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[Obo-svn-commit] SF.net SVN: obo:[4020] ontologies/trunk/UBERON
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From: <cmu...@us...> - 2011-09-03 18:52:41
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Revision: 4020
http://obo.svn.sourceforge.net/obo/?rev=4020&view=rev
Author: cmungall
Date: 2011-09-03 18:52:30 +0000 (Sat, 03 Sep 2011)
Log Message:
-----------
Modified Paths:
--------------
ontologies/trunk/UBERON/basic.obo
ontologies/trunk/UBERON/core.obo
ontologies/trunk/UBERON/merged.obo
Modified: ontologies/trunk/UBERON/basic.obo
===================================================================
--- ontologies/trunk/UBERON/basic.obo 2011-09-03 18:50:18 UTC (rev 4019)
+++ ontologies/trunk/UBERON/basic.obo 2011-09-03 18:52:30 UTC (rev 4020)
@@ -1,6 +1,6 @@
format-version: 1.2
-data-version: 2011-08-31
-date: 30:08:2011 16:10
+data-version: 2011-09-04
+date: 03:09:2011 16:43
saved-by: cjm
subsetdef: defined_by_ordinal_series "classes that are defined by relative position counting from first in a series in an individual organism rather than by homology"
subsetdef: developmental_classification "developmental_classification"
@@ -143,7 +143,6 @@
xref: OpenCyc:Mx4rvViCbJwpEbGdrcN5Y29ycA
xref: SCTID:181195007
xref: TAO:0000047
-xref: XAO:0003172
xref: ZFA:0000047
is_a: UBERON:0002268 ! olfactory organ
relationship: develops_from UBERON:0003050 ! olfactory placode
@@ -166,7 +165,7 @@
id: UBERON:0000006
name: islet of Langerhans
def: "Regions of the pancreas that contain its endocrine (i.e., hormone-producing) cells." [Wikipedia:Islet_of_Langerhans]
-comment: TODO - is plural equivalent to endocrine pancreas? It has been recognized that the cytoarchitecture of pancreatic islets differs between species[WP].
+comment: A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986)[PMID:16417468]
subset: uberon_slim
synonym: "island of Langerhans" RELATED [BTO:0000991]
synonym: "island of pancreas" RELATED [BTO:0000991]
@@ -481,7 +480,7 @@
id: UBERON:0000019
name: camera-type eye
alt_id: UBERON:FMA_12513-MIAA_0000283-XAO_0000181
-def: "GO: The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field. Organ with organ cavity which is connected to the optic nerve, allowing light to enter it and project onto a light-sensitive panel of cells, known as the retina, at the rear of the eye [FMA]." [FMA:12513, GO:0043010, Image:http\://genome.cshlp.org/content/14/8/1555/F1.large.jpg, Image:http\://www.pnas.org/content/94/6/2098/F1.large.jpg]
+def: "GO: The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field[FMA]." [GO:0043010, Image:http\://genome.cshlp.org/content/14/8/1555/F1.large.jpg, Image:http\://www.pnas.org/content/94/6/2098/F1.large.jpg]
comment: FMA distinguishes Eye (subdivision of face) from Eyeball (organ). Here we are referring to the organ but we also include Eye as being subsumed
subset: uberon_slim
subset: vertebrate_core
@@ -3154,7 +3153,6 @@
xref: BTO:0000213
xref: FMA:14998
is_a: UBERON:0000064 ! organ part
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0000317 ! implied link automatically realized ! colonic mucosa
relationship: part_of UBERON:0001153
@@ -4270,7 +4268,6 @@
xref: FMA:14949
xref: SCTID:362151009
is_a: UBERON:0000064 ! organ part
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0001204 ! implied link automatically realized ! mucosa of small intestine
relationship: part_of UBERON:0002115
@@ -4281,7 +4278,6 @@
xref: BTO:0001743
xref: FMA:17232
xref: SCTID:57300004
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0001902 {source="BTO"} ! epithelium of small intestine
relationship: part_of UBERON:0002115
relationship: part_of UBERON:0008343 {source="FMA"} ! intestinal villus of jejunum
@@ -8916,9 +8912,7 @@
xref: SCTID:361410004
xref: TGMA:0001036
xref: XAO:0000103
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0004921 ! subdivision of digestive tract
-relationship: develops_from UBERON:0003104 {source="Wikipedia"} ! mesenchyme
[Term]
id: UBERON:0001046
@@ -11291,7 +11285,6 @@
xref: OG:0001559
xref: OpenCyc:Mx4rve6u4JwpEbGdrcN5Y29ycA
xref: SCTID:181256004
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0004921 ! subdivision of digestive tract
relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut
relationship: part_of UBERON:0000059 {source="MA"} ! large intestine
@@ -11325,7 +11318,7 @@
xref: OpenCyc:Mx4rvVjGgJwpEbGdrcN5Y29ycA
xref: SCTID:181255000
is_a: UBERON:0000062 ! organ
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
+is_a: UBERON:0004119 ! implied link automatically realized ! endoderm-derived structure
relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut
relationship: part_of UBERON:0001153 ! caecum
@@ -11383,7 +11376,6 @@
xref: ncithesaurus:Ascending_Colon
xref: OpenCyc:Mx4rv3H0FZwpEbGdrcN5Y29ycA
xref: SCTID:362162009
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0000168 {source="FMA"} ! segment of colon
relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut
@@ -11405,7 +11397,6 @@
xref: ncithesaurus:Transverse_Colon
xref: OpenCyc:Mx4rvg7qyJwpEbGdrcN5Y29ycA
xref: SCTID:362163004
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0000168 {source="FMA"} ! segment of colon
relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut
@@ -12457,7 +12448,7 @@
xref: ncithesaurus:Small_Intestinal_Submucosa
xref: SCTID:691000
is_a: UBERON:0000009 ! submucosa
-is_a: UBERON:0004119 ! implied link automatically realized ! endoderm-derived structure
+is_a: UBERON:0009566 ! implied link automatically realized ! intestinal submucosa
relationship: part_of UBERON:0002108
relationship: part_of UBERON:0001168 ! wall of small intestine
@@ -12523,7 +12514,7 @@
xref: MA:0002690
xref: ncithesaurus:Large_Intestinal_Submucosa
is_a: UBERON:0000009 ! submucosa
-is_a: UBERON:0004119 ! implied link automatically realized ! endoderm-derived structure
+is_a: UBERON:0009566 ! implied link automatically realized ! intestinal submucosa
relationship: part_of UBERON:0000059
relationship: part_of UBERON:0001169 ! wall of large intestine
@@ -13198,8 +13189,7 @@
id: UBERON:0001242
name: intestinal mucosa
alt_id: UBERON:FMA_15695-MA_0001537
-def: "." [Wikipedia:Intestinal_mucosa]
-comment: This class was created automatically from a combination of ontologies
+def: "The innermost membrane of the four coats of the intestinal wall, the other three being the submucosa, muscular layers, and serosa. (Berk et al., Gastroenterology, 4th ed, v.3, p1479)" [MESH:A.03.492.411.369]
subset: uberon_slim
synonym: "bowel mucosa" EXACT [OBOL:automatic]
synonym: "bowel mucosa of organ" EXACT [OBOL:automatic]
@@ -13224,7 +13214,6 @@
xref: MESH:A.03.492.411.369
xref: ncithesaurus:Intestinal_Mucosa
xref: SCTID:362080002
-is_a: UBERON:0004119 ! implied link automatically realized ! endoderm-derived structure
is_a: UBERON:0004786 ! implied link automatically realized ! gastrointestinal system mucosa
relationship: part_of UBERON:0000160
relationship: part_of UBERON:0001262 ! wall of intestine
@@ -13746,7 +13735,8 @@
id: UBERON:0001264
name: pancreas
alt_id: UBERON:FMA_16017-FMA_16018-FMA_7198-MA_0000120-MA_0001582-MA_0002415-MIAA_0000075-XAO_0000136-XAO_0000137-ZFA_0000140-ZFA_0001249-ZFA_0001260
-def: "An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. The mature pancreas of higher vertebrates and mam- mals comprises two major functional units: the exo- crine pancreas, which is responsible for the pro- duction of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductu- lar cells. The endocrine portion, which comprises only 1–2% of the total mass, contains five different cell types, which are organized into mixed functional as- semblies referred to as the islets of Langerhans[PMID]." [GO:0031016, PMID:16417468, Wikipedia:Pancreas]
+def: "An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1–2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans[PMID]." [GO:0031016, PMID:16417468, Wikipedia:Pancreas]
+comment: taxon notes: As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468]
subset: major_organ
subset: uberon_slim
subset: vertebrate_core
@@ -22809,12 +22799,9 @@
xref: OpenCyc:Mx4rvVjJv5wpEbGdrcN5Y29ycA
xref: SCTID:72651009
xref: XAO:0003103
-is_a: UBERON:0000026 ! appendage
-is_a: UBERON:0004120 ! implied link automatically realized ! mesoderm-derived structure
-is_a: UBERON:0004121 ! implied link automatically realized ! ectoderm-derived structure
+is_a: UBERON:0009564 ! distal limb integumentary appendage
relationship: part_of UBERON:0001003 {source="FMA"} ! epidermis
relationship: part_of UBERON:0002097 {source="FMA"} ! skin of body
-relationship: part_of UBERON:0002544 ! digit
[Term]
id: UBERON:0001706
@@ -31431,8 +31418,7 @@
id: UBERON:0002082
name: cardiac ventricle
alt_id: UBERON:FMA_7100-MA_0000091-ZFA_0000009
-def: "Cardiac chamber which consists of a wall that surrounds the cavity of a ventricle. // One of four heart chambers." [Wikipedia:Cardiac_ventricle, ZFIN:curator]
-comment: This class was created automatically from a combination of ontologies
+def: "Cardiac chamber which consists of a wall that surrounds the cavity of a ventricle." [FMA:7100]
subset: uberon_slim
subset: vertebrate_core
synonym: "heart ventricle" EXACT []
@@ -32295,7 +32281,6 @@
xref: OG:0000053
xref: OpenCyc:Mx4rwATkPJwpEbGdrcN5Y29ycA
xref: SCTID:181248002
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0004921 ! subdivision of digestive tract
relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut
relationship: part_of UBERON:0002108 ! small intestine
@@ -51351,9 +51336,11 @@
id: UBERON:0003112
name: olfactory region
alt_id: UBERON:ZFA_0000351-XAO_0003172
+def: "Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the olfactory organ." [TAO:0000351]
synonym: "ethmoid region" EXACT [ZFA:0000351]
xref: AAO:0010206
xref: EFO:0003525
+xref: TAO:0000351
xref: XAO:0003172
xref: ZFA:0000351
is_a: UBERON:0000477 ! anatomical cluster
@@ -53301,8 +53288,8 @@
xref: EHDAA2:0001194
xref: EMAPA:16257
xref: OG:0001080
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0000925 ! implied link automatically realized ! endoderm
+is_a: UBERON:0004119 ! implied link automatically realized ! endoderm-derived structure
relationship: part_of UBERON:0001045
[Term]
@@ -53740,7 +53727,6 @@
xref: EHDAA:3937
xref: EHDAA2:0001189
xref: EMAPA:17193
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0002114 ! implied link automatically realized ! duodenum
relationship: part_of UBERON:0001045
@@ -54600,7 +54586,6 @@
xref: EMAPA:27351
xref: FMA:14950
xref: SCTID:70192009
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0001205 ! implied link automatically realized ! submucosa of small intestine
relationship: part_of UBERON:0002115
@@ -54902,7 +54887,6 @@
xref: BTO:0005053
xref: EHDAA2:0001195
xref: EMAPA:16569
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0003929 ! implied link automatically realized ! gut epithelium
relationship: part_of UBERON:0001045
relationship: part_of UBERON:0001045 {source="BTO"} ! midgut
@@ -55153,8 +55137,13 @@
[Term]
id: UBERON:0003371
name: hindlimb bud ectoderm
+alt_id: UBERON:0005232
+synonym: "hindlimb ectoderm" EXACT [OG:0001048]
synonym: "leg ectoderm" RELATED [OBOL:automatic]
+synonym: "lower limb bud ectoderm" EXACT [EHDAA2:0001034]
+xref: EHDAA2:0001034
xref: EMAPA:17254
+xref: OG:0001048
is_a: UBERON:0000924 ! implied link automatically realized ! ectoderm
is_a: UBERON:0004120 ! implied link automatically realized ! mesoderm-derived structure
relationship: part_of UBERON:0005418
@@ -55162,10 +55151,14 @@
[Term]
id: UBERON:0003372
name: forelimb bud ectoderm
+alt_id: UBERON:0005231
alt_id: UBERON:0005663
synonym: "arm ectoderm" RELATED [OBOL:automatic]
+synonym: "forelimb ectoderm" EXACT [OG:0001047]
+synonym: "upper limb bud ectoderm" EXACT [EHDAA2:0002134]
xref: EHDAA2:0002134
xref: EMAPA:17243
+xref: OG:0001047
is_a: UBERON:0000924 ! implied link automatically realized ! ectoderm
is_a: UBERON:0004120 ! implied link automatically realized ! mesoderm-derived structure
relationship: part_of UBERON:0005417
@@ -61316,6 +61309,7 @@
id: UBERON:0003695
name: metacarpophalangeal joint
def: "The metacarpophalangeal joints (MCP) are of the condyloid kind, formed by the reception of the rounded heads of the metacarpal bones into shallow cavities on the proximal ends of the first phalanges, with the exception of that of the thumb, which presents more of the characters of a ginglymoid joint. Arthritis of the MCP is a distinguishing feature of Rheumatoid Arthritis, as opposed to the distal interphalangeal joint in osteoarthritis. [WP,unvetted]." [Wikipedia:Metacarpophalangeal_joint]
+comment: we follow FMA in making these joints part of digits
synonym: "metacarpal joint" EXACT [FMA:35246]
synonym: "metacarpo-phalangeal joint" EXACT [MA:0000453]
synonym: "mp joint" EXACT [FMA:35246]
@@ -61329,15 +61323,18 @@
xref: ncithesaurus:Metacarpophalangeal_Joint
xref: OpenCyc:Mx4rwNt8wJwpEbGdrcN5Y29ycA
xref: SCTID:280995004
-is_a: UBERON:0002217 ! synovial joint
+is_a: UBERON:0001489 ! implied link automatically realized ! joint of hand
+relationship: part_of UBERON:0002389
[Term]
id: UBERON:0003696
name: metatarsophalangeal joint
def: "The metatarsophalangeal articulations are the joints between the metatarsal bones of the foot and the proximal bones of the toes . They are condyloid joints meaning an elliptical or rounded surface (of the metatarsal bones) come close to the shallow cavities (of the proximal phalanges). The ligaments are the plantar and two collateral." [Wikipedia:Metatarsophalangeal_articulations]
+comment: we follow FMA in making these joints part of digits
synonym: "metatarsal joint" EXACT [FMA:35222]
synonym: "metatarsalphalangeal joint" RELATED [Wikipedia:Metatarsophalangeal_articulations]
synonym: "metatarsophalangeal" RELATED [Wikipedia:Metatarsophalangeal_articulations]
+synonym: "metatarsophalangeal articulation" RELATED [Wikipedia:Metatarsophalangeal_articulations]
xref: FMA:35222
xref: GAID:258
xref: galen:MetatarsoPhalangealJoint
@@ -61345,7 +61342,8 @@
xref: ncithesaurus:Metatarsophalangeal_Joint
xref: OpenCyc:Mx4rwCtS0pwpEbGdrcN5Y29ycA
xref: SCTID:239747005
-is_a: UBERON:0001487 ! joint of foot
+is_a: UBERON:0001487 ! implied link automatically realized ! joint of foot
+relationship: part_of UBERON:0001466
[Term]
id: UBERON:0003697
@@ -61890,6 +61888,7 @@
[Term]
id: UBERON:0003821
name: metacarpal/metatarsal bone
+synonym: "cannon bone" NARROW SENSU [UBERON:cjm]
synonym: "metacarpal or metatarsal bone" EXACT []
synonym: "metacarpal/metatarsal" EXACT []
synonym: "metapodium bone" EXACT [http://en.wiktionary.org/wiki/metapodial, UBERON:cjm]
@@ -63256,11 +63255,12 @@
is_a: UBERON:0001048 {source="Obol"} ! primordium
relationship: develops_from UBERON:0000925 ! endoderm
relationship: part_of UBERON:0000922 ! embryo
+relationship: part_of UBERON:0007026 ! primitive gut
[Term]
id: UBERON:0003922
name: pancreatic bud
-def: "embryonic structure that gives rise to the adult pancreas[CJM]. In humans, an embryonic structure that is an outgrowth of the duodenum during embryogenesis - joins together to form the adult pancreas[WP]." [Wikipedia:Pancreatic_bud]
+def: "The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]. In humans, an embryonic structure that is an outgrowth of the duodenum during embryogenesis - joins together to form the adult pancreas[WP]." [PMID:16417468, Wikipedia:Pancreatic_bud]
xref: EFO:0003470
xref: http://upload.wikimedia.org/wikipedia/commons/thumb/d/db/Gray982.png/200px-Gray982.png
xref: ncithesaurus:Pancreatic_Bud
@@ -63268,6 +63268,7 @@
xref: ZFA:0001390
is_a: UBERON:0005423 ! developing anatomical structure
relationship: develops_from UBERON:0001041 {source="Wikipedia:Pancreas#Embryological_development"} ! foregut
+relationship: develops_from UBERON:0001555 ! digestive tract
relationship: develops_from UBERON:0002114 {exception="zebrafish", source="Wikipedia:Pancreatic_bud"} ! duodenum
relationship: develops_from UBERON:0003921 ! pancreas primordium
relationship: part_of UBERON:0000922 ! embryo
@@ -63296,6 +63297,7 @@
id: UBERON:0003924
name: ventral pancreatic bud
def: "pancreatic bud that gives rise to the major pancreatic duct." [Wikipedia:Pancreatic_bud]
+comment: the ventral pancreas and liver are derived from a common precursor cell population[PMID:16417468]. TODO - add this relationship
subset: vertebrate_core
synonym: "anterior pancreatic anlage" RELATED []
synonym: "anterior pancreatic bud" RELATED []
@@ -65180,16 +65182,6 @@
relationship: part_of UBERON:0000949 ! endocrine system
[Term]
-id: UBERON:0004093
-name: fingertip
-def: "." [HP:0001211]
-xref: OpenCyc:Mx4rvVjpf5wpEbGdrcN5Y29ycA
-xref: SCTID:312543003
-is_a: UBERON:0000061 ! anatomical structure
-is_a: UBERON:0004120 ! implied link automatically realized ! mesoderm-derived structure
-relationship: part_of UBERON:0002389 ! hand digit
-
-[Term]
id: UBERON:0004095
name: corticospinal tract
def: "The corticospinal or pyramidal tract is a collection of axons that travel between the cerebral cortex of the brain and the spinal cord. The corticospinal tract mostly contains motor axons. It actually consists of two separate tracts in the spinal cord: the lateral corticospinal tract and the medial corticospinal tract. An understanding of these tracts leads to an understanding of why for the most part, one side of the body is controlled by the opposite side of the brain. Also the corticobulbar tract is considered to be a pyramidal tract. The corticobulbar tract carries signals that control motor neurons located in cranial nerve brain nuclei rather than motor neurons located in the spinal cord. The neurons of the pyramidal tracts are pyramidal neurons, but that is not how the pyramidal tract got its name, as most of the pyramidal neurons send their axons elsewhere. Instead, it got its name from the shape of the corticospinal axon tracts: when the pyramidal tract passes the medulla, it forms a dense bundle of nerve fibres that is shaped somewhat like a pyramid. [WP,unvetted]." [HP:0002492, Wikipedia:Corticospinal_tract]
@@ -74153,22 +74145,18 @@
[Term]
id: UBERON:0004786
name: gastrointestinal system mucosa
-def: "A mucosa that is part of a digestive system [Obol]." [OBOL:automatic]
-synonym: "digestive system mucosa" EXACT [OBOL:automatic]
-synonym: "digestive system mucosa of organ" EXACT [OBOL:automatic]
-synonym: "digestive system mucous membrane" EXACT [OBOL:automatic]
-synonym: "gastrointestinal system mucosa of organ" EXACT [OBOL:automatic]
-synonym: "gastrointestinal system mucous membrane" EXACT [OBOL:automatic]
-synonym: "mucosa of digestive system" EXACT [OBOL:automatic]
-synonym: "mucosa of gastrointestinal system" EXACT [OBOL:automatic]
-synonym: "mucosa of organ of digestive system" EXACT [OBOL:automatic]
-synonym: "mucosa of organ of gastrointestinal system" EXACT [OBOL:automatic]
-synonym: "mucous membrane of digestive system" EXACT [OBOL:automatic]
-synonym: "mucous membrane of gastrointestinal system" EXACT [OBOL:automatic]
+comment: The gut mucosa of amphioxus has insulin-secreting cells. PMID:16417468
+synonym: "digestive tract mucosa" EXACT [UBERON:cjm]
+synonym: "gut mucosa" EXACT [BTO:0000546]
+synonym: "gut mucuous membrane" EXACT [UBERON:cjm]
+synonym: "mucosa of gut" EXACT [UBERON:cjm]
+xref: BTO:0000546
xref: MA:0001521
xref: SCTID:410433007
is_a: UBERON:0000344 ! implied link automatically realized ! mucosa
+is_a: UBERON:0004119 ! implied link automatically realized ! endoderm-derived structure
relationship: part_of UBERON:0005409
+relationship: part_of UBERON:0001555 ! digestive tract
[Term]
id: UBERON:0004787
@@ -75713,9 +75701,9 @@
xref: OG:0001351
is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0003914 ! epithelial tube
-is_a: UBERON:0005911 ! implied link automatically realized ! endo-epithelium
-relationship: develops_from UBERON:0001041 ! foregut
-relationship: develops_from UBERON:0004161 {source="EHDAA2"} ! septum transversum
+is_a: UBERON:0009497 ! implied link automatically realized ! epithelium of foregut-midgut junction
+relationship: develops_from UBERON:0004161 {source="EHDAA2-modified"} ! septum transversum
+relationship: part_of UBERON:0006235 {source="EMAPA"} ! foregut-midgut junction
[Term]
id: UBERON:0004913
@@ -75917,7 +75905,6 @@
synonym: "submucosa of caecum" EXACT [OBOL:automatic]
synonym: "submucosa of intestinum crassum caecum" EXACT [OBOL:automatic]
xref: FMA:14999
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0003331 ! implied link automatically realized ! submucosa of colon
relationship: part_of UBERON:0001153
@@ -75944,7 +75931,6 @@
def: "A submucosa that is part of an ascending colon [Obol]." [OBOL:automatic]
synonym: "ascending colon submucosa" EXACT [OBOL:automatic]
xref: FMA:15006
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0003331 ! implied link automatically realized ! submucosa of colon
relationship: part_of UBERON:0001156
@@ -75954,7 +75940,6 @@
def: "A submucosa that is part of a transverse colon [Obol]." [OBOL:automatic]
synonym: "transverse colon submucosa" EXACT [OBOL:automatic]
xref: FMA:15013
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0003331 ! implied link automatically realized ! submucosa of colon
relationship: part_of UBERON:0001157
@@ -76506,7 +76491,6 @@
synonym: "mucous membrane of ascending colon" EXACT [OBOL:automatic]
synonym: "organ mucosa of ascending colon" EXACT [OBOL:automatic]
xref: FMA:15005
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0000317 ! implied link automatically realized ! colonic mucosa
relationship: part_of UBERON:0001156
@@ -76522,7 +76506,6 @@
synonym: "transverse colon mucous membrane" EXACT [OBOL:automatic]
synonym: "transverse colon organ mucosa" EXACT [OBOL:automatic]
xref: FMA:15012
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0000317 ! implied link automatically realized ! colonic mucosa
relationship: part_of UBERON:0001157
@@ -79576,24 +79559,6 @@
is_obsolete: true
[Term]
-id: UBERON:0005231
-name: forelimb ectoderm
-def: "An ectoderm that is part of a forelimb [Obol]." [OBOL:automatic]
-xref: OG:0001047
-is_a: UBERON:0000924 ! implied link automatically realized ! ectoderm
-is_a: UBERON:0004120 ! implied link automatically realized ! mesoderm-derived structure
-relationship: part_of UBERON:0002102
-
-[Term]
-id: UBERON:0005232
-name: hindlimb ectoderm
-def: "An ectoderm that is part of a hindlimb [Obol]." [OBOL:automatic]
-xref: OG:0001048
-is_a: UBERON:0000924 ! implied link automatically realized ! ectoderm
-is_a: UBERON:0004120 ! implied link automatically realized ! mesoderm-derived structure
-relationship: part_of UBERON:0002103
-
-[Term]
id: UBERON:0005233
name: medial-nasal process ectoderm
def: "An ectoderm that is part of a medial nasal prominence [Obol]." [OBOL:automatic]
@@ -79983,7 +79948,9 @@
xref: MA:0002706
xref: OG:0001362
xref: SCTID:181578005
+is_a: UBERON:0004121 ! implied link automatically realized ! ectoderm-derived structure
is_a: UBERON:0005275 ! dorsal skin of digit
+relationship: part_of UBERON:0001705 {source="MA"} ! nail
[Term]
id: UBERON:0005274
@@ -83976,7 +83943,6 @@
id: UBERON:0005636
name: caecum epithelium
xref: EHDAA2:0000209
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0000397 ! implied link automatically realized ! colonic epithelium
relationship: part_of UBERON:0001153
@@ -84385,16 +84351,16 @@
xref: EMAPA:17046
xref: EMAPA:18671
xref: SCTID:361434009
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0002296 ! implied link automatically realized ! dorsal mesentery
+is_a: UBERON:0004119 ! implied link automatically realized ! endoderm-derived structure
relationship: part_of UBERON:0001045
[Term]
id: UBERON:0005686
name: caecum dorsal mesentery
xref: EHDAA2:0000208
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0002296 ! implied link automatically realized ! dorsal mesentery
+is_a: UBERON:0004119 ! implied link automatically realized ! endoderm-derived structure
relationship: part_of UBERON:0001153
[Term]
@@ -91819,6 +91785,7 @@
[Term]
id: UBERON:0006658
name: inter-phalangeal joint
+synonym: "interphalangeal joint" EXACT [galen:InterphalangealJoint]
xref: FMA:42765
xref: galen:InterphalangealJoint
is_a: UBERON:0002217 ! synovial joint
@@ -94484,7 +94451,7 @@
xref: MESH:A.16.254.891
xref: Wikipedia:Vitelline_duct
is_a: UBERON:0000058 ! duct
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
+is_a: UBERON:0004119 ! implied link automatically realized ! endoderm-derived structure
relationship: develops_from UBERON:0001045 ! midgut
[Term]
@@ -97870,7 +97837,6 @@
xref: EMAPA:25057
xref: FMA:35249
xref: SCTID:361844001
-is_a: UBERON:0001489 ! implied link automatically realized ! joint of hand
is_a: UBERON:0003695 ! implied link automatically realized ! metacarpophalangeal joint
relationship: part_of UBERON:0001463
@@ -97882,7 +97848,6 @@
xref: EMAPA:25060
xref: FMA:35252
xref: SCTID:361845000
-is_a: UBERON:0001489 ! implied link automatically realized ! joint of hand
is_a: UBERON:0003695 ! implied link automatically realized ! metacarpophalangeal joint
relationship: part_of UBERON:0003622
@@ -97894,7 +97859,6 @@
xref: EMAPA:25063
xref: FMA:35255
xref: SCTID:361846004
-is_a: UBERON:0001489 ! implied link automatically realized ! joint of hand
is_a: UBERON:0003695 ! implied link automatically realized ! metacarpophalangeal joint
relationship: part_of UBERON:0003623
@@ -97906,7 +97870,6 @@
xref: EMAPA:25066
xref: FMA:35258
xref: SCTID:361847008
-is_a: UBERON:0001489 ! implied link automatically realized ! joint of hand
is_a: UBERON:0003695 ! implied link automatically realized ! metacarpophalangeal joint
relationship: part_of UBERON:0003624
@@ -97918,7 +97881,6 @@
xref: EMAPA:25069
xref: FMA:35261
xref: SCTID:361848003
-is_a: UBERON:0001489 ! implied link automatically realized ! joint of hand
is_a: UBERON:0003695 ! implied link automatically realized ! metacarpophalangeal joint
relationship: part_of UBERON:0003625
@@ -99592,7 +99554,6 @@
id: UBERON:0008343
name: intestinal villus of jejunum
xref: FMA:63301
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
is_a: UBERON:0001213 {source="FMA"} ! intestinal villus
is_a: UBERON:0007607 ! implied link automatically realized ! small intestine villus
relationship: part_of UBERON:0000399 {source="FMA"} ! jejunal mucosa
@@ -101357,6 +101318,8 @@
xref: SCTID:362132003
is_a: UBERON:0001135 {source="MP"} ! smooth muscle tissue
is_a: UBERON:0004222 ! implied link automatically realized ! stomach smooth muscle
+is_a: UBERON:0006660 ! implied link automatically realized ! muscle layer
+relationship: part_of UBERON:0001167
relationship: part_of UBERON:0001167 {source="FMA"} ! wall of stomach
[Term]
@@ -102192,13 +102155,10 @@
id: UBERON:0008963
name: hoof
def: "The tip of a toe of an ungulate mammal, strengthened by a thick horny (keratin) covering. The hoof consists of a hard or rubbery sole, and a hard wall formed by a thick nail rolled around the tip of the toe. The weight of the animal is normally borne by both the sole and the edge of the hoof wall. Hooves grow continuously, and are constantly worn down by use." [Wikipedia:Hoof]
+comment: The hoof is the integument of the foot. Like skin, the integument of the foot has three layers, namely the epidermis, dermis, and SC tissue.
xref: BTO:0003994
xref: SCTID:410026002
-is_a: UBERON:0000026 ! appendage
-is_a: UBERON:0004120 ! implied link automatically realized ! mesoderm-derived structure
-is_a: UBERON:0004121 ! implied link automatically realized ! ectoderm-derived structure
-relationship: part_of UBERON:0001003 ! epidermis
-relationship: part_of UBERON:0002544 ! digit
+is_a: UBERON:0009564 ! distal limb integumentary appendage
[Term]
id: UBERON:0008964
@@ -102254,7 +102214,7 @@
xref: BTO:0000649
xref: SCTID:362161002
is_a: UBERON:0000064 ! organ part
-is_a: UBERON:0000077 ! implied link automatically realized ! mixed endoderm/mesoderm-derived structure
+is_a: UBERON:0004119 ! implied link automatically realized ! endoderm-derived structure
relationship: develops_from UBERON:0001045 {source="BTO"} ! midgut
relationship: part_of UBERON:0001155 {source="BTO"} ! colon
@@ -103921,6 +103881,143 @@
is_a: UBERON:0004119 ! implied link automatically realized ! endoderm-derived structure
relationship: part_of UBERON:0006235
+[Term]
+id: UBERON:0009551
+name: distal segment of digit
+def: "A segment of a digit containing the distal phalanx, and overlapping the interphalangeal joint[CJM]. The digit tip is derived from multiple and distinct embryonic origins, and includes the distal bone with associated marrow cavity and haematopoietic cells, ventral (flexor) and dorsal (extensor) tendons, sweat glands with myoepithelial and luminal secreting cells and associated neurons for innervation, dermis with resident melanocytes and dendritic cells, mesenchyme with resident fibroblasts, skin epidermis with hair follicles, a nail organ composed of six specific parts (the root, nail bed, nail plate, eponychium (cuticle), perionychium and hyponychium)." [doi:10.1038/nature10346]
+comment: Newborn and adult mice are able to regrow forelimb (finger) and hindlimb (toe) digit tips after their amputation through the distal interphalangeal joint. Regeneration of the digit tip involves the integrated regrowth of multiple tissues within 2–3 months, reaching an external morphology that is cosmetically and functionally similar to normal digits. Most importantly, regeneration of the mouse distal digit shares morphological similarities with clinical cases documenting regrowth of missing distal portions of fingers in both children and adults
+synonym: "digit tip" EXACT [UBERON:cjm]
+synonym: "distal digit segment" EXACT [UBERON:cjm]
+synonym: "tip of digit" EXACT [UBERON:cjm]
+is_a: UBERON:0000914 ! organismal segment
+is_a: UBERON:0004120 ! implied link automatically realized ! mesoderm-derived structure
+relationship: part_of UBERON:0002544 ! digit
+
+[Term]
+id: UBERON:0009552
+name: distal segment of hand digit
+alt_id: UBERON:0004093
+def: "." [HP:0001211]
+comment: in SNOMED this is a surface region. Here we intend it to be the entire distal segment
+synonym: "finger digit tip" EXACT [doi:10.1038/nature10346]
+synonym: "finger distal segment" EXACT [UBERON:cjm]
+synonym: "finger tip" EXACT [UBERON:cjm]
+synonym: "fingertip" EXACT [HP:0001211]
+synonym: "forelimb digit tip" EXACT [doi:10.1038/nature10346]
+synonym: "tip of finger" EXACT [SCTID:312543003]
+xref: OpenCyc:Mx4rvVjpf5wpEbGdrcN5Y29ycA
+xref: SCTID:312543003
+is_a: UBERON:0009551 ! implied link automatically realized ! distal segment of digit
+relationship: part_of UBERON:0002389
+
+[Term]
+id: UBERON:0009553
+name: distal segment of foot digit
+synonym: "hindlimb digit tip" EXACT [doi:10.1038/nature10346]
+synonym: "tip of toe" EXACT [UBERON:cjm]
+synonym: "toe digit tip" EXACT [doi:10.1038/nature10346]
+synonym: "toe distal segment" EXACT [UBERON:cjm]
+is_a: UBERON:0009551 ! implied link automatically realized ! distal segment of digit
+relationship: part_of UBERON:0001466
+
+[Term]
+id: UBERON:0009554
+name: coffin bone
+def: "the bottommost bone in the equine leg and is encased by the hoof capsule. The distal phalanx articulates with both the middle phalanx and the distal sesamoid, forming the distal interphalangeal joint " [Wikipedia:Coffin_bone]
+synonym: "equine distal phalanx" EXACT [UBERON:cjm]
+synonym: "pedal bone" EXACT [Wikipedia:Coffin_bone, Wikipedia:Equine_forelimb_anatomy#Distal_phalanx]
+is_a: UBERON:0004300 ! distal phalanx
+
+[Term]
+id: UBERON:0009555
+name: short pastern bone
+def: "." [Wikipedia:Equine_forelimb_anatomy#Middle_phalanx]
+synonym: "equine middle phalanx" EXACT [UBERON:cjm]
+is_a: UBERON:0004301 ! middle phalanx
+is_a: UBERON:0009558 ! pastern bone
+
+[Term]
+id: UBERON:0009556
+name: long pastern bone
+def: "." [Wikipedia:Equine_forelimb_anatomy#Proximal_phalanx]
+synonym: "equine proximal phalanx" EXACT [UBERON:cjm]
+is_a: UBERON:0004302 ! proximal phalanx
+is_a: UBERON:0009558 ! pastern bone
+
+[Term]
+id: UBERON:0009557
+name: coffin joint
+synonym: "distal interphalangeal joint" EXACT [UBERON:cjm]
+xref: SCTID:196392002
+is_a: UBERON:0006658 ! inter-phalangeal joint
+
+[Term]
+id: UBERON:0009558
+name: pastern bone
+is_a: UBERON:0003221 ! phalanx
+relationship: part_of UBERON:0009563 ! pastern region of limb
+
+[Term]
+id: UBERON:0009559
+name: metacarpal/tarsal-phalangeal joint
+synonym: "fetlock" NARROW SENSU [UBERON:cjm, Wikipedia:Fetlock]
+synonym: "metacarpo-tarsophalangeal joint" EXACT [UBERON:cjm]
+is_a: UBERON:0002217 ! implied link automatically realized ! synovial joint
+is_a: UBERON:0003841 ! implied link automatically realized ! autopod joint
+relationship: part_of UBERON:0002544
+
+[Term]
+id: UBERON:0009563
+name: pastern region of limb
+comment: note that digit is used very generically in uberon, to include the homologous region in ungulates
+xref: SCTID:370725009
+is_a: UBERON:0000914 ! organismal segment
+is_a: UBERON:0004120 ! implied link automatically realized ! mesoderm-derived structure
+relationship: part_of UBERON:0002544 ! digit
+
+[Term]
+id: UBERON:0009564
+name: distal limb integumentary appendage
+def: "A nail, hoof or claw." [PMID:11710767]
+xref: MESH:A.13.491
+is_a: UBERON:0000026 ! appendage
+is_a: UBERON:0004120 ! implied link automatically realized ! mesoderm-derived structure
+is_a: UBERON:0004121 ! implied link automatically realized ! ectoderm-derived structure
+relationship: part_of UBERON:0001003 ! epidermis
+relationship: part_of UBERON:0009551 {source="cjm"} ! distal segment of digit
+
+[Term]
+id: UBERON:0009565
+name: nail of forelimb digit
+synonym: "finger nail" EXACT [FMA:54327]
+synonym: "fingernail" EXACT [FMA:54327]
+synonym: "nail of finger" EXACT [FMA:54327]
+xref: FMA:54327
+is_a: UBERON:0001705 ! implied link automatically realized ! nail
+relationship: part_of UBERON:0002389
+relationship: part_of UBERON:0005276 {source="FMA"} ! dorsal skin of finger
+
+[Term]
+id: UBERON:0009566
+name: intestinal submucosa
+synonym: "submucosa of intestine" EXACT [FMA:15696]
+xref: FMA:15696
+is_a: UBERON:0000009 ! implied link automatically realized ! submucosa
+is_a: UBERON:0004119 ! implied link automatically realized ! endoderm-derived structure
+relationship: part_of UBERON:0000160
+relationship: part_of UBERON:0001262 {source="FMA"} ! wall of intestine
+
+[Term]
+id: UBERON:0009567
+name: nail of hindlimb digit
+synonym: "nail of toe" EXACT [FMA:54328]
+synonym: "toe nail" EXACT [FMA:54328]
+synonym: "toenail" EXACT [FMA:54328]
+xref: FMA:54328
+is_a: UBERON:0001705 ! implied link automatically realized ! nail
+relationship: part_of UBERON:0001466
+relationship: part_of UBERON:0005277 {source="FMA"} ! dorsal skin of toe
+
[Typedef]
id: adjacent_to
name: adjacent_to
@@ -103959,7 +104056,7 @@
namespace: CL
def: "A relation between a material entity (such as a cell) and a process. This is a shortcut relation, translation rule for which is: capable_of P <-> bearer_of (some realized_by only P). Example: osteoclast capable of bone resorption." [GOC:cjm]
comment: At the CL meeting we discussed a separate case, capable_of P <-> bearer_of (some realized_by only (P or part_of some P)). We need to look at specific cases.
-expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000053 some (http://purl.obolibrary.org/obo/BFO_0000054 only ?Y)" []
+expand_expression_to: "BFO_0000053 some (BFO_0000054 only ?Y)" []
[Typedef]
id: capable_of_part_of
@@ -104203,7 +104300,6 @@
[Typedef]
id: only_in_taxon
name: only_in_taxon
-is_class_level: true
[Typedef]
id: output_of
@@ -104214,7 +104310,7 @@
name: overlaps
def: "A overlaps B if they share some part in common." []
xref: RO:0002131
-expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" []
+expand_expression_to: "BFO_0000051 some (BFO_0000050 some ?Y)" []
[Typedef]
id: part_of
Modified: ontologies/trunk/UBERON/core.obo
===================================================================
--- ontologies/trunk/UBERON/core.obo 2011-09-03 18:50:18 UTC (rev 4019)
+++ ontologies/trunk/UBERON/core.obo 2011-09-03 18:52:30 UTC (rev 4020)
@@ -270,7 +270,6 @@
xref: OpenCyc:Mx4rvViCbJwpEbGdrcN5Y29ycA
xref: TAO:0000047 ! peripheral olfactory organ
xref: ZFA:0000047 ! peripheral olfactory organ
-xref: XAO:0003172 ! olfactory region
xref: ncithesaurus:Nose ! Nose
xref: galen:Nose ! nose
xref: OpenCyc:Mx4rvViCbJwpEbGdrcN5Y29ycA ! nose
@@ -560,7 +559,7 @@
id: UBERON:0000006
name: islet of Langerhans
def: "Regions of the pancreas that contain its endocrine (i.e., hormone-producing) cells." [Wikipedia:Islet_of_Langerhans]
-comment: TODO - is plural equivalent to endocrine pancreas? It has been recognized that the cytoarchitecture of pancreatic islets differs between species[WP].
+comment: A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986)[PMID:16417468]
subset: uberon_slim
synonym: "islets of langerhans" RELATED []
synonym: "pancreatic insula" EXACT []
@@ -584,6 +583,11 @@
xref: EV:0100130 ! islets of Langerhans
is_a: UBERON:0000064 ! organ part
relationship: part_of UBERON:0000016 ! endocrine pancreas
+relationship: has_part CL:0002067 {source="PMID:16417468"} ! type A enterocrine cell
+relationship: has_part CL:0000168 {source="PMID:16417468"} ! insulin secreting cell
+relationship: has_part CL:0000172 {source="PMID:16417468"} ! somatostatin secreting cell
+relationship: has_part CL:0000696 {gci_relation="part_of", gci_filler="NCBITaxon:117570", source="PMID:16417468"} ! PP cell
+relationship: has_part CL:0000696 {gci_relation="part_of", gci_filler="NCBITaxon:7778", source="PMID:16417468"} ! PP cell
xref: AAO:0010406 ! islet of Langerhans
[Term]
@@ -856,11 +860,12 @@
is_a: UBERON:0001048 {source="Obol"} ! primordium
relationship: part_of UBERON:0000922 ! embryo
relationship: develops_from UBERON:0000925 ! endoderm
+relationship: part_of UBERON:0007026 ! primitive gut
[Term]
id: UBERON:0003922 ! pancreatic bud
name: pancreatic bud
-def: "embryonic structure that gives rise to the adult pancreas[CJM]. In humans, an embryonic structure that is an outgrowth of the duodenum during embryogenesis - joins together to form the adult pancreas[WP]." [Wikipedia:Pancreatic_bud]
+def: "The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]. In humans, an embryonic structure that is an outgrowth of the duodenum during embryogenesis - joins together to form the adult pancreas[WP]." [Wikipedia:Pancreatic_bud, PMID:16417468]
xref: ZFA:0001390 ! pancreatic bud
xref: ncithesaurus:Pancreatic_Bud ! Pancreatic Bud
xref: http://upload.wikimedia.org/wikipedia/commons/thumb/d/db/Gray982.png/200px-Gray982.png
@@ -868,6 +873,7 @@
is_a: UBERON:0005423 ! developing anatomical structure
relationship: part_of UBERON:0000922 ! embryo
relationship: develops_from UBERON:0003921 ! pancreas primordium
+relationship: develops_from UBERON:0001555 ! digestive tract
relationship: develops_from UBERON:0001041 {source="Wikipedia:Pancreas#Embryological_development"} ! foregut
relationship: develops_from UBERON:0002114 {exception="zebrafish", source="Wikipedia:Pancreatic_bud"} ! duodenum
xref: SCTID:360398004 ! Pancreatic bud
@@ -889,6 +895,8 @@
xref: EFO:0003465 ! posterior pancreatic bud
is_a: UBERON:0003922 ! pancreatic bud
relationship: develops_from UBERON:0001045 {source="XAO"} ! midgut
+relationship: induced_by UBERON:0002328 {gci_relation="part_of", gci_filler="NCBITaxon:10088", source="PMID:16417468"} ! notochord
+relationship: induced_by UBERON:0005805 {gci_relation="part_of", gci_filler="NCBITaxon:10088", source="PMID:16417468"} ! dorsal aorta
xref: AAO:0011031 ! dorsal pancreatic bud
xref: SCTID:361435005 ! Dorsal pancreatic bud
@@ -896,6 +904,7 @@
id: UBERON:0003924
name: ventral pancreatic bud
def: "pancreatic bud that gives rise to the major pancreatic duct." [Wikipedia:Pancreatic_bud]
+comment: the ventral pancreas and liver are derived from a common precursor cell population[PMID:16417468]. TODO - add this relationship
subset: vertebrate_core
synonym: "ventral pancreatic anlage" RELATED []
synonym: "anterior pancreatic anlage" RELATED []
@@ -933,7 +942,7 @@
id: UBERON:0000019
name: camera-type eye
alt_id: UBERON:FMA_12513-MIAA_0000283-XAO_0000181
-def: "GO: The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field. Organ with organ cavity which is connected to the optic nerve, allowing light to enter it and project onto a light-sensitive panel of cells, known as the retina, at the rear of the eye [FMA]." [FMA:12513, GO:0043010, Image:http\://genome.cshlp.org/content/14/8/1555/F1.large.jpg, Image:http\://www.pnas.org/content/94/6/2098/F1.large.jpg]
+def: "GO: The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field[FMA]." [GO:0043010, Image:http\://genome.cshlp.org/content/14/8/1555/F1.large.jpg, Image:http\://www.pnas.org/content/94/6/2098/F1.large.jpg]
comment: FMA distinguishes Eye (subdivision of face) from Eyeball (organ). Here we are referring to the organ but we also include Eye as being subsumed
subset: uberon_slim
subset: vertebrate_core
@@ -1849,6 +1858,7 @@
xref: NIF_GrossAnatomy:birnlex_4 ! Organ
is_a: UBERON:0000061 ! anatomical structure
relationship: part_of UBERON:0000467 ! anatomical system
+relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} ! Xenoturbella
[Term]
id: UBERON:0000064
@@ -10282,6 +10292,7 @@
xref: galen:UrinaryTract
xref: AAO:0010257 ! urinary system
xref: SCTID:362204003 ! Entire urinary system
+relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} ! Xenoturbella
[Term]
id: UBERON:0001009 ! circulatory system
@@ -11795,7 +11806,6 @@
xref: TGMA:0001036 ! adult midgut
xref: EMAPA:16255 ! midgut
is_a: UBERON:0004921 ! subdivision of digestive tract
-relationship: develops_from UBERON:0003104 {source="Wikipedia"} ! mesenchyme
xref: SCTID:361410004 ! primitive midgut
[Term]
@@ -16541,6 +16551,7 @@
relationship: part_of UBERON:0002294 ! biliary system
relationship: develops_from UBERON:0008835 {source="XAO"} ! hepatic diverticulum
relationship: part_of UBERON:0001173 {source="MA"} ! biliary tree
+relationship: has_part CL:0000168 {gci_relation="part_of", gci_filler="NCBITaxon:7769", source="PMID:16417468"} ! insulin secreting cell
xref: AAO:0011019 ! bile duct
xref: SCTID:276157007 ! Entire bile duct
@@ -18428,8 +18439,7 @@
id: UBERON:0001242
name: intestinal mucosa
alt_id: UBERON:FMA_15695-MA_0001537
-def: "." [Wikipedia:Intestinal_mucosa]
-comment: This class was created automatically from a combination of ontologies
+def: "The innermost membrane of the four coats of the intestinal wall, the other three being the submucosa, muscular layers, and serosa. (Berk et al., Gastroenterology, 4th ed, v.3, p1479)" [MESH:A.03.492.411.369]
subset: uberon_slim
synonym: "intestine mucosa" EXACT []
synonym: "mucosa of intestine" EXACT []
@@ -18459,6 +18469,15 @@
xref: SCTID:362080002 ! Entire intestinal mucous membrane
[Term]
+id: UBERON:0009566
+name: intestinal submucosa
+synonym: "submucosa of intestine" EXACT [FMA:15696]
+intersection_of: UBERON:0000009 ! submucosa
+intersection_of: part_of UBERON:0000160 ! intestine
+relationship: part_of UBERON:0001262 {source="FMA"} ! wall of intestine
+xref: FMA:15696 ! intestinal submucosa
+
+[Term]
id: UBERON:0001243
name: serosa of intestine
alt_id: UBERON:FMA_15701-MA_0001538
@@ -18923,7 +18942,8 @@
id: UBERON:0001264
name: pancreas
alt_id: UBERON:FMA_16017-FMA_16018-FMA_7198-MA_0000120-MA_0001582-MA_0002415-MIAA_0000075-XAO_0000136-XAO_0000137-ZFA_0000140-ZFA_0001249-ZFA_0001260
-def: "An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. The mature pancreas of higher vertebrates and mam- mals comprises two major functional units: the exo- crine pancreas, which is responsible for the pro- duction of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductu- lar cells. The endocrine portion, which comprises only 1–2% of the total mass, contains five different cell types, which are organized into mixed functional as- semblies referred to as the islets of Langerhans[PMID]." [Wikipedia:Pancreas, PMID:16417468, GO:0031016]
+def: "An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1–2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans[PMID]." [Wikipedia:Pancreas, PMID:16417468, GO:0031016]
+comment: taxon notes: As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468]
subset: uberon_slim
subset: vertebrate_core
subset: major_organ
@@ -18954,6 +18974,7 @@
relationship: part_of UBERON:0000949 ! endocrine system
relationship: develops_from UBERON:0003923 {source="Wikipedia"} ! dorsal pancreatic bud
relationship: develops_from UBERON:0003924 {source="Wikipedia"} ! ventral pancreatic bud
+relationship: only_in_taxon NCBITaxon:7742 {source="PMID:16417468"} ! Vertebrata
xref: AAO:0010112 ! pancreas
xref: SCTID:181277001 ! Entire pancreas
@@ -23373,6 +23394,7 @@
synonym: "metacarpal/metatarsal" EXACT []
synonym: "metacarpal or metatarsal bone" EXACT []
synonym: "metapodium bone" EXACT [UBERON:cjm, http://en.wiktionary.org/wiki/metapodial]
+synonym: "cannon bone" NARROW SENSU [UBERON:cjm]
xref: MA:0000301 ! metacarpal/metatarsal bone
is_a: UBERON:0002495 ! long bone
relationship: part_of UBERON:0002470 ! autopod
@@ -39819,8 +39841,7 @@
id: UBERON:0002082
name: cardiac ventricle
alt_id: UBERON:FMA_7100-MA_0000091-ZFA_0000009
-def: "Cardiac chamber which consists of a wall that surrounds the cavity of a ventricle. // One of four heart chambers." [Wikipedia:Cardiac_ventricle, ZFIN:curator]
-comment: This class was created automatically from a combination of ontologies
+def: "Cardiac chamber which consists of a wall that surrounds the cavity of a ventricle." [FMA:7100]
subset: uberon_slim
subset: vertebrate_core
synonym: "heart ventricle" EXACT []
@@ -62945,7 +62966,9 @@
id: UBERON:0003112
name: olfactory region
alt_id: UBERON:ZFA_0000351-XAO_0003172
+def: "Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the olfactory organ." [TAO:0000351]
synonym: "ethmoid region" EXACT [ZFA:0000351]
+xref: TAO:0000351
xref: XAO:0003172 ! olfactory region
xref: ZFA:0000351 ! olfactory region
xref: EFO:0003525 ! olfactory region
@@ -65120,7 +65143,7 @@
comment: TODO - check
synonym: "foregut endoderm" EXACT [OBOL:automatic]
xref: EHDAA:524 ! endoderm
-xref: EHDAA2:0000566 ! foregut endoderm
+xref: EHDAA2:0000566 ! lower foregut region endoderm
intersection_of: UBERON:0000925 ! endoderm
intersection_of: part_of UBERON:0001041 ! foregut
@@ -66894,8 +66917,14 @@
[Term]
id: UBERON:0003371
name: hindlimb bud ectoderm
+alt_id: UBERON:0005232
synonym: "leg ectoderm" RELATED [OBOL:automatic]
+synonym: "lower limb bud ectoderm" EXACT [EHDAA2:0001034]
+synonym: "hindlimb ectoderm" EXACT [OG:0001048]
xref: EMAPA:17254 ! ectoderm of leg of hindlimb bud
+xref: OG:0001048 ! hindlimb ectoderm
+xref: EHDAA2:0001034 ! lower limb bud ectoderm
+synonym: "hindlimb ectoderm" EXACT [OG:0001048]
intersection_of: UBERON:0000924 ! ectoderm
intersection_of: part_of UBERON:0005418 ! hindlimb bud
@@ -66903,9 +66932,13 @@
id: UBERON:0003372
name: forelimb bud ectoderm
alt_id: UBERON:0005663
+alt_id: UBERON:0005231
synonym: "arm ectoderm" RELATED [OBOL:automatic]
+synonym: "upper limb bud ectoderm" EXACT [EHDAA2:0002134]
+synonym: "forelimb ectoderm" EXACT [OG:0001047]
xref: EMAPA:17243 ! ectoderm of arm of forelimb bud
xref: EHDAA2:0002134 ! upper limb bud ectoderm
+xref: OG:0001047 ! forelimb ectoderm
intersection_of: UBERON:0000924 ! ectoderm
intersection_of: part_of UBERON:0005417 ! forelimb bud
@@ -73331,10 +73364,21 @@
is_a: UBERON:0000982 ! joint
xref: SCTID:361832004 ! Entire atlantoaxial joint
+
[Term]
+id: UBERON:0009559
+name: metacarpal/tarsal-phalangeal joint
+intersection_of: UBERON:0002217 ! synovial joint
+intersection_of: attached_to UBERON:0003656 ! carpal/tarsal bone
+intersection_of: part_of UBERON:0002544 ! digit
+synonym: "metacarpo-tarsophalangeal joint" EXACT [UBERON:cjm]
+synonym: "fetlock" NARROW SENSU [UBERON:cjm, Wikipedia:Fetlock]
+
+[Term]
id: UBERON:0003695
name: metacarpophalangeal joint
def: "The metacarpophalangeal joints (MCP) are of the condyloid kind, formed by the reception of the rounded heads of the metacarpal bones into shallow cavities on the proximal ends of the first phalanges, with the exception of that of the thumb, which presents more of the characters of a ginglymoid joint. Arthritis of the MCP is a distinguishing feature of Rheumatoid Arthritis, as opposed to the distal interphalangeal joint in osteoarthritis. [WP,unvetted]." [Wikipedia:Metacarpophalangeal_joint]
+comment: we follow FMA in making these joints part of digits
synonym: "metacarpal joint" EXACT [FMA:35246]
synonym: "mp joint" EXACT [FMA:35246]
synonym: "metacarpo-phalangeal joint" EXACT [MA:0000453]
@@ -73346,8 +73390,9 @@
xref: http://upload.wikimedia.org/wikipedia/commons/thumb/5/53/Gray337.png/200px-Gray337.png
xref: EMAPA:19302 ! metacarpo-phalangeal
xref: MESH:A.02.835.583.345.512 ! metacarpophalangeal joint
-is_a: UBERON:0002217 ! synovial joint
-relationship: attached_to UBERON:0002374 ! metacarpal bone
+intersection_of: UBERON:0002217 ! synovial joint
+intersection_of: attached_to UBERON:0002374 ! metacarpal bone
+intersection_of: part_of UBERON:0002389 ! hand digit
xref: galen:MetacarpoPhalangealJoint
xref: SCTID:280995004 ! Entire metacarpophalangeal joint
@@ -73409,6 +73454,8 @@
id: UBERON:0003696
name: metatarsophalangeal joint
def: "The metatarsophalangeal articulations are the joints between the metatarsal bones of the foot and the proximal bones of the toes . They are condyloid joints meaning an elliptical or rounded surface (of the metatarsal bones) come close to the shallow cavities (of the proximal phalanges). The ligaments are the plantar and two collateral." [Wikipedia:Metatarsophalangeal_articulations]
+comment: we follow FMA in making these joints part of digits
+synonym: "metatarsophalangeal articulation" RELATED [Wikipedia:Metatarsophalangeal_articulations]
synonym: "metatarsalphalangeal joint" RELATED [Wikipedia:Metatarsophalangeal_articulations]
synonym: "metatarsophalangeal" RELATED [Wikipedia:Metatarsophalangeal_articulations]
synonym: "metatarsal joint" EXACT [FMA:35222]
@@ -73417,8 +73464,9 @@
xref: ncithesaurus:Metatarsophalangeal_Joint ! Metatarsophalangeal Joint
xref: OpenCyc:Mx4rwCtS0pwpEbGdrcN5Y29ycA ! metatarsophalangeal joint
xref: MESH:A.02.835.583.378.531 ! metatarsophalangeal joint
-is_a: UBERON:0001487 ! joint of foot
-relationship: attached_to UBERON:0001448 ! metatarsal bone
+intersection_of: UBERON:0002217 ! synovial joint
+intersection_of: attached_to UBERON:0001448 ! metatarsal bone
+intersection_of: part_of UBERON:0001466 ! foot digit
xref: galen:MetatarsoPhalangealJoint
xref: SCTID:239747005 ! Entire metatarsal joint
@@ -74631,8 +74679,8 @@
xref: EHDAA2:0000171 ! biliary bud
xref: http://upload.wikimedia.org/wikipedia/commons/thumb/4/4f/Gray1088.png/200px-Gray1088.png
is_a: UBERON:0003914 ! epithelial tube
-relationship: develops_from UBERON:0001041 ! foregut
-relationship: develops_from UBERON:0004161 {source="EHDAA2"} ! septum transversum
+relationship: part_of UBERON:0006235 {source="EMAPA"} ! foregut-midgut junction
+relationship: develops_from UBERON:0004161 {source="EHDAA2-modified"} ! septum transversum
[Term]
id: UBERON:0008835 ! hepatic diverticulum
@@ -76956,15 +77004,6 @@
relationship: part_of UBERON:0000949 ! endocrine system
[Term]
-id: UBERON:0004093
-name: fingertip
-def: "." [HP:0001211]
-xref: OpenCyc:Mx4rvVjpf5wpEbGdrcN5Y29ycA ! fingertip
-is_a: UBERON:0000061 ! anatomical structure
-relationship: part_of UBERON:0002389 ! hand digit
-xref: SCTID:312543003 ! Tip of finger
-
-[Term]
id: UBERON:0003662
name: forelimb muscle
alt_id: UBERON:0005634
@@ -85646,24 +85685,24 @@
intersection_of: part_of UBERON:0002082 ! part_of cardiac ventricle
[Term]
-id: UBERON:0004786
+id: UBERON:0004786 ! gastrointestinal system mucosa
name: gastrointestinal system mucosa
-def: "A mucosa that is part of a digestive system [Obol]." [OBOL:automatic]
-synonym: "digestive system mucosa" EXACT [OBOL:automatic]
-synonym: "digestive system mucosa of organ" EXACT [OBOL:automatic]
-synonym: "digestive system mucous membrane" EXACT [OBOL:automatic]
-synonym: "gastrointestinal system mucosa of organ" EXACT [OBOL:automatic]
-synonym: "gastrointestinal system mucous membrane" EXACT [OBOL:automatic]
-synonym: "mucosa of digestive system" EXACT [OBOL:automatic]
-synonym: "mucosa of gastrointestinal system" EXACT [OBOL:automatic]
-synonym: "mucosa of organ of digestive system" EXACT [OBOL:automatic]
-synonym: "mucosa of organ of gastrointestinal system" EXACT [OBOL:automatic]
-synonym: "mucous membrane of digestive system" EXACT [OBOL:automatic]
-synonym: "mucous membrane of gastrointestinal system" EXACT [OBOL:automatic]
-xref: MA:0001521 ! gastrointestinal system mucosa
+comment: The gut mucosa of amphioxus has insulin-secreting cells. PMID:16417468
+synonym: "gut mucosa" EXACT [BTO:0000546]
+synonym: "mucosa of gut" EXACT [UBERON:cjm]
+synonym: "gut mucuous membrane" EXACT [UBERON:cjm]
+synonym: "digestive tract mucosa" EXACT [UBERON:cjm]
intersection_of: UBERON:0000344 ! mucosa
intersection_of: part_of UBERON:0005409 ! gastrointestinal system
+relationship: part_of UBERON:0001555 ! digestive tract
+relationship: adjacent_to UBERON:0006909 {source="BTO-modified"} ! lumen of gut
+relationship: has_part CL:0002067 {source="PMID:16417468"} ! type A enterocrine cell
+relationship: has_part CL:0000168 {gci_relation="part_of", gci_filler="NCBITaxon:7737", source="PMID:16417468"} ! insulin secreting cell
+relationship: has_part CL:0000172 {source="PMID:16417468"} ! somatostatin secreting cell
+relationship: has_part CL:0000696 {source="PMID:16417468"} ! PP cell
xref: SCTID:410433007 ! Structure of digestive system mucous membrane
+xref: BTO:0000546 ! gut mucosa
+xref: MA:0001521 ! gastrointestinal system mucosa
[Term]
id: UBERON:0004789
@@ -90207,22 +90246,6 @@
is_obsolete: true
[Term]
-id: UBERON:0005231
-name: forelimb ectoderm
-def: "An ectoderm that is part of a forelimb [Obol]." [OBOL:automatic]
-xref: OG:0001047
-intersection_of: UBERON:0000924
-intersection_of: part_of UBERON:0002102
-
-[Term]
-id: UBERON:0005232
-name: hindlimb ectoderm
-def: "An ectoderm that is part of a hindlimb [Obol]." [OBOL:automatic]
-xref: OG:0001048
-intersection_of: UBERON:0000924
-intersection_of: part_of UBERON:0002103
-
-[Term]
id: UBERON:0005233
name: medial-nasal process ectoderm
def: "An ectoderm that is part of a medial nasal prominence [Obol]." [OBOL:automatic]
@@ -90594,6 +90617,37 @@
relationship: has_function_in GO:0070293 {source="Wikipedia"} ! renal reabsorption
[Term]
+id: UBERON:0009564 ! distal limb integumentary appendage
+name: distal limb integumentary appendage
+def: "A nail, hoof or claw." [PMID:11710767]
+xref: MESH:A.13.491 ! hoof and claw
+is_a: UBERON:0000026 ! appendage
+relationship: part_of UBERON:0009551 {source="cjm"} ! distal segment of digit
+relationship: part_of UBERON:0001003 ! epidermis
+
+[Term]
+id: UBERON:0009565
+name: nail of forelimb digit
+synonym: "finger nail" EXACT [FMA:54327]
+synonym: "fingernail" EXACT [FMA:54327]
+intersection_of: UBERON:0001705 ! nail
+intersection_of: part_of UBERON:0002389 ! hand digit
+relationship: part_of UBERON:0005276 {source="FMA"} ! dorsal skin of f...
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