium - UBERON:0011156 - - facial skeleton - http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg + UBERON:0015007 + cervical vertebra endochondral element - - - - FMA - - - - - - - - - - - FMA - - - + - Subdivision of skull that consists of the facial bones. - - - - MP:0005274 - - - - - facial skeleton - FMA:53673 - - - - - facial bone - MA:0000318 - - - - - ossa facialia - - + A vertebral endochondral element in the cervical region of the vertebral column. + - - - ossa faciei - - + + + cervical vertebra skeletal element + - - - viscerocranium - MA:0000318 - + + + cervical vertebra element + - + - - + + + + + + + + + + + + + + + + + + + + + + + + - + - The skull can be divided into two: the neurocranium and the facial skeleton - FMA:54964 - skull subdivision - subdivision of skull + A vertebral endochondral element in the thoracic region of the vertebral column. + thoracic vertebra skeletal element + thoracic vertebra element uberon - UBERON:0011158 - - primary subdivision of skull + UBERON:0015008 + thoracic vertebra endochondral element - - - - FMA - - - + - The skull can be divided into two: the neurocranium and the facial skeleton + A vertebral endochondral element in the thoracic region of the vertebral column. - - - skull subdivision - FMA:54964 + + + thoracic vertebra skeletal element + - + - subdivision of skull - FMA:54964 + thoracic vertebra element + - + - - + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + + A forelimb bone or its cartilage or pre-cartilage precursor. + forelimb skeletal element uberon - UBERON:0011159 - - primary subdivision of cranial skeletal system + UBERON:0015021 + forelimb endochondral element - - - - FMA + + + A forelimb bone or its cartilage or pre-cartilage precursor. + + + + + + forelimb skeletal element + - + - + - + - + - + + + + + + + + + + - + - A bone that is part of a neurocranium [Automatically generated definition]. - - EMAPA:35238 - MA:0001478 - chondrocranium bone + + + + + + + A hindlimb bone or its cartilage or pre-cartilage precursor. + hindlimb bone skeletal element uberon - UBERON:0011164 - neurocranium bone + UBERON:0015022 + hindlimb endochondral element - + - A bone that is part of a neurocranium [Automatically generated definition]. - OBOL:automatic + A hindlimb bone or its cartilage or pre-cartilage precursor. + - - - chondrocranium bone - MA:0001478 + + + hindlimb bone skeletal element + - + - + - + - + - + + + + + + + + + + + - + - 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 limb bone or its cartilage or pre-cartilage precursor. + limb bone skeletal element + limb bone endochondral element + uberon + UBERON:0015061 + limb endochondral element + - + - A lamina propria that is part of a large intestine. - OBOL:automatic - - - - - UMLS:C1708644 - ncithesaurus:Large_Intestinal_Lamina_Propria + A limb bone or its cartilage or pre-cartilage precursor. + - - - lamina propria of mucosa of large intestine - FMA:15654 + + + limb bone skeletal element + - + - large intestine lamina propria - FMA:15654 + limb bone endochondral element + - + - - - - - - - - - - - - - + + + - + - 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 + consider merging into myocardial compact layer + FMA:83105 + perimysial connective tissue of subepicardium + subepicardial connective tissue uberon - UBERON:0011198 - muscle layer of large intestine + UBERON:0015128 + subepicardial layer of epicardium - + + + + FMA + + + - + 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 + perimysial connective tissue of subepicardium + FMA:83105 - + - tunica muscularis intestini crassi - FMA:TA - + subepicardial connective tissue + FMA:83105 - + - + - + - - + + + + + + + + + + - + + + - + - A multi cell part structure that is part of a central nervous system. - FMA:83143 - cell part cluster of neuraxis - neuraxis layer + + + + + + + + + + + + + + + + + + + + + + + + + Visceral intrapericardial fat contiguous with the myocardial surface. + + FMA:9871 + epicardial adipose tissue + pericardial adipose tissue uberon - UBERON:0011215 - - central nervous system cell part cluster + UBERON:0015129 + epicardial fat - + - 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 + Visceral intrapericardial fat contiguous with the myocardial surface. + - + - - + + + + + + + + + + + + + - + - A subdivision of an anatomical system. - - FBbt:00007330 - FMA:67509 - uberon - UBERON:0011216 - - organ system subdivision - - - - - - 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 + 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 - UBERON:0011222 - intra-ocular muscle + orbital gland + UBERON:0015152 + gland of ocular region - + - + - EMAPA - - - - - Muscles within the eye (bulbus oculi).[AAO] - 2012-06-20 - AAO:0010038 - AAO - AAO:EJS + inferred - - - intrinsic ocular muscle - EMAPA:18808 + + + 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. + + - + - - - - - - - - - - - - - - - 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 + + + 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:0011249 - appendicular skeletal system - https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton + UBERON:0015154 + lateral gland of orbital region - + - 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 gland that is located in or around the ocular region, nearer the outer canthi. + - + - - + + + + + + + + + + + + + - - + + - 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 - + + + + + + + An eye consisting of multiple light-sensing organs. + + + + + uberon + UBERON:0015165 + multi-unit eye + - + - The part of the trunk that is in the dorsum[cjm]. - - UBERONREF:0000006 + An eye consisting of multiple light-sensing organs. + + - - - back of trunk - FMA:25056 + + + + present on tentacular crown + - - - dorsum of trunk - FMA:25056 + + + + present on mantle edge in arcacean Bivalvia + - - - trunk back - FMA:25056 + + + + 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 + - + - - - + + + + + + + + + + + + + + + + + + - + - - + + - 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 + A region of somite adjacent to presomitic mesoderm. + TAO:0001462 + XAO:0004074 + ZFA:0001462 uberon - basal cell layer of skin - outer epithelium of body - UBERON:0011272 - embryonic skin basal layer + inter-somited border + intersomitic boundary + intersomitic fissure + intersomitic junction + segmental border + somite boundary + UBERON:0015178 + + somite border - - - - EHDAA2 - - - - - - - - - - - EHDAA2 + + + A region of somite adjacent to presomitic mesoderm. + - - - - - - - - - EHDAA2 + + + intersomitic junction + XAO:0004074 - + - outer epithelium of body - Wikipathways:WP2062 + somite boundary + ZFA:0001462 - + - + - + - + - - - 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 + + + + + + + + + Epithelium located in the intersomitic region. + XAO:0004077 + intersomitic epithelium + intersomitic membrane uberon - cranial blood vessels - UBERON:0011362 - cranial blood vasculature + UBERON:0015179 + somite boundary epithelium - + - 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 + Epithelium located in the intersomitic region. + XAO:0004077 + XAO:EJS - + - cranial blood vessel - ZFA:0005297 + intersomitic epithelium + XAO:0004077 - - - cranial blood vessels - TAO:0005297 - + + + intersomitic membrane + XAO:0004077 - + - + - + - - + + - + - + - - + + - A tube lumen that is part of a mesonephric duct. - EHDAA2:0001244 - nephric duct lumen + + + + + + + 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 - cavity of nephric duct - UBERON:0011574 - mesonephric duct lumen + UBERON:0015212 + + + lateral structure - + - A tube lumen that is part of a mesonephric duct. - OBOL:automatic + 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 + - - - nephric duct lumen - EHDAA2:0001244 + + + 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. + - + - + - + - - + + - - + - + - - - - - - - - - - - - - + - 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 + A basement membrane of epithelium that is part of a respiratory system. + EMAPA:37570 + MA:0001815 uberon - UBERON:0011582 - - paired limb/fin skeleton + UBERON:0015329 + respiratory system basement membrane - + - - + + - ISBN:9780878932504 + MA - + - The collection of all skeletal elements in an individual limb or fin. - + A basement membrane of epithelium that is part of a respiratory system. + OBOL:automatic - - - 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 + + + EMAPA:37570 + MA:th + + + + + + + + + + + + + + + EMAPA:37597 + MA:0002449 + heart/pericardium + uberon + UBERON:0015410 + heart plus pericardium + + + + + + MA - + + + EMAPA:37597 + MA:th + + + - limb/fin skeleton - VSAO:0000301 + heart/pericardium + MA:0002449 - + - - - 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 + + + + + + + + + + + + + + + + + + + + + A mesenchyme that is part of a urethra. + EMAPA:37786 + MA:0002648 uberon - UBERON:0011585 - cell condensation + UBERON:0015418 + urethra mesenchymal layer - - - - VSAO + + + A mesenchyme that is part of a urethra. + OBOL:automatic - - - 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 + + + EMAPA:37786 + MA:th - + - + - + - - + + - - + + - + - - + + - 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 + A valve that is part of a ureter. + EMAPA:37781 + MA:0002658 + ureteral valve + valve or ureter uberon - UBERON:0011595 - jaw region - http://eol.org/collections/11578 + UBERON:0015420 + ureteral valve - - - + + + A valve that is part of a ureter. + OBOL:automatic + + + + + EMAPA:37781 + MA:th + + + + + ureteral valve + MA:0002658 + + + + + + + + + + + + + + + + + + + + + - + - - EMAPA - FMA-abduced - ZFA-abduced - + + An 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 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. - + An epithelium that is part of a anal canal. + OBOL:automatic + + + + + anal canal epithelium + FMA:17511 + + + + + epithelium of anal canal + FMA:17511 - + - - - - - - - - - - EHDAA2:0001020 - lower jaw future lip + + + FMA:62798 + portion of heterogeneous tissue uberon - UBERON:0011596 - future lower lip + UBERON:0015757 + heterogeneous tissue - - - - EHDAA2 - - - + - - - - - - - + + FMA - + - lower jaw future lip - EHDAA2:0001020 + portion of heterogeneous tissue + FMA:62798 - + - + - + - - - - - + - - - + - - + + - An epithelium that develops_from a ectoderm and is part of a oral epithelium. - EHDAA2:0004137 + 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:0011642 - oral epithelium from ectoderm + UBERON:0015783 + smooth muscle layer in fatty layer of subcutaneous tissue - - - - EHDAA2 + + + A smooth muscle tissue that is part of a hypodermis. + OBOL:automatic - - - - - - - - - EHDAA2 + + + muscle layer in fatty layer of subcutaneous tissue + FMA:77862 - - - An epithelium that develops_from a ectoderm and is part of a oral epithelium. - OBOL:automatic + + + stratum musculosum panniculi adiposi telae subcutaneae + FMA:77862 + FMA:TA + - + - - + + + + + + + + + + + + + + - + - 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 + An epithelium that is part of a camera-type eye. + EMAPA:35957 + MA:0003162 uberon - body segment - main body segment - UBERON:0011676 - - subdivision of organism along main body axis + UBERON:0015808 + eye epithelium - + - 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. - + An epithelium that is part of a camera-type eye. + OBOL:automatic - + - + - + - + - + - + - A cardiovascular system that is part of a conceptus. - EHDAA2:0000216 - FMA:305965 - NCIT:C34148 - conceptus cardiovascular system + An epithelium that is part of a foregut. + EMAPA:32922 + MA:0003204 uberon - embryonic circulatory system - fetal circulatory system - UBERON:0011695 - embryonic cardiovascular system + UBERON:0015833 + foregut epithelium - + - A cardiovascular system that is part of a conceptus. + An epithelium that is part of a foregut. OBOL:automatic - + - + - + - - + + - + + - - - - - - - + - An anatomical space that is part of a bone of lower jaw. - AAO:0000273 + A capillary that is part of a lung. + FMA:14121 + capillary of lung uberon - UBERON:0011772 - lower jaw opening + UBERON:0016405 + + pulmonary capillary - + - An anatomical space that is part of a bone of lower jaw. + A capillary that is part of a lung. 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. - - + + + capillary of lung + FMA:14121 - + - + - + - - - - - + - - + + - - + + - - - - - - - + - - + + - An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart. - EHDAA2:0004149 - FMA:85125 + A hole in the diaphragm through which the esophagus passes. + FMA:58289 + esophageal hiatus of diaphragm + oesophageal aperture + oesophageal hiatus uberon - AV region - AV segment - atrial ventricular junction - atrioventricular junction - atrioventricular segment - UBERON:0011820 - atrioventricular region + UBERON:0016458 + + esophageal hiatus - + - An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart. - - - - - - AV region - - - - - - AV segment - + A hole in the diaphragm through which the esophagus passes. + HP:0002036 - - - atrial ventricular junction - GO:0003294 + + + esophageal hiatus of diaphragm + FMA:58289 - - - atrioventricular junction - FMA:85125 - GO:0003294 + + + oesophageal aperture + FMA:58289 - - - atrioventricular segment - + + + oesophageal hiatus + FMA:58289 - + - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + + 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:0011821 - irregular connective tissue + UBERON:0016490 + auditory system - - - - FMA + + + Is the sensory system for the sense of hearing. + NLXANAT:090817 - - - 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 + + + Auditory system is general anatomical term in FMA + FMA + + + + + UMLS:C0587901 + ncithesaurus:Auditory_System - + - - - - 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) + + + + + + + + + + + + + + + + + + + + + + + + + + Luminal space of the right ventricle of the heart. + EMAPA:26047 + FMA:9291 + right ventricle lumen + right ventricular cavity uberon - UBERON:0011822 - dense irregular connective tissue + UBERON:0016509 + cavity of right ventricle - - - - 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 + Luminal space of the right ventricle of the heart. + - - - UMLS:C0738366 - ncithesaurus:Irregular_Dense_Connective_Tissue + + + right ventricle lumen + EMAPA:26047 - + - typus irregularis (textus connectivus collagenosus compactus) - FMA:20109 + right ventricular cavity + FMA:FMA - + - + - + - - + + - + - - + + - - 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 + + + + + + + Luminal space of the left atrium of the heart. + EMAPA:26011 + FMA:9465 + left atrial cavity + left atrium lumen uberon - UBERON:0011823 - dense connective tissue + UBERON:0016513 + cavity of left atrium - + - 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 - + Luminal space of the left atrium of the heart. + - - - 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 + + + left atrial cavity + FMA:FMA - - - UMLS:C1511770 - ncithesaurus:Dense_Connective_Tissue + + + left atrium lumen + EMAPA:26011 - + - - - - FMA:75634 + + + + + + + + + + + + + + + + + + + + + + + + + + Luminal space of the left ventricle of the heart. + EMAPA:26038 + FMA:9466 + left ventricular cavity uberon - UBERON:0011824 - fibrous connective tissue + UBERON:0016514 + cavity of left ventricle - - - - FMA + + + Luminal space of the left ventricle of the heart. + + + + + + left ventricular cavity + FMA: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 + + + + + + + + + + + + + + + + + + + + An epithelium that is part of a female urethra. + EMAPA:30470 + FMA:19774 + female urethral epithelium + urethral epithelium of female 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 - + UBERON:0016520 + epithelium of female urethra + - - - UMLS:C1253917 - ncithesaurus:Loose_Connective_Tissue + + + An epithelium that is part of a female urethra. + OBOL:automatic - + - textus connectivus collagenosus laxus - FMA:19783 - FMA:TA - + female urethral epithelium + FMA:FMA - + - textus connectivus laxus - FMA:19783 - FMA:TA - + urethral epithelium of female + EMAPA:30470 - + - + - + - - + + - - - + - + - An acinus that is part of a lacrimal gland. - FMA:85250 - lacrimal gland acinus + + + + + + + Luminal space of the right atrium of the heart. + EMAPA:26020 + FMA:11359 + right atrial cavity uberon - UBERON:0011857 - acinus of lacrimal gland + UBERON:0016522 + cavity of right atrium - + - An acinus that is part of a lacrimal gland. - OBOL:automatic + Luminal space of the right atrium of the heart. + - + - lacrimal gland acinus - FMA:85250 + right atrial cavity + FMA:FMA - + - + - + - + + + + + - + + + - + - An acinus that is part of a exocrine gland. - exocrine gland acinus + + + + + + + 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:0011858 - acinus of exocrine gland + UBERON:0016545 + pharyngeal ectoderm - + - An acinus that is part of a exocrine gland. - OBOL:automatic + The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches. + + - + - - - the FMA class specifically refers to ureter - FMA:63212 - MESH:D024022 - NCIT:C32339 - NIF_Subcellular:sao7547390221 + + + + + + + + + + + + + + + + + + + + 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:0011860 - collection of collagen fibrils - + UBERON:0016548 + central nervous system gray matter layer - - - - ZFA + + + A layer of of the central nervous system that is part of gray matter. + - - - the FMA class specifically refers to ureter - FMA + + + gray matter layer of neuraxis + FMA:83142 - + - + - + - - + + - + - - + + - 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 + Mucus produced in the respiratory tract. + + NCIT:C93171 uberon - UBERON:0011863 - - bone collagen fibril + UBERON:0016552 + phlegm - + - 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 + Mucus produced in the respiratory tract. + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + - - + + - 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 + 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 - ciliary body and iris - vasculosa oculi - UBERON:0011892 - - anterior uvea + UBERON:0016553 + respiratory system mucus - - - - 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 + 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). + + - + - - - 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 + + + An roughly circular indentation in a surface. + AEO:0000204 uberon - coelem - coelomic cavity - UBERON:0011997 - coelom + UBERON:0016566 + + pit - - - - EHDAA2 - - - + - The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. - - - UBERON:cjm - - - - - enterocoelom - NCBITaxon:33511 - - - - - coelomic cavity - EHDAA2:0004731 + An roughly circular indentation in a surface. + AEO:0000204 + AEO:JB - + - - - - 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 + + + + + + + + + + + + + + + + + + + + + + + FMA:68861 + rexed lamina uberon - UBERON:0012075 - replacement bone + UBERON:0016570 + lamina of gray matter of spinal cord - - - - ZFA - - - - - - ZFA + + + rexed lamina + FMA:68861 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - + - 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 + The dorsal region of the optic cup that gives rise to the dorsal part of the retina. + - - - 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 + + + dorsal optic cup + - + - replacement bones - ZFA:0001628 - + 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. + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - + + - Anatomical system that consists of the integumental system plus all mucosae and submucosae. - - + Primordium that develops into the nervous system. + UBERON:3000477 + AAO:0000477 + presumptive nervous system uberon - dermatological system - UBERON:0012125 - dermatological-muscosal system + UBERON:0016880 + future nervous system - + - Anatomical system that consists of the integumental system plus all mucosae and submucosae. - + Primordium that develops into the nervous system. + - - - dermatological system - OBI:MC + + + presumptive nervous system + AAO:0000477 - + - + - + - + - + - + - A zone of skin that is part of a craniocervical region. - - EMAPA:37276 - MA:0000574 - NCIT:C12294 - UMLS:C1522650 + Epithelium lining the distalmost portion of the digestive tract. + BTO:0005445 + WBbt:0005800 + rectum epithelium uberon - UBERON:0012180 - head or neck skin + UBERON:0016885 + epithelium of terminal part of digestive tract - + - A zone of skin that is part of a craniocervical region. - OBOL:automatic - - - - - EMAPA:37276 - MA:th + Epithelium lining the distalmost portion of the digestive tract. + - - - UMLS:C1522650 - ncithesaurus:Skin_of_the_Scalp_and_Neck + + + 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. + + + + + + + + + + + + + + - - + + - 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 + + + + + + + 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 - blood vessel of bladder - UBERON:0012239 - - urinary bladder vasculature + UBERON:0016887 + entire extraembryonic component - - + + + + AEO + + + + - - - - - - - - - + + + + - EMAPA + AEO - + - 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 + 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 - + - blood vessels of bladder - EMAPA:28679 + 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 - - - blood vessel of bladder - EMAPA:28679 + + + An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development. + AEO:0000132 + AEO:JB - + - + - + - - - - - - - - - + - - + - + + The dorsal part of the body wall. + uberon + UBERON:0017649 + dorsal body wall + + + + + The dorsal part of the body wall. + + + + + + + + + + + + + + + + + + + + - - + + + A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. + AEO:0001016 + uberon + UBERON:0017650 + developing mesenchymal structure + + + + + A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. + AEO:0001016 + AEO:JB + + + + + + + + + + + + + + + + + + + + - - + + - 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 + A viscus that is part of a abdomen. + FMA:32413 + FMA:67355 + abdominal viscera + abdominal viscera set + set of abdominal viscera uberon - urinary meatus - UBERON:0012240 + UBERON:0017672 - urethral meatus + abdominal viscera - + - 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 - + A viscus that is part of a abdomen. + OBOL:automatic - + - orificium urethrae externum - + abdominal viscera + FMA:32413 - + - orificium urethræ externum - + abdominal viscera set + FMA:32413 - + - urethral meatus - FMA:19650 + set of abdominal viscera + FMA:32413 - + - + - + - - - - - - - - - + - - + - - - - - - - - - - - - - + - 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 + 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 - internal urethral ostium - internal urinary meatus - UBERON:0012242 - - internal urethral orifice + UBERON:0018111 + muscle layer of rectum - + - 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 + A muscle layer that is part of the rectum. + - + - internal urethral ostium - FMA:85263 + muscular coat of rectum + FMA:15035 - + - orificium urethrae internum - MP:0011782 - + muscularis externa of rectum + FMA:15035 - + - ostium orificium internum - + rectal muscularis propria + FMA:15035 - + - ostium urethrae internum - - + tunica muscularis (rectum) + FMA:15035 - + - vesicourethral orifice - FMA:85263 - - - - - internal urethral ostium - MP:0011782 - - - - - internal urinary meatus - MP:0011782 + tunica muscularis recti + FMA:TA - + - - - 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] - + + + + + + + + + + + + + + + + + + + + + + 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:0012274 - columnar epithelium + UBERON:0018112 + rectum smooth muscle tissue - + - 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] - + Any portion of smooth muscle tissue that is part of the rectum. + - + - + - + - - + + - + - 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 - - - - - - - - - - - - - - - - - - - - - + - 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 + A renal pelvis that is part of a left ureter. + + FMA:15579 + pelvis of left ureter + renal pelvis of left kidney 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 + UBERON:0018115 + left renal pelvis - - - - - - - - - EHDAA2 + + + A renal pelvis that is part of a left ureter. + OBOL:automatic - - - 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 + + + pelvis of left ureter + FMA:15579 - - - cloacal fold - EHDAA2:0004009 + + + renal pelvis of left kidney + FMA:15579 - + - + - + - + - + - + - A mucosa that is part of a urethra. - - EMAPA:37912 - FMA:76904 - mucous membrane of urethra - tunica mucosa urethrae - urethral mucosa + A renal pelvis that is part of a right ureter. + + FMA:15578 + pelvis of right kidney + pelvis of right ureter uberon - UBERON:0012299 - mucosa of urethra + UBERON:0018116 + right renal pelvis - + - A mucosa that is part of a urethra. + A renal pelvis that is part of a right ureter. OBOL:automatic - - - EMAPA:37912 - MA:th - - - - - mucous membrane of urethra - FMA:76904 - - - + - tunica mucosa urethrae - FMA:TA + pelvis of right kidney + FMA:15578 - + - urethral mucosa - FMA:76904 + pelvis of right ureter + FMA:15578 - + - - + + + + + + + + + + + + + - - + + - One of five swellings formed during the development of the face - - FMA:293103 + FMA:83521 uberon - embryonic facial process - facial primordium - primordium of face - UBERON:0012314 - embryonic facial prominence + UBERON:0018135 + fibrocollagenous connective tissue - - - - One of five swellings formed during the development of the face - - - + - + - + - + - - - An artery of the neck - - EMAPA:37075 - NCIT:C52850 - UMLS:C1707349 + + + + + + + + + + + + + + + + + + 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:0012320 - cervical artery + UBERON:0018142 + caudal vertebra endochondral element - + - An artery of the neck - - - - - - EMAPA:37075 - MA:th - - - - - UMLS:C1707349 - ncithesaurus:Cervical_Artery + Any vertebra endochondral element that is part of the caudal region of the vertebral column (tail or coccyx). + - + - + - + - + - - - - - - - + + - - - - - - - + - The deep cervical artery (Profunda cervicalis) is an artery of the neck. - - - FMA:10659 + A zone of skin that is part of a lower lip. + + FMA:24767 + lower lip skin uberon - profunda cervicalis - UBERON:0012321 - deep cervical artery + UBERON:0018150 + skin of lower lip - - - - - - - - - FMA - - - + - The deep cervical artery (Profunda cervicalis) is an artery of the neck. - + A zone of skin that is part of a lower lip. + OBOL:automatic - - - profunda cervicalis - + + + lower lip skin + FMA:24767 - + - + - + - - + + - - + + - + - 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 + + + + + + + A boundary delimiting a rhombomere. + rhombomere junction uberon - UBERON:0012360 - bone of jaw + UBERON:0018239 + rhombomere boundary - + - A bone element that is part of a jaw region. - OBOL:automatic + A boundary delimiting a rhombomere. + GO:0021654 - + - - + + + - + - EHDAA2:0004588 + + + + + + + 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:0012361 - internal anal region + UBERON:0018254 + + skeletal musculature - + - + - EHDAA2 + MA - + - + - + - - + + - + - + - 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 vein that drains a lacrimal gland. + + FMA:51779 + uberon + UBERON:0018256 + lacrimal vein + - + - A muscle layer that is part of an intestine. + A vein that drains a lacrimal gland. OBOL:automatic - - - - intestinal muscularis propria - FMA:15697 - - - - - muscularis externa of intestine - FMA:15697 - - + - + - - - - - + - - + + - - - - - - - + + - - + + - A layer of tissue between the muscularis and serosa. - - - - FMA:45636 - NCIT:C94494 - UMLS:C0225334 + Any portion of submucosa that lines the digestive tract. uberon - UBERON:0012375 - Contains nerves, blood vessels, lymphatics and lymph nodes - subserosa + UBERON:0018257 + submucosa of digestive tract - + - A layer of tissue between the muscularis and serosa. - - - - - - UMLS:C0225334 - ncithesaurus:Subserosa + Any portion of submucosa that lines the digestive tract. + - + - + - + - - + + - - - - - - - - + + - - + + - 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) + Any organ component layer that consists of muscle tissue. + NCITA class may refer to smooth muscle only + + FMA:45634 + NCIT:C75444 uberon - UBERON:0012378 - muscle layer of urinary bladder + UBERON:0018260 + layer of muscle tissue - - - - - - - - - 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 + Any organ component layer that consists of muscle tissue. + - - - tunica muscularis (vesica urinaria) - FMA:TA + + + NCITA class may refer to smooth muscle only + NCIT - + - + - + - + - - + - + - EMAPA:37567 - MA:0001802 + + + + + + + A muscular coat that is part of a digestive tract. + responsible for gut movement, such as peristalsis + tunica muscularis of digestive tract uberon - UBERON:0012416 - respiratory system arterial smooth muscle + muscular layer of digestive tract + muscularis externa of digestive tract + tunica externa of digestive tract + UBERON:0018261 + muscular coat of digestive tract - - - EMAPA:37567 - MA:th + + + A muscular coat that is part of a digestive tract. + OBOL:automatic - + - + - + - - + + - + - + - A smooth muscle tissue that is part of a respiratory system venous blood vessel. - EMAPA:37586 - MA:0001812 + + + + + + + Foramen that allows the passge of the glossopharyngeal nerve (cranial nerve IX). + UBERONTEMP:9ca0bda7-9111-4f59-bc72-5d47bc3d7d61 uberon - UBERON:0012418 - respiratory system venous smooth muscle + UBERON:0018321 + foramen for glossopharyngeal nerve - + - A smooth muscle tissue that is part of a respiratory system venous blood vessel. - OBOL:automatic - - - - - EMAPA:37586 - MA:th + Foramen that allows the passge of the glossopharyngeal nerve (cranial nerve IX). + PHENOSCAPE:alex - + - - - - + + + + + + + + + + + + + + - - - - - - - + - - + + - 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 + 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 - corneosclera - fibrous tunic - UBERON:0012430 - tunica fibrosa of eyeball + gut lumen + UBERON:0018543 + lumen of intestine - - - - 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. - - - - - - - + The anatomical space within the intestine. + - + - fibrous layer of eyeball - FMA:58102 + intestinal lumen + FMA:14586 - - - corneosclera - + + + intestine lumen + ZFA:0005807 - + - fibrous tunic - + gut lumen + ZFA:0005807 - + - + - + - - + + - - - - - - - + + + - - + + - - + + - 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 + 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:0012463 - cloacal lumen + UBERON:0018544 + trigeminal nerve muscle - - - - - - - - - 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 + Muscle innervated by the trigeminal nerve (Cranial Nerve V). + MFMO:0000072 - + - cloacal chamber - ZFA:0000330 + muscles innervated by the trigeminal nerve + MFMO:0000072 + - + - + - + - + - + - + - The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives. - cloacal opening + + + + + + + FMA:83450 + ventricular cardiac muscle tissue + ventricular heart muscle uberon - cloacal orifice - vent - UBERON:0012464 - cloacal vent + ventricular muscle + UBERON:0018649 + cardiac muscle tissue of ventricle - - - The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives. + + + ventricular cardiac muscle tissue + + + + + + ventricular heart muscle + + + + + + ventricular muscle - + - + - + - - + + - + + + - - - - - - - + - A anatomical space that is enclosed by a terminal part of digestive tract. - includes the cloacal lumen, in species where this is present + An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart. + FMA:73747 + ZFA:0005811 + cardiac vasculature uberon - UBERON:0012465 - lumen of terminal part of digestive tract + UBERON:0018674 + heart vasculature - + - A anatomical space that is enclosed by a terminal part of digestive tract. - OBOL:automatic + An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart. + ZFA:0005811 + ZFA:CVS + + + + + cardiac vasculature + FMA:73747 - + - + - + - - + + - + - + + + + + + + + + + + + + - 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 + UBERON:0018692 + dorsal side of post-anal tail - - - - An anatomical space with no opening to another space or to the exterior. - AEO:0000222 - - + - - + + + - - + + - EHDAA2:0004589 + + + + + + + + + + + + + A membranous sac in animals that serves as the receptacle of a liquid or contains gas. + BTO:0000123 + bladder uberon - UBERON:0012469 - external anal region + UBERON:0018707 + bladder organ - - - - - - - - - EHDAA2 + + + A membranous sac in animals that serves as the receptacle of a liquid or contains gas. + BTO:0000123 + + + + + bladder + BTO:0000123 - + - + - + - - + + - - - - - - - + + - - - - - - - + - The collection of all skeletal elements in a pectoral complex - i.e. the combination of free limb or fin plus pectoral girdle. - FMA:24139 + BTO:0002439 + genital mucosa 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 + UBERON:0019042 + reproductive system mucosa - - - - - - - - - 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 + + + genital mucosa + BTO:0002439 - + - + - + - - + + - - - - - - - + - - - - - - - + - The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle. - FMA:24140 + 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 - 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 + intramuscular fat + UBERON:0019143 + intramuscular adipose tissue - - - - - - - - - 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 + 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 - + - skeleton of posterior limb/fin and girdle - + intramuscular fat + BTO:0004043 - + - + - + - + - + - + - A gland that is part of a cloaca. + BTO:0004626 uberon - UBERON:0012478 - cloacal gland + carotid endothelium + carotid epithelium + UBERON:0019189 + carotid artery endothelium - - - A gland that is part of a cloaca. - OBOL:automatic + + + carotid endothelium + BTO:0004626 - + - + - + - + - + + + + - + - 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 + + BTO:0004638 + FMA:13119 + bronchial gland + bronchial mucous gland + peribronchial gland uberon - UBERON:0012480 - cloacal mucosa + UBERON:0019190 + mucous gland of lung - - - A mucosa that is part of a cloaca [Automatically generated definition]. - OBOL:automatic + + + bronchial gland + FMA:13119 + + + + + bronchial mucous gland + FMA:13119 + + + + + peribronchial gland + BTO:0004638 - + - + - + - - + - + - 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 + Any region of epithelium that is part of a skin region. + BTO:0004382 uberon - cloacal endoderm - UBERON:0012481 - cloacal epithelium + UBERON:0019204 + skin epithelium - + - An epithelium that is part of a cloaca. + Any region of epithelium that is part of a skin region. + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + - - - 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 + + + The part of the eye that consists of both the retina and the optic choroid. + + UBERON:drseb - + - + - + - + - + - + - A submucosa that is part of a cloaca [Automatically generated definition]. - cloaca submucosa - cloacal submucosa + DHBA:10654 + FMA:268630 + gray matter of the hindbrain uberon - UBERON:0012482 - submucosa of cloaca + UBERON:0019263 + gray matter of hindbrain - - - A submucosa that is part of a cloaca [Automatically generated definition]. - OBOL:automatic + + + gray matter of the hindbrain + DHBA:HGM - + - + - + - + - + - + - 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 + DHBA:10649 + FMA:83913 uberon - UBERON:0012483 - serosa of cloaca + UBERON:0019267 + gray matter of midbrain - - - - A serous membrane that is part of a cloaca [Automatically generated definition]. - OBOL:automatic - - + - + - + - + - + - + - A muscular coat that is part of a cloaca. - muscularis externa of cloaca + EMAPA:35952 + MA:0003174 uberon - smooth muscle of cloaca - UBERON:0012486 - muscle layer of cloaca + UBERON:0019304 + sensory organ epithelium - - - - A muscular coat that is part of a cloaca. - OBOL:automatic - - + - + - + - + - + + - + - 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 + An exocrine gland that is part of a integumental system. + integumental exocrine gland + integumental system exocrine gland uberon - colon muscularis - UBERON:0012489 - muscle layer of colon + UBERON:0019319 + exocrine gland of integumental system - + - A muscular coat that is part of a colon. - OBOL:automatic + An exocrine gland that is part of a integumental system. + + GOC:dos - + - colonic muscularis propria - FMA:14986 + integumental exocrine gland + - + - muscular coat of colon - FMA:14986 + 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 - - - muscular layer of colon - FMA:14986 + + + + MA - - - muscularis externa of colon - FMA:14986 + + + + + + + + + MA - + + + 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 + + + - tunica muscularis coli - FMA:TA + accessory neural nucleus + FMA:83965 - + - colon muscularis - MA:0003198 + 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 + - + - + + + + + + + + + + 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 + + + + + + + - + - - + + - - + + - + - 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 + + + + + + + FMA:58315 uberon - UBERON:0012490 - muscle layer of anal canal + surface of region of wall of eyeball + UBERON:0022288 + surface of eyeball - - - A muscular coat that is part of a anal canal. - OBOL:automatic - - - - - anal muscularis propria - FMA:15708 - - - - - muscularis propria of anal canal - FMA:15708 + + + surface of region of wall of eyeball + FMA:58315 - + - + - + - - - - - - - - - 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 + + + + + + + + + + + + + + A portion of organism substance that is secreted by a reproductive gland. uberon - UBERON:0013126 - - vein of abdomen + genital fluid + genital secretion + reproductive system fluid + reproductive system fluid/secretion + reproductive system secretion + UBERON:0022293 + reproductive gland secretion - + - A vein that is part of a abdomen. - OBOL:automatic + A portion of organism substance that is secreted by a reproductive gland. + UBERON:cjm - + - + - + - - + + + + + + - - - + + - - - - - - - + - - + + - A vein that drains a lip. - - labial vein of face - lip vein - vena labialis + 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 - labial vein - UBERON:0013136 - vein of lip + UBERON:0022303 + + nervous system cell part layer - - - - - - - - - FMA - - - + - A vein that drains a lip. - OBOL:automatic + 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 - - - lip vein - OBOL:automatic + + + lamina + CUMBO:CUMBO - - - vena labialis - + + + layer + CUMBO:CUMBO - + - + - + - + + + + + - + + - + - 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 + + + + + + + Serous membrane layer that is adjacent to and lines an organ. + FMA:15860 + visceral wall of serous membrane uberon - UBERON:0013140 - systemic vein + UBERON:0022350 + visceral serous membrane - + - 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 + Serous membrane layer that is adjacent to and lines an organ. + - + - systemic venous tree organ part - FMA:66644 + visceral wall of serous membrane + FMA:15860 - + - + - + - + + + + + - + + - + - A gland that is part of a foregut-midgut junction. - EHDAA2:0000574 - EMAPA:17065 - gland of foregut-midgut junction + + + + + + + Serous membrane layer that lines to a body cavity. + cavity lining + FMA:15859 + MA:0002448 + parietal wall of serous membrane uberon - UBERON:0013158 - foregut-midgut junction gland + UBERON:0022351 + parietal serous membrane - + - A gland that is part of a foregut-midgut junction. - OBOL:automatic + Serous membrane layer that lines to a body cavity. + - + + + cavity lining + MA:0002448 + + + - gland of foregut-midgut junction - EMAPA:17065 + parietal wall of serous membrane + FMA:15859 - + - + - + - - + + - + + - + - The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells. - FMA:86279 - acinus of serous gland + + + + + + + A specific region of the foregut into the area in which the lung will develop. + + lung field uberon - UBERON:0013232 - serous acinus + UBERON:0022361 + lung field - + - The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells. - - + A specific region of the foregut into the area in which the lung will develop. + GOC:dph + GOC:mtg_lung - + - - + + + - - + + - 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 + 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:0013241 - embryonic urethral groove + 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 + + + - - - - - - - Wikipedia + + AEO - + - The precursor of the urethra - + 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 + - - - 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 - + + + + AEO - - - sulcus urethralis primarius - - + + + A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells. + AEO:0001010 - + - + - + - - + + - + + - - - - - - - + - 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 + DHBA:12694 + EMAPA:32916 + marginal zone of hindbrain uberon - intracranial cavity - intracranial space - UBERON:0013411 - cranial cavity - http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg + MZH + UBERON:0034709 + hindbrain marginal layer - + - cavitas cranii - FMA:9644 - FMA:TA - - - - - - intracranial cavity - + marginal zone of hindbrain + DHBA:12694 - + - intracranial space - - - - - - - - - - - - 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 + MZH + DHBA:12694 + - + - + - + - - + + - + - - + + - The space that surrounds an organism. - external to organism - outside of body + + + + + + + EHDAA2:0001267 + EMAPA:17585 + spinal cord lateral wall ventricular layer uberon - UBERON:0013514 - space surrounding organism + UBERON:0034710 + spinal cord ventricular layer - - - The space that surrounds an organism. - + + + + + + + + + EHDAA2 + + + + + spinal cord lateral wall ventricular layer + EHDAA2:0001267 - + - - + + - + - - + + + + + + + + - - + + - - + + + 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 - UBERON:0013522 - subdivision of tube + 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 + + - + - + - + - + - + - + - Anatomical space that is an opening in a bone of the skull. - - - FMA:53165 - foramen of skull - cranial conduit - cranial foramen + A taste bud that is located external to the digestive tube, on the head or body, as found in species such as goldfish. uberon - foramina of the skull - UBERON:0013685 - foramen of skull + UBERON:0034717 + integumental taste bud - + - Anatomical space that is an opening in a bone of the skull. + A taste bud that is located external to the digestive tube, on the head or body, as found in species such as goldfish. - 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 + A taste bud that is located on a lip. + uberon - UBERON:0013686 - anatomical conduit space + UBERON:0034719 + lip taste bud - - - - FMA - - - + - An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]. + A taste bud that is located on a lip. - FMA:9338 + - + - + - + - + - - + + - + - Vascular endothelium found in blood vessels of the blood-brain-barrier. - BTO:0001852 - BTO:0003248 - CALOHA:TS-0092 + A taste bud that is located on the skin of the head. uberon - cerebromicrovascular endothelium - UBERON:0013694 - brain endothelium + UBERON:0034720 + head taste bud - + - Vascular endothelium found in blood vessels of the blood-brain-barrier. - CALOHA:TS-0092 - - - - - cerebromicrovascular endothelium - CALOHA:TS-0092 + A taste bud that is located on the skin of the head. + - + - + - + - + - - - Vascular endothelium found in colon blood vessels. - CALOHA:TS-0162 + + + + + + + + + + + + + + + A taste bud that is located in the pharynx. + uberon - colon endothelial cell - colon endothelial cells - colonic endothelial cell - colonic endothelium - colorectal endothelial cell - colorectal endothelium - UBERON:0013695 - colon endothelium + UBERON:0034721 + pharyngeal taste bud - + - 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 + A taste bud that is located in the pharynx. + - + - + - + - - - - - + - + + + - - - - - - - + - Musculature of the head and neck, spine, and ribs. - EHDAA2:0000159 - EMAPA:18166 + A taste bud that is located in the esophagus. + uberon - UBERON:0013700 - axial musculature + UBERON:0034724 + esophageal taste bud - + - Musculature of the head and neck, spine, and ribs. - HP:0003327 + A taste bud that is located in the esophagus. + - + - - - 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. + + + + + + + + + + + + + + + + + + + + + + A taste bud that is located on the skin of the trunk. uberon - UBERON:0013701 - - main body axis + UBERON:0034726 + trunk taste bud - + - 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. - + A taste bud that is located on the skin of the trunk. + - + - - + + - + - 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 + + + + + + + + + + + + + + + + + + + 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 - body - whole body - UBERON:0013702 - - body proper + UBERON:0034728 + autonomic nerve - - - - AEO - - - + - The region of the organism associated with the visceral organs. - AEO:0000103 + 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. + - - - 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 + + + EMAPA:37957 + MA:th - - - body - AEO:0000103 + + + nervus visceralis + FMA:5866 - - - whole body - BTO:0001489 + + + visceral nerve + FMA:5866 - + - + - + - + - - + - + - 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 + + EMAPA:37958 uberon - UBERON:0013727 - Distinct feature of coelocanths - notochordal fluid + UBERON:0034729 + sympathetic nerve - - - Fluid contained within the notochordal canal - - + + + EMAPA:37958 + MA:th - + - + + + FMA:79770 + NCIT:C41168 + uberon + UBERON:0034769 + lymphomyeloid tissue + + + + + + FMA + + + + + + + - + - - + + - + - - + + - A organ component layer that is part of a integumental system. - - layer of skin - skin layer + 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:0013754 - - integumentary system layer + UBERON:0034873 + bodily gas - + - A organ component layer that is part of a integumental system. - OBOL:automatic + Any substance in the body or expelled from the body that is in a gaseous state. + + + + + + portion of gas in anatomical space + FMA:84580 - + - + - + - - + + + + + + - + - - + + - A blood that is part of a artery. - FMA:83066 - arterial blood - blood in artery - portion of arterial blood + + + + + + + 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:0013755 - - arterial blood + UBERON:0034874 + air in respiratory system - + - A blood that is part of a artery. - OBOL:automatic - - - - - arterial blood - FMA:83066 - - - - - blood in artery - FMA:83066 + Any portion of gas located in a part of the respiratory system that is composed primarily of air. + - + - portion of arterial blood - FMA:83066 + respiratory air + FMA:84581 - + - + - + - + + + + + - + + - + - A blood that is part of a vein. - FMA:83067 - blood in vein - portion of venous blood - venous blood + + + + + + + The area of axial mesoderm that develops into the prechordal plate. + prechordal mesenchyme uberon - UBERON:0013756 - venous blood + UBERON:0034878 + prechordal mesoderm - + - 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 + The area of axial mesoderm that develops into the prechordal plate. + MGI:anna - + - + - + - + - + - + - A blood that is part of a capillary. - FMA:263901 - NCIT:C32212 - blood in capillary - portion of blood in capillary - portion of capillary blood + 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 - UBERON:0013757 - capillary blood + left atrium endocardial tissue + UBERON:0034903 + left atrium endocardium - + - A blood that is part of a capillary. - OBOL:automatic + 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 + + + - portion of blood in capillary - FMA:263901 + endocardium of left atrium + FMA:7286 + + + + + left atrium endocardial tissue + VHOG:0001226 - + - + - + - - + + - + - + - 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 + + + + + + + lumen of gland uberon - UBERON:0013765 - - - digestive system element + UBERON:0034905 + gland lumen + + + + + + + + + + + + + + + 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 + + + - Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. - + An multicellular anatomical structure that has subparts of multiple organs as a part. + CARO:0020001 - - - EMAPA:37843 - MA:th + + + anatomical cluster + CARO:0020001 - + - - - 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 + + + + + + + + + A cluster of cells, largely surrounded by a morphological boundary. + CARO:0020002 + FMA:62807 uberon - UBERON:0013768 - - Groupings may vary - typically pulmonary vessels and aorta and vena cavae - great vessel of heart + UBERON:0034922 + cell cluster - + + + + CARO + + + - Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart. - + A cluster of cells, largely surrounded by a morphological boundary. + CARO:0020002 - + - - - - - - - - - - - - - - - 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 + + + + + + + + + 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:0014387 - mesenchyme derived from neural crest + UBERON:0034925 + anatomical collection - + - Mesenchyme that develops_from the neural crest[Automatically generated definition]. - - OBOL:automatic + A collection of anatomical structures that are alike in terms of their morphology or developmental origin. + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + + + + + + + + - + - - + + - - - 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 + + + + + + + + Any organ component layer that consists of smooth muscle tissue. uberon - kidney venous system - UBERON:0014401 - - renal venous blood vessel + UBERON:0034933 + layer of smooth muscle tissue - + - Any member of the network of tubes that return blood from the renal tissues to the systemic circulation. - MGI:csmith + Any organ component layer that consists of smooth muscle tissue. + + + + + + + + + FMA:55268 + organ sector + organ zonal region + organ zone + uberon + organ region with floating fiat boundary + UBERON:0034944 + zone of organ + - - - 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 + + + organ sector + FMA:55268 - + - kidney venous blood vessel - MA:0002591 + organ zone + FMA:55268 - + - kidney venous system - EMAPA:31450 + organ region with floating fiat boundary + FMA:55268 - + - + - + - - - - - - + + - - - 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 + + + + + + + + + Any gaseous product of an excretory process. uberon - UBERON:0014455 - subcutaneous abdominal adipose tissue + UBERON:0034945 + excreted gas - + - Subcutaneous adipose tissue that is located in the abdominal region. + Any gaseous product of an excretory process. - - CALOHA:paula - MGI:csmith - + - - - - - - - - + + + + + + + + + + + + + - - + + - 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 + Any excreted gas that is produced by the digestive tract. + FMA:78440 + flatulence + flatus + intestinal gas uberon - UBERON:0014477 - - thoracic skeleton + UBERON:0034946 + In mammals, mostly produced as a byproduct of bacterial fermentation in the gastrointestinal (GI) tract, especially the colon, and excreted through the rectum + gas excreted from digestive tract - + - 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. - - + Any excreted gas that is produced by the digestive tract. + - - - thoracic skeleton - EHDAA2:0002013 + + + flatulence + FMA:78440 + + + + + flatus + + - + - + - - - - - + - - + + - - + - - + + - A unilaminar epithelium that develops_from a ectoderm and is part of a anal region. - EHDAA2:0004019 - EMAPA:25040 + Any portion of gas located in a part of the respiratory system. + respiratory gas + respiratory system gas uberon - UBERON:0014703 - anal membrane ectodermal component + UBERON:0034947 + gas in respiratory system - + - A unilaminar epithelium that develops_from a ectoderm and is part of a anal region. - OBOL:automatic + Any portion of gas located in a part of the respiratory system. + - + - + - + - + - + - + - The secretory unit of a mucous gland. The acinar portion is composed of mucous secreting cells. - FMA:86278 - acinus of mucuous gland - mucus acinus + + + + + + + + NCIT:C25787 uberon - UBERON:0014717 - mucous acinus + duct epithelium + ductal epithelium + UBERON:0034969 + epithelial layer of duct - - - - The secretory unit of a mucous gland. The acinar portion is composed of mucous secreting cells. - - - - + - + - + - + - + + - + - 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 + Mesenchyme that is part of a developing jaw [Automatically generated definition]. + EMAPA:32907 + EMAPA:35454 uberon - future mesencephalon - mesomere group - UBERON:0014776 - midbrain neuromere + UBERON:0034995 + jaw mesenchyme - + - A neuromere that is part of the presumptive midbrain - - - - - - mesomere group - EHDAA2:0004352 + Mesenchyme that is part of a developing jaw [Automatically generated definition]. + OBOL:automatic - + - + - + - + - + - + - A neuromere that is part of the presumptive spinal cord - TAO:0001332 - ZFA:0001332 - spinal cord metameric segment - spinal neuromeres + EMAPA:32904 + MA:0003220 uberon - spinal cord segment - UBERON:0014777 - spinal neuromere + UBERON:0035037 + jaw epithelium - - - - 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. + + + + + + + + hemorrhoidal artery uberon - UBERON:0014783 - cloacal muscle + UBERON:0035039 + rectal artery - - - - Any muscle organ that is part of a cloaca. - OBOL:automatic - - + - + - + - - + + - + - - + + - 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 + A post-anal tail that attaches outside the tail. uberon - UBERON:0014792 - musculature of pelvic complex + UBERON:0035091 + extrinsic post-anal tail muscle - + - 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 + A post-anal tail that attaches outside the tail. + - + - + - + - - + + - + - - + + - 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 + 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 - UBERON:0014793 - musculature of pectoral complex + ingested material entity + UBERON:0035118 + material entity in digestive tract - + - 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 + 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. + - - - upper limb musculature - FMA:71296 + + + digestive tract contents + - + - + - + - - + + - - - - - - - + - - + + - A portion of tissue that will develop into vasculature. - EFO:0003708 - TAO:0005076 - ZFA:0005076 + 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:0014903 - primordial vasculature + UBERON:0035159 + entire surface of organism - + - A portion of tissue that will develop into vasculature. - ZFA:0005076 - ZFA:curator + 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 - + - + - + - - + + - - - - - - - - - - + + + - + - A forelimb bone or its cartilage or pre-cartilage precursor. - forelimb skeletal element + + + + + + + + + FMA:70506 + NCIT:C32837 + internal carotid arterial subdivision + subdivision of internal carotid artery uberon - UBERON:0015021 - forelimb endochondral element + UBERON:0035237 + branch of internal carotid artery - - - A forelimb bone or its cartilage or pre-cartilage precursor. - + + + internal carotid arterial subdivision + FMA:70506 - - - forelimb skeletal element - + + + subdivision of internal carotid artery + FMA:70506 - + - + - + - - + + - - - - - - - - - - + + - + - A hindlimb bone or its cartilage or pre-cartilage precursor. - hindlimb bone skeletal element + + + + + + + + + FMA:70505 + NCIT:C32552 + external carotid arterial subdivision + subdivision of external carotid artery uberon - UBERON:0015022 - hindlimb endochondral element + UBERON:0035398 + branch of external carotid artery - - - A hindlimb bone or its cartilage or pre-cartilage precursor. - + + + external carotid arterial subdivision + FMA:70505 - - - hindlimb bone skeletal element - + + + subdivision of external carotid artery + FMA:70505 - + - + - + - - + + + + + + - - - - - - - - - - - + + - + - A limb bone or its cartilage or pre-cartilage precursor. - limb bone skeletal element - limb bone endochondral element + + + + + + + + + + + + + + + FMA:15590 + NCIT:C32895 + facies posterior (Ren) + facies posterior renis uberon - UBERON:0015061 - limb endochondral element + UBERON:0035471 + posterior surface of kidney - - - A limb bone or its cartilage or pre-cartilage precursor. - - - - - - limb bone skeletal element - + + + facies posterior (Ren) + FMA:15590 - + - limb bone endochondral element - + facies posterior renis + FMA:15590 + FMA:TA + - + - - + + + + + + + + + + + + + + - + - consider merging into myocardial compact layer - FMA:83105 - perimysial connective tissue of subepicardium - subepicardial connective tissue + + + + + + + + + + + + + + + + + + + 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:0015128 - subepicardial layer of epicardium + UBERON:0035539 + esophageal artery - + + + + FMA + + + - - + + FMA - + + + Any of several arteries that arise from the aorta and supply blood to the esophagus. + ncithesaurus:Esophageal_Artery + + + - perimysial connective tissue of subepicardium - FMA:83105 + aortic esophageal artery + FMA:4149 - + - subepicardial connective tissue - FMA:83105 + oesophageal artery + FMA:4149 - + - + - - - - - + - - + + + + + + + + + + + + + + + + + + + + FMA:51797 + ciliary vein + uberon + UBERON:0035546 + uveal vein + + + + + ciliary vein + FMA:51797 + + + + + + + + + + + - - + + - - - + - + - - + + + + uberon + UBERON:0035548 + colic artery + + + + + + + + + + + + + + + + + + + - - + + - Visceral intrapericardial fat contiguous with the myocardial surface. - - FMA:9871 - epicardial adipose tissue - pericardial adipose tissue + + + + + + + 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 - UBERON:0015129 - epicardial fat + skin vasculature + subcutaneous vasculature + vasculature of skin + UBERON:0035549 + vasculature of integument - + - Visceral intrapericardial fat contiguous with the myocardial surface. - + 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 - + - + - + - + - + - + - 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 + Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers. + + + + FMA:76719 + NCIT:C33666 uberon - orbital gland - UBERON:0015152 - gland of ocular region + superfical vein + superficial veins + superficial vessels + UBERON:0035550 + superficial vein - - - - - - - - - inferred + + + Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers. + ncithesaurus:Superficial_Vein - - - 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. - - + + + superfical vein + - - - - - - - - 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. - + + + superficial veins + + + + + + superficial vessels + - + - + - + - - + + - + - - + + - An eye consisting of multiple light-sensing organs - - - + 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:0015165 - multi-unit eye + UBERON:0035551 + deep vasculature - + - An eye consisting of multiple light-sensing organs + The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin. - - - - - - - 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 region of somite adjacent to presomitic mesoderm. - TAO:0001462 - XAO:0004074 - ZFA:0001462 + A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery. + + + + FMA:76718 + NCIT:C32444 uberon - inter-somited border - intersomitic boundary - intersomitic fissure - intersomitic junction - segmental border - somite boundary - UBERON:0015178 - - somite border + deep veins + deep vessels + UBERON:0035552 + deep vein - + - A region of somite adjacent to presomitic mesoderm. - + A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery. + ncithesaurus:Deep_Vein - + - intersomitic junction - XAO:0004074 + deep veins + - + - somite boundary - ZFA:0001462 + deep vessels + - + - + - + - - + + - + + - - + + - Epithelium located in the intersomitic region. - XAO:0004077 - intersomitic epithelium - intersomitic membrane + Any chamber of the left side of the heart. + + FMA:7166 uberon - UBERON:0015179 - somite boundary epithelium + UBERON:0035553 + left cardiac chamber - + - Epithelium located in the intersomitic region. - XAO:0004077 - XAO:EJS - - - - - intersomitic epithelium - XAO:0004077 - - - - - intersomitic membrane - XAO:0004077 + Any chamber of the left side of the heart. + - + - + - + - - + + - + + - - + + - 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. + Any chamber of the right side of the heart. + + FMA:7165 uberon - UBERON:0015212 - - - lateral structure + UBERON:0035554 + right cardiac chamber - + - Any structure that is placed on one side of the left-right axis of a bilaterian. + Any chamber of the right side of the heart. - + - - + + - + - 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 + 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 - cardiac structure - UBERON:0015228 - - circulatory organ + UBERON:0035597 + profundal placode - + - 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. - + 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 - + - + + + + + + + + + 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 + + + + + + + + + - + - - + + - + + - - + + - A basement membrane of epithelium that is part of a respiratory system. - EMAPA:37570 - MA:0001815 + Any nerve that innervates the larynx. + + MESH:A08.800.050.050.925.450 uberon - UBERON:0015329 - respiratory system basement membrane + UBERON:0035642 + laryngeal nerve - - - - - - - - - MA - - - + - A basement membrane of epithelium that is part of a respiratory system. - OBOL:automatic - - - - - EMAPA:37570 - MA:th + Any nerve that innervates the larynx. + UBERON:cjm - + - - + + + + + + + + + + + + + + - + - EMAPA:37597 - MA:0002449 - heart/pericardium + + + + + + + + + + + + + EHDAA2:0004181 + FMA:9464 + cardiac chamber cavity + heart cavity + heart lumen uberon - UBERON:0015410 - heart plus pericardium + UBERON:0035763 + cavity of cardiac chamber - + - - MA + + + + + + + FMA - - - EMAPA:37597 - MA:th + + + cardiac chamber cavity + FMA:9464 - + - heart/pericardium - MA:0002449 + heart cavity + FMA:9464 + + + + + heart lumen + EHDAA2:0004181 - + - - - - - - - - - - - - - - + + + + + + + + + + + + + + + - - + + - A mesenchyme that is part of a urethra. - EMAPA:37786 - MA:0002648 + The primordial mouth region of the developing head. + FMA:293105 + primitive mouth + primordial mouth uberon - UBERON:0015418 - urethra mesenchymal layer + UBERON:0035804 + future mouth - + - A mesenchyme that is part of a urethra. - OBOL:automatic + The primordial mouth region of the developing head. + MP:0003119 - - - EMAPA:37786 - MA:th + + + primitive mouth + FMA:293105 - + - + - + - + - - + - + - A valve that is part of a ureter. - EMAPA:37781 - MA:0002658 - ureteral valve - valve or ureter + 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 - UBERON:0015420 - ureteral valve + sigmoideum muscularis + tunica muscularis colon sigmoideum + UBERON:0035805 + muscle layer of sigmoid colon - + - A valve that is part of a ureter. - OBOL:automatic - - - - - EMAPA:37781 - MA:th + A muscle layer that is part of the sigmoid colon. + - + - ureteral valve - MA:0002658 + muscularis externa of sigmoid colon + FMA:15028 - + - + - + - - + + - - + - + - A epithelium that is part of a anal canal. - EMAPA:18835 - FMA:17511 - anal canal epithelium - epithelium of anal canal + + + + + + + + FMA:12241 uberon - UBERON:0015716 - anal canal epithelium + UBERON:0035809 + serous cavity - - - - 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 hypodermis. - FMA:77862 - muscle layer in fatty layer of subcutaneous tissue - stratum musculosum panniculi adiposi telae subcutaneae + The sum of epicardial and paracardial fat deposits. + + ZFA:0005765 uberon - UBERON:0015783 - smooth muscle layer in fatty layer of subcutaneous tissue + UBERON:0035814 + pericardial fat - + - 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 sum of epicardial and paracardial fat deposits. + - + - + - + - - + + + + + + - - + - - + + - A epithelium that is part of a camera-type eye. - EMAPA:35957 - MA:0003162 + + + + + + + Fat deposits in the mediastinum outside the parietal pericardium . + intrathoracic fat uberon - UBERON:0015808 - eye epithelium + UBERON:0035815 + paracardial fat - + - A epithelium that is part of a camera-type eye. - OBOL:automatic + Fat deposits in the mediastinum outside the parietal pericardium . + + + + + + intrathoracic fat + - + - + - + - - + + - + - - + + - A epithelium that is part of a foregut. - EMAPA:32922 - MA:0003204 + Any fat deposit surrounding a visceral organ. uberon - UBERON:0015833 - foregut epithelium + UBERON:0035818 + visceral fat - + - A epithelium that is part of a foregut. - OBOL:automatic + Any fat deposit surrounding a visceral organ. + UBERON:cjm - + - + - + - + - - + + - - - + + - + - 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 + + + + + + + + + + + + + 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:0016545 - pharyngeal ectoderm + UBERON:0035819 + abdominopelvic cavity - + - The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches. - - + 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 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 + + + + + + + + + + + + + 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 - UBERON:0016548 - central nervous system gray matter layer + peritoneal component + UBERON:0035820 + peritoneal sac - + - A layer of of the central nervous system that is part of gray matter. - + A serous sac that is the aggregate of the peritoneum and the peritoneal cavity, located in the abdominal cavity. + - - - gray matter layer of neuraxis - FMA:83142 + + + peritoneal component + EMAPA:16137 - + - - - - - - - - - - - - - + + + + - - + + - 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). + + + + + + + + + + + + + + + + + + + The domain of the diaphragm that is a thin domed sheet of muscle composed of a radial array of myofibers extending laterally from the ribs and medially to a central tendon. + + FMA:58277 + costal part of diaphragm + pars costalis diaphragmatis uberon - UBERON:0016553 - respiratory system mucus + UBERON:0035831 + costal diaphragm - - - 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). - - + + + + + + + + + - - - - - - - - An roughly circular indentation in a surface. - AEO:0000204 - uberon - UBERON:0016566 - - pit - - + + + + + + + + + + + + - An roughly circular indentation in a surface. - AEO:0000204 - AEO:JB + The domain of the diaphragm that is a thin domed sheet of muscle composed of a radial array of myofibers extending laterally from the ribs and medially to a central tendon. + + + + + + costal part of diaphragm + FMA:58277 + + + + + pars costalis diaphragmatis + FMA:TA + - + - + - + - + - - + + - + - - - FMA:68861 - rexed lamina + + + + + + + BTO:0004378 + EMAPA:37987 + FMA:67473 + blood vessel wall uberon - UBERON:0016570 - lamina of gray matter of spinal cord + vascular wall + UBERON:0035965 + wall of blood vessel - + + + EMAPA:37987 + MA:th + + + - rexed lamina - FMA:68861 + blood vessel wall + FMA:67473 + + + + + vascular wall + BTO:0004378 - + - + - + - - + + - + + + + + - + - - - - - - - + - Primordium that develops into the central nervous system - UBERON:3000469 - future CNS - presumptive central nervous system + EHDAA2:0004070 uberon - UBERON:0016879 - future central nervous system + UBERON:0036072 + respiratory primordium epithelium - - - Primordium that develops into the central nervous system - + + + + + + + + + EHDAA2 - + - + - + - - + + - + + - - + + - - + + - Primordium that develops into the nervous system - UBERON:3000477 - AAO:0000477 - presumptive nervous system + EHDAA2:0004071 + respiratory primordium associated mesenchyme uberon - UBERON:0016880 - future nervous system + UBERON:0036073 + respiratory primordium mesenchyme - - - Primordium that develops into the nervous system - + + + + + + + + + EHDAA2 - + - presumptive nervous system - AAO:0000477 + respiratory primordium associated mesenchyme + EHDAA2:0004071 - + - - - - - - - - - - - - - + + + + + - + - Epithelium lining the distalmost portion of the digestive tract. - BTO:0005445 - WBbt:0005800 - rectum epithelium + + + + + + + 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:0016885 - epithelium of terminal part of digestive tract + UBERON:0036146 + cardiopharyngeal field - + - Epithelium lining the distalmost portion of the digestive tract. - - - - - - rectum epithelium - BTO:0005445 + 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 - + - + - + - - + + - + + - - + + - Any muscle tissue of the distalmost portion of the digestive tract. - rectum muscle - rectum muscle structure + FMA:83520 uberon - UBERON:0016886 - muscle tissue of terminal part of digestive tract + UBERON:0036186 + fibroelastic connective tissue - - - - 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 + An anatomical junction that is between the sigmoid colon and rectum. + + NCIT:C54188 uberon - UBERON:0016887 - entire extraembryonic component + rectosigmoid region + UBERON:0036214 + rectosigmoid junction - - - - 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 anatomical junction that is between the sigmoid colon and rectum. + + + NCIT:C54188 - - - 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 + + + rectosigmoid region + NCIT:C54188 - + - - - - - - - - - - - - - + + - + + + + + + + - The dorsal part of the body wall + Material anatomical entity that forms the outermost boundary of an anatomical structure. + AAO:0010270 + AEO:0000154 + ZFA:0005594 uberon - UBERON:0017649 - dorsal body wall + UBERON:0036215 + anatomical surface region - + - The dorsal part of the body wall - + Material anatomical entity that forms the outermost boundary of an anatomical structure. + - + - + - + - - + + - + - - + + - A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. - AEO:0001016 + 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:0017650 - developing mesenchymal structure + UBERON:0036217 + coelomic fluid - + - A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. - AEO:0001016 - AEO:JB + A bodily fluid that is located in the coelom. + + - + - + - + - + - - - A viscus that is part of a abdomen. - FMA:32413 - FMA:67355 - abdominal viscera - abdominal viscera set - set of abdominal viscera + + + + + + + + Any gland that is part os the respiratory system. uberon - UBERON:0017672 - - abdominal viscera + UBERON:0036225 + respiratory system gland - + - 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 + Any gland that is part os the respiratory system. + UBERON:cjm - + - + - + - + - + - + - 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 + + + + + + + A notochord that has persisted beyond the embryonic stage. + + + + + + uberon - UBERON:0018111 - muscle layer of rectum + UBERON:0036242 + post-embryonic notochord - + - 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 + A notochord that has persisted beyond the embryonic stage. + UBERON:cjm - + - + - + - - + + - - - + - - + + - Any portion of smooth muscle tissue that is part of the rectum - rectal smooth muscle tissue - rectum smooth muscle - smooth muscle of rectum + + + + + + + A transudate found in the serous sac. + serous fluid + FMA:20932 + serous sac fluid uberon - UBERON:0018112 - rectum smooth muscle tissue + UBERON:0036244 + secretion of serous membrane - + - Any portion of smooth muscle tissue that is part of the rectum - + A transudate found in the serous sac. + FMA:20932 + + + + + serous fluid + FMA:20932 - + - + - + - + - - + - + - A zone of skin that is part of a lower lip. - - FMA:24767 - lower lip skin + FMA:53133 + cranial orifice + skull orifice uberon - UBERON:0018150 - skin of lower lip + UBERON:0036253 + orifice of skull - - - A zone of skin that is part of a lower lip. - OBOL:automatic + + + cranial orifice + FMA:53133 - + - lower lip skin - FMA:24767 + skull orifice + FMA:53133 - + - - - - - - - - - - - - - - + + - + - - + + - A boundary delimiting a rhombomere. - rhombomere junction + 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 - UBERON:0018239 - rhombomere boundary + zygomaticotemporal + zygomaticotemporal branch + UBERON:0036264 + zygomaticotemporal nerve - + - A boundary delimiting a rhombomere. - GO:0021654 + 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 + - + - + - + + + + + + + - + - A vein that drains a lacrimal gland. - - FMA:51779 + uberon - UBERON:0018256 - lacrimal vein + UBERON:0036268 + pelvic vein - - - - A vein that drains a lacrimal gland. - OBOL:automatic - - + - + - + - + - + - + - Any portion of submucosa that lines the digestive tract. + Wall of ventricle which is continuous with the wall of aorta. + FMA:9556 + left ventricular wall uberon - UBERON:0018257 - submucosa of digestive tract + UBERON:0036285 + wall of left ventricle - - - Any portion of submucosa that lines the digestive tract. - + + + + FMA - - - - - - - - - - - - - - - - - - - + + + + - - + + - - 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 - + + FMA + - + - Any organ component layer that consists of muscle tissue. - + Wall of ventricle which is continuous with the wall of aorta. + FMA:9556 - - - NCITA class may refer to smooth muscle only - NCIT + + + left ventricular wall + FMA:9556 - + - + - + - + - + - + - A muscular coat that is part of a digestive tract. - responsible for gut movement, such as peristalsis - tunica muscularis of digestive tract + Wall of ventricle which is continuous with the wall of pulmonary trunk. + FMA:9533 + right ventricular wall uberon - muscular layer of digestive tract - muscularis externa of digestive tract - tunica externa of digestive tract - UBERON:0018261 - muscular coat of digestive tract + UBERON:0036286 + wall of right ventricle - + + + + FMA + + + + + + + + + + + FMA + + + - A muscular coat that is part of a digestive tract. - OBOL:automatic + Wall of ventricle which is continuous with the wall of pulmonary trunk. + FMA:9533 + + + + + right ventricular wall + FMA:9533 - + - + - + - - + + - + - + - - + + - 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 + FMA:9560 uberon - gut lumen - UBERON:0018543 - lumen of intestine + UBERON:0036288 + anterior wall of left ventricle - - - The anatomical space within the intestine. - - - - - - intestinal lumen - FMA:14586 - - - - - intestine lumen - ZFA:0005807 - - - - - gut lumen - ZFA:0005807 + + + + + + + + + FMA - + - + - + - - + + - + - - + + - FMA:83450 - ventricular cardiac muscle tissue - ventricular heart muscle + Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle. + FMA:9553 uberon - ventricular muscle - UBERON:0018649 - cardiac muscle tissue of ventricle + UBERON:0036289 + anterior wall of right ventricle - - - ventricular cardiac muscle tissue - - - - - - ventricular heart muscle - - - - - - ventricular muscle - + + + Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle. + FMA:9553 - + - + - + - + - - + - - - - 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 - - - - - - - - - - - - - + - A membranous sac in animals that serves as the receptacle of a liquid or contains gas. - BTO:0000123 - bladder + FMA:87177 uberon - UBERON:0018707 - bladder organ + UBERON:0036290 + myocardium of anterior wall of left ventricle - - - - 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 + + + + + + + + FMA:260877 uberon - UBERON:0019042 - reproductive system mucosa + UBERON:0036291 + myocardium of anterior wall of right ventricle - - - - genital mucosa - BTO:0002439 - - + - + - + - + - + + - + - Any region of epithelium that is part of a skin region. - BTO:0004382 + A mucosa that is part of a lip region [Automatically generated definition]. + NCIT:C12226 + labial mucosa uberon - UBERON:0019204 - skin epithelium + UBERON:0036294 + mucosa of lip - + - Any region of epithelium that is part of a skin region. - + A mucosa that is part of a lip region [Automatically generated definition]. + OBOL:automatic + + + + + labial mucosa + UBERON:cjm - + - - - - + + - - - - - - - - - - - - - + - The part of the eye that consists of both the retina and the optic choroid - - chorioretina - choroid and retina - retinachoroid - retinachoroidal region + 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:0019207 - - chorioretinal region + UBERON:0036295 + renal pelvis/ureter - + + + + + + + + + NCIT + + + - The part of the eye that consists of both the retina and the optic choroid - - UBERON:drseb + 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 - + - + - - - - - - - + + + + - - - - - - - - DHBA:10654 - FMA:268630 - gray matter of the hindbrain + uberon - UBERON:0019263 - gray matter of hindbrain + UBERON:0036302 + vasculature of central nervous system plus retina - - - - gray matter of the hindbrain - DHBA:HGM - - + - + - + - + - + + - + - DHBA:10649 - FMA:83913 + FMA:259905 uberon - UBERON:0019267 - gray matter of midbrain + UBERON:0036303 + vasculature of central nervous system - + - + - + - + + + + + - + + + - + - EMAPA:35952 - MA:0003174 + + + + + + + FMA:15704 + anal canal wall uberon - UBERON:0019304 - sensory organ epithelium + UBERON:0036362 + wall of anal canal + + + + + FMA + + + + + + + + + + + FMA + + + + + + + + + + + FMA + + + + + anal canal wall + FMA:15704 + - + - + - + - + - - - An exocrine gland that is part of a integumental system. - integumental exocrine gland - integumental system exocrine gland + + + + + + + + FMA:15889 + right ureteral wall uberon - UBERON:0019319 - exocrine gland of integumental system + UBERON:0036375 + wall of right ureter - - - An exocrine gland that is part of a integumental system. - - GOC:dos - - - - - integumental exocrine gland - + + + + FMA - - - integumental system exocrine gland - - - - - - - - - - - + + + - + - - 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 - + + FMA + - - - 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 + + + right ureteral wall + FMA:15889 - + - + - + - - + + - + - - - - - - - + - FMA:58315 + FMA:15890 + left ureteral wall uberon - surface of region of wall of eyeball - UBERON:0022288 - surface of eyeball + UBERON:0036376 + wall of left ureter - - - surface of region of wall of eyeball - FMA:58315 + + + + FMA + + + + + + + + + + + FMA + + + + + left ureteral wall + FMA:15890 - + - + - + - - + + - + + - - + + - A portion of organism substance that is secreted by a reproductive gland. + FMA:18211 + pulmonary arterial wall uberon - genital fluid - genital secretion - reproductive system fluid - reproductive system fluid/secretion - reproductive system secretion - UBERON:0022293 - reproductive gland secretion + UBERON:0036422 + wall of pulmonary artery - - - A portion of organism substance that is secreted by a reproductive gland. - UBERON:cjm + + + + FMA - - - - - - - - + + + + - + - - 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 + + FMA - - - layer - CUMBO:CUMBO + + + pulmonary arterial wall + FMA:18211 - + - + - + - - - - - + + - - - - - - - - + - Serous membrane layer that is adjacent to and lines an organ. - FMA:15860 - visceral wall of serous membrane + FMA:19779 + urethral wall uberon - UBERON:0022350 - visceral serous membrane + UBERON:0036521 + wall of urethra - - - Serous membrane layer that is adjacent to and lines an organ. - + + + + FMA - + + + + + + + + + FMA + + + - visceral wall of serous membrane - FMA:15860 + urethral wall + FMA:19779 - + - + - + - - - - - + - - + + - - - - - - - + - Serous membrane layer that lines to a body cavity. - cavity lining - FMA:15859 - MA:0002448 - parietal wall of serous membrane + FMA:231590 uberon - UBERON:0022351 - parietal serous membrane + UBERON:0036553 + wall of synovial tendon sheath - - - Serous membrane layer that lines to a body cavity. - - - - - - cavity lining - MA:0002448 + + + + FMA - - - parietal wall of serous membrane - FMA:15859 + + + + + + + + + FMA - + - - + + + + + + + + + + + + + + - + - 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 + FMA:58098 + eyeball wall uberon - UBERON:0034705 - developing neuroepithelium + UBERON:0036925 + wall of eyeball - - - An embryonic or larval epithelium that is committed to form part of the nervous system. - AEO:0001008 - AEO:JB - - - - - neurepithelium - BTO:0000314 + + + + FMA - - - embryonic neuroepithelium - + + + + + + + + + FMA - + - neuroepithelium - AEO:0001008 + eyeball wall + FMA:58098 - + - - - An epithelium that is undergoing proliferation to provide large numbers of neuronal cells. - AEO:0001009 + + + + + + + + + + + + + + + + + + + + + FMA:66284 + common carotid arterial wall uberon - UBERON:0034706 - proliferating neuroepithelium + UBERON:0037094 + wall of common carotid artery - + - - AEO - - - - - An epithelium that is undergoing proliferation to provide large numbers of neuronal cells. - AEO:0001009 + + FMA - - - - - - - - A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells. - AEO:0001010 - uberon - UBERON:0034707 - differentiating neuroepithelium - - + - - AEO + + + + + + + FMA - - - A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells. - AEO:0001010 + + + common carotid arterial wall + FMA:66284 - + - + - + - + - - + + + - + - DHBA:12694 - EMAPA:32916 - marginal zone of hindbrain + + + + + + + + + + + + + + + + + + + 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 - MZH - UBERON:0034709 - hindbrain marginal layer + UBERON:0037144 + wall of heart - - - marginal zone of hindbrain - DHBA:12694 + + + + FMA - - - MZH - DHBA:12694 - + + + + + + + + + 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 - + - + - + - + - - - - - - - + - - - - EHDAA2:0001267 - EMAPA:17585 - spinal cord lateral wall ventricular layer + + + + FMA:19780 + female urethral wall uberon - UBERON:0034710 - spinal cord ventricular layer + UBERON:0037455 + wall of female urethra - + + + + FMA + + + - + - EHDAA2 + FMA - + - spinal cord lateral wall ventricular layer - EHDAA2:0001267 + female urethral wall + FMA:19780 - + - + - - - - - + - - + + - + - + - - + + - the area of axial mesoderm that develops into the prechordal plate - prechordal mesenchyme + + + + + + + FMA:15395 uberon - UBERON:0034878 - prechordal mesoderm + UBERON:0039228 + sigmoid vein - - - the area of axial mesoderm that develops into the prechordal plate - MGI:anna + + + + + + + + + FMA - + - + - + - - + + - + - - - - - - - + - lumen of gland + 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 - UBERON:0034905 - gland lumen + 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 + - + - - + + + + + + + + + + + + + - - + + - An multicellular anatomical structure that has subparts of multiple organs as a part. - CARO:0020001 + An anatomical junction between two parts of the digestive tract. + + 2021-02-05T11:19:31Z uberon - anatomical cluster - UBERON:0034921 - multi organ part structure + UBERON:1100000 + digestive tract junction - - - - CARO - - - + - An multicellular anatomical structure that has subparts of multiple organs as a part. - CARO:0020001 - - - - - anatomical cluster - CARO:0020001 + An anatomical junction between two parts of the digestive tract. + - + - - + + + - - + + - A cluster of cells, largely surrounded by a morphological boundary. - CARO:0020002 - FMA:62807 + + + + + + + EFO:0003612 + TAO:0001053 + ZFA:0001053 + PICA + primitive internal carotid artery uberon - UBERON:0034922 - cell cluster + UBERON:2001053 + future internal carotid artery - + - - CARO + + + + + + + EHDAA2 - - - A cluster of cells, largely surrounded by a morphological boundary. - CARO:0020002 + + + PICA + TAO:0001053 + + + + + primitive internal carotid artery + ZFA:0001053 - + - - - - - - - - - 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 + + + 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 - UBERON:0034925 - anatomical collection + UBERON:2001073 + axial vasculature - - - - A collection of anatomical structures that are alike in terms of their morphology or developmental origin. - - - + - + - + - - + + - + - - + + - Any organ component layer that consists of smooth muscle tissue. + 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 - UBERON:0034933 - layer of smooth muscle tissue + UBERON:2001457 + postcranial axial cartilage - + - Any organ component layer that consists of smooth muscle tissue. - + Cartilage which is part of the axial skeleton. + ZFIN:curator - + - - - FMA:55268 - organ sector - organ zonal region - organ zone - uberon - organ region with floating fiat boundary - UBERON:0034944 - zone of organ - + + + + 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 + - - - organ sector - FMA:55268 + + + + ZFA - - - organ zone - FMA:55268 + + + 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. + + - - - organ region with floating fiat boundary - FMA:55268 + + + fenestrated blood vessel endothelium + ZFA:0005260 + + + + + UMLS:C1179615 + ncithesaurus:Fenestrated_Capillary + + + + + fenestrated capillary vessel + FMA:63196 - + - - - - - - - - - - - - - - - - - - - - - NCIT:C25787 + + + 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 - duct epithelium - ductal epithelium - UBERON:0034969 - epithelial layer of duct + UBERON:2007013 + preplacodal ectoderm + + + + Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes. + ZFIN:curator + - + - + - + - + - + - + - Mesenchyme that is part of a developing jaw [Automatically generated definition]. - EMAPA:32907 - EMAPA:35454 + 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 - UBERON:0034995 - jaw mesenchyme + UBERON:3000961 + Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305 + external integument structure - + - Mesenchyme that is part of a developing jaw [Automatically generated definition]. - OBOL:automatic + Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument. + AAO:EJS - + - + - + - + - + - - - - EMAPA:32904 - MA:0003220 - uberon - UBERON:0035037 - jaw epithelium - - - - - - - - - - - - - - - - - - - - - - - + - 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 + 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 - ingested material entity - UBERON:0035118 - material entity in digestive tract + UBERON:3000972 + head external integument structure - + - 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 - + Dermal, epidermal, glandular and pigment structures of the external head integument. + AAO:EJS - + - + - + - - + + - + - - + + - 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 + 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 - UBERON:0035159 - entire surface of organism + UBERON:3000977 + body external integument structure - + - 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 + Dermal, epidermal, glandular and pigment structures of the body integument. + AAO:EJS - + - + - - - - - + - - + + - + - - - - - - - - - - - - - + - - - FMA:15590 - NCIT:C32895 - facies posterior (Ren) - facies posterior renis + 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 - UBERON:0035471 - posterior surface of kidney + UBERON:3000981 + limb external integument structure - - - facies posterior (Ren) - FMA:15590 - - - - - facies posterior renis - FMA:15590 - FMA:TA - + + + Dermal, epidermal, glandular and pigment structures of the limb integument. + AAO:EJS - + - + - + - - + + - + - - + + - - FMA:51797 - ciliary vein + 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 - UBERON:0035546 - uveal vein - - - - - ciliary vein - FMA:51797 + UBERON:3000982 + tail external integument structure + + + + + Dermal, epidermal, glandular and pigment structures of the tail integument. + AAO:EJS - + - + - + - + + + + + - + - + + + + + + + - 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 + Blood vessels in respiratory skin. + Modified from the original AAO source + amphibian_anatomy_curators uberon - skin vasculature - subcutaneous vasculature - vasculature of skin - UBERON:0035549 - vasculature of integument + UBERON:3010200 + vasculature of respiratory 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 + Blood vessels in respiratory skin. + AAO:EJS - + - + - + - + - + - + - Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers. - - - - FMA:76719 - NCIT:C33666 + An anatomical surface that is part of a bone. + bone surface uberon - superfical vein - superficial veins - superficial vessels - UBERON:0035550 - superficial vein + UBERON:4200230 + surface of bone + surface of bone - + - Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers. - ncithesaurus:Superficial_Vein - - - - - superfical vein - - - - - - superficial veins - - - - - - superficial vessels - + An anatomical surface that is part of a bone. + PHENOSCAPE - + - + - + - - + + - + + - - + + - 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 + Mesenchyme that is part of a forelimb bud. + WD uberon - UBERON:0035551 - deep vasculature + UBERON:4300226 + forelimb bud mesenchyme - + - The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin. - + Mesenchyme that is part of a forelimb bud. + PHENOSCAPE - + - + - + - + - + + - + - A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery. - - - - FMA:76718 - NCIT:C32444 + Mesenchyme that is part of a hindlimb bud. + WD uberon - deep veins - deep vessels - UBERON:0035552 - deep vein + UBERON:4300227 + hindlimb bud mesenchyme - + - A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery. - ncithesaurus:Deep_Vein - - - - - deep veins - - - - - - deep vessels - + Mesenchyme that is part of a hindlimb bud. + PHENOSCAPE - + - - + + + + + + + + + + + + + + - - + + - 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 + 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 - 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 + UBERON:8000006 + left side of back - + - 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 - - + Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. + - + - + - + - - + + - - - - - - - - - - - - - + + - - + + - EHDAA2:0004181 - FMA:9464 - cardiac chamber cavity - heart cavity - heart lumen + 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:0035763 - cavity of cardiac chamber + UBERON:8000007 + right side of back - - - - - - - - - FMA - - - - - cardiac chamber cavity - FMA:9464 - - - - - heart cavity - FMA:9464 - - - - - heart lumen - EHDAA2:0004181 + + + Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. + - + - - - - - - - - - - - - - - + + + + + + + + + + + + + + - - + + - The primordial mouth region of the developing head. - FMA:293105 - primitive mouth - primordial mouth + 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:0035804 - future mouth + UBERON:8300001 + right forelimb - + - The primordial mouth region of the developing head. - MP:0003119 - - - - - primitive mouth - FMA:293105 + A forelimb that is on the right side of a pectoral complex. + UBERONREF:0000003 - + - + - + - - + + - + + - - + + - 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 + 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 - sigmoideum muscularis - tunica muscularis colon sigmoideum - UBERON:0035805 - muscle layer of sigmoid colon + UBERON:8300002 + left forelimb - + - A muscle layer that is part of the sigmoid colon - - - - - - muscularis externa of sigmoid colon - FMA:15028 + A forelimb that is on the left side of a pectoral complex. + UBERONREF:0000003 - + - + - + - - + + - - - - - - - + + - - + + - - FMA:12241 + 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:0035809 - serous cavity + UBERON:8300003 + right hindlimb + + + + A hindlimb that is on the right side of a pelvic complex. + UBERONREF:0000003 + - + - + - + - - + + - + + - - + + - The sum of epicardial and paracardial fat deposits. - - ZFA:0005765 + 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:0035814 - pericardial fat + UBERON:8300004 + left hindlimb - + - The sum of epicardial and paracardial fat deposits. - + A hindlimb that is on the left side of a pelvic complex. + UBERONREF:0000003 - + - + - - - - - + - - + + - + - - + + - Fat deposits in the mediastinum outside the parietal pericardium . - intrathoracic fat + A venule that is located in the anorectum. + http://orcid.org/0000-0002-2825-0621 + anorectum venule uberon - UBERON:0035815 - paracardial fat + UBERON:8410008 + venule of anorectum - + - Fat deposits in the mediastinum outside the parietal pericardium . - - - - - - intrathoracic fat - + A venule that is located in the anorectum. + - + - + - + - - + + - + - - + + - Any fat deposit surrounding a visceral organ. + An arteriole that is located in the anorectum. + http://orcid.org/0000-0002-2825-0621 + anorectum arteriole uberon - UBERON:0035818 - visceral fat + UBERON:8410009 + arteriole of anorectum - + - Any fat deposit surrounding a visceral organ. - UBERON:cjm + An arteriole that is located in the anorectum. + - + - + - + - - - - - + - - - - - - - + - - - - - - - + - 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 + An arteriole located in the colon. + http://orcid.org/0000-0002-2825-0621 uberon - UBERON:0035819 - abdominopelvic cavity + UBERON:8410015 + arteriole of colon - + - 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 - + An arteriole located in the colon. + + - + - + - + - + + + + + - - + + - + - - + + - BTO:0004378 - EMAPA:37987 - FMA:67473 - blood vessel wall + An anatomical junction between two parts of the intestine. + http://orcid.org/0000-0002-2825-0621 + junction of intestine uberon - vascular wall - UBERON:0035965 - wall of blood vessel + UBERON:8410024 + intestinal junction - - - EMAPA:37987 - MA:th - - - - - blood vessel wall - FMA:67473 - - - - - vascular wall - BTO:0004378 + + + An anatomical junction between two parts of the intestine. + - + - - - - - - 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. + + + + + + + + + + + + + + + + + + + + A venule located in the colon. + http://orcid.org/0000-0002-2825-0621 uberon - UBERON:0036146 - cardiopharyngeal field + UBERON:8410048 + venule of colon - + - 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 + A venule located in the colon. + + - + - + - + - + + + + + - - + + - + - + + + + + + + + + + + + + - - + + - An anatomical junction that is between the sigmoid colon and rectum. - - NCIT:C54188 + A subdivision of the digestive tract in humans that includes the rectum, the anal canal and the anus. + The anatomy, pathology and medical community considers the anus to be part of the large intestine, and supports the use of 'anorectum' to include rectum, anal canal and anus. Although a few resources seem to only include the distal part of the rectum in 'anorectum', this UBERON grouping term is meant to refer more broadly to the whole of rectum. + Homo sapiens + anorectal + http://orcid.org/0000-0002-2825-0621 + anorectal canal uberon - rectosigmoid region - UBERON:0036214 - rectosigmoid junction + UBERON:8410050 + anorectum - + - An anatomical junction that is between the sigmoid colon and rectum. - - - NCIT:C54188 - - - - - rectosigmoid region - NCIT:C54188 + A subdivision of the digestive tract in humans that includes the rectum, the anal canal and the anus. + + + + + - + - - + + + + + + + + + + + + + - + + A capillary that is part of the anorectum. + http://orcid.org/0000-0002-2825-0621 + blood vessel capillary of anorectum + uberon + UBERON:8410056 + capillary of anorectum + + + + + A capillary that is part of the anorectum. + + + + + + + + + + + + + + + + + + + + - - + + - Material anatomical entity that forms the outermost boundary of an anatomical structure. - AAO:0010270 - AEO:0000154 - ZFA:0005594 + A capillary that is part of the colon. + http://orcid.org/0000-0002-2825-0621 + blood vessel capillary of colon uberon - UBERON:0036215 - anatomical surface region + UBERON:8410057 + capillary of colon - + - Material anatomical entity that forms the outermost boundary of an anatomical structure. - + A capillary that is part of the colon. + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - + + + + + + - - - - - - - - A bodily fluid that is located in the coelom. - he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste [Wikipedia:Coelom#Coelomic_fluid] - BTO:0001708 - uberon - UBERON:0036217 - coelomic fluid - - - - - A bodily fluid that is located in the coelom. - - - - - - - - - - - + + + + + - - - - - - - - Any gland that is part os the respiratory system. - uberon - UBERON:0036225 - respiratory system gland - - - - - Any gland that is part os the respiratory system. - UBERON:cjm - - - - - - - - - + + + + + - - - - - - - - A notochord that has persisted beyond the embryonic stage. - - - - - - uberon - UBERON:0036242 - post-embryonic notochord - - - - - A notochord that has persisted beyond the embryonic stage. - UBERON:cjm - - - - - - - - - - + + + + + + - - - - - - - - - - - - - - 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 - - - - - - - - - + + + + + - - - - - - - - FMA:53133 - cranial orifice - skull orifice - uberon - UBERON:0036253 - orifice of skull - - - - - cranial orifice - FMA:53133 - - - - - skull orifice - FMA:53133 - - - - - - - - - - + + + + + + + + + + + - - - - - - - - - uberon - UBERON:0036268 - pelvic vein - - - - - - - - - + + + + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + - 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 - - - - - - - - - - - - - - - - - uberon - UBERON:0036302 - vasculature of central nervous system plus retina + + + + + + + - - - - - - - + + - + - + + + + + + + - - - + + + - - + + - - FMA:259905 - uberon - UBERON:0036303 - vasculature of central nervous system - - - - - - - - + + FMA-abduced-lr + + + - + - + + + - - + + - + - - - - - - - - - - FMA:15704 - anal canal wall - uberon - UBERON:0036362 - wall of anal canal - - - + - - + + - FMA + definitional - - - anal canal wall - FMA:15704 - - - - - - - - + - + - + + + + + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + - FMA:19779 - urethral wall - uberon - UBERON:0036521 - wall of urethra - - - - - FMA - - - - - + + + - + - - FMA - + + + + + + + + - - - urethral wall - FMA:19779 - - - - - - - - + - + - + + + + + + + - - - - - - - - - - FMA:58098 - eyeball wall - uberon - UBERON:0036925 - wall of eyeball - - - - - - FMA - - - + - - + + - FMA + only in species that have a stomach - - - eyeball wall - FMA:58098 - - - - - - - - + - + - + + + + + + + - - - - + + + + + + + + + + + + + - + + + + + + + + + + + + + + + + - - + + + + + + + + + + + - - + + - 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 - - - - - - - - - - - - - - - - - - - + + + + + + + + + + - + + + + + + + - 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 - - - - - - - - - - - - - - - - - - - + + + + + + + + - + - 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 - - - - - - - - - - - - - - - - - - - - + + + - + + + + + + + - 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 + + FMA - - - - - - - + + - + - + + + + + + + - - - + + + + + + + + + cjm + + + + - + + + + + + + - 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 - - - - - - - - + - + - + + + - - + + - + - - - + + + - - + + - - 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 + + + AAO - - - - - - - + + - + - + + + + + + + - - - + + + - - + + - - An anatomical surface that is part of a bone - bone surface - surface of bone - - - - - - - - + + ISBN:9780878932504 + + + - + - + + + + + + + - - - - + + + - - + + - - Mesenchyme that is part of a forelimb bud. - WD - forelimb bud mesenchyme - - - - - - - - + + Mammals + + + - + - + + + + + + + - - - - + + + - - + + - - Mesenchyme that is part of a hindlimb bud. - WD - hindlimb bud mesenchyme - - - - - - + + conservatively place at deuterostome, excluding acoelomates + - - - - - - - - - - - - - + + - + - - + + - - + + - + - - - - - + + - + - - + + - - + + - + - + + - - - - - + - - + + - - + + + + + + + - + - - - - - + + - + - - + + - + - + - - - - - + + - + - - + + - + - + - - - - - + + - + - - + + - - + + - + - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + - - + + - - + + EHDAA2 + @@ -90177,6 +166649,26 @@ + + + + + + + + + + + + + + + + + + + + @@ -90187,6 +166679,26 @@ + + + + + + + + + + + + + + + + + + + + @@ -90207,6 +166719,33 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -90217,6 +166756,1366 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 can't be added as a property chain because it causes a circularity violation for 'part of'. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This can't be added as a property chain because it causes a circularity violation for 'part of'. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This can't be added as a property chain because it causes a circularity violation for 'part of'. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +