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vccf.obo
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format-version: 1.2
data-version: releases/2024-06-04
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam ""
subsetdef: ro-eco ""
subsetdef: RO:0002259 ""
synonymtypedef: OMO:0003000 "abbreviation"
synonymtypedef: OMO:0003001 "ambiguous synonym"
synonymtypedef: OMO:0003002 "dubious synonym"
synonymtypedef: OMO:0003003 "layperson synonym"
synonymtypedef: OMO:0003004 "plural form"
synonymtypedef: OMO:0003005 "UK spelling synonym"
synonymtypedef: OMO:0003006 "misspelling"
synonymtypedef: OMO:0003007 "misnomer"
synonymtypedef: OMO:0003008 "previous name"
synonymtypedef: OMO:0003009 "legal name"
synonymtypedef: OMO:0003010 "International Nonproprietary Name"
synonymtypedef: OMO:0003011 "latin term"
synonymtypedef: OMO:0003012 "acronym"
ontology: vccf
property_value: http://purl.org/dc/terms/description "None" xsd:string
property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/unspecified
property_value: http://purl.org/dc/terms/title "Vasculature Common Coordinate Framework Ontology" xsd:string
property_value: owl:versionInfo "2024-06-04" xsd:string
[Term]
id: IAO:0000027
name: data item
is_a: IAO:0000030 ! information content entity
property_value: IAO:0000111 "data item" xsd:string
[Term]
id: IAO:0000030
name: information content entity
is_a: BFO:0000031
property_value: IAO:0000111 "information content entity" xsd:string
[Term]
id: IAO:0000078
name: curation status specification
def: "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." []
is_a: IAO:0000102 ! data about an ontology part
property_value: IAO:0000111 "curation status specification" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string
property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string
property_value: IAO:0000119 "GROUP:OBI:<http://purl.obolibrary.org/obo/obi>" xsd:string
property_value: IAO:0000119 "OBI_0000266" xsd:string
[Term]
id: IAO:0000102
name: data about an ontology part
def: "Data about an ontology part is a data item about a part of an ontology, for example a term" []
is_a: IAO:0000027 ! data item
property_value: IAO:0000111 "data about an ontology part" xsd:string
property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string
[Term]
id: IAO:0000225
name: obsolescence reason specification
def: "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." []
is_a: IAO:0000102 ! data about an ontology part
property_value: IAO:0000111 "obsolescence reason specification" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
[Term]
id: IAO:0000409
name: denotator type
def: "A denotator type indicates how a term should be interpreted from an ontological perspective." []
is_a: IAO:0000102 ! data about an ontology part
property_value: IAO:0000111 "denotator type" xsd:string
property_value: IAO:0000112 "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." xsd:string
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string
[Term]
id: IAO:8000000
name: ontology module
is_a: IAO:0000102 ! data about an ontology part
property_value: IAO:0000111 "ontology module" xsd:string
property_value: IAO:0000116 "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." xsd:string
property_value: IAO:0000118 "ontology file" xsd:string
property_value: IAO:0000232 "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." xsd:string
[Term]
id: IAO:8000001
name: base ontology module
def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "base ontology module" xsd:string
property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50
[Term]
id: IAO:8000002
name: editors ontology module
def: "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "editors ontology module" xsd:string
property_value: IAO:0000118 "source ontology module" xsd:string
[Term]
id: IAO:8000003
name: main release ontology module
def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "main release ontology module" xsd:string
property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string
[Term]
id: IAO:8000004
name: bridge ontology module
def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "bridge ontology module" xsd:string
property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies
[Term]
id: IAO:8000005
name: import ontology module
def: "A subset ontology module that is intended to be imported from another ontology." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "import ontology module" xsd:string
property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string
property_value: IAO:0000118 "import file" xsd:string
property_value: seeAlso http://robot.obolibrary.org/extract
[Term]
id: IAO:8000006
name: subset ontology module
def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "subset ontology module" xsd:string
property_value: IAO:0000118 "ontology slim" xsd:string
property_value: IAO:0000118 "subset ontology" xsd:string
property_value: seeAlso http://robot.obolibrary.org/filter
property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide
[Term]
id: IAO:8000007
name: curation subset ontology module
def: "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "curation subset ontology module" xsd:string
[Term]
id: IAO:8000008
name: analysis subset ontology module
def: "An ontology module that is intended for usage in analysis or discovery applications." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "analysis ontology module" xsd:string
[Term]
id: IAO:8000009
name: single layer subset ontology module
def: "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "single layer ontology module" xsd:string
property_value: IAO:0000118 "ribbon subset" xsd:string
[Term]
id: IAO:8000010
name: exclusion subset ontology module
def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "exclusion subset ontology module" xsd:string
property_value: IAO:0000118 "antislim" xsd:string
[Term]
id: IAO:8000011
name: external import ontology module
def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." []
is_a: IAO:8000005 ! import ontology module
property_value: IAO:0000111 "external import ontology module" xsd:string
property_value: IAO:0000118 "external import" xsd:string
[Term]
id: IAO:8000012
name: species subset ontology module
def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "species subset ontology module" xsd:string
property_value: IAO:0000118 "taxon subset" xsd:string
property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints
[Term]
id: IAO:8000013
name: reasoned ontology module
def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "reasoned ontology module" xsd:string
property_value: seeAlso http://robot.obolibrary.org/reason
[Term]
id: IAO:8000014
name: generated ontology module
def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "generated ontology module" xsd:string
property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string
[Term]
id: IAO:8000015
name: template generated ontology module
def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." []
is_a: IAO:8000014 ! generated ontology module
property_value: IAO:0000111 "template generated ontology module" xsd:string
property_value: seeAlso http://robot.obolibrary.org/template
property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0
property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/
[Term]
id: IAO:8000016
name: taxonomic bridge ontology module
is_a: IAO:8000004 ! bridge ontology module
property_value: IAO:0000111 "taxonomic bridge ontology module" xsd:string
[Term]
id: IAO:8000017
name: ontology module subsetted by expressivity
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "ontology module subsetted by expressivity" xsd:string
[Term]
id: IAO:8000018
name: obo basic subset ontology module
def: "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" []
is_a: IAO:8000017 ! ontology module subsetted by expressivity
property_value: IAO:0000111 "obo basic subset ontology module" xsd:string
property_value: seeAlso 6.2
[Term]
id: IAO:8000019
name: ontology module subsetted by OWL profile
is_a: IAO:8000017 ! ontology module subsetted by expressivity
property_value: IAO:0000111 "ontology module subsetted by OWL profile" xsd:string
[Term]
id: IAO:8000020
name: EL++ ontology module
is_a: IAO:8000019 ! ontology module subsetted by OWL profile
property_value: IAO:0000111 "EL++ ontology module" xsd:string
[Term]
id: RO:0002577
name: system
def: "A material entity consisting of multiple components that are causally integrated." []
is_a: BFO:0000040
property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000119 "http://www.jbiomedsem.com/content/4/1/43" xsd:string
[Term]
id: UBERON:0000004
name: nose
def: "The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity." [UBERON:cjm]
synonym: "peripheral olfactory organ" EXACT [ZFA:0000047]
xref: BTO:0000840
xref: CALOHA:TS-2037
xref: EHDAA2:0001274
xref: EHDAA:1502
xref: EMAPA:16542
xref: EV:0100037
xref: EV:0100370
xref: FMA:46472
xref: GAID:77
xref: galen:Nose
xref: MA:0000281
xref: MAT:0000139
xref: MESH:D009666
xref: MIAA:0000139
xref: NCIT:C12756
xref: SCTID:181195007
xref: TAO:0000047
xref: Wikipedia:Nose
xref: ZFA:0000047
relationship: BFO:0000050 UBERON:0001456 ! part of face
relationship: RO:0002433 UBERON:0001456 ! face
[Term]
id: UBERON:0000006
name: islet of Langerhans
def: "The clusters of hormone-producing cells that are scattered throughout the pancreas." [MA:0000127, MESH:A03.734.414, MP:0005215]
synonym: "pancreatic insula" EXACT []
synonym: "pancreatic islet" EXACT []
xref: AAO:0010406
xref: BTO:0000991
xref: CALOHA:TS-0741
xref: EFO:0000856
xref: EMAPA:32927
xref: EV:0100130
xref: FMA:16016
xref: GAID:324
xref: MA:0000127
xref: MAT:0000076
xref: MESH:D007515
xref: MIAA:0000076
xref: NCIT:C12608
xref: VHOG:0000646
xref: Wikipedia:Islets_of_Langerhans
xref: XAO:0000159
relationship: BFO:0000050 UBERON:0000016 ! part of endocrine pancreas
relationship: RO:0002433 UBERON:0000016 ! endocrine pancreas
[Term]
id: UBERON:0000007
name: pituitary gland
def: "The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]." [Wikipedia:Pituitary_gland, ZFIN:curator]
synonym: "pituitary" EXACT [BTO:0001073]
synonym: "pituitary body" EXACT [BTO:0001073]
xref: AAO:0010536
xref: BAMS:PIT
xref: BAMS:Pit
xref: BIRNLEX:1353
xref: BM:Die-Hy-HY
xref: BTO:0001073
xref: CALOHA:TS-0798
xref: DHBA:10505
xref: EFO:0000857
xref: EHDAA2:0001471
xref: EHDAA:2183
xref: EHDAA:4477
xref: EMAPA:35998
xref: EV:0100132
xref: FMA:13889
xref: GAID:457
xref: HBA:4634
xref: MA:0000176
xref: MAT:0000077
xref: MESH:D010902
xref: MIAA:0000077
xref: NCIT:C12399
xref: SCTID:181125003
xref: TAO:0000118
xref: VHOG:0000143
xref: Wikipedia:Pituitary_gland
xref: XAO:0000017
xref: ZFA:0000118
[Term]
id: UBERON:0000016
name: endocrine pancreas
def: "The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin." [GO:GO, http://orcid.org/0000-0002-6601-2165]
synonym: "endocrine pancreas" EXACT []
synonym: "pars endocrina pancreatis" EXACT []
xref: BTO:0000650
xref: CALOHA:TS-1302
xref: EFO:0002542
xref: EMAPA:35305
xref: EV:0100129
xref: FMA:16018
xref: MA:0001582
xref: NCIT:C32509
xref: SCTID:361339003
xref: TAO:0001260
xref: VHOG:0000049
xref: Wikipedia:Islets_of_Langerhans
xref: ZFA:0001260
relationship: BFO:0000050 UBERON:0001264 ! part of pancreas
relationship: RO:0002433 UBERON:0001264 ! pancreas
relationship: RO:0002473 UBERON:0000006 ! islet of Langerhans
[Term]
id: UBERON:0000017
name: exocrine pancreas
def: "The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO]." [GOC:GO, http://orcid.org/0000-0002-6601-2165]
synonym: "exocrine pancreas" EXACT []
synonym: "pars exocrina pancreatis" EXACT []
xref: AAO:0010407
xref: BTO:0000434
xref: CALOHA:TS-1241
xref: EMAPA:35328
xref: EV:0100093
xref: FMA:16017
xref: MA:0002415
xref: NCIT:C32546
xref: SCTID:248202004
xref: TAO:0001249
xref: VHOG:0000048
xref: Wikipedia:Exocrine_component_of_pancreas
xref: XAO:0000137
xref: ZFA:0001249
relationship: BFO:0000050 UBERON:0001264 ! part of pancreas
relationship: BFO:0000051 UBERON:0001263 ! has part pancreatic acinus
relationship: RO:0002433 UBERON:0001264 ! pancreas
[Term]
id: UBERON:0000033
name: head
def: "The head is the anterior-most division of the body [GO]." [GO:0060322, Wikipedia:Head]
synonym: "head (volume)" EXACT [FMA:7154]
xref: AAO:0010335
xref: AEO:0000106
xref: BILA:0000115
xref: BIRNLEX:1230
xref: BTO:0000282
xref: CALOHA:TS-0436
xref: EFO:0000964
xref: EHDAA2:0003106
xref: EMAPA:31858
xref: FMA:7154
xref: GAID:61
xref: galen:Head
xref: HAO:0000397
xref: MA:0000023
xref: MAT:0000294
xref: MESH:D006257
xref: MIAA:0000294
xref: NCIT:C12419
xref: SCTID:302548004
xref: SPD:0000016
xref: TAO:0001114
xref: TGMA:0000002
xref: VHOG:0001644
xref: WBbt:0005739
xref: Wikipedia:Head
xref: XAO:0003024
xref: ZFA:0001114
[Term]
id: UBERON:0000056
name: ureter
def: "Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs." [GO:0090189, Wikipedia:Ureter]
xref: AAO:0010254
xref: BTO:0001409
xref: CALOHA:TS-1084
xref: EFO:0000930
xref: EHDAA2:0002139
xref: EHDAA:9341
xref: EMAPA:17950
xref: EV:0100097
xref: FMA:9704
xref: GAID:438
xref: galen:Ureter
xref: MA:0000378
xref: MAT:0000120
xref: MESH:D014513
xref: MIAA:0000120
xref: NCIT:C12416
xref: SCTID:302511008
xref: VHOG:0000605
xref: Wikipedia:Ureter
xref: XAO:0000144
relationship: BFO:0000050 UBERON:0002355 ! part of pelvic region of trunk
relationship: channels_into UBERON:0001255 ! urinary bladder
[Term]
id: UBERON:0000059
name: large intestine
def: "A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]." [ISBN:0073040584, Wikipedia:Large_intestine_(anatomy)]
xref: AAO:0010396
xref: BTO:0000706
xref: CALOHA:TS-1306
xref: EFO:0000840
xref: EMAPA:19252
xref: EV:0100077
xref: FMA:7201
xref: GAID:306
xref: galen:LargeIntestine
xref: MA:0000333
xref: MESH:D007420
xref: MIAA:0000046
xref: NCIT:C12379
xref: SCTID:181254001
xref: VHOG:0000054
xref: Wikipedia:Large_intestine_(anatomy)
xref: XAO:0000131
[Term]
id: UBERON:0000362
name: renal medulla
def: "The inner portion of the kidney consisting of the renal pyramids." [ISBN:0-683-40008-8, MGI:smb, MP:0003014]
synonym: "kidney medulla" EXACT [OBOL:automatic]
synonym: "medulla of kidney" EXACT [OBOL:automatic]
xref: BTO:0001167
xref: CALOHA:TS-1157
xref: EMAPA:19279
xref: GAID:425
xref: galen:MedullaOfKidney
xref: MA:0000373
xref: MESH:D007679
xref: NCIT:C12740
xref: SCTID:30737000
xref: Wikipedia:Renal_medulla
relationship: BFO:0000050 UBERON:0002113 ! part of kidney
relationship: RO:0002433 UBERON:0002113 ! kidney
[Term]
id: UBERON:0000442
name: right testicular vein
def: "A vein that drains the left pampiniform plexus and empties into the left renal vein." [Dorlands_Medical_Dictionary:MerckSource]
synonym: "right spermatic vein" EXACT [MA:0002220]
synonym: "vena testicularis (adrenalis) dextra" EXACT [FMA:14341]
xref: BTO:0002679
xref: FMA:14341
xref: MA:0002220
xref: NCIT:C52697
xref: SCTID:53500001
is_a: UBERON:0001638 ! vein
relationship: RO:0002170 UBERON:0001072 ! connected to posterior vena cava
relationship: RO:0002170 UBERON:0001142 ! connected to left renal vein
relationship: RO:0002170 UBERON:0001330 ! connected to pampiniform plexus
relationship: RO:0002179 UBERON:0000473 ! drains testis
[Term]
id: UBERON:0000443
name: left testicular vein
def: "A vein that drains the right pampiniform plexus and empties into the inferior vena cava." [Dorlands_Medical_Dictionary:MerckSource]
synonym: "left spermatic vein" EXACT [MA:0002219]
xref: BTO:0002680
xref: FMA:14345
xref: MA:0002219
xref: NCIT:C52696
xref: SCTID:90988008
is_a: UBERON:0001638 ! vein
relationship: RO:0002170 UBERON:0001072 ! connected to posterior vena cava
relationship: RO:0002170 UBERON:0001142 ! connected to left renal vein
relationship: RO:0002170 UBERON:0001330 ! connected to pampiniform plexus
relationship: RO:0002179 UBERON:0000473 ! drains testis
[Term]
id: UBERON:0000473
name: testis
def: "A gonad of a male animal. A gonad produces and releases sperm." [http://orcid.org/0000-0002-6601-2165]
synonym: "gonad of male genitalia" EXACT [OBOL:automatic]
synonym: "gonad of male reproductive system" EXACT [OBOL:automatic]
synonym: "male gonad" EXACT [OBOL:automatic]
synonym: "testicle" EXACT [FMA:7210]
xref: AAO:0000606
xref: BILA:0000124
xref: BSA:0000085
xref: BTO:0001363
xref: CALOHA:TS-1030
xref: EFO:0000984
xref: EHDAA2:0002007
xref: EHDAA:8146
xref: EMAPA:17972
xref: EV:0100102
xref: FMA:7210
xref: GAID:396
xref: galen:Testis
xref: HAO:0001007
xref: MA:0000411
xref: MAT:0000132
xref: MESH:D013737
xref: MIAA:0000132
xref: NCIT:C12412
xref: SCTID:181431007
xref: TAO:0000598
xref: VHOG:0000252
xref: WBbt:0006794
xref: Wikipedia:Testis
xref: XAO:0000157
xref: ZFA:0000598
disjoint_from: UBERON:0000992 ! ovary
[Term]
id: UBERON:0000945
name: stomach
def: "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." [https://orcid.org/0000-0002-6601-2165, ISBN:0073040584, Wikipedia:Stomach]
xref: AAO:0000579
xref: ANISEED:1235297
xref: BTO:0001307
xref: CALOHA:TS-0980
xref: EFO:0000837
xref: EHDAA2:0001915
xref: EHDAA:2993
xref: EMAPA:17021
xref: EV:0100070
xref: FMA:7148
xref: GAID:293
xref: galen:Stomach
xref: MA:0000353
xref: MAT:0000051
xref: MESH:D013270
xref: MIAA:0000051
xref: NCIT:C12391
xref: SCTID:181246003
xref: TAO:0002121
xref: VHOG:0000408
xref: Wikipedia:Stomach
xref: XAO:0000128
[Term]
id: UBERON:0000947
name: aorta
def: "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." [http://orcid.org/0000-0002-6601-2165, ISBN:0-683-40008-8, MESH:A07.231.114.056, MP:0000272, Wikipedia:Aorta]
synonym: "trunk of aortic tree" EXACT []
synonym: "trunk of systemic arterial tree" EXACT []
xref: AAO:0010213
xref: BTO:0000135
xref: CALOHA:TS-0046
xref: EFO:0000265
xref: EMAPA:18601
xref: EV:0100027
xref: FMA:3734
xref: GAID:469
xref: galen:Aorta
xref: MA:0000062
xref: MAT:0000035
xref: MESH:D001011
xref: MIAA:0000035
xref: NCIT:C12669
xref: SCTID:181298001
xref: VHOG:0001523
xref: Wikipedia:Aorta
xref: XAO:0003010
is_a: BFO:0000004
relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity
relationship: RO:0002170 UBERON:0002084 ! connected to heart left ventricle
[Term]
id: UBERON:0000948
name: heart
def: "A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Heart]
synonym: "chambered heart" EXACT [https://orcid.org/0000-0002-6601-2165]
synonym: "vertebrate heart" EXACT []
xref: AAO:0010210
xref: BILA:0000020
xref: BTO:0000562
xref: CALOHA:TS-0445
xref: EFO:0000815
xref: EHDAA2:0000738
xref: EHDAA:420
xref: EMAPA:16105
xref: EV:0100018
xref: FMA:7088
xref: GAID:174
xref: galen:Heart
xref: MA:0000072
xref: MAT:0000036
xref: MESH:D006321
xref: MIAA:0000036
xref: NCIT:C12727
xref: SCTID:302509004
xref: TAO:0000114
xref: VHOG:0000276
xref: Wikipedia:Heart
xref: XAO:0000064
xref: ZFA:0000114
relationship: BFO:0000051 UBERON:0004151 ! has part cardiac chamber
[Term]
id: UBERON:0000955
name: brain
def: "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]." [https://github.com/obophenotype/uberon/issues/300, Wikipedia:Brain]
xref: AAO:0010478
xref: ABA:Brain
xref: BAMS:Br
xref: BAMS:Brain
xref: BILA:0000135
xref: BIRNLEX:796
xref: BTO:0000142
xref: CALOHA:TS-0095
xref: DHBA:10155
xref: EFO:0000302
xref: EHDAA2:0000183
xref: EHDAA:2641
xref: EHDAA:6485
xref: EMAPA:16894
xref: EV:0100164
xref: FMA:50801
xref: GAID:571
xref: galen:Brain
xref: HBA:4005
xref: MA:0000168
xref: MAT:0000098
xref: MBA:8
xref: MBA:997
xref: MESH:D001921
xref: MIAA:0000098
xref: NCIT:C12439
xref: PBA:3999
xref: SCTID:258335003
xref: TAO:0000008
xref: VHOG:0000157
xref: Wikipedia:Brain
xref: XAO:0000010
xref: ZFA:0000008
[Term]
id: UBERON:0000970
name: eye
def: "An organ that detects light." [https://orcid.org/0000-0002-6601-2165]
xref: BILA:0000017
xref: BTO:0000439
xref: CALOHA:TS-0309
xref: EFO:0000827
xref: EV:0100336
xref: GAID:69
xref: MAT:0000140
xref: MESH:D005123
xref: MIAA:0000140
xref: Wikipedia:Eye
[Term]
id: UBERON:0000974
name: neck
def: "An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column." [http://orcid.org/0000-0002-6601-2165]
xref: AEO:0000108
xref: BTO:0000420
xref: CALOHA:TS-2045
xref: EFO:0000967
xref: EHDAA2:0003108
xref: EMAPA:35587
xref: FMA:7155
xref: GAID:86
xref: galen:Neck
xref: MA:0000024
xref: MAT:0000297
xref: MESH:D009333
xref: MIAA:0000297
xref: NCIT:C13063
xref: SCTID:302550007
xref: Wikipedia:Neck
relationship: anteriorly_connected_to UBERON:0000033 ! head
[Term]
id: UBERON:0000976
name: humerus
def: "Paired endochondral long bone that extends between the pectoral girdle and the skeletal parts of the forelimb. [PHENOSCAPE:mah]." [AAO:0000679, https://github.com/obophenotype/uberon/issues/106, PHENOSCAPE:mah]
synonym: "humerus bone" EXACT []
xref: AAO:0000679
xref: CALOHA:TS-2202
xref: EFO:0001398
xref: EMAPA:19106
xref: FMA:13303
xref: GAID:183
xref: galen:Humerus
xref: MA:0001356
xref: MESH:D006811
xref: NCIT:C12731
xref: SCTID:181923006
xref: VHOG:0001158
xref: Wikipedia:Humerus
xref: XAO:0003210
relationship: BFO:0000050 UBERON:0001460 ! part of arm
[Term]
id: UBERON:0000978
name: leg
def: "The portion of the hindlimb that contains both the stylopod and zeugopod." [Wikipedia:Leg#Limb]
synonym: "tetrapod leg" EXACT []
xref: BTO:0000721
xref: CALOHA:TS-2206
xref: EFO:0001411
xref: EHDAA2:0000972
xref: EHDAA:5151
xref: EHDAA:6176
xref: EHDAA:8289
xref: EMAPA:17489
xref: GAID:49
xref: MA:0000047
xref: MESH:D035002
xref: VHOG:0000345
xref: Wikipedia:Leg#Limb
relationship: distally_connected_to UBERON:0002387 ! pes
[Term]
id: UBERON:0000985
name: axillary vein
def: "Vein that drains the axilla." [http://orcid.org/0000-0002-6601-2165]
xref: EMAPA:18758
xref: FMA:13329
xref: GAID:527
xref: galen:AxillaryVein
xref: MA:0002084
xref: MESH:D001367
xref: NCIT:C32171
xref: SCTID:181389002
xref: Wikipedia:Axillary_vein
is_a: UBERON:0001638 ! vein
relationship: BFO:0000050 UBERON:0001467 ! part of shoulder
relationship: RO:0002170 UBERON:0001587 ! connected to subclavian vein
[Term]
id: UBERON:0000989
name: penis
def: "An intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination." [http://orcid.org/0000-0002-6601-2165, ISBN:0-683-40008-8, MP:0005187, Wikipedia:Penis]
xref: BTO:0000405
xref: CALOHA:TS-0758
xref: EFO:0000987
xref: EHDAA2:0001433
xref: EHDAA:9380
xref: EMAPA:18682
xref: EMAPA_RETIRED:18996
xref: EV:0100107
xref: FMA:9707
xref: GAID:389
xref: galen:Penis
xref: MA:0000408
xref: MAT:0000186
xref: MESH:D010413
xref: MIAA:0000186
xref: NCIT:C12409
xref: SCTID:265793009
xref: VHOG:0000727
xref: Wikipedia:Penis
[Term]
id: UBERON:0000992
name: ovary
def: "The gonad of a female organism which contains germ cells." [ISBN:0-683-40008-8, MP:0001126, Wikipedia:Ovary]
synonym: "animal ovary" EXACT [EFO:0000973]
synonym: "female gonad" EXACT []
synonym: "female organism genitalia gonad" EXACT [OBOL:automatic]
synonym: "female organism genitalia gonada" EXACT [OBOL:automatic]
synonym: "female organism reproductive system gonad" EXACT [OBOL:automatic]
synonym: "female organism reproductive system gonada" EXACT [OBOL:automatic]
synonym: "female reproductive system gonad" EXACT [OBOL:automatic]
synonym: "female reproductive system gonada" EXACT [OBOL:automatic]
synonym: "genitalia of female organism gonad" EXACT [OBOL:automatic]
synonym: "genitalia of female organism gonada" EXACT [OBOL:automatic]
synonym: "gonad of female organism genitalia" EXACT [OBOL:automatic]
synonym: "gonad of female organism reproductive system" EXACT [OBOL:automatic]
synonym: "gonad of female reproductive system" EXACT [OBOL:automatic]
synonym: "gonad of genitalia of female organism" EXACT [OBOL:automatic]
synonym: "gonad of reproductive system of female organism" EXACT [OBOL:automatic]
synonym: "gonada of female organism genitalia" EXACT [OBOL:automatic]
synonym: "gonada of female organism reproductive system" EXACT [OBOL:automatic]
synonym: "gonada of female reproductive system" EXACT [OBOL:automatic]
synonym: "gonada of genitalia of female organism" EXACT [OBOL:automatic]
synonym: "gonada of reproductive system of female organism" EXACT [OBOL:automatic]
synonym: "reproductive system of female organism gonad" EXACT [OBOL:automatic]
synonym: "reproductive system of female organism gonada" EXACT [OBOL:automatic]
xref: AAO:0000371
xref: BILA:0000125
xref: BSA:0000080
xref: BTO:0000975
xref: CALOHA:TS-0730
xref: EFO:0000973
xref: EHDAA2:0001360
xref: EHDAA:8124
xref: EMAPA:17962
xref: EV:0100111
xref: FMA:7209
xref: GAID:367
xref: MA:0000384
xref: MESH:D010053
xref: MIAA:0000125
xref: NCIT:C12404
xref: SCTID:181464007
xref: TAO:0000403
xref: VHOG:0000251
xref: Wikipedia:Ovary
xref: XAO:0000258
xref: ZFA:0000403
[Term]
id: UBERON:0000995
name: uterus
def: "The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth." [MGI:csmith, MP:0001120]
xref: BTO:0001424
xref: CALOHA:TS-1102
xref: EFO:0000975
xref: EMAPA:29915
xref: EV:0100113
xref: FMA:17558
xref: GAID:172
xref: galen:Uterus
xref: MA:0000389
xref: MAT:0000127
xref: MESH:D014599
xref: MIAA:0000127
xref: NCIT:C12405
xref: SCTID:181452004
xref: VHOG:0001137
xref: Wikipedia:Uterus
[Term]
id: UBERON:0000996
name: vagina
def: "A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Vagina]
xref: BTO:0000243
xref: CALOHA:TS-1103
xref: EFO:0000976
xref: EMAPA:18986
xref: EV:0100117
xref: FMA:19949
xref: GAID:381
xref: galen:Vagina
xref: MA:0000394
xref: MAT:0000128
xref: MESH:D014621
xref: MIAA:0000128
xref: NCIT:C12407
xref: SCTID:181441005
xref: VHOG:0001138
xref: Wikipedia:Vagina
[Term]
id: UBERON:0001043
name: esophagus
def: "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)." [http://www.rivm.nl/interspeciesinfo/inter/oesophagus/, Wikipedia:Esophagus]
synonym: "gullet" EXACT []
synonym: "oesophagus" EXACT []
xref: AAO:0000145
xref: ANISEED:1235301
xref: BTO:0000959
xref: CALOHA:TS-0700
xref: EFO:0000835
xref: EHDAA2:0001285
xref: EHDAA:2937
xref: EMAPA:16833
xref: EV:0100069
xref: FMA:7131
xref: GAID:291
xref: galen:Esophagus
xref: MA:0000352
xref: MAT:0000048
xref: MESH:D004947
xref: MIAA:0000048
xref: NCIT:C12389
xref: SCTID:181245004
xref: TAO:0000204
xref: VHOG:0000450
xref: Wikipedia:Esophagus
xref: XAO:0000127
xref: ZFA:0000204
is_a: BFO:0000004
relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity
[Term]
id: UBERON:0001052
name: rectum
def: "The terminal portion of the intestinal tube, terminating with the anus." [http://orcid.org/0000-0002-6601-2165, ISBN:0-683-40008-8, MP:0000492]
synonym: "terminal portion of intestine" EXACT []
xref: AAO:0010401
xref: BTO:0001158
xref: CALOHA:TS-1180
xref: EFO:0000848
xref: EHDAA2:0001592
xref: EHDAA:5836
xref: EMAPA:17896
xref: EV:0100081
xref: FMA:14544
xref: GAID:311
xref: galen:Rectum
xref: MA:0000336
xref: MAT:0000050
xref: MESH:D012007
xref: MIAA:0000050
xref: NCIT:C12390
xref: SCTID:181261002
xref: VHOG:0001751
xref: Wikipedia:Rectum
xref: XAO:0000238
relationship: BFO:0000050 UBERON:0000059 ! part of large intestine
relationship: BSPO:0001108 UBERON:0000059 ! large intestine
relationship: RO:0002433 UBERON:0000059 ! large intestine
[Term]
id: UBERON:0001064
name: ventral pancreatic duct
def: "A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla." [Wikipedia:Pancreatic_duct]
synonym: "chief pancreatic duct" EXACT [FMA:16003]
synonym: "duct of Wirsung" EXACT [Wikipedia:Pancreatic_duct]
synonym: "main pancreatic duct" EXACT [MA:0000126]
xref: BTO:0002362
xref: EHDAA2:0001396
xref: EHDAA:6905
xref: EMAPA:17510
xref: FMA:16003
xref: GAID:337
xref: MA:0000126
xref: MESH:D010183
xref: NCIT:C12272
xref: RETIRED_EHDAA2:0002177
xref: SCTID:245385001
xref: VHOG:0000256
xref: Wikipedia:Pancreatic_duct
relationship: BFO:0000050 UBERON:0000017 ! part of exocrine pancreas
relationship: RO:0002433 UBERON:0000017 ! exocrine pancreas
[Term]
id: UBERON:0001069
name: head of pancreas
def: "The head of pancreas is a portion of the pancreas that is lodged within the curve of the duodenum, and is flattened anteriorly (from before). The other parts of the pancreas are the body and the tail. Its upper border is overlapped by the superior part of the duodenum and its lower overlaps the horizontal part; its right and left borders overlap in front, and insinuate themselves behind, the descending and ascending parts of the duodenum respectively. [WP,unvetted]." [Wikipedia:Head_of_pancreas]
synonym: "pancreas head" EXACT []
synonym: "pancreatic head" EXACT []
synonym: "right extremity of pancreas" EXACT []
xref: EHDAA2:0001374
xref: EMAPA:17507
xref: FMA:10468
xref: MA:0000122
xref: NCIT:C12269
xref: SCTID:362201006
xref: VHOG:0000448
xref: Wikipedia:Head_of_pancreas
relationship: BFO:0000050 UBERON:0001264 ! part of pancreas
[Term]
id: UBERON:0001070
name: external carotid artery
def: "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]
synonym: "external carotid" EXACT [AAO:0010218]