external_definition
type: AnnotationProperty
is metadata tag: 1
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.
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO
database_cross_reference: UBPROP:0000001
id: external_definition
shorthand: external_definition
has_obo_namespace: uberon

never_in_taxon
type: AnnotationProperty
is class level: 1
is metadata tag: 1
expand assertion to: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y)
database_cross_reference: RO:0002161
definition: S never_in_taxon T iff: S SubClassOf in_taxon only not T
shorthand: never_in_taxon
id: never_in_taxon
has_obo_namespace: uberon

shorthand
type: AnnotationProperty

in_subset
type: AnnotationProperty

definition
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

expand assertion to
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

taxon_notes
type: AnnotationProperty
is metadata tag: 1
database_cross_reference: UBPROP:0000008
id: taxon_notes
shorthand: taxon_notes
has_obo_namespace: uberon

has_obo_namespace
type: AnnotationProperty

has_relational_adjective
type: AnnotationProperty
is metadata tag: 1
database_cross_reference: UBPROP:0000007
comment: 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_obo_namespace: uberon

axiom_lost_from_external_ontology
type: AnnotationProperty
is metadata tag: 1
definition: A textual description of an axiom loss in this ontology compared to an external ontology.
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO
database_cross_reference: UBPROP:0000002
id: axiom_lost_from_external_ontology
shorthand: axiom_lost_from_external_ontology
has_obo_namespace: uberon

homology_notes
type: AnnotationProperty
is metadata tag: 1
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
database_cross_reference: UBPROP:0000003
shorthand: homology_notes
id: homology_notes
has_obo_namespace: uberon

has_exact_synonym
type: AnnotationProperty

spatially_disjoint_from
type: AnnotationProperty
is metadata tag: 1
is class level: 1
definition: A is spatially_disjoint_from B if they have no parts in common.
expand assertion to: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
has_exact_synonym: non_overlapping_with
has_exact_synonym: shares_no_parts_with
id: spatially_disjoint_from
has_obo_namespace: uberon

has_related_synonym
type: AnnotationProperty

homologous_in
type: AnnotationProperty
is metadata tag: 1
comment: Status: experimental
id: homologous_in
has_obo_namespace: uberon

imported from
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

fma_set_term
type: AnnotationProperty
is metadata tag: 1
comment: 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
id: fma_set_term
has_obo_namespace: uberon

dubious_for_taxon
type: AnnotationProperty
is class level: 1
is metadata tag: 1
definition: S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
id: dubious_for_taxon
comment: this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost
has_obo_namespace: uberon

has_broad_synonym
type: AnnotationProperty

uterine cervix
type: Class
subclass of: anatomical entity
database_cross_reference: BTO:0001421
database_cross_reference: BTO:0002249
database_cross_reference: CALOHA:TS-0134
database_cross_reference: EFO:0000979
database_cross_reference: EMAPA:29927
database_cross_reference: EV:0100114
database_cross_reference: FMA:17740
database_cross_reference: GAID:376
definition: Lower, narrow portion of the uterus where it joins with the top end of the vagina.
database_cross_reference: MA:0000392
database_cross_reference: MAT:0000292
database_cross_reference: MESH:A05.360.319.679.256
database_cross_reference: OpenCyc:Mx4rvVipEJwpEbGdrcN5Y29ycA
database_cross_reference: SCTID:245494008
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]
external_definition: The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG]
id: UBERON:0000002
database_cross_reference: UMLS:C0007874
database_cross_reference: VHOG:0001359
database_cross_reference: Wikipedia:Cervix
has_exact_synonym: canalis cervicis uteri
has_exact_synonym: caudal segment of uterus
has_relational_adjective: cervical
has_related_synonym: cervical canal
has_exact_synonym: cervical canal of uterus
has_broad_synonym: cervix
has_related_synonym: cervix of uterus
has_exact_synonym: cervix uteri
database_cross_reference: galen:CervixUteri
database_cross_reference: ncithesaurus:Cervix
has_exact_synonym: neck of uterus
has_obo_namespace: uberon
has_exact_synonym: uterine cervix
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: efo slim
in_subset: uberon slim

dorsal root ganglion
type: Class
subclass of: nervous system
database_cross_reference: AAO:0011032
database_cross_reference: BTO:0001264
database_cross_reference: CALOHA:TS-0954
has_related_synonym: DRG
comment: Development notes: The sensory ganglia of spinal nerves arise only from the neural crest, whereas many sensory ganglia of the 'dorsal' cranial nerves arise from epibranchial placodes as well as the neural crest[doi: 10.1093/icb/icn065]. Other ontology notes: FMA treats dorsal root ganglion and spinal ganglion as equivalent labels. MA is the only ontology to introduce two classes here (also EHDAA2)
database_cross_reference: EFO:0000900
database_cross_reference: EHDAA2:0000418
database_cross_reference: EHDAA2:0001897
database_cross_reference: EHDAA:2899
database_cross_reference: EMAPA:16668
database_cross_reference: EMAPA:18372
database_cross_reference: EV:0100373
database_cross_reference: FMA:5888
homology_notes: From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG]
database_cross_reference: MA:0000231
database_cross_reference: MA:0000232
database_cross_reference: MAT:0000162
database_cross_reference: MIAA:0000162
database_cross_reference: NIF_GrossAnatomy:birnlex_2596
database_cross_reference: SCTID:244455004
database_cross_reference: TAO:0000200
external_definition: Trunk ganglion which is located adjacent to the spine on a dorsal root and contains the cell bodies of afferent sensory nerves.[TAO]
id: UBERON:0000044
database_cross_reference: UMLS:C0017070
database_cross_reference: VHOG:0000222
database_cross_reference: Wikipedia:Dorsal_root_ganglion
database_cross_reference: XAO:0000210
database_cross_reference: ZFA:0000200
has_related_synonym: dorsal root ganglia
has_exact_synonym: dorsal root ganglion
has_exact_synonym: ganglion of dorsal root
definition: ganglion on the dorsal root of each spinal nerve that is one of a series of ganglia lodging cell bodies of sensory neurons[BTO]. Trunk ganglion which is located adjacent to the spine on a dorsal root and contains the cell bodies of afferent sensory nerves[..]. one on the posterior root of each spinal nerve, composed of unipolar nerve cell bodies of the sensory neurons of the nerve[TFD].
has_related_synonym: ganglion sensorium nervi spinalis
has_related_synonym: ganglion spinale
has_exact_synonym: ganglion spinalis
database_cross_reference: ncithesaurus:Dorsal_Root_Ganglion
has_exact_synonym: spinal ganglion
has_obo_namespace: uberon
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: efo slim
in_subset: uberon slim
in_subset: vertebrate core

ureter
type: Class
subclass of: anatomical entity
database_cross_reference: AAO:0010254
external_definition: Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]
database_cross_reference: BTO:0001409
database_cross_reference: CALOHA:TS-1084
database_cross_reference: EFO:0000930
database_cross_reference: EHDAA2:0002139
database_cross_reference: EHDAA:9341
database_cross_reference: EMAPA:17950
database_cross_reference: EV:0100097
database_cross_reference: FMA:9704
database_cross_reference: GAID:438
database_cross_reference: MA:0000378
database_cross_reference: MAT:0000120
database_cross_reference: MESH:A05.810.776
database_cross_reference: MIAA:0000120
definition: Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. In humans, organ with organ cavity which connects the renal sinus to the urinary bladder. Examples: the right and the left ureters.
database_cross_reference: OpenCyc:Mx4rvhmm6JwpEbGdrcN5Y29ycA
database_cross_reference: SCTID:302511008
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]
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]
id: UBERON:0000056
database_cross_reference: UMLS:C0041951
database_cross_reference: VHOG:0000605
database_cross_reference: Wikipedia:Ureter
database_cross_reference: XAO:0000144
database_cross_reference: galen:Ureter
has_related_synonym: metanephric duct
database_cross_reference: ncithesaurus:Ureter
has_obo_namespace: uberon
has_relational_adjective: ureteral
has_relational_adjective: ureteric
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: efo slim
in_subset: major organ
in_subset: organ slim
in_subset: uberon slim

embryo stage
type: Class
subclass of: life cycle stage
definition: A life cycle stage that starts with fertilization and ends with the fully formed embryo.
database_cross_reference: BilaDO:0000002
database_cross_reference: EV:0300001
database_cross_reference: FBdv:00005289
database_cross_reference: HsapDv:0000002
database_cross_reference: MmusDv:0000002
database_cross_reference: OGES:000000
database_cross_reference: OGES:000022
database_cross_reference: SCTID:296280003
id: UBERON:0000068
database_cross_reference: XAO:1000012
has_related_synonym: embryogenesis
has_exact_synonym: embryonic stage
has_obo_namespace: uberon
imported from: uberon.owl

life cycle stage
type: Class
subclass of: PATO_0000011
definition: A spatiotemporal region encompassing some part of the life cycle of an organism.
database_cross_reference: BILS:0000105
database_cross_reference: EFO:0000399
comment: Editor notes: we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
database_cross_reference: MmusDv:0000001
database_cross_reference: OlatDv:0000010
database_cross_reference: PdumDv:0000090
id: UBERON:0000105
database_cross_reference: WBls:0000002
database_cross_reference: XAO:1000000
database_cross_reference: ZFS:0000000
database_cross_reference: ZFS:0100000
has_narrow_synonym: developmental stage
database_cross_reference: ncithesaurus:Developmental_Stage
has_narrow_synonym: stage
has_obo_namespace: uberon
imported from: uberon.owl
in_subset: efo slim
in_subset: upper level

gastrula stage
type: Class
subclass of: embryo stage
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.
database_cross_reference: BILS:0000109
database_cross_reference: BilaDO:0000008
database_cross_reference: EFO:0001296
database_cross_reference: FBdv:00005317
database_cross_reference: HsapDv:0000010
database_cross_reference: MmusDv:0000013
database_cross_reference: OGES:000004
database_cross_reference: OGES:000019
id: UBERON:0000109
database_cross_reference: XAO:1000005
database_cross_reference: ZFS:0000047
has_related_synonym: blastocystis trilaminaris stage
has_related_synonym: trilaminar blastocyst stage
has_related_synonym: trilaminar blastoderm stage
has_related_synonym: trilaminar disk stage
has_related_synonym: trilaminar germ stage
has_related_synonym: trilaminar stage
has_obo_namespace: uberon
imported from: uberon.owl
in_subset: efo slim

neurula stage
type: Class
subclass of: embryo stage
database_cross_reference: BILS:0000110
database_cross_reference: BilaDO:0000009
database_cross_reference: HsapDv:0000012
database_cross_reference: MmusDv:0000017
definition: Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
id: UBERON:0000110
database_cross_reference: XAO:1000006
has_obo_namespace: uberon
imported from: uberon.owl

organogenesis stage
type: Class
subclass of: embryo stage
definition: A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
database_cross_reference: BILS:0000111
database_cross_reference: BilaDO:0000010
database_cross_reference: HsapDv:0000015
database_cross_reference: MmusDv:0000018
database_cross_reference: OGES:000005
database_cross_reference: OGES:000032
id: UBERON:0000111
database_cross_reference: Wikipedia:Organogenesis
has_related_synonym: segmentation stage
has_obo_namespace: uberon
imported from: uberon.owl

juvenile stage
type: Class
subclass of: EFO_0002948
database_cross_reference: BILS:0000112
database_cross_reference: BTO:0002168
comment: Consider renaming this to '(sexually) immature stage'; in mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother)
database_cross_reference: EFO:0001300
database_cross_reference: EV:0300051
database_cross_reference: MmusDv:0000043
database_cross_reference: OGES:000009
database_cross_reference: TS28
external_definition: The stage of being a sexually immature adult animal[XAO:1000010].
id: UBERON:0000112
database_cross_reference: XAO:1000010
database_cross_reference: XtroDO:0000083
database_cross_reference: ZFS:0000051
has_exact_synonym: immature stage
has_obo_namespace: uberon
imported from: uberon.owl
in_subset: efo slim

post-juvenile adult stage
type: Class
subclass of: EFO_0002948
database_cross_reference: BILS:0000113
database_cross_reference: EV:0300064
database_cross_reference: EV:0300070
database_cross_reference: MIAA:0000403
database_cross_reference: MmusDv:0000110
database_cross_reference: OGES:000026
database_cross_reference: OGES:000027
definition: The stage of being a sexually mature adult animal.
id: UBERON:0000113
database_cross_reference: XAO:1000009
database_cross_reference: ZFS:0000044
has_broad_synonym: adult stage
has_obo_namespace: uberon
imported from: uberon.owl

intestine
type: Class
subclass of: anatomical entity
database_cross_reference: AAO:0000246
database_cross_reference: ANISEED:1235303
database_cross_reference: BSA:0000093
database_cross_reference: BTO:0000648
database_cross_reference: CALOHA:TS-0490
database_cross_reference: EFO:0000834
database_cross_reference: EMAPA:32874
database_cross_reference: EV:0100071
database_cross_reference: FMA:7199
database_cross_reference: GAID:295
comment: MA also has a class MA:0001524 bowel, not clear how this is different. Usage notes: this class is currently very general, encompassing the C elegans 'intestine', which is a tube of epithelial cells extending from the 'pharynx' to 'rectum'. 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.
database_cross_reference: MA:0000328
database_cross_reference: MA:0001524
database_cross_reference: MESH:A03.492.411
database_cross_reference: MIAA:0000043
external_definition: Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
database_cross_reference: SCTID:256876008
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.
database_cross_reference: TAO:0001338
external_definition: The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
id: UBERON:0000160
database_cross_reference: UMLS:C0021853
database_cross_reference: VHOG:0000056
database_cross_reference: WBbt:0005772
database_cross_reference: Wikipedia:Intestine
database_cross_reference: XAO:0000129
database_cross_reference: ZFA:0001338
has_exact_synonym: bowel
database_cross_reference: galen:Intestine
has_relational_adjective: intestinal
database_cross_reference: ncithesaurus:Intestine
has_obo_namespace: uberon
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: efo slim
in_subset: uberon slim
in_subset: vertebrate core

breast
type: Class
subclass of: anatomical entity
database_cross_reference: BTO:0000149
database_cross_reference: CALOHA:TS-2083
database_cross_reference: EV:0100124
database_cross_reference: FMA:9601
database_cross_reference: GAID:33
database_cross_reference: MESH:A01.236
database_cross_reference: OpenCyc:Mx4rvVjV7ZwpEbGdrcN5Y29ycA
database_cross_reference: SCTID:181131000
definition: The breast is the upper ventral region of an animal's torso, particularly that of mammals, including human beings. The breasts of a female primate’s body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's. [WP,unvetted].
id: UBERON:0000310
database_cross_reference: UMLS:C0006141
database_cross_reference: Wikipedia:Breast
database_cross_reference: galen:Breast
has_related_synonym: mamma
has_exact_synonym: mammary part of chest
has_exact_synonym: mammary region
database_cross_reference: ncithesaurus:Breast
has_obo_namespace: uberon
imported from: uberon.owl

testis
type: Class
subclass of: anatomical entity
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]
database_cross_reference: AAO:0000606
database_cross_reference: BILA:0000124
database_cross_reference: BSA:0000085
database_cross_reference: BTO:0001363
database_cross_reference: CALOHA:TS-1030
database_cross_reference: EFO:0000984
database_cross_reference: EHDAA2:0002007
database_cross_reference: EHDAA:8146
database_cross_reference: EMAPA:17972
database_cross_reference: EV:0100102
external_definition: Either of paired male reproductive organs which are involved in the production of sperm and male sex hormones.[AAO]
database_cross_reference: FBbt:00004928
database_cross_reference: FMA:7210
database_cross_reference: GAID:396
database_cross_reference: HAO:0001007
database_cross_reference: MA:0000411
database_cross_reference: MAT:0000132
database_cross_reference: MESH:A05.360.444.849
database_cross_reference: MIAA:0000132
external_definition: Male reproductive organ.[TAO]
database_cross_reference: OpenCyc:Mx4rvVjM25wpEbGdrcN5Y29ycA
database_cross_reference: SCTID:181431007
database_cross_reference: TAO:0000598
taxon_notes: The testes are descended in metatherian and eutherian mammals.
id: UBERON:0000473
has_alternative_id: UBERON:0002117
database_cross_reference: UMLS:C0039597
database_cross_reference: VHOG:0000252
database_cross_reference: WBbt:0006794
database_cross_reference: Wikipedia:Testis
database_cross_reference: XAO:0000157
database_cross_reference: ZFA:0000598
database_cross_reference: galen:Testis
has_exact_synonym: genitalia of male organism gonad
has_exact_synonym: genitalia of male organism gonada
definition: gonad of a male animal, produces and releases sperm.
has_exact_synonym: gonad of genitalia of male organism
has_exact_synonym: gonad of male genitalia
has_exact_synonym: gonad of male genitals
has_exact_synonym: gonad of male organism genitalia
has_exact_synonym: gonad of male organism reproductive system
has_exact_synonym: gonad of male reproductive system
has_exact_synonym: gonad of reproductive system of male organism
has_exact_synonym: gonada of genitalia of male organism
has_exact_synonym: gonada of male genitalia
has_exact_synonym: gonada of male genitals
has_exact_synonym: gonada of male organism genitalia
has_exact_synonym: gonada of male organism reproductive system
has_exact_synonym: gonada of male reproductive system
has_exact_synonym: gonada of reproductive system of male organism
has_exact_synonym: male genitalia gonad
has_exact_synonym: male genitalia gonada
has_exact_synonym: male genitals gonad
has_exact_synonym: male gonad
has_exact_synonym: male organism genitalia gonad
has_exact_synonym: male organism genitalia gonada
has_exact_synonym: male organism reproductive system gonad
has_exact_synonym: male organism reproductive system gonada
has_exact_synonym: male reproductive system gonad
has_exact_synonym: male reproductive system gonada
database_cross_reference: ncithesaurus:Testis
has_related_synonym: orchis
has_exact_synonym: reproductive system of male organism gonad
has_exact_synonym: reproductive system of male organism gonada
has_related_synonym: testes
has_exact_synonym: testicle
has_relational_adjective: testicular
has_related_synonym: testiculus
has_obo_namespace: uberon
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: efo slim
in_subset: organ slim
in_subset: uberon slim
in_subset: vertebrate core

stomach
type: Class
subclass of: anatomical entity
database_cross_reference: AAO:0000579
database_cross_reference: ANISEED:1235297
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.
database_cross_reference: BSA:0000123
database_cross_reference: BTO:0001307
database_cross_reference: CALOHA:TS-0980
database_cross_reference: EFO:0000837
database_cross_reference: EHDAA2:0001915
database_cross_reference: EHDAA:2993
database_cross_reference: EMAPA:17021
database_cross_reference: EMAPA:18889
database_cross_reference: EV:0100070
database_cross_reference: FMA:7148
database_cross_reference: GAID:293
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]
database_cross_reference: MA:0000353
database_cross_reference: MAT:0000051
database_cross_reference: MESH:A03.492.766
database_cross_reference: MIAA:0000051
database_cross_reference: OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA
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]
database_cross_reference: SCTID:181246003
database_cross_reference: TAO:0002121
comment: 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 -- Stomach#In_other_animals
id: UBERON:0000945
database_cross_reference: UMLS:C0038351
database_cross_reference: VHOG:0000408
has_related_synonym: Ventricular
database_cross_reference: Wikipedia:Stomach
database_cross_reference: XAO:0000128
has_related_synonym: anterior intestine
database_cross_reference: galen:Stomach
has_related_synonym: gaster
has_related_synonym: mesenteron
database_cross_reference: ncithesaurus:Stomach
has_narrow_synonym: stomach chamber
has_obo_namespace: uberon
has_related_synonym: ventriculus
homologous_in: NCBITaxon 7742
never_in_taxon: NCBITaxon 7955
imported from: uberon.owl
in_subset: efo slim
in_subset: major organ
in_subset: organ slim
in_subset: uberon slim
in_subset: vertebrate core

brain
type: Class
subclass of: anatomical entity
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]
database_cross_reference: AAO:0010478
database_cross_reference: ABA:Brain
database_cross_reference: BILA:0000135
database_cross_reference: BTO:0000142
database_cross_reference: CALOHA:TS-0095
external_definition: Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
database_cross_reference: EFO:0000302
database_cross_reference: EHDAA2:0000183
database_cross_reference: EHDAA:2641
database_cross_reference: EHDAA:6485
database_cross_reference: EMAPA:16894
database_cross_reference: EV:0100164
database_cross_reference: FBbt:00005095
database_cross_reference: FMA:50801
database_cross_reference: GAID:571
database_cross_reference: MA:0000168
database_cross_reference: MAT:0000098
database_cross_reference: MESH:A08.186.211
database_cross_reference: MIAA:0000098
database_cross_reference: NIF_GrossAnatomy:birnlex_796
database_cross_reference: NeuroNames:21
database_cross_reference: OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA
external_definition: Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
database_cross_reference: SCTID:258335003
database_cross_reference: TAO: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].
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)
id: UBERON:0000955
database_cross_reference: UMLS:C0006104
database_cross_reference: UMLS:C1269537
database_cross_reference: VHOG:0000157
database_cross_reference: Wikipedia:Brain
database_cross_reference: XAO:0000010
database_cross_reference: ZFA:0000008
has_related_synonym: encephalon
database_cross_reference: galen:Brain
comment: include synganglion?
database_cross_reference: ncithesaurus:Brain
has_related_synonym: suprasegmental levels of nervous system
has_related_synonym: suprasegmental structures
has_related_synonym: synganglion
has_related_synonym: the brain
has_obo_namespace: uberon
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: cumbo
in_subset: efo slim
in_subset: major organ
in_subset: uberon slim
in_subset: vertebrate core

cerebral cortex
type: Class
subclass of: brain
database_cross_reference: ABA:CTX
database_cross_reference: BM:Tel-Cx
database_cross_reference: BTO:0000233
database_cross_reference: CALOHA:TS-0091
database_cross_reference: EFO:0000328
database_cross_reference: EHDAA2:0000234
database_cross_reference: EHDAA:5464
database_cross_reference: EMAPA:17544
database_cross_reference: EV:0100166
database_cross_reference: FMA:61830
database_cross_reference: GAID:629
database_cross_reference: MA:0000185
database_cross_reference: MAT:0000108
database_cross_reference: MESH:A08.186.211.730.885.213
database_cross_reference: MIAA:0000108
homology_notes: Migration of neurons from the basal or striatal portions of the anterior part of the neural tube occurs to varying degrees in different vertebrate classes, but a true cerebral cortex is generally acknowledged to have made its first appearance in reptiles. The definition can be unambiguous, since 'cortex' simply implies the existence of a surface neuronal layer with an overlying 'zonal lamina' or 'molecular' layer containing dendrites and axons, which is separated from the underlying basal 'matrix' by white matter. Although reptilian cerebral cortex does indeed fulfill these conditions in certain locations, the separation from striatal structures is often indistinct, so that it may even be argued that some primitive dipnoans possess a pallium or cortex. Nevertheless, an extensive laminated layer separated by underlying white matter is well represented only in reptiles and mammals.[well established][VHOG]
database_cross_reference: NIF_GrossAnatomy:birnlex_1494
database_cross_reference: NeuroNames:39
database_cross_reference: SCTID:362880003
external_definition: The cerebral cortex is a structure within the brain that plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It constitutes the outermost layer of the cerebrum. In preserved brains, it has a grey color, hence the name 'grey matter'. Grey matter is formed by neurons and their unmyelinated fibers, whereas the white matter below the grey matter of the cortex is formed predominantly by myelinated axons interconnecting different regions of the central nervous system. The human cerebral cortex is 2–4 mm (0.08–0.16 inches) thick. The surface of the cerebral cortex is folded in large mammals, such that more than two-thirds of the cortical surface is buried in the grooves, called 'sulci. ' The phylogenetically most recent part of the cerebral cortex, the neocortex, also called isocortex, is differentiated into six horizontal layers; the more ancient part of the cerebral cortex, the hippocampus (also called archicortex), has at most three cellular layers, and is divided into subfields. Relative variations in thickness or cell type (among other parameters) allow us to distinguish between different neocortical architectonic fields. The geometry of at least some of these fields seems to be related to the anatomy of the cortical folds, and, for example, layers in the upper part of the cortical ridges seem to be more clearly differentiated than in its deeper parts. [WP,unvetted][Wikipedia:Cerebral_cortex].
definition: The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex.
id: UBERON:0000956
database_cross_reference: UMLS:C0007776
database_cross_reference: VHOG:0000722
database_cross_reference: Wikipedia:Cerebral_cortex
has_related_synonym: brain cortex
has_related_synonym: cortex cerebralis
has_related_synonym: cortex cerebri
has_exact_synonym: cortex of cerebral hemisphere
has_related_synonym: cortical plate (CTXpl)
has_related_synonym: cortical plate (areas)
database_cross_reference: ncithesaurus:Cortex
has_related_synonym: pallium of the brain
has_obo_namespace: uberon
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: efo slim
in_subset: uberon slim

female gonad
type: Class
subclass of: anatomical entity
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]
database_cross_reference: AAO:0000371
database_cross_reference: BILA:0000125
database_cross_reference: BSA:0000080
database_cross_reference: BTO:0000975
database_cross_reference: CALOHA:TS-0730
database_cross_reference: EFO:0000973
database_cross_reference: EHDAA2:0001360
database_cross_reference: EHDAA:8124
database_cross_reference: EMAPA:17962
database_cross_reference: EV:0100111
external_definition: Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]
database_cross_reference: FBbt:00004865
database_cross_reference: FMA:7209
external_definition: Female reproductive organ.[TAO]
database_cross_reference: GAID:367
database_cross_reference: MA:0000384
database_cross_reference: MESH:A05.360.319.114.630
database_cross_reference: MIAA:0000125
database_cross_reference: OpenCyc:Mx4rvVi9QJwpEbGdrcN5Y29ycA
comment: Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo[WP].
definition: Ovum-producing female reproductive organ.
database_cross_reference: SCTID:181464007
database_cross_reference: TAO:0000403
id: UBERON:0000992
database_cross_reference: UMLS:C0029939
database_cross_reference: VHOG:0000251
database_cross_reference: Wikipedia:Ovary
database_cross_reference: XAO:0000258
database_cross_reference: ZFA:0000403
has_exact_synonym: female organism genitalia gonad
has_exact_synonym: female organism genitalia gonada
has_exact_synonym: female organism reproductive system gonad
has_exact_synonym: female organism reproductive system gonada
has_exact_synonym: female reproductive system gonad
has_exact_synonym: female reproductive system gonada
has_exact_synonym: genitalia of female organism gonad
has_exact_synonym: genitalia of female organism gonada
has_exact_synonym: gonad of female organism genitalia
has_exact_synonym: gonad of female organism reproductive system
has_exact_synonym: gonad of female reproductive system
has_exact_synonym: gonad of genitalia of female organism
has_exact_synonym: gonad of reproductive system of female organism
has_exact_synonym: gonada of female organism genitalia
has_exact_synonym: gonada of female organism reproductive system
has_exact_synonym: gonada of female reproductive system
has_exact_synonym: gonada of genitalia of female organism
has_exact_synonym: gonada of reproductive system of female organism
database_cross_reference: ncithesaurus:Ovary
has_relational_adjective: ovarian
has_related_synonym: ovaries
has_related_synonym: ovarium
has_exact_synonym: ovary
has_exact_synonym: ovum-producing ovary
axiom_lost_from_external_ontology: relationship type change: subclass gonad (TAO:0000413) CHANGED TO: develops_from gonad (UBERON:0000991)[TAO]
has_exact_synonym: reproductive system of female organism gonad
has_exact_synonym: reproductive system of female organism gonada
has_obo_namespace: uberon
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: efo slim
in_subset: organ slim
in_subset: uberon slim
in_subset: vertebrate core

uterus
type: Class
subclass of: anatomical entity
homology_notes: An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]
database_cross_reference: BTO:0001424
database_cross_reference: CALOHA:TS-1102
database_cross_reference: EFO:0000975
database_cross_reference: EMAPA:29915
database_cross_reference: EV:0100113
database_cross_reference: FMA:17558
database_cross_reference: GAID:172
database_cross_reference: MA:0000389
database_cross_reference: MAT:0000127
database_cross_reference: MESH:A05.360.319.679
database_cross_reference: MIAA:0000127
comment: 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.
database_cross_reference: OpenCyc:Mx4rvViojJwpEbGdrcN5Y29ycA
database_cross_reference: SCTID:181452004
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
database_cross_reference: UMLS:C0042149
database_cross_reference: VHOG:0001137
database_cross_reference: Wikipedia:Uterus
definition: a major female hormone-responsive reproductive sex organ of most mammals including humans. One end, the cervix, opens into the vagina, while the other is connected to one or both fallopian tubes, depending on the species. It is within the uterus that the fetus develops during gestation, usually developing completely in placental mammals such as humans and partially in marsupials such as kangaroos and opossums. 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[WP].
database_cross_reference: galen:Uterus
database_cross_reference: ncithesaurus:Uterus
has_obo_namespace: uberon
has_relational_adjective: uterine
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: efo slim
in_subset: organ slim
in_subset: uberon slim

mammalian vulva
type: Class
subclass of: anatomical entity
database_cross_reference: BTO:0003101
database_cross_reference: CALOHA:TS-1168
database_cross_reference: EFO:0000978
database_cross_reference: EV:0100118
database_cross_reference: FMA:20462
database_cross_reference: GAID:383
database_cross_reference: MA:0000395
database_cross_reference: MAT:0000169
database_cross_reference: MESH:A05.360.319.887
database_cross_reference: MIAA:0000169
database_cross_reference: OpenCyc:Mx4rvgAWeJwpEbGdrcN5Y29ycA
database_cross_reference: SCTID:265796001
external_definition: The external genital organs of the female, including the labia majora, labia minora, clitoris, and vestibule of the vagina. [TFD][VHOG]
id: UBERON:0000997
database_cross_reference: UMLS:C0042993
database_cross_reference: VHOG:0001458
database_cross_reference: Wikipedia:Vulva
comment: editor note: todo - add pudendum
definition: external genital organs of the female mammal[WP].
has_exact_synonym: female pudendum
database_cross_reference: galen:Vulva
has_exact_synonym: mammalian vulva
database_cross_reference: ncithesaurus:Vulva
has_exact_synonym: puboperineal region
has_related_synonym: pudendum
has_exact_synonym: pudendum femininum
has_related_synonym: pudendum femininum
has_related_synonym: pudendum muliebre
has_exact_synonym: skin of female pudendum
has_exact_synonym: skin of vulva
has_obo_namespace: uberon
has_exact_synonym: vulva
has_relational_adjective: vulval
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: efo slim
in_subset: uberon slim

nervous system
type: Class
subclass of: anatomical entity
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]
database_cross_reference: AAO:0000324
external_definition: Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
database_cross_reference: BILA:0000079
database_cross_reference: BTO:0001484
database_cross_reference: CALOHA:TS-1313
database_cross_reference: EFO:0000802
database_cross_reference: EHDAA2:0001246
database_cross_reference: EHDAA:826
database_cross_reference: EMAPA:16469
database_cross_reference: EV:0100162
database_cross_reference: FBbt:00005093
database_cross_reference: FMA:7157
database_cross_reference: GAID:466
database_cross_reference: MA:0000016
database_cross_reference: MAT:0000026
database_cross_reference: MESH:A08
database_cross_reference: MIAA:0000026
database_cross_reference: NIF_GrossAnatomy:birnlex_844
has_related_synonym: Nervensystem
homology_notes: Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
database_cross_reference: NeuroNames:3236
database_cross_reference: OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA
database_cross_reference: SCTID:278196006
database_cross_reference: TAO:0000396
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].
comment: This class was created automatically from a combination of ontologies
id: UBERON:0001016
database_cross_reference: UMLS:C0027763
database_cross_reference: VHOG:0000402
database_cross_reference: WBbt:0005735
database_cross_reference: Wikipedia:Nervous_system
database_cross_reference: XAO:0000177
database_cross_reference: ZFA:0000396
database_cross_reference: ncithesaurus:Nervous_System
has_narrow_synonym: nerve net
has_relational_adjective: nervous
has_relational_adjective: neural
axiom_lost_from_external_ontology: relationship type change: differentiates_from ectoderm (AAO:0000137) CHANGED TO: develops_from ectoderm (UBERON:0000924)[AAO]
has_related_synonym: systema nervosum
has_obo_namespace: uberon
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: cumbo
in_subset: efo slim
in_subset: uberon slim
in_subset: vertebrate core

esophagus
type: Class
subclass of: anatomical entity
database_cross_reference: AAO:0000145
database_cross_reference: ANISEED:1235301
comment: AO 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)
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]
database_cross_reference: BSA:0000074
database_cross_reference: BTO:0000959
database_cross_reference: CALOHA:TS-0700
database_cross_reference: EFO:0000835
database_cross_reference: EHDAA2:0001285
database_cross_reference: EHDAA:2937
database_cross_reference: EMAPA:16833
database_cross_reference: EMAPA:18860
database_cross_reference: EV:0100069
database_cross_reference: FMA:7131
database_cross_reference: GAID:291
database_cross_reference: MA:0000352
database_cross_reference: MAT:0000048
database_cross_reference: MESH:A03.365
database_cross_reference: MIAA:0000048
database_cross_reference: OpenCyc:Mx4rvVj9Q5wpEbGdrcN5Y29ycA
database_cross_reference: SCTID:181245004
database_cross_reference: TAO:0000204
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]
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
database_cross_reference: UMLS:C0014876
database_cross_reference: VHOG:0000450
database_cross_reference: Wikipedia:Esophagus
database_cross_reference: XAO:0000127
database_cross_reference: ZFA:0000204
has_relational_adjective: esophageal
database_cross_reference: galen:Esophagus
has_exact_synonym: gullet
database_cross_reference: ncithesaurus:Esophagus
has_exact_synonym: oesophagus
has_obo_namespace: uberon
has_related_synonym: Åsophagus
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: efo slim
in_subset: major organ
in_subset: organ slim
in_subset: uberon slim
in_subset: vertebrate core

anatomical entity
type: Class
database_cross_reference: AAO:0010841
database_cross_reference: AEO:0000000
database_cross_reference: BILA:0000000
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.
database_cross_reference: CARO:0000000
database_cross_reference: EHDAA2:0002229
database_cross_reference: FBbt:10000000
database_cross_reference: FBbt_root:00000000
database_cross_reference: FMA:62955
database_cross_reference: HAO:0000000
database_cross_reference: MA:0000001
database_cross_reference: NIF_GrossAnatomy:birnlex_6
database_cross_reference: TAO:0100000
database_cross_reference: TGMA:0001822
id: UBERON:0001062
database_cross_reference: UMLS:C1515976
database_cross_reference: ZFA:0100000
database_cross_reference: ncithesaurus:Anatomic_Structure_System_or_Substance
has_obo_namespace: uberon
imported from: uberon.owl
in_subset: upper level

urinary bladder
type: Class
subclass of: anatomical entity
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]
database_cross_reference: AAO:0000623
external_definition: Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]
database_cross_reference: BTO:0001418
database_cross_reference: CALOHA:TS-1090
database_cross_reference: EFO:0000290
database_cross_reference: EHDAA2:0000174
database_cross_reference: EHDAA:9328
database_cross_reference: EMAPA:18321
database_cross_reference: EV:0100098
database_cross_reference: FMA:15900
database_cross_reference: GAID:0000004
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]
database_cross_reference: MA:0000380
database_cross_reference: MAT:0000122
database_cross_reference: MESH:A05.810.161
database_cross_reference: MIAA:0000122
database_cross_reference: OpenCyc:Mx4rvVjMmZwpEbGdrcN5Y29ycA
database_cross_reference: SCTID:302512001
id: UBERON:0001255
database_cross_reference: UMLS:C0005682
database_cross_reference: VHOG:0000740
database_cross_reference: Wikipedia:Urinary_bladder
database_cross_reference: XAO:0000154
has_exact_synonym: bladder
definition: distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
database_cross_reference: galen:UrinaryBladder
database_cross_reference: ncithesaurus:Bladder
has_obo_namespace: uberon
has_related_synonym: urocyst
has_related_synonym: vesica
has_exact_synonym: vesica urinaria
has_relational_adjective: vesical
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: efo slim
in_subset: major organ
in_subset: organ slim
in_subset: uberon slim

pancreas
type: Class
subclass of: anatomical entity
database_cross_reference: AAO:0010112
definition: An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1–2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans[PMID].
database_cross_reference: BTO:0000988
database_cross_reference: CALOHA:TS-0736
database_cross_reference: EFO:0000855
database_cross_reference: EHDAA2:0001367
database_cross_reference: EHDAA:6893
database_cross_reference: EMAPA:17503
database_cross_reference: EMAPA:18816
database_cross_reference: EV:0100092
database_cross_reference: FMA:7198
database_cross_reference: GAID:334
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]
database_cross_reference: MA:0000120
database_cross_reference: MAT:0000075
database_cross_reference: MESH:A03.734
database_cross_reference: MIAA:0000075
database_cross_reference: OpenCyc:Mx4rvVimZZwpEbGdrcN5Y29ycA
external_definition: Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]
database_cross_reference: SCTID:181277001
database_cross_reference: TAO:0000140
id: UBERON:0001264
database_cross_reference: UMLS:C0030274
database_cross_reference: VHOG:0000050
database_cross_reference: Wikipedia:Pancreas
database_cross_reference: XAO:0000136
database_cross_reference: ZFA:0000140
database_cross_reference: galen:Pancreas
database_cross_reference: ncithesaurus:Pancreas
has_relational_adjective: pancreatic
comment: 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) [PMID:20959416]. The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract (Figures 16 and 17 ). The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm
has_obo_namespace: uberon
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: efo slim
in_subset: major organ
in_subset: organ slim
in_subset: uberon slim
in_subset: vertebrate core

bone element
type: Class
subclass of: anatomical entity
database_cross_reference: AAO:0000047
database_cross_reference: AEO:0000082
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]
comment: Alternate definition: Organ with cavitated organ parts, which primarily consists of compact (cortical) and cancellous bone, which surround bone marrow cavities; together with other bones, cartilages and joints, it constitutes the skeletal system. Examples: femur, sternum, maxilla, vertebra, talus[FMA]
database_cross_reference: BTO:0000140
database_cross_reference: CALOHA:TS-0088
database_cross_reference: EFO:0000298
database_cross_reference: EHDAA2:0003082
database_cross_reference: EMAPA:32782
database_cross_reference: ENVO:00002039
database_cross_reference: EV:0100140
database_cross_reference: FMA:30317
database_cross_reference: FMA:5018
database_cross_reference: GAID:92
database_cross_reference: MA:0001459
database_cross_reference: MAT:0000299
database_cross_reference: MIAA:0000299
database_cross_reference: OpenCyc:Mx4rvViDlpwpEbGdrcN5Y29ycA
database_cross_reference: OpenCyc:Mx4rvVkCG5wpEbGdrcN5Y29ycA
external_definition: Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]
database_cross_reference: SCTID:90780006
definition: Skeletal element that is composed of bone tissue.
external_definition: Skeletal element that is composed of bone tissue.[VSAO]
database_cross_reference: TAO:0001514
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]
id: UBERON:0001474
database_cross_reference: UMLS:C0262950
database_cross_reference: VHOG:0001190
database_cross_reference: VSAO:0000057
database_cross_reference: Wikipedia:Bone
database_cross_reference: XAO:0000169
database_cross_reference: ZFA:0001514
has_related_synonym: bone
has_exact_synonym: bone element
has_exact_synonym: bone organ
database_cross_reference: galen:Bone
database_cross_reference: ncithesaurus:Bone
axiom_lost_from_external_ontology: relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
has_obo_namespace: uberon
homologous_in: NCBITaxon 7742
spatially_disjoint_from: UBERON_0001015
spatially_disjoint_from: UBERON_0001630
spatially_disjoint_from: muscle tissue
imported from: uberon.owl
in_subset: efo slim
in_subset: major organ
in_subset: organ slim
in_subset: uberon slim
in_subset: vertebrate core

neocortex
type: Class
subclass of: cerebral cortex
database_cross_reference: ABA:Isocortex
database_cross_reference: BTO:0000920
database_cross_reference: EHDAA2:0004662
database_cross_reference: EMAPA:32842
database_cross_reference: FMA:62429
database_cross_reference: GAID:677
database_cross_reference: MA:0002754
database_cross_reference: MESH:A08.186.211.730.885.213.420
database_cross_reference: NIF_GrossAnatomy:birnlex_2547
database_cross_reference: NeuroNames:757
homology_notes: The 6-layer neocortex is well conserved in all extant mammals, but not present in birds or reptils
definition: The term neocortex refers to those areas of cerebral cortex defined on the basis of cytoarchitecture that have six layers. Starting from the cortical surface the layers are: molecular layer (I), external granular layer (II), external pyramidal layer (III), internal granular layer (IV), internal pyramidal layer (V), and multiform layer (VI). Neocortex is most prominent in the frontal lobe, the parietal lobe, the temporal lobe and the occipital lobe, less so in the cingulate gyrus, the parahippocampal gyrus and the insula. It is composed of two subdivisions: true isocortex and proisocortex (Carpenter-83)(NN)
id: UBERON:0001950
database_cross_reference: UMLS:C0175173
database_cross_reference: Wikipedia:Neocortex
has_exact_synonym: cerebral neocortex
has_exact_synonym: homogenetic cortex
has_exact_synonym: homotypical cortex
has_exact_synonym: isocortex
has_exact_synonym: isocortex (sensu lato)
has_exact_synonym: neopallial cortex
has_exact_synonym: neopallium
has_related_synonym: nonolfactory cortex
has_related_synonym: nucleus hypoglossalis
has_obo_namespace: uberon
spatially_disjoint_from: UBERON_0002264
spatially_disjoint_from: hippocampal formation
imported from: uberon.owl
in_subset: uberon slim

blood plasma
type: Class
subclass of: anatomical entity
database_cross_reference: BTO:0000131
definition: Body substance in liquid state contained in the lumen of arterial and venous trees, blood capillary and the cardiac chambers; constitutes the liquid phase of blood.[FMA]
database_cross_reference: CALOHA:TS-0800
database_cross_reference: EFO:0001905
database_cross_reference: FMA:62970
database_cross_reference: GAID:1178
database_cross_reference: MA:0002501
database_cross_reference: MAT:0000052
database_cross_reference: MESH:A12.207.152.693
database_cross_reference: MIAA:0000052
database_cross_reference: OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw
id: UBERON:0001969
database_cross_reference: UMLS:C0032105
database_cross_reference: Wikipedia:Blood_plasma
database_cross_reference: ncithesaurus:Plasma
has_exact_synonym: plasma
has_exact_synonym: portion of blood plasma
has_exact_synonym: portion of plasma
has_obo_namespace: uberon
imported from: uberon.owl
in_subset: efo slim
in_subset: uberon slim

thyroid gland
type: Class
subclass of: anatomical entity
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]
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].
database_cross_reference: AAO:0010544
database_cross_reference: BTO:0001379
database_cross_reference: CALOHA:TS-1047
database_cross_reference: EFO:0000861
database_cross_reference: EHDAA2:0002028
database_cross_reference: EHDAA:2148
database_cross_reference: EHDAA:2975
database_cross_reference: EMAPA:17068
database_cross_reference: EMAPA:18827
database_cross_reference: EV:0100133
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]
database_cross_reference: FMA:9603
database_cross_reference: GAID:465
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
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)
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
database_cross_reference: MA:0000129
database_cross_reference: MAT:0000081
database_cross_reference: MESH:A06.407.900
database_cross_reference: MIAA:0000081
database_cross_reference: OpenCyc:Mx4rvVjLT5wpEbGdrcN5Y29ycA
database_cross_reference: SCTID:181117000
id: UBERON:0002046
database_cross_reference: UMLS:C0040132
database_cross_reference: VHOG:0000418
database_cross_reference: Wikipedia:Thyroid
database_cross_reference: XAO:0000162
database_cross_reference: galen:ThyroidGland
has_related_synonym: glandula thyroidea
database_cross_reference: ncithesaurus:Thyroid_Gland
has_exact_synonym: thyroid
has_obo_namespace: uberon
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: efo slim
in_subset: organ slim
in_subset: uberon slim

lung
type: Class
subclass of: anatomical entity
database_cross_reference: AAO:0000275
database_cross_reference: AAO:0010567
database_cross_reference: BTO:0000763
database_cross_reference: CALOHA:TS-0568
database_cross_reference: EFO:0000934
database_cross_reference: EHDAA2:0001042
database_cross_reference: EHDAA:1554
database_cross_reference: EHDAA:2205
database_cross_reference: EMAPA:16728
database_cross_reference: EV:0100042
external_definition: Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]
database_cross_reference: FMA:7195
database_cross_reference: GAID:345
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]
database_cross_reference: MA:0000415
database_cross_reference: MAT:0000135
database_cross_reference: MESH:A04.411
database_cross_reference: MIAA:0000135
database_cross_reference: OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA
definition: Respiration organ present in all air-breathing animals whose principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere[WP]. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax[GO].
database_cross_reference: SCTID:181216001
id: UBERON:0002048
database_cross_reference: UMLS:C0024109
database_cross_reference: VHOG:0000310
database_cross_reference: Wikipedia:Lung
database_cross_reference: XAO:0000119
database_cross_reference: galen:Lung
database_cross_reference: ncithesaurus:Lung
has_exact_synonym: pulmo
has_relational_adjective: pulmonary
comment: 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 // 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_obo_namespace: uberon
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: efo slim
in_subset: major organ
in_subset: organ slim
in_subset: uberon slim

skin of body
type: Class
subclass of: anatomical entity
database_cross_reference: BTO:0001253
database_cross_reference: CALOHA:TS-0934
database_cross_reference: EFO:0000962
database_cross_reference: EHDAA2:0001844
database_cross_reference: EMAPA:17525
database_cross_reference: FMA:7163
database_cross_reference: MESH:A17.815
definition: Nonparenchymatous organ that consists of the dermis and epidermis. Subdivisions of the skin surround various body parts; as a whole, the skin constitutes the external layer of the body. Examples: There is only one skin[FMA]. Surface structure that consists of the external membranous integument of the animal.
comment: Note that FMA uses 'skin' for the entire organ. XAO seems consistent. MA seems to use it analagously to zone of skin
database_cross_reference: OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA
database_cross_reference: SCTID:181469002
id: UBERON:0002097
database_cross_reference: UMLS:C1123023
database_cross_reference: Wikipedia:Skin
database_cross_reference: XAO:0000023
has_exact_synonym: entire skin
database_cross_reference: galen:Skin
has_related_synonym: integument
database_cross_reference: ncithesaurus:Skin
has_related_synonym: pelt
has_related_synonym: skin
has_obo_namespace: uberon
imported from: uberon.owl
in_subset: efo slim
in_subset: major organ
in_subset: uberon slim

liver
type: Class
subclass of: anatomical entity
database_cross_reference: AAO:0010111
comment: AO 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. Taxon notes: WP: 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.[7] 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).
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]
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].
database_cross_reference: BTO:0000759
database_cross_reference: CALOHA:TS-0564
database_cross_reference: EFO:0000887
database_cross_reference: EHDAA2:0000997
database_cross_reference: EHDAA:2197
database_cross_reference: EMAPA:16846
database_cross_reference: EV:0100089
database_cross_reference: FMA:7197
database_cross_reference: GAID:288
database_cross_reference: MA:0000358
database_cross_reference: MAT:0000097
database_cross_reference: MESH:A03.620
database_cross_reference: MIAA:0000097
database_cross_reference: OpenCyc:Mx4rvVimppwpEbGdrcN5Y29ycA
external_definition: Organ which secretes bile and participates in formation of certain blood proteins.[AAO]
database_cross_reference: SCTID:181268008
database_cross_reference: TAO:0000123
id: UBERON:0002107
database_cross_reference: UMLS:C0023884
database_cross_reference: VHOG:0000257
database_cross_reference: Wikipedia:Liver
database_cross_reference: XAO:0000133
database_cross_reference: ZFA:0000123
database_cross_reference: galen:Liver
has_relational_adjective: hepatic
has_related_synonym: iecur
has_related_synonym: jecur
database_cross_reference: ncithesaurus:Liver
axiom_lost_from_external_ontology: relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
has_obo_namespace: uberon
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: efo slim
in_subset: major organ
in_subset: organ slim
in_subset: uberon slim
in_subset: vertebrate core

gallbladder
type: Class
subclass of: anatomical entity
database_cross_reference: AAO:0010114
database_cross_reference: BTO:0000493
database_cross_reference: CALOHA:TS-0394
database_cross_reference: EFO:0000853
database_cross_reference: EHDAA2:0000699
database_cross_reference: EHDAA:8062
database_cross_reference: EMAPA:17202
database_cross_reference: EV:0100090
database_cross_reference: FMA:7202
database_cross_reference: MA:0000356
database_cross_reference: MAT:0000072
database_cross_reference: MESH:A03.159.439
database_cross_reference: MIAA:0000072
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]
database_cross_reference: OpenCyc:Mx4rvVkGr5wpEbGdrcN5Y29ycA
external_definition: Organ attached to the liver which stores bile and empties into the duodenum via the bile duct as needed for digestion.[AAO]
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)
database_cross_reference: SCTID:181269000
database_cross_reference: TAO:0000208
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]
id: UBERON:0002110
database_cross_reference: UMLS:C0016976
database_cross_reference: VHOG:0000221
database_cross_reference: Wikipedia:Gallbladder
database_cross_reference: XAO:0000135
database_cross_reference: ZFA:0000208
definition: a small organ that aids digestion and stores bile produced by the liver[WP]. Organ with organ cavity which is continuous proximally with the cystic duct and distally terminates in the fundus of the gallbladder[FMA].
database_cross_reference: galen:Gallbladder
has_exact_synonym: gall bladder
database_cross_reference: ncithesaurus:Gallbladder
axiom_lost_from_external_ontology: relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
has_obo_namespace: uberon
has_related_synonym: vesica fellea; vesica biliaris
never_in_taxon: NCBITaxon_10114
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: efo slim
in_subset: organ slim
in_subset: uberon slim
in_subset: vertebrate core

kidney
type: Class
subclass of: anatomical entity
definition: A paired organ which has the production of urine as its primary function.
database_cross_reference: AAO:0000250
database_cross_reference: BTO:0000671
database_cross_reference: CALOHA:TS-0510
database_cross_reference: EFO:0000929
database_cross_reference: EV:0100096
database_cross_reference: FMA:7203
database_cross_reference: GAID:423
database_cross_reference: MA:0000368
database_cross_reference: MAT:0000119
database_cross_reference: MESH:A05.810.453
database_cross_reference: MIAA:0000119
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]
database_cross_reference: OpenCyc:Mx4rvVjlYpwpEbGdrcN5Y29ycA
database_cross_reference: SCTID:181414000
id: UBERON:0002113
database_cross_reference: UMLS:C0022646
database_cross_reference: Wikipedia:Kidney
database_cross_reference: XAO:0003267
database_cross_reference: galen:Kidney
database_cross_reference: ncithesaurus:Kidney
has_relational_adjective: renal
has_narrow_synonym: reniculate kidney
has_obo_namespace: uberon
fma_set_term: FMA_264815
spatially_disjoint_from: intestine
imported from: uberon.owl
in_subset: efo slim
in_subset: major organ
in_subset: organ slim
in_subset: uberon slim
in_subset: vertebrate core

duodenum
type: Class
subclass of: anatomical entity
database_cross_reference: AAO:0010402
database_cross_reference: BTO:0000365
database_cross_reference: CALOHA:TS-0214
database_cross_reference: EFO:0000851
database_cross_reference: EMAPA:18852
database_cross_reference: EV:0100073
database_cross_reference: FMA:7206
database_cross_reference: GAID:284
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.
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.
database_cross_reference: MA:0000338
database_cross_reference: MAT:0000044
database_cross_reference: MESH:A03.492.411.620.270
database_cross_reference: MIAA:0000044
database_cross_reference: OpenCyc:Mx4rv4LJDpwpEbGdrcN5Y29ycA
database_cross_reference: SCTID:181247007
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).
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]
id: UBERON:0002114
database_cross_reference: UMLS:C0013303
database_cross_reference: VHOG:0000052
database_cross_reference: Wikipedia:Duodenum
database_cross_reference: XAO:0000236
has_relational_adjective: duodenal
database_cross_reference: galen:Duodenum
database_cross_reference: ncithesaurus:Duodenum
has_related_synonym: proximal intestine
has_obo_namespace: uberon
has_related_synonym: upper intestine
homologous_in: NCBITaxon 7742
dubious_for_taxon: NCBITaxon 7955
imported from: uberon.owl
in_subset: efo slim
in_subset: uberon slim
in_subset: vertebrate core

prostate gland
type: Class
subclass of: anatomical entity
database_cross_reference: BTO:0001129
database_cross_reference: CALOHA:TS-0828
database_cross_reference: EFO:0000858
database_cross_reference: EMAPA:19287
database_cross_reference: EV:0100104
database_cross_reference: FMA:9600
database_cross_reference: GAID:392
database_cross_reference: MA:0000404
database_cross_reference: MAT:0000078
database_cross_reference: MESH:A05.360.444.575
database_cross_reference: MIAA:0000078
database_cross_reference: OpenCyc:Mx4rv6trqZwpEbGdrcN5Y29ycA
database_cross_reference: SCTID:181422007
comment: TODO - FMA treats the gland as part of the prostate - see also FMA:74119.
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.
id: UBERON:0002367
database_cross_reference: UMLS:C0033572
database_cross_reference: VHOG:0001261
database_cross_reference: Wikipedia:Prostate
database_cross_reference: galen:ProstateGland
has_exact_synonym: male prostate
database_cross_reference: ncithesaurus:Prostate_Gland
has_related_synonym: prostata
has_exact_synonym: prostate
has_relational_adjective: prostatic
has_obo_namespace: uberon
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: efo slim
in_subset: major organ
in_subset: organ slim
in_subset: uberon slim

adrenal gland
type: Class
subclass of: anatomical entity
database_cross_reference: AAO:0010551
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]
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]
database_cross_reference: BTO:0000047
database_cross_reference: CALOHA:TS-0016
database_cross_reference: EFO:0000238
database_cross_reference: EMAPA:18426
database_cross_reference: EV:0100135
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].
database_cross_reference: FMA:9604
database_cross_reference: GAID:446
database_cross_reference: MA:0000116
database_cross_reference: MAT:0000071
database_cross_reference: MESH:A06.407.071
database_cross_reference: MIAA:0000071
database_cross_reference: OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA
database_cross_reference: SCTID:181127006
comment: 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
id: UBERON:0002369
database_cross_reference: UMLS:C0001625
database_cross_reference: VHOG:0001141
database_cross_reference: Wikipedia:Adrenal_gland
database_cross_reference: XAO:0000164
has_related_synonym: adrenal
has_related_synonym: adrenal capsule
has_related_synonym: adrenal medulla cell
has_related_synonym: atrabiliary capsule
has_related_synonym: epinephric gland
has_related_synonym: epinephros
database_cross_reference: galen:AdrenalGland
has_exact_synonym: glandula adrenalis
has_related_synonym: glandula suprarenalis
has_exact_synonym: glandula suprarenalis
has_related_synonym: interrenal gland
database_cross_reference: ncithesaurus:Adrenal_Gland
has_related_synonym: suprarenal capsule
has_related_synonym: suprarenal gland
has_obo_namespace: uberon
homologous_in: NCBITaxon 7742
imported from: uberon.owl
in_subset: organ slim
in_subset: uberon slim

muscle tissue
type: Class
subclass of: anatomical entity
database_cross_reference: AAO:0000306
database_cross_reference: AEO:0000122
database_cross_reference: CALOHA:TS-0642
database_cross_reference: EHDAA2:0003122
database_cross_reference: FMA:9641
database_cross_reference: MA:0002437
database_cross_reference: MESH:A02.633
definition: Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
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]
database_cross_reference: SCTID:91727004
id: UBERON:0002385
database_cross_reference: UMLS:C2328219
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.
database_cross_reference: Wikipedia:Muscle_tissue
database_cross_reference: galen:MuscleTissue
has_exact_synonym: muscular tissue
database_cross_reference: ncithesaurus:Muscle_Tissue
has_exact_synonym: portion of muscle tissue
has_exact_synonym: textus muscularis
has_obo_namespace: uberon
spatially_disjoint_from: UBERON_0003714
imported from: uberon.owl
in_subset: uberon slim

hippocampal formation
type: Class
subclass of: brain
database_cross_reference: ABA:HPF
database_cross_reference: BM:Tel-HF
database_cross_reference: BTO:0000601
database_cross_reference: EMAPA:32772
database_cross_reference: EMAPA:32845
database_cross_reference: FMA:74038
definition: Hippocampus (proper) plus dentate gyrus and subiculum[definition derived from NIF comments and ontology alignment].
database_cross_reference: MA:0000189
database_cross_reference: NIF_GrossAnatomy:birnlex_715
database_cross_reference: NeuroNames:177
database_cross_reference: SCTID:422867004
id: UBERON:0002421
database_cross_reference: UMLS:C0175202
comment: Usage notes: The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum[NIF]. BTO:0000601 is placed here since it includes the DG. GO also includes dentate gyrus development as part of hippocampus development, so we assume when GO says "hippocampus" it means "hippocampal formation". In ABA HPF = (.. subiculum) + HIP, HIP = DG + AH.
has_related_synonym: archipallium
has_related_synonym: formatio hippocampi
has_narrow_synonym: hippocampus
has_exact_synonym: hippocampus (crosby)
has_related_synonym: major hippocampus
has_related_synonym: primal cortex
has_related_synonym: seahorse
has_obo_namespace: uberon
spatially_disjoint_from: neocortex
spatially_disjoint_from: UBERON_0002264
imported from: uberon.owl
in_subset: uberon slim

granular layer of cerebellar cortex
type: Class
subclass of: brain
database_cross_reference: ABA:CBXgr
database_cross_reference: BTO:0004425
database_cross_reference: CALOHA:TS-1247
database_cross_reference: FMA:83140
database_cross_reference: MA:0000993
database_cross_reference: NIF_GrossAnatomy:birnlex_779
database_cross_reference: NeuroNames:363
definition: The granular layer is the innermost layer of the cerebellar cortex. This layer contains densely packed small neurons, mostly granule cells. Some Golgi cells are found at the outer border. Granule neurons send parallel fibers to the upper molecular layer, where they synapse with Purkinje cell dendrites. Mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons at cerebellar glomeruli in the granule cell layer.
id: UBERON:0002956
database_cross_reference: UMLS:C1708253
has_exact_synonym: cerebellar granular layer
has_exact_synonym: cerebellar granule cell layer
has_exact_synonym: cerebellar granule layer
has_exact_synonym: cerebellum granule cell layer
has_exact_synonym: cerebellum granule layer
has_related_synonym: granular layer of cerebellum
has_exact_synonym: granule cell layer of cerebellar cortex
database_cross_reference: ncithesaurus:Granular_Layer_of_the_Cerebellum
has_exact_synonym: stratum granulosum cerebelli
has_obo_namespace: uberon
spatially_disjoint_from: UBERON_0002979
imported from: uberon.owl

pharyngula stage
type: Class
subclass of: embryo stage
definition: A stage that follows the blastula, gastrula and neurula stages. At the pharyngula stage, all vertebrate embryos show remarkable similarities.
comment: Corresponds to E7-E11 in Mouse (Galis et al, TREE, 2001)
database_cross_reference: DrerDO:0000052
database_cross_reference: EFO:0001310
database_cross_reference: OGES:000006
id: UBERON:0004707
database_cross_reference: Wikipedia:Pharyngula
database_cross_reference: ZFS:0000050
has_related_synonym: pharyngula
has_exact_synonym: phylotypic stage
has_obo_namespace: uberon
imported from: uberon.owl
in_subset: efo slim

late embryonic stage
type: Class
subclass of: embryo stage
database_cross_reference: EV:0300011
database_cross_reference: EVM:2990031
database_cross_reference: FBdv:00005333
database_cross_reference: MIAA:0000399
database_cross_reference: MmusDv:0000031
database_cross_reference: OGES:000023
database_cross_reference: SCTID:367619004
id: UBERON:0007220
has_exact_synonym: embryo late (growth) stage
has_related_synonym: embryo late growth stage
has_related_synonym: embryo late stage
has_narrow_synonym: fetal stage
has_narrow_synonym: fetus
has_narrow_synonym: fetus stage
has_obo_namespace: uberon
imported from: uberon.owl

neonate stage
type: Class
subclass of: EFO_0002948
database_cross_reference: BTO:0001762
database_cross_reference: EV:0300037
comment: Editor note: consider splitting infant/newborn
database_cross_reference: HsapDv:0000082
database_cross_reference: HsapDv:0000083
database_cross_reference: MmusDv:0000038
database_cross_reference: NIF_Organism:birnlex_695
database_cross_reference: OGES:000025
definition: Of or pertaining to the period of time immediately following birth, or to the newborn.
id: UBERON:0007221
database_cross_reference: Wikipedia:Infant
has_narrow_synonym: fledgling stage
has_narrow_synonym: hatchling
has_narrow_synonym: hatchling stage
database_cross_reference: http://neurolex.org/wiki/Category:Infant_organism
database_cross_reference: http://neurolex.org/wiki/Category:Newborn_organism
has_narrow_synonym: infant stage
has_exact_synonym: neonatal stage
has_narrow_synonym: nestling stage
has_related_synonym: newborn stage
has_obo_namespace: uberon
imported from: uberon.owl

late adult stage
type: Class
subclass of: post-juvenile adult stage
database_cross_reference: EV:0300123
database_cross_reference: HsapDv:0000093
database_cross_reference: NIF_Organism:birnlex_691
id: UBERON:0007222
database_cross_reference: UMLS:C0001792
has_related_synonym: elderly
has_related_synonym: elderly stage
has_related_synonym: geriatric
has_related_synonym: geriatric stage
database_cross_reference: ncithesaurus:Elderly
has_obo_namespace: uberon
imported from: uberon.owl

craniocervical region
type: Class
subclass of: anatomical entity
database_cross_reference: CALOHA:TS-2356
database_cross_reference: EV:0100009
database_cross_reference: FMA:280881
database_cross_reference: MA:0000006
database_cross_reference: SCTID:361355005
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.
id: UBERON:0007811
database_cross_reference: UMLS:C0460004
database_cross_reference: WikipediaCategory:Head_and_neck
database_cross_reference: galen:HeadAndNeck
has_exact_synonym: head and neck
has_related_synonym: head or neck
database_cross_reference: ncithesaurus:Head_and_Neck
has_obo_namespace: uberon
imported from: uberon.owl

perinatal stage
type: Class
subclass of: life cycle stage
comment: In birds, the paranatal stage starts when the beak penetrates into the air pocket (air cell) between the inner and outer shell membranes
id: UBERON:0012101
has_narrow_synonym: paranatal stage
definition: the period spanning the range immediately before and after birth
has_obo_namespace: uberon
imported from: uberon.owl