contributor
type: AnnotationProperty
is metadata tag: true
id: dc-contributor
shorthand: dc-contributor

see also
type: AnnotationProperty
is metadata tag: true
shorthand: seeAlso
id: seeAlso

function_notes
type: AnnotationProperty
is metadata tag: true
has cross-reference: UBPROP:0000009
editor note: This annotation property may be replaced with an annotation property from an external ontology such as IAO
id: function_notes
shorthand: function_notes
definition: Notes on the evolved function of instances of this class.

has_related_synonym
type: AnnotationProperty
label: has related synonym
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/21
definition: An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.

taxon_notes
type: AnnotationProperty
is metadata tag: true
definition: Notes on the how instances of this class vary across species.
id: taxon_notes
has cross-reference: UBPROP:0000008
shorthand: taxon_notes

has_relational_adjective
type: AnnotationProperty
is metadata tag: true
curator note: Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.
shorthand: has_relational_adjective
id: has_relational_adjective
has cross-reference: UBPROP:0000007

fma_set_term
type: AnnotationProperty
is metadata tag: true
id: fma_set_term
shorthand: fma_set_term
has cross-reference: UBPROP:0000202
external_ontology_notes: FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term

homology_notes
type: AnnotationProperty
is metadata tag: true
definition: Notes on the homology status of this class.
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO
shorthand: homology_notes
has cross-reference: UBPROP:0000003
id: homology_notes

axiom_lost_from_external_ontology
type: AnnotationProperty
is metadata tag: true
shorthand: axiom_lost_from_external_ontology
id: axiom_lost_from_external_ontology
has cross-reference: UBPROP:0000002
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO
definition: A textual description of an axiom loss in this ontology compared to an external ontology.

external_definition
type: AnnotationProperty
is metadata tag: true
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO
has cross-reference: UBPROP:0000001
shorthand: external_definition
definition: An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
id: external_definition

never in taxon
type: AnnotationProperty
is class level: true
is metadata tag: true
id: never_in_taxon
definition: x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
has cross-reference: RO:0002161
shorthand: never_in_taxon
example of usage: tooth SubClassOf 'never in taxon' value 'Aves'
OMO_0002000: PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> CONSTRUCT { in_taxon: a owl:ObjectProperty . a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . ?x rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom [ a owl:Class ; owl:complementOf ?taxon ] ] . } WHERE { ?x never_in_taxon: ?taxon . }

has_alternative_id
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty
label: has narrow synonym
definition: An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/19

in_subset
type: AnnotationProperty

editor note
type: AnnotationProperty
is metadata tag: true
id: editor_note
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
has cross-reference: IAO:0000116
shorthand: editor_note

imported from
type: AnnotationProperty

definition
type: AnnotationProperty
editor note: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.

has cross-reference
type: AnnotationProperty
label: database_cross_reference
example of usage: disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string
definition: An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/123
contributor: https://orcid.org/0000-0002-7356-1779

example of usage
type: AnnotationProperty
is metadata tag: true
id: example_of_usage
has cross-reference: IAO:0000112
definition: A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
shorthand: example_of_usage

term tracker item
type: AnnotationProperty
is metadata tag: true
has cross-reference: IAO:0000233
shorthand: term_tracker_item
definition: An IRI or similar locator for a request or discussion of an ontology term.
id: term_tracker_item
comment: The 'tracker item' can associate a tracker with a specific ontology term.
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/

curator note
type: AnnotationProperty
label: curator notes
is metadata tag: true
id: curator_notes
has cross-reference: IAO:0000232
definition: An administrative note of use for a curator but of no use for a user
shorthand: curator_notes

id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty
label: has broad synonym
definition: An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/18

external_ontology_notes
type: AnnotationProperty
is metadata tag: true
definition: Notes on how similar or equivalent classes are represented in other ontologies.
id: external_ontology_notes
editor note: This annotation property may be replaced with an annotation property from an external ontology such as IAO
shorthand: external_ontology_notes
has cross-reference: UBPROP:0000012

development_notes
type: AnnotationProperty
is metadata tag: true
definition: Notes on the ontogenic development of instances of this class.
id: development_notes
has cross-reference: UBPROP:0000011
editor note: This annotation property may be replaced with an annotation property from an external ontology such as IAO
shorthand: development_notes

structure_notes
type: AnnotationProperty
is metadata tag: true
definition: Notes on the structure, composition or histology of instances of this class.
shorthand: structure_notes
has cross-reference: UBPROP:0000010
editor note: This annotation property may be replaced with an annotation property from an external ontology such as IAO
id: structure_notes

mutually spatially disjoint with
type: AnnotationProperty
is metadata tag: true
is class level: true
OMO_0002000: PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> CONSTRUCT { part_of: a owl:ObjectProperty . [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?x ; a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?y ] ] } WHERE { ?x mutually_spatially_disjoint_with: ?y . }
definition: A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.
shorthand: mutually_spatially_disjoint_with
has cross-reference: RO:0002171
id: mutually_spatially_disjoint_with

has_exact_synonym
type: AnnotationProperty
label: has exact synonym
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/20
definition: An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.

shorthand
type: AnnotationProperty

depiction
type: AnnotationProperty
is metadata tag: true
id: depiction
shorthand: depiction

present in taxon
type: AnnotationProperty
is class level: true
is metadata tag: true
has cross-reference: RO:0002175
OMO_0002000: PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?witness rdfs:label ?label . ?witness rdfs:subClassOf ?x . ?witness rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . } WHERE { ?x present_in_taxon: ?taxon . BIND(IRI(CONCAT( "http://purl.obolibrary.org/obo/RO_0002175#", MD5(STR(?x)), "-", MD5(STR(?taxon)) )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) }
id: present_in_taxon
comment: The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology.
definition: S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
shorthand: present_in_taxon

uterine cervix
type: Class
subclass of: organ
has cross-reference: EMAPA:29927
has_related_synonym: cervix of uterus
has cross-reference: UMLS:C0007874
has cross-reference: MESH:D002584
has_exact_synonym: cervical canal of uterus
has_related_synonym: cervical canal
has_exact_synonym: cervix uteri
has cross-reference: BTO:0002249
has_exact_synonym: uterine cervix
has cross-reference: FMA:17740
has cross-reference: NCIT:C12311
has cross-reference: EFO:0000979
homology_notes: The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG]
has cross-reference: GAID:376
has_broad_synonym: cervix
has cross-reference: galen:CervixUteri
has cross-reference: MAT:0000292
id: UBERON:0000002
has_exact_synonym: caudal segment of uterus
external_definition: The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG]
has cross-reference: VHOG:0001359
has cross-reference: Wikipedia:Cervix
has cross-reference: EV:0100114
has cross-reference: SCTID:181453009
has cross-reference: BTO:0001421
has cross-reference: CALOHA:TS-0134
has_exact_synonym: canalis cervicis uteri
has_exact_synonym: neck of uterus
has_relational_adjective: cervical
has cross-reference: MA:0000392
definition: Lower, narrow portion of the uterus where it joins with the top end of the vagina.
in_subset: efo slim
in_subset: human reference atlas
in_subset: human subset
in_subset: mouse subset
in_subset: pheno slim
in_subset: uberon slim
present in taxon: NCBITaxon 9606
imported from: uberon.owl

ureter
type: Class
subclass of: organ
has cross-reference: BTO:0001409
has cross-reference: EHDAA:9341
has cross-reference: MIAA:0000120
homology_notes: The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]
has_related_synonym: metanephric duct
definition: Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs.
id: UBERON:0000056
has cross-reference: UMLS:C0041951
has cross-reference: MAT:0000120
has cross-reference: EFO:0000930
has cross-reference: GAID:438
has cross-reference: NCIT:C12416
has cross-reference: FMA:9704
has cross-reference: galen:Ureter
structure_notes: in humans, consists of adventitial, muscular and mucoa layers
has cross-reference: VHOG:0000605
has cross-reference: AAO:0010254
has cross-reference: EHDAA2:0002139
has cross-reference: MA:0000378
external_definition: Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]
has_relational_adjective: ureteric
has cross-reference: EMAPA:17950
has cross-reference: XAO:0000144
has cross-reference: Wikipedia:Ureter
external_definition: The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
has cross-reference: EV:0100097
has cross-reference: CALOHA:TS-1084
has cross-reference: MESH:D014513
has cross-reference: SCTID:302511008
has_relational_adjective: ureteral
in_subset: efo slim
in_subset: human reference atlas
in_subset: human subset
in_subset: major organ
in_subset: mouse subset
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
present in taxon: NCBITaxon 9606
imported from: uberon.owl

anatomical structure
type: Class
subclass of: anatomical entity
has cross-reference: HAO:0000003
has cross-reference: XAO:0003000
has_exact_synonym: biological structure
has cross-reference: ZFA:0000037
has cross-reference: TGMA:0001823
has cross-reference: AAO:0010825
has cross-reference: FMA:305751
has cross-reference: BILA:0000003
definition: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
has cross-reference: http://dbpedia.org/ontology/AnatomicalStructure
has cross-reference: MA:0003000
has cross-reference: AEO:0000003
has cross-reference: TAO:0000037
has cross-reference: SCTID:362889002
has cross-reference: FMA:67135
has cross-reference: FBbt:00007001
id: UBERON:0000061
has cross-reference: GAID:781
has_exact_synonym: connected biological structure
has cross-reference: CARO:0000003
has cross-reference: FAO:0000001
has cross-reference: EMAPA:0
has cross-reference: EHDAA2:0003003
has cross-reference: VHOG:0001759
has cross-reference: MESH:D000825
in_subset: common anatomy
in_subset: human reference atlas
in_subset: human subset
in_subset: mouse subset
in_subset: upper level
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon_33208
present in taxon: NCBITaxon 4751
present in taxon: NCBITaxon 9606
imported from: uberon.owl

organ
type: Class
subclass of: multicellular anatomical structure
has_related_synonym: element
has cross-reference: EMAPA:35949
has cross-reference: SCTID:272625005
has cross-reference: CARO:0020004
has cross-reference: FMA:67498
has cross-reference: WBbt:0003760
external_ontology_notes: CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
has_related_synonym: body organ
id: UBERON:0000062
has_related_synonym: anatomical unit
has cross-reference: MA:0003001
has cross-reference: NCIT:C13018
has cross-reference: BIRNLEX:4
external_definition: Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
has cross-reference: EFO:0000634
has cross-reference: UMLS:C0178784
definition: Anatomical structure that performs a specific function or group of functions [WP].
has cross-reference: Wikipedia:Organ_(anatomy)
has cross-reference: ENVO:01000162
in_subset: common anatomy
in_subset: human subset
in_subset: mouse subset
in_subset: upper level
never in taxon: NCBITaxon_110815
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon_33208
present in taxon: NCBITaxon 4751
imported from: uberon.owl

embryo stage
type: Class
subclass of: life cycle stage
has cross-reference: OGES:000000
has cross-reference: OGES:000022
has cross-reference: FBdv:00005289
has cross-reference: OcunDv:0000002
has cross-reference: AcarDv:0000002
has cross-reference: WBls:0000102
has cross-reference: WBls:0000003
has cross-reference: CfamDv:0000002
has cross-reference: PtroDv:0000002
has cross-reference: MdomDv:0000002
has cross-reference: OariDv:0000002
has cross-reference: FMA:72652
has cross-reference: XAO:1000012
has cross-reference: CporDv:0000002
has cross-reference: ChirDv:0000002
has cross-reference: MmusDv:0000042
has cross-reference: HsapDv:0000045
has cross-reference: DpseDv:0000002
has cross-reference: WBls:0000092
has cross-reference: GgorDv:0000002
has cross-reference: SsalDv:0000002
has cross-reference: SCTID:296280003
has cross-reference: OanaDv:0000002
has cross-reference: SscrDv:0000002
has_related_synonym: embryogenesis
has cross-reference: RnorDv:0000002
has cross-reference: EV:0300001
has cross-reference: MmulDv:0000002
has cross-reference: BtauDv:0000002
has cross-reference: GgalDv:0000002
has cross-reference: BilaDO:0000002
has cross-reference: EcabDv:0000002
has cross-reference: FcatDv:0000002
has cross-reference: DsimDv:0000002
id: UBERON:0000068
has_exact_synonym: embryonic stage
definition: A life cycle stage that starts with fertilization and ends with the fully formed embryo.
has cross-reference: PpanDv:0000002
imported from: uberon.owl

life cycle stage
type: Class
subclass of: BAO_0003114
has_narrow_synonym: developmental stage
external_ontology_notes: the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
has cross-reference: BILS:0000105
has cross-reference: PtroDv:0000000
has cross-reference: MmulDv:0000000
has cross-reference: ncithesaurus:Developmental_Stage
id: UBERON:0000105
has cross-reference: DpseDv:0000000
has cross-reference: PpanDv:0000000
has cross-reference: XAO:1000000
has cross-reference: DsimDv:0000000
has cross-reference: MESH:D008018
definition: A spatiotemporal region encompassing some part of the life cycle of an organism.
has cross-reference: ZFS:0000000
has cross-reference: PdumDv:0000090
has cross-reference: EFO:0000399
has cross-reference: OanaDv:0000000
has cross-reference: OcunDv:0000000
has cross-reference: CfamDv:0000000
has cross-reference: FMA:24120
has_narrow_synonym: stage
has cross-reference: MdomDv:0000000
has cross-reference: RnorDv:0000000
editor note: this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
has cross-reference: BtauDv:0000000
has cross-reference: ChirDv:0000000
has cross-reference: OariDv:0000000
has cross-reference: ZFS:0100000
has cross-reference: EcabDv:0000000
has cross-reference: CporDv:0000000
has cross-reference: SsalDv:0000000
has cross-reference: SscrDv:0000000
has cross-reference: WBls:0000002
has cross-reference: GgalDv:0000000
has cross-reference: MmusDv:0000000
has cross-reference: FcatDv:0000000
external_ontology_notes: we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
has cross-reference: FBdv:00007012
has cross-reference: GgorDv:0000000
has cross-reference: AcarDv:0000000
has cross-reference: HsapDv:0000000
in_subset: common anatomy
in_subset: efo slim
in_subset: upper level
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon_33208
present in taxon: NCBITaxon 4751
imported from: uberon.owl

gastrula stage
type: Class
subclass of: life cycle stage
has cross-reference: OGES:000019
has cross-reference: FBdv:00005317
has cross-reference: RnorDv:0000005
has cross-reference: ChirDv:0000011
has cross-reference: SscrDv:0000090
definition: A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
has_related_synonym: trilaminar blastocyst stage
has cross-reference: WBls:0000010
has cross-reference: OGES:000004
has cross-reference: GgalDv:0000092
has_related_synonym: trilaminar stage
has cross-reference: SsalDv:0000016
has cross-reference: EFO:0001296
has cross-reference: MmusDv:0000013
has cross-reference: OariDv:0000026
has cross-reference: BILS:0000109
has cross-reference: XAO:1000005
has cross-reference: HsapDv:0000010
has cross-reference: BilaDO:0000008
has_related_synonym: trilaminar blastoderm stage
has_related_synonym: trilaminar germ stage
has cross-reference: ZFS:0000047
has_related_synonym: trilaminar disk stage
id: UBERON:0000109
has_related_synonym: blastocystis trilaminaris stage
in_subset: efo slim
imported from: uberon.owl

post-juvenile adult stage
type: Class
subclass of: life cycle stage
has cross-reference: FcatDv:0000004
has cross-reference: ZFS:0000044
has cross-reference: EV:0300070
has cross-reference: BtauDv:0000004
has cross-reference: HsapDv:0000258
has cross-reference: CfamDv:0000004
has_broad_synonym: adult stage
has cross-reference: OanaDv:0000004
has cross-reference: AcarDv:0000004
definition: The stage of being a sexually mature adult animal.
has cross-reference: ChirDv:0000035
has cross-reference: GgorDv:0000006
has cross-reference: MdomDv:0000006
has cross-reference: MmusDv:0000110
has cross-reference: EV:0300064
has cross-reference: PtroDv:0000011
has cross-reference: BILS:0000113
has cross-reference: GgalDv:0000006
has cross-reference: EcabDv:0000004
has cross-reference: SsalDv:0000042
has cross-reference: CporDv:0000004
has cross-reference: SscrDv:0000006
id: UBERON:0000113
has cross-reference: OcunDv:0000004
has cross-reference: OGES:000027
has cross-reference: OGES:000026
has cross-reference: PpanDv:0000016
has cross-reference: MmulDv:0000021
has cross-reference: XAO:1000093
has cross-reference: RnorDv:0000015
has cross-reference: MIAA:0000403
has cross-reference: OariDv:0000006
imported from: uberon.owl

intestine
type: Class
subclass of: organ
has cross-reference: ZFA:0001338
has cross-reference: BTO:0000648
id: UBERON:0000160
has_related_synonym: intestinal tract
has cross-reference: galen:Intestine
has cross-reference: XAO:0000129
has cross-reference: AAO:0000246
has cross-reference: UMLS:C0021853
has cross-reference: EV:0100071
taxon_notes: In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type.
has cross-reference: WBbt:0005772
has_exact_synonym: bowel
external_definition: Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
has cross-reference: EFO:0000834
has cross-reference: SCTID:256876008
has cross-reference: TAO:0001338
has cross-reference: FMA:7199
editor note: This class is probably too inclusive
has cross-reference: NCIT:C12736
has cross-reference: MA:0000328
has cross-reference: GAID:295
has cross-reference: MIAA:0000043
has cross-reference: ANISEED:1235303
definition: Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.
has cross-reference: EMAPA:32874
has cross-reference: CALOHA:TS-0490
external_definition: The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
has cross-reference: BSA:0000093
has cross-reference: MA:0001524
has cross-reference: VHOG:0000056
has cross-reference: MESH:D007422
has_relational_adjective: intestinal
has cross-reference: Wikipedia:Intestine
in_subset: efo slim
in_subset: human subset
in_subset: mouse subset
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
imported from: uberon.owl

blood
type: Class
subclass of: hemolymphoid system
has cross-reference: XAO:0000124
curator note: This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
external_definition: A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
has cross-reference: MA:0000059
has cross-reference: CALOHA:TS-0079
id: UBERON:0000178
has_exact_synonym: vertebrate blood
has cross-reference: EV:0100047
has cross-reference: EHDAA:418
has cross-reference: EFO:0000296
has cross-reference: BTO:0000089
has cross-reference: NCIT:C12434
has cross-reference: MESH:D001769
has cross-reference: EMAPA:16332
has cross-reference: AAO:0000046
has cross-reference: Wikipedia:Blood
has_related_synonym: whole blood
has_exact_synonym: portion of blood
homology_notes: Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
has cross-reference: UMLS:C0005767
has cross-reference: ZFA:0000007
has cross-reference: ENVO:02000027
has cross-reference: galen:Blood
definition: A fluid that is composed of blood plasma and erythrocytes.
has cross-reference: GAID:965
external_definition: Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
has cross-reference: EHDAA2:0000176
has cross-reference: FMA:9670
has cross-reference: VHOG:0000224
has cross-reference: TAO:0000007
axiom_lost_from_external_ontology: relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
has cross-reference: MIAA:0000315
in_subset: efo slim
in_subset: human reference atlas
in_subset: human subset
in_subset: mouse subset
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
present in taxon: NCBITaxon 9606
imported from: uberon.owl
contributor: https://orcid.org/0000-0002-6601-2165
contributor: https://orcid.org/0000-0003-1980-3228

breast
type: Class
subclass of: multicellular anatomical structure
has cross-reference: MESH:D001940
definition: The upper ventral region of the torso of an organism.
has cross-reference: GAID:33
has cross-reference: UMLS:C0006141
id: UBERON:0000310
taxon_notes: The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's.
has cross-reference: galen:Breast
has_exact_synonym: mammary region
has_related_synonym: mamma
has cross-reference: SCTID:181131000
has cross-reference: Wikipedia:Breast
has cross-reference: NCIT:C12971
has_exact_synonym: mammary part of chest
has cross-reference: FMA:9601
has cross-reference: BTO:0000149
has cross-reference: EV:0100124
has cross-reference: CALOHA:TS-2083
in_subset: human subset
in_subset: mouse subset
in_subset: pheno slim
imported from: uberon.owl

organism substance
type: Class
subclass of: anatomical entity
has cross-reference: XAO:0004001
has cross-reference: FBbt:00007019
has cross-reference: TGMA:0001824
has cross-reference: AEO:0000004
has cross-reference: TAO:0001487
has cross-reference: MA:0002450
has cross-reference: SPD:0000008
has_exact_synonym: body substance
has cross-reference: BILA:0000004
has cross-reference: VHOG:0001726
definition: Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
has cross-reference: EMAPA:35178
has_exact_synonym: organism substance
id: UBERON:0000463
has_exact_synonym: body fluid or substance
has cross-reference: FMA:9669
has cross-reference: AAO:0010839
has_exact_synonym: portion of organism substance
has cross-reference: galen:BodySubstance
has cross-reference: NCIT:C13236
has cross-reference: ZFA:0001487
has cross-reference: CARO:0000004
has cross-reference: EHDAA2:0003004
has cross-reference: CALOHA:TS-2101
has cross-reference: HAO:0000004
has_exact_synonym: portion of body substance
in_subset: common anatomy
in_subset: human subset
in_subset: mouse subset
in_subset: pheno slim
in_subset: upper level
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon_33208
present in taxon: NCBITaxon 4751
imported from: uberon.owl

anatomical system
type: Class
subclass of: anatomical structure
has_exact_synonym: organ system
has cross-reference: FBbt:00004856
has cross-reference: FMA:7149
has cross-reference: UMLS:C0460002
has cross-reference: AAO:0000007
has cross-reference: MA:0000003
has_exact_synonym: connected anatomical system
has cross-reference: galen:AnatomicalSystem
has cross-reference: NCIT:C12919
has_broad_synonym: system
has_related_synonym: anatomical systems
has cross-reference: EHDAA:392
has cross-reference: CARO:0000011
has cross-reference: WBbt:0005746
has cross-reference: TAO:0001439
has cross-reference: ZFA:0001439
has cross-reference: HAO:0000011
id: UBERON:0000467
has_exact_synonym: body system
has cross-reference: IDOMAL:0002460
has cross-reference: TGMA:0001831
has cross-reference: BSA:0000049
has cross-reference: EV:0100000
has cross-reference: AEO:0000011
has cross-reference: CALOHA:TS-2088
has cross-reference: BILA:0000011
has cross-reference: EMAPA:16103
definition: Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
has cross-reference: SCTID:278195005
has cross-reference: Wikipedia:Organ_system
has cross-reference: VHOG:0001725
has cross-reference: WBbt:0005763
has cross-reference: EHDAA2:0003011
has cross-reference: BIRNLEX:14
has cross-reference: XAO:0003002
in_subset: common anatomy
in_subset: human reference atlas
in_subset: human subset
in_subset: mouse subset
in_subset: pheno slim
in_subset: uberon slim
in_subset: upper level
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon_33208
present in taxon: NCBITaxon 4751
present in taxon: NCBITaxon 9606
imported from: uberon.owl

testis
type: Class
subclass of: organ
has_related_synonym: orchis
has cross-reference: EHDAA2:0002007
has cross-reference: BILA:0000124
has cross-reference: EHDAA:8146
homology_notes: (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]
taxon_notes: The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally
has cross-reference: MA:0000411
has cross-reference: MIAA:0000132
has_related_synonym: testiculus
has cross-reference: FBbt:00004928
has_related_synonym: testes
has cross-reference: CALOHA:TS-1030
has cross-reference: EV:0100102
has cross-reference: EMAPA:17972
has cross-reference: TAO:0000598
has_exact_synonym: gonad of male reproductive system
has cross-reference: MESH:D013737
has cross-reference: ZFA:0000598
id: UBERON:0000473
has_relational_adjective: testicular
has cross-reference: galen:Testis
has cross-reference: NCIT:C12412
has cross-reference: Wikipedia:Testis
has cross-reference: GAID:396
has cross-reference: FMA:7210
has cross-reference: VHOG:0000252
has cross-reference: XAO:0000157
has cross-reference: HAO:0001007
has cross-reference: EFO:0000984
has cross-reference: SCTID:181431007
has cross-reference: MAT:0000132
has cross-reference: WBbt:0006794
has_exact_synonym: testicle
definition: A gonad of a male animal. A gonad produces and releases sperm.
has_exact_synonym: male gonad
has cross-reference: BTO:0001363
has_exact_synonym: gonad of male genitalia
has cross-reference: UMLS:C0039597
external_definition: Male reproductive organ.[TAO]
has cross-reference: AAO:0000606
has cross-reference: BSA:0000085
has_alternative_id: UBERON:0002117
in_subset: efo slim
in_subset: human subset
in_subset: mouse subset
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
imported from: uberon.owl

tissue
type: Class
subclass of: multicellular anatomical structure
has cross-reference: HAO:0000043
has cross-reference: XAO:0003040
has cross-reference: galen:Tissue
has cross-reference: VHOG:0001757
has cross-reference: NCIT:C12801
has cross-reference: EHDAA2:0003043
has_narrow_synonym: simple tissue
has cross-reference: TAO:0001477
has cross-reference: CARO:0000043
has cross-reference: FBbt:00007003
has cross-reference: AAO:0000607
has cross-reference: AAO:0010054
id: UBERON:0000479
has cross-reference: AEO:0000043
has cross-reference: CALOHA:TS-2090
has cross-reference: MESH:D014024
has cross-reference: FMA:9637
has cross-reference: EMAPA:35868
definition: Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
has cross-reference: TGMA:0001844
has cross-reference: ZFA:0001477
has cross-reference: MA:0003002
editor note: changed label and definition to reflect CARO2
has_exact_synonym: portion of tissue
has cross-reference: BIRNLEX:19
has_exact_synonym: tissue portion
has cross-reference: UMLS:C0040300
has cross-reference: WBbt:0005729
has cross-reference: BILA:0000043
in_subset: common anatomy
in_subset: human subset
in_subset: mouse subset
in_subset: pheno slim
in_subset: upper level
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon_33208
present in taxon: NCBITaxon 4751
imported from: uberon.owl

stomach
type: Class
subclass of: organ
has cross-reference: MA:0000353
taxon_notes: We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa
id: UBERON:0000945
has cross-reference: MIAA:0000051
has cross-reference: FMA:7148
has cross-reference: EMAPA:17021
has_related_synonym: ventriculus
has cross-reference: CALOHA:TS-0980
has cross-reference: EHDAA:2993
has cross-reference: XAO:0000128
definition: 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.
has cross-reference: EV:0100070
has cross-reference: EHDAA2:0001915
has cross-reference: BTO:0001307
has_related_synonym: mesenteron
has cross-reference: GAID:293
has cross-reference: SCTID:181246003
has cross-reference: Wikipedia:Stomach
has_narrow_synonym: stomach chamber
has cross-reference: AAO:0000579
has cross-reference: MESH:D013270
has cross-reference: NCIT:C12391
has cross-reference: VHOG:0000408
has_related_synonym: anterior intestine
has cross-reference: ANISEED:1235297
external_definition: Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
has_related_synonym: gaster
has cross-reference: galen:Stomach
has cross-reference: MAT:0000051
homology_notes: It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]
has cross-reference: EFO:0000837
has cross-reference: TAO:0002121
has cross-reference: UMLS:C0038351
in_subset: efo slim
in_subset: human reference atlas
in_subset: human subset
in_subset: major organ
in_subset: mouse subset
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
never in taxon: NCBITaxon 7864
never in taxon: NCBITaxon 7878
never in taxon: NCBITaxon 7955
never in taxon: NCBITaxon 9259
present in taxon: NCBITaxon 9606
imported from: uberon.owl

brain
type: Class
subclass of: nervous system
has cross-reference: NCIT:C12439
external_definition: The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
editor note: requires review for applicability to invertebrate structures, e.g. synganglion
has cross-reference: DHBA:10155
has cross-reference: GAID:571
has cross-reference: EMAPA:16894
has cross-reference: BTO:0000142
external_definition: Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
has cross-reference: MESH:D001921
has cross-reference: EHDAA:6485
has cross-reference: CALOHA:TS-0095
has cross-reference: VHOG:0000157
has cross-reference: EHDAA2:0000183
has cross-reference: XAO:0000010
has cross-reference: BAMS:Brain
has_related_synonym: suprasegmental levels of nervous system
has cross-reference: Wikipedia:Brain
has cross-reference: FMA:50801
homology_notes: (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
has cross-reference: MBA:997
has cross-reference: SCTID:258335003
has cross-reference: EHDAA:2641
has cross-reference: BAMS:Br
has_related_synonym: synganglion
has cross-reference: galen:Brain
has cross-reference: TAO:0000008
has cross-reference: MBA:8
external_definition: Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
has cross-reference: BILA:0000135
has cross-reference: EV:0100164
has cross-reference: EFO:0000302
has cross-reference: HBA:4005
has cross-reference: MAT:0000098
has cross-reference: UMLS:C0006104
has cross-reference: PBA:3999
has cross-reference: ABA:Brain
has cross-reference: FBbt:00005095
has cross-reference: ZFA:0000008
definition: 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].
has cross-reference: MIAA:0000098
has cross-reference: AAO:0010478
id: UBERON:0000955
has cross-reference: neuronames:21
has cross-reference: BIRNLEX:796
has_related_synonym: suprasegmental structures
has_related_synonym: encephalon
has_related_synonym: the brain
has cross-reference: UMLS:C1269537
has cross-reference: MA:0000168
in_subset: cumbo
in_subset: efo slim
in_subset: human reference atlas
in_subset: human subset
in_subset: major organ
in_subset: mouse subset
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
present in taxon: NCBITaxon 9606
imported from: uberon.owl
contributor: https://orcid.org/0000-0002-6601-2165

ovary
type: Class
subclass of: organ
has cross-reference: UMLS:C0029939
has cross-reference: XAO:0000258
has_exact_synonym: gonada of female organism genitalia
homology_notes: (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]
has cross-reference: ZFA:0000403
has cross-reference: GAID:367
external_definition: Female reproductive organ.[TAO]
has_exact_synonym: gonada of genitalia of female organism
definition: The gonad of a female organism which contains germ cells.
has_exact_synonym: female organism reproductive system gonad
has cross-reference: AAO:0000371
has cross-reference: BTO:0000975
has cross-reference: Wikipedia:Ovary
has_exact_synonym: female organism reproductive system gonada
has cross-reference: FBbt:00004865
has_exact_synonym: female reproductive system gonad
has_exact_synonym: female reproductive system gonada
has_exact_synonym: reproductive system of female organism gonada
has_exact_synonym: animal ovary
has cross-reference: BSA:0000080
has_exact_synonym: gonada of female organism reproductive system
has cross-reference: EHDAA2:0001360
has_exact_synonym: genitalia of female organism gonad
has_exact_synonym: female organism genitalia gonada
has cross-reference: BILA:0000125
has_exact_synonym: gonad of female organism genitalia
has_related_synonym: ovarium
has_exact_synonym: gonad of reproductive system of female organism
has_relational_adjective: ovarian
has_exact_synonym: female gonad
has cross-reference: EMAPA:17962
has cross-reference: FMA:7209
has cross-reference: EFO:0000973
has cross-reference: MA:0000384
has cross-reference: SCTID:181464007
has_related_synonym: ovaries
has_exact_synonym: gonad of female reproductive system
has cross-reference: VHOG:0000251
has_exact_synonym: gonad of female organism reproductive system
has cross-reference: TAO:0000403
has_exact_synonym: gonada of female reproductive system
has_exact_synonym: ovum-producing ovary
has cross-reference: EV:0100111
has cross-reference: NCIT:C12404
has cross-reference: MESH:D010053
has_exact_synonym: genitalia of female organism gonada
has_exact_synonym: female organism genitalia gonad
id: UBERON:0000992
has cross-reference: CALOHA:TS-0730
has_exact_synonym: reproductive system of female organism gonad
has_exact_synonym: gonad of genitalia of female organism
has cross-reference: EHDAA:8124
external_definition: Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]
has_exact_synonym: gonada of reproductive system of female organism
taxon_notes: Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo
has cross-reference: MIAA:0000125
in_subset: efo slim
in_subset: human reference atlas
in_subset: human subset
in_subset: mouse subset
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
present in taxon: NCBITaxon 9606
imported from: uberon.owl

uterus
type: Class
subclass of: organ
has cross-reference: NCIT:C12405
has cross-reference: EMAPA:29915
has cross-reference: EV:0100113
definition: The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth.
has cross-reference: EFO:0000975
has cross-reference: MA:0000389
has cross-reference: BTO:0001424
has cross-reference: galen:Uterus
has cross-reference: MAT:0000127
external_definition: The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG]
id: UBERON:0000995
has cross-reference: VHOG:0001137
homology_notes: An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]
has cross-reference: MESH:D014599
has cross-reference: Wikipedia:Uterus
has cross-reference: SCTID:181452004
has cross-reference: MIAA:0000127
development_notes: Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus]
has cross-reference: GAID:172
has_relational_adjective: uterine
has cross-reference: CALOHA:TS-1102
has cross-reference: UMLS:C0042149
has cross-reference: FMA:17558
taxon_notes: Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream.
in_subset: efo slim
in_subset: human reference atlas
in_subset: human subset
in_subset: mouse subset
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
present in taxon: NCBITaxon 9606
imported from: uberon.owl

mammalian vulva
type: Class
subclass of: organ
has cross-reference: BTO:0003101
has_exact_synonym: puboperineal region
has cross-reference: EFO:0000978
has_exact_synonym: mammalian vulva
has_related_synonym: pudendum femininum
has_relational_adjective: vulval
has cross-reference: UMLS:C0042993
has_exact_synonym: female pudendum
has cross-reference: SCTID:265796001
has cross-reference: GAID:383
has cross-reference: EV:0100118
has cross-reference: NCIT:C12408
has cross-reference: FMA:20462
has cross-reference: MIAA:0000169
has cross-reference: MA:0000395
has cross-reference: MAT:0000169
has cross-reference: EMAPA:36631
has_related_synonym: pudendum muliebre
definition: External genital organs of the female mammal[WP].
has cross-reference: CALOHA:TS-1168
has cross-reference: VHOG:0001458
id: UBERON:0000997
external_definition: The external genital organs of the female, including the labia majora, labia minora, clitoris, and vestibule of the vagina. [TFD][VHOG]
has_exact_synonym: vulva
has_exact_synonym: pudendum femininum
has cross-reference: Wikipedia:Vulva
has cross-reference: galen:Vulva
has_related_synonym: pudendum
has cross-reference: MESH:D014844
in_subset: efo slim
in_subset: human subset
in_subset: mouse subset
in_subset: pheno slim
in_subset: uberon slim
imported from: uberon.owl

nervous system
type: Class
subclass of: anatomical system
has_related_synonym: systema nervosum
has cross-reference: Wikipedia:Nervous_system
has cross-reference: XAO:0000177
id: UBERON:0001016
has_exact_synonym: neurological system
has cross-reference: AAO:0000324
has cross-reference: NCIT:C12755
has_relational_adjective: nervous
has cross-reference: UMLS:C0027763
has cross-reference: FMA:7157
has_narrow_synonym: nerve net
has cross-reference: MAT:0000026
has cross-reference: CALOHA:TS-1313
has cross-reference: MA:0000016
external_definition: Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
has cross-reference: BILA:0000079
has cross-reference: BIRNLEX:844
has cross-reference: GAID:466
has cross-reference: EHDAA2:0001246
has cross-reference: SCTID:278196006
has cross-reference: TAO:0000396
has cross-reference: ZFA:0000396
has cross-reference: EV:0100162
definition: The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
has cross-reference: MIAA:0000026
external_definition: A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
has cross-reference: WBbt:0005735
has cross-reference: EFO:0000802
has cross-reference: neuronames:3236
has cross-reference: EMAPA:16469
has cross-reference: VHOG:0000402
homology_notes: Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
has cross-reference: BTO:0001484
has cross-reference: FBbt:00005093
has_relational_adjective: neural
has cross-reference: MESH:D009420
has cross-reference: EHDAA:826
in_subset: cumbo
in_subset: efo slim
in_subset: human reference atlas
in_subset: human subset
in_subset: mouse subset
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
never in taxon: NCBITaxon 6040
present in taxon: NCBITaxon 9606
imported from: uberon.owl

esophagus
type: Class
subclass of: organ
has cross-reference: EHDAA2:0001285
has cross-reference: NCIT:C12389
has_relational_adjective: esophageal
external_definition: Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO]
homology_notes: The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG]
has cross-reference: MA:0000352
has cross-reference: MAT:0000048
has_exact_synonym: oesophagus
has_exact_synonym: gullet
has cross-reference: ZFA:0000204
has cross-reference: AAO:0000145
has cross-reference: MIAA:0000048
has cross-reference: EMAPA:16833
has cross-reference: GAID:291
has cross-reference: SCTID:181245004
has cross-reference: TAO:0000204
has cross-reference: EV:0100069
has cross-reference: UMLS:C0014876
has cross-reference: CALOHA:TS-0700
has cross-reference: VHOG:0000450
definition: 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).
id: UBERON:0001043
has cross-reference: BTO:0000959
has cross-reference: EFO:0000835
has cross-reference: Wikipedia:Esophagus
has cross-reference: EHDAA:2937
has cross-reference: MESH:D004947
has cross-reference: ANISEED:1235301
has cross-reference: galen:Esophagus
has cross-reference: XAO:0000127
has cross-reference: FMA:7131
external_ontology_notes: esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995)
in_subset: efo slim
in_subset: human reference atlas
in_subset: human subset
in_subset: major organ
in_subset: mouse subset
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
present in taxon: NCBITaxon 9606
imported from: uberon.owl

anatomical entity
type: Class
subclass of: BAO_0003114
has cross-reference: UMLS:C1515976
has cross-reference: ZFA:0100000
has cross-reference: BFO:0000004
has cross-reference: MA:0000001
definition: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
has cross-reference: HAO:0000000
has cross-reference: CARO:0000000
has cross-reference: TAO:0100000
id: UBERON:0001062
has cross-reference: TGMA:0001822
has cross-reference: EHDAA2:0002229
has cross-reference: NCIT:C12219
has cross-reference: AAO:0010841
has cross-reference: AEO:0000000
has cross-reference: XAO:0000000
has cross-reference: WBbt:0000100
has cross-reference: FBbt:10000000
has cross-reference: FMA:62955
has cross-reference: BILA:0000000
has cross-reference: BIRNLEX:6
in_subset: common anatomy
in_subset: human subset
in_subset: mouse subset
in_subset: upper level
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon_33208
present in taxon: NCBITaxon 4751
imported from: uberon.owl

urinary bladder
type: Class
subclass of: organ
has cross-reference: NCIT:C12414
external_definition: Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]
has_related_synonym: urocyst
has_broad_synonym: bladder
has cross-reference: GAID:0000004
has cross-reference: MIAA:0000122
definition: Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
has cross-reference: Wikipedia:Urinary_bladder
has cross-reference: MESH:D001743
has cross-reference: CALOHA:TS-1090
has cross-reference: XAO:0000154
has cross-reference: MA:0000380
has cross-reference: EV:0100098
has_related_synonym: vesica
has cross-reference: EHDAA:9328
has cross-reference: galen:UrinaryBladder
has cross-reference: EMAPA:18321
homology_notes: In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]
has cross-reference: MAT:0000122
external_definition: A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
has cross-reference: SCTID:302512001
has cross-reference: UMLS:C0005682
has cross-reference: EFO:0000290
id: UBERON:0001255
has_relational_adjective: vesical
has cross-reference: AAO:0000623
has cross-reference: BTO:0001418
has cross-reference: VHOG:0000740
has_exact_synonym: vesica urinaria
has cross-reference: FMA:15900
has cross-reference: EHDAA2:0000174
taxon_notes: The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454]
in_subset: efo slim
in_subset: human reference atlas
in_subset: human subset
in_subset: major organ
in_subset: mouse subset
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
never in taxon: NCBITaxon 8782
present in taxon: NCBITaxon 9606
imported from: uberon.owl

pancreas
type: Class
subclass of: organ
taxon_notes: The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm
has cross-reference: ZFA:0000140
has cross-reference: UMLS:C0030274
has cross-reference: BTO:0000988
function_notes: 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
has cross-reference: EHDAA2:0001367
has cross-reference: CALOHA:TS-0736
has cross-reference: EV:0100092
has cross-reference: SCTID:181277001
has cross-reference: AAO:0010112
external_definition: Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]
definition: An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO].
id: UBERON:0001264
has cross-reference: MA:0000120
has cross-reference: GAID:334
has cross-reference: EFO:0000855
has cross-reference: MESH:D010179
has cross-reference: EHDAA:6893
has cross-reference: NCIT:C12393
has cross-reference: Wikipedia:Pancreas
has_relational_adjective: pancreatic
has cross-reference: XAO:0000136
homology_notes: In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]
has cross-reference: EMAPA:17503
has cross-reference: TAO:0000140
has cross-reference: MIAA:0000075
has cross-reference: galen:Pancreas
has cross-reference: FMA:7198
has cross-reference: MAT:0000075
taxon_notes: As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52)
has cross-reference: VHOG:0000050
in_subset: efo slim
in_subset: human reference atlas
in_subset: human subset
in_subset: major organ
in_subset: mouse subset
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
present in taxon: NCBITaxon 9606
imported from: uberon.owl

skeletal system
type: Class
subclass of: anatomical system
has cross-reference: VHOG:0001254
external_definition: Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]
has_narrow_synonym: set of all bones and joints
has cross-reference: MA:0000018
has cross-reference: CALOHA:TS-1320
has cross-reference: NCIT:C12788
has cross-reference: TAO:0000434
external_definition: System that provides physical support to the organism.[AAO]
homology_notes: By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]
has_exact_synonym: skeleton system
has_relational_adjective: skeletal
has cross-reference: EHDAA2:0003168
has_related_synonym: Skelettsystem
has cross-reference: AAO:0000566
has cross-reference: BTO:0001486
has cross-reference: UMLS:C0037253
has cross-reference: ZFA:0000434
has cross-reference: VSAO:0000027
has cross-reference: FMA:23881
has cross-reference: XAO:0003060
external_ontology_notes: GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates
definition: Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.
id: UBERON:0001434
external_definition: Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]
has cross-reference: EMAPA:35773
has cross-reference: EFO:0000806
in_subset: efo slim
in_subset: human reference atlas
in_subset: human subset
in_subset: mouse subset
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
present in taxon: NCBITaxon 9606
mutually spatially disjoint with: nervous system
imported from: uberon.owl

bone element
type: Class
subclass of: skeletal system
definition: Skeletal element that is composed of bone tissue.
has cross-reference: galen:Bone
id: UBERON:0001474
has cross-reference: MAT:0000299
has cross-reference: SCTID:90780006
has cross-reference: EFO:0000298
has cross-reference: FMA:30317
has cross-reference: EMAPA:32782
has cross-reference: EHDAA2:0003082
has cross-reference: XAO:0000169
has cross-reference: VHOG:0001190
has cross-reference: ENVO:00002039
has cross-reference: AEO:0000082
has cross-reference: FMA:5018
external_definition: Skeletal element that is composed of bone tissue.[VSAO]
has_related_synonym: bones
has cross-reference: VSAO:0000057
external_definition: Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]
homology_notes: The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]
has cross-reference: MIAA:0000299
has cross-reference: NCIT:C12366
has cross-reference: CALOHA:TS-0088
has cross-reference: MA:0001459
has cross-reference: TAO:0001514
has cross-reference: AAO:0000047
has_related_synonym: bone
has cross-reference: BTO:0000140
has cross-reference: EV:0100140
has cross-reference: ZFA:0001514
external_definition: Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]
has cross-reference: Wikipedia:Bone
has cross-reference: GAID:92
axiom_lost_from_external_ontology: relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
has cross-reference: UMLS:C0262950
has_exact_synonym: bone organ
in_subset: efo slim
in_subset: human subset
in_subset: major organ
in_subset: mouse subset
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
mutually spatially disjoint with: UBERON_0001015
mutually spatially disjoint with: UBERON_0001630
mutually spatially disjoint with: muscle tissue
imported from: uberon.owl

blood plasma
type: Class
subclass of: blood
has cross-reference: MESH:D010949
has cross-reference: Wikipedia:Blood_plasma
has cross-reference: EMAPA:35690
has cross-reference: MIAA:0000052
has cross-reference: NCIT:C13356
has cross-reference: MAT:0000052
has_exact_synonym: portion of blood plasma
has_broad_synonym: portion of plasma
has cross-reference: FMA:62970
has_broad_synonym: plasma
has cross-reference: CALOHA:TS-0800
definition: The liquid component of blood, in which erythrocytes are suspended.
has cross-reference: BTO:0000131
id: UBERON:0001969
has_exact_synonym: blood plasm
has cross-reference: EFO:0001905
has cross-reference: GAID:1178
has cross-reference: UMLS:C0032105
has cross-reference: MA:0002501
in_subset: efo slim
in_subset: human subset
in_subset: mouse subset
in_subset: pheno slim
in_subset: uberon slim
imported from: uberon.owl

blood serum
type: Class
subclass of: blood
has cross-reference: MESH:D044967
has cross-reference: UMLS:C0229671
has cross-reference: EHDAA2:0004728
has_exact_synonym: serum
has cross-reference: FMA:63083
definition: The portion of blood plasma that excludes clotting factors.
has cross-reference: MA:0002502
has cross-reference: BTO:0001239
has cross-reference: NCIT:C13325
has cross-reference: Wikipedia:Serum_(blood)
has cross-reference: BTO:0000133
has cross-reference: CALOHA:TS-0923
id: UBERON:0001977
has cross-reference: EMAPA:35770
in_subset: human subset
in_subset: mouse subset
in_subset: pheno slim
in_subset: uberon slim
imported from: uberon.owl

thyroid gland
type: Class
subclass of: organ
has cross-reference: CALOHA:TS-1047
has cross-reference: EHDAA:2148
has cross-reference: NCIT:C12400
has cross-reference: BTO:0001379
has cross-reference: EV:0100133
has cross-reference: GAID:465
has cross-reference: EFO:0000861
has_exact_synonym: thyroid
taxon_notes: In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine)
has cross-reference: galen:ThyroidGland
has cross-reference: XAO:0000162
has cross-reference: UMLS:C0040132
has cross-reference: MA:0000129
has cross-reference: AAO:0010544
has cross-reference: MESH:D013961
taxon_notes: In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species
has cross-reference: MAT:0000081
has cross-reference: SCTID:181117000
has cross-reference: EHDAA:2975
has_related_synonym: glandula thyroidea
homology_notes: (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG]
taxon_notes: In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes
external_definition: Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO]
id: UBERON:0002046
has cross-reference: FMA:9603
has cross-reference: EMAPA:17068
has cross-reference: EHDAA2:0002028
has cross-reference: VHOG:0000418
definition: A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO].
has cross-reference: Wikipedia:Thyroid
has cross-reference: MIAA:0000081
in_subset: efo slim
in_subset: human subset
in_subset: mouse subset
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
imported from: uberon.owl

lung
type: Class
subclass of: organ
has cross-reference: SCTID:181216001
has cross-reference: MAT:0000135
id: UBERON:0002048
has cross-reference: UMLS:C0024109
has_relational_adjective: pulmonary
has cross-reference: EHDAA2:0001042
has cross-reference: galen:Lung
has cross-reference: MA:0000415
has cross-reference: EMAPA:16728
comment: Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
has cross-reference: GAID:345
has cross-reference: NCIT:C12468
taxon_notes: respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi
has cross-reference: MIAA:0000135
has cross-reference: Wikipedia:Lung
definition: Respiration organ that develops as an outpocketing of the esophagus.
has cross-reference: AAO:0000275
homology_notes: Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]
has cross-reference: FMA:7195
has cross-reference: CALOHA:TS-0568
external_definition: Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]
has cross-reference: XAO:0000119
has_exact_synonym: pulmo
has cross-reference: BTO:0000763
has cross-reference: EV:0100042
has cross-reference: EFO:0000934
has cross-reference: AAO:0010567
has cross-reference: EHDAA:2205
has cross-reference: MESH:D008168
has cross-reference: EHDAA:1554
in_subset: efo slim
in_subset: human reference atlas
in_subset: human subset
in_subset: major organ
in_subset: mouse subset
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
never in taxon: NCBITaxon_32443
never in taxon: NCBITaxon 7777
present in taxon: NCBITaxon 9606
imported from: uberon.owl

skin of body
type: Class
subclass of: organ
has cross-reference: CALOHA:TS-0934
has cross-reference: FMA:7163
has cross-reference: MESH:D012867
has_related_synonym: integumental organ
has cross-reference: XAO:0000023
has_exact_synonym: skin organ
has cross-reference: Wikipedia:Skin
has cross-reference: MFMO:0000099
has_related_synonym: pelt
has_related_synonym: skin
external_ontology_notes: MA uses the term skin to refer to what is called here: zone of skin
has_related_synonym: integument
has cross-reference: EFO:0000962
has cross-reference: EHDAA2:0001844
has_exact_synonym: entire skin
has cross-reference: galen:Skin
has cross-reference: UMLS:C1123023
has cross-reference: NCIT:C12470
definition: The organ covering the body that consists of the dermis and epidermis.
id: UBERON:0002097
has cross-reference: EMAPA:17525
has_related_synonym: entire integument
has cross-reference: BTO:0001253
curator note: consider 'integumentary system' for invertebrates
has cross-reference: SCTID:181469002
in_subset: efo slim
in_subset: human reference atlas
in_subset: human subset
in_subset: major organ
in_subset: mouse subset
in_subset: pheno slim
in_subset: uberon slim
present in taxon: NCBITaxon 9606
imported from: uberon.owl

liver
type: Class
subclass of: organ
has cross-reference: EV:0100089
external_definition: Organ which secretes bile and participates in formation of certain blood proteins.[AAO]
has cross-reference: BTO:0000759
has cross-reference: MAT:0000097
has cross-reference: TAO:0000123
has cross-reference: EHDAA2:0000997
function_notes: secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
has cross-reference: EFO:0000887
definition: An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
has cross-reference: galen:Liver
has_relational_adjective: hepatic
has cross-reference: GAID:288
has cross-reference: MESH:D008099
taxon_notes: The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates.
has cross-reference: Wikipedia:Liver
has cross-reference: VHOG:0000257
has cross-reference: MA:0000358
has cross-reference: NCIT:C12392
has cross-reference: EHDAA:2197
has cross-reference: MIAA:0000097
homology_notes: All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG]
has cross-reference: FMA:7197
has cross-reference: AAO:0010111
has cross-reference: SCTID:181268008
taxon_notes: An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003).
has cross-reference: CALOHA:TS-0564
external_ontology_notes: Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function.
has_related_synonym: iecur
has cross-reference: EMAPA:16846
has cross-reference: ZFA:0000123
axiom_lost_from_external_ontology: relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
has cross-reference: XAO:0000133
id: UBERON:0002107
has_related_synonym: jecur
has cross-reference: UMLS:C0023884
in_subset: efo slim
in_subset: human reference atlas
in_subset: human subset
in_subset: major organ
in_subset: mouse subset
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
present in taxon: NCBITaxon 9606
imported from: uberon.owl

gallbladder
type: Class
subclass of: organ
has cross-reference: VHOG:0000221
has cross-reference: SCTID:181269000
has cross-reference: ZFA:0000208
has cross-reference: MA:0000356
has cross-reference: CALOHA:TS-0394
has cross-reference: XAO:0000135
axiom_lost_from_external_ontology: relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
has_related_synonym: vesica biliaris
has cross-reference: NCIT:C12377
has cross-reference: UMLS:C0016976
has cross-reference: galen:Gallbladder
has cross-reference: EFO:0000853
has cross-reference: TAO:0000208
has_related_synonym: vesica fellea
has cross-reference: MAT:0000072
has cross-reference: EHDAA2:0000699
has cross-reference: AAO:0010114
has cross-reference: BTO:0000493
has_exact_synonym: gall bladder
external_definition: Membranous muscular sac in which the bile from the liver remains stored until it is required. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
external_definition: Organ attached to the liver which stores bile and empties into the duodenum via the bile duct as needed for digestion.[AAO]
has_exact_synonym: cholecyst
has cross-reference: EHDAA:8062
definition: An organ that aids digestion and stores bile produced by the liver[WP].
has cross-reference: MESH:D005704
has cross-reference: Wikipedia:Gallbladder
has cross-reference: EMAPA:17202
has cross-reference: FMA:7202
id: UBERON:0002110
homology_notes: The presence of a gallbladder appears to be a primitive trait. It is found in most fish and all adult reptiles and amphibians and has been well conserved in mammals, for the most part.[well established][VHOG]
has cross-reference: EV:0100090
has cross-reference: MIAA:0000072
comment: Rats do not have a gallbladder, but produce bile. The bile flows directly from the liver through the (hepatic) bile duct into the small intestine (Hebel and Stromberg, 1988)
in_subset: efo slim
in_subset: human subset
in_subset: mouse subset
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
never in taxon: NCBITaxon_10114
never in taxon: NCBITaxon 8801
never in taxon: NCBITaxon 8930
imported from: uberon.owl

kidney
type: Class
subclass of: organ
has cross-reference: AAO:0000250
external_definition: One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]
has cross-reference: GAID:423
has cross-reference: Wikipedia:Kidney
has cross-reference: MESH:D007668
has cross-reference: CALOHA:TS-0510
has cross-reference: MAT:0000119
has cross-reference: XAO:0003267
has cross-reference: BTO:0000671
has cross-reference: galen:Kidney
has_relational_adjective: renal
has cross-reference: UMLS:C0022646
has cross-reference: MIAA:0000119
definition: A paired organ of the urinary tract that produces urine and maintains bodily fluid homeostasis, blood pressure, pH levels, red blood cell production and skeleton mineralization.
id: UBERON:0002113
has_narrow_synonym: reniculate kidney
in_subset: efo slim
in_subset: human reference atlas
in_subset: human subset
in_subset: major organ
in_subset: mouse subset
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
fma_set_term: FMA_264815
present in taxon: NCBITaxon 9606
mutually spatially disjoint with: intestine
imported from: uberon.owl
contributor: https://orcid.org/0000-0001-7655-4833
contributor: 0000-0003-2804-127X

duodenum
type: Class
subclass of: organ
has_relational_adjective: duodenal
has cross-reference: VHOG:0000052
has_related_synonym: proximal intestine
has cross-reference: SCTID:181247007
has cross-reference: UMLS:C0013303
has cross-reference: EFO:0000851
has cross-reference: MESH:D004386
id: UBERON:0002114
has_related_synonym: upper intestine
has cross-reference: EV:0100073
has cross-reference: NCIT:C12263
has cross-reference: GAID:284
has cross-reference: BTO:0000365
has cross-reference: CALOHA:TS-0214
has cross-reference: MA:0000338
has cross-reference: MAT:0000044
definition: The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one).
has cross-reference: FMA:7206
has cross-reference: galen:Duodenum
has cross-reference: AAO:0010402
has cross-reference: MIAA:0000044
taxon_notes: In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum.
has cross-reference: EMAPA:18852
external_definition: The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
has cross-reference: Wikipedia:Duodenum
has cross-reference: XAO:0000236
taxon_notes: In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz.
in_subset: efo slim
in_subset: human reference atlas
in_subset: human subset
in_subset: mouse subset
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
never in taxon: NCBITaxon 7955
present in taxon: NCBITaxon 9606
imported from: uberon.owl

hemolymphoid system
type: Class
subclass of: anatomical system
has cross-reference: EMAPA:18765
has cross-reference: MA:0000013
definition: Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
has_exact_synonym: hematolymphoid system
has_exact_synonym: lymphomyeloid complex
has cross-reference: CALOHA:TS-2018
id: UBERON:0002193
has cross-reference: EHDAA2:0004615
has cross-reference: FMA:74562
has_related_synonym: haemolymphoid system
in_subset: human subset
in_subset: mouse subset
imported from: uberon.owl

prostate gland
type: Class
subclass of: organ
id: UBERON:0002367
has cross-reference: MAT:0000078
has cross-reference: EMAPA:19287
has cross-reference: MIAA:0000078
has_relational_adjective: prostatic
has_exact_synonym: male prostate
has cross-reference: VHOG:0001261
definition: The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
has_related_synonym: prostata
has cross-reference: MESH:D011467
has cross-reference: Wikipedia:Prostate
has cross-reference: SCTID:181422007
has cross-reference: BTO:0001129
editor note: TODO - FMA treats the gland as part of the prostate - see also FMA:74119.
has cross-reference: CALOHA:TS-0828
has_exact_synonym: prostate
has cross-reference: galen:ProstateGland
has cross-reference: NCIT:C12410
has cross-reference: MA:0000404
has cross-reference: EFO:0000858
has cross-reference: GAID:392
has cross-reference: FMA:9600
has cross-reference: EV:0100104
has cross-reference: UMLS:C0033572
in_subset: efo slim
in_subset: human reference atlas
in_subset: human subset
in_subset: major organ
in_subset: mouse subset
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
present in taxon: NCBITaxon 9606
imported from: uberon.owl

adrenal gland
type: Class
subclass of: organ
external_definition: Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO]
has cross-reference: EFO:0000238
has_related_synonym: suprarenal gland
has_related_synonym: glandula suprarenalis
has cross-reference: Wikipedia:Adrenal_gland
has_related_synonym: epinephric gland
has cross-reference: MESH:D000311
has cross-reference: SCTID:181127006
has_exact_synonym: glandula adrenalis
definition: Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO].
has_related_synonym: atrabiliary capsule
id: UBERON:0002369
has_related_synonym: adrenal medulla cell
has cross-reference: CALOHA:TS-0016
has cross-reference: MA:0000116
has_exact_synonym: glandula suprarenalis
has cross-reference: AAO:0010551
has cross-reference: galen:AdrenalGland
has cross-reference: GAID:446
function_notes: suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n.
has cross-reference: MAT:0000071
has_related_synonym: adrenal
has_related_synonym: adrenal capsule
has cross-reference: BTO:0000047
has cross-reference: NCIT:C12666
has cross-reference: EV:0100135
has_related_synonym: interrenal gland
has cross-reference: FMA:9604
homology_notes: All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]
has cross-reference: MIAA:0000071
has cross-reference: EMAPA:18426
has cross-reference: UMLS:C0001625
has cross-reference: XAO:0000164
taxon_notes: The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole
has_related_synonym: epinephros
has_related_synonym: suprarenal capsule
in_subset: human subset
in_subset: mouse subset
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
imported from: uberon.owl

muscle tissue
type: Class
subclass of: tissue
has cross-reference: AEO:0000122
has cross-reference: SCTID:91727004
has cross-reference: Wikipedia:Muscle_tissue
has cross-reference: EHDAA2:0003122
has cross-reference: MESH:D009132
has cross-reference: NCIT:C12435
has cross-reference: CALOHA:TS-0642
has_exact_synonym: portion of muscle tissue
comment: Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach.
has cross-reference: galen:MuscleTissue
has cross-reference: AAO:0000306
has cross-reference: FMA:9641
has_exact_synonym: muscular tissue
has cross-reference: MA:0002437
has cross-reference: UMLS:C2328219
has_exact_synonym: textus muscularis
definition: Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
id: UBERON:0002385
has cross-reference: EMAPA:32715
external_definition: One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]
in_subset: human subset
in_subset: mouse subset
in_subset: uberon slim
mutually spatially disjoint with: UBERON_0003714
imported from: uberon.owl

lymph
type: Class
subclass of: organism substance
has cross-reference: MAT:0000055
has cross-reference: UMLS:C0024202
has cross-reference: MIAA:0000055
has cross-reference: BTO:0000855
has cross-reference: Wikipedia:Lymph
has cross-reference: ENVO:02000041
has cross-reference: GAID:1186
has cross-reference: MESH:D008196
has cross-reference: ZFA:0005658
has_related_synonym: lympha
definition: Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP].
has cross-reference: VHOG:0001590
has cross-reference: FMA:9671
has cross-reference: NCIT:C13252
has cross-reference: EV:0100049
has cross-reference: galen:Lymph
id: UBERON:0002391
has cross-reference: MA:0002520
has cross-reference: CALOHA:TS-0580
has cross-reference: EFO:0000871
in_subset: efo slim
in_subset: human subset
in_subset: mouse subset
in_subset: pheno slim
in_subset: uberon slim
imported from: uberon.owl

craniocervical region
type: Class
subclass of: multicellular anatomical structure
has cross-reference: ZFA:0001114
has cross-reference: EV:0100009
has cross-reference: MA:0000006
has cross-reference: CALOHA:TS-2356
has cross-reference: UMLS:C0460004
has cross-reference: FMA:280881
definition: The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae.
has_related_synonym: cephalic region
has cross-reference: WikipediaCategory:Head_and_neck
id: UBERON:0007811
has_related_synonym: cephalic area
has cross-reference: SCTID:361355005
has_related_synonym: cephalic part of animal
has_related_synonym: head and neck
has_related_synonym: head or neck
has cross-reference: galen:HeadAndNeck
has cross-reference: NCIT:C12418
in_subset: human subset
in_subset: mouse subset
in_subset: pheno slim
imported from: uberon.owl

multicellular anatomical structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that has more than one cell as a part.
has cross-reference: CARO:0010000
has_exact_synonym: multicellular structure
has cross-reference: FBbt:00100313
id: UBERON:0010000
in_subset: common anatomy
in_subset: human subset
in_subset: mouse subset
in_subset: upper level
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon_33208
present in taxon: NCBITaxon 4751
imported from: uberon.owl