processual entity
type: Class
disjoint with: anatomical entity
IAO_0000115: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: BFO:0000003
has OBO namespace: uberon
id: UBERON:0000000
in subset: common anatomy
in subset: upper level
comment: This term is being aligned with COB

Axiom
annotated source: processual entity
annotated property: IAO_0000115
annotated target: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
has db xref: span:ProcessualEntity

uterine cervix
type: Class
equivalent class: Class
  intersection of: UBERON_0001560
  intersection of: Restriction
    on property: BFO_0000050
    some values from: uterus
  intersection of: Restriction
    on property: RO_0002150
    some values from: vagina
subclass of: UBERON_0001560
subclass of: UBERON_0005156
subclass of: Restriction
  on property: BFO_0000050
  some values from: uterus
subclass of: Restriction
  on property: RO_0002150
  some values from: vagina
subclass of: Restriction
  on property: RO_0002433
  some values from: uterus
IAO_0000115: Lower, narrow portion of the uterus where it joins with the top end of the vagina.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG]
UBPROP_0000003: 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]
UBPROP_0000007: cervical
has broad synonym: cervix
has db xref: BTO:0001421
has db xref: BTO:0002249
has db xref: CALOHA:TS-0134
has db xref: EFO:0000979
has db xref: EMAPA:29927
has db xref: EV:0100114
has db xref: FMA:17740
has db xref: GAID:376
has db xref: MA:0000392
has db xref: MAT:0000292
has db xref: MESH:D002584
has db xref: NCIT:C12311
has db xref: SCTID:181453009
has db xref: UMLS:C0007874
has db xref: VHOG:0001359
has db xref: Wikipedia:Cervix
has db xref: galen:CervixUteri
has exact synonym: canalis cervicis uteri
has exact synonym: caudal segment of uterus
has exact synonym: cervical canal of uterus
has exact synonym: cervix uteri
has exact synonym: neck of uterus
has exact synonym: uterine cervix
has OBO namespace: uberon
has related synonym: cervical canal
has related synonym: cervix of uterus
id: UBERON:0000002
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: uterine cervix
annotated property: IAO_0000115
annotated target: Lower, narrow portion of the uterus where it joins with the top end of the vagina.
has db xref: Wikipedia:Cervix
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: uterine cervix
annotated property: UBPROP_0000001
annotated target: The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001359
ontology: VHOG
source: http://bgee.unil.ch/
source: http://medical-dictionary.thefreedictionary.com/uterine+cervix

Axiom
annotated source: uterine cervix
annotated property: UBPROP_0000003
annotated target: 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]
date retrieved: 2012-09-17
external class: VHOG:0001359
ontology: VHOG
source: DOI:10.1098/rspb.2004.2848 Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004)
source: http://bgee.unil.ch/

Axiom
annotated source: uterine cervix
annotated property: hasBroadSynonym
annotated target: cervix
has db xref: EFO:0000979

Axiom
annotated source: uterine cervix
annotated property: hasDbXref
annotated target: UMLS:C0007874
source: ncithesaurus:Cervix

Axiom
annotated source: uterine cervix
annotated property: hasExactSynonym
annotated target: canalis cervicis uteri
has db xref: FMA:17740
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: uterine cervix
annotated property: hasExactSynonym
annotated target: cervical canal of uterus
has db xref: FMA:17740

Axiom
annotated source: uterine cervix
annotated property: hasExactSynonym
annotated target: cervix uteri
has db xref: EMAPA:29927
has synonym type: OMO_0003011

Axiom
annotated source: uterine cervix
annotated property: hasExactSynonym
annotated target: neck of uterus
has db xref: FMA:17740

Axiom
annotated source: uterine cervix
annotated property: hasExactSynonym
annotated target: uterine cervix
has db xref: FMA:17740

Axiom
annotated source: uterine cervix
annotated property: hasRelatedSynonym
annotated target: cervical canal
has db xref: FMA:17740

Axiom
annotated source: uterine cervix
annotated property: hasRelatedSynonym
annotated target: cervix of uterus
has db xref: BTO:0001421

naris
type: Class
equivalent class: Class
  intersection of: orifice
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0005725
  intersection of: Restriction
    on property: RO_0002176
    some values from: UBERON_0001707
subclass of: orifice
subclass of: Restriction
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0005725
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7711
subclass of: Restriction
  on property: RO_0002176
  some values from: UBERON_0001707
IAO_0000115: Orifice of the olfactory system. The naris is the route by which odorants enter the olfactory system[MAH].
UBPROP_0000001: One of paired external openings of the nasal chamber.[AAO]
UBPROP_0000003: Naris refer to the external and interior naris (choana) of tetrapods, and to anterior and posterior naris of zebrafish. It seems now accepted that the structure is homologous: The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG]
UBPROP_0000008: in actinopterygians, both pairs of nares are external. In tetrapods, the exhalant empties into the buccal cavity
UBPROP_0000012: we have classified this as an orifice, according to FMA. Note that in FMA, orifices are immaterial entities, but in ZFA this is a surface structure
has db xref: AAO:0000311
has db xref: EHDAA2:0001225
has db xref: EHDAA:9083
has db xref: EMAPA:17847
has db xref: MA:0000282
has db xref: SCTID:272650008
has db xref: VHOG:0000663
has db xref: galen:Naris
has OBO namespace: uberon
id: UBERON:0000003
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: naris
annotated property: subClassOf
annotated target: Restriction
source: ZFA

Axiom
annotated source: naris
annotated property: IAO_0000115
annotated target: Orifice of the olfactory system. The naris is the route by which odorants enter the olfactory system[MAH].
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: naris
annotated property: UBPROP_0000001
annotated target: One of paired external openings of the nasal chamber.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000311
ontology: AAO
source: AAO:EJS

Axiom
annotated source: naris
annotated property: UBPROP_0000003
annotated target: Naris refer to the external and interior naris (choana) of tetrapods, and to anterior and posterior naris of zebrafish. It seems now accepted that the structure is homologous: The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000663
ontology: VHOG
source: DOI:10.1038/nature02843 Zhu M, Ahlberg PE, The origin of the internal nostril in tetrapodes. Nature (2004)
source: http://bgee.unil.ch/

Axiom
annotated source: naris
annotated property: UBPROP_0000012
annotated target: we have classified this as an orifice, according to FMA. Note that in FMA, orifices are immaterial entities, but in ZFA this is a surface structure
external ontology: FMA

nose
type: Class
subclass of: UBERON_0002268
subclass of: UBERON_0004121
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7742
subclass of: Restriction
  on property: RO_0002216
  some values from: GO_0007608
subclass of: Restriction
  on property: RO_0002433
  some values from: respiratory system
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0001456
subclass of: Restriction
  on property: RO_0002551
  some values from: UBERON_0006813
IAO_0000115: The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity.
UBPROP_0000001: Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047].
UBPROP_0000001: a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose].
UBPROP_0000001: the organ that is specialized for smell and is part of the respiratory system
UBPROP_0000008: the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359]
has db xref: BTO:0000840
has db xref: CALOHA:TS-2037
has db xref: EHDAA2:0001274
has db xref: EHDAA:1502
has db xref: EMAPA:16542
has db xref: EV:0100037
has db xref: EV:0100370
has db xref: FMA:46472
has db xref: GAID:77
has db xref: MA:0000281
has db xref: MAT:0000139
has db xref: MESH:D009666
has db xref: MIAA:0000139
has db xref: NCIT:C12756
has db xref: SCTID:181195007
has db xref: TAO:0000047
has db xref: UMLS:C0028429
has db xref: Wikipedia:Nose
has db xref: ZFA:0000047
has db xref: galen:Nose
has exact synonym: nasal sac
has exact synonym: nose
has exact synonym: peripheral olfactory organ
has OBO namespace: uberon
has related synonym: nasus
has related synonym: olfactory apparatus
has related synonym: proboscis
id: UBERON:0000004
in subset: efo slim
in subset: major organ
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: nose
annotated property: subClassOf
annotated target: Restriction
source: FMA
source: ZFA-def

Axiom
annotated source: nose
annotated property: subClassOf
annotated target: Restriction
source: ZFA

Axiom
annotated source: nose
annotated property: IAO_0000115
annotated target: The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity.
has db xref: UBERON:cjm

Axiom
annotated source: nose
annotated property: UBPROP_0000001
annotated target: Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047].
source: ZFA:0000047

Axiom
annotated source: nose
annotated property: UBPROP_0000001
annotated target: a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose].
source: Wikipedia:Nose

Axiom
annotated source: nose
annotated property: UBPROP_0000001
annotated target: the organ that is specialized for smell and is part of the respiratory system
source: MP:0002233

Axiom
annotated source: nose
annotated property: hasDbXref
annotated target: UMLS:C0028429
source: ncithesaurus:Nose

Axiom
annotated source: nose
annotated property: hasExactSynonym
annotated target: nasal sac
has db xref: ZFA:0000047
has synonym type: SENSU

Axiom
annotated source: nose
annotated property: hasExactSynonym
annotated target: nose
has db xref: MA:0000281
has synonym type: HUMAN PREFERRED

Axiom
annotated source: nose
annotated property: hasExactSynonym
annotated target: peripheral olfactory organ
has db xref: ZFA:0000047

Axiom
annotated source: nose
annotated property: hasRelatedSynonym
annotated target: nasus
has db xref: Wikipedia:Nose
has synonym type: OMO_0003011

Axiom
annotated source: nose
annotated property: hasRelatedSynonym
annotated target: olfactory apparatus
has db xref: UBERON:cjm

chemosensory organ
type: Class
equivalent class: Class
  intersection of: sense organ
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0007606
subclass of: sense organ
subclass of: Restriction
  on property: BFO_0000050
  some values from: nervous system
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0005726
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0007606
has db xref: FBbt:00005157
has exact synonym: chemosensory sensory organ
has OBO namespace: uberon
id: UBERON:0000005
in subset: functional classification
in subset: uberon slim

Axiom
annotated source: chemosensory organ
annotated property: hasDbXref
annotated target: FBbt:00005157
mapping justification: ManualMappingCuration

Axiom
annotated source: chemosensory organ
annotated property: hasExactSynonym
annotated target: chemosensory sensory organ
has db xref: FBbt:00005157

islet of Langerhans
type: Class
subclass of: UBERON_0034922
subclass of: Restriction
  on property: BFO_0000050
  some values from: endocrine pancreas
subclass of: Restriction
  on property: RO_0002433
  some values from: endocrine pancreas
IAO_0000115: The clusters of hormone-producing cells that are scattered throughout the pancreas.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO]
UBPROP_0000003: Mammals, birds, reptiles and amphibians have a pancreas with similar histology and mode of development, while in some fish, the islet cells are segregated as Brockmann bodies.[well established][VHOG]
UBPROP_0000008: A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986)
UBPROP_0000202: FMA_76489
has db xref: AAO:0010406
has db xref: BTO:0000991
has db xref: CALOHA:TS-0741
has db xref: EFO:0000856
has db xref: EMAPA:32927
has db xref: EV:0100130
has db xref: FMA:16016
has db xref: GAID:324
has db xref: MA:0000127
has db xref: MAT:0000076
has db xref: MESH:D007515
has db xref: MIAA:0000076
has db xref: NCIT:C12608
has db xref: UMLS:C0022131
has db xref: VHOG:0000646
has db xref: Wikipedia:Islets_of_Langerhans
has db xref: XAO:0000159
has exact synonym: pancreatic insula
has exact synonym: pancreatic islet
has OBO namespace: uberon
has related synonym: island of Langerhans
has related synonym: island of pancreas
has related synonym: islets of Langerhans
id: UBERON:0000006
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: islet of Langerhans
annotated property: subClassOf
annotated target: Restriction
source: PMID:16417468

Axiom
annotated source: islet of Langerhans
annotated property: subClassOf
annotated target: Restriction
source: PMID:16417468

Axiom
annotated source: islet of Langerhans
annotated property: subClassOf
annotated target: Restriction
source: PMID:16417468

Axiom
annotated source: islet of Langerhans
annotated property: IAO_0000115
annotated target: The clusters of hormone-producing cells that are scattered throughout the pancreas.
has db xref: MA:0000127
has db xref: MESH:A03.734.414
has db xref: MP:0005215

Axiom
annotated source: islet of Langerhans
annotated property: UBPROP_0000001
annotated target: Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010406
ontology: AAO
source: AAO:BJB

Axiom
annotated source: islet of Langerhans
annotated property: UBPROP_0000003
annotated target: Mammals, birds, reptiles and amphibians have a pancreas with similar histology and mode of development, while in some fish, the islet cells are segregated as Brockmann bodies.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000646
ontology: VHOG
source: PMID:7600975 Slack JMW, Developmental biology of the pancreas. Development (1995)
source: http://bgee.unil.ch/

Axiom
annotated source: islet of Langerhans
annotated property: UBPROP_0000008
annotated target: A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986)
source: PMID:16417468

Axiom
annotated source: islet of Langerhans
annotated property: hasDbXref
annotated target: UMLS:C0022131
source: ncithesaurus:Islet_of_Langerhans

Axiom
annotated source: islet of Langerhans
annotated property: hasRelatedSynonym
annotated target: island of Langerhans
has db xref: BTO:0000991

Axiom
annotated source: islet of Langerhans
annotated property: hasRelatedSynonym
annotated target: island of pancreas
has db xref: BTO:0000991

pituitary gland
type: Class
subclass of: UBERON_0002368
subclass of: UBERON_0003133
subclass of: UBERON_0003296
subclass of: UBERON_0003937
subclass of: UBERON_0004121
subclass of: Restriction
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0002196
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0002198
subclass of: Restriction
  on property: RO_0002216
  some values from: GO_0007276
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0001894
IAO_0000115: The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN].
UBPROP_0000001: An endocrine gland derived from infundibulum of the floor of the diencephalon and an ectodermal dorsal protrusion from the buccal cavity which controls the secretion of many hormones influencing the function of various organs of the body.[AAO]
UBPROP_0000001: An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin.[TAO]
UBPROP_0000003: It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]
UBPROP_0000008: The lamprey possesses a distinct pituitary organ and hormones, the ascidian does not show distinct evidence of them [Sower S, Freamat M, Kavanaugh S. The origins of the vertebrate hypothalamic-pituitary-gonadal (HPG) and hypothalamic-pituitary-thyroid (HPT) endocrine systems: new insights from lampreys. Gen Comp Endocrinol 2009;161:20-9]
has broad synonym: Hp
has db xref: AAO:0010536
has db xref: BAMS:PIT
has db xref: BAMS:Pit
has db xref: BIRNLEX:1353
has db xref: BM:Die-Hy-HY
has db xref: BTO:0001073
has db xref: CALOHA:TS-0798
has db xref: DHBA:10505
has db xref: EFO:0000857
has db xref: EHDAA2:0001471
has db xref: EHDAA:2183
has db xref: EHDAA:4477
has db xref: EMAPA:35998
has db xref: EV:0100132
has db xref: FMA:13889
has db xref: GAID:457
has db xref: HBA:4634
has db xref: MA:0000176
has db xref: MAT:0000077
has db xref: MESH:D010902
has db xref: MIAA:0000077
has db xref: NCIT:C12399
has db xref: SCTID:181125003
has db xref: TAO:0000118
has db xref: UMLS:C0032005
has db xref: VHOG:0000143
has db xref: Wikipedia:Pituitary_gland
has db xref: XAO:0000017
has db xref: ZFA:0000118
has db xref: neuronames:399
has exact synonym: glandula pituitaria
has exact synonym: pituitary
has exact synonym: pituitary body
has OBO namespace: uberon
has related synonym: hypophysis
has related synonym: hypophysis cerebri
id: UBERON:0000007
in subset: efo slim
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core
comment: Terminology note: hypophysis and pituitary gland are often used informally as synonyms, but the hypophysis also includes the small infundibular or pituitary stalk[Neumann 2020]

Axiom
annotated source: pituitary gland
annotated property: hasDbXref
annotated target: neuronames:399
source: BIRNLEX:1353

Axiom
annotated source: pituitary gland
annotated property: hasExactSynonym
annotated target: glandula pituitaria
has db xref: Wikipedia:Pituitary_gland
has synonym type: OMO_0003011

Axiom
annotated source: pituitary gland
annotated property: hasExactSynonym
annotated target: pituitary
has db xref: BTO:0001073

Axiom
annotated source: pituitary gland
annotated property: hasExactSynonym
annotated target: pituitary body
has db xref: BTO:0001073

Axiom
annotated source: pituitary gland
annotated property: hasRelatedSynonym
annotated target: hypophysis
has db xref: ZFA:0000118

Axiom
annotated source: pituitary gland
annotated property: hasRelatedSynonym
annotated target: hypophysis cerebri
has db xref: MA:0000176

Axiom
annotated source: pituitary gland
annotated property: subClassOf
annotated target: UBERON_0002368
source: BTO
source: EFO
source: VHOG

Axiom
annotated source: pituitary gland
annotated property: subClassOf
annotated target: Restriction
source: ZFA

Axiom
annotated source: pituitary gland
annotated property: subClassOf
annotated target: Restriction
source: ZFA

Axiom
annotated source: pituitary gland
annotated property: subClassOf
annotated target: Restriction
source: PMID:19084529

Axiom
annotated source: pituitary gland
annotated property: IAO_0000115
annotated target: The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN].
has db xref: Wikipedia:Pituitary_gland
has db xref: ZFIN:curator

Axiom
annotated source: pituitary gland
annotated property: UBPROP_0000001
annotated target: An endocrine gland derived from infundibulum of the floor of the diencephalon and an ectodermal dorsal protrusion from the buccal cavity which controls the secretion of many hormones influencing the function of various organs of the body.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010536
ontology: AAO
source: AAO:BJB

Axiom
annotated source: pituitary gland
annotated property: UBPROP_0000001
annotated target: An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000118
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: pituitary gland
annotated property: UBPROP_0000003
annotated target: It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000143
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510
source: http://bgee.unil.ch/

Axiom
annotated source: pituitary gland
annotated property: hasBroadSynonym
annotated target: Hp
has db xref: BIRNLEX:1353
has db xref: NIFSTD:NeuroNames_abbrevSource
has synonym type: OMO_0003000

Axiom
annotated source: pituitary gland
annotated property: hasDbXref
annotated target: UMLS:C0032005
source: BIRNLEX:1353
source: ncithesaurus:Pituitary_Gland

submucosa
type: Class
subclass of: UBERON_0004923
subclass of: Restriction
  on property: BSPO_0001107
  some values from: mucosa
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7711
subclass of: Restriction
  on property: RO_0002473
  some values from: UBERON_0002384
IAO_0000115: A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted].
UBPROP_0000007: submucosal
has db xref: BTO:0002107
has db xref: FMA:85391
has db xref: FMA:85392
has db xref: NCIT:C13167
has db xref: SCTID:68439008
has db xref: UMLS:C0225344
has db xref: Wikipedia:Submucosa
has exact synonym: organ submucosa
has exact synonym: region of submucosa
has exact synonym: submucosa of organ
has exact synonym: submucosa of region of organ
has OBO namespace: uberon
has related synonym: submucous layer
has related synonym: tela submucosa
has related synonym: tunica submucosa
id: UBERON:0000009
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: submucosa
annotated property: IAO_0000115
annotated target: A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted].
has db xref: Wikipedia:Submucosa

Axiom
annotated source: submucosa
annotated property: hasDbXref
annotated target: UMLS:C0225344
source: ncithesaurus:Submucosa

Axiom
annotated source: submucosa
annotated property: hasExactSynonym
annotated target: organ submucosa
has db xref: FMA:85391

Axiom
annotated source: submucosa
annotated property: hasExactSynonym
annotated target: region of submucosa
has db xref: FMA:85392

Axiom
annotated source: submucosa
annotated property: hasExactSynonym
annotated target: submucosa of organ
has db xref: FMA:85391

Axiom
annotated source: submucosa
annotated property: hasExactSynonym
annotated target: submucosa of region of organ
has db xref: FMA:85392

Axiom
annotated source: submucosa
annotated property: hasRelatedSynonym
annotated target: submucous layer
has db xref: BTO:0002107

Axiom
annotated source: submucosa
annotated property: hasRelatedSynonym
annotated target: tela submucosa
has db xref: BTO:0002107

peripheral nervous system
type: Class
subclass of: UBERON_0011216
subclass of: Restriction
  on property: BFO_0000050
  some values from: nervous system
IAO_0000115: A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]
UBPROP_0000001: Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]
UBPROP_0000001: The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)
UBPROP_0000003: (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]
has broad synonym: PNS
has db xref: AAO:0000429
has db xref: BAMS:PNS
has db xref: BILA:0000081
has db xref: BIRNLEX:1111
has db xref: BTO:0001028
has db xref: CALOHA:TS-0808
has db xref: EFO:0000891
has db xref: EHDAA2:0001445
has db xref: EHDAA:2893
has db xref: EMAPA:16665
has db xref: EV:0100335
has db xref: FBbt:00005098
has db xref: FMA:9903
has db xref: GAID:715
has db xref: MA:0000218
has db xref: MAT:0000338
has db xref: MESH:D017933
has db xref: MIAA:0000338
has db xref: NCIT:C12465
has db xref: SCTID:362292005
has db xref: TAO:0000142
has db xref: UMLS:C0206417
has db xref: UMLS:C1305921
has db xref: VHOG:0000399
has db xref: Wikipedia:Peripheral_nervous_system
has db xref: XAO:0000178
has db xref: ZFA:0000142
has db xref: neuronames:3232
has exact synonym: pars peripherica
has exact synonym: systema nervosum periphericum
has OBO namespace: uberon
id: UBERON:0000010
in subset: cumbo
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: peripheral nervous system
annotated property: subClassOf
annotated target: UBERON_0011216
source: cjm

Axiom
annotated source: peripheral nervous system
annotated property: IAO_0000115
annotated target: A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
has db xref: GO:0007422

Axiom
annotated source: peripheral nervous system
annotated property: UBPROP_0000001
annotated target: Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000142
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: peripheral nervous system
annotated property: UBPROP_0000001
annotated target: Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000429
ontology: AAO
source: AAO:BJB

Axiom
annotated source: peripheral nervous system
annotated property: UBPROP_0000001
annotated target: The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)
source: http://neurolex.org/wiki/Cumbo_terms

Axiom
annotated source: peripheral nervous system
annotated property: UBPROP_0000003
annotated target: (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000399
ontology: VHOG
source: DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006)
source: http://bgee.unil.ch/

Axiom
annotated source: peripheral nervous system
annotated property: hasBroadSynonym
annotated target: PNS
has synonym type: OMO_0003000

Axiom
annotated source: peripheral nervous system
annotated property: hasDbXref
annotated target: FBbt:00005098
mapping justification: ManualMappingCuration

Axiom
annotated source: peripheral nervous system
annotated property: hasDbXref
annotated target: UMLS:C0206417
source: BIRNLEX:1111
source: ncithesaurus:Peripheral_Nervous_System

Axiom
annotated source: peripheral nervous system
annotated property: hasDbXref
annotated target: UMLS:C1305921
source: BIRNLEX:1111

Axiom
annotated source: peripheral nervous system
annotated property: hasExactSynonym
annotated target: pars peripherica
has db xref: FMA:9903
has db xref: FMA:TA
has db xref: Wikipedia:Peripheral_nervous_system
has synonym type: OMO_0003011

Axiom
annotated source: peripheral nervous system
annotated property: hasExactSynonym
annotated target: systema nervosum periphericum
has db xref: FMA:9903
has db xref: FMA:TA
has db xref: Wikipedia:Peripheral_nervous_system
has synonym type: OMO_0003011

parasympathetic nervous system
type: Class
subclass of: UBERON_0010314
subclass of: UBERON_0011216
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0002410
IAO_0000115: The parasympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system. Parasympathetic nerves emerge cranially as pre ganglionic fibers from oculomotor, facial, glossopharyngeal and vagus and from the sacral region of the spinal cord. Most neurons are cholinergic and responses are mediated by muscarinic receptors. The parasympathetic system innervates, for example: salivary glands, thoracic and abdominal viscera, bladder and genitalia[GO].
UBPROP_0000001: Part of the autonomic nervous system which has opposing physiological effects of the sympathetic nervous system. Examples include decreasing the heart rate or dilating the blood vessels.[AAO]
UBPROP_0000003: In mammals, the autonomic nervous system is divided into two contrasting, antagonistic systems of control over visceral activity: the sympathetic system and the parasympathetic system (reference 1); In general, the teleosts may be considered phylogenetically the first class of vertebrates in which the heart is regulated by both sympathetic and parasympathetic neural pathways (reference 2).[well established][VHOG]
has db xref: AAO:0010488
has db xref: BIRNLEX:2517
has db xref: BTO:0001833
has db xref: CALOHA:TS-2094
has db xref: EFO:0000894
has db xref: EHDA:10096
has db xref: EHDAA2:0001402
has db xref: EHDAA:4655
has db xref: EMAPA:17270
has db xref: FMA:9907
has db xref: GAID:708
has db xref: MA:0000223
has db xref: MAT:0000101
has db xref: MESH:D010275
has db xref: MIAA:0000101
has db xref: NCIT:C12764
has db xref: SCTID:362496006
has db xref: TAO:0001575
has db xref: UMLS:C0030510
has db xref: UMLS:C1305770
has db xref: VHOG:0000755
has db xref: Wikipedia:Parasympathetic_nervous_system
has db xref: ZFA:0001575
has exact synonym: PNS - parasympathetic
has exact synonym: parasympathetic part of autonomic division of nervous system
has exact synonym: pars parasympathica divisionis autonomici systematis nervosi
has OBO namespace: uberon
has related synonym: pars parasympathica divisionis autonomici systematis nervosi
id: UBERON:0000011
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: parasympathetic nervous system
annotated property: subClassOf
annotated target: UBERON_0011216
source: cjm

Axiom
annotated source: parasympathetic nervous system
annotated property: subClassOf
annotated target: Restriction
source: FMA
source: MA
source: WP
source: ZFA-modified-from-isa

Axiom
annotated source: parasympathetic nervous system
annotated property: IAO_0000115
annotated target: The parasympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system. Parasympathetic nerves emerge cranially as pre ganglionic fibers from oculomotor, facial, glossopharyngeal and vagus and from the sacral region of the spinal cord. Most neurons are cholinergic and responses are mediated by muscarinic receptors. The parasympathetic system innervates, for example: salivary glands, thoracic and abdominal viscera, bladder and genitalia[GO].
has db xref: GO:0048486

Axiom
annotated source: parasympathetic nervous system
annotated property: UBPROP_0000001
annotated target: Part of the autonomic nervous system which has opposing physiological effects of the sympathetic nervous system. Examples include decreasing the heart rate or dilating the blood vessels.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010488
ontology: AAO
source: AAO:BJB

Axiom
annotated source: parasympathetic nervous system
annotated property: UBPROP_0000003
annotated target: In mammals, the autonomic nervous system is divided into two contrasting, antagonistic systems of control over visceral activity: the sympathetic system and the parasympathetic system (reference 1); In general, the teleosts may be considered phylogenetically the first class of vertebrates in which the heart is regulated by both sympathetic and parasympathetic neural pathways (reference 2).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000755
ontology: VHOG
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.634, DOI:10.1016/S0306-4530(98)00057-2 Porges SW, Love: an emergent property of the mammalian autonomic nervous system. Psychoneuroendocrinology (1998)
source: http://bgee.unil.ch/

Axiom
annotated source: parasympathetic nervous system
annotated property: hasDbXref
annotated target: UMLS:C0030510
source: BIRNLEX:2517
source: ncithesaurus:Parasympathetic_Nervous_System

Axiom
annotated source: parasympathetic nervous system
annotated property: hasDbXref
annotated target: UMLS:C1305770
source: BIRNLEX:2517

Axiom
annotated source: parasympathetic nervous system
annotated property: hasExactSynonym
annotated target: pars parasympathica divisionis autonomici systematis nervosi
has db xref: FMA:9907
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: parasympathetic nervous system
annotated property: hasRelatedSynonym
annotated target: pars parasympathica divisionis autonomici systematis nervosi
has db xref: Wikipedia:Parasympathetic_nervous_system
has synonym type: OMO_0003011

somatic nervous system
type: Class
subclass of: UBERON_0011216
subclass of: Restriction
  on property: BFO_0000050
  some values from: peripheral nervous system
subclass of: Restriction
  on property: RO_0002433
  some values from: nervous system
IAO_0000115: Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors.
has db xref: EFO:0000892
has db xref: FMA:9904
has db xref: MA:0002850
has db xref: MAT:0000099
has db xref: MIAA:0000099
has db xref: NLXANAT:100301
has db xref: Wikipedia:Somatic_nervous_system
has exact synonym: PNS - somatic
has exact synonym: somatic nervous system, somatic division
has exact synonym: somatic part of peripheral nervous system
has exact synonym: somatic peripheral nervous system
has OBO namespace: uberon
id: UBERON:0000012
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: somatic nervous system
annotated property: subClassOf
annotated target: UBERON_0011216
source: cjm

Axiom
annotated source: somatic nervous system
annotated property: IAO_0000115
annotated target: Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors.
has db xref: NLXANAT:100301

Axiom
annotated source: somatic nervous system
annotated property: hasExactSynonym
annotated target: somatic nervous system, somatic division
has db xref: NLXANAT:100301

Axiom
annotated source: somatic nervous system
annotated property: hasExactSynonym
annotated target: somatic part of peripheral nervous system
has db xref: UBERON:cjm

Axiom
annotated source: somatic nervous system
annotated property: hasExactSynonym
annotated target: somatic peripheral nervous system
has db xref: NLXANAT:100301

sympathetic nervous system
type: Class
subclass of: UBERON_0011216
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0002410
IAO_0000115: The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO].
UBPROP_0000001: Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO]
UBPROP_0000001: The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
UBPROP_0000003: The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG]
UBPROP_0000011: has developmental contribution from NC in verteberates (https://github.com/obophenotype/uberon/wiki/The-neural-crest)
has db xref: AAO:0010487
has db xref: BIRNLEX:2516
has db xref: BTO:0001832
has db xref: CALOHA:TS-2050
has db xref: EFO:0000893
has db xref: EHDAA2:0001971
has db xref: EHDAA:3769
has db xref: EMAPA:16985
has db xref: FMA:9906
has db xref: GAID:710
has db xref: MA:0000225
has db xref: MESH:D013564
has db xref: MIAA:0000100
has db xref: NCIT:C12795
has db xref: SCTID:362484004
has db xref: TAO:0001576
has db xref: UMLS:C0039044
has db xref: UMLS:C1269646
has db xref: VHOG:0000384
has db xref: Wikipedia:Sympathetic_nervous_system
has db xref: ZFA:0001576
has exact synonym: pars sympathica divisionis autonomici systematis nervosi
has exact synonym: sympathetic nervous system
has exact synonym: sympathetic part of autonomic division of nervous system
has OBO namespace: uberon
has related synonym: pars sympathica divisionis autonomici systematis nervosi
id: UBERON:0000013
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: sympathetic nervous system
annotated property: subClassOf
annotated target: UBERON_0011216
source: cjm

Axiom
annotated source: sympathetic nervous system
annotated property: subClassOf
annotated target: Restriction
source: FMA
source: MA
source: ZFA-modified-from-isa

Axiom
annotated source: sympathetic nervous system
annotated property: IAO_0000115
annotated target: The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO].
has db xref: GO:0048485

Axiom
annotated source: sympathetic nervous system
annotated property: UBPROP_0000001
annotated target: Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010487
ontology: AAO
source: AAO:BJB

Axiom
annotated source: sympathetic nervous system
annotated property: UBPROP_0000001
annotated target: The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000384
ontology: VHOG
source: http://bgee.unil.ch/

Axiom
annotated source: sympathetic nervous system
annotated property: UBPROP_0000003
annotated target: The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000384
ontology: VHOG
source: ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.461-463
source: http://bgee.unil.ch/

Axiom
annotated source: sympathetic nervous system
annotated property: hasDbXref
annotated target: UMLS:C0039044
source: BIRNLEX:2516
source: ncithesaurus:Sympathetic_Nervous_System

Axiom
annotated source: sympathetic nervous system
annotated property: hasDbXref
annotated target: UMLS:C1269646
source: BIRNLEX:2516

Axiom
annotated source: sympathetic nervous system
annotated property: hasExactSynonym
annotated target: pars sympathica divisionis autonomici systematis nervosi
has db xref: FMA:9906
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: sympathetic nervous system
annotated property: hasRelatedSynonym
annotated target: pars sympathica divisionis autonomici systematis nervosi
has db xref: Wikipedia:Sympathetic_nervous_system
has synonym type: OMO_0003011

zone of skin
type: Class
subclass of: UBERON_0010314
subclass of: UBERON_0034944
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002097
subclass of: Restriction
  on property: BFO_0000051
  some values from: skin epidermis
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0002067
IAO_0000115: Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
IAO_0000232: Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
UBPROP_0000003: (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]
UBPROP_0000012: we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive
has db xref: EHDAA:6530
has db xref: EV:0100152
has db xref: FMA:86166
has db xref: GAID:933
has db xref: MA:0000151
has db xref: MAT:0000284
has db xref: MESH:D012867
has db xref: MIAA:0000284
has db xref: SCTID:20795001
has db xref: VHOG:0000860
has db xref: Wikipedia:Skin
has exact synonym: portion of skin
has exact synonym: region of skin
has exact synonym: skin
has exact synonym: skin region
has exact synonym: skin zone
has OBO namespace: uberon
id: UBERON:0000014
in subset: pheno slim

Axiom
annotated source: zone of skin
annotated property: subClassOf
annotated target: UBERON_0034944
source: FMA

Axiom
annotated source: zone of skin
annotated property: IAO_0000115
annotated target: Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
has db xref: Wikipedia:Skin
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: zone of skin
annotated property: UBPROP_0000003
annotated target: (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000860
ontology: VHOG
source: DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)
source: http://bgee.unil.ch/

Axiom
annotated source: zone of skin
annotated property: hasExactSynonym
annotated target: skin
has db xref: MA:0000151

non-material anatomical boundary
type: Class
subclass of: immaterial anatomical entity
IAO_0000115: A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: AEO:0000192
has db xref: CARO:0000010
has db xref: FMA:50705
has exact synonym: anatomical boundary
has OBO namespace: uberon
id: UBERON:0000015
in subset: common anatomy
in subset: upper level
comment: Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms.

Axiom
annotated source: non-material anatomical boundary
annotated property: subClassOf
annotated target: immaterial anatomical entity
source: CARO

Axiom
annotated source: non-material anatomical boundary
annotated property: IAO_0000115
annotated target: A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
has db xref: CARO:0000010

Axiom
annotated source: non-material anatomical boundary
annotated property: hasExactSynonym
annotated target: anatomical boundary
has db xref: CARO:0000010

endocrine pancreas
type: Class
subclass of: compound organ component
subclass of: UBERON_0004119
subclass of: Restriction
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001264
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0003923
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0001264
subclass of: Restriction
  on property: RO_0002473
  some values from: islet of Langerhans
IAO_0000115: The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin.
IAO_0000116: create a separate class for distributed pancreas, eg cyclostomes?
RO_0002175: NCBITaxon 9606
UBPROP_0000001: The part of the pancreas that acts as an endocrine gland, consisting of the islets of Langerhans, which secrete insulin and other hormones. [TFD][VHOG]
UBPROP_0000001: The zebrafish endocrine pancreas is composed of small groups of islet cells that are distributed throughout the exocrine pancreas. The islet cells produce insulin, glucagon and somatostatin.[TAO]
UBPROP_0000003: 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]
UBPROP_0000008: endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys
has db xref: BTO:0000650
has db xref: CALOHA:TS-1302
has db xref: EFO:0002542
has db xref: EMAPA:35305
has db xref: EV:0100129
has db xref: FMA:16018
has db xref: MA:0001582
has db xref: MESH:D007515
has db xref: NCIT:C32509
has db xref: SCTID:361339003
has db xref: TAO:0001260
has db xref: VHOG:0000049
has db xref: Wikipedia:Islets_of_Langerhans
has db xref: ZFA:0001260
has exact synonym: endocrine pancreas
has exact synonym: pars endocrina pancreatis
has OBO namespace: uberon
has related synonym: endocrine part of pancreas
has related synonym: islets of Langerhans part of pancreas
id: UBERON:0000016
in subset: efo slim
in subset: human reference atlas
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: endocrine pancreas
annotated property: subClassOf
annotated target: compound organ component
source: ZFA

Axiom
annotated source: endocrine pancreas
annotated property: subClassOf
annotated target: Restriction
source: AAO
source: FMA
source: XAO

Axiom
annotated source: endocrine pancreas
annotated property: subClassOf
annotated target: Restriction
source: GO

Axiom
annotated source: endocrine pancreas
annotated property: subClassOf
annotated target: Restriction
source: GO

Axiom
annotated source: endocrine pancreas
annotated property: subClassOf
annotated target: Restriction
source: GO

Axiom
annotated source: endocrine pancreas
annotated property: IAO_0000115
annotated target: The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin.
has db xref: GO:GO
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: endocrine pancreas
annotated property: UBPROP_0000001
annotated target: The part of the pancreas that acts as an endocrine gland, consisting of the islets of Langerhans, which secrete insulin and other hormones. [TFD][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000049
ontology: VHOG
source: http://bgee.unil.ch/
source: http://medical-dictionary.thefreedictionary.com/Pancreas

Axiom
annotated source: endocrine pancreas
annotated property: UBPROP_0000001
annotated target: The zebrafish endocrine pancreas is composed of small groups of islet cells that are distributed throughout the exocrine pancreas. The islet cells produce insulin, glucagon and somatostatin.[TAO]
date retrieved: 2012-08-14
external class: TAO:0001260
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: endocrine pancreas
annotated property: UBPROP_0000003
annotated target: 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]
date retrieved: 2012-09-17
external class: VHOG:0000049
ontology: VHOG
source: DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)
source: http://bgee.unil.ch/

Axiom
annotated source: endocrine pancreas
annotated property: UBPROP_0000008
annotated target: endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys
source: PMID:20959416

Axiom
annotated source: endocrine pancreas
annotated property: hasDbXref
annotated target: MESH:D007515
mapping justification: LexicalMatching
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: endocrine pancreas
annotated property: hasRelatedSynonym
annotated target: endocrine part of pancreas
has db xref: BTO:0000650

exocrine pancreas
type: Class
subclass of: serous gland
subclass of: UBERON_0004119
subclass of: UBERON_0005177
subclass of: UBERON_0013765
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001264
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0001263
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0007329
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0003924
subclass of: Restriction
  on property: RO_0002216
  some values from: GO_0007586
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0001264
IAO_0000115: The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO].
RO_0002175: NCBITaxon 9606
UBPROP_0000001: The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO]
UBPROP_0000001: The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG]
UBPROP_0000003: In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]
has db xref: AAO:0010407
has db xref: BTO:0000434
has db xref: CALOHA:TS-1241
has db xref: EMAPA:35328
has db xref: EV:0100093
has db xref: FMA:16017
has db xref: MA:0002415
has db xref: MESH:D046790
has db xref: NCIT:C32546
has db xref: SCTID:248202004
has db xref: TAO:0001249
has db xref: UMLS:C0553695
has db xref: VHOG:0000048
has db xref: Wikipedia:Exocrine_component_of_pancreas
has db xref: XAO:0000137
has db xref: ZFA:0001249
has exact synonym: exocrine pancreas
has exact synonym: pars exocrina pancreatis
has OBO namespace: uberon
has related synonym: exocrine component of pancreas
has related synonym: exocrine part of pancreas
id: UBERON:0000017
in subset: human reference atlas
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: exocrine pancreas
annotated property: IAO_0000115
annotated target: The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO].
has db xref: GOC:GO
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: exocrine pancreas
annotated property: UBPROP_0000001
annotated target: The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO]
date retrieved: 2012-08-14
external class: TAO:0001249
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: exocrine pancreas
annotated property: UBPROP_0000001
annotated target: The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000048
ontology: VHOG
source: http://bgee.unil.ch/
source: http://medical-dictionary.thefreedictionary.com/Pancreas

Axiom
annotated source: exocrine pancreas
annotated property: UBPROP_0000003
annotated target: 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]
date retrieved: 2012-09-17
external class: VHOG:0000048
ontology: VHOG
source: DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)
source: http://bgee.unil.ch/

Axiom
annotated source: exocrine pancreas
annotated property: hasDbXref
annotated target: MESH:D046790
author id: https://orcid.org/0000-0001-9439-5346
mapping justification: ManualMappingCuration
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: exocrine pancreas
annotated property: hasDbXref
annotated target: UMLS:C0553695
source: ncithesaurus:Exocrine_Pancreas

Axiom
annotated source: exocrine pancreas
annotated property: hasRelatedSynonym
annotated target: exocrine part of pancreas
has db xref: BTO:0000434

compound eye
type: Class
equivalent class: Class
  intersection of: eye
  intersection of: Restriction
    on property: RO_0002473
    some values from: ommatidium
subclass of: UBERON_0015165
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002473
  some values from: ommatidium
IAO_0000115: A light sensing organ composed of ommatidia.
UBPROP_0000008: The term compound eye is sometimes used for the multi-unit eyes of annelids, bivalves, echinoderms. We follow Richter et al and restrict this class to the arthropod structure for these structures
has db xref: BTO:0001921
has db xref: FBbt:00004508
has db xref: HAO:0000217
has db xref: IDOMAL:0002421
has db xref: TGMA:0000024
has db xref: Wikipedia:Compound_eye
has OBO namespace: uberon
has related synonym: Facettenauge
has related synonym: Komplexauge
has related synonym: adult compound eye
has related synonym: faceted eye
has related synonym: insect eye
has related synonym: zusammengesetztes Auge
id: UBERON:0000018
in subset: organ slim
in subset: uberon slim

Axiom
annotated source: compound eye
annotated property: subClassOf
annotated target: Restriction
source: PMID:21062451

Axiom
annotated source: compound eye
annotated property: IAO_0000115
annotated target: A light sensing organ composed of ommatidia.
has db xref: FB:gg
has db xref: Wikipedia:Compound_eye

Axiom
annotated source: compound eye
annotated property: UBPROP_0000008
annotated target: The term compound eye is sometimes used for the multi-unit eyes of annelids, bivalves, echinoderms. We follow Richter et al and restrict this class to the arthropod structure for these structures
source: PMID:21062451

Axiom
annotated source: compound eye
annotated property: hasDbXref
annotated target: FBbt:00004508
mapping justification: ManualMappingCuration

Axiom
annotated source: compound eye
annotated property: hasDbXref
annotated target: IDOMAL:0002421
author id: https://orcid.org/0000-0003-4423-4370
mapping justification: ManualMappingCuration
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: compound eye
annotated property: hasRelatedSynonym
annotated target: Facettenauge
has db xref: BTO:0001921

Axiom
annotated source: compound eye
annotated property: hasRelatedSynonym
annotated target: Komplexauge
has db xref: BTO:0001921

Axiom
annotated source: compound eye
annotated property: hasRelatedSynonym
annotated target: zusammengesetztes Auge
has db xref: BTO:0001921

camera-type eye
type: Class
subclass of: simple eye
subclass of: UBERON_0004121
subclass of: UBERON_0010314
subclass of: UBERON_0015212
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0004088
subclass of: Restriction
  on property: BFO_0000051
  some values from: lens of camera-type eye
subclass of: Restriction
  on property: BFO_0000051
  some values from: retina
subclass of: Restriction
  on property: BSPO_0000126
  some values from: head
subclass of: Restriction
  on property: RO_0002492
  some values from: fully formed stage
IAO_0000115: An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid.
UBPROP_0000001: A cavitated compound organ that transduces light waves into neural signals.[TAO]
UBPROP_0000003: The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
UBPROP_0000012: FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this
has broad synonym: eye
has db xref: AAO:0010340
has db xref: BIRNLEX:1169
has db xref: BTO:0004688
has db xref: EHDAA2:0000484
has db xref: EHDAA:936
has db xref: EMAPA:16198
has db xref: FMA:54448
has db xref: MA:0000261
has db xref: NCIT:C12401
has db xref: SCTID:181143004
has db xref: TAO:0000107
has db xref: UMLS:C0015392
has db xref: UMLS:C1280202
has db xref: VHOG:0000275
has db xref: XAO:0000179
has db xref: ZFA:0000107
has exact synonym: regio orbitalis
has narrow synonym: vertebrate eye
has OBO namespace: uberon
has related synonym: camera-type eye plus associated structures
has related synonym: eyes
has related synonym: orbital part of face
has related synonym: orbital region
id: UBERON:0000019
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: camera-type eye
annotated property: subClassOf
annotated target: Restriction
evidence: definitional

Axiom
annotated source: camera-type eye
annotated property: IAO_0000115
annotated target: An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid.
has db xref: GO:0043010
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: camera-type eye
annotated property: UBPROP_0000001
annotated target: A cavitated compound organ that transduces light waves into neural signals.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000107
ontology: TAO
source: TAO:wd

Axiom
annotated source: camera-type eye
annotated property: UBPROP_0000003
annotated target: The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000275
ontology: VHOG
source: DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
source: http://bgee.unil.ch/

Axiom
annotated source: camera-type eye
annotated property: UBPROP_0000012
annotated target: FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this
external ontology: FMA

Axiom
annotated source: camera-type eye
annotated property: hasBroadSynonym
annotated target: eye
has db xref: FMA:54448

Axiom
annotated source: camera-type eye
annotated property: hasDbXref
annotated target: UMLS:C0015392
source: BIRNLEX:1169
source: ncithesaurus:Eye

Axiom
annotated source: camera-type eye
annotated property: hasDbXref
annotated target: UMLS:C1280202
source: BIRNLEX:1169

Axiom
annotated source: camera-type eye
annotated property: hasExactSynonym
annotated target: regio orbitalis
has db xref: FMA:54448
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: camera-type eye
annotated property: hasRelatedSynonym
annotated target: eyes
has db xref: TAO:0000107
has synonym type: OMO_0003004

Axiom
annotated source: camera-type eye
annotated property: hasRelatedSynonym
annotated target: orbital part of face
has db xref: FMA:54448

Axiom
annotated source: camera-type eye
annotated property: hasRelatedSynonym
annotated target: orbital region
has db xref: FMA:54448

sense organ
type: Class
equivalent class: Class
  intersection of: organ
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050906
subclass of: organ
subclass of: Restriction
  on property: BFO_0000050
  some values from: sensory system
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0050906
IAO_0000115: An organ that is capable of transducing sensory stimulus to the nervous system.
has db xref: AEO:0000094
has db xref: BSA:0000121
has db xref: BTO:0000202
has db xref: CALOHA:TS-2043
has db xref: EHDAA2:0001824
has db xref: EHDAA:500
has db xref: EMAPA:35955
has db xref: FBbt:00005155
has db xref: GAID:63
has db xref: HAO:0000930
has db xref: MA:0000017
has db xref: MESH:D012679
has db xref: NCIT:C33224
has db xref: SCTID:244485009
has db xref: UMLS:C0935626
has db xref: VHOG:0001407
has db xref: WBbt:0006929
has exact synonym: organ of sense organ system
has exact synonym: organ of sensory organ system
has exact synonym: organ of sensory system
has exact synonym: sense organ system organ
has exact synonym: sensory organ
has exact synonym: sensory organ system organ
has exact synonym: sensory system organ
has narrow synonym: sensillum
has OBO namespace: uberon
has related synonym: Sinnesorgan
has related synonym: sensor
id: UBERON:0000020
in subset: uberon slim

Axiom
annotated source: sense organ
annotated property: IAO_0000115
annotated target: An organ that is capable of transducing sensory stimulus to the nervous system.
has db xref: https://github.com/obophenotype/uberon/issues/549
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: sense organ
annotated property: hasDbXref
annotated target: FBbt:00005155
mapping justification: ManualMappingCuration

Axiom
annotated source: sense organ
annotated property: hasDbXref
annotated target: UMLS:C0935626
source: ncithesaurus:Organ_of_the_Special_Sense

Axiom
annotated source: sense organ
annotated property: hasExactSynonym
annotated target: organ of sense organ system
has db xref: OBOL:accepted

Axiom
annotated source: sense organ
annotated property: hasExactSynonym
annotated target: organ of sensory organ system
has db xref: OBOL:accepted

Axiom
annotated source: sense organ
annotated property: hasExactSynonym
annotated target: organ of sensory system
has db xref: OBOL:accepted

Axiom
annotated source: sense organ
annotated property: hasExactSynonym
annotated target: sense organ system organ
has db xref: OBOL:automatic

Axiom
annotated source: sense organ
annotated property: hasExactSynonym
annotated target: sensory organ system organ
has db xref: OBOL:automatic

Axiom
annotated source: sense organ
annotated property: hasExactSynonym
annotated target: sensory system organ
has db xref: OBOL:accepted

Axiom
annotated source: sense organ
annotated property: hasNarrowSynonym
annotated target: sensillum
has db xref: WBbt:0006929

Axiom
annotated source: sense organ
annotated property: hasRelatedSynonym
annotated target: Sinnesorgan
has db xref: BTO:0000202

cutaneous appendage
type: Class
subclass of: UBERON_0013703
subclass of: Restriction
  on property: RO_0002371
  some values from: UBERON_0002097
IAO_0000115: Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales.
IAO_0000116: Mammary glands develop by similar mechanisms, and there is an argument for including them here (e.g. http://www.ncbi.nlm.nih.gov/pubmed/20484386), but these structures do not fit the current definition (lactiferous glands are part of the integumentary system in FMA). Note the FMA class is a subdivision of epidermis, which may be too restrictive for our purposes here.
has db xref: CALOHA:TS-0051
has db xref: FMA:71012
has db xref: SCTID:276160000
has exact synonym: skin appendage
has narrow synonym: epidermal appendage
has OBO namespace: uberon
has related synonym: epidermal growth
id: UBERON:0000021
in subset: uberon slim

Axiom
annotated source: cutaneous appendage
annotated property: IAO_0000115
annotated target: Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales.
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: cutaneous appendage
annotated property: hasExactSynonym
annotated target: skin appendage
has db xref: FMA:71012

wing
type: Class
equivalent class: Class
  intersection of: appendage
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002236
subclass of: appendage
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0002236
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_33213
subclass of: Restriction
  on property: RO_0002216
  some values from: GO_0060361
IAO_0000115: Appendage that is shaped in order to produce lift for flight through the air.
RO_0002161: NCBITaxon_118072
RO_0002161: NCBITaxon_186634
RO_0002161: NCBITaxon_314147
RO_0002161: NCBITaxon 6231
RO_0002161: NCBITaxon 7878
RO_0002161: NCBITaxon 8292
RO_0002161: NCBITaxon_91561
RO_0002161: NCBITaxon 9254
RO_0002161: NCBITaxon 9263
RO_0002161: NCBITaxon 9443
RO_0002161: NCBITaxon 9606
UBPROP_0000007: alar
UBPROP_0000008: This class is not monophyletic. See also: GO:0007629
has db xref: BTO:0001463
has db xref: EFO:0000885
has db xref: GAID:1217
has db xref: MAT:0000202
has db xref: MESH:D014921
has db xref: MIAA:0000202
has db xref: Wikipedia:Wing
has exact synonym: aliform appendage
has OBO namespace: uberon
id: UBERON:0000023
in subset: efo slim
in subset: grouping class
in subset: uberon slim

Axiom
annotated source: wing
annotated property: IAO_0000115
annotated target: Appendage that is shaped in order to produce lift for flight through the air.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: wing
annotated property: RO_0002161
annotated target: NCBITaxon_118072
source: bgee

Axiom
annotated source: wing
annotated property: RO_0002161
annotated target: NCBITaxon_186634
source: bgee

Axiom
annotated source: wing
annotated property: RO_0002161
annotated target: NCBITaxon_314147
source: bgee

Axiom
annotated source: wing
annotated property: RO_0002161
annotated target: NCBITaxon 6231
source: bgee

Axiom
annotated source: wing
annotated property: RO_0002161
annotated target: NCBITaxon 7878
source: bgee

Axiom
annotated source: wing
annotated property: RO_0002161
annotated target: NCBITaxon 8292
notes: we do not consider flying frogs to have wings
source: bgee

Axiom
annotated source: wing
annotated property: RO_0002161
annotated target: NCBITaxon_91561
source: bgee

Axiom
annotated source: wing
annotated property: RO_0002161
annotated target: NCBITaxon 9254
source: bgee

Axiom
annotated source: wing
annotated property: RO_0002161
annotated target: NCBITaxon 9263
source: bgee

Axiom
annotated source: wing
annotated property: RO_0002161
annotated target: NCBITaxon 9443
source: bgee

Axiom
annotated source: wing
annotated property: hasExactSynonym
annotated target: aliform appendage
has db xref: http://orcid.org/0000-0002-6601-2165

forelimb wing
type: Class
equivalent class: Class
  intersection of: UBERON_0002102
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002236
subclass of: wing
subclass of: UBERON_0002102
IAO_0000115: Forelimb that is used to produce lift for flight through the air.
has OBO namespace: uberon
id: UBERON:0000024
comment: Examples: bat wing, bird wing

Axiom
annotated source: forelimb wing
annotated property: IAO_0000115
annotated target: Forelimb that is used to produce lift for flight through the air.
has db xref: http://orcid.org/0000-0002-6601-2165

tube
type: Class
equivalent class: Class
  intersection of: UBERON_0004111
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002299
subclass of: UBERON_0004111
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0013522
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0002299
IAO_0000115: Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
IAO_0000232: not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)
UBPROP_0000007: tubular
has db xref: galen:Tube
has exact synonym: anatomical tube
has narrow synonym: duct
has OBO namespace: uberon
id: UBERON:0000025

Axiom
annotated source: tube
annotated property: IAO_0000115
annotated target: Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
has db xref: http://orcid.org/0000-0002-6601-2165

appendage
type: Class
subclass of: organism subdivision
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6072
IAO_0000115: Major subdivision of an organism that protrudes from the body[DOS, CARO].
UBPROP_0000001: An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018].
UBPROP_0000001: Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736].
UBPROP_0000007: appendicular
UBPROP_0000008: this is currently a subtype of organism subdivision - which would exclude feathers
has db xref: AEO:0000193
has db xref: BILA:0000018
has db xref: BTO:0001492
has db xref: CARO:0010003
has db xref: EFO:0000799
has db xref: EHDAA2:0003193
has db xref: EMAPA:37283
has db xref: EV:0100155
has db xref: FBbt:00007000
has db xref: HAO:0000144
has db xref: MAT:0000023
has db xref: MESH:D005121
has db xref: MIAA:0000023
has db xref: NCIT:C61460
has db xref: UMLS:C0598782
has db xref: VSAO:0000075
has db xref: Wikipedia:Appendage
has db xref: XAO:0000218
has OBO namespace: uberon
has related synonym: appendages
has related synonym: extremitaet
has related synonym: extremity
has related synonym: limbs/digits/tail
id: UBERON:0000026
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: appendage
annotated property: IAO_0000115
annotated target: Major subdivision of an organism that protrudes from the body[DOS, CARO].
has db xref: CARO:DOS

Axiom
annotated source: appendage
annotated property: UBPROP_0000001
annotated target: An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018].
source: BILA:0000018

Axiom
annotated source: appendage
annotated property: UBPROP_0000001
annotated target: Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736].
source: GO:0048736

Axiom
annotated source: appendage
annotated property: hasDbXref
annotated target: EMAPA:37283
source: MA:th

Axiom
annotated source: appendage
annotated property: hasDbXref
annotated target: FBbt:00007000
mapping justification: ManualMappingCuration

Axiom
annotated source: appendage
annotated property: hasDbXref
annotated target: UMLS:C0598782
source: ncithesaurus:Appendage

Axiom
annotated source: appendage
annotated property: hasRelatedSynonym
annotated target: appendages
has db xref: XAO:0000218
has synonym type: OMO_0003004

Axiom
annotated source: appendage
annotated property: hasRelatedSynonym
annotated target: extremitaet
has db xref: BTO:0001492

Axiom
annotated source: appendage
annotated property: hasRelatedSynonym
annotated target: limbs/digits/tail
has db xref: MP:0000001

lymph node
type: Class
equivalent class: Class
  intersection of: organ
  intersection of: Restriction
    on property: RO_0002150
    some values from: UBERON_0001473
  intersection of: Restriction
    on property: RO_0002473
    some values from: UBERON_0001744
subclass of: UBERON_0005057
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002465
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0002006
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0002007
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0002194
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0002391
subclass of: Restriction
  on property: RO_0002150
  some values from: UBERON_0001473
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_40674
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0034953
subclass of: Restriction
  on property: RO_0002473
  some values from: UBERON_0001744
IAO_0000115: Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph.
RO_0002175: NCBITaxon 9606
UBPROP_0000003: Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG]
has db xref: BTO:0000784
has db xref: CALOHA:TS-0579
has db xref: EFO:0000872
has db xref: EMAPA:35523
has db xref: EV:0100050
has db xref: FMA:5034
has db xref: GAID:947
has db xref: MA:0000139
has db xref: MAT:0000442
has db xref: MESH:D008198
has db xref: NCIT:C12745
has db xref: NCIT:C33027
has db xref: SCTID:181756000
has db xref: TAO_RETIRED:0005318
has db xref: UMLS:C0024204
has db xref: VHOG:0001273
has db xref: Wikipedia:Lymph_node
has db xref: ZFA_RETIRED:0005318
has db xref: galen:Lymphnode
has OBO namespace: uberon
has related synonym: lymph gland
has related synonym: nodus lymphaticus
id: UBERON:0000029
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: lymph node
annotated property: IAO_0000115
annotated target: Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph.
has db xref: BTO:0000784

Axiom
annotated source: lymph node
annotated property: UBPROP_0000003
annotated target: Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001273
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.630
source: http://bgee.unil.ch/

Axiom
annotated source: lymph node
annotated property: hasDbXref
annotated target: UMLS:C0024204
source: ncithesaurus:Lymph_Node

Axiom
annotated source: lymph node
annotated property: hasRelatedSynonym
annotated target: lymph gland
has db xref: VHOG:0001273

Axiom
annotated source: lymph node
annotated property: hasRelatedSynonym
annotated target: nodus lymphaticus
has db xref: Wikipedia:Lymph_node
has synonym type: OMO_0003011

lamina propria
type: Class
subclass of: UBERON_0004923
subclass of: Restriction
  on property: BFO_0000050
  some values from: mucosa
subclass of: Restriction
  on property: BSPO_0001107
  some values from: epithelium
subclass of: Restriction
  on property: RO_0002473
  some values from: UBERON_0011825
IAO_0000115: A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions.
has db xref: BTO:0002330
has db xref: FMA:62517
has db xref: NCIT:C32918
has db xref: SCTID:298225002
has db xref: UMLS:C1179187
has db xref: Wikipedia:Lamina_propria
has exact synonym: lamina propria mucosa
has exact synonym: lamina propria mucosae
has OBO namespace: uberon
has related synonym: tunica propria
id: UBERON:0000030
in subset: uberon slim

Axiom
annotated source: lamina propria
annotated property: IAO_0000115
annotated target: A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions.
has db xref: Wikipedia:Lamina_propria

Axiom
annotated source: lamina propria
annotated property: hasDbXref
annotated target: UMLS:C1179187
source: ncithesaurus:Lamina_Propria

Axiom
annotated source: lamina propria
annotated property: hasRelatedSynonym
annotated target: tunica propria
has db xref: BTO:0002330

lamina propria of trachea
type: Class
equivalent class: Class
  intersection of: lamina propria
  intersection of: Restriction
    on property: BFO_0000050
    some values from: respiratory airway
subclass of: UBERON_0004779
subclass of: Restriction
IAO_0000115: A lamina propria that is part of a respiratory airway.
has db xref: EMAPA:35877
has db xref: FMA:265157
has db xref: MA:0001858
has db xref: NCIT:C49305
has db xref: UMLS:C1710457
has exact synonym: lamina propria mucosa of trachea
has exact synonym: lamina propria mucosa of windpipe
has exact synonym: lamina propria mucosae of trachea
has exact synonym: lamina propria mucosae of windpipe
has exact synonym: lamina propria of windpipe
has exact synonym: trachea lamina propria
has exact synonym: trachea lamina propria mucosa
has exact synonym: trachea lamina propria mucosae
has exact synonym: tracheal lamina propria
has exact synonym: windpipe lamina propria
has exact synonym: windpipe lamina propria mucosa
has exact synonym: windpipe lamina propria mucosae
has OBO namespace: uberon
id: UBERON:0000031

Axiom
annotated source: lamina propria of trachea
annotated property: subClassOf
annotated target: Restriction
is inferred: true
source: https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships

Axiom
annotated source: lamina propria of trachea
annotated property: IAO_0000115
annotated target: A lamina propria that is part of a respiratory airway.
has db xref: OBOL:automatic

Axiom
annotated source: lamina propria of trachea
annotated property: hasDbXref
annotated target: UMLS:C1710457
source: ncithesaurus:Trachea_Lamina_Propria

Axiom
annotated source: lamina propria of trachea
annotated property: hasExactSynonym
annotated target: lamina propria mucosa of trachea
has db xref: OBOL:automatic

Axiom
annotated source: lamina propria of trachea
annotated property: hasExactSynonym
annotated target: lamina propria mucosa of windpipe
has db xref: OBOL:automatic

Axiom
annotated source: lamina propria of trachea
annotated property: hasExactSynonym
annotated target: lamina propria mucosae of trachea
has db xref: OBOL:automatic

Axiom
annotated source: lamina propria of trachea
annotated property: hasExactSynonym
annotated target: lamina propria mucosae of windpipe
has db xref: OBOL:automatic

Axiom
annotated source: lamina propria of trachea
annotated property: hasExactSynonym
annotated target: lamina propria of windpipe
has db xref: OBOL:automatic

Axiom
annotated source: lamina propria of trachea
annotated property: hasExactSynonym
annotated target: trachea lamina propria mucosa
has db xref: OBOL:automatic

Axiom
annotated source: lamina propria of trachea
annotated property: hasExactSynonym
annotated target: trachea lamina propria mucosae
has db xref: OBOL:automatic

Axiom
annotated source: lamina propria of trachea
annotated property: hasExactSynonym
annotated target: windpipe lamina propria
has db xref: OBOL:automatic

Axiom
annotated source: lamina propria of trachea
annotated property: hasExactSynonym
annotated target: windpipe lamina propria mucosa
has db xref: OBOL:automatic

Axiom
annotated source: lamina propria of trachea
annotated property: hasExactSynonym
annotated target: windpipe lamina propria mucosae
has db xref: OBOL:automatic

head
type: Class
subclass of: UBERON_0011676
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0007811
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_33213
IAO_0000115: The head is the anterior-most division of the body [GO].
RO_0002171: heart
UBPROP_0000001: Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]
UBPROP_0000001: Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]
UBPROP_0000003: Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]
has db xref: AAO:0010335
has db xref: AEO:0000106
has db xref: BILA:0000115
has db xref: BIRNLEX:1230
has db xref: BTO:0000282
has db xref: CALOHA:TS-0436
has db xref: EFO:0000964
has db xref: EHDAA2:0003106
has db xref: EMAPA:31858
has db xref: FMA:7154
has db xref: GAID:61
has db xref: HAO:0000397
has db xref: MA:0000023
has db xref: MAT:0000294
has db xref: MESH:D006257
has db xref: MIAA:0000294
has db xref: NCIT:C12419
has db xref: SCTID:302548004
has db xref: SPD:0000016
has db xref: TAO:0001114
has db xref: TGMA:0000002
has db xref: UMLS:C0018670
has db xref: VHOG:0001644
has db xref: WBbt:0005739
has db xref: Wikipedia:Head
has db xref: XAO:0003024
has db xref: galen:Head
has exact synonym: head (volume)
has narrow synonym: adult head
has OBO namespace: uberon
has related synonym: cephalic area
id: UBERON:0000033
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: head
annotated property: IAO_0000115
annotated target: The head is the anterior-most division of the body [GO].
has db xref: GO:0060322
has db xref: Wikipedia:Head

Axiom
annotated source: head
annotated property: UBPROP_0000001
annotated target: Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010335
ontology: AAO
source: AAO:BJB

Axiom
annotated source: head
annotated property: UBPROP_0000001
annotated target: Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]
date retrieved: 2012-08-14
external class: TAO:0001114
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: head
annotated property: UBPROP_0000003
annotated target: Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001644
ontology: VHOG
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82
source: http://bgee.unil.ch/

Axiom
annotated source: head
annotated property: hasDbXref
annotated target: UMLS:C0018670
source: BIRNLEX:1230
source: ncithesaurus:Head

Axiom
annotated source: head
annotated property: hasExactSynonym
annotated target: head (volume)
has db xref: FMA:7154

Axiom
annotated source: head
annotated property: hasRelatedSynonym
annotated target: cephalic area
has db xref: SPD:0000016

primary ovarian follicle
type: Class
equivalent class: Class
  intersection of: UBERON_0001305
  intersection of: Restriction
    on property: RO_0002180
    qualified cardinality: 1
    on class: UBERON_0005170
subclass of: UBERON_0001305
subclass of: Restriction
  on property: RO_0002180
  some values from: UBERON_0005170
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0003981
IAO_0000115: An ovarian follicle that has one layer of granulosa cells.
RO_0002175: NCBITaxon 9606
has db xref: BTO:0000410
has db xref: EMAPA:35631
has db xref: FMA:18634
has db xref: MA:0002907
has db xref: SCTID:258665002
has exact synonym: folliculus ovaricus primarius
has exact synonym: ovary primary follicle
has exact synonym: primary follicle of ovary
has exact synonym: primary ovarian follicle
has OBO namespace: uberon
has related synonym: preantral follicle of ovary
has related synonym: primary egg follicle
has related synonym: primary follicle
id: UBERON:0000035
in subset: human reference atlas
in subset: pheno slim

Axiom
annotated source: primary ovarian follicle
annotated property: IAO_0000115
annotated target: An ovarian follicle that has one layer of granulosa cells.
has db xref: GO:0001545
has db xref: GOC:mtg_mpo
has db xref: http://ovary.stanford.edu

Axiom
annotated source: primary ovarian follicle
annotated property: hasExactSynonym
annotated target: folliculus ovaricus primarius
has db xref: FMA:18634
has synonym type: OMO_0003011

Axiom
annotated source: primary ovarian follicle
annotated property: hasExactSynonym
annotated target: ovary primary follicle
has db xref: EMAPA:35631
has db xref: MA:0002907

Axiom
annotated source: primary ovarian follicle
annotated property: hasExactSynonym
annotated target: primary follicle of ovary
has db xref: FMA:18634

Axiom
annotated source: primary ovarian follicle
annotated property: hasExactSynonym
annotated target: primary ovarian follicle
has db xref: FMA:18634

Axiom
annotated source: primary ovarian follicle
annotated property: hasRelatedSynonym
annotated target: primary follicle
has db xref: EMAPA:35631

secondary ovarian follicle
type: Class
equivalent class: Class
  intersection of: UBERON_0001305
  intersection of: Restriction
    on property: RO_0002387
    some values from: tertiary ovarian follicle
  intersection of: Restriction
    on property: RO_0002180
    min qualified cardinality: 2
    on class: UBERON_0005170
subclass of: UBERON_0001305
subclass of: Restriction
  on property: RO_0002180
  some values from: UBERON_0005170
subclass of: Restriction
  on property: RO_0002202
  some values from: primary ovarian follicle
subclass of: Restriction
  on property: RO_0002387
  some values from: tertiary ovarian follicle
IAO_0000115: A maturing ovarian follicle that has two more more layers of granulosa cells, up to the onset of antrum formation.
IAO_0000116: consider adopting distinction in MA
RO_0002175: NCBITaxon 9606
has db xref: EMAPA:35632
has db xref: FMA:18637
has db xref: MA:0002908
has exact synonym: folliculus ovaricus secondarius
has exact synonym: ovary secondary follicle
has exact synonym: pre-antral follicle
has exact synonym: preantral follicle
has exact synonym: secondary follicle of ovary
has OBO namespace: uberon
has related synonym: antral follicle of ovary
has related synonym: pre-ovulatory follicle
has related synonym: secondary egg follicle
has related synonym: secondary follicle
id: UBERON:0000036
in subset: human reference atlas
in subset: pheno slim

Axiom
annotated source: secondary ovarian follicle
annotated property: IAO_0000115
annotated target: A maturing ovarian follicle that has two more more layers of granulosa cells, up to the onset of antrum formation.
has db xref: GO:0001546
has db xref: http://ovary.stanford.edu
has db xref: http://www.repropedia.org/secondary-ovarian-follicle

Axiom
annotated source: secondary ovarian follicle
annotated property: hasExactSynonym
annotated target: ovary secondary follicle
has db xref: MA:0002908

Axiom
annotated source: secondary ovarian follicle
annotated property: hasExactSynonym
annotated target: pre-antral follicle
has db xref: GO:0001546

Axiom
annotated source: secondary ovarian follicle
annotated property: hasExactSynonym
annotated target: preantral follicle
has db xref: GO:0001546

Axiom
annotated source: secondary ovarian follicle
annotated property: hasRelatedSynonym
annotated target: antral follicle of ovary
has db xref: FMA:18637

Axiom
annotated source: secondary ovarian follicle
annotated property: hasRelatedSynonym
annotated target: pre-ovulatory follicle
has db xref: EMAPA:30777

Axiom
annotated source: secondary ovarian follicle
annotated property: hasRelatedSynonym
annotated target: secondary follicle
has db xref: EMAPA:35632

tertiary ovarian follicle
type: Class
equivalent class: Class
  intersection of: UBERON_0001305
  intersection of: Restriction
    on property: BFO_0000051
    some values from: follicular antrum
  intersection of: Restriction
    on property: RO_0002180
    min qualified cardinality: 2
    on class: UBERON_0005170
subclass of: UBERON_0001305
subclass of: Restriction
  on property: BFO_0000051
  some values from: follicular antrum
subclass of: Restriction
  on property: RO_0002180
  some values from: UBERON_0005170
subclass of: Restriction
  on property: RO_0002202
  some values from: secondary ovarian follicle
IAO_0000115: A follicle that has reached the most mature stage of folliculogenesis, characterized by the presence of the antrum.
has broad synonym: antral follicle
has db xref: EMAPA:30763
has db xref: FMA:18641
has db xref: MA:0002909
has db xref: NCIT:C32692
has db xref: SCTID:362261008
has db xref: UMLS:C0600225
has exact synonym: Graafian follicle
has exact synonym: antral ovarian follicle
has exact synonym: folliculi ovarici vesiculosi
has exact synonym: folliculus ovaricus tertiarius
has exact synonym: folliculus ovaricus tertiarius (vesiculosus)
has exact synonym: folliculus ovaricus tertiarius (vesiculous)
has exact synonym: ovary antral follicle
has exact synonym: tertiary follicle of ovary
has exact synonym: vesicular follicle of ovary
has exact synonym: vesicular ovarian follicle
has OBO namespace: uberon
has related synonym: tertiary egg follicle
id: UBERON:0000037
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: tertiary ovarian follicle
annotated property: IAO_0000115
annotated target: A follicle that has reached the most mature stage of folliculogenesis, characterized by the presence of the antrum.
has db xref: http://orcid.org/0000-0002-6601-2165
has db xref: http://www.repropedia.org/antral-follicle

Axiom
annotated source: tertiary ovarian follicle
annotated property: hasDbXref
annotated target: UMLS:C0600225
source: ncithesaurus:Graafian_Follicle

Axiom
annotated source: tertiary ovarian follicle
annotated property: hasExactSynonym
annotated target: Graafian follicle
has db xref: http://www.repropedia.org/antral-follicle

Axiom
annotated source: tertiary ovarian follicle
annotated property: hasExactSynonym
annotated target: antral ovarian follicle
has db xref: GO:0001547

Axiom
annotated source: tertiary ovarian follicle
annotated property: hasExactSynonym
annotated target: folliculi ovarici vesiculosi
has db xref: FMA:18641
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: tertiary ovarian follicle
annotated property: hasExactSynonym
annotated target: folliculus ovaricus tertiarius (vesiculosus)
has db xref: FMA:18641

Axiom
annotated source: tertiary ovarian follicle
annotated property: hasExactSynonym
annotated target: ovary antral follicle
has db xref: MA:0002909
has db xref: http://www.repropedia.org/antral-follicle

Axiom
annotated source: tertiary ovarian follicle
annotated property: hasExactSynonym
annotated target: tertiary follicle of ovary
has db xref: FMA:18641
has db xref: http://www.repropedia.org/antral-follicle

Axiom
annotated source: tertiary ovarian follicle
annotated property: hasExactSynonym
annotated target: vesicular follicle of ovary
has db xref: FMA:18641

Axiom
annotated source: tertiary ovarian follicle
annotated property: hasExactSynonym
annotated target: vesicular ovarian follicle
has db xref: FMA:18641

follicular fluid
type: Class
subclass of: organism substance
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001305
subclass of: Restriction
  on property: BFO_0000051
  some values from: CHEBI_17089
subclass of: Restriction
  on property: BFO_0000051
  some values from: secretion of exocrine gland
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0007779
subclass of: Restriction
  on property: RO_0001025
  some values from: follicular antrum
subclass of: Restriction
  on property: RO_0002221
  some values from: CL_0000025
IAO_0000115: The fluid surrounding the ovum and granulosa cells in the ovarian follicle.
RO_0002175: NCBITaxon 9606
UBPROP_0000008: Generally, larger species such as ovine, equine, porcine, human, and bovine have larger follicles, with the fluid comprising a substantial proportion of the volume of the follicles at ovulation (estimated at >95% in bovine [3]). Smaller species such as rats and mice have smaller follicles with fractionally less follicular fluid[20164441]
UBPROP_0000010: The follicular fluid contains sex steroids, glycoprotein hormones, plasma proteins, mucopolysaccharides, and enzymes and is rich in hyaluronic acid.
has db xref: BTO:0004383
has db xref: CALOHA:TS-0728
has db xref: FMA:18665
has db xref: GAID:372
has db xref: MA:0002511
has db xref: MESH:D015571
has db xref: NCIT:C52556
has db xref: UMLS:C1709369
has db xref: Wikipedia:Follicular_fluid
has exact synonym: liquor follicularis
has exact synonym: liquor folliculi
has exact synonym: ovary follicle fluid
has OBO namespace: uberon
has related synonym: antral fluid, ovarian follicle
has related synonym: liquor folliculi
has related synonym: ovarian follicular fluid
has related synonym: ovary follicular fluid
id: UBERON:0000038
in subset: human reference atlas
in subset: uberon slim

Axiom
annotated source: follicular fluid
annotated property: IAO_0000115
annotated target: The fluid surrounding the ovum and granulosa cells in the ovarian follicle.
has db xref: ISBN:145114847X
has db xref: MESH:D015571
has db xref: Wikipedia:Follicular_fluid

Axiom
annotated source: follicular fluid
annotated property: hasDbXref
annotated target: UMLS:C1709369
source: ncithesaurus:Ovarian_Follicle_Fluid

Axiom
annotated source: follicular fluid
annotated property: hasExactSynonym
annotated target: liquor follicularis
has db xref: FMA:18665

Axiom
annotated source: follicular fluid
annotated property: hasExactSynonym
annotated target: liquor folliculi
has synonym type: OMO_0003011

Axiom
annotated source: follicular fluid
annotated property: hasExactSynonym
annotated target: ovary follicle fluid
has db xref: MA:0002511

Axiom
annotated source: follicular fluid
annotated property: hasRelatedSynonym
annotated target: liquor folliculi
has db xref: Wikipedia:Follicular_fluid
has synonym type: OMO_0003011

Axiom
annotated source: follicular fluid
annotated property: hasRelatedSynonym
annotated target: ovarian follicular fluid
has db xref: BTO:0004383

Axiom
annotated source: follicular fluid
annotated property: hasRelatedSynonym
annotated target: ovary follicular fluid
has db xref: BTO:0004383

follicular antrum
type: Class
equivalent class: Class
  intersection of: anatomical space
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001305
  intersection of: Restriction
    on property: RO_0001015
    some values from: follicular fluid
subclass of: anatomical space
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001305
subclass of: Restriction
  on property: RO_0001015
  some values from: follicular fluid
IAO_0000115: Region of ovarian follicle filled with follicular fluid.
RO_0002175: NCBITaxon 9606
has db xref: EMAPA:37867
has db xref: FMA:18675
has db xref: Wikipedia:Follicular_antrum
has exact synonym: antral cavity
has exact synonym: antrum folliculare
has exact synonym: ovarian follicle antrum
has OBO namespace: uberon
has related synonym: antrum follicularum
id: UBERON:0000039
in subset: human reference atlas
in subset: uberon slim

Axiom
annotated source: follicular antrum
annotated property: IAO_0000115
annotated target: Region of ovarian follicle filled with follicular fluid.
has db xref: Wikipedia:Follicular_antrum

Axiom
annotated source: follicular antrum
annotated property: hasDbXref
annotated target: EMAPA:37867
source: MA:th

Axiom
annotated source: follicular antrum
annotated property: hasExactSynonym
annotated target: antral cavity
has db xref: FMA:18675

Axiom
annotated source: follicular antrum
annotated property: hasExactSynonym
annotated target: antrum folliculare
has db xref: FMA:18675

Axiom
annotated source: follicular antrum
annotated property: hasExactSynonym
annotated target: ovarian follicle antrum
has db xref: GO:0001548

Axiom
annotated source: follicular antrum
annotated property: hasRelatedSynonym
annotated target: antrum follicularum
has db xref: Wikipedia:Follicular_antrum
has synonym type: OMO_0003011

serous membrane
type: Class
subclass of: multi-tissue structure
subclass of: UBERON_0004120
subclass of: Restriction
  on property: BFO_0000050
  some values from: anatomical wall
subclass of: Restriction
  on property: BFO_0000051
  some values from: mesothelium
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0002384
IAO_0000115: Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
UBPROP_0000001: A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
UBPROP_0000001: a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]
UBPROP_0000012: in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.
has db xref: FMA:9581
has db xref: GAID:19
has db xref: MESH:D012704
has db xref: NCIT:C13169
has db xref: SCTID:362878009
has db xref: TAO:0005425
has db xref: UMLS:C0036760
has db xref: Wikipedia:Serous_membrane
has db xref: ZFA:0005425
has exact synonym: tunica serosa
has exact synonym: wall of serous sac
has OBO namespace: uberon
has related synonym: serosa
id: UBERON:0000042
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: serous membrane
annotated property: IAO_0000115
annotated target: Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
has db xref: Wikipedia:Serous_membrane
has db xref: https://github.com/obophenotype/uberon/issues/86

Axiom
annotated source: serous membrane
annotated property: UBPROP_0000001
annotated target: A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
date retrieved: 2012-08-14
external class: TAO:0005425
ontology: TAO
source: Wikipedia:Serous_membrane

Axiom
annotated source: serous membrane
annotated property: UBPROP_0000001
annotated target: a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]
source: Wikipedia:Serous_membrane

Axiom
annotated source: serous membrane
annotated property: UBPROP_0000012
annotated target: in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.
external ontology: FMA

Axiom
annotated source: serous membrane
annotated property: hasDbXref
annotated target: UMLS:C0036760
source: ncithesaurus:Serosa

Axiom
annotated source: serous membrane
annotated property: hasExactSynonym
annotated target: tunica serosa
has db xref: FMA:9581
has synonym type: OMO_0003011

Axiom
annotated source: serous membrane
annotated property: hasExactSynonym
annotated target: wall of serous sac
has db xref: FMA:9581

Axiom
annotated source: serous membrane
annotated property: hasRelatedSynonym
annotated target: serosa
has db xref: Wikipedia:Serous_membrane

tendon
type: Class
subclass of: UBERON_0007846
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7742
subclass of: Restriction
  on property: RO_0002176
  some values from: UBERON_0001474
subclass of: Restriction
  on property: RO_0002176
  some values from: UBERON_0001630
IAO_0000115: Dense regular connective tissue that connects muscle to bone[VSAO].
UBPROP_0000001: Dense regular connective tissue that connects muscle to bone.[VSAO]
UBPROP_0000003: Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]
UBPROP_0000012: in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis
has db xref: AEO:0000091
has db xref: BTO:0001356
has db xref: CALOHA:TS-1021
has db xref: EHDAA2:0003091
has db xref: EMAPA:35854
has db xref: EV:0100149
has db xref: FMA:9721
has db xref: GAID:276
has db xref: MA:0000115
has db xref: MESH:D013710
has db xref: NCIT:C13045
has db xref: SCTID:256667004
has db xref: UMLS:C0039508
has db xref: VHOG:0001286
has db xref: VSAO:0000073
has db xref: Wikipedia:Tendon
has db xref: XAO:0000173
has db xref: ZFA:0005647
has db xref: galen:Tendon
has OBO namespace: uberon
has related synonym: sinew
has related synonym: tendo
id: UBERON:0000043
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: tendon
annotated property: subClassOf
annotated target: UBERON_0007846
source: VSAO

Axiom
annotated source: tendon
annotated property: subClassOf
annotated target: Restriction
source: OG

Axiom
annotated source: tendon
annotated property: subClassOf
annotated target: Restriction
source: AEO

Axiom
annotated source: tendon
annotated property: IAO_0000115
annotated target: Dense regular connective tissue that connects muscle to bone[VSAO].
has db xref: GO_REF:0000034
has db xref: VSAO:0000073
has db xref: Wikipedia:Tendon
has db xref: http://dx.plos.org/10.1371/journal.pone.0051070

Axiom
annotated source: tendon
annotated property: UBPROP_0000001
annotated target: Dense regular connective tissue that connects muscle to bone.[VSAO]
date retrieved: 2012-08-14
external class: VSAO:0000073
ontology: VSAO
source: PSPUB:0000170

Axiom
annotated source: tendon
annotated property: UBPROP_0000003
annotated target: Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001286
ontology: VHOG
source: DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002)
source: http://bgee.unil.ch/

Axiom
annotated source: tendon
annotated property: UBPROP_0000012
annotated target: in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis
external ontology: FMA

Axiom
annotated source: tendon
annotated property: hasDbXref
annotated target: UMLS:C0039508
source: ncithesaurus:Tendon

Axiom
annotated source: tendon
annotated property: hasRelatedSynonym
annotated target: sinew
has db xref: Wikipedia:Tendon

Axiom
annotated source: tendon
annotated property: hasRelatedSynonym
annotated target: tendo
has db xref: Wikipedia:Tendon
has synonym type: OMO_0003011

dorsal root ganglion
type: Class
equivalent class: Class
  intersection of: ganglion
  intersection of: Restriction
    on property: extends fibers into
    some values from: UBERON_0001780
  intersection of: Restriction
    on property: extends fibers into
    some values from: UBERON_0002261
subclass of: UBERON_0001800
subclass of: Restriction
subclass of: Restriction
  on property: extends fibers into
  some values from: UBERON_0001780
subclass of: Restriction
  on property: extends fibers into
  some values from: UBERON_0002261
IAO_0000115: Sensory ganglia located on the dorsal spinal roots within the vertebral column. The spinal ganglion cells are pseudounipolar. The single primary branch bifurcates sending a peripheral process to carry sensory information from the periphery and a central branch which relays that information to the spinal cord or brain. (MSH) * ganglion found on the posterior root of each spinal nerve, composed of the unipolar nerve cell bodies of the sensory neurons of the nerve. (CSP).
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Trunk ganglion which is located adjacent to the spine on a dorsal root and contains the cell bodies of afferent sensory nerves.[TAO]
UBPROP_0000003: 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]
UBPROP_0000011: 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]
UBPROP_0000012: MA and EMAPA introduce distinct classes for what appears to be the same thing
has alternative id: UBERON:0026602
has db xref: AAO:0011032
has db xref: BIRNLEX:2596
has db xref: BIRNLEX:2598
has db xref: BTO:0001264
has db xref: CALOHA:TS-0954
has db xref: EFO:0000900
has db xref: EHDAA2:0000418
has db xref: EHDAA2:0001897
has db xref: EHDAA:2899
has db xref: EMAPA:16667
has db xref: EMAPA:16668
has db xref: EMAPA:18372
has db xref: EV:0100373
has db xref: FMA:5888
has db xref: MA:0000231
has db xref: MA:0000232
has db xref: MAT:0000162
has db xref: MESH:D005727
has db xref: MIAA:0000162
has db xref: NCIT:C12462
has db xref: SCTID:244455004
has db xref: TAO:0000200
has db xref: UMLS:C0017070
has db xref: VHOG:0000222
has db xref: Wikipedia:Dorsal_root_ganglion
has db xref: XAO:0000210
has db xref: ZFA:0000200
has exact synonym: dorsal root ganglion
has exact synonym: ganglion of dorsal root
has exact synonym: ganglion spinalis
has exact synonym: spinal ganglion
has exact synonym: spinal ganglion part of peripheral nervous system
has OBO namespace: uberon
has related synonym: DRG
has related synonym: dorsal root ganglia
has related synonym: ganglion sensorium nervi spinalis
has related synonym: ganglion spinale
has related synonym: posterior root ganglion
id: UBERON:0000044
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: dorsal root ganglion
annotated property: subClassOf
annotated target: UBERON_0001800
source: MA

Axiom
annotated source: dorsal root ganglion
annotated property: subClassOf
annotated target: Restriction
source: DOI:10.1101/gr.157586.113
source: ZFA
source: https://github.com/obophenotype/uberon/wiki/The-neural-crest

Axiom
annotated source: dorsal root ganglion
annotated property: IAO_0000115
annotated target: Sensory ganglia located on the dorsal spinal roots within the vertebral column. The spinal ganglion cells are pseudounipolar. The single primary branch bifurcates sending a peripheral process to carry sensory information from the periphery and a central branch which relays that information to the spinal cord or brain. (MSH) * ganglion found on the posterior root of each spinal nerve, composed of the unipolar nerve cell bodies of the sensory neurons of the nerve. (CSP).
has db xref: BIRNLEX:2596

Axiom
annotated source: dorsal root ganglion
annotated property: UBPROP_0000001
annotated target: Trunk ganglion which is located adjacent to the spine on a dorsal root and contains the cell bodies of afferent sensory nerves.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000200
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: dorsal root ganglion
annotated property: UBPROP_0000003
annotated target: 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]
date retrieved: 2012-09-17
external class: VHOG:0000222
ontology: VHOG
source: DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000)
source: http://bgee.unil.ch/

Axiom
annotated source: dorsal root ganglion
annotated property: UBPROP_0000012
annotated target: MA and EMAPA introduce distinct classes for what appears to be the same thing
external ontology: FMA

Axiom
annotated source: dorsal root ganglion
annotated property: hasDbXref
annotated target: MESH:D005727
mapping justification: LexicalMatching
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: dorsal root ganglion
annotated property: hasDbXref
annotated target: UMLS:C0017070
source: BIRNLEX:2596
source: ncithesaurus:Dorsal_Root_Ganglion

Axiom
annotated source: dorsal root ganglion
annotated property: hasExactSynonym
annotated target: dorsal root ganglion
has db xref: BTO:0001264

Axiom
annotated source: dorsal root ganglion
annotated property: hasExactSynonym
annotated target: ganglion of dorsal root
has db xref: OBOL:automatic

Axiom
annotated source: dorsal root ganglion
annotated property: hasExactSynonym
annotated target: ganglion spinalis
has db xref: FMA:5888

Axiom
annotated source: dorsal root ganglion
annotated property: hasExactSynonym
annotated target: spinal ganglion
has db xref: FMA:5888

Axiom
annotated source: dorsal root ganglion
annotated property: hasExactSynonym
annotated target: spinal ganglion part of peripheral nervous system
has db xref: BIRNLEX:2598

Axiom
annotated source: dorsal root ganglion
annotated property: hasRelatedSynonym
annotated target: DRG
has synonym type: OMO_0003000

Axiom
annotated source: dorsal root ganglion
annotated property: hasRelatedSynonym
annotated target: dorsal root ganglia
has synonym type: OMO_0003004

Axiom
annotated source: dorsal root ganglion
annotated property: hasRelatedSynonym
annotated target: ganglion sensorium nervi spinalis
has db xref: BTO:0001264
has db xref: Wikipedia:Dorsal_root_ganglion
has synonym type: OMO_0003011

Axiom
annotated source: dorsal root ganglion
annotated property: hasRelatedSynonym
annotated target: ganglion spinale
has db xref: BTO:0001264

Axiom
annotated source: dorsal root ganglion
annotated property: hasRelatedSynonym
annotated target: posterior root ganglion
has db xref: EMAPA:16668

ganglion
type: Class
subclass of: anatomical structure
subclass of: Restriction
  on property: BFO_0000050
  some values from: nervous system
disjoint with: UBERON_0002420
IAO_0000115: A biological tissue mass, most commonly a mass of nerve cell bodies.
IAO_0000116: TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures
UBPROP_0000001: Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO]
UBPROP_0000001: Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO]
UBPROP_0000001: Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302].
UBPROP_0000003: Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG]
UBPROP_0000007: ganglionic
has db xref: AAO:0010426
has db xref: AEO:0000135
has db xref: BAMS:G
has db xref: BTO:0000497
has db xref: CALOHA:TS-0397
has db xref: EFO:0000899
has db xref: EHDAA2:0003135
has db xref: EHDAA:2897
has db xref: EHDAA:4662
has db xref: EHDAA:5621
has db xref: EHDAA:918
has db xref: EMAPA:32846
has db xref: EV:0100372
has db xref: FMA:5884
has db xref: MA:0002406
has db xref: MAT:0000207
has db xref: MAT:0000343
has db xref: MESH:D005724
has db xref: MIAA:0000207
has db xref: MIAA:0000343
has db xref: NCIT:C12719
has db xref: NLXANAT:100302
has db xref: TAO:0000190
has db xref: TGMA:0001016
has db xref: UMLS:C0017067
has db xref: VHOG:0000156
has db xref: WBbt:0005189
has db xref: Wikipedia:Ganglion
has db xref: XAO:0000209
has db xref: ZFA:0000190
has OBO namespace: uberon
has related synonym: ganglia
has related synonym: neural ganglion
id: UBERON:0000045
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: ganglion
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: ganglion
annotated property: subClassOf
annotated target: Restriction
source: Bgee:AN

Axiom
annotated source: ganglion
annotated property: disjointWith
annotated target: UBERON_0002420
inconsistent with: BTO

Axiom
annotated source: ganglion
annotated property: IAO_0000115
annotated target: A biological tissue mass, most commonly a mass of nerve cell bodies.
has db xref: Wikipedia:Ganglion
has db xref: https://github.com/obophenotype/uberon/issues/300

Axiom
annotated source: ganglion
annotated property: UBPROP_0000001
annotated target: A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures
source: PMID:21062451

Axiom
annotated source: ganglion
annotated property: UBPROP_0000001
annotated target: Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010426
ontology: AAO
source: AAO:EJS

Axiom
annotated source: ganglion
annotated property: UBPROP_0000001
annotated target: Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO]
date retrieved: 2012-08-14
external class: TAO:0000190
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: ganglion
annotated property: UBPROP_0000001
annotated target: Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302].
source: NLXANAT:100302

Axiom
annotated source: ganglion
annotated property: UBPROP_0000003
annotated target: Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000156
ontology: VHOG
source: DOI:10.1016/j.ydbio.2005.02.021 Mazet F, Hutt JA, Milloz J, Millard J, Graham A, Shimeld SM, Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Developmental Biology (2005)
source: http://bgee.unil.ch/

Axiom
annotated source: ganglion
annotated property: hasDbXref
annotated target: UMLS:C0017067
source: ncithesaurus:Ganglion

Axiom
annotated source: ganglion
annotated property: hasRelatedSynonym
annotated target: neural ganglion
has db xref: BTO:0000497

simple eye
type: Class
subclass of: eye
IAO_0000115: An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity.
has db xref: TGMA:0000729
has db xref: Wikipedia:Eye#Simple_eyes
has OBO namespace: uberon
id: UBERON:0000047
in subset: grouping class
in subset: uberon slim

Axiom
annotated source: simple eye
annotated property: IAO_0000115
annotated target: An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity.
has db xref: Wikipedia:Eye#Simple_eyes

vessel
type: Class
subclass of: UBERON_0004111
subclass of: Restriction
  on property: channel for
  some values from: UBERON_0006314
IAO_0000115: A tubular structure that contains, conveys body fluid, such as blood or lymph.
RO_0002175: NCBITaxon 9606
has OBO namespace: uberon
id: UBERON:0000055
in subset: grouping class
in subset: human reference atlas
in subset: pheno slim

Axiom
annotated source: vessel
annotated property: IAO_0000115
annotated target: A tubular structure that contains, conveys body fluid, such as blood or lymph.
has db xref: https://orcid.org/0000-0002-6601-2165

ureter
type: Class
subclass of: UBERON_0004120
subclass of: UBERON_0005179
subclass of: UBERON_0006555
subclass of: UBERON_0015212
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0036295
subclass of: Restriction
  on property: BSPO_0000126
  some values from: multicellular organism
subclass of: Restriction
  on property: channel for
  some values from: urine
subclass of: Restriction
  on property: channels from
  some values from: UBERON_0001224
subclass of: Restriction
  on property: channels into
  some values from: UBERON_0001255
IAO_0000115: Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]
UBPROP_0000001: 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]
UBPROP_0000003: 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]
UBPROP_0000007: ureteral
UBPROP_0000007: ureteric
UBPROP_0000010: in humans, consists of adventitial, muscular and mucoa layers
has db xref: AAO:0010254
has db xref: BTO:0001409
has db xref: CALOHA:TS-1084
has db xref: EFO:0000930
has db xref: EHDAA2:0002139
has db xref: EHDAA:9341
has db xref: EMAPA:17950
has db xref: EV:0100097
has db xref: FMA:9704
has db xref: GAID:438
has db xref: MA:0000378
has db xref: MAT:0000120
has db xref: MESH:D014513
has db xref: MIAA:0000120
has db xref: NCIT:C12416
has db xref: SCTID:302511008
has db xref: UMLS:C0041951
has db xref: VHOG:0000605
has db xref: Wikipedia:Ureter
has db xref: XAO:0000144
has db xref: galen:Ureter
has OBO namespace: uberon
has related synonym: metanephric duct
id: UBERON:0000056
in subset: efo slim
in subset: human reference atlas
in subset: major organ
in subset: organ slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: ureter
annotated property: subClassOf
annotated target: Restriction
source: GO

Axiom
annotated source: ureter
annotated property: IAO_0000115
annotated target: Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs.
has db xref: GO:0090189
has db xref: Wikipedia:Ureter

Axiom
annotated source: ureter
annotated property: UBPROP_0000001
annotated target: Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010254
ontology: AAO
source: AAO:BJB

Axiom
annotated source: ureter
annotated property: UBPROP_0000001
annotated target: 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]
date retrieved: 2012-09-17
external class: VHOG:0000605
ontology: VHOG
source: http://bgee.unil.ch/

Axiom
annotated source: ureter
annotated property: UBPROP_0000003
annotated target: 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]
date retrieved: 2012-09-17
external class: VHOG:0000605
ontology: VHOG
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543
source: http://bgee.unil.ch/

Axiom
annotated source: ureter
annotated property: hasDbXref
annotated target: UMLS:C0041951
source: ncithesaurus:Ureter

Axiom
annotated source: ureter
annotated property: hasRelatedSynonym
annotated target: metanephric duct
has db xref: ISBN:0073040584
has db xref: VHOG:0000605

urethra
type: Class
subclass of: organ
subclass of: UBERON_0004111
subclass of: UBERON_0004120
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001556
subclass of: Restriction
  on property: RO_0002150
  some values from: UBERON_0001255
subclass of: Restriction
  on property: RO_0002216
  some values from: GO_0060073
subclass of: Restriction
  on property: channel for
  some values from: urine
subclass of: Restriction
  on property: channels from
  some values from: UBERON_0001255
IAO_0000115: The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening.
UBPROP_0000007: urethral
UBPROP_0000008: In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening.
has db xref: BTO:0001426
has db xref: CALOHA:TS-1132
has db xref: EFO:0000931
has db xref: EMAPA:30901
has db xref: EV:0100099
has db xref: FMA:19667
has db xref: GAID:390
has db xref: MA:0000379
has db xref: MAT:0000121
has db xref: MESH:D014521
has db xref: MIAA:0000121
has db xref: NCIT:C12417
has db xref: SCTID:302513006
has db xref: UMLS:C0041967
has db xref: VHOG:0001264
has db xref: Wikipedia:Urethra
has db xref: XAO:0000153
has db xref: galen:Urethra
has OBO namespace: uberon
id: UBERON:0000057
in subset: efo slim
in subset: major organ
in subset: organ slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: urethra
annotated property: subClassOf
annotated target: Restriction
notes: pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra
source: Wikipedia

Axiom
annotated source: urethra
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: urethra
annotated property: IAO_0000115
annotated target: The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening.
has db xref: MGI:anna
has db xref: MP:0000537

Axiom
annotated source: urethra
annotated property: hasDbXref
annotated target: UMLS:C0041967
source: ncithesaurus:Urethra

duct
type: Class
subclass of: organ subunit
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0034969
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0002299
subclass of: Restriction
  on property: RO_0002570
  some values from: organism substance
IAO_0000115: A tubular structure that transports secreted or excreted substances.
UBPROP_0000001: A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171].
UBPROP_0000012: Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here.
has db xref: AAO:0011123
has db xref: FBbt:00100314
has db xref: FMA:30320
has db xref: NCIT:C12948
has db xref: SCTID:91726008
has db xref: TAO:0005171
has db xref: UMLS:C0687028
has db xref: Wikipedia:Duct_(anatomy)
has db xref: XAO:0004000
has db xref: ZFA:0005171
has db xref: galen:Duct
has exact synonym: anatomical duct
has narrow synonym: exocrine duct
has narrow synonym: exocrine gland duct
has OBO namespace: uberon
has related synonym: ducts
id: UBERON:0000058
in subset: grouping class

Axiom
annotated source: duct
annotated property: IAO_0000115
annotated target: A tubular structure that transports secreted or excreted substances.
has db xref: http://orcid.org/0000-0002-6601-2165
has db xref: http://www.siumed.edu/~dking2/intro/glands.htm#ducts

Axiom
annotated source: duct
annotated property: UBPROP_0000001
annotated target: A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171].
source: ZFA:0005171

Axiom
annotated source: duct
annotated property: hasDbXref
annotated target: FBbt:00100314
mapping justification: ManualMappingCuration

Axiom
annotated source: duct
annotated property: hasDbXref
annotated target: UMLS:C0687028
source: ncithesaurus:Duct

Axiom
annotated source: duct
annotated property: hasRelatedSynonym
annotated target: ducts
has db xref: XAO:0004000
has synonym type: OMO_0003004

large intestine
type: Class
subclass of: UBERON_0004921
subclass of: UBERON_0013765
subclass of: Restriction
  on property: BFO_0000050
  some values from: intestine
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0004907
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7742
subclass of: Restriction
  on property: RO_0002433
  some values from: intestine
IAO_0000115: A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong].
RO_0002175: NCBITaxon 9606
UBPROP_0000003: Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]
has db xref: AAO:0010396
has db xref: BTO:0000706
has db xref: CALOHA:TS-1306
has db xref: EFO:0000840
has db xref: EMAPA:19252
has db xref: EV:0100077
has db xref: FMA:7201
has db xref: GAID:306
has db xref: MA:0000333
has db xref: MESH:D007420
has db xref: MIAA:0000046
has db xref: NCIT:C12379
has db xref: SCTID:181254001
has db xref: UMLS:C0021851
has db xref: VHOG:0000054
has db xref: Wikipedia:Large_intestine_(anatomy)
has db xref: XAO:0000131
has db xref: galen:LargeIntestine
has OBO namespace: uberon
has related synonym: intestinum crassum
id: UBERON:0000059
in subset: efo slim
in subset: human reference atlas
in subset: major organ
in subset: organ slim
in subset: pheno slim

Axiom
annotated source: large intestine
annotated property: subClassOf
annotated target: UBERON_0004921
source: cjm

Axiom
annotated source: large intestine
annotated property: IAO_0000115
annotated target: A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong].
has db xref: ISBN:0073040584
has db xref: Wikipedia:Large_intestine_(anatomy)

Axiom
annotated source: large intestine
annotated property: UBPROP_0000003
annotated target: Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000054
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566
source: http://bgee.unil.ch/

Axiom
annotated source: large intestine
annotated property: hasDbXref
annotated target: UMLS:C0021851
source: ncithesaurus:Large_Intestine

Axiom
annotated source: large intestine
annotated property: hasRelatedSynonym
annotated target: intestinum crassum
has db xref: BTO:0000706

anatomical wall
type: Class
subclass of: organ part
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0004923
subclass of: Restriction
  on property: RO_0002220
  some values from: UBERON_0002553
IAO_0000115: Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
UBPROP_0000012: in FMA, serosa is a wall
has alternative id: UBERON:0009915
has broad synonym: wall
has db xref: FMA:82482
has db xref: galen:Wall
has exact synonym: wall of organ
has OBO namespace: uberon
has related synonym: organ wall
id: UBERON:0000060
in subset: upper level

Axiom
annotated source: anatomical wall
annotated property: IAO_0000115
annotated target: Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
has db xref: FMA:82482

Axiom
annotated source: anatomical wall
annotated property: UBPROP_0000012
annotated target: in FMA, serosa is a wall
external ontology: FMA

Axiom
annotated source: anatomical wall
annotated property: hasExactSynonym
annotated target: wall of organ
has db xref: FMA:82482

Axiom
annotated source: anatomical wall
annotated property: hasRelatedSynonym
annotated target: organ wall
has db xref: FMA:82482

anatomical structure
type: Class
subclass of: material anatomical entity
subclass of: Restriction
  on property: RO_0002497
  some values from: death stage
IAO_0000115: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
RO_0002175: NCBITaxon 9606
has db xref: AAO:0010825
has db xref: AEO:0000003
has db xref: BILA:0000003
has db xref: CARO:0000003
has db xref: EHDAA2:0003003
has db xref: EMAPA:0
has db xref: FBbt:00007001
has db xref: FMA:305751
has db xref: FMA:67135
has db xref: GAID:781
has db xref: HAO:0000003
has db xref: MA:0003000
has db xref: MESH:D000825
has db xref: SCTID:362889002
has db xref: TAO:0000037
has db xref: TGMA:0001823
has db xref: VHOG:0001759
has db xref: XAO:0003000
has db xref: ZFA:0000037
has db xref: http://dbpedia.org/ontology/AnatomicalStructure
has exact synonym: biological structure
has exact synonym: connected biological structure
has OBO namespace: uberon
id: UBERON:0000061
in subset: common anatomy
in subset: human reference atlas
in subset: upper level

Axiom
annotated source: anatomical structure
annotated property: IAO_0000115
annotated target: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
has db xref: CARO:0000003

Axiom
annotated source: anatomical structure
annotated property: hasDbXref
annotated target: FBbt:00007001
mapping justification: ManualMappingCuration

Axiom
annotated source: anatomical structure
annotated property: hasExactSynonym
annotated target: connected biological structure
has db xref: CARO:0000003

organ
type: Class
subclass of: UBERON_0010000
subclass of: Restriction
  on property: BFO_0000050
  some values from: anatomical system
subclass of: Restriction
  on property: RO_0002002
  some values from: UBERON_0006984
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0008150
disjoint with: UBERON_0002095
disjoint with: UBERON_0034921
IAO_0000115: Anatomical structure that performs a specific function or group of functions [WP].
RO_0002161: NCBITaxon_110815
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
UBPROP_0000001: Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
UBPROP_0000012: CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
has db xref: BIRNLEX:4
has db xref: CARO:0020004
has db xref: EFO:0000634
has db xref: EMAPA:35949
has db xref: ENVO:01000162
has db xref: FMA:67498
has db xref: MA:0003001
has db xref: NCIT:C13018
has db xref: SCTID:272625005
has db xref: UMLS:C0178784
has db xref: WBbt:0003760
has db xref: Wikipedia:Organ_(anatomy)
has OBO namespace: uberon
has related synonym: anatomical unit
has related synonym: body organ
has related synonym: element
id: UBERON:0000062
in subset: common anatomy
in subset: upper level

Axiom
annotated source: organ
annotated property: disjointWith
annotated target: UBERON_0002095
source: PMID:28192867

Axiom
annotated source: organ
annotated property: IAO_0000115
annotated target: Anatomical structure that performs a specific function or group of functions [WP].
has db xref: Wikipedia:Organ_(anatomy)

Axiom
annotated source: organ
annotated property: RO_0002161
annotated target: NCBITaxon_110815
source: Wikipedia

Axiom
annotated source: organ
annotated property: UBPROP_0000001
annotated target: Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
source: GO:0048513

Axiom
annotated source: organ
annotated property: hasDbXref
annotated target: UMLS:C0178784
source: ncithesaurus:Organ

Axiom
annotated source: organ
annotated property: hasRelatedSynonym
annotated target: element
has db xref: http://orcid.org/0000-0002-6601-2165

organ subunit
type: Class
subclass of: organ part
IAO_0000115: A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.
IAO_0000116: FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction
UBPROP_0000001: Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball.
UBPROP_0000001: Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal.
has db xref: FMA:86140
has OBO namespace: uberon
has related synonym: organ region with fixed fiat boundary
has related synonym: organ segment
has related synonym: segment of organ
id: UBERON:0000063
in subset: upper level

Axiom
annotated source: organ subunit
annotated property: IAO_0000115
annotated target: A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: organ subunit
annotated property: UBPROP_0000001
annotated target: Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball.
source: FMA:86140
version: 3

Axiom
annotated source: organ subunit
annotated property: UBPROP_0000001
annotated target: Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal.
source: FMA:86140
version: 1

Axiom
annotated source: organ subunit
annotated property: hasRelatedSynonym
annotated target: organ region with fixed fiat boundary
has db xref: FMA:86140

Axiom
annotated source: organ subunit
annotated property: hasRelatedSynonym
annotated target: organ segment
has db xref: FMA:86140

Axiom
annotated source: organ subunit
annotated property: hasRelatedSynonym
annotated target: segment of organ
has db xref: FMA:86140

organ part
type: Class
subclass of: UBERON_0010000
subclass of: Restriction
  on property: BFO_0000050
  some values from: organ
IAO_0000115: A multicellular structure that is a part of an organ.
IAO_0000232: currently defined in a very broad sense, may be replaced by more specific classes in the future
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: AAO:0011124
has db xref: BIRNLEX:16
has db xref: EFO:0000635
has db xref: FMA:82472
has db xref: SCTID:113343008
has db xref: SCTID:91717005
has exact synonym: cardinal organ part
has OBO namespace: uberon
has related synonym: regional part of organ
id: UBERON:0000064
in subset: common anatomy
in subset: efo slim
in subset: non informative
in subset: upper level

Axiom
annotated source: organ part
annotated property: IAO_0000115
annotated target: A multicellular structure that is a part of an organ.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: organ part
annotated property: hasExactSynonym
annotated target: cardinal organ part
has db xref: FMA:82472

Axiom
annotated source: organ part
annotated property: hasRelatedSynonym
annotated target: regional part of organ
has db xref: BIRNLEX:16

respiratory tract
type: Class
subclass of: respiratory airway
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0008947
IAO_0000115: Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts.
RO_0002175: NCBITaxon 9606
has db xref: EHDAA2:0001606
has db xref: EHDAA:1568
has db xref: EHDAA:2219
has db xref: EMAPA:16737
has db xref: FMA:265130
has db xref: SCTID:361110005
has db xref: VHOG:0000393
has OBO namespace: uberon
id: UBERON:0000065
in subset: human reference atlas

Axiom
annotated source: respiratory tract
annotated property: subClassOf
annotated target: Restriction
source: NCBIBook:NBK10107

Axiom
annotated source: respiratory tract
annotated property: IAO_0000115
annotated target: Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts.
has db xref: https://orcid.org/0000-0002-6601-2165

fully formed stage
type: Class
subclass of: BFO_0000003
subclass of: life cycle stage
subclass of: Restriction
  on property: BFO_0000050
  some values from: post-embryonic stage
subclass of: Restriction
  on property: BFO_0000062
  some values from: organogenesis stage
subclass of: Restriction
  on property: BFO_0000063
  some values from: death stage
IAO_0000115: The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
has broad synonym: adult stage
has db xref: BTO:0001043
has db xref: BilaDO:0000004
has db xref: BtauDv:0000078
has db xref: CfamDv:0000007
has db xref: ChirDv:0000014
has db xref: DpseDv:0000005
has db xref: DsimDv:0000005
has db xref: EFO:0001272
has db xref: EcabDv:0000007
has db xref: FBdv:00005369
has db xref: FcatDv:0000007
has db xref: GgalDv:0000076
has db xref: GgorDv:0000032
has db xref: HsapDv:0010000
has db xref: MmulDv:0000052
has db xref: MmusDv:0000092
has db xref: OanaDv:0000007
has db xref: OariDv:0000024
has db xref: PpanDv:0000041
has db xref: PtroDv:0000052
has db xref: RnorDv:0000061
has db xref: SsalDv:0000040
has db xref: SscrDv:0000084
has db xref: WBls:0000041
has db xref: XtroDO:0000084
has exact synonym: fully formed animal stage
has exact synonym: juvenile-adult stage
has OBO namespace: uberon
id: UBERON:0000066
in subset: efo slim

Axiom
annotated source: fully formed stage
annotated property: IAO_0000115
annotated target: The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: BtauDv:0000078
mapping justification: UnspecifiedMatching

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: CfamDv:0000007
mapping justification: UnspecifiedMatching

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: ChirDv:0000014
mapping justification: UnspecifiedMatching

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: DpseDv:0000005
mapping justification: UnspecifiedMatching

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: DsimDv:0000005
mapping justification: UnspecifiedMatching

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: EcabDv:0000007
mapping justification: UnspecifiedMatching

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: FcatDv:0000007
mapping justification: UnspecifiedMatching

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: GgalDv:0000076
mapping justification: UnspecifiedMatching

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: GgorDv:0000032
mapping justification: UnspecifiedMatching

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: HsapDv:0010000
mapping justification: UnspecifiedMatching

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: MmulDv:0000052
mapping justification: UnspecifiedMatching

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: MmusDv:0000092
mapping justification: UnspecifiedMatching

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: OanaDv:0000007
mapping justification: UnspecifiedMatching

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: OariDv:0000024
mapping justification: UnspecifiedMatching

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: PpanDv:0000041
mapping justification: UnspecifiedMatching

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: PtroDv:0000052
mapping justification: UnspecifiedMatching

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: RnorDv:0000061
mapping justification: UnspecifiedMatching

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: SsalDv:0000040
mapping justification: UnspecifiedMatching

Axiom
annotated source: fully formed stage
annotated property: hasDbXref
annotated target: SscrDv:0000084
mapping justification: UnspecifiedMatching

embryo stage
type: Class
subclass of: BFO_0000003
subclass of: life cycle stage
subclass of: Restriction
  on property: BFO_0000063
  some values from: fully formed stage
subclass of: Restriction
  on property: BFO_0000063
  some values from: post-embryonic stage
subclass of: Restriction
  on property: RO_0002082
  some values from: GO_0009790
disjoint with: post-embryonic stage
IAO_0000115: A life cycle stage that starts with fertilization and ends with the fully formed embryo.
has db xref: AcarDv:0000002
has db xref: BilaDO:0000002
has db xref: BtauDv:0000002
has db xref: CfamDv:0000002
has db xref: ChirDv:0000002
has db xref: CporDv:0000002
has db xref: DpseDv:0000002
has db xref: DsimDv:0000002
has db xref: EV:0300001
has db xref: EcabDv:0000002
has db xref: FBdv:00005289
has db xref: FMA:72652
has db xref: FcatDv:0000002
has db xref: GgalDv:0000002
has db xref: GgorDv:0000002
has db xref: HsapDv:0000045
has db xref: MdomDv:0000002
has db xref: MmulDv:0000002
has db xref: MmusDv:0000042
has db xref: OGES:000000
has db xref: OGES:000022
has db xref: OanaDv:0000002
has db xref: OariDv:0000002
has db xref: OcunDv:0000002
has db xref: PpanDv:0000002
has db xref: PtroDv:0000002
has db xref: RnorDv:0000002
has db xref: SCTID:296280003
has db xref: SsalDv:0000002
has db xref: SscrDv:0000002
has db xref: WBls:0000003
has db xref: WBls:0000092
has db xref: WBls:0000102
has db xref: XAO:1000012
has exact synonym: embryonic stage
has OBO namespace: uberon
has related synonym: embryogenesis
id: UBERON:0000068

Axiom
annotated source: embryo stage
annotated property: IAO_0000115
annotated target: A life cycle stage that starts with fertilization and ends with the fully formed embryo.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: AcarDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: BtauDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: CfamDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: ChirDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: CporDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: DpseDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: DsimDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: EcabDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: FcatDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: GgalDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: GgorDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: HsapDv:0000045
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: MdomDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: MmulDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: MmusDv:0000042
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: OanaDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: OariDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: OcunDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: PpanDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: PtroDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: RnorDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: SsalDv:0000002
mapping justification: UnspecifiedMatching

Axiom
annotated source: embryo stage
annotated property: hasDbXref
annotated target: SscrDv:0000002
mapping justification: UnspecifiedMatching

larval stage
type: Class
subclass of: BFO_0000003
subclass of: life cycle stage
subclass of: Restriction
  on property: BFO_0000050
  some values from: post-embryonic stage
subclass of: Restriction
  on property: RO_0002082
  some values from: GO_0002164
subclass of: Restriction
  on property: RO_0002087
  some values from: embryo stage
IAO_0000115: A distinct juvenile stage many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.
IAO_0000232: Uberon includes clade-specific subclasses, e.g. nematod larva
RO_0002161: NCBITaxon_32524
UBPROP_0000008: It is a misunderstanding that the larval form always reflects the group's evolutionary history. It could be the case, but often the larval stage has evolved secondarily, as in insects. In these cases the larval form might differ more from the group's common origin than the adult form
has db xref: BTO:0000915
has db xref: BTO:0000954
has db xref: DpseDv:0000003
has db xref: DsimDv:0000003
has db xref: EFO:0001303
has db xref: MIAA:0000400
has db xref: OGES:000008
has db xref: SsalDv:0000039
has db xref: Wikipedia:Larva
has db xref: ZFS:0000048
has exact synonym: larva stage
has narrow synonym: ammocoete
has narrow synonym: ammocoete stage
has narrow synonym: bipinnaria
has narrow synonym: bipinnaria stage
has narrow synonym: caterpillar
has narrow synonym: caterpillar stage
has narrow synonym: glochidium
has narrow synonym: glochidium stage
has narrow synonym: grub
has narrow synonym: grub stage
has narrow synonym: leptocephalus
has narrow synonym: leptocephalus stage
has narrow synonym: maggot
has narrow synonym: maggot stage
has narrow synonym: metacestode
has narrow synonym: naiad, nymph
has narrow synonym: naiad, nymph stage
has narrow synonym: nauplius
has narrow synonym: nauplius stage
has narrow synonym: nymph
has narrow synonym: nymph stage
has narrow synonym: planula
has narrow synonym: planula stage
has narrow synonym: tornaria
has narrow synonym: trochophore
has narrow synonym: trochophore stage
has narrow synonym: veliger
has narrow synonym: veliger stage
has narrow synonym: wriggler
has narrow synonym: wriggler stage
has narrow synonym: zoea
has narrow synonym: zoea stage
has OBO namespace: uberon
has related synonym: larva
id: UBERON:0000069
in subset: efo slim

Axiom
annotated source: larval stage
annotated property: IAO_0000115
annotated target: A distinct juvenile stage many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.
has db xref: Wikipedia:Larva

Axiom
annotated source: larval stage
annotated property: UBPROP_0000008
annotated target: It is a misunderstanding that the larval form always reflects the group's evolutionary history. It could be the case, but often the larval stage has evolved secondarily, as in insects. In these cases the larval form might differ more from the group's common origin than the adult form
source: WP

Axiom
annotated source: larval stage
annotated property: hasDbXref
annotated target: DpseDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: larval stage
annotated property: hasDbXref
annotated target: DsimDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: larval stage
annotated property: hasDbXref
annotated target: SsalDv:0000039
mapping justification: UnspecifiedMatching

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: ammocoete
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: ammocoete stage
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: bipinnaria
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: bipinnaria stage
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: caterpillar
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: caterpillar stage
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: glochidium
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: glochidium stage
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: grub
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: grub stage
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: leptocephalus
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: leptocephalus stage
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: maggot
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: maggot stage
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: metacestode
has db xref: BTO:0000859
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: naiad, nymph
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: naiad, nymph stage
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: nauplius
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: nauplius stage
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: nymph
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: nymph stage
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: planula
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: planula stage
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: tornaria
has db xref: NCBITaxon:10219
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: trochophore
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: trochophore stage
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: veliger
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: veliger stage
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: wriggler
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: wriggler stage
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: zoea
has db xref: Wikipedia:Larva
has synonym type: SENSU

Axiom
annotated source: larval stage
annotated property: hasNarrowSynonym
annotated target: zoea stage
has db xref: Wikipedia:Larva
has synonym type: SENSU

pupal stage
type: Class
subclass of: BFO_0000003
subclass of: life cycle stage
subclass of: Restriction
  on property: BFO_0000050
  some values from: post-embryonic stage
subclass of: Restriction
  on property: RO_0002087
  some values from: larval stage
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_33392
IAO_0000115: A life cycle stage of holometabolous insects in which the organism is a pupa and starts with the larval-pupal apolysis and ends with pupal-adult apolysis.
UBPROP_0000008: The pupal stage is found only in holometabolous insects, those that undergo a complete metamorphosis, going through four life stages; embryo, larva, pupa and imago
has db xref: DpseDv:0000004
has db xref: DsimDv:0000004
has db xref: FBdv:00005349
has db xref: Wikipedia:Pupa
has exact synonym: pupa stage
has narrow synonym: aurelia stage
has narrow synonym: chrysalides stage
has narrow synonym: chrysalis stage
has OBO namespace: uberon
id: UBERON:0000070

Axiom
annotated source: pupal stage
annotated property: subClassOf
annotated target: Restriction
notes: may be better to model pupal development as including the pre-pupal stage

Axiom
annotated source: pupal stage
annotated property: IAO_0000115
annotated target: A life cycle stage of holometabolous insects in which the organism is a pupa and starts with the larval-pupal apolysis and ends with pupal-adult apolysis.
has db xref: Wikipedia:Pupa
has db xref: https://github.com/obophenotype/uberon/issues/562

Axiom
annotated source: pupal stage
annotated property: hasDbXref
annotated target: DpseDv:0000004
mapping justification: UnspecifiedMatching

Axiom
annotated source: pupal stage
annotated property: hasDbXref
annotated target: DsimDv:0000004
mapping justification: UnspecifiedMatching

Axiom
annotated source: pupal stage
annotated property: hasNarrowSynonym
annotated target: aurelia stage
has db xref: NCBITaxon:37572
has db xref: Wikipedia:Pupa

Axiom
annotated source: pupal stage
annotated property: hasNarrowSynonym
annotated target: chrysalides stage
has db xref: NCBITaxon:37572
has db xref: Wikipedia:Pupa

Axiom
annotated source: pupal stage
annotated property: hasNarrowSynonym
annotated target: chrysalis stage
has db xref: NCBITaxon:37572
has db xref: Wikipedia:Pupa

death stage
type: Class
subclass of: BFO_0000003
subclass of: life cycle stage
subclass of: Restriction
  on property: RO_0002229
  some values from: life cycle
IAO_0000115: End of the life of an organism.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
UBPROP_0000012: ncit:Death is an outcome
has db xref: XAO:0000437
has db xref: XtroDO:0000085
has OBO namespace: uberon
has related synonym: death
id: UBERON:0000071
in subset: common anatomy

Axiom
annotated source: death stage
annotated property: IAO_0000115
annotated target: End of the life of an organism.
has db xref: XAO:0000437

Axiom
annotated source: death stage
annotated property: UBPROP_0000012
annotated target: ncit:Death is an outcome
external ontology: ncit

proximo-distal subdivision of respiratory tract
type: Class
equivalent class: Class
  intersection of: UBERON_0013522
  intersection of: Restriction
    on property: BFO_0000050
    some values from: respiratory tract
subclass of: UBERON_0013522
subclass of: Restriction
  on property: BFO_0000050
  some values from: respiratory tract
IAO_0000115: An section of a respiratory tract.
RO_0002175: NCBITaxon 9606
UBPROP_0000012: MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole
has db xref: FMA:45660
has db xref: MA:0000434
has OBO namespace: uberon
has related synonym: respiratory tract
has related synonym: subdivision of respiratory tract
id: UBERON:0000072
in subset: human reference atlas
in subset: non informative

Axiom
annotated source: proximo-distal subdivision of respiratory tract
annotated property: IAO_0000115
annotated target: An section of a respiratory tract.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: proximo-distal subdivision of respiratory tract
annotated property: UBPROP_0000012
annotated target: MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole
external ontology: MA

Axiom
annotated source: proximo-distal subdivision of respiratory tract
annotated property: hasRelatedSynonym
annotated target: respiratory tract
has db xref: MA:0000434

regional part of nervous system
type: Class
equivalent class: Class
  intersection of: multi-tissue structure
  intersection of: Restriction
    on property: BFO_0000050
    some values from: nervous system
subclass of: multi-tissue structure
subclass of: Restriction
  on property: BFO_0000050
  some values from: nervous system
IAO_0000115: Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS.
contributor: https://orcid.org/0000-0001-9114-8737
creation date: 2009-06-18T09:00:04Z
has db xref: BIRNLEX:1157
has db xref: NCIT:C13040
has db xref: SCTID:25087005
has db xref: UMLS:C1518256
has exact synonym: part of nervous system
has OBO namespace: uberon
id: UBERON:0000073
in subset: non informative
in subset: upper level

Axiom
annotated source: regional part of nervous system
annotated property: IAO_0000115
annotated target: Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS.
has db xref: BIRNLEX:1157

Axiom
annotated source: regional part of nervous system
annotated property: hasDbXref
annotated target: UMLS:C1518256
source: ncithesaurus:Nervous_System_Part

Axiom
annotated source: regional part of nervous system
annotated property: hasExactSynonym
annotated target: part of nervous system
has db xref: BIRNLEX:1157

renal glomerulus
type: Class
subclass of: organ part
subclass of: UBERON_0004120
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0005749
subclass of: Restriction
  on property: RO_0002219
  some values from: UBERON_0001230
IAO_0000115: A capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney[GO].
RO_0002175: NCBITaxon 9606
UBPROP_0000012: ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule?
contributor: https://orcid.org/0000-0001-9114-8737
creation date: 2009-06-18T09:26:37Z
has broad synonym: glomerulus
has db xref: BTO:0000530
has db xref: CALOHA:TS-0862
has db xref: EFO:0003667
has db xref: EMAPA:28329
has db xref: EV:0100386
has db xref: FMA:15624
has db xref: MA:0001657
has db xref: MESH:D007678
has db xref: NCIT:C13250
has db xref: SCTID:362217000
has db xref: TAO:0001288
has db xref: UMLS:C0022663
has db xref: Wikipedia:Glomerulus
has db xref: ZFA:0001288
has exact synonym: renal glomeruli
has OBO namespace: uberon
has related synonym: Malphigian glomerulus
has related synonym: Malpighian glomerulus
has related synonym: Malpighian tuft
has related synonym: glomerular capillary tuft
has related synonym: glomerular tuft
has related synonym: glomerulus renis
has related synonym: renal corpuscle
id: UBERON:0000074
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: vertebrate core

Axiom
annotated source: renal glomerulus
annotated property: subClassOf
annotated target: Restriction
source: FMA
source: MA

Axiom
annotated source: renal glomerulus
annotated property: IAO_0000115
annotated target: A capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney[GO].
has db xref: MP:0005325
has db xref: Wikipedia:Glomerulus

Axiom
annotated source: renal glomerulus
annotated property: UBPROP_0000012
annotated target: ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule?
external ontology: ZFA

Axiom
annotated source: renal glomerulus
annotated property: hasDbXref
annotated target: UMLS:C0022663
source: ncithesaurus:Glomerulus

Axiom
annotated source: renal glomerulus
annotated property: hasExactSynonym
annotated target: renal glomeruli
has db xref: TAO:0001288

Axiom
annotated source: renal glomerulus
annotated property: hasRelatedSynonym
annotated target: Malphigian glomerulus
has db xref: BTO:0000530
has synonym type: MISSPELLING

Axiom
annotated source: renal glomerulus
annotated property: hasRelatedSynonym
annotated target: Malpighian glomerulus
has db xref: http://medical-dictionary.thefreedictionary.com/malpighian+glomerulus

Axiom
annotated source: renal glomerulus
annotated property: hasRelatedSynonym
annotated target: Malpighian tuft
has db xref: http://medical-dictionary.thefreedictionary.com/malpighian+glomerulus

Axiom
annotated source: renal glomerulus
annotated property: hasRelatedSynonym
annotated target: glomerular capillary tuft
has db xref: ZFA:0001288

Axiom
annotated source: renal glomerulus
annotated property: hasRelatedSynonym
annotated target: glomerular tuft
has synonym type: INCONSISTENT

Axiom
annotated source: renal glomerulus
annotated property: hasRelatedSynonym
annotated target: glomerulus renis
has db xref: Wikipedia:Glomerulus
has synonym type: OMO_0003011

Axiom
annotated source: renal glomerulus
annotated property: hasRelatedSynonym
annotated target: renal corpuscle
has synonym type: INCONSISTENT

subdivision of skeletal system
type: Class
subclass of: UBERON_0011216
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001434
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7711
subclass of: Restriction
  on property: RO_0002473
  some values from: UBERON_0004765
IAO_0000115: Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
has alternative id: UBERON:0010322
has db xref: FMA:85544
has db xref: NCIT:C34076
has db xref: SCTID:118966000
has db xref: UMLS:C1519343
has db xref: galen:ComplexSkeletalStructure
has exact synonym: skeletal system subdivision
has OBO namespace: uberon
has related synonym: skeletal system part
id: UBERON:0000075
in subset: non informative

Axiom
annotated source: subdivision of skeletal system
annotated property: subClassOf
annotated target: UBERON_0011216
source: cjm

Axiom
annotated source: subdivision of skeletal system
annotated property: IAO_0000115
annotated target: Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
has db xref: UBERONREF:0000003
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: subdivision of skeletal system
annotated property: hasDbXref
annotated target: UMLS:C1519343
source: ncithesaurus:Skeletal_System_Part

Axiom
annotated source: subdivision of skeletal system
annotated property: hasExactSynonym
annotated target: skeletal system subdivision
has db xref: FMA:85544

external ectoderm
type: Class
subclass of: unilaminar epithelium
subclass of: UBERON_0005291
subclass of: Restriction
IAO_0000115: The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
IAO_0000116: merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)
RO_0002171: UBERON_0002346
UBPROP_0000011: (or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis
has db xref: BTO:0006242
has db xref: EHDAA2:0001968
has db xref: EHDAA:1494
has db xref: EHDAA:350
has db xref: EHDAA:4784
has db xref: EHDAA:4790
has db xref: EHDAA:4796
has db xref: EHDAA:7860
has db xref: EMAPA:16096
has db xref: FMA:87656
has db xref: NCIT:C34309
has db xref: UMLS:C1515087
has db xref: Wikipedia:External_ectoderm
has exact synonym: surface (external) ectoderm
has exact synonym: surface ectoderm
has OBO namespace: uberon
id: UBERON:0000076
in subset: pheno slim

Axiom
annotated source: external ectoderm
annotated property: subClassOf
annotated target: unilaminar epithelium
source: EHDAA2

Axiom
annotated source: external ectoderm
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: external ectoderm
annotated property: IAO_0000115
annotated target: The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
has db xref: MGI:anna
has db xref: MP:0012532

Axiom
annotated source: external ectoderm
annotated property: hasDbXref
annotated target: BTO:0006242
author id: https://orcid.org/0000-0003-4423-4370
mapping justification: ManualMappingCuration
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: external ectoderm
annotated property: hasDbXref
annotated target: UMLS:C1515087
source: ncithesaurus:Surface_Ectoderm

Axiom
annotated source: external ectoderm
annotated property: hasExactSynonym
annotated target: surface ectoderm
has db xref: MP:0012532

mixed endoderm/mesoderm-derived structure
type: Class
equivalent class: Class
  intersection of: anatomical structure
  intersection of: Restriction
    on property: RO_0002202
    some values from: endoderm
  intersection of: Restriction
    on property: RO_0002202
    some values from: mesoderm
subclass of: UBERON_0004119
subclass of: UBERON_0004120
IAO_0000115: An anatomical structure that develops from the endoderm and the mesoderm.
IAO_0000232: Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple
has OBO namespace: uberon
id: UBERON:0000077
in subset: grouping class

Axiom
annotated source: mixed endoderm/mesoderm-derived structure
annotated property: IAO_0000115
annotated target: An anatomical structure that develops from the endoderm and the mesoderm.
has db xref: https://orcid.org/0000-0002-6601-2165

mixed ectoderm/mesoderm/endoderm-derived structure
type: Class
equivalent class: Class
  intersection of: anatomical structure
  intersection of: Restriction
    on property: RO_0002202
    some values from: ectoderm
  intersection of: Restriction
    on property: RO_0002202
    some values from: endoderm
  intersection of: Restriction
    on property: RO_0002202
    some values from: mesoderm
subclass of: mixed endoderm/mesoderm-derived structure
subclass of: UBERON_0004121
IAO_0000115: An anatomical structure that develops from the ectoderm, mesoderm and endoderm.
IAO_0000232: Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple
has OBO namespace: uberon
id: UBERON:0000078
in subset: grouping class

Axiom
annotated source: mixed ectoderm/mesoderm/endoderm-derived structure
annotated property: IAO_0000115
annotated target: An anatomical structure that develops from the ectoderm, mesoderm and endoderm.
has db xref: https://orcid.org/0000-0002-6601-2165

male reproductive system
type: Class
equivalent class: Class
  intersection of: reproductive system
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0003101
subclass of: reproductive system
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0003101
disjoint with: female reproductive system
IAO_0000115: The organs associated with producing offspring in the gender that produces spermatozoa.
RO_0002175: NCBITaxon 9606
UBPROP_0000003: By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]
has db xref: BTO:0000082
has db xref: CALOHA:TS-1310
has db xref: EFO:0000970
has db xref: EHDAA2:0001054
has db xref: EHDAA:8136
has db xref: EMAPA:17968
has db xref: EV:0100101
has db xref: FBbt:00004927
has db xref: FMA:45664
has db xref: GAID:386
has db xref: HAO:0000505
has db xref: MA:0000396
has db xref: MESH:D005837
has db xref: NCIT:C12722
has db xref: SCTID:361340001
has db xref: TGMA:0000634
has db xref: UMLS:C0017422
has db xref: UMLS:C1963704
has db xref: VHOG:0000725
has db xref: Wikipedia:Male_reproductive_system_(human)
has db xref: XAO:0000155
has exact synonym: genitalia of male organism
has exact synonym: male genital system
has exact synonym: male genitalia
has exact synonym: male genitals
has exact synonym: male organism genitalia
has exact synonym: male organism reproductive system
has exact synonym: reproductive system of male organism
has OBO namespace: uberon
has related synonym: male genital organ
has related synonym: male genital tract
has related synonym: male reproductive tract
has related synonym: systema genitale masculinum
id: UBERON:0000079
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim

Axiom
annotated source: male reproductive system
annotated property: IAO_0000115
annotated target: The organs associated with producing offspring in the gender that produces spermatozoa.
has db xref: MP:0001145

Axiom
annotated source: male reproductive system
annotated property: UBPROP_0000003
annotated target: By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000725
ontology: VHOG
source: ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43
source: http://bgee.unil.ch/

Axiom
annotated source: male reproductive system
annotated property: hasDbXref
annotated target: FBbt:00004927
mapping justification: ManualMappingCuration

Axiom
annotated source: male reproductive system
annotated property: hasDbXref
annotated target: UMLS:C0017422
source: ncithesaurus:Male_Genitalia

Axiom
annotated source: male reproductive system
annotated property: hasDbXref
annotated target: UMLS:C1963704
source: ncithesaurus:Male_Reproductive_System

Axiom
annotated source: male reproductive system
annotated property: hasExactSynonym
annotated target: genitalia of male organism
has db xref: OBOL:automatic

Axiom
annotated source: male reproductive system
annotated property: hasExactSynonym
annotated target: male genital system
has db xref: FMA:45664

Axiom
annotated source: male reproductive system
annotated property: hasExactSynonym
annotated target: male organism genitalia
has db xref: OBOL:automatic

Axiom
annotated source: male reproductive system
annotated property: hasExactSynonym
annotated target: male organism reproductive system
has db xref: OBOL:automatic

Axiom
annotated source: male reproductive system
annotated property: hasExactSynonym
annotated target: reproductive system of male organism
has db xref: OBOL:automatic

Axiom
annotated source: male reproductive system
annotated property: hasRelatedSynonym
annotated target: male genital organ
has db xref: BTO:0000082

Axiom
annotated source: male reproductive system
annotated property: hasRelatedSynonym
annotated target: male reproductive tract
has db xref: MA:0000396

Axiom
annotated source: male reproductive system
annotated property: hasRelatedSynonym
annotated target: systema genitale masculinum
has db xref: BTO:0000082

mesonephros
type: Class
subclass of: UBERON_0002113
subclass of: UBERON_0004120
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0002120
IAO_0000115: The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo.
UBPROP_0000001: A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]
UBPROP_0000001: Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO]
UBPROP_0000003: As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]
UBPROP_0000007: mesonephric
UBPROP_0000008: In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney
UBPROP_0000009: By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified]
has db xref: AAO:0010384
has db xref: BTO:0001542
has db xref: CALOHA:TS-0624
has db xref: EFO:0000928
has db xref: EHDAA2:0001130
has db xref: EHDAA:1581
has db xref: EHDAA:5903
has db xref: EMAPA:16744
has db xref: FMA:72171
has db xref: GAID:1308
has db xref: MESH:D001755
has db xref: NCIT:C26467
has db xref: SCTID:308799002
has db xref: TAO:0000529
has db xref: UMLS:C0025492
has db xref: VHOG:0000038
has db xref: Wikipedia:Mesonephros
has db xref: XAO:0000141
has db xref: ZFA:0000529
has exact synonym: Wolffian body
has exact synonym: mesonephric kidney
has exact synonym: mesonephroi
has OBO namespace: uberon
has related synonym: amphibian adult kidney
has related synonym: corpus Wolffi
has related synonym: middle kidney
has related synonym: opisthonephros
has related synonym: opisto nephros
has related synonym: opistonephros
id: UBERON:0000080
in subset: efo slim
in subset: organ slim
in subset: pheno slim
in subset: vertebrate core

Axiom
annotated source: mesonephros
annotated property: IAO_0000115
annotated target: The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo.
has db xref: GO:0001823
has db xref: Wikipedia:Mesonephros

Axiom
annotated source: mesonephros
annotated property: UBPROP_0000001
annotated target: A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000038
ontology: VHOG
source: http://bgee.unil.ch/

Axiom
annotated source: mesonephros
annotated property: UBPROP_0000001
annotated target: Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010384
ontology: AAO
source: AAO:BJB

Axiom
annotated source: mesonephros
annotated property: UBPROP_0000003
annotated target: As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000038
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639
source: http://bgee.unil.ch/

Axiom
annotated source: mesonephros
annotated property: hasDbXref
annotated target: UMLS:C0025492
source: ncithesaurus:Mesonephros

Axiom
annotated source: mesonephros
annotated property: hasExactSynonym
annotated target: Wolffian body
has db xref: BTO:0001542
has db xref: GOC:yaf
has db xref: MESH:A16.254.500
has db xref: Wikipedia:Mesonephros

Axiom
annotated source: mesonephros
annotated property: hasExactSynonym
annotated target: mesonephric kidney
has db xref: XAO:0000141

Axiom
annotated source: mesonephros
annotated property: hasExactSynonym
annotated target: mesonephroi
has db xref: http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron
has synonym type: OMO_0003004

Axiom
annotated source: mesonephros
annotated property: hasRelatedSynonym
annotated target: amphibian adult kidney
has db xref: XAO:0000141

Axiom
annotated source: mesonephros
annotated property: hasRelatedSynonym
annotated target: corpus Wolffi
has db xref: BTO:0001542

Axiom
annotated source: mesonephros
annotated property: hasRelatedSynonym
annotated target: middle kidney
has db xref: BTO:0001542

Axiom
annotated source: mesonephros
annotated property: hasRelatedSynonym
annotated target: opisthonephros
has db xref: VHOG:0000038
has db xref: XAO:0000141

Axiom
annotated source: mesonephros
annotated property: hasRelatedSynonym
annotated target: opistonephros
has db xref: http://www.usm.maine.edu/bio/courses/bio205/bio205_26_sex.html

metanephros
type: Class
subclass of: UBERON_0002113
subclass of: UBERON_0004120
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0005753
subclass of: Restriction
  on property: RO_0002492
  some values from: fully formed stage
IAO_0000115: In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO].
IAO_0000116: TODO check developmental relationships
UBPROP_0000001: A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]
UBPROP_0000003: The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG]
UBPROP_0000007: metanephric
UBPROP_0000011: During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis
has db xref: BTO:0001543
has db xref: EHDAA2:0001137
has db xref: EHDAA:3089
has db xref: EHDAA:5911
has db xref: EMAPA:17373
has db xref: EMAPA_RETIRED:17207
has db xref: FMA:72172
has db xref: NCIT:C34209
has db xref: SCTID:308797000
has db xref: UMLS:C0231049
has db xref: VHOG:0000039
has db xref: Wikipedia:Metanephros#Metanephros
has exact synonym: metanephron
has OBO namespace: uberon
has related synonym: definite kidney
has related synonym: definitive kidney
has related synonym: hind kidney
has related synonym: metanephric kidney
id: UBERON:0000081
in subset: organ slim
in subset: pheno slim

Axiom
annotated source: metanephros
annotated property: subClassOf
annotated target: Restriction
evidence: definitional

Axiom
annotated source: metanephros
annotated property: subClassOf
annotated target: Restriction
source: GO

Axiom
annotated source: metanephros
annotated property: subClassOf
annotated target: Restriction
source: ISBN:9780878932504

Axiom
annotated source: metanephros
annotated property: IAO_0000115
annotated target: In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO].
has db xref: GO:0001656
has db xref: Wikipedia:Metanephros#Metanephros

Axiom
annotated source: metanephros
annotated property: UBPROP_0000001
annotated target: A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000039
ontology: VHOG
source: http://bgee.unil.ch/

Axiom
annotated source: metanephros
annotated property: UBPROP_0000003
annotated target: The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000039
ontology: VHOG
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543
source: http://bgee.unil.ch/

Axiom
annotated source: metanephros
annotated property: hasDbXref
annotated target: UMLS:C0231049
source: ncithesaurus:Metanephros

Axiom
annotated source: metanephros
annotated property: hasExactSynonym
annotated target: metanephron
has db xref: BTO:0001543

Axiom
annotated source: metanephros
annotated property: hasRelatedSynonym
annotated target: definite kidney
has db xref: BTO:0001543

Axiom
annotated source: metanephros
annotated property: hasRelatedSynonym
annotated target: definitive kidney
has db xref: BTO:0001543

Axiom
annotated source: metanephros
annotated property: hasRelatedSynonym
annotated target: hind kidney
has db xref: BTO:0001543

Axiom
annotated source: metanephros
annotated property: hasRelatedSynonym
annotated target: metanephric kidney
has db xref: VHOG:0000039

mesonephric tubule
type: Class
equivalent class: Class
  intersection of: UBERON_0003914
  intersection of: Restriction
    on property: BFO_0000050
    some values from: mesonephros
subclass of: UBERON_0003914
subclass of: UBERON_0005103
subclass of: UBERON_0006555
IAO_0000115: A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP].
IAO_0000116: TODO check
UBPROP_0000001: Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG]
UBPROP_0000003: As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG]
has db xref: AAO:0010389
has db xref: EHDAA2:0001134
has db xref: EMAPA:16747
has db xref: VHOG:0000500
has db xref: Wikipedia:Mesonephric_tubules
has db xref: XAO:0000148
has OBO namespace: uberon
has related synonym: renal tubules
has related synonym: tubuli mesonephrici
id: UBERON:0000083

Axiom
annotated source: mesonephric tubule
annotated property: IAO_0000115
annotated target: A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP].
has db xref: Wikipedia:Mesonephric_tubules

Axiom
annotated source: mesonephric tubule
annotated property: UBPROP_0000001
annotated target: Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000500
ontology: VHOG
source: http://bgee.unil.ch/
source: http://medical-dictionary.thefreedictionary.com/mesonephric+tubule

Axiom
annotated source: mesonephric tubule
annotated property: UBPROP_0000003
annotated target: As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000500
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639
source: http://bgee.unil.ch/

Axiom
annotated source: mesonephric tubule
annotated property: hasRelatedSynonym
annotated target: renal tubules
has db xref: VHOG:0000500
has synonym type: OMO_0003004

Axiom
annotated source: mesonephric tubule
annotated property: hasRelatedSynonym
annotated target: tubuli mesonephrici
has db xref: Wikipedia:Mesonephric_tubules
has synonym type: OMO_0003011

ureteric bud
type: Class
subclass of: mesonephric tubule
subclass of: UBERON_0007499
subclass of: UBERON_0012275
subclass of: UBERON_0034969
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0003074
IAO_0000115: An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP].
UBPROP_0000001: Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG]
UBPROP_0000001: Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541].
UBPROP_0000003: The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]
has db xref: BTO:0001646
has db xref: EHDAA2:0002140
has db xref: EHDAA:3091
has db xref: EHDAA:5917
has db xref: EMAPA:17209
has db xref: NCIT:C34207
has db xref: SCTID:361528000
has db xref: UMLS:C1284058
has db xref: VHOG:0000541
has db xref: Wikipedia:Ureteric_bud
has OBO namespace: uberon
has related synonym: diverticulum
has related synonym: diverticulum metanephricum
has related synonym: gemma ureterica
has related synonym: metanephric bud
has related synonym: metanephric diverticulum
has related synonym: ureteric ampulla
has related synonym: ureteric diverticulum
id: UBERON:0000084
in subset: pheno slim

Axiom
annotated source: ureteric bud
annotated property: subClassOf
annotated target: UBERON_0007499
source: EHDAA2

Axiom
annotated source: ureteric bud
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: ureteric bud
annotated property: subClassOf
annotated target: Restriction
source: ISBN:9780878932504

Axiom
annotated source: ureteric bud
annotated property: IAO_0000115
annotated target: An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP].
has db xref: MP:0010979
has db xref: PMID:19828308

Axiom
annotated source: ureteric bud
annotated property: UBPROP_0000001
annotated target: Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000541
ontology: VHOG
source: http://bgee.unil.ch/

Axiom
annotated source: ureteric bud
annotated property: UBPROP_0000001
annotated target: Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541].
source: VHOG:0000541

Axiom
annotated source: ureteric bud
annotated property: UBPROP_0000003
annotated target: 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]
date retrieved: 2012-09-17
external class: VHOG:0000541
ontology: VHOG
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543
source: http://bgee.unil.ch/

Axiom
annotated source: ureteric bud
annotated property: hasDbXref
annotated target: UMLS:C1284058
source: ncithesaurus:Metanephric_Diverticulum

Axiom
annotated source: ureteric bud
annotated property: hasRelatedSynonym
annotated target: diverticulum
has db xref: BTO:0001646

Axiom
annotated source: ureteric bud
annotated property: hasRelatedSynonym
annotated target: diverticulum metanephricum
has db xref: Wikipedia:Ureteric_bud
has synonym type: OMO_0003011

Axiom
annotated source: ureteric bud
annotated property: hasRelatedSynonym
annotated target: gemma ureterica
has db xref: Wikipedia:Ureteric_bud
has synonym type: OMO_0003011

Axiom
annotated source: ureteric bud
annotated property: hasRelatedSynonym
annotated target: metanephric bud
has db xref: BTO:0001646

Axiom
annotated source: ureteric bud
annotated property: hasRelatedSynonym
annotated target: metanephric diverticulum
has db xref: Wikipedia:Metanephros#Metanephros

Axiom
annotated source: ureteric bud
annotated property: hasRelatedSynonym
annotated target: ureteric diverticulum
has db xref: VHOG:0000541

morula
type: Class
subclass of: embryo
subclass of: Restriction
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0000353
subclass of: Restriction
  on property: RO_0002219
  some values from: zona pellucida
subclass of: Restriction
  on property: RO_0002488
  some values from: cleavage stage
subclass of: Restriction
  on property: RO_0002492
  some values from: cleavage stage
IAO_0000115: A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum.
UBPROP_0000012: EHDAA2 has embryo starting later
has db xref: BTO:0001508
has db xref: EHDAA2:0000005
has db xref: FMA:292334
has db xref: GAID:1295
has db xref: MESH:D009028
has db xref: NCIT:C34212
has db xref: SCTID:361474003
has db xref: UMLS:C0026573
has db xref: Wikipedia:Morula
has OBO namespace: uberon
has related synonym: morula (2-16 cells)
id: UBERON:0000085
in subset: pheno slim

Axiom
annotated source: morula
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: morula
annotated property: IAO_0000115
annotated target: A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum.
has db xref: MP:0012130

Axiom
annotated source: morula
annotated property: UBPROP_0000012
annotated target: EHDAA2 has embryo starting later
external ontology: EHDAA2

Axiom
annotated source: morula
annotated property: hasDbXref
annotated target: UMLS:C0026573
source: ncithesaurus:Morula

Axiom
annotated source: morula
annotated property: hasRelatedSynonym
annotated target: morula (2-16 cells)
has db xref: EHDAA2:0000005

zona pellucida
type: Class
subclass of: UBERON_0005764
subclass of: Restriction
  on property: BFO_0000050
  some values from: ovary
subclass of: Restriction
  on property: BFO_0000051
  some values from: CHEBI_17089
subclass of: Restriction
  on property: RO_0002007
  some values from: CL_0000023
IAO_0000115: A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes.
RO_0002175: NCBITaxon 9606
UBPROP_0000003: Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG]
has broad synonym: zona pellucida - vitelline membrane
has db xref: BTO:0003135
has db xref: EHDAA2:0002220
has db xref: EHDAA:31
has db xref: EHDAA:62
has db xref: EMAPA:16035
has db xref: FMA:18674
has db xref: GAID:410
has db xref: MA:0001715
has db xref: MESH:D015044
has db xref: NCIT:C33896
has db xref: TAO:0001111
has db xref: UMLS:C0043519
has db xref: Wikipedia:Zona_pellucida
has db xref: ZFA:0001111
has OBO namespace: uberon
has related synonym: oolemma
has related synonym: pellucid zone
has related synonym: striated membrane
has related synonym: vitelline envelope
has related synonym: vitelline membrane
has related synonym: zona radiata
has related synonym: zona striata
id: UBERON:0000086
in subset: human reference atlas
in subset: pheno slim
in subset: vertebrate core

Axiom
annotated source: zona pellucida
annotated property: IAO_0000115
annotated target: A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes.
has db xref: Wikipedia:Zona_pellucida

Axiom
annotated source: zona pellucida
annotated property: UBPROP_0000003
annotated target: Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000720
ontology: VHOG
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.159
source: http://bgee.unil.ch/

Axiom
annotated source: zona pellucida
annotated property: hasBroadSynonym
annotated target: zona pellucida - vitelline membrane
has db xref: VHOG:0000720

Axiom
annotated source: zona pellucida
annotated property: hasDbXref
annotated target: UMLS:C0043519
source: ncithesaurus:Zona_Pellucida

Axiom
annotated source: zona pellucida
annotated property: hasRelatedSynonym
annotated target: oolemma
has db xref: BTO:0003135

Axiom
annotated source: zona pellucida
annotated property: hasRelatedSynonym
annotated target: pellucid zone
has db xref: BTO:0003135

Axiom
annotated source: zona pellucida
annotated property: hasRelatedSynonym
annotated target: striated membrane
has db xref: BTO:0003135

Axiom
annotated source: zona pellucida
annotated property: hasRelatedSynonym
annotated target: zona radiata
has db xref: BTO:0003135

Axiom
annotated source: zona pellucida
annotated property: hasRelatedSynonym
annotated target: zona striata
has db xref: BTO:0003135

inner cell mass
type: Class
subclass of: UBERON_0002050
subclass of: Restriction
IAO_0000115: A mass of cells that develop into the body of the embryo and some extraembryonic tissues.
UBPROP_0000001: A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG]
UBPROP_0000003: A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG]
UBPROP_0000011: This structure forms in the earliest steps of development, before implantation into the endometrium of the uterus has occurred.The ICM lies within the blastocyst cavity and is entirely surrounded by the single layer of cells called trophoblast. [Wikipedia:Inner_cell_mass]
has db xref: EFO:0000547
has db xref: EHDAA2:0000830
has db xref: EHDAA:40
has db xref: EMAPA:16041
has db xref: FMA:86557
has db xref: NCIT:C13740
has db xref: SCTID:361456007
has db xref: UMLS:C1283994
has db xref: VHOG:0000742
has db xref: Wikipedia:Inner_cell_mass
has OBO namespace: uberon
has related synonym: ICM
has related synonym: early embryoblast
has related synonym: embryoblast
has related synonym: embryoblastus; massa cellularis interna; pluriblastus senior
has related synonym: pluriblast
id: UBERON:0000087
in subset: early development
in subset: efo slim
in subset: pheno slim

Axiom
annotated source: inner cell mass
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: inner cell mass
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: inner cell mass
annotated property: IAO_0000115
annotated target: A mass of cells that develop into the body of the embryo and some extraembryonic tissues.
has db xref: ISBN:0-683-40008-8
has db xref: MGI:pvb

Axiom
annotated source: inner cell mass
annotated property: UBPROP_0000001
annotated target: A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000742
ontology: VHOG
source: http://bgee.unil.ch/

Axiom
annotated source: inner cell mass
annotated property: UBPROP_0000003
annotated target: A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000742
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144
source: http://bgee.unil.ch/

Axiom
annotated source: inner cell mass
annotated property: hasDbXref
annotated target: UMLS:C1283994
source: ncithesaurus:Inner_Cell_Mass

Axiom
annotated source: inner cell mass
annotated property: hasRelatedSynonym
annotated target: ICM
has db xref: VHOG:0000742

Axiom
annotated source: inner cell mass
annotated property: hasRelatedSynonym
annotated target: early embryoblast
has db xref: FMA:86557

Axiom
annotated source: inner cell mass
annotated property: hasRelatedSynonym
annotated target: embryoblastus; massa cellularis interna; pluriblastus senior
has db xref: Wikipedia:Inner_cell_mass
has synonym type: OMO_0003011

trophoblast
type: Class
subclass of: UBERON_0002050
subclass of: Restriction
  on property: BFO_0000050
  some values from: blastocyst
subclass of: Restriction
  on property: RO_0002473
  some values from: CL_0000351
IAO_0000115: The mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta.
UBPROP_0000001: the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta[MP]
UBPROP_0000007: trophoblastic
UBPROP_0000011: The postimplantation derivatives of the trophectoderm, which make up most of the fetal part of the placenta
has db xref: BTO:0001079
has db xref: CALOHA:TS-1070
has db xref: EV:0100120
has db xref: FMA:83029
has db xref: GAID:1152
has db xref: MESH:D014327
has db xref: NCIT:C93292
has db xref: SCTID:362839005
has db xref: UMLS:C0041178
has db xref: Wikipedia:Trophoblast
has exact synonym: trophoblast layer
has OBO namespace: uberon
has related synonym: massa cellularis externa
has related synonym: trophoblastus
has related synonym: trophoderm
id: UBERON:0000088
in subset: early development
in subset: pheno slim
comment: Aggregate of cells forming the outer layer of a blastocyst, which provide nutrients to the embryo and develop into a large part of the placenta. They are formed during the first stage of pregnancy and are the first cells to differentiate from the fertilized egg. [Wikipedia:Trophoblast]

Axiom
annotated source: trophoblast
annotated property: subClassOf
annotated target: Restriction
source: MP-def
source: PMID:19829370

Axiom
annotated source: trophoblast
annotated property: IAO_0000115
annotated target: The mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta.
has db xref: ISBN:0-683-40008-8
has db xref: MP:0005031

Axiom
annotated source: trophoblast
annotated property: UBPROP_0000001
annotated target: the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta[MP]
date retrieved: 2012-08-23
external class: MP:0005031
external class label: trophoblast layer
ontology: MP
source: ISBN:0-683-40008-8

Axiom
annotated source: trophoblast
annotated property: UBPROP_0000011
annotated target: The postimplantation derivatives of the trophectoderm, which make up most of the fetal part of the placenta
source: PMID:19829370

Axiom
annotated source: trophoblast
annotated property: hasDbXref
annotated target: UMLS:C0041178
source: ncithesaurus:Trophoblast

Axiom
annotated source: trophoblast
annotated property: hasExactSynonym
annotated target: trophoblast layer
has db xref: MP:0005031

Axiom
annotated source: trophoblast
annotated property: hasRelatedSynonym
annotated target: massa cellularis externa
has db xref: Wikipedia:Trophoblast
has synonym type: OMO_0003011

Axiom
annotated source: trophoblast
annotated property: hasRelatedSynonym
annotated target: trophoblastus
has db xref: Wikipedia:Trophoblast
has synonym type: OMO_0003011

Axiom
annotated source: trophoblast
annotated property: hasRelatedSynonym
annotated target: trophoderm
has db xref: BTO:0001079

hypoblast (generic)
type: Class
subclass of: UBERON_0002050
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0004750
IAO_0000115: Missing definition for term UBERON:0000089. Please replace it using linked reference.
IAO_0000116: TODO - consider relationship to UBERON:0000091 ! bilaminar disc
IAO_0000232: this term groups together disparate structures with different relationships.
IAO_0000233: https://sourceforge.net/p/geneontology/ontology-requests/9676/
UBPROP_0000001: A primary germ layer that can give rise to both mesoderm and endoderm.[AAO]
UBPROP_0000001: The inner of the two layers of the blastoderm that forms during gastrulation and give rise to the definitive mesoderm and endoderm. Kimmel et al, 1995.[TAO]
UBPROP_0000003: In mammal and avian, extraembryonic endoderm such as visceral endoderm and hypoblast play essential roles in the embryonic axis formation and germ layer development. These extraembryonic tissues are generally considered to have been created in ancestral amniotes evolved from the Xenopus-type ancestor (reference 1); The endomesoderm secretes as yet unidentified signals that posteriorize the ectoderm, which would otherwise adopt an anterior fate. Our results point to a conserved function at the base of deuterostomes for beta-catenin in germ layer specification and to a causal link in the definition of the posterior part of the embryonic ectoderm by way of activating posteriorizing endomesodermal factors (reference 2).[well established][VHOG]
has db xref: AAO:0000229
has db xref: AAO:0010619
has db xref: BTO:0003953
has db xref: EFO:0001930
has db xref: EMAPA:32762
has db xref: FMA:293873
has db xref: MAT:0000418
has db xref: MIAA:0000418
has db xref: NCIT:C34190
has db xref: TAO:0000117
has db xref: UMLS:C1512561
has db xref: VHOG:0001222
has db xref: Wikipedia:Hypoblast
has db xref: XAO:0003044
has db xref: ZFA:0000117
has exact synonym: hypoblast
has OBO namespace: uberon
has related synonym: endomesoderm
has related synonym: future endoderm and mesoderm
has related synonym: hypoblastus
has related synonym: mesendoderm
id: UBERON:0000089
in subset: early development
in subset: efo slim
in subset: grouping class
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: hypoblast (generic)
annotated property: IAO_0000115
annotated target: Missing definition for term UBERON:0000089. Please replace it using linked reference.
has db xref: GO:dph
has db xref: ZFIN:cvs

Axiom
annotated source: hypoblast (generic)
annotated property: UBPROP_0000001
annotated target: A primary germ layer that can give rise to both mesoderm and endoderm.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010619
ontology: AAO
source: AAO:EJS

Axiom
annotated source: hypoblast (generic)
annotated property: UBPROP_0000001
annotated target: The inner of the two layers of the blastoderm that forms during gastrulation and give rise to the definitive mesoderm and endoderm. Kimmel et al, 1995.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000117
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: hypoblast (generic)
annotated property: UBPROP_0000003
annotated target: In mammal and avian, extraembryonic endoderm such as visceral endoderm and hypoblast play essential roles in the embryonic axis formation and germ layer development. These extraembryonic tissues are generally considered to have been created in ancestral amniotes evolved from the Xenopus-type ancestor (reference 1); The endomesoderm secretes as yet unidentified signals that posteriorize the ectoderm, which would otherwise adopt an anterior fate. Our results point to a conserved function at the base of deuterostomes for beta-catenin in germ layer specification and to a causal link in the definition of the posterior part of the embryonic ectoderm by way of activating posteriorizing endomesodermal factors (reference 2).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001222
ontology: VHOG
source: DOI:10.1016/j.ydbio.2009.05.543 Takeuchi M, Takahashi M, Okabe M, Aizawa S, Germ layer patterning in bichir and lamprey; an insight into its evolution in vertebrates. Developmental Biology (2009) (reference 1), Darras S, Gerhart J, Terasaki M, Kirschner M, Lowe CJ, Beta-catenin specifies the endomesoderm and defines the posterior organizer of the hemichordate Saccoglossus kowalevskii. Development (2011) (reference 2)
source: http://bgee.unil.ch/

Axiom
annotated source: hypoblast (generic)
annotated property: hasDbXref
annotated target: UMLS:C1512561
source: ncithesaurus:Hypoblast

Axiom
annotated source: hypoblast (generic)
annotated property: hasExactSynonym
annotated target: hypoblast
has db xref: VHOG:0001222

Axiom
annotated source: hypoblast (generic)
annotated property: hasRelatedSynonym
annotated target: endomesoderm
has db xref: ISBN:0073040584
has db xref: VHOG:0001222

Axiom
annotated source: hypoblast (generic)
annotated property: hasRelatedSynonym
annotated target: future endoderm and mesoderm
has db xref: ISBN:0073040584

Axiom
annotated source: hypoblast (generic)
annotated property: hasRelatedSynonym
annotated target: hypoblastus
has db xref: Wikipedia:Hypoblast
has synonym type: OMO_0003011

Axiom
annotated source: hypoblast (generic)
annotated property: hasRelatedSynonym
annotated target: mesendoderm
has db xref: ZFIN:ZDB-PUB-961014-576

bilaminar disc
type: Class
subclass of: UBERON_0002050
subclass of: Restriction
IAO_0000115: A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc.
has broad synonym: embryonic disc
has broad synonym: embryonic shield
has broad synonym: germinal disc
has broad synonym: germinal disk
has db xref: FMA:293863
has db xref: NCIT:C34112
has db xref: UMLS:C1283997
has db xref: Wikipedia:Bilaminar_disc
has exact synonym: bilaminary embryonic disc
has exact synonym: bilaminary germ disc
has OBO namespace: uberon
has related synonym: bilaminar disk
id: UBERON:0000091
in subset: early development
in subset: pheno slim

Axiom
annotated source: bilaminar disc
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: bilaminar disc
annotated property: IAO_0000115
annotated target: A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc.
has db xref: MP:0003886

Axiom
annotated source: bilaminar disc
annotated property: hasBroadSynonym
annotated target: embryonic disc
has db xref: MP:0003886

Axiom
annotated source: bilaminar disc
annotated property: hasBroadSynonym
annotated target: embryonic shield
has db xref: MP:0003886

Axiom
annotated source: bilaminar disc
annotated property: hasBroadSynonym
annotated target: germinal disc
has db xref: MP:0003886

Axiom
annotated source: bilaminar disc
annotated property: hasBroadSynonym
annotated target: germinal disk
has db xref: MP:0003886

Axiom
annotated source: bilaminar disc
annotated property: hasDbXref
annotated target: UMLS:C1283997
source: ncithesaurus:Bilaminar_Embryonic_Disc

Axiom
annotated source: bilaminar disc
annotated property: hasExactSynonym
annotated target: bilaminary germ disc
has db xref: ISBN:9780878932504

Axiom
annotated source: bilaminar disc
annotated property: hasRelatedSynonym
annotated target: bilaminar disk
has db xref: Wikipedia:Bilaminar_disc

post-embryonic stage
type: Class
subclass of: BFO_0000003
subclass of: life cycle stage
subclass of: Restriction
  on property: BFO_0000062
  some values from: embryo stage
subclass of: Restriction
  on property: RO_0002082
  some values from: GO_0009791
IAO_0000115: Stage succeeding embryo, including mature structure.
UBPROP_0000008: In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
has db xref: BilaDO:0000003
has db xref: OGES:000010
has db xref: OGES:000014
has db xref: OGES:000024
has db xref: SsalDv:0000038
has db xref: WBls:0000022
has db xref: WBls:0000093
has db xref: WBls:0000103
has exact synonym: postembryonic stage
has narrow synonym: post-hatching stage
has OBO namespace: uberon
has related synonym: postembryonic
id: UBERON:0000092

Axiom
annotated source: post-embryonic stage
annotated property: IAO_0000115
annotated target: Stage succeeding embryo, including mature structure.
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: post-embryonic stage
annotated property: hasDbXref
annotated target: SsalDv:0000038
mapping justification: UnspecifiedMatching

sulcus
type: Class
subclass of: anatomical space
IAO_0000115: A depression or fissure in the surface of an organ.
contributor: https://orcid.org/0000-0002-6601-2165
creation date: 2009-04-09T06:23:22Z
has db xref: Wikipedia:Sulcus_(anatomy)
has OBO namespace: uberon
id: UBERON:0000093
in subset: grouping class
in subset: non informative

Axiom
annotated source: sulcus
annotated property: IAO_0000115
annotated target: A depression or fissure in the surface of an organ.
has db xref: Wikipedia:Sulcus_(anatomy)

membrane organ
type: Class
subclass of: organ
subclass of: Restriction
IAO_0000115: Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA].
contributor: https://orcid.org/0000-0002-6601-2165
creation date: 2009-07-30T05:19:13Z
has broad synonym: membrane
has db xref: FMA:7145
has exact synonym: membrane of organ
has OBO namespace: uberon
id: UBERON:0000094

Axiom
annotated source: membrane organ
annotated property: subClassOf
annotated target: Restriction
source: FMA-def

Axiom
annotated source: membrane organ
annotated property: IAO_0000115
annotated target: Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA].
has db xref: FMA:7145

cardiac neural crest
type: Class
subclass of: UBERON_0005291
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002342
IAO_0000115: Portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia].
UBPROP_0000001: A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751].
UBPROP_0000012: ZFA treats this as a subtype of NC.
contributor: https://orcid.org/0000-0002-6601-2165
creation date: 2009-07-30T07:57:38Z
has db xref: TAO:0002173
has db xref: Wikipedia:Cardiac_neural_crest
has db xref: XAO:0004190
has db xref: ZFA:0001648
has OBO namespace: uberon
has related synonym: cardiac neural crest complex
has related synonym: complexus cristae neuralis cardiacus
id: UBERON:0000095
in subset: vertebrate core

Axiom
annotated source: cardiac neural crest
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: cardiac neural crest
annotated property: IAO_0000115
annotated target: Portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia].
has db xref: Wikipedia:Cardiac_neural_crest

Axiom
annotated source: cardiac neural crest
annotated property: UBPROP_0000001
annotated target: A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751].
source: DOI:10.1242/dev.091751

Axiom
annotated source: cardiac neural crest
annotated property: UBPROP_0000012
annotated target: ZFA treats this as a subtype of NC.
external ontology: ZFA

Axiom
annotated source: cardiac neural crest
annotated property: hasRelatedSynonym
annotated target: cardiac neural crest complex
has db xref: Wikipedia:Cardiac_neural_crest

Axiom
annotated source: cardiac neural crest
annotated property: hasRelatedSynonym
annotated target: complexus cristae neuralis cardiacus
has db xref: Wikipedia:Cardiac_neural_crest

lobe of lung
type: Class
subclass of: UBERON_0009912
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002048
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0002048
IAO_0000115: A lung lobe is one of the rounded projections that compose the lung[GO].
has db xref: EMAPA:36281
has db xref: FMA:7311
has db xref: MA:0003098
has db xref: NCIT:C34021
has db xref: SCTID:245524004
has db xref: UMLS:C0225752
has db xref: galen:LobeOfLung
has exact synonym: lung lobe
has exact synonym: pulminory lobe
has exact synonym: pulmonary lobe
has OBO namespace: uberon
id: UBERON:0000101
in subset: pheno slim

Axiom
annotated source: lobe of lung
annotated property: subClassOf
annotated target: UBERON_0009912
source: FMA

Axiom
annotated source: lobe of lung
annotated property: IAO_0000115
annotated target: A lung lobe is one of the rounded projections that compose the lung[GO].
has db xref: GOC:GO

Axiom
annotated source: lobe of lung
annotated property: hasDbXref
annotated target: UMLS:C0225752
source: ncithesaurus:Lung_Lobe

Axiom
annotated source: lobe of lung
annotated property: hasExactSynonym
annotated target: pulmonary lobe
has db xref: FMA:7311

lung vasculature
type: Class
equivalent class: Class
  intersection of: UBERON_0002049
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002048
subclass of: UBERON_0002201
subclass of: UBERON_0006876
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002048
IAO_0000115: The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO].
has db xref: FMA:73750
has exact synonym: lung vascular network
has exact synonym: pulmonary vasculature
has exact synonym: vascular network of lung
has exact synonym: vasculature of lung
has OBO namespace: uberon
id: UBERON:0000102
in subset: pheno slim

Axiom
annotated source: lung vasculature
annotated property: IAO_0000115
annotated target: The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO].
has db xref: GOC:GO

Axiom
annotated source: lung vasculature
annotated property: hasExactSynonym
annotated target: lung vascular network
has db xref: OBOL:automatic

Axiom
annotated source: lung vasculature
annotated property: hasExactSynonym
annotated target: pulmonary vasculature
has db xref: FMA:73750

Axiom
annotated source: lung vasculature
annotated property: hasExactSynonym
annotated target: vascular network of lung
has db xref: OBOL:automatic

Axiom
annotated source: lung vasculature
annotated property: hasExactSynonym
annotated target: vasculature of lung
has db xref: OBOL:automatic

life cycle
type: Class
subclass of: BFO_0000003
subclass of: processual entity
subclass of: Restriction
  on property: BFO_0000051
  some values from: life cycle stage
subclass of: Restriction
  on property: RO_0002230
  some values from: death stage
IAO_0000115: An entire span of an organism's life. In metazoans, commences with the zygote stage and ends with the death of the organism.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: AcarDv:0000001
has db xref: BtauDv:0000001
has db xref: CfamDv:0000001
has db xref: ChirDv:0000001
has db xref: CporDv:0000001
has db xref: DpseDv:0000001
has db xref: DsimDv:0000001
has db xref: EcabDv:0000001
has db xref: FBdv:00000000
has db xref: FcatDv:0000001
has db xref: GgalDv:0000001
has db xref: GgorDv:0000001
has db xref: HsapDv:0000001
has db xref: MdomDv:0000001
has db xref: MmulDv:0000001
has db xref: MmusDv:0000001
has db xref: OGES:000011
has db xref: OanaDv:0000001
has db xref: OariDv:0000001
has db xref: OcunDv:0000001
has db xref: PpanDv:0000001
has db xref: PtroDv:0000001
has db xref: RnorDv:0000001
has db xref: SsalDv:0000001
has db xref: SscrDv:0000001
has db xref: ncithesaurus:Life
has exact synonym: entire life cycle
has exact synonym: entire lifespan
has exact synonym: life
has exact synonym: lifespan
has OBO namespace: uberon
id: UBERON:0000104
in subset: common anatomy
in subset: upper level

Axiom
annotated source: life cycle
annotated property: IAO_0000115
annotated target: An entire span of an organism's life. In metazoans, commences with the zygote stage and ends with the death of the organism.
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: AcarDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: BtauDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: CfamDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: ChirDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: CporDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: DpseDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: DsimDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: EcabDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: FcatDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: GgalDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: GgorDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: HsapDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: MdomDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: MmulDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: MmusDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: OanaDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: OariDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: OcunDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: PpanDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: PtroDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: RnorDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: SsalDv:0000001
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle
annotated property: hasDbXref
annotated target: SscrDv:0000001
mapping justification: UnspecifiedMatching

life cycle stage
type: Class
subclass of: processual entity
subclass of: Restriction
  on property: BFO_0000050
  some values from: life cycle
IAO_0000115: A spatiotemporal region encompassing some part of the life cycle of an organism.
IAO_0000116: this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
UBPROP_0000012: the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
UBPROP_0000012: we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
has db xref: AcarDv:0000000
has db xref: BILS:0000105
has db xref: BtauDv:0000000
has db xref: CfamDv:0000000
has db xref: ChirDv:0000000
has db xref: CporDv:0000000
has db xref: DpseDv:0000000
has db xref: DsimDv:0000000
has db xref: EFO:0000399
has db xref: EcabDv:0000000
has db xref: FBdv:00007012
has db xref: FMA:24120
has db xref: FcatDv:0000000
has db xref: GgalDv:0000000
has db xref: GgorDv:0000000
has db xref: HsapDv:0000000
has db xref: MESH:D008018
has db xref: MdomDv:0000000
has db xref: MmulDv:0000000
has db xref: MmusDv:0000000
has db xref: OanaDv:0000000
has db xref: OariDv:0000000
has db xref: OcunDv:0000000
has db xref: PdumDv:0000090
has db xref: PpanDv:0000000
has db xref: PtroDv:0000000
has db xref: RnorDv:0000000
has db xref: SsalDv:0000000
has db xref: SscrDv:0000000
has db xref: WBls:0000002
has db xref: XAO:1000000
has db xref: ZFS:0000000
has db xref: ZFS:0100000
has db xref: ncithesaurus:Developmental_Stage
has narrow synonym: developmental stage
has narrow synonym: stage
has OBO namespace: uberon
id: UBERON:0000105
in subset: common anatomy
in subset: efo slim
in subset: upper level

Axiom
annotated source: life cycle stage
annotated property: IAO_0000115
annotated target: A spatiotemporal region encompassing some part of the life cycle of an organism.
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: AcarDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: BtauDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: CfamDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: ChirDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: CporDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: DpseDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: DsimDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: EcabDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: FcatDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: GgalDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: GgorDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: HsapDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: MdomDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: MmulDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: MmusDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: OanaDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: OariDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: OcunDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: PpanDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: PtroDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: RnorDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: SsalDv:0000000
mapping justification: UnspecifiedMatching

Axiom
annotated source: life cycle stage
annotated property: hasDbXref
annotated target: SscrDv:0000000
mapping justification: UnspecifiedMatching

zygote stage
type: Class
subclass of: BFO_0000003
subclass of: life cycle stage
subclass of: Restriction
  on property: BFO_0000050
  some values from: embryo stage
subclass of: Restriction
  on property: RO_0002223
  some values from: life cycle
IAO_0000115: A stage at which the organism is a single cell produced by means of sexual reproduction.
UBPROP_0000003: As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
has db xref: BILS:0000106
has db xref: BilaDO:0000005
has db xref: ChirDv:0000003
has db xref: EFO:0001322
has db xref: EHDAA:27
has db xref: FBdv:00005288
has db xref: HsapDv:0000003
has db xref: IDOMAL:0000302
has db xref: MmusDv:0000003
has db xref: NCIT:C12601
has db xref: OariDv:0000009
has db xref: PdumDv:0000100
has db xref: RnorDv:0000048
has db xref: SsalDv:0000003
has db xref: SscrDv:0000087
has db xref: VHOG:0000745
has db xref: Wikipedia:Zygote
has db xref: XAO:1000001
has db xref: ZFS:0000001
has exact synonym: 1-cell stage
has exact synonym: fertilized egg stage
has exact synonym: one cell stage
has OBO namespace: uberon
has related synonym: fertilized egg stage
has related synonym: one-cell stage
has related synonym: zygote
has related synonym: zygotum
id: UBERON:0000106
in subset: efo slim

Axiom
annotated source: zygote stage
annotated property: IAO_0000115
annotated target: A stage at which the organism is a single cell produced by means of sexual reproduction.
has db xref: Wikipedia:Zygote

Axiom
annotated source: zygote stage
annotated property: UBPROP_0000003
annotated target: As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000745
ontology: VHOG
source: ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107
source: http://bgee.unil.ch/

Axiom
annotated source: zygote stage
annotated property: hasDbXref
annotated target: ChirDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: zygote stage
annotated property: hasDbXref
annotated target: HsapDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: zygote stage
annotated property: hasDbXref
annotated target: IDOMAL:0000302
author id: https://orcid.org/0000-0003-4423-4370
mapping justification: ManualMappingCuration
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: zygote stage
annotated property: hasDbXref
annotated target: MmusDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: zygote stage
annotated property: hasDbXref
annotated target: OariDv:0000009
mapping justification: UnspecifiedMatching

Axiom
annotated source: zygote stage
annotated property: hasDbXref
annotated target: RnorDv:0000048
mapping justification: UnspecifiedMatching

Axiom
annotated source: zygote stage
annotated property: hasDbXref
annotated target: SsalDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: zygote stage
annotated property: hasDbXref
annotated target: SscrDv:0000087
mapping justification: UnspecifiedMatching

Axiom
annotated source: zygote stage
annotated property: hasExactSynonym
annotated target: fertilized egg stage
has db xref: BTO:0000854

Axiom
annotated source: zygote stage
annotated property: hasRelatedSynonym
annotated target: one-cell stage
has db xref: VHOG:0000745

Axiom
annotated source: zygote stage
annotated property: hasRelatedSynonym
annotated target: zygote
has db xref: VHOG:0000745

Axiom
annotated source: zygote stage
annotated property: hasRelatedSynonym
annotated target: zygotum
has db xref: Wikipedia:Zygote
has synonym type: OMO_0003011

cleavage stage
type: Class
equivalent class: Class
  intersection of: life cycle stage
  intersection of: Restriction
    on property: RO_0002082
    some values from: GO_0040016
subclass of: BFO_0000003
subclass of: life cycle stage
subclass of: Restriction
  on property: BFO_0000050
  some values from: embryo stage
subclass of: Restriction
  on property: RO_0002082
  some values from: GO_0040016
subclass of: Restriction
  on property: RO_0002087
  some values from: zygote stage
IAO_0000115: The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
has db xref: BILS:0000107
has db xref: BilaDO:0000006
has db xref: ChirDv:0000004
has db xref: EFO:0001290
has db xref: FBdv:00000054
has db xref: GgalDv:0000064
has db xref: HsapDv:0000005
has db xref: MESH:D002970
has db xref: MmusDv:0000004
has db xref: OGES:000015
has db xref: OGES:000020
has db xref: OariDv:0000010
has db xref: PdumDv:0000200
has db xref: RnorDv:0000049
has db xref: SsalDv:0000004
has db xref: SscrDv:0000088
has db xref: Wikipedia:Cleavage_(embryo)
has db xref: XAO:1000004
has db xref: ZFS:0000046
has OBO namespace: uberon
id: UBERON:0000107
in subset: efo slim

Axiom
annotated source: cleavage stage
annotated property: IAO_0000115
annotated target: The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
has db xref: GO:0040016
has db xref: Wikipedia:Cleavage_(embryo)

Axiom
annotated source: cleavage stage
annotated property: hasDbXref
annotated target: ChirDv:0000004
mapping justification: UnspecifiedMatching

Axiom
annotated source: cleavage stage
annotated property: hasDbXref
annotated target: GgalDv:0000064
mapping justification: UnspecifiedMatching

Axiom
annotated source: cleavage stage
annotated property: hasDbXref
annotated target: HsapDv:0000005
mapping justification: UnspecifiedMatching

Axiom
annotated source: cleavage stage
annotated property: hasDbXref
annotated target: MmusDv:0000004
mapping justification: UnspecifiedMatching

Axiom
annotated source: cleavage stage
annotated property: hasDbXref
annotated target: OariDv:0000010
mapping justification: UnspecifiedMatching

Axiom
annotated source: cleavage stage
annotated property: hasDbXref
annotated target: RnorDv:0000049
mapping justification: UnspecifiedMatching

Axiom
annotated source: cleavage stage
annotated property: hasDbXref
annotated target: SsalDv:0000004
mapping justification: UnspecifiedMatching

Axiom
annotated source: cleavage stage
annotated property: hasDbXref
annotated target: SscrDv:0000088
mapping justification: UnspecifiedMatching

blastula stage
type: Class
subclass of: BFO_0000003
subclass of: life cycle stage
subclass of: Restriction
  on property: BFO_0000050
  some values from: embryo stage
subclass of: Restriction
  on property: BFO_0000062
  some values from: cleavage stage
IAO_0000115: An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
IAO_0000116: consider adding a preceding stage 'morula stage' as part of cleavage
has db xref: BILS:0000108
has db xref: BilaDO:0000007
has db xref: ChirDv:0000010
has db xref: EFO:0001282
has db xref: GgalDv:0000091
has db xref: HsapDv:0000006
has db xref: MmusDv:0000007
has db xref: OGES:000003
has db xref: OGES:000016
has db xref: OGES:000021
has db xref: OariDv:0000025
has db xref: RnorDv:0000054
has db xref: SsalDv:0000012
has db xref: SscrDv:0000089
has db xref: WBls:0000005
has db xref: Wikipedia:Blastula
has db xref: XAO:1000003
has db xref: ZFS:0000045
has OBO namespace: uberon
id: UBERON:0000108
in subset: efo slim

Axiom
annotated source: blastula stage
annotated property: hasDbXref
annotated target: SscrDv:0000089
mapping justification: UnspecifiedMatching

Axiom
annotated source: blastula stage
annotated property: IAO_0000115
annotated target: An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
has db xref: Wikipedia:Blastula

Axiom
annotated source: blastula stage
annotated property: hasDbXref
annotated target: ChirDv:0000010
mapping justification: UnspecifiedMatching

Axiom
annotated source: blastula stage
annotated property: hasDbXref
annotated target: GgalDv:0000091
mapping justification: UnspecifiedMatching

Axiom
annotated source: blastula stage
annotated property: hasDbXref
annotated target: HsapDv:0000006
mapping justification: UnspecifiedMatching

Axiom
annotated source: blastula stage
annotated property: hasDbXref
annotated target: MmusDv:0000007
mapping justification: UnspecifiedMatching

Axiom
annotated source: blastula stage
annotated property: hasDbXref
annotated target: OariDv:0000025
mapping justification: UnspecifiedMatching

Axiom
annotated source: blastula stage
annotated property: hasDbXref
annotated target: RnorDv:0000054
mapping justification: UnspecifiedMatching

Axiom
annotated source: blastula stage
annotated property: hasDbXref
annotated target: SsalDv:0000012
mapping justification: UnspecifiedMatching

gastrula stage
type: Class
subclass of: BFO_0000003
subclass of: life cycle stage
subclass of: Restriction
  on property: BFO_0000050
  some values from: embryo stage
subclass of: Restriction
  on property: RO_0002082
  some values from: GO_0007369
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6072
IAO_0000115: A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
has db xref: BILS:0000109
has db xref: BilaDO:0000008
has db xref: ChirDv:0000011
has db xref: EFO:0001296
has db xref: FBdv:00005317
has db xref: GgalDv:0000092
has db xref: HsapDv:0000010
has db xref: MmusDv:0000013
has db xref: OGES:000004
has db xref: OGES:000019
has db xref: OariDv:0000026
has db xref: RnorDv:0000005
has db xref: SsalDv:0000016
has db xref: SscrDv:0000090
has db xref: WBls:0000010
has db xref: XAO:1000005
has db xref: ZFS:0000047
has OBO namespace: uberon
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
id: UBERON:0000109
in subset: efo slim

Axiom
annotated source: gastrula stage
annotated property: subClassOf
annotated target: Restriction
source: BILS

Axiom
annotated source: gastrula stage
annotated property: IAO_0000115
annotated target: A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
has db xref: GO:0007369

Axiom
annotated source: gastrula stage
annotated property: hasDbXref
annotated target: ChirDv:0000011
mapping justification: UnspecifiedMatching

Axiom
annotated source: gastrula stage
annotated property: hasDbXref
annotated target: GgalDv:0000092
mapping justification: UnspecifiedMatching

Axiom
annotated source: gastrula stage
annotated property: hasDbXref
annotated target: HsapDv:0000010
mapping justification: UnspecifiedMatching

Axiom
annotated source: gastrula stage
annotated property: hasDbXref
annotated target: MmusDv:0000013
mapping justification: UnspecifiedMatching

Axiom
annotated source: gastrula stage
annotated property: hasDbXref
annotated target: OariDv:0000026
mapping justification: UnspecifiedMatching

Axiom
annotated source: gastrula stage
annotated property: hasDbXref
annotated target: RnorDv:0000005
mapping justification: UnspecifiedMatching

Axiom
annotated source: gastrula stage
annotated property: hasDbXref
annotated target: SsalDv:0000016
mapping justification: UnspecifiedMatching

Axiom
annotated source: gastrula stage
annotated property: hasDbXref
annotated target: SscrDv:0000090
mapping justification: UnspecifiedMatching

Axiom
annotated source: gastrula stage
annotated property: hasRelatedSynonym
annotated target: blastocystis trilaminaris stage
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: gastrula stage
annotated property: hasRelatedSynonym
annotated target: trilaminar blastocyst stage
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: gastrula stage
annotated property: hasRelatedSynonym
annotated target: trilaminar blastoderm stage
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: gastrula stage
annotated property: hasRelatedSynonym
annotated target: trilaminar disk stage
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: gastrula stage
annotated property: hasRelatedSynonym
annotated target: trilaminar germ stage
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: gastrula stage
annotated property: hasRelatedSynonym
annotated target: trilaminar stage
has db xref: https://orcid.org/0000-0002-6601-2165

neurula stage
type: Class
subclass of: BFO_0000003
subclass of: life cycle stage
subclass of: Restriction
  on property: BFO_0000050
  some values from: embryo stage
subclass of: Restriction
  on property: BFO_0000062
  some values from: gastrula stage
subclass of: Restriction
  on property: RO_0002082
  some values from: GO_0001841
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7711
IAO_0000115: A chordate developmental stage 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.
RO_0002174: NCBITaxon 7955
UBPROP_0000008: In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos.
has db xref: BILS:0000110
has db xref: BilaDO:0000009
has db xref: ChirDv:0000012
has db xref: GgalDv:0000093
has db xref: HsapDv:0000012
has db xref: MmusDv:0000017
has db xref: OariDv:0000027
has db xref: RnorDv:0000007
has db xref: SscrDv:0000091
has db xref: XAO:1000006
has OBO namespace: uberon
id: UBERON:0000110

Axiom
annotated source: neurula stage
annotated property: IAO_0000115
annotated target: A chordate developmental stage 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.
has db xref: GO:0001841

Axiom
annotated source: neurula stage
annotated property: hasDbXref
annotated target: ChirDv:0000012
mapping justification: UnspecifiedMatching

Axiom
annotated source: neurula stage
annotated property: hasDbXref
annotated target: GgalDv:0000093
mapping justification: UnspecifiedMatching

Axiom
annotated source: neurula stage
annotated property: hasDbXref
annotated target: HsapDv:0000012
mapping justification: UnspecifiedMatching

Axiom
annotated source: neurula stage
annotated property: hasDbXref
annotated target: MmusDv:0000017
mapping justification: UnspecifiedMatching

Axiom
annotated source: neurula stage
annotated property: hasDbXref
annotated target: OariDv:0000027
mapping justification: UnspecifiedMatching

Axiom
annotated source: neurula stage
annotated property: hasDbXref
annotated target: RnorDv:0000007
mapping justification: UnspecifiedMatching

Axiom
annotated source: neurula stage
annotated property: hasDbXref
annotated target: SscrDv:0000091
mapping justification: UnspecifiedMatching

organogenesis stage
type: Class
subclass of: BFO_0000003
subclass of: life cycle stage
subclass of: Restriction
  on property: BFO_0000050
  some values from: embryo stage
subclass of: Restriction
  on property: RO_0002082
  some values from: GO_0048513
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6072
IAO_0000115: A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
has db xref: BILS:0000111
has db xref: BilaDO:0000010
has db xref: ChirDv:0000013
has db xref: GgalDv:0000094
has db xref: HsapDv:0000015
has db xref: MmusDv:0000018
has db xref: OGES:000005
has db xref: OGES:000032
has db xref: OariDv:0000028
has db xref: RnorDv:0000055
has db xref: SsalDv:0000022
has db xref: SscrDv:0000086
has db xref: Wikipedia:Organogenesis
has OBO namespace: uberon
has related synonym: segmentation stage
id: UBERON:0000111

Axiom
annotated source: organogenesis stage
annotated property: IAO_0000115
annotated target: A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
has db xref: Wikipedia:Organogenesis

Axiom
annotated source: organogenesis stage
annotated property: hasDbXref
annotated target: ChirDv:0000013
mapping justification: UnspecifiedMatching

Axiom
annotated source: organogenesis stage
annotated property: hasDbXref
annotated target: GgalDv:0000094
mapping justification: UnspecifiedMatching

Axiom
annotated source: organogenesis stage
annotated property: hasDbXref
annotated target: HsapDv:0000015
mapping justification: UnspecifiedMatching

Axiom
annotated source: organogenesis stage
annotated property: hasDbXref
annotated target: MmusDv:0000018
mapping justification: UnspecifiedMatching

Axiom
annotated source: organogenesis stage
annotated property: hasDbXref
annotated target: OariDv:0000028
mapping justification: UnspecifiedMatching

Axiom
annotated source: organogenesis stage
annotated property: hasDbXref
annotated target: RnorDv:0000055
mapping justification: UnspecifiedMatching

Axiom
annotated source: organogenesis stage
annotated property: hasDbXref
annotated target: SsalDv:0000022
mapping justification: UnspecifiedMatching

Axiom
annotated source: organogenesis stage
annotated property: hasDbXref
annotated target: SscrDv:0000086
mapping justification: UnspecifiedMatching

sexually immature stage
type: Class
subclass of: BFO_0000003
subclass of: life cycle stage
subclass of: Restriction
  on property: BFO_0000050
  some values from: fully formed stage
UBPROP_0000001: The stage of being a sexually immature adult animal[XAO:1000010].
UBPROP_0000008: In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother)
has db xref: AcarDv:0000003
has db xref: BILS:0000112
has db xref: BTO:0002168
has db xref: BtauDv:0000003
has db xref: CfamDv:0000003
has db xref: ChirDv:0000015
has db xref: CporDv:0000003
has db xref: EFO:0001300
has db xref: EV:0300051
has db xref: EcabDv:0000003
has db xref: FcatDv:0000003
has db xref: GgalDv:0000003
has db xref: GgorDv:0000003
has db xref: HsapDv:0000264
has db xref: MdomDv:0000003
has db xref: MmulDv:0000003
has db xref: MmusDv:0000043
has db xref: OGES:000009
has db xref: OanaDv:0000003
has db xref: OariDv:0000003
has db xref: OcunDv:0000003
has db xref: PpanDv:0000003
has db xref: PtroDv:0000003
has db xref: RnorDv:0000012
has db xref: SsalDv:0000041
has db xref: SscrDv:0000003
has db xref: XAO:1000010
has db xref: XtroDO:0000083
has db xref: ZFS:0000051
has exact synonym: immature stage
has narrow synonym: juvenile stage
has OBO namespace: uberon
has related synonym: subadult stage
id: UBERON:0000112
in subset: efo slim

Axiom
annotated source: sexually immature stage
annotated property: UBPROP_0000001
annotated target: The stage of being a sexually immature adult animal[XAO:1000010].
source: XAO:1000010

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: AcarDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: BtauDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: CfamDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: ChirDv:0000015
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: CporDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: EcabDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: FcatDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: GgalDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: GgorDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: HsapDv:0000264
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: MdomDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: MmulDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: MmusDv:0000043
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: OanaDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: OariDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: OcunDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: PpanDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: PtroDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: RnorDv:0000012
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: SsalDv:0000041
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasDbXref
annotated target: SscrDv:0000003
mapping justification: UnspecifiedMatching

Axiom
annotated source: sexually immature stage
annotated property: hasExactSynonym
annotated target: immature stage
has db xref: VHOG:FB

Axiom
annotated source: sexually immature stage
annotated property: hasNarrowSynonym
annotated target: juvenile stage
has db xref: XAO:1000010

Axiom
annotated source: sexually immature stage
annotated property: hasRelatedSynonym
annotated target: subadult stage
has db xref: http://eol.org/schema/terms/subadult

post-juvenile adult stage
type: Class
subclass of: BFO_0000003
subclass of: life cycle stage
subclass of: Restriction
  on property: BFO_0000050
  some values from: fully formed stage
subclass of: Restriction
  on property: BFO_0000062
  some values from: sexually immature stage
IAO_0000115: The stage of being a sexually mature adult animal.
has broad synonym: adult stage
has db xref: AcarDv:0000004
has db xref: BILS:0000113
has db xref: BtauDv:0000004
has db xref: CfamDv:0000004
has db xref: ChirDv:0000035
has db xref: CporDv:0000004
has db xref: EV:0300064
has db xref: EV:0300070
has db xref: EcabDv:0000004
has db xref: FcatDv:0000004
has db xref: GgalDv:0000006
has db xref: GgorDv:0000006
has db xref: HsapDv:0000258
has db xref: MIAA:0000403
has db xref: MdomDv:0000006
has db xref: MmulDv:0000021
has db xref: MmusDv:0000110
has db xref: OGES:000026
has db xref: OGES:000027
has db xref: OanaDv:0000004
has db xref: OariDv:0000006
has db xref: OcunDv:0000004
has db xref: PpanDv:0000016
has db xref: PtroDv:0000011
has db xref: RnorDv:0000015
has db xref: SsalDv:0000042
has db xref: SscrDv:0000006
has db xref: XAO:1000093
has db xref: ZFS:0000044
has OBO namespace: uberon
id: UBERON:0000113

Axiom
annotated source: post-juvenile adult stage
annotated property: IAO_0000115
annotated target: The stage of being a sexually mature adult animal.
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: AcarDv:0000004
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: BtauDv:0000004
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: CfamDv:0000004
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: ChirDv:0000035
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: CporDv:0000004
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: EcabDv:0000004
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: FcatDv:0000004
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: GgalDv:0000006
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: GgorDv:0000006
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: HsapDv:0000258
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: MdomDv:0000006
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: MmulDv:0000021
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: MmusDv:0000110
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: OanaDv:0000004
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: OariDv:0000006
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: OcunDv:0000004
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: PpanDv:0000016
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: PtroDv:0000011
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: RnorDv:0000015
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: SsalDv:0000042
mapping justification: UnspecifiedMatching

Axiom
annotated source: post-juvenile adult stage
annotated property: hasDbXref
annotated target: SscrDv:0000006
mapping justification: UnspecifiedMatching

lung connective tissue
type: Class
equivalent class: Class
  intersection of: UBERON_0002384
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002048
subclass of: UBERON_0003580
subclass of: UBERON_0003837
subclass of: UBERON_0004120
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002048
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0002048
subclass of: Restriction
  on property: RO_0002494
  some values from: UBERON_0004883
IAO_0000115: The connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin.
RO_0002175: NCBITaxon 9606
UBPROP_0000009: it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces
has db xref: EMAPA:35521
has db xref: FMA:27533
has db xref: MA:0001782
has db xref: SCTID:201609008
has exact synonym: connective tissue of lung
has exact synonym: pulmonary interstitium
has OBO namespace: uberon
has related synonym: lung interstitial tissue
has related synonym: lung interstitium
has related synonym: pulmonary connective tissue
has related synonym: pulmonary interstitial tissue
id: UBERON:0000114
in subset: human reference atlas
in subset: pheno slim

Axiom
annotated source: lung connective tissue
annotated property: IAO_0000115
annotated target: The connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin.
has db xref: ISBN:0-683-40008-8
has db xref: MGI:anna
has db xref: MP:0002276
has db xref: PMID:14635660

Axiom
annotated source: lung connective tissue
annotated property: hasExactSynonym
annotated target: connective tissue of lung
has db xref: OBOL:automatic

Axiom
annotated source: lung connective tissue
annotated property: hasExactSynonym
annotated target: pulmonary interstitium
has db xref: FMA:27533

Axiom
annotated source: lung connective tissue
annotated property: hasRelatedSynonym
annotated target: lung interstitial tissue
has db xref: MA:0001782

Axiom
annotated source: lung connective tissue
annotated property: hasRelatedSynonym
annotated target: pulmonary connective tissue
has db xref: EMAPA:35521

lung epithelium
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002048
subclass of: UBERON_0004815
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002048
subclass of: Restriction
  on property: RO_0002202
  some values from: foregut
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0002048
IAO_0000115: The epithelial layer of the lung.
UBPROP_0000008: A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469]
has db xref: BTO:0001653
has db xref: EMAPA:32860
has db xref: MA:0001783
has exact synonym: epithelial tissue of lung
has exact synonym: epithelium of lung
has exact synonym: lung epithelial tissue
has OBO namespace: uberon
has related synonym: pulmonary epithelium
id: UBERON:0000115
in subset: pheno slim

Axiom
annotated source: lung epithelium
annotated property: IAO_0000115
annotated target: The epithelial layer of the lung.
has db xref: MP:0006382

Axiom
annotated source: lung epithelium
annotated property: hasExactSynonym
annotated target: epithelial tissue of lung
has db xref: OBOL:automatic

Axiom
annotated source: lung epithelium
annotated property: hasExactSynonym
annotated target: epithelium of lung
has db xref: OBOL:automatic

Axiom
annotated source: lung epithelium
annotated property: hasExactSynonym
annotated target: lung epithelial tissue
has db xref: OBOL:automatic

Axiom
annotated source: lung epithelium
annotated property: hasRelatedSynonym
annotated target: pulmonary epithelium
has db xref: BTO:0001653

lung saccule
type: Class
subclass of: organ part
subclass of: Restriction
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0000322
IAO_0000115: Primitive gas exchange portion of the lung composed of type I and type II cells[GO].
has OBO namespace: uberon
id: UBERON:0000116
in subset: pheno slim

Axiom
annotated source: lung saccule
annotated property: subClassOf
annotated target: Restriction
source: GO

Axiom
annotated source: lung saccule
annotated property: IAO_0000115
annotated target: Primitive gas exchange portion of the lung composed of type I and type II cells[GO].
has db xref: GO:0060430

respiratory tube
type: Class
equivalent class: Class
  intersection of: tube
  intersection of: Restriction
    on property: BFO_0000050
    some values from: respiratory tract
subclass of: tube
subclass of: Restriction
  on property: BFO_0000050
  some values from: respiratory tract
subclass of: Restriction
  on property: BFO_0000051
  some values from: epithelium
IAO_0000115: A tube in the respiratory system. Examples: bronchus, bronchiole, trachea.
UBPROP_0000012: in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class)
has db xref: EMAPA:37946
has db xref: FMA:12224
has exact synonym: segment of tracheobronchial tree
has narrow synonym: respiratory conducting tube
has narrow synonym: segment of tracheobronchial tree
has narrow synonym: tracheobronchial tree segment
has OBO namespace: uberon
has related synonym: airway
id: UBERON:0000117

Axiom
annotated source: respiratory tube
annotated property: IAO_0000115
annotated target: A tube in the respiratory system. Examples: bronchus, bronchiole, trachea.
has db xref: GO:0030323
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: respiratory tube
annotated property: UBPROP_0000012
annotated target: in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class)
external ontology: GO

Axiom
annotated source: respiratory tube
annotated property: hasDbXref
annotated target: EMAPA:37946
source: MA:th

Axiom
annotated source: respiratory tube
annotated property: hasExactSynonym
annotated target: segment of tracheobronchial tree
has db xref: FMA:12224

Axiom
annotated source: respiratory tube
annotated property: hasNarrowSynonym
annotated target: respiratory conducting tube
has db xref: MP:0004391

Axiom
annotated source: respiratory tube
annotated property: hasNarrowSynonym
annotated target: segment of tracheobronchial tree
has db xref: FMA:12224

Axiom
annotated source: respiratory tube
annotated property: hasNarrowSynonym
annotated target: tracheobronchial tree segment
has db xref: FMA:12224

lung bud
type: Class
subclass of: UBERON_0005153
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0005597
subclass of: Restriction
  on property: RO_0002220
  some values from: UBERON_0004872
IAO_0000115: Structure derived from foregut that becomes a lung[GO].
IAO_0000116: clarify successors - include bronchi?
has db xref: BTO:0001643
has db xref: EHDAA2:0004089
has db xref: NCIT:C34260
has db xref: NCIT:C34282
has db xref: SCTID:361427007
has db xref: UMLS:C1514420
has db xref: UMLS:C1514897
has db xref: Wikipedia:Respiratory_bud
has OBO namespace: uberon
has related synonym: gemma pulmonalis
has related synonym: gemma respiratoria
has related synonym: lung bud
has related synonym: primary lung bud
has related synonym: respiratory diverticulum
id: UBERON:0000118
in subset: pheno slim

Axiom
annotated source: lung bud
annotated property: subClassOf
annotated target: UBERON_0005153
source: GO:0060441

Axiom
annotated source: lung bud
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: lung bud
annotated property: IAO_0000115
annotated target: Structure derived from foregut that becomes a lung[GO].
has db xref: GO:0060431
has db xref: Wikipedia:Respiratory_bud

Axiom
annotated source: lung bud
annotated property: hasDbXref
annotated target: UMLS:C1514420
source: ncithesaurus:Primary_Bronchial_Bud

Axiom
annotated source: lung bud
annotated property: hasDbXref
annotated target: UMLS:C1514897
source: ncithesaurus:Respiratory_Diverticulum

Axiom
annotated source: lung bud
annotated property: hasRelatedSynonym
annotated target: gemma pulmonalis
has db xref: Wikipedia:Lung_buds
has synonym type: OMO_0003011

Axiom
annotated source: lung bud
annotated property: hasRelatedSynonym
annotated target: gemma respiratoria
has db xref: Wikipedia:Lung_buds
has synonym type: OMO_0003011

Axiom
annotated source: lung bud
annotated property: hasRelatedSynonym
annotated target: lung bud
has synonym type: OMO_0003004

Axiom
annotated source: lung bud
annotated property: hasRelatedSynonym
annotated target: primary lung bud
has db xref: GO:0060572

Axiom
annotated source: lung bud
annotated property: hasRelatedSynonym
annotated target: respiratory diverticulum
has db xref: Wikipedia:Lung_buds

cell layer
type: Class
subclass of: lamina
IAO_0000115: Portion of tissue, that consists of single layer of cells connected to each other by cell junctions. Examples: layer of glial cells; epithelium.
IAO_0000116: consider adding to caro
has broad synonym: layer
has db xref: NCIT:C66831
has exact synonym: layer of cells
has OBO namespace: uberon
has related synonym: cell sheath
has related synonym: sheath of cells
id: UBERON:0000119
in subset: upper level

Axiom
annotated source: cell layer
annotated property: IAO_0000115
annotated target: Portion of tissue, that consists of single layer of cells connected to each other by cell junctions. Examples: layer of glial cells; epithelium.
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: cell layer
annotated property: hasBroadSynonym
annotated target: layer
has db xref: NCIT:C66831

blood brain barrier
type: Class
subclass of: cell layer
subclass of: Restriction
  on property: BFO_0000050
  some values from: nervous system
subclass of: Restriction
  on property: RO_0002220
  some values from: haemolymphatic fluid
subclass of: Restriction
  on property: RO_0002220
  some values from: brain
IAO_0000115: Cell layer consisting of lining cells that separates the central nervous system and the bloodstream. The BBB may consist of endothelial cells or glial cells. An endothelial barrier may have arisen independently several times during evolution. In bichir and lungfish the barrier is formed by brain endothelial cells, while in sturgeon it is formed by a complex perivascular glial sheath, but with no detectable tight junctions.
has db xref: MESH:D001812
has db xref: NCIT:C13194
has db xref: UMLS:C0005854
has db xref: Wikipedia:Blood-brain_barrier
has db xref: http://uri.neuinfo.org/nif/nifstd/nlx_subcell_100205
has exact synonym: blood-brain barrier
has OBO namespace: uberon
has related synonym: BBB
id: UBERON:0000120

Axiom
annotated source: blood brain barrier
annotated property: IAO_0000115
annotated target: Cell layer consisting of lining cells that separates the central nervous system and the bloodstream. The BBB may consist of endothelial cells or glial cells. An endothelial barrier may have arisen independently several times during evolution. In bichir and lungfish the barrier is formed by brain endothelial cells, while in sturgeon it is formed by a complex perivascular glial sheath, but with no detectable tight junctions.
has db xref: DOI:10.1002/glia.20642
has db xref: Wikipedia:Blood-brain_barrier

Axiom
annotated source: blood brain barrier
annotated property: hasDbXref
annotated target: MESH:D001812
author id: https://orcid.org/0000-0001-9439-5346
mapping justification: ManualMappingCuration
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: blood brain barrier
annotated property: hasDbXref
annotated target: UMLS:C0005854
source: ncithesaurus:Blood-Brain_Barrier

neuron projection bundle
type: Class
subclass of: UBERON_0005162
subclass of: Restriction
  on property: BFO_0000050
  some values from: nervous system
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0043005
IAO_0000115: A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
has alternative id: UBERON:0005163
has db xref: CARO:0001001
has db xref: FBbt:00005099
has db xref: NLX:147821
has exact synonym: funiculus
has exact synonym: nerve fiber bundle
has exact synonym: neural fiber bundle
has OBO namespace: uberon
id: UBERON:0000122

Axiom
annotated source: neuron projection bundle
annotated property: IAO_0000115
annotated target: A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
has db xref: CARO:0001001
has db xref: FBC:DOS
has db xref: FBbt:00005099

Axiom
annotated source: neuron projection bundle
annotated property: hasDbXref
annotated target: FBbt:00005099
mapping justification: ManualMappingCuration

Axiom
annotated source: neuron projection bundle
annotated property: hasExactSynonym
annotated target: nerve fiber bundle
has db xref: FBbt:00005099

neural nucleus
type: Class
subclass of: UBERON_0011215
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002473
  some values from: UBERON_0002020
IAO_0000115: A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO).
UBPROP_0000001: Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021].
UBPROP_0000012: Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate.
has broad synonym: nucleus
has db xref: AEO:0000136
has db xref: FMA:83686
has db xref: NCIT:C13197
has db xref: NLX:28443
has db xref: Wikipedia:Nucleus_(neuroanatomy)
has exact synonym: nervous system nucleus
has exact synonym: neuraxis nucleus
has exact synonym: neuronal nucleus
has exact synonym: nucleus of CNS
has OBO namespace: uberon
has related synonym: nucleus of neuraxis
id: UBERON:0000125
in subset: cumbo

Axiom
annotated source: neural nucleus
annotated property: subClassOf
annotated target: Restriction
notes: we limit this structure by definition to chordate and vertebrate nervous systems

Axiom
annotated source: neural nucleus
annotated property: IAO_0000115
annotated target: A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO).
has db xref: NLX:28443

Axiom
annotated source: neural nucleus
annotated property: UBPROP_0000001
annotated target: Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021].
source: GO_REF:0000021

Axiom
annotated source: neural nucleus
annotated property: hasExactSynonym
annotated target: neuraxis nucleus
has db xref: FMA:83686

Axiom
annotated source: neural nucleus
annotated property: hasExactSynonym
annotated target: neuronal nucleus
has db xref: AEO:0000136

Axiom
annotated source: neural nucleus
annotated property: hasExactSynonym
annotated target: nucleus of CNS
has db xref: NLX:28443

cranial nerve nucleus
type: Class
equivalent class: Class
  intersection of: UBERON_0002308
  intersection of: Restriction
    on property: extends fibers into
    some values from: UBERON_0001785
subclass of: UBERON_0002308
subclass of: Restriction
  on property: extends fibers into
  some values from: UBERON_0001785
IAO_0000115: Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves.
has db xref: EMAPA:37066
has db xref: FMA:54501
has db xref: NLX:28532
has db xref: SCTID:280160003
has db xref: Wikipedia:Cranial_nerve_nucleus
has exact synonym: cranial neural nucleus
has exact synonym: nucleus of cranial nerve
has OBO namespace: uberon
has related synonym: nucleus nervi cranialis
id: UBERON:0000126

Axiom
annotated source: cranial nerve nucleus
annotated property: IAO_0000115
annotated target: Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves.
has db xref: NLX:28532

Axiom
annotated source: cranial nerve nucleus
annotated property: hasDbXref
annotated target: EMAPA:37066
source: MA:th

Axiom
annotated source: cranial nerve nucleus
annotated property: hasExactSynonym
annotated target: cranial neural nucleus
has db xref: FMA:54501

Axiom
annotated source: cranial nerve nucleus
annotated property: hasRelatedSynonym
annotated target: nucleus nervi cranialis
has db xref: Wikipedia:Cranial_nerve_nucleus
has synonym type: OMO_0003011

facial nucleus
type: Class
equivalent class: Class
  intersection of: cranial nerve nucleus
  intersection of: Restriction
    on property: extends fibers into
    some values from: UBERON_0001647
subclass of: cranial nerve nucleus
subclass of: UBERON_0004121
subclass of: UBERON_0006331
subclass of: UBERON_0009662
subclass of: Restriction
  on property: BFO_0000050
  some values from: pons
subclass of: Restriction
  on property: RO_0002433
  some values from: pons
subclass of: Restriction
  on property: extends fibers into
  some values from: UBERON_0001647
IAO_0000115: The group of motor neurons residing in the pons that innervate the muscles of facial expression.
UBPROP_0000012: FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It's not clear how facial nucleus is distinct from facial motor nucleus.
has db xref: BAMS:7
has db xref: BAMS:7N
has db xref: BAMS:VII
has db xref: BM:Pons-VII
has db xref: DHBA:12420
has db xref: EHDAA2:0004638
has db xref: EMAPA:35338
has db xref: EV:0100267
has db xref: FMA:54572
has db xref: MA:0001014
has db xref: MESH:D065828
has db xref: NCIT:C12898
has db xref: SCTID:280166009
has db xref: UMLS:C0228740
has db xref: VHOG:0001412
has exact synonym: facial VII nucleus
has exact synonym: facial nerve nucleus
has exact synonym: nucleus of facial nerve
has OBO namespace: uberon
has related synonym: facial VII motor nucleus
id: UBERON:0000127
in subset: pheno slim

Axiom
annotated source: facial nucleus
annotated property: subClassOf
annotated target: Restriction
evidence: definitional

Axiom
annotated source: facial nucleus
annotated property: IAO_0000115
annotated target: The group of motor neurons residing in the pons that innervate the muscles of facial expression.
has db xref: ISBN:0838580343
has db xref: MP:0000909

Axiom
annotated source: facial nucleus
annotated property: UBPROP_0000012
annotated target: FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It's not clear how facial nucleus is distinct from facial motor nucleus.
external ontology: FMA

Axiom
annotated source: facial nucleus
annotated property: hasDbXref
annotated target: UMLS:C0228740
source: ncithesaurus:Facial_Nerve_Nucleus

Axiom
annotated source: facial nucleus
annotated property: hasExactSynonym
annotated target: facial VII nucleus
has db xref: MA:0001014

Axiom
annotated source: facial nucleus
annotated property: hasExactSynonym
annotated target: nucleus of facial nerve
has db xref: FMA:54572

Axiom
annotated source: facial nucleus
annotated property: hasRelatedSynonym
annotated target: facial VII motor nucleus
has db xref: MA:0001014

olivary body
type: Class
subclass of: UBERON_0010000
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001896
IAO_0000115: Prominent oval structure in the medulla oblongata, present in pairs, the lower portion of the brainstem. They contain the olivary nuclei.
has db xref: BTO:0002299
has db xref: SCTID:279293003
has db xref: Wikipedia:Olivary_body
has exact synonym: olive body
has OBO namespace: uberon
has related synonym: oliva
has related synonym: olivary nucleus
has related synonym: olive
id: UBERON:0000128
in subset: pheno slim

Axiom
annotated source: olivary body
annotated property: IAO_0000115
annotated target: Prominent oval structure in the medulla oblongata, present in pairs, the lower portion of the brainstem. They contain the olivary nuclei.
has db xref: Wikipedia:Olivary_body

Axiom
annotated source: olivary body
annotated property: hasRelatedSynonym
annotated target: oliva
has db xref: Wikipedia:Olivary_body
has synonym type: OMO_0003011

Axiom
annotated source: olivary body
annotated property: hasRelatedSynonym
annotated target: olivary nucleus
has db xref: BTO:0002299

pectoral fin
type: Class
equivalent class: Class
  intersection of: UBERON_0002534
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0010708
subclass of: UBERON_0002534
subclass of: UBERON_0004710
subclass of: Restriction
  on property: RO_0002551
  some values from: UBERON_0010710
IAO_0000115: Paired fin that is located in the thoracic region of the body.
UBPROP_0000001: Paired fin that is located in the thoracic region of the body.[TAO]
UBPROP_0000001: Paired fin that is located in the thoracic region of the body.[VSAO]
has db xref: BTO:0004653
has db xref: SCTID:416982006
has db xref: TAO:0001161
has db xref: VSAO:0000147
has db xref: Wikipedia:Pectoral_fin#Fins
has db xref: ZFA:0001161
has exact synonym: forefin
has OBO namespace: uberon
has related synonym: pectoral fins
id: UBERON:0000151

Axiom
annotated source: pectoral fin
annotated property: subClassOf
annotated target: UBERON_0004710
is entailed: true

Axiom
annotated source: pectoral fin
annotated property: IAO_0000115
annotated target: Paired fin that is located in the thoracic region of the body.
has db xref: TAO:curator
has db xref: VSAO:0000147

Axiom
annotated source: pectoral fin
annotated property: UBPROP_0000001
annotated target: Paired fin that is located in the thoracic region of the body.[TAO]
date retrieved: 2012-08-14
external class: TAO:0001161
ontology: TAO
source: TAO:wd

Axiom
annotated source: pectoral fin
annotated property: UBPROP_0000001
annotated target: Paired fin that is located in the thoracic region of the body.[VSAO]
date retrieved: 2012-08-14
external class: VSAO:0000147
ontology: VSAO
source: TAO:curator

Axiom
annotated source: pectoral fin
annotated property: hasExactSynonym
annotated target: forefin
has db xref: VSAO:0000147

Axiom
annotated source: pectoral fin
annotated property: hasRelatedSynonym
annotated target: pectoral fins
has db xref: ZFA:0001161
has synonym type: OMO_0003004

pelvic fin
type: Class
equivalent class: Class
  intersection of: UBERON_0002534
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0010709
subclass of: UBERON_0002534
subclass of: UBERON_0004709
subclass of: Restriction
  on property: RO_0002551
  some values from: UBERON_0010711
IAO_0000115: Paired fin located in the abdominal position of the body.
UBPROP_0000001: Paired fin located in the abdominal position of the body.[TAO]
UBPROP_0000001: Paired fin located in the abdominal position of the body.[VSAO]
has db xref: BTO:0004651
has db xref: EFO:0003644
has db xref: TAO:0001184
has db xref: VSAO:0000129
has db xref: Wikipedia:Pectoral_fin#Fins
has db xref: ZFA:0001184
has OBO namespace: uberon
has related synonym: pelvic fins
id: UBERON:0000152
in subset: efo slim

Axiom
annotated source: pelvic fin
annotated property: subClassOf
annotated target: UBERON_0004709
is entailed: true

Axiom
annotated source: pelvic fin
annotated property: IAO_0000115
annotated target: Paired fin located in the abdominal position of the body.
has db xref: TAO:curator
has db xref: VSAO:0000129

Axiom
annotated source: pelvic fin
annotated property: UBPROP_0000001
annotated target: Paired fin located in the abdominal position of the body.[TAO]
date retrieved: 2012-08-14
external class: TAO:0001184
ontology: TAO
source: TAO:wd

Axiom
annotated source: pelvic fin
annotated property: UBPROP_0000001
annotated target: Paired fin located in the abdominal position of the body.[VSAO]
date retrieved: 2012-08-14
external class: VSAO:0000129
ontology: VSAO
source: TAO:curator

Axiom
annotated source: pelvic fin
annotated property: hasRelatedSynonym
annotated target: pelvic fins
has db xref: ZFA:0001184
has synonym type: OMO_0003004

anterior region of body
type: Class
subclass of: organism subdivision
subclass of: Restriction
  on property: BSPO_0000096
  some values from: posterior region of body
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_33213
disjoint with: posterior region of body
has OBO namespace: uberon
id: UBERON:0000153

Axiom
annotated source: anterior region of body
annotated property: disjointWith
annotated target: posterior region of body
source: lexical

posterior region of body
type: Class
subclass of: organism subdivision
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_33213
has OBO namespace: uberon
id: UBERON:0000154

membranous layer
type: Class
subclass of: UBERON_0004923
subclass of: Restriction
  on property: RO_0002007
  some values from: organ part
UBPROP_0000001: A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures.
has broad synonym: membrane
has db xref: FMA:30322
has db xref: FMA:82500
has db xref: MESH:D008566
has db xref: NCIT:C12749
has exact synonym: membranous organ component
has OBO namespace: uberon
id: UBERON:0000158

Axiom
annotated source: membranous layer
annotated property: UBPROP_0000001
annotated target: A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures.
source: ncithesaurus:Membrane

Axiom
annotated source: membranous layer
annotated property: hasExactSynonym
annotated target: membranous organ component
has db xref: FMA:82500

anal canal
type: Class
subclass of: UBERON_0004111
subclass of: Restriction
  on property: BFO_0000050
  some values from: large intestine
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001353
subclass of: Restriction
  on property: RO_0002150
  some values from: rectum
subclass of: Restriction
  on property: RO_0002150
  some values from: UBERON_0001245
subclass of: Restriction
  on property: channel for
  some values from: UBERON_0001988
IAO_0000115: The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus.
IAO_0000116: requires alignment with EHDAA2 and complete developmental relationships
RO_0002175: NCBITaxon 9606
has db xref: BTO:0001978
has db xref: CALOHA:TS-2160
has db xref: EMAPA:18256
has db xref: FMA:15703
has db xref: MA:0000330
has db xref: MESH:D001003
has db xref: NCIT:C12375
has db xref: SCTID:245438008
has db xref: UMLS:C0227411
has db xref: Wikipedia:Anal_canal
has db xref: galen:AnalCanal
has exact synonym: anal canal
has exact synonym: anal canal viewed anatomically
has exact synonym: anatomical anal canal
has OBO namespace: uberon
has related synonym: anal pad
has related synonym: anus
has related synonym: canalis analis
has related synonym: cloaca
has related synonym: cloacal chamber
has related synonym: mesenteron
has related synonym: pars analis recti
id: UBERON:0000159
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: anal canal
annotated property: subClassOf
annotated target: Restriction
source: Wikipathways:WP2062

Axiom
annotated source: anal canal
annotated property: IAO_0000115
annotated target: The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus.
has db xref: Wikipedia:Anal_canal

Axiom
annotated source: anal canal
annotated property: hasDbXref
annotated target: MESH:D001003
author id: https://orcid.org/0000-0001-9439-5346
mapping justification: ManualMappingCuration
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: anal canal
annotated property: hasDbXref
annotated target: UMLS:C0227411
source: ncithesaurus:Anal_Canal

Axiom
annotated source: anal canal
annotated property: hasRelatedSynonym
annotated target: canalis analis
has db xref: BTO:0001978
has db xref: Wikipedia:Anal_canal
has synonym type: OMO_0003011

Axiom
annotated source: anal canal
annotated property: hasRelatedSynonym
annotated target: pars analis recti
has db xref: BTO:0001978

intestine
type: Class
subclass of: UBERON_0004921
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0005409
subclass of: Restriction
  on property: RO_0002433
  some values from: digestive system
IAO_0000115: 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.
IAO_0000116: This class is probably too inclusive
UBPROP_0000001: Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
UBPROP_0000001: The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
UBPROP_0000007: intestinal
UBPROP_0000008: In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type.
has db xref: AAO:0000246
has db xref: ANISEED:1235303
has db xref: BSA:0000093
has db xref: BTO:0000648
has db xref: CALOHA:TS-0490
has db xref: EFO:0000834
has db xref: EMAPA:32874
has db xref: EV:0100071
has db xref: FMA:7199
has db xref: GAID:295
has db xref: MA:0000328
has db xref: MA:0001524
has db xref: MESH:D007422
has db xref: MIAA:0000043
has db xref: NCIT:C12736
has db xref: SCTID:256876008
has db xref: TAO:0001338
has db xref: UMLS:C0021853
has db xref: VHOG:0000056
has db xref: WBbt:0005772
has db xref: Wikipedia:Intestine
has db xref: XAO:0000129
has db xref: ZFA:0001338
has db xref: galen:Intestine
has exact synonym: bowel
has OBO namespace: uberon
has related synonym: intestinal tract
id: UBERON:0000160
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: intestine
annotated property: subClassOf
annotated target: UBERON_0004921
source: cjm

Axiom
annotated source: intestine
annotated property: IAO_0000115
annotated target: Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.
has db xref: GOC:GO
has db xref: Wikipedia:Intestine

Axiom
annotated source: intestine
annotated property: UBPROP_0000001
annotated target: Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000246
ontology: AAO
source: AAO:EJS

Axiom
annotated source: intestine
annotated property: UBPROP_0000001
annotated target: The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000056
ontology: VHOG
source: http://bgee.unil.ch/

Axiom
annotated source: intestine
annotated property: hasDbXref
annotated target: UMLS:C0021853
source: ncithesaurus:Intestine

orifice
type: Class
subclass of: UBERON_0004111
IAO_0000115: Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified].
UBPROP_0000012: in FMA, this is an anatomical conduit *space*, rather than anatomical conduit
has broad synonym: anatomical ostium
has broad synonym: ostium
has db xref: FMA:3724
has db xref: SCTID:91837002
has exact synonym: anatomical orifice
has narrow synonym: hilum
has OBO namespace: uberon
id: UBERON:0000161

Axiom
annotated source: orifice
annotated property: IAO_0000115
annotated target: Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified].
has db xref: FMA:3724

Axiom
annotated source: orifice
annotated property: UBPROP_0000012
annotated target: in FMA, this is an anatomical conduit *space*, rather than anatomical conduit
external ontology: FMA

Axiom
annotated source: orifice
annotated property: hasBroadSynonym
annotated target: anatomical ostium
has db xref: FMA:3724

Axiom
annotated source: orifice
annotated property: hasExactSynonym
annotated target: anatomical orifice
has db xref: FMA:3724

cloaca
type: Class
subclass of: UBERON_0013522
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7742
IAO_0000115: Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures.
IAO_0000116: adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca
RO_0002175: NCBITaxon 9369
UBPROP_0000001: A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG]
UBPROP_0000001: Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO]
UBPROP_0000003: A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG]
UBPROP_0000007: cloacal
UBPROP_0000008: Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs
UBPROP_0000011: hindgut endoderm and proctodeal ectoderm.
has db xref: AAO:0000095
has db xref: GAID:1206
has db xref: MESH:D002988
has db xref: NCIT:C34127
has db xref: SCTID:362857006
has db xref: SCTID:370631000
has db xref: UMLS:C0008987
has db xref: VHOG:0001186
has db xref: Wikipedia:Cloaca
has db xref: XAO:0000244
has db xref: ZFA:0005781
has OBO namespace: uberon
has related synonym: cloacal chamber
has related synonym: vent
id: UBERON:0000162

Axiom
annotated source: cloaca
annotated property: subClassOf
annotated target: Restriction
source: ZFA

Axiom
annotated source: cloaca
annotated property: subClassOf
annotated target: Restriction
source: AAO

Axiom
annotated source: cloaca
annotated property: IAO_0000115
annotated target: Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures.
has db xref: ISBN:0073040584
has db xref: Wikipedia:Cloaca

Axiom
annotated source: cloaca
annotated property: RO_0002175
annotated target: NCBITaxon 9369
notes: most adult placentals have no trace of a cloaca. However, the tenrecs and golden moles, small placental mammals native to Africa, retain a cloaca as adults.

Axiom
annotated source: cloaca
annotated property: UBPROP_0000001
annotated target: A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001186
ontology: VHOG
source: http://bgee.unil.ch/
source: http://medical-dictionary.thefreedictionary.com/cloaca

Axiom
annotated source: cloaca
annotated property: UBPROP_0000001
annotated target: Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000095
ontology: AAO
source: AAO:BJB

Axiom
annotated source: cloaca
annotated property: UBPROP_0000003
annotated target: A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001186
ontology: VHOG
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572
source: http://bgee.unil.ch/

Axiom
annotated source: cloaca
annotated property: UBPROP_0000011
annotated target: hindgut endoderm and proctodeal ectoderm.
source: WP

Axiom
annotated source: cloaca
annotated property: hasDbXref
annotated target: UMLS:C0008987
source: ncithesaurus:Cloaca

Axiom
annotated source: cloaca
annotated property: hasRelatedSynonym
annotated target: cloacal chamber
has db xref: AAO:0000095

Axiom
annotated source: cloaca
annotated property: hasRelatedSynonym
annotated target: vent
has db xref: XAO:0000244

embryonic cloaca
type: Class
subclass of: cloaca
subclass of: Restriction
  on property: BFO_0000050
  some values from: embryo
subclass of: Restriction
  on property: RO_0002254
  some values from: UBERON_0003064
IAO_0000115: Endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP].
IAO_0000232: this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals.
has db xref: EHDAA2:0000256
has db xref: EHDAA:4895
has db xref: EMAPA:27573
has db xref: Wikipedia:Cloaca_(embryology)
has OBO namespace: uberon
has related synonym: cloaca
id: UBERON:0000163
in subset: pheno slim

Axiom
annotated source: embryonic cloaca
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: embryonic cloaca
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: embryonic cloaca
annotated property: IAO_0000115
annotated target: Endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP].
has db xref: MP:0010115
has db xref: Wikipedia:Cloaca_(embryology)

Axiom
annotated source: embryonic cloaca
annotated property: hasRelatedSynonym
annotated target: cloaca
has synonym type: SENSU

primitive urogenital sinus
type: Class
subclass of: UBERON_0002050
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7742
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0003064
subclass of: Restriction
  on property: RO_0002433
  some values from: embryonic cloaca
IAO_0000115: The ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females.
UBPROP_0000001: The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG]
UBPROP_0000003: In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]
UBPROP_0000013: the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal
has broad synonym: urogenital sinus
has db xref: EHDAA2:0004060
has db xref: EHDAA:5029
has db xref: EHDAA:5919
has db xref: EMAPA:17379
has db xref: NCIT:C34322
has db xref: SCTID:50961009
has db xref: UMLS:C0231057
has db xref: VHOG:0000414
has db xref: Wikipedia:Definitive_urogenital_sinus
has exact synonym: UGS
has exact synonym: fetal UGS
has exact synonym: sinus urogenitalis
has OBO namespace: uberon
id: UBERON:0000164
in subset: pheno slim

Axiom
annotated source: primitive urogenital sinus
annotated property: subClassOf
annotated target: Restriction
source: MP-def

Axiom
annotated source: primitive urogenital sinus
annotated property: IAO_0000115
annotated target: The ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females.
has db xref: ISBN:0-683-40008-8
has db xref: MP:0010116

Axiom
annotated source: primitive urogenital sinus
annotated property: UBPROP_0000001
annotated target: The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000414
ontology: VHOG
source: http://bgee.unil.ch/
source: http://medical-dictionary.thefreedictionary.com/urogenital+sinus

Axiom
annotated source: primitive urogenital sinus
annotated property: UBPROP_0000003
annotated target: In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000414
ontology: VHOG
source: ISBN:978-0721676678 Romer AS, Vertebrate body (1970)p.388-89 and Figure 300
source: http://bgee.unil.ch/

Axiom
annotated source: primitive urogenital sinus
annotated property: UBPROP_0000013
annotated target: the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal
source: MP

Axiom
annotated source: primitive urogenital sinus
annotated property: hasBroadSynonym
annotated target: urogenital sinus
has db xref: MP:0010116

Axiom
annotated source: primitive urogenital sinus
annotated property: hasDbXref
annotated target: UMLS:C0231057
source: ncithesaurus:Urogenital_Sinus

Axiom
annotated source: primitive urogenital sinus
annotated property: hasExactSynonym
annotated target: UGS
has db xref: MP:0010116

Axiom
annotated source: primitive urogenital sinus
annotated property: hasExactSynonym
annotated target: fetal UGS
has db xref: PMID:18977204

Axiom
annotated source: primitive urogenital sinus
annotated property: hasExactSynonym
annotated target: sinus urogenitalis
has synonym type: OMO_0003011

mouth
type: Class
equivalent class: Class
  intersection of: UBERON_0004921
  intersection of: Restriction
    on property: BSPO_0001106
    some values from: UBERON_0001555
subclass of: UBERON_0004921
subclass of: Restriction
  on property: BSPO_0001106
  some values from: UBERON_0001555
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6072
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0035804
IAO_0000115: The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
UBPROP_0000003: Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]
UBPROP_0000007: oral
UBPROP_0000011: some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
UBPROP_0000012: in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips
has db xref: AAO:0010355
has db xref: BTO:0001090
has db xref: BTO:0004698
has db xref: CALOHA:TS-1315
has db xref: EFO:0000825
has db xref: EHDAA2:0001326
has db xref: EHDAA:542
has db xref: EMAPA:16262
has db xref: FBbt:00003126
has db xref: FMA:49184
has db xref: GAID:75
has db xref: MA:0000341
has db xref: MA:0002474
has db xref: MAT:0000038
has db xref: MESH:D009055
has db xref: MIAA:0000038
has db xref: SCTID:21082005
has db xref: TADS:0000040
has db xref: TAO:0000547
has db xref: TAO:0000590
has db xref: TGMA:0000131
has db xref: VHOG:0000280
has db xref: VHOG:0000812
has db xref: Wikipedia:Mouth
has db xref: XAO:0003029
has db xref: ZFA:0000547
has db xref: ZFA:0000590
has db xref: galen:Mouth
has exact synonym: regio oralis
has narrow synonym: adult mouth
has OBO namespace: uberon
has related synonym: cavital oralis
has related synonym: cavitas oris
has related synonym: cavum oris
has related synonym: mouth cavity
has related synonym: oral region
has related synonym: oral vestibule
has related synonym: rima oris
has related synonym: stoma
has related synonym: stomatodaeum
has related synonym: trophic apparatus
has related synonym: vestibule of mouth
has related synonym: vestibulum oris
id: UBERON:0000165
in subset: efo slim
in subset: human reference atlas
in subset: major organ
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: mouth
annotated property: subClassOf
annotated target: UBERON_0004921
notes: the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts

Axiom
annotated source: mouth
annotated property: IAO_0000115
annotated target: The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
has db xref: Wikipedia:Mouth
has db xref: https://github.com/obophenotype/uberon/wiki/The-digestive-tract

Axiom
annotated source: mouth
annotated property: UBPROP_0000001
annotated target: Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010355
ontology: AAO
source: AAO:BJB

Axiom
annotated source: mouth
annotated property: UBPROP_0000003
annotated target: Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000812
ontology: VHOG
source: DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)
source: http://bgee.unil.ch/

Axiom
annotated source: mouth
annotated property: UBPROP_0000012
annotated target: in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips
external ontology: FMA

Axiom
annotated source: mouth
annotated property: hasDbXref
annotated target: FBbt:00003126
mapping justification: ManualMappingCuration

Axiom
annotated source: mouth
annotated property: hasExactSynonym
annotated target: regio oralis
has db xref: BTO:0004698
has db xref: FMA:49184
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: mouth
annotated property: hasRelatedSynonym
annotated target: cavital oralis
has db xref: Wikipedia:Mouth
has synonym type: OMO_0003011

Axiom
annotated source: mouth
annotated property: hasRelatedSynonym
annotated target: cavitas oris
has db xref: BTO:0001090

Axiom
annotated source: mouth
annotated property: hasRelatedSynonym
annotated target: cavum oris
has db xref: BTO:0001090

Axiom
annotated source: mouth
annotated property: hasRelatedSynonym
annotated target: mouth cavity
has db xref: BTO:0001090

Axiom
annotated source: mouth
annotated property: hasRelatedSynonym
annotated target: oral region
has db xref: EHDAA2:0001326

Axiom
annotated source: mouth
annotated property: hasRelatedSynonym
annotated target: oral vestibule
has db xref: BTO:0001090

Axiom
annotated source: mouth
annotated property: hasRelatedSynonym
annotated target: rima oris
has db xref: BTO:0001090

Axiom
annotated source: mouth
annotated property: hasRelatedSynonym
annotated target: stomatodaeum
has db xref: VHOG:0000812

Axiom
annotated source: mouth
annotated property: hasRelatedSynonym
annotated target: trophic apparatus
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: mouth
annotated property: hasRelatedSynonym
annotated target: vestibule of mouth
has db xref: BTO:0001090

Axiom
annotated source: mouth
annotated property: hasRelatedSynonym
annotated target: vestibulum oris
has db xref: BTO:0001090

oral opening
type: Class
subclass of: orifice
subclass of: Restriction
  on property: BFO_0000050
  some values from: mouth
IAO_0000115: The orifice that connects the mouth to the exterior of the body.
UBPROP_0000003: (...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG]
has db xref: FMA:59806
has exact synonym: oral fissure
has exact synonym: oral orifice
has OBO namespace: uberon
has related synonym: mouth
has related synonym: oral part of face
id: UBERON:0000166
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: oral opening
annotated property: subClassOf
annotated target: orifice
source: FMA

Axiom
annotated source: oral opening
annotated property: IAO_0000115
annotated target: The orifice that connects the mouth to the exterior of the body.
has db xref: https://github.com/obophenotype/uberon/wiki/The-digestive-tract

Axiom
annotated source: oral opening
annotated property: UBPROP_0000003
annotated target: (...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000280
ontology: VHOG
source: DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007)
source: http://bgee.unil.ch/

Axiom
annotated source: oral opening
annotated property: hasExactSynonym
annotated target: oral fissure
has db xref: FMA:59806

Axiom
annotated source: oral opening
annotated property: hasExactSynonym
annotated target: oral orifice
has db xref: FMA:59806

Axiom
annotated source: oral opening
annotated property: hasRelatedSynonym
annotated target: mouth
has synonym type: INCONSISTENT

oral cavity
type: Class
equivalent class: Class
  intersection of: anatomical space
  intersection of: Restriction
    on property: RO_0002572
    some values from: mouth
subclass of: UBERON_0002553
subclass of: Restriction
  on property: BFO_0000050
  some values from: mouth
subclass of: Restriction
  on property: RO_0002433
  some values from: mouth
subclass of: Restriction
  on property: RO_0002572
  some values from: mouth
IAO_0000115: Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present).
UBPROP_0000001: Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO]
UBPROP_0000001: The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG]
UBPROP_0000003: Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG]
has db xref: AAO:0000053
has db xref: AAO:0000960
has db xref: BSA:0000107
has db xref: CALOHA:TS-1315
has db xref: EFO:0001975
has db xref: EHDAA2:0001324
has db xref: EHDAA:6970
has db xref: EMAPA:17411
has db xref: EMAPA:18399
has db xref: EV:0100057
has db xref: FMA:20292
has db xref: HAO:0000669
has db xref: MESH:D009055
has db xref: NCIT:C12421
has db xref: SCTID:181220002
has db xref: TAO:0001027
has db xref: TGMA:0000102
has db xref: UMLS:C0226896
has db xref: VHOG:0000188
has db xref: WBbt:0005255
has db xref: XAO:0000126
has db xref: ZFA:0001027
has exact synonym: buccal cavity
has exact synonym: cavity of mouth
has OBO namespace: uberon
has related synonym: bucca
id: UBERON:0000167
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: oral cavity
annotated property: IAO_0000115
annotated target: Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present).
has db xref: ISBN:0073040584
has db xref: https://github.com/obophenotype/uberon/wiki/The-digestive-tract
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: oral cavity
annotated property: UBPROP_0000001
annotated target: Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000960
ontology: AAO
source: AAO:EJS

Axiom
annotated source: oral cavity
annotated property: UBPROP_0000001
annotated target: The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000188
ontology: VHOG
source: http://bgee.unil.ch/
source: http://medical-dictionary.thefreedictionary.com/oral+cavity

Axiom
annotated source: oral cavity
annotated property: UBPROP_0000003
annotated target: Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000188
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32
source: http://bgee.unil.ch/

Axiom
annotated source: oral cavity
annotated property: hasDbXref
annotated target: MESH:D009055
mapping justification: LexicalMatching
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: oral cavity
annotated property: hasDbXref
annotated target: UMLS:C0226896
source: ncithesaurus:Oral_Cavity

Axiom
annotated source: oral cavity
annotated property: hasExactSynonym
annotated target: buccal cavity
has db xref: FMA:20292
has db xref: ISBN:0073040584

proximal-distal subdivision of colon
type: Class
equivalent class: Class
  intersection of: UBERON_0013522
  intersection of: Restriction
    on property: subdivision of
    some values from: colon
subclass of: UBERON_0004921
subclass of: Restriction
  on property: BFO_0000050
  some values from: colon
subclass of: Restriction
  on property: subdivision of
  some values from: colon
IAO_0000115: A section dividing a colon along a proximal-distal axis.
has db xref: FMA:222905
has OBO namespace: uberon
has related synonym: segment of colon
id: UBERON:0000168
in subset: non informative

Axiom
annotated source: proximal-distal subdivision of colon
annotated property: subClassOf
annotated target: UBERON_0004921
order: 4
source: cjm

Axiom
annotated source: proximal-distal subdivision of colon
annotated property: IAO_0000115
annotated target: A section dividing a colon along a proximal-distal axis.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: proximal-distal subdivision of colon
annotated property: hasRelatedSynonym
annotated target: segment of colon
has db xref: FMA:222905

pair of lungs
type: Class
equivalent class: Class
  intersection of: UBERON_0034925
  intersection of: Restriction
    on property: RO_0002351
    some values from: UBERON_0002167
  intersection of: Restriction
    on property: RO_0002351
    some values from: UBERON_0002168
subclass of: UBERON_0034925
subclass of: Restriction
subclass of: Restriction
  on property: RO_0001025
  some values from: UBERON_0002224
subclass of: Restriction
  on property: RO_0002351
  some values from: UBERON_0002167
subclass of: Restriction
  on property: RO_0002351
  some values from: UBERON_0002168
subclass of: Restriction
  on property: RO_0002351
  qualified cardinality: 1
  on class: UBERON_0002167
subclass of: Restriction
  on property: RO_0002351
  qualified cardinality: 1
  on class: UBERON_0002168
IAO_0000115: The pair of anatomical structures comprised of a left lung and right lung.
RO_0002175: NCBITaxon 9606
has db xref: FMA:68877
has exact synonym: lungs
has exact synonym: lungs pair
has exact synonym: pulmones
has exact synonym: set of lungs
has OBO namespace: uberon
id: UBERON:0000170
in subset: human reference atlas
in subset: pheno slim

Axiom
annotated source: pair of lungs
annotated property: subClassOf
annotated target: Restriction
source: FMA-abduced

Axiom
annotated source: pair of lungs
annotated property: IAO_0000115
annotated target: The pair of anatomical structures comprised of a left lung and right lung.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: pair of lungs
annotated property: hasExactSynonym
annotated target: pulmones
has db xref: FMA:68877
has db xref: FMA:TA
has synonym type: OMO_0003011

respiration organ
type: Class
equivalent class: Class
  intersection of: organ
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0007585
subclass of: organ
subclass of: Restriction
  on property: BFO_0000050
  some values from: respiratory system
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0007585
IAO_0000115: Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
has db xref: SCTID:272626006
has db xref: SPD:0000428
has db xref: TGMA:0001247
has exact synonym: apparatus respiratorius organ
has exact synonym: breathing organ
has exact synonym: organ of apparatus respiratorius
has exact synonym: organ of respiratory system
has exact synonym: respiratory organ
has exact synonym: respiratory system organ
has OBO namespace: uberon
has related synonym: gas exchange organ
id: UBERON:0000171
in subset: functional classification
in subset: organ slim

Axiom
annotated source: respiration organ
annotated property: IAO_0000115
annotated target: Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
has db xref: GO:0007585

Axiom
annotated source: respiration organ
annotated property: hasExactSynonym
annotated target: apparatus respiratorius organ
has db xref: OBOL:automatic

Axiom
annotated source: respiration organ
annotated property: hasExactSynonym
annotated target: organ of apparatus respiratorius
has db xref: OBOL:automatic

Axiom
annotated source: respiration organ
annotated property: hasExactSynonym
annotated target: organ of respiratory system
has db xref: OBOL:automatic

Axiom
annotated source: respiration organ
annotated property: hasExactSynonym
annotated target: respiratory system organ
has db xref: OBOL:automatic

excreta
type: Class
equivalent class: Class
  intersection of: organism substance
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0007588
subclass of: organism substance
subclass of: Restriction
  on property: RO_0002353
  some values from: GO_0007588
IAO_0000115: A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity.
has alternative id: UBERON:0000324
has alternative id: UBERON:0007550
has db xref: AEO:0000184
has db xref: BTO:0000491
has db xref: EHDAA2_RETIRED:0003184
has db xref: ENVO:02000022
has db xref: FMA:9674
has db xref: galen:Excretion
has exact synonym: excreted substance
has exact synonym: portion of excreted substance
has exact synonym: waste substance
has OBO namespace: uberon
has related synonym: excretion
id: UBERON:0000174

Axiom
annotated source: excreta
annotated property: IAO_0000115
annotated target: A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity.
has db xref: GO:0007588
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: excreta
annotated property: hasExactSynonym
annotated target: portion of excreted substance
has db xref: FMA:9674

Axiom
annotated source: excreta
annotated property: hasExactSynonym
annotated target: waste substance
has db xref: AEO:0000184

Axiom
annotated source: excreta
annotated property: hasRelatedSynonym
annotated target: excretion
has db xref: BTO:0000491

blood
type: Class
subclass of: haemolymphatic fluid
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002390
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0001969
IAO_0000115: A fluid that is composed of blood plasma and erythrocytes.
IAO_0000232: This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
UBPROP_0000001: Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
UBPROP_0000002: relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
UBPROP_0000003: Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
has db xref: AAO:0000046
has db xref: BTO:0000089
has db xref: CALOHA:TS-0079
has db xref: EFO:0000296
has db xref: EHDAA2:0000176
has db xref: EHDAA:418
has db xref: EMAPA:16332
has db xref: ENVO:02000027
has db xref: EV:0100047
has db xref: FMA:9670
has db xref: GAID:965
has db xref: MA:0000059
has db xref: MESH:D001769
has db xref: MIAA:0000315
has db xref: NCIT:C12434
has db xref: TAO:0000007
has db xref: UMLS:C0005767
has db xref: VHOG:0000224
has db xref: Wikipedia:Blood
has db xref: XAO:0000124
has db xref: ZFA:0000007
has db xref: galen:Blood
has exact synonym: portion of blood
has exact synonym: vertebrate blood
has OBO namespace: uberon
has related synonym: whole blood
id: UBERON:0000178
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: blood
annotated property: subClassOf
annotated target: Restriction
source: CL:tm

Axiom
annotated source: blood
annotated property: subClassOf
annotated target: Restriction
source: Bgee:AN

Axiom
annotated source: blood
annotated property: IAO_0000115
annotated target: A fluid that is composed of blood plasma and erythrocytes.
has db xref: FMA:9670
has db xref: Wikipedia:Blood
has db xref: http://orcid.org/0000-0002-6601-2165
has db xref: https://github.com/obophenotype/uberon/issues/9

Axiom
annotated source: blood
annotated property: UBPROP_0000001
annotated target: A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
date retrieved: 2012-08-14
external class: TAO:0000007
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: blood
annotated property: UBPROP_0000001
annotated target: Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000046
ontology: AAO
source: AAO:LAP

Axiom
annotated source: blood
annotated property: UBPROP_0000002
annotated target: relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
date retrieved: 2012-06-20
external class: AAO:0000046
ontology: AAO

Axiom
annotated source: blood
annotated property: UBPROP_0000003
annotated target: Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000224
ontology: VHOG
source: DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006)
source: http://bgee.unil.ch/

Axiom
annotated source: blood
annotated property: hasDbXref
annotated target: UMLS:C0005767
source: ncithesaurus:Blood

Axiom
annotated source: blood
annotated property: hasRelatedSynonym
annotated target: whole blood
has db xref: BTO:0000089

haemolymphatic fluid
type: Class
equivalent class: Class
  intersection of: organism substance
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002193
subclass of: UBERON_0006314
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002193
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6072
IAO_0000115: Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
contributor: https://orcid.org/0000-0002-6601-2165
creation date: 2009-04-08T04:38:19Z
has db xref: CARO:0000081
has OBO namespace: uberon
has related synonym: blood or blood analog
has related synonym: circulating fluid
id: UBERON:0000179

Axiom
annotated source: haemolymphatic fluid
annotated property: IAO_0000115
annotated target: Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
has db xref: http://orcid.org/0000-0002-6601-2165

gyrus
type: Class
subclass of: UBERON_0034768
subclass of: Restriction
  on property: BFO_0000050
  some values from: cerebral cortex
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_40674
subclass of: Restriction
  on property: RO_0002219
  some values from: UBERON_0013118
IAO_0000115: A ridge on the cerebral cortex. It is generally surrounded by one or more sulci .
RO_0002174: NCBITaxon_10088
UBPROP_0000202: FMA_72015
has db xref: BTO:0002495
has db xref: FMA:83874
has db xref: NCIT:C32290
has db xref: SCTID:279165009
has db xref: UMLS:C0458308
has db xref: Wikipedia:Gyrus
has db xref: neuronames:1211
has exact synonym: cerebral gyrus
has exact synonym: gyrus of neuraxis
has exact synonym: neuraxis gyrus
has OBO namespace: uberon
has related synonym: folia
has related synonym: folium
has related synonym: folium of brain
has related synonym: gyri
has related synonym: gyri of cerebrum
has related synonym: gyrus of cerebral hemisphere
has related synonym: gyrus of cerebrum
id: UBERON:0000200
in subset: pheno slim

Axiom
annotated source: gyrus
annotated property: IAO_0000115
annotated target: A ridge on the cerebral cortex. It is generally surrounded by one or more sulci .
has db xref: Wikipedia:Gyrus
has db xref: https://github.com/obophenotype/uberon/issues/573

Axiom
annotated source: gyrus
annotated property: hasDbXref
annotated target: UMLS:C0458308
source: ncithesaurus:Cerebral_Gyrus

Axiom
annotated source: gyrus
annotated property: hasExactSynonym
annotated target: cerebral gyrus
has db xref: BTO:0002495

Axiom
annotated source: gyrus
annotated property: hasExactSynonym
annotated target: gyrus of neuraxis
has db xref: FMA:83874

Axiom
annotated source: gyrus
annotated property: hasExactSynonym
annotated target: neuraxis gyrus
has db xref: FMA:83874

Axiom
annotated source: gyrus
annotated property: hasRelatedSynonym
annotated target: folia
has synonym type: OMO_0003004

Axiom
annotated source: gyrus
annotated property: hasRelatedSynonym
annotated target: folium
has db xref: PHENOSCAPE:wd

Axiom
annotated source: gyrus
annotated property: hasRelatedSynonym
annotated target: gyri
has db xref: BTO:0002495
has synonym type: OMO_0003004

Axiom
annotated source: gyrus
annotated property: hasRelatedSynonym
annotated target: gyri of cerebrum
has db xref: BTO:0002495
has synonym type: OMO_0003004

Axiom
annotated source: gyrus
annotated property: hasRelatedSynonym
annotated target: gyrus of cerebral hemisphere
has db xref: FMA:83874

Axiom
annotated source: gyrus
annotated property: hasRelatedSynonym
annotated target: gyrus of cerebrum
has db xref: BTO:0002495

endothelial blood brain barrier
type: Class
equivalent class: Class
  intersection of: blood brain barrier
  intersection of: Restriction
    on property: RO_0002473
    some values from: CL_0000115
subclass of: blood brain barrier
subclass of: Restriction
  on property: RO_0002473
  some values from: CL_0000115
IAO_0000115: A blood brain barrier that is composed of endothelial cells.
contributor: https://orcid.org/0000-0002-6601-2165
creation date: 2009-04-10T08:15:44Z
has db xref: NIF_Subcellular:nlx_subcell_100205
has OBO namespace: uberon
id: UBERON:0000201

Axiom
annotated source: endothelial blood brain barrier
annotated property: IAO_0000115
annotated target: A blood brain barrier that is composed of endothelial cells.
has db xref: https://orcid.org/0000-0002-6601-2165

glial blood brain barrier
type: Class
equivalent class: Class
  intersection of: blood brain barrier
  intersection of: Restriction
    on property: RO_0002473
    some values from: CL_0000125
subclass of: blood brain barrier
subclass of: Restriction
  on property: RO_0002473
  some values from: CL_0000125
IAO_0000115: A blood brain barrier composed of glial cells.
contributor: https://orcid.org/0000-0002-6601-2165
creation date: 2009-04-10T08:42:24Z
has db xref: FBbt:00007091
has OBO namespace: uberon
id: UBERON:0000202

Axiom
annotated source: glial blood brain barrier
annotated property: IAO_0000115
annotated target: A blood brain barrier composed of glial cells.
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: glial blood brain barrier
annotated property: hasDbXref
annotated target: FBbt:00007091
mapping justification: ManualMappingCuration

pallium
type: Class
subclass of: UBERON_0002616
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001893
IAO_0000115: Dorsal part (roof region) of the telencephalon[GO].
RO_0002175: NCBITaxon 7762
UBPROP_0000003: In the anatomy of animals, an avian pallium is the dorsal telencephalon of a bird's brain. Pallium of avian species tend to be relatively large, comprising ~75% of the telencephalic volume.
UBPROP_0000008: In humans the cerebrum has three parts: the archipallium, the paleopallium and the neopallium. The developing telencephalon or forebrain is divided into pallium and subpallium. In amphibians, the cerebrum includes archipallium, paleopallium and some of the basal nuclei. Reptiles first developed a neopallium, which continued to develop in the brains of more recent species to become the neocortex of humans and Old World monkeys. In fish, the archipallium is the largest part of the cerebrum. Some researchers suggest the early archipallium gave rise to the human hippocampus
contributor: https://orcid.org/0000-0002-6601-2165
creation date: 2009-04-18T12:03:09Z
has alternative id: UBERON:0007333
has db xref: BTO:0003399
has db xref: DMBA:15903
has db xref: EFO:0003534
has db xref: SCTID:369224000
has db xref: TAO:0000505
has db xref: TAO:0007007
has db xref: Wikipedia:Avian_pallium
has db xref: Wikipedia:Pallium_(neuroanatomy)
has db xref: ZFA:0000505
has db xref: neuronames:3240
has exact synonym: area dorsalis telencephali
has exact synonym: dorsal part of telencephalon
has exact synonym: dorsal telencephalic area
has exact synonym: dorsal telencephalon
has OBO namespace: uberon
id: UBERON:0000203
in subset: developmental classification
in subset: efo slim

Axiom
annotated source: pallium
annotated property: IAO_0000115
annotated target: Dorsal part (roof region) of the telencephalon[GO].
has db xref: GO:0021543
has db xref: ISBN:0471888893
has db xref: Wikipedia:Pallium_(neuroanatomy)
has db xref: https://github.com/obophenotype/uberon/issues/287

Axiom
annotated source: pallium
annotated property: RO_0002175
annotated target: NCBITaxon 7762
source: PMID:8932866

Axiom
annotated source: pallium
annotated property: UBPROP_0000003
annotated target: In the anatomy of animals, an avian pallium is the dorsal telencephalon of a bird's brain. Pallium of avian species tend to be relatively large, comprising ~75% of the telencephalic volume.
source: Wikipedia:Avian_pallium
taxon: NCBITaxon:8782

Axiom
annotated source: pallium
annotated property: UBPROP_0000008
annotated target: In humans the cerebrum has three parts: the archipallium, the paleopallium and the neopallium. The developing telencephalon or forebrain is divided into pallium and subpallium. In amphibians, the cerebrum includes archipallium, paleopallium and some of the basal nuclei. Reptiles first developed a neopallium, which continued to develop in the brains of more recent species to become the neocortex of humans and Old World monkeys. In fish, the archipallium is the largest part of the cerebrum. Some researchers suggest the early archipallium gave rise to the human hippocampus
source: WP

Axiom
annotated source: pallium
annotated property: hasExactSynonym
annotated target: area dorsalis telencephali
has db xref: ZFA:0000505

Axiom
annotated source: pallium
annotated property: hasExactSynonym
annotated target: dorsal part of telencephalon
has db xref: ISBN:0471888893

Axiom
annotated source: pallium
annotated property: hasExactSynonym
annotated target: dorsal telencephalic area
has db xref: ZFA:0000505

Axiom
annotated source: pallium
annotated property: hasExactSynonym
annotated target: dorsal telencephalon
has db xref: ZFA:0000505

ventral part of telencephalon
type: Class
subclass of: UBERON_0002616
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001893
IAO_0000115: Ventral part (base region) of the telencephalon.
UBPROP_0000012: BTO term refers specifically to the avian structure
contributor: https://orcid.org/0000-0002-6601-2165
creation date: 2009-04-18T12:12:27Z
has db xref: BTO:0003401
has db xref: DMBA:15751
has db xref: EFO:0003522
has db xref: TAO:0000304
has db xref: ZFA:0000304
has exact synonym: area ventralis telencephali
has exact synonym: subpallium
has exact synonym: ventral telencephalon
has narrow synonym: subpallium
has OBO namespace: uberon
id: UBERON:0000204
in subset: developmental classification
in subset: efo slim

Axiom
annotated source: ventral part of telencephalon
annotated property: subClassOf
annotated target: Restriction
notes: separated by cell-free region

Axiom
annotated source: ventral part of telencephalon
annotated property: IAO_0000115
annotated target: Ventral part (base region) of the telencephalon.
has db xref: GO:0021544
has db xref: GO_REF:0000021
has db xref: ISBN:0471888893
has db xref: PMID:12626695

Axiom
annotated source: ventral part of telencephalon
annotated property: UBPROP_0000012
annotated target: BTO term refers specifically to the avian structure
external ontology: BTO

Axiom
annotated source: ventral part of telencephalon
annotated property: hasExactSynonym
annotated target: area ventralis telencephali
has db xref: ZFA:0000304

Axiom
annotated source: ventral part of telencephalon
annotated property: hasExactSynonym
annotated target: subpallium
has db xref: GO:0021544
has db xref: ZFA:0000304

Axiom
annotated source: ventral part of telencephalon
annotated property: hasExactSynonym
annotated target: ventral telencephalon
has db xref: ZFA:0000304

Axiom
annotated source: ventral part of telencephalon
annotated property: hasNarrowSynonym
annotated target: subpallium
has db xref: BTO:0003401
has db xref: NCBITaxon:8782

compound eye corneal lens
type: Class
subclass of: acellular anatomical structure
subclass of: UBERON_0005389
subclass of: Restriction
  on property: BFO_0000050
  some values from: compound eye
disjoint with: lens of camera-type eye
IAO_0000115: A chitinous extracellular secretion of the four underlying cone cells and the pigment cells.
contributor: https://orcid.org/0000-0002-6601-2165
creation date: 2009-04-18T01:35:32Z
has db xref: FBbt:00004199
has db xref: TADS:0000304
has OBO namespace: uberon
has related synonym: acellular lens
id: UBERON:0000207

Axiom
annotated source: compound eye corneal lens
annotated property: IAO_0000115
annotated target: A chitinous extracellular secretion of the four underlying cone cells and the pigment cells.
has db xref: GO:0048058

Axiom
annotated source: compound eye corneal lens
annotated property: hasDbXref
annotated target: FBbt:00004199
mapping justification: ManualMappingCuration

tetrapod frontal bone
type: Class
subclass of: UBERON_0002514
subclass of: UBERON_0008907
subclass of: UBERON_0010428
subclass of: UBERON_0011164
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002131
  some values from: UBERON_0001697
IAO_0000115: The bone forming the forehead and roof of the eye orbit.
RO_0002175: NCBITaxon 9606
UBPROP_0000008: fused in humans, paired in other animals
UBPROP_0000011: In the mouse the parietal originates from cephalic paraxial mesoderm (Jiang 2000; Morriss-Kay 2001), whereas in the chicken it is traced back to either mesodermal (Noden 1978) or neural crest (Couly 1992, 1993).
has db xref: AAO:0000206
has db xref: EMAPA:19016
has db xref: FMA:52734
has db xref: GAID:226
has db xref: MA:0001466
has db xref: MESH:D005624
has db xref: NCIT:C32635
has db xref: SCTID:181793006
has db xref: UMLS:C0016732
has db xref: VSAO:0000208
has db xref: Wikipedia:Frontal_bone
has narrow synonym: frontal
has narrow synonym: frontal bone
has narrow synonym: os frontal
has OBO namespace: uberon
has related synonym: os frontale
id: UBERON:0000209
in subset: human reference atlas
in subset: pheno slim

Axiom
annotated source: tetrapod frontal bone
annotated property: subClassOf
annotated target: UBERON_0010428
source: FMA

Axiom
annotated source: tetrapod frontal bone
annotated property: subClassOf
annotated target: Restriction
source: cjm

Axiom
annotated source: tetrapod frontal bone
annotated property: IAO_0000115
annotated target: The bone forming the forehead and roof of the eye orbit.
has db xref: ISBN:0-683-40008-8
has db xref: MP:0000107
has db xref: PMID:7914451
has db xref: Wikipedia:Frontal_bone

Axiom
annotated source: tetrapod frontal bone
annotated property: hasDbXref
annotated target: UMLS:C0016732
source: ncithesaurus:Frontal_Bone

Axiom
annotated source: tetrapod frontal bone
annotated property: hasNarrowSynonym
annotated target: frontal
has db xref: AAO:0000206

Axiom
annotated source: tetrapod frontal bone
annotated property: hasNarrowSynonym
annotated target: frontal bone
has db xref: FMA:52734
has db xref: MA:0001466
has synonym type: SENSU

Axiom
annotated source: tetrapod frontal bone
annotated property: hasNarrowSynonym
annotated target: os frontal
has db xref: Wikipedia:Frontal_bone
has synonym type: SENSU

Axiom
annotated source: tetrapod frontal bone
annotated property: hasRelatedSynonym
annotated target: os frontale
has db xref: Wikipedia:Frontal_bone
has synonym type: OMO_0003011

tetrapod parietal bone
type: Class
subclass of: UBERON_0002514
subclass of: UBERON_0010428
subclass of: UBERON_0011164
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0004339
IAO_0000115: In humans: bone forming side and roof of cranium. Each bone is irregularly quadrilateral in form, and has two surfaces, four borders, and four angles.
RO_0002175: NCBITaxon 9606
UBPROP_0000003: The homologization of cranial bones of actinopterygians with those of sarcopterygians based on the bone names established in human anatomy is favored in order to permit the building of phylogenetic relationship schemes beyond the taxonomic boundaries of osteichthyans (including tetrapods). (...) In actinopterygians, the terms parietal and postparietal bones have to replace the commonly used terms 'frontal' and 'parietal' bones for the two paired bones on the skull roof.[well established][VHOG]
UBPROP_0000008: The frontal bone in teleost fish is the homolog of the parietal bone in tetrapods[various]. In many non-mammalian tetrapods, they are bordered to the rear by a pair of postparietal bones that may be solely in the roof of the skull, or slope downwards to contribute to the back of the skull, depending on the species. In the living tuatara, and many fossil species, a small opening, the parietal foramen, lies between the two parietal bones. This opening is the location of a third eye in the midline of the skull, which is much smaller than the two main eyes
has db xref: AAO:0000390
has db xref: EMAPA:18715
has db xref: FMA:9613
has db xref: GAID:229
has db xref: MA:0001469
has db xref: MESH:D010294
has db xref: NCIT:C12766
has db xref: SCTID:181794000
has db xref: UMLS:C0030558
has db xref: VHOG:0001326
has db xref: Wikipedia:Parietal_bone
has narrow synonym: actinopterygian frontal bone
has narrow synonym: frontal bone
has narrow synonym: parietal
has narrow synonym: parietal bone
has OBO namespace: uberon
has related synonym: os parietale
id: UBERON:0000210
in subset: human reference atlas
in subset: pheno slim

Axiom
annotated source: tetrapod parietal bone
annotated property: subClassOf
annotated target: UBERON_0010428
source: FMA

Axiom
annotated source: tetrapod parietal bone
annotated property: subClassOf
annotated target: Restriction
source: PMID:11523816

Axiom
annotated source: tetrapod parietal bone
annotated property: IAO_0000115
annotated target: In humans: bone forming side and roof of cranium. Each bone is irregularly quadrilateral in form, and has two surfaces, four borders, and four angles.
has db xref: Wikipedia:Parietal_bone
has db xref: ZFA:0000514

Axiom
annotated source: tetrapod parietal bone
annotated property: UBPROP_0000003
annotated target: The homologization of cranial bones of actinopterygians with those of sarcopterygians based on the bone names established in human anatomy is favored in order to permit the building of phylogenetic relationship schemes beyond the taxonomic boundaries of osteichthyans (including tetrapods). (...) In actinopterygians, the terms parietal and postparietal bones have to replace the commonly used terms 'frontal' and 'parietal' bones for the two paired bones on the skull roof.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001326
ontology: VHOG
source: ISBN:978-3899370805 Arratia G, Schultze HP, Wilson MVH, Mesozoic Fishes 4 - Homology and Phylogeny (2008) p.23-48
source: http://bgee.unil.ch/

Axiom
annotated source: tetrapod parietal bone
annotated property: UBPROP_0000008
annotated target: The frontal bone in teleost fish is the homolog of the parietal bone in tetrapods[various]. In many non-mammalian tetrapods, they are bordered to the rear by a pair of postparietal bones that may be solely in the roof of the skull, or slope downwards to contribute to the back of the skull, depending on the species. In the living tuatara, and many fossil species, a small opening, the parietal foramen, lies between the two parietal bones. This opening is the location of a third eye in the midline of the skull, which is much smaller than the two main eyes
source: WP

Axiom
annotated source: tetrapod parietal bone
annotated property: hasDbXref
annotated target: UMLS:C0030558
source: ncithesaurus:Parietal_Bone

Axiom
annotated source: tetrapod parietal bone
annotated property: hasNarrowSynonym
annotated target: actinopterygian frontal bone
has db xref: TAO:0000514

Axiom
annotated source: tetrapod parietal bone
annotated property: hasNarrowSynonym
annotated target: frontal bone
has db xref: TAO:0000514

Axiom
annotated source: tetrapod parietal bone
annotated property: hasNarrowSynonym
annotated target: parietal
has db xref: AAO:0000390
has synonym type: SENSU

Axiom
annotated source: tetrapod parietal bone
annotated property: hasNarrowSynonym
annotated target: parietal bone
has db xref: FMA:9613
has synonym type: SENSU

Axiom
annotated source: tetrapod parietal bone
annotated property: hasRelatedSynonym
annotated target: os parietale
has db xref: Wikipedia:Parietal_bone
has synonym type: OMO_0003011

ligament
type: Class
subclass of: organ
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0002384
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_33213
IAO_0000115: Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.
UBPROP_0000001: Nonparenchymatous organ that primarily consists of dense connective tissue aggregated into fasciculi by connective tissue. Examples: sutural ligament, radiate sternocostal ligament, ligament of liver, ovarian ligament[FMA][FMA:21496].
UBPROP_0000001: Portion of connective tissue that connects bone or cartilage.[TAO]
UBPROP_0000003: Compared with their Ediacarian predecessor, Cambrian animals in general were characterized by their much stouter bodies. The stoutness of the body is likely due to the formation of ligaments and tendons, which in turn requires the crosslinking of collagen triple helices.[well established][VHOG]
UBPROP_0000012: this groups both skeletal and non-skeletal ligaments. What is called a 'ligament' in many AOs is actually a skeletal ligament
has db xref: CALOHA:TS-2145
has db xref: EFO:0001966
has db xref: EMAPA:35493
has db xref: FMA:21496
has db xref: FMA:30319
has db xref: MA:0000113
has db xref: MESH:D008022
has db xref: NCIT:C13046
has db xref: SCTID:182358004
has db xref: TAO:0001682
has db xref: UMLS:C0023685
has db xref: VHOG:0001272
has db xref: Wikipedia:Ligament
has db xref: XAO:0004031
has db xref: ZFA:0001675
has db xref: galen:Ligament
has exact synonym: ligament organ
has OBO namespace: uberon
id: UBERON:0000211
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: ligament
annotated property: IAO_0000115
annotated target: Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.
has db xref: GO_REF:0000034
has db xref: VSAO:0000073
has db xref: http://dx.plos.org/10.1371/journal.pone.0051070

Axiom
annotated source: ligament
annotated property: UBPROP_0000001
annotated target: Nonparenchymatous organ that primarily consists of dense connective tissue aggregated into fasciculi by connective tissue. Examples: sutural ligament, radiate sternocostal ligament, ligament of liver, ovarian ligament[FMA][FMA:21496].
source: FMA:21496

Axiom
annotated source: ligament
annotated property: UBPROP_0000001
annotated target: Portion of connective tissue that connects bone or cartilage.[TAO]
date retrieved: 2012-08-14
external class: TAO:0001682
ontology: TAO
source: TAO:wd

Axiom
annotated source: ligament
annotated property: UBPROP_0000003
annotated target: Compared with their Ediacarian predecessor, Cambrian animals in general were characterized by their much stouter bodies. The stoutness of the body is likely due to the formation of ligaments and tendons, which in turn requires the crosslinking of collagen triple helices.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001272
ontology: VHOG
source: PMID:8710894 Ohno S, The notion of the Cambrian pananimalia genome. PNAS (1996)
source: http://bgee.unil.ch/

Axiom
annotated source: ligament
annotated property: hasDbXref
annotated target: UMLS:C0023685
source: ncithesaurus:Ligament

Axiom
annotated source: ligament
annotated property: hasExactSynonym
annotated target: ligament organ
has db xref: FMA:21496

vertebral arch of axis
type: Class
equivalent class: Class
  intersection of: UBERON_0003861
  intersection of: Restriction
    on property: BFO_0000050
    some values from: vertebral bone 2
subclass of: UBERON_0003861
subclass of: Restriction
  on property: BFO_0000050
  some values from: vertebral bone 2
IAO_0000115: A neural arch that is part of a vertebral bone 2.
has db xref: FMA:24053
has exact synonym: vertebral foramen of cervical vertebra 2
has OBO namespace: uberon
id: UBERON:0000218

Axiom
annotated source: vertebral arch of axis
annotated property: IAO_0000115
annotated target: A neural arch that is part of a vertebral bone 2.
has db xref: OBOL:automatic

atlanto-occipital joint
type: Class
equivalent class: Class
  intersection of: UBERON_0002217
  intersection of: Restriction
    on property: RO_0002176
    some values from: vertebral bone 1
  intersection of: Restriction
    on property: RO_0002176
    some values from: UBERON_0001676
subclass of: UBERON_0002217
subclass of: UBERON_0015212
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0011138
subclass of: Restriction
  on property: RO_0002176
  some values from: vertebral bone 1
subclass of: Restriction
  on property: RO_0002176
  some values from: UBERON_0001676
IAO_0000115: The Atlanto-occipital joint (articulation between the atlas and the occipital bone) consists of a pair of condyloid joints. The atlanto-occipital joint is a synovial joint. The ligaments connecting the bones are: Two Articular capsules; Posterior atlantoöccipital membrane; Anterior atlantoöccipital membrane; Lateral atlantoöccipital.
has db xref: FMA:24939
has db xref: MESH:D001269
has db xref: NCIT:C32158
has db xref: SCTID:361831006
has db xref: UMLS:C0004169
has db xref: Wikipedia:Atlanto-occipital_joint
has db xref: ncithesaurus:Atlanto-occipital_Joint-Atlanto
has exact synonym: articulatio atlanto-occipitalis
has exact synonym: atlanto occipital joint
has exact synonym: atlantooccipital joint
has exact synonym: craniovertebral joint
has exact synonym: occipito atlantal joint
has exact synonym: occipito-atlantal joint
has OBO namespace: uberon
has related synonym: articulatio atlantooccipitalis
id: UBERON:0000220

Axiom
annotated source: atlanto-occipital joint
annotated property: subClassOf
annotated target: Restriction
source: FMA-abduced-lr

Axiom
annotated source: atlanto-occipital joint
annotated property: IAO_0000115
annotated target: The Atlanto-occipital joint (articulation between the atlas and the occipital bone) consists of a pair of condyloid joints. The atlanto-occipital joint is a synovial joint. The ligaments connecting the bones are: Two Articular capsules; Posterior atlantoöccipital membrane; Anterior atlantoöccipital membrane; Lateral atlantoöccipital.
has db xref: Wikipedia:Atlanto-occipital_joint

Axiom
annotated source: atlanto-occipital joint
annotated property: hasDbXref
annotated target: MESH:D001269
author id: https://orcid.org/0000-0001-9439-5346
mapping justification: ManualMappingCuration
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: atlanto-occipital joint
annotated property: hasDbXref
annotated target: UMLS:C0004169
source: ncithesaurus:Atlanto-occipital_Joint

Axiom
annotated source: atlanto-occipital joint
annotated property: hasExactSynonym
annotated target: articulatio atlanto-occipitalis
has db xref: FMA:24939

Axiom
annotated source: atlanto-occipital joint
annotated property: hasExactSynonym
annotated target: craniovertebral joint
has db xref: FMA:24939

Axiom
annotated source: atlanto-occipital joint
annotated property: hasRelatedSynonym
annotated target: articulatio atlantooccipitalis
has db xref: Wikipedia:Atlanto-occipital_joint
has synonym type: OMO_0003011

tendon sheath
type: Class
equivalent class: Class
  intersection of: UBERON_0004923
  intersection of: Restriction
    on property: RO_0002007
    some values from: tendon
subclass of: UBERON_0004923
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0011233
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0011234
subclass of: Restriction
  on property: RO_0002007
  some values from: tendon
IAO_0000115: A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath.
IAO_0000116: TODO - add layer relations. 'tendon sheath' GAT in FMA.
has db xref: BTO:0000051
has db xref: FMA:45087
has db xref: FMA:76715
has db xref: NCIT:C96299
has db xref: SCTID:361885006
has db xref: UMLS:C0224856
has db xref: Wikipedia:Tendon_sheath
has exact synonym: synovial tendon sheath
has OBO namespace: uberon
has related synonym: vagina tendinis
id: UBERON:0000304

Axiom
annotated source: tendon sheath
annotated property: IAO_0000115
annotated target: A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath.
has db xref: Wikipedia:Tendon_sheath

Axiom
annotated source: tendon sheath
annotated property: hasDbXref
annotated target: UMLS:C0224856
source: ncithesaurus:Tendon_Sheath

Axiom
annotated source: tendon sheath
annotated property: hasExactSynonym
annotated target: synovial tendon sheath
has db xref: FMA:45087

Axiom
annotated source: tendon sheath
annotated property: hasRelatedSynonym
annotated target: vagina tendinis
has db xref: Wikipedia:Tendon_sheath
has synonym type: OMO_0003011

blastula
type: Class
equivalent class: Class
  intersection of: multicellular organism
  intersection of: Restriction
    on property: RO_0002491
    some values from: blastula stage
subclass of: embryo
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0007010
subclass of: Restriction
  on property: RO_0002491
  some values from: blastula stage
IAO_0000115: Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
IAO_0000116: TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula
has alternative id: UBERON:0007011
has db xref: BILA:0000059
has db xref: BTO:0000128
has db xref: GAID:1294
has db xref: MESH:D036703
has db xref: OGEM:000006
has db xref: Wikipedia:Blastula
has exact synonym: blastula embryo
has OBO namespace: uberon
has related synonym: blastosphere
id: UBERON:0000307
in subset: inconsistent with fma

Axiom
annotated source: blastula
annotated property: IAO_0000115
annotated target: Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
has db xref: Wikipedia:Blastula

Axiom
annotated source: blastula
annotated property: hasExactSynonym
annotated target: blastula embryo
has db xref: BILA:0000059

Axiom
annotated source: blastula
annotated property: hasRelatedSynonym
annotated target: blastosphere
has db xref: Wikipedia:Blastula

body wall
type: Class
subclass of: organism subdivision
IAO_0000115: The external portion of an animal body derived from ectoderm and mesoderm layers that encloses the body cavity.
UBPROP_0000008: defined generically to encompass both vertebrates and invertebrates
UBPROP_0000012: the BTO class refers to earthworms.
has db xref: BTO:0000139
has db xref: EMAPA:32761
has db xref: FMA:10427
has db xref: SCTID:281483004
has db xref: galen:BodyWall
has exact synonym: wall fo trunk
has narrow synonym: trunk wall
has narrow synonym: wall of trunk
has OBO namespace: uberon
id: UBERON:0000309
in subset: pheno slim

Axiom
annotated source: body wall
annotated property: IAO_0000115
annotated target: The external portion of an animal body derived from ectoderm and mesoderm layers that encloses the body cavity.
has db xref: MP:0003385

Axiom
annotated source: body wall
annotated property: UBPROP_0000012
annotated target: the BTO class refers to earthworms.
external ontology: BTO

Axiom
annotated source: body wall
annotated property: hasExactSynonym
annotated target: wall fo trunk
has db xref: FMA:10427

Axiom
annotated source: body wall
annotated property: hasNarrowSynonym
annotated target: trunk wall
has db xref: FMA:10427

Axiom
annotated source: body wall
annotated property: hasNarrowSynonym
annotated target: wall of trunk
has db xref: FMA:10427

breast
type: Class
subclass of: UBERON_0034929
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001443
IAO_0000115: The upper ventral region of the torso of an organism.
UBPROP_0000008: The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's.
has db xref: BTO:0000149
has db xref: CALOHA:TS-2083
has db xref: EV:0100124
has db xref: FMA:9601
has db xref: GAID:33
has db xref: MESH:D001940
has db xref: NCIT:C12971
has db xref: SCTID:181131000
has db xref: UMLS:C0006141
has db xref: Wikipedia:Breast
has db xref: galen:Breast
has exact synonym: mammary part of chest
has exact synonym: mammary region
has OBO namespace: uberon
has related synonym: mamma
id: UBERON:0000310
in subset: pheno slim

Axiom
annotated source: breast
annotated property: IAO_0000115
annotated target: The upper ventral region of the torso of an organism.
has db xref: Wikipedia:Breast

Axiom
annotated source: breast
annotated property: UBPROP_0000008
annotated target: 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.
source: WP,unvetted

Axiom
annotated source: breast
annotated property: hasDbXref
annotated target: UMLS:C0006141
source: ncithesaurus:Breast

Axiom
annotated source: breast
annotated property: hasExactSynonym
annotated target: mammary part of chest
has db xref: FMA:9601

Axiom
annotated source: breast
annotated property: hasExactSynonym
annotated target: mammary region
has db xref: FMA:9601

Axiom
annotated source: breast
annotated property: hasRelatedSynonym
annotated target: mamma
has db xref: Wikipedia:Breast
has synonym type: OMO_0003011

portion of cartilage tissue in tibia
type: Class
equivalent class: Class
  intersection of: UBERON_0002418
  intersection of: Restriction
    on property: BFO_0000050
    some values from: tibia
subclass of: UBERON_0004270
subclass of: UBERON_0007391
subclass of: Restriction
  on property: BFO_0000050
  some values from: tibia
IAO_0000115: Cartilage pertaining to the tibia.
IAO_0000232: This class represents a portion of cartilage tissue located in the tibia, *not* the cartilaginous condensation of an emrbyonic tibia
has db xref: BTO:0000207
has db xref: FMA:33923
has exact synonym: tibial cartilage
has OBO namespace: uberon
has related synonym: cartilage of tibia
id: UBERON:0000313

Axiom
annotated source: portion of cartilage tissue in tibia
annotated property: IAO_0000115
annotated target: Cartilage pertaining to the tibia.
has db xref: Dorlands_Medical_Dictionary:MerckSource

Axiom
annotated source: portion of cartilage tissue in tibia
annotated property: hasRelatedSynonym
annotated target: cartilage of tibia
has db xref: FMA:33923

cecum mucosa
type: Class
equivalent class: Class
  intersection of: mucosa
  intersection of: Restriction
    on property: BFO_0000050
    some values from: caecum
subclass of: colonic mucosa
subclass of: Restriction
  on property: BFO_0000050
  some values from: caecum
IAO_0000115: A mucosa that is part of a cecum [Automatically generated definition].
RO_0002175: NCBITaxon 9606
has db xref: BTO:0000213
has db xref: FMA:14998
has exact synonym: caecum mucosa
has exact synonym: caecum mucosa of organ
has exact synonym: caecum mucous membrane
has exact synonym: caecum organ mucosa
has exact synonym: cecal mucosa
has exact synonym: cecum mucosa of organ
has exact synonym: cecum mucous membrane
has exact synonym: cecum organ mucosa
has exact synonym: intestinum crassum caecum mucosa
has exact synonym: intestinum crassum caecum mucosa of organ
has exact synonym: intestinum crassum caecum mucous membrane
has exact synonym: intestinum crassum caecum organ mucosa
has exact synonym: mucosa of caecum
has exact synonym: mucosa of cecum
has exact synonym: mucosa of intestinum crassum caecum
has exact synonym: mucosa of organ of caecum
has exact synonym: mucosa of organ of cecum
has exact synonym: mucosa of organ of intestinum crassum caecum
has exact synonym: mucous membrane of caecum
has exact synonym: mucous membrane of cecum
has exact synonym: mucous membrane of intestinum crassum caecum
has exact synonym: organ mucosa of caecum
has exact synonym: organ mucosa of cecum
has exact synonym: organ mucosa of intestinum crassum caecum
has OBO namespace: uberon
id: UBERON:0000314
in subset: human reference atlas

Axiom
annotated source: cecum mucosa
annotated property: IAO_0000115
annotated target: A mucosa that is part of a cecum [Automatically generated definition].
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: caecum mucosa
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: caecum mucosa of organ
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: caecum mucous membrane
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: caecum organ mucosa
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: cecal mucosa
has db xref: FMA:14998

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: cecum mucosa of organ
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: cecum mucous membrane
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: cecum organ mucosa
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: intestinum crassum caecum mucosa
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: intestinum crassum caecum mucosa of organ
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: intestinum crassum caecum mucous membrane
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: intestinum crassum caecum organ mucosa
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: mucosa of caecum
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: mucosa of cecum
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: mucosa of intestinum crassum caecum
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: mucosa of organ of caecum
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: mucosa of organ of cecum
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: mucosa of organ of intestinum crassum caecum
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: mucous membrane of caecum
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: mucous membrane of cecum
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: mucous membrane of intestinum crassum caecum
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: organ mucosa of caecum
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: organ mucosa of cecum
has db xref: OBOL:automatic

Axiom
annotated source: cecum mucosa
annotated property: hasExactSynonym
annotated target: organ mucosa of intestinum crassum caecum
has db xref: OBOL:automatic

subarachnoid space
type: Class
equivalent class: Class
  intersection of: anatomical space
  intersection of: Restriction
    on property: RO_0002220
    some values from: UBERON_0002361
  intersection of: Restriction
    on property: RO_0002220
    some values from: UBERON_0002362
subclass of: anatomical space
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0010743
subclass of: Restriction
  on property: RO_0001015
  some values from: UBERON_0001359
subclass of: Restriction
  on property: RO_0002220
  some values from: UBERON_0002361
subclass of: Restriction
  on property: RO_0002220
  some values from: UBERON_0002362
IAO_0000115: The space between the arachnoid and pia mater.
has db xref: BTO:0000230
has db xref: EMAPA:32666
has db xref: FMA:83716
has db xref: GAID:689
has db xref: MESH:D013346
has db xref: SCTID:362311001
has db xref: Wikipedia:Subarachnoid_space
has exact synonym: subarachnoid space of CNS
has exact synonym: subarachnoid space of central nervous system
has exact synonym: subarachnoid space of neuraxis
has OBO namespace: uberon
has related synonym: cavitas subarachnoidea
has related synonym: cavum subarachnoideale
has related synonym: spatium leptomeningeum
has related synonym: spatium subarachnoideum
has related synonym: subarachnoid cavity
id: UBERON:0000315
in subset: pheno slim

Axiom
annotated source: subarachnoid space
annotated property: subClassOf
annotated target: Restriction
source: ISBN:0471888893

Axiom
annotated source: subarachnoid space
annotated property: IAO_0000115
annotated target: The space between the arachnoid and pia mater.
has db xref: GOC:add
has db xref: Wikipedia:Subarachnoid_space
has db xref: https://sourceforge.net/p/obo/mammalian-phenotype-requests/1168/

Axiom
annotated source: subarachnoid space
annotated property: hasExactSynonym
annotated target: subarachnoid space of neuraxis
has db xref: FMA:322060

Axiom
annotated source: subarachnoid space
annotated property: hasRelatedSynonym
annotated target: cavitas subarachnoidea
has db xref: BTO:0000230
has synonym type: OMO_0003011

Axiom
annotated source: subarachnoid space
annotated property: hasRelatedSynonym
annotated target: cavum subarachnoideale
has db xref: Wikipedia:Subarachnoid_space
has synonym type: OMO_0003011

Axiom
annotated source: subarachnoid space
annotated property: hasRelatedSynonym
annotated target: spatium leptomeningeum
has db xref: BTO:0000230
has synonym type: OMO_0003011

Axiom
annotated source: subarachnoid space
annotated property: hasRelatedSynonym
annotated target: spatium subarachnoideum
has db xref: BTO:0000230
has db xref: Wikipedia:Subarachnoid_space
has synonym type: OMO_0003011

Axiom
annotated source: subarachnoid space
annotated property: hasRelatedSynonym
annotated target: subarachnoid cavity
has db xref: BTO:0000230

cervical mucus
type: Class
equivalent class: Class
  intersection of: mucus
  intersection of: Restriction
    on property: RO_0003001
    some values from: uterine cervix
subclass of: mucus
subclass of: Restriction
  on property: RO_0003001
  some values from: uterine cervix
IAO_0000115: A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus.
has db xref: BTO:0000242
has db xref: FMA:83689
has db xref: MESH:D002582
has db xref: Wikipedia:Mucus#Reproductive_system
has exact synonym: cervix mucus
has OBO namespace: uberon
id: UBERON:0000316

Axiom
annotated source: cervical mucus
annotated property: IAO_0000115
annotated target: A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus.
has db xref: BTO:0000242
has db xref: Wikipedia:Cervix#Cervical_mucus
has db xref: Wikipedia:Mucus#Reproductive_system

Axiom
annotated source: cervical mucus
annotated property: hasExactSynonym
annotated target: cervix mucus
has db xref: OBOL:automatic

colonic mucosa
type: Class
equivalent class: Class
  intersection of: mucosa
  intersection of: Restriction
    on property: BFO_0000050
    some values from: colon
subclass of: UBERON_0001207
subclass of: Restriction
  on property: BFO_0000050
  some values from: colon
IAO_0000115: Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells.
RO_0002175: NCBITaxon 9606
has alternative id: UBERON:0003347
has alternative id: UBERON:0004981
has db xref: BTO:0000271
has db xref: CALOHA:TS-0164
has db xref: EFO:0003038
has db xref: EMAPA:27375
has db xref: FMA:14984
has db xref: FMA:85388
has db xref: MA:0003194
has db xref: SCTID:362157008
has exact synonym: colon mucosa
has exact synonym: colon mucous membrane
has exact synonym: colonic mucosa
has exact synonym: colonic mucous membrane
has exact synonym: large bowel mucosa
has exact synonym: mucosa of colon
has exact synonym: mucosa of large bowel
has OBO namespace: uberon
id: UBERON:0000317
in subset: efo slim
in subset: human reference atlas

Axiom
annotated source: colonic mucosa
annotated property: IAO_0000115
annotated target: Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: colonic mucosa
annotated property: hasExactSynonym
annotated target: colon mucosa
has db xref: FMA:14984

Axiom
annotated source: colonic mucosa
annotated property: hasExactSynonym
annotated target: colon mucous membrane
has db xref: OBOL:automatic

Axiom
annotated source: colonic mucosa
annotated property: hasExactSynonym
annotated target: colonic mucous membrane
has db xref: FMA:14984

Axiom
annotated source: colonic mucosa
annotated property: hasExactSynonym
annotated target: large bowel mucosa
has db xref: OBOL:automatic

Axiom
annotated source: colonic mucosa
annotated property: hasExactSynonym
annotated target: mucosa of colon
has db xref: FMA:14984

Axiom
annotated source: colonic mucosa
annotated property: hasExactSynonym
annotated target: mucosa of large bowel
has db xref: OBOL:automatic

duodenal mucosa
type: Class
equivalent class: Class
  intersection of: mucosa
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002114
subclass of: UBERON_0001204
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002114
IAO_0000115: A mucosa that is part of a duodenum [Automatically generated definition].
RO_0002175: NCBITaxon 9606
has alternative id: UBERON:0003348
has db xref: BTO:0000367
has db xref: CALOHA:TS-0213
has db xref: EMAPA:27235
has db xref: FMA:14942
has db xref: MA:0003207
has db xref: SCTID:362146003
has exact synonym: doudenal mucosa
has exact synonym: duodenal mucous membrane
has exact synonym: mucosa of duodenum
has exact synonym: mucous membrane of duodenum
has OBO namespace: uberon
has related synonym: duodenum mucosa
id: UBERON:0000320
in subset: human reference atlas

Axiom
annotated source: duodenal mucosa
annotated property: IAO_0000115
annotated target: A mucosa that is part of a duodenum [Automatically generated definition].
has db xref: OBOL:automatic

Axiom
annotated source: duodenal mucosa
annotated property: hasExactSynonym
annotated target: doudenal mucosa
has db xref: FMA:14942

Axiom
annotated source: duodenal mucosa
annotated property: hasExactSynonym
annotated target: duodenal mucous membrane
has db xref: FMA:14942

Axiom
annotated source: duodenal mucosa
annotated property: hasExactSynonym
annotated target: mucosa of duodenum
has db xref: OBOL:automatic

Axiom
annotated source: duodenal mucosa
annotated property: hasExactSynonym
annotated target: mucous membrane of duodenum
has db xref: OBOL:automatic

Axiom
annotated source: duodenal mucosa
annotated property: hasRelatedSynonym
annotated target: duodenum mucosa
has db xref: BTO:0000367

late embryo
type: Class
equivalent class: Class
  intersection of: embryo
  intersection of: Restriction
    on property: RO_0002491
    some values from: UBERON_0007220
subclass of: embryo
subclass of: Restriction
  on property: RO_0002491
  some values from: UBERON_0007220
IAO_0000115: An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching.
IAO_0000116: TODO - check fetus/embryo. WP: An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination. In humans, it is called an embryo until about eight weeks after fertilization (i.e. ten weeks LMP), and from then it is instead called a fetus.
UBPROP_0000001: Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus[FMA:63919].
has db xref: BTO:0000449
has db xref: CALOHA:TS-0360
has db xref: EFO:0001323
has db xref: FBbt:00005333
has db xref: FMA:63919
has db xref: GAID:552
has db xref: MESH:D005333
has db xref: NCIT:C13235
has db xref: SCTID:83418008
has db xref: UMLS:C0015965
has narrow synonym: fetus
has OBO namespace: uberon
has related synonym: embryo late growth stage
has related synonym: embryo late stage
id: UBERON:0000323
in subset: efo slim
in subset: pheno slim

Axiom
annotated source: late embryo
annotated property: IAO_0000115
annotated target: An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching.
has db xref: https://orcid.org/0000-0003-3308-6245

Axiom
annotated source: late embryo
annotated property: UBPROP_0000001
annotated target: Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus[FMA:63919].
source: FMA:63919

Axiom
annotated source: late embryo
annotated property: hasDbXref
annotated target: FBbt:00005333
mapping justification: ManualMappingCuration

Axiom
annotated source: late embryo
annotated property: hasDbXref
annotated target: UMLS:C0015965
source: ncithesaurus:Fetus

Axiom
annotated source: late embryo
annotated property: hasNarrowSynonym
annotated target: fetus
has db xref: BTO:0000449

Axiom
annotated source: late embryo
annotated property: hasRelatedSynonym
annotated target: embryo late growth stage
has db xref: BTO:0000449

Axiom
annotated source: late embryo
annotated property: hasRelatedSynonym
annotated target: embryo late stage
has db xref: BTO:0000449

gastric gland
type: Class
subclass of: UBERON_0002365
subclass of: UBERON_0003294
subclass of: Restriction
IAO_0000115: The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin.
has db xref: BTO:0000503
has db xref: EMAPA:27181
has db xref: FMA:14919
has OBO namespace: uberon
id: UBERON:0000325
in subset: organ slim
in subset: pheno slim

Axiom
annotated source: gastric gland
annotated property: subClassOf
annotated target: UBERON_0002365
source: cjm

Axiom
annotated source: gastric gland
annotated property: subClassOf
annotated target: Restriction
source: ISBN:0073040584

Axiom
annotated source: gastric gland
annotated property: IAO_0000115
annotated target: The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin.
has db xref: MGI:anna

pancreatic juice
type: Class
equivalent class: Class
  intersection of: secretion of exocrine gland
  intersection of: Restriction
    on property: RO_0003001
    some values from: UBERON_0001264
subclass of: secretion of exocrine gland
subclass of: Restriction
  on property: RO_0003001
  some values from: UBERON_0001264
IAO_0000115: Pancreatic juice is slightly alkaline and contains numerous enzymes and inactive enzyme precursors including alpha-amylase, chymotrypsinogen, lipase, procarboxypeptidase, proelastase, prophospholipase A2, ribonuclease, and trypsinogen. Its high concentration of bicarbonate ions helps to neutralize the acid from the stomach.
has db xref: BTO:0000504
has db xref: CALOHA:TS-2235
has db xref: FMA:62973
has db xref: GAID:1166
has db xref: MESH:D010189
has OBO namespace: uberon
has related synonym: pancreatic fluid
has related synonym: pancreatic secretion
has related synonym: succus pancreaticus
id: UBERON:0000326

Axiom
annotated source: pancreatic juice
annotated property: IAO_0000115
annotated target: Pancreatic juice is slightly alkaline and contains numerous enzymes and inactive enzyme precursors including alpha-amylase, chymotrypsinogen, lipase, procarboxypeptidase, proelastase, prophospholipase A2, ribonuclease, and trypsinogen. Its high concentration of bicarbonate ions helps to neutralize the acid from the stomach.
has db xref: GO:0030157

Axiom
annotated source: pancreatic juice
annotated property: hasRelatedSynonym
annotated target: succus pancreaticus
has db xref: BTO:0000504

gut wall
type: Class
equivalent class: Class
  intersection of: anatomical wall
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001555
subclass of: anatomical wall
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001555
IAO_0000115: The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity).
IAO_0000232: We model the digestive tract as consisting of two parts: the wall and the lumen.
has db xref: BTO:0000547
has db xref: FMA:45653
has exact synonym: digestive tract wall
has exact synonym: wall of digestive tract
has exact synonym: wall of gut
has OBO namespace: uberon
has related synonym: wall of alimentary tract
id: UBERON:0000328

Axiom
annotated source: gut wall
annotated property: IAO_0000115
annotated target: The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity).
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: gut wall
annotated property: hasExactSynonym
annotated target: wall of gut
has db xref: FMA:45653

yellow bone marrow
type: Class
equivalent class: Class
  intersection of: UBERON_0002371
  intersection of: Restriction
    on property: RO_0002473
    some values from: CL_0000136
subclass of: UBERON_0002371
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0007195
subclass of: Restriction
  on property: RO_0002473
  some values from: CL_0000136
IAO_0000115: Bone marrow in which the fat cells predominate in the meshes of the reticular network.
has db xref: BTO:0000635
has db xref: FMA:74596
has db xref: SCTID:328639002
has db xref: SCTID:5023006
has exact synonym: medulla ossium flava
has exact synonym: yellow marrow
has OBO namespace: uberon
has related synonym: fat marrow
id: UBERON:0000332

Axiom
annotated source: yellow bone marrow
annotated property: IAO_0000115
annotated target: Bone marrow in which the fat cells predominate in the meshes of the reticular network.
has db xref: http://medical-dictionary.thefreedictionary.com/Yellow+Marrow

Axiom
annotated source: yellow bone marrow
annotated property: hasExactSynonym
annotated target: medulla ossium flava
has db xref: BTO:0000635
has synonym type: OMO_0003011

Axiom
annotated source: yellow bone marrow
annotated property: hasExactSynonym
annotated target: yellow marrow
has db xref: BTO:0000635

Axiom
annotated source: yellow bone marrow
annotated property: hasRelatedSynonym
annotated target: fat marrow
has db xref: BTO:0000635

intestinal gland
type: Class
equivalent class: Class
  intersection of: UBERON_0002530
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001242
subclass of: UBERON_0003408
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001242
IAO_0000115: A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm].
UBPROP_0000012: Note that some sources treat 'intestinal gland' as synonymous with crypts
has db xref: BTO:0000640
has db xref: FMA:15052
has db xref: SCTID:266297002
has exact synonym: bowel mucosa gland
has exact synonym: bowel mucosa of organ gland
has exact synonym: bowel mucous membrane gland
has exact synonym: bowel organ mucosa gland
has exact synonym: gland of bowel mucosa
has exact synonym: gland of bowel mucosa of organ
has exact synonym: gland of bowel mucous membrane
has exact synonym: gland of bowel organ mucosa
has exact synonym: gland of intestinal mucosa
has exact synonym: gland of intestine mucosa
has exact synonym: gland of intestine mucosa of organ
has exact synonym: gland of intestine mucous membrane
has exact synonym: gland of intestine organ mucosa
has exact synonym: gland of mucosa of bowel
has exact synonym: gland of mucosa of intestine
has exact synonym: gland of mucosa of organ of bowel
has exact synonym: gland of mucosa of organ of intestine
has exact synonym: gland of mucous membrane of bowel
has exact synonym: gland of mucous membrane of intestine
has exact synonym: gland of organ mucosa of bowel
has exact synonym: gland of organ mucosa of intestine
has exact synonym: glandula intestinalis
has exact synonym: intestinal mucosa gland
has exact synonym: intestine mucosa gland
has exact synonym: intestine mucosa of organ gland
has exact synonym: intestine mucous membrane gland
has exact synonym: intestine organ mucosa gland
has exact synonym: mucosa of bowel gland
has exact synonym: mucosa of intestine gland
has exact synonym: mucosa of organ of bowel gland
has exact synonym: mucosa of organ of intestine gland
has exact synonym: mucous membrane of bowel gland
has exact synonym: mucous membrane of intestine gland
has exact synonym: organ mucosa of bowel gland
has exact synonym: organ mucosa of intestine gland
has OBO namespace: uberon
has related synonym: glandulae intestinales
id: UBERON:0000333
in subset: organ slim

Axiom
annotated source: intestinal gland
annotated property: IAO_0000115
annotated target: A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm].
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: bowel mucosa gland
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: bowel mucosa of organ gland
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: bowel mucous membrane gland
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: bowel organ mucosa gland
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: gland of bowel mucosa
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: gland of bowel mucosa of organ
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: gland of bowel mucous membrane
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: gland of bowel organ mucosa
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: gland of intestinal mucosa
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: gland of intestine mucosa
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: gland of intestine mucosa of organ
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: gland of intestine mucous membrane
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: gland of intestine organ mucosa
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: gland of mucosa of bowel
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: gland of mucosa of intestine
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: gland of mucosa of organ of bowel
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: gland of mucosa of organ of intestine
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: gland of mucous membrane of bowel
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: gland of mucous membrane of intestine
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: gland of organ mucosa of bowel
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: gland of organ mucosa of intestine
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: glandula intestinalis
has db xref: FMA:15052

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: intestinal mucosa gland
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: intestine mucosa gland
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: intestine mucosa of organ gland
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: intestine mucous membrane gland
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: intestine organ mucosa gland
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: mucosa of bowel gland
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: mucosa of intestine gland
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: mucosa of organ of bowel gland
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: mucosa of organ of intestine gland
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: mucous membrane of bowel gland
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: mucous membrane of intestine gland
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: organ mucosa of bowel gland
has db xref: OBOL:automatic

Axiom
annotated source: intestinal gland
annotated property: hasExactSynonym
annotated target: organ mucosa of intestine gland
has db xref: OBOL:automatic

mucosa
type: Class
subclass of: UBERON_0004923
subclass of: Restriction
  on property: BFO_0000051
  some values from: epithelium
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0002384
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7711
IAO_0000115: A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP].
RO_0002171: submucosa
UBPROP_0000007: mucosal
UBPROP_0000012: FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately
has db xref: AEO:0000199
has db xref: BTO:0000886
has db xref: CALOHA:TS-2031
has db xref: EHDAA2_RETIRED:0003234
has db xref: EV:0100382
has db xref: FMA:85355
has db xref: FMA:85358
has db xref: GAID:297
has db xref: MESH:D009092
has db xref: NCIT:C13166
has db xref: SCTID:361693009
has db xref: UMLS:C0026724
has db xref: Wikipedia:Mucous_membrane
has db xref: galen:Mucosa
has exact synonym: mucosa of organ
has exact synonym: mucosa of organ part
has exact synonym: mucosal region
has exact synonym: mucous membrane
has exact synonym: organ mucosa
has OBO namespace: uberon
has related synonym: region of mucosa
has related synonym: tunica mucosa
id: UBERON:0000344
in subset: pheno slim

Axiom
annotated source: mucosa
annotated property: IAO_0000115
annotated target: A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP].
has db xref: Wikipedia:Mucous_membrane

Axiom
annotated source: mucosa
annotated property: UBPROP_0000012
annotated target: FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately
external ontology: FMA

Axiom
annotated source: mucosa
annotated property: hasDbXref
annotated target: UMLS:C0026724
source: ncithesaurus:Mucosa

Axiom
annotated source: mucosa
annotated property: hasExactSynonym
annotated target: mucosa of organ
has db xref: FMA:85355

Axiom
annotated source: mucosa
annotated property: hasExactSynonym
annotated target: mucosa of organ part
has db xref: FMA:85358

Axiom
annotated source: mucosa
annotated property: hasExactSynonym
annotated target: mucosal region
has db xref: FMA:85358

Axiom
annotated source: mucosa
annotated property: hasExactSynonym
annotated target: mucous membrane
has db xref: FMA:85355

Axiom
annotated source: mucosa
annotated property: hasExactSynonym
annotated target: organ mucosa
has db xref: FMA:85355

Axiom
annotated source: mucosa
annotated property: hasRelatedSynonym
annotated target: region of mucosa
has db xref: FMA:85358

Axiom
annotated source: mucosa
annotated property: hasRelatedSynonym
annotated target: tunica mucosa
has db xref: BTO:0000886
has db xref: Wikipedia:Mucous_membrane
has synonym type: OMO_0003011

ophthalmic nerve
type: Class
subclass of: UBERON_0004121
subclass of: UBERON_0011779
subclass of: Restriction
  on property: RO_0002134
  some values from: UBERON_1000021
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0035597
IAO_0000115: The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the orbit and its contents, the nasal cavity and the skin of the nose and forehead.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Sensory medial ramus of the trigeminal nerve.[AAO]
UBPROP_0000003: The profundus nerve is a distinct nerve only in fishes. (...) In mammals, the profundus nerve is the same as the most rostral (ophthalmic) branch of the trigeminal nerve.[well established][VHOG]
has db xref: AAO:0010648
has db xref: BTO:0000926
has db xref: EHDAA2:0002088
has db xref: EHDAA:3744
has db xref: EMAPA:17800
has db xref: FMA:52621
has db xref: GAID:837
has db xref: MA:0001104
has db xref: MESH:D009882
has db xref: NCIT:C33215
has db xref: SCTID:280210000
has db xref: UMLS:C0029082
has db xref: VHOG:0001349
has db xref: Wikipedia:Ophthalmic_nerve
has exact synonym: cranial nerve V, branch V1
has exact synonym: first branch of fifth cranial nerve
has exact synonym: first division of fifth cranial nerve
has exact synonym: first division of trigeminal nerve
has exact synonym: nervus ophthalmicus (V1)
has exact synonym: nervus ophthalmicus (Va)
has exact synonym: nervus ophthalmicus [v1]
has exact synonym: nervus ophthalmicus [va]
has exact synonym: ophthalmic division [V1]
has exact synonym: ophthalmic division [Va]
has exact synonym: ophthalmic division of fifth cranial nerve
has exact synonym: ophthalmic division of trigeminal nerve (V1)
has exact synonym: ophthalmic division of trigeminal nerve (Va)
has exact synonym: ophthalmic nerve [V1]
has exact synonym: ophthalmic nerve [Va]
has exact synonym: opthalmic nerve
has exact synonym: ramus opthalmicus profundus (ramus V1)
has exact synonym: rostral branch of trigeminal nerve
has exact synonym: trigeminal V nerve ophthalmic division
has OBO namespace: uberon
has related synonym: ciliary nerve
has related synonym: ethmoidal nerve
has related synonym: ophthalmic division
has related synonym: profundal nerve
has related synonym: profundus
has related synonym: profundus nerve
has related synonym: trigeminal nerve ophthalmic division
id: UBERON:0000348
in subset: human reference atlas
in subset: pheno slim
comment: Terminology notes. This nerve is known by a ridiculous number of names[http://palaeos.com/vertebrates/glossary/glossaryPo.html]

Axiom
annotated source: ophthalmic nerve
annotated property: subClassOf
annotated target: Restriction
notes: may be a distinct nerve in teleosts
source: multiple

Axiom
annotated source: ophthalmic nerve
annotated property: IAO_0000115
annotated target: The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the orbit and its contents, the nasal cavity and the skin of the nose and forehead.
has db xref: MP:0009798
has db xref: Wikipedia:Ophthalmic_nerve

Axiom
annotated source: ophthalmic nerve
annotated property: UBPROP_0000001
annotated target: Sensory medial ramus of the trigeminal nerve.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010648
ontology: AAO
source: AAO:EJS

Axiom
annotated source: ophthalmic nerve
annotated property: UBPROP_0000003
annotated target: The profundus nerve is a distinct nerve only in fishes. (...) In mammals, the profundus nerve is the same as the most rostral (ophthalmic) branch of the trigeminal nerve.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001349
ontology: VHOG
source: ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.177
source: http://bgee.unil.ch/

Axiom
annotated source: ophthalmic nerve
annotated property: hasDbXref
annotated target: UMLS:C0029082
source: ncithesaurus:Ophthalmic_Nerve

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: cranial nerve V, branch V1
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: first branch of fifth cranial nerve
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: first division of fifth cranial nerve
has db xref: FMA:52621

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: first division of trigeminal nerve
has db xref: FMA:52621

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: nervus ophthalmicus (V1)
has db xref: FMA:52621

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: nervus ophthalmicus (Va)
has db xref: FMA:52621

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: nervus ophthalmicus [v1]
has db xref: FMA:52621
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: nervus ophthalmicus [va]
has db xref: FMA:52621
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: ophthalmic division [V1]
has db xref: FMA:52621

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: ophthalmic division [Va]
has db xref: FMA:52621

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: ophthalmic division of fifth cranial nerve
has db xref: FMA:52621

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: ophthalmic division of trigeminal nerve (V1)
has db xref: FMA:52621

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: ophthalmic division of trigeminal nerve (Va)
has db xref: FMA:52621

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: ophthalmic nerve [V1]
has db xref: FMA:52621

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: ophthalmic nerve [Va]
has db xref: FMA:52621

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: opthalmic nerve
has db xref: Wikipedia:Ophthalmic_nerve

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: ramus opthalmicus profundus (ramus V1)
has db xref: AAO:0010648

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: rostral branch of trigeminal nerve
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: ophthalmic nerve
annotated property: hasExactSynonym
annotated target: trigeminal V nerve ophthalmic division
has db xref: MA:0001104

Axiom
annotated source: ophthalmic nerve
annotated property: hasRelatedSynonym
annotated target: ciliary nerve
has db xref: http://palaeos.com/vertebrates/glossary/glossaryPo.html

Axiom
annotated source: ophthalmic nerve
annotated property: hasRelatedSynonym
annotated target: ethmoidal nerve
has db xref: Wikipedia:Ophthalmic_nerve

Axiom
annotated source: ophthalmic nerve
annotated property: hasRelatedSynonym
annotated target: ophthalmic division
has db xref: BTO:0000926
has db xref: Wikipedia:Ophthalmic_nerve

Axiom
annotated source: ophthalmic nerve
annotated property: hasRelatedSynonym
annotated target: profundal nerve
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: ophthalmic nerve
annotated property: hasRelatedSynonym
annotated target: profundus
has db xref: http://palaeos.com/vertebrates/glossary/glossaryPo.html

Axiom
annotated source: ophthalmic nerve
annotated property: hasRelatedSynonym
annotated target: profundus nerve
has db xref: http://palaeos.com/vertebrates/glossary/glossaryPo.html

Axiom
annotated source: ophthalmic nerve
annotated property: hasRelatedSynonym
annotated target: trigeminal nerve ophthalmic division
has db xref: EMAPA:17800

limbic system
type: Class
subclass of: UBERON_0011216
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001890
IAO_0000115: A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex].
IAO_0000116: obsoletion proposes. The current part_of children were chosen as the intersection of what is stated in wikipedia and in the FMA. NIF: We are including Limbic System because it is still used by neuroscientists and others, but as a data annotation term, it is very poor because it is not a clearly defined entity.
has db xref: BTO:0000928
has db xref: CALOHA:TS-1307
has db xref: FMA:242000
has db xref: GAID:615
has db xref: MESH:D008032
has db xref: NCIT:C94541
has db xref: SCTID:361342009
has db xref: UMLS:C0023715
has db xref: Wikipedia:Limbic_system
has db xref: neuronames:2055
has OBO namespace: uberon
has related synonym: visceral brain
id: UBERON:0000349
in subset: non informative
in subset: pheno slim
comment: includes the hippocampus, amygdala, anterior thalamic nuclei, and limbic cortex, which support a variety of functions including emotion, behavior, long term memory, and olfaction [Wikipedia]

Axiom
annotated source: limbic system
annotated property: IAO_0000115
annotated target: A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex].
has db xref: BIRNLEX:Limbic_system
has db xref: Wikipedia:Limbic_system

Axiom
annotated source: limbic system
annotated property: hasDbXref
annotated target: UMLS:C0023715
source: ncithesaurus:Limbic_System

Axiom
annotated source: limbic system
annotated property: hasRelatedSynonym
annotated target: visceral brain
has db xref: ISBN:0123813611

nuchal ligament
type: Class
subclass of: UBERON_0005174
subclass of: UBERON_0008846
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002371
  some values from: UBERON_0001676
IAO_0000115: A fibrous membrane, which, in the neck, represents the supraspinal ligaments of the upper vertebrae.
RO_0002161: NCBITaxon 9596
RO_0002175: NCBITaxon 9606
RO_0002175: NCBITaxon 9608
RO_0002175: NCBITaxon 9788
RO_0002175: NCBITaxon 9895
UBPROP_0000008: In humans it is a tendon-like structure that has developed independently in humans and other animals well adapted for running. In some four legged animals, particularly ungulates, the nuchal ligament serves to sustain the weight of the head
UBPROP_0000009: As it is required for running, not all animals have a nuchal ligament
has db xref: BTO:0000952
has db xref: EMAPA:19207
has db xref: FMA:13427
has db xref: SCTID:166962007
has db xref: Wikipedia:Nuchal_ligament
has exact synonym: ligament of neck
has exact synonym: ligamentum nuchae
has narrow synonym: paddywhack
has OBO namespace: uberon
has related synonym: paxwax
id: UBERON:0000351

Axiom
annotated source: nuchal ligament
annotated property: subClassOf
annotated target: Restriction
source: BTO

Axiom
annotated source: nuchal ligament
annotated property: subClassOf
annotated target: Restriction
notes: C7 in humans

Axiom
annotated source: nuchal ligament
annotated property: IAO_0000115
annotated target: A fibrous membrane, which, in the neck, represents the supraspinal ligaments of the upper vertebrae.
has db xref: Wikipedia:Nuchal_ligament

Axiom
annotated source: nuchal ligament
annotated property: hasExactSynonym
annotated target: ligament of neck
has db xref: FMA:13427

Axiom
annotated source: nuchal ligament
annotated property: hasExactSynonym
annotated target: ligamentum nuchae
has db xref: FMA:13427
has synonym type: OMO_0003011

Axiom
annotated source: nuchal ligament
annotated property: hasNarrowSynonym
annotated target: paddywhack
has db xref: NCBITaxon:9895
has db xref: Wikipedia:Paddywhack

parenchyma
type: Class
subclass of: organ part
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6072
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032501
disjoint with: UBERON_0003891
IAO_0000115: Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues.
UBPROP_0000007: parenchymal
UBPROP_0000011: Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin
UBPROP_0000012: the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated
has db xref: BTO:0000999
has db xref: BTO:0001539
has db xref: EHDAA:3015
has db xref: EHDAA:3905
has db xref: EHDAA:3999
has db xref: EHDAA:4005
has db xref: EHDAA:6899
has db xref: EHDAA:6903
has db xref: EHDAA:6994
has db xref: EHDAA:8086
has db xref: EHDAA:9182
has db xref: EHDAA:9190
has db xref: EHDAA:9196
has db xref: EHDAA:9202
has db xref: FMA:45732
has db xref: NCIT:C74601
has db xref: UMLS:C0933845
has db xref: Wikipedia:Parenchyma
has OBO namespace: uberon
id: UBERON:0000353

Axiom
annotated source: parenchyma
annotated property: IAO_0000115
annotated target: Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues.
has db xref: Wikipedia:Parenchyma

Axiom
annotated source: parenchyma
annotated property: UBPROP_0000011
annotated target: Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin
source: WP

Axiom
annotated source: parenchyma
annotated property: UBPROP_0000012
annotated target: the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated
external ontology: FMA

Axiom
annotated source: parenchyma
annotated property: hasDbXref
annotated target: BTO:0000999
author id: https://orcid.org/0000-0003-4423-4370
mapping justification: ManualMappingCuration
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: parenchyma
annotated property: hasDbXref
annotated target: BTO:0001539
author id: https://orcid.org/0000-0003-4423-4370
mapping justification: ManualMappingCuration
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: parenchyma
annotated property: hasDbXref
annotated target: UMLS:C0933845
source: ncithesaurus:Parenchyma

pharyngeal mucosa
type: Class
equivalent class: Class
  intersection of: mucosa
  intersection of: Restriction
    on property: BFO_0000050
    some values from: chordate pharynx
subclass of: UBERON_0004785
subclass of: Restriction
  on property: BFO_0000050
  some values from: chordate pharynx
IAO_0000115: A mucosa that is part of a pharynx [Automatically generated definition].
has alternative id: UBERON:0003344
has db xref: BTO:0001047
has db xref: EMAPA:26957
has db xref: FMA:55031
has db xref: MA:0003143
has db xref: SCTID:362121003
has exact synonym: mucosa of organ of pharynx
has exact synonym: mucosa of pharynx
has exact synonym: mucous membrane of pharynx
has exact synonym: organ mucosa of pharynx
has exact synonym: pharynx mucosa
has exact synonym: pharynx mucosa of organ
has exact synonym: pharynx mucous membrane
has exact synonym: pharynx organ mucosa
has exact synonym: tunica mucosa pharyngea
has exact synonym: tunica mucosa pharyngis
has OBO namespace: uberon
has related synonym: mucous membrane of the pharynx
id: UBERON:0000355

Axiom
annotated source: pharyngeal mucosa
annotated property: IAO_0000115
annotated target: A mucosa that is part of a pharynx [Automatically generated definition].
has db xref: OBOL:automatic

Axiom
annotated source: pharyngeal mucosa
annotated property: hasExactSynonym
annotated target: mucosa of organ of pharynx
has db xref: OBOL:automatic

Axiom
annotated source: pharyngeal mucosa
annotated property: hasExactSynonym
annotated target: mucosa of pharynx
has db xref: OBOL:automatic

Axiom
annotated source: pharyngeal mucosa
annotated property: hasExactSynonym
annotated target: mucous membrane of pharynx
has db xref: FMA:55031
has db xref: OBOL:automatic

Axiom
annotated source: pharyngeal mucosa
annotated property: hasExactSynonym
annotated target: organ mucosa of pharynx
has db xref: OBOL:automatic

Axiom
annotated source: pharyngeal mucosa
annotated property: hasExactSynonym
annotated target: pharynx mucosa
has db xref: OBOL:automatic

Axiom
annotated source: pharyngeal mucosa
annotated property: hasExactSynonym
annotated target: pharynx mucosa of organ
has db xref: OBOL:automatic

Axiom
annotated source: pharyngeal mucosa
annotated property: hasExactSynonym
annotated target: pharynx mucous membrane
has db xref: OBOL:automatic

Axiom
annotated source: pharyngeal mucosa
annotated property: hasExactSynonym
annotated target: pharynx organ mucosa
has db xref: OBOL:automatic

Axiom
annotated source: pharyngeal mucosa
annotated property: hasExactSynonym
annotated target: tunica mucosa pharyngea
has db xref: FMA:55031
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: pharyngeal mucosa
annotated property: hasRelatedSynonym
annotated target: mucous membrane of the pharynx
has db xref: BTO:0001047

blastocyst
type: Class
subclass of: UBERON_0002050
subclass of: Restriction
  on property: BFO_0000050
  some values from: blastula
subclass of: Restriction
  on property: BFO_0000051
  some values from: inner cell mass
subclass of: Restriction
  on property: BFO_0000051
  some values from: trophoblast
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_32525
subclass of: Restriction
  on property: RO_0002202
  some values from: morula
subclass of: Restriction
  on property: RO_0002491
  some values from: blastula stage
IAO_0000115: The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO].
IAO_0000116: Gilbert fig11.32 has blastocyst has giving rise to ICM and trophoblast (which in this source is a synonym for trophectoderm)
has db xref: BTO:0001099
has db xref: CALOHA:TS-0076
has db xref: EFO:0000295
has db xref: EMAPA:36035
has db xref: EV:0100394
has db xref: FMA:83041
has db xref: GAID:1153
has db xref: MESH:D001755
has db xref: NCIT:C13739
has db xref: SCTID:308837009
has db xref: UMLS:C1281743
has db xref: Wikipedia:Blastocyst
has OBO namespace: uberon
has related synonym: blastocystis
has related synonym: blastula
id: UBERON:0000358
in subset: efo slim

Axiom
annotated source: blastocyst
annotated property: IAO_0000115
annotated target: The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO].
has db xref: GO:0001824
has db xref: Wikipedia:Blastocyst

Axiom
annotated source: blastocyst
annotated property: hasDbXref
annotated target: UMLS:C1281743
source: ncithesaurus:Blastocyst

Axiom
annotated source: blastocyst
annotated property: hasRelatedSynonym
annotated target: blastocystis
has db xref: Wikipedia:Blastocyst
has synonym type: OMO_0003011

Axiom
annotated source: blastocyst
annotated property: hasRelatedSynonym
annotated target: blastula
has db xref: FMA:83041

red bone marrow
type: Class
equivalent class: Class
  intersection of: UBERON_0002371
  intersection of: Restriction
    on property: RO_0002473
    some values from: CL_0000988
subclass of: UBERON_0002371
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0012429
subclass of: Restriction
  on property: RO_0002473
  some values from: CL_0000988
IAO_0000115: The red vascular substance consisting of connective tissue and blood vessels, containing primitive blood cells, macrophages, megakaryocytes, and fat cells. Red marrow is found in the cavities of many bones. It manufactures and releases leukocytes and erythrocytes into the bloodstream.
has db xref: BTO:0001160
has db xref: FMA:74595
has db xref: SCTID:328538003
has db xref: SCTID:75330005
has exact synonym: medulla ossium rubra
has exact synonym: parenchymal red marrow
has exact synonym: red marrow
has OBO namespace: uberon
has related synonym: parenchyma of none marrow marrow
id: UBERON:0000361

Axiom
annotated source: red bone marrow
annotated property: IAO_0000115
annotated target: The red vascular substance consisting of connective tissue and blood vessels, containing primitive blood cells, macrophages, megakaryocytes, and fat cells. Red marrow is found in the cavities of many bones. It manufactures and releases leukocytes and erythrocytes into the bloodstream.
has db xref: http://medical-dictionary.thefreedictionary.com/red+marrow

Axiom
annotated source: red bone marrow
annotated property: hasExactSynonym
annotated target: medulla ossium rubra
has db xref: BTO:0001160
has synonym type: OMO_0003011

Axiom
annotated source: red bone marrow
annotated property: hasExactSynonym
annotated target: parenchymal red marrow
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: red bone marrow
annotated property: hasExactSynonym
annotated target: red marrow
has db xref: BTO:0001160

Axiom
annotated source: red bone marrow
annotated property: hasRelatedSynonym
annotated target: parenchyma of none marrow marrow
has db xref: http://orcid.org/0000-0002-6601-2165

renal medulla
type: Class
equivalent class: Class
  intersection of: medulla of organ
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002113
subclass of: medulla of organ
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002113
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0004200
subclass of: Restriction
  on property: RO_0002216
  some values from: GO_0070295
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0002113
IAO_0000115: The inner portion of the kidney consisting of the renal pyramids.
RO_0002175: NCBITaxon 9606
UBPROP_0000010: The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water
has db xref: BTO:0001167
has db xref: CALOHA:TS-1157
has db xref: EMAPA:19279
has db xref: GAID:425
has db xref: MA:0000373
has db xref: MESH:D007679
has db xref: NCIT:C12740
has db xref: SCTID:30737000
has db xref: UMLS:C0022664
has db xref: Wikipedia:Renal_medulla
has db xref: galen:MedullaOfKidney
has exact synonym: kidney medulla
has exact synonym: medulla of kidney
has exact synonym: medulla renalis
has exact synonym: pyramides renales
has exact synonym: renal medullae
has exact synonym: renal medullae set
has exact synonym: renal pyramids
has exact synonym: renal pyramids set
has OBO namespace: uberon
has related synonym: medullary pyramids
has related synonym: renal marrow
id: UBERON:0000362
in subset: human reference atlas
in subset: pheno slim
comment: Note that 'renal medulla' is not synonymous with 'medullary region of kidney'. The former is composed of kidney pyramids only, while the latter covers kidney pyramids and renal columns, which are histologically different.

Axiom
annotated source: renal medulla
annotated property: IAO_0000115
annotated target: The inner portion of the kidney consisting of the renal pyramids.
has db xref: ISBN:0-683-40008-8
has db xref: MGI:smb
has db xref: MP:0003014

Axiom
annotated source: renal medulla
annotated property: hasDbXref
annotated target: UMLS:C0022664
source: ncithesaurus:Renal_Medulla

Axiom
annotated source: renal medulla
annotated property: hasExactSynonym
annotated target: kidney medulla
has db xref: OBOL:automatic

Axiom
annotated source: renal medulla
annotated property: hasExactSynonym
annotated target: medulla of kidney
has db xref: OBOL:automatic

Axiom
annotated source: renal medulla
annotated property: hasExactSynonym
annotated target: medulla renalis
has db xref: FMA:74268
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: renal medulla
annotated property: hasExactSynonym
annotated target: pyramides renales
has db xref: FMA:74268
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: renal medulla
annotated property: hasExactSynonym
annotated target: renal medullae
has db xref: FMA:86327
has synonym type: OMO_0003004

Axiom
annotated source: renal medulla
annotated property: hasExactSynonym
annotated target: renal medullae set
has db xref: FMA:86327
has synonym type: OMO_0003004

Axiom
annotated source: renal medulla
annotated property: hasExactSynonym
annotated target: renal pyramids
has db xref: FMA:74268
has synonym type: OMO_0003004

Axiom
annotated source: renal medulla
annotated property: hasExactSynonym
annotated target: renal pyramids set
has db xref: FMA:74268
has synonym type: OMO_0003004

Axiom
annotated source: renal medulla
annotated property: hasRelatedSynonym
annotated target: medullary pyramids
has db xref: FMA:74268
has synonym type: OMO_0003004

Axiom
annotated source: renal medulla
annotated property: hasRelatedSynonym
annotated target: renal marrow
has db xref: BTO:0001167

urothelium
type: Class
subclass of: multilaminar epithelium
subclass of: UBERON_0005911
subclass of: Restriction
  on property: BFO_0000050
  some values from: renal system
IAO_0000115: An epithelial tissue layer that lines much of the urinary tract, including the renal pelvis, the ureters, the bladder, and parts of the urethra.
UBPROP_0000007: urothelial
has broad synonym: transitional epithelium
has db xref: BTO:0003906
has db xref: CALOHA:TS-1096
has db xref: EMAPA:37978
has db xref: FMA:63914
has db xref: FMA:67695
has db xref: GAID:935
has db xref: MESH:D019459
has db xref: NCIT:C12884
has db xref: SCTID:30117005
has db xref: SCTID:57789003
has db xref: UMLS:C0225339
has db xref: UMLS:C0227598
has db xref: Wikipedia:Transitional_epithelium
has db xref: Wikipedia:Urothelium
has exact synonym: epithelium transitionale
has exact synonym: transitional epithelium
has exact synonym: uroepithelium
has OBO namespace: uberon
id: UBERON:0000365
in subset: pheno slim

Axiom
annotated source: urothelium
annotated property: IAO_0000115
annotated target: An epithelial tissue layer that lines much of the urinary tract, including the renal pelvis, the ureters, the bladder, and parts of the urethra.
has db xref: Wikipedia:Urothelium
has db xref: https://github.com/obophenotype/uberon/issues/92

Axiom
annotated source: urothelium
annotated property: hasBroadSynonym
annotated target: transitional epithelium
has synonym type: INCONSISTENT

Axiom
annotated source: urothelium
annotated property: hasDbXref
annotated target: EMAPA:37978
source: MA:th

Axiom
annotated source: urothelium
annotated property: hasDbXref
annotated target: UMLS:C0225339
source: ncithesaurus:Transitional_Epithelium

Axiom
annotated source: urothelium
annotated property: hasDbXref
annotated target: UMLS:C0227598
source: ncithesaurus:Urothelium

Axiom
annotated source: urothelium
annotated property: hasExactSynonym
annotated target: epithelium transitionale
has db xref: FMA:63914

Axiom
annotated source: urothelium
annotated property: hasExactSynonym
annotated target: transitional epithelium
has db xref: FMA:63914
has db xref: https://github.com/obophenotype/uberon/issues/92

Axiom
annotated source: urothelium
annotated property: hasExactSynonym
annotated target: uroepithelium
has db xref: FMA:67695

corpus striatum
type: Class
subclass of: UBERON_0002616
subclass of: Restriction
IAO_0000115: The corpus striatum (striated body) is a compound structure consisting of the caudate nucleus and the lentiform nucleus, which consists of the putamen and the globus pallidus[WP].
UBPROP_0000003: Thus, certain telencephalic characters - such as the presence of a pallium divided into lateral, dorsal, and medial formations and a subpallium divided into striatum and septum - appear to characterize all vertebrates. They are primitive characters and are homologous among all vertebrates.[well established][VHOG]
UBPROP_0000013: The term has been used in a few different ways: * It is a pair of nuclear masses which form the basal ganglia, along with the subthalamic nucleus and the substantia nigra. * It may also refer to both the basal ganglia and internal capsule collectively.[2]
has alternative id: UBERON:0010082
has db xref: BAMS:CSTR
has db xref: BTO:0001311
has db xref: CALOHA:TS-0183
has db xref: EFO:0000381
has db xref: EHDAA2:0000596
has db xref: EMAPA:17549
has db xref: EV:0100184
has db xref: FMA:77616
has db xref: GAID:667
has db xref: MESH:D003342
has db xref: NCIT:C12448
has db xref: SCTID:279318005
has db xref: UMLS:C0010097
has db xref: VHOG:0001175
has db xref: Wikipedia:Corpus_striatum
has db xref: neuronames:2339
has OBO namespace: uberon
has related synonym: striate body
has related synonym: striated body
id: UBERON:0000369
in subset: efo slim
comment: * According to the 1917 version of Gray's Anatomy, it is the combination of the lentiform nucleus (also known as the lenticular nucleus) and the caudate nucleus * According to BrainInfo it is a part of the basal ganglia comprising the globus pallidus and striatum

Axiom
annotated source: corpus striatum
annotated property: subClassOf
annotated target: Restriction
source: MA

Axiom
annotated source: corpus striatum
annotated property: IAO_0000115
annotated target: The corpus striatum (striated body) is a compound structure consisting of the caudate nucleus and the lentiform nucleus, which consists of the putamen and the globus pallidus[WP].
has db xref: Wikipedia:Corpus_striatum

Axiom
annotated source: corpus striatum
annotated property: UBPROP_0000003
annotated target: Thus, certain telencephalic characters - such as the presence of a pallium divided into lateral, dorsal, and medial formations and a subpallium divided into striatum and septum - appear to characterize all vertebrates. They are primitive characters and are homologous among all vertebrates.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001175
ontology: VHOG
source: DOI:10.1146/annurev.ne.04.030181.001505, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.487 Figure 14-10
source: http://bgee.unil.ch/

Axiom
annotated source: corpus striatum
annotated property: hasDbXref
annotated target: UMLS:C0010097
source: ncithesaurus:Corpus_Striatum

Axiom
annotated source: corpus striatum
annotated property: hasRelatedSynonym
annotated target: striate body
has db xref: BTO:0001311

Axiom
annotated source: corpus striatum
annotated property: hasRelatedSynonym
annotated target: striated body
has db xref: BTO:0001311

mandibular nerve
type: Class
subclass of: UBERON_0011779
subclass of: Restriction
  on property: RO_0002380
  some values from: UBERON_0001645
IAO_0000115: The motor and sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the auricle, the external acoustic meatus, tympanic membrane, temporal region, the cheek, the skin overlying the mandible, the anterior portion of the tongue, the floor of the mouth, lower teeth and gingiva and transmits motor information from the muscles of mastication, the mylohyoid muscle and digastric muscle and the muscles tensor tympani and tensor veli palatini.
RO_0002175: NCBITaxon 9606
has db xref: AAO:0010688
has db xref: AAO:0010703
has db xref: BTO:0001375
has db xref: EHDAA2:0002086
has db xref: EMAPA:17798
has db xref: FMA:52996
has db xref: GAID:834
has db xref: MA:0001101
has db xref: MESH:D008340
has db xref: NCIT:C32779
has db xref: SCTID:280212008
has db xref: UMLS:C0024695
has db xref: VHOG:0001345
has db xref: Wikipedia:Mandibular_nerve
has exact synonym: inferior maxillary nerve
has exact synonym: mandibular division [V3]
has exact synonym: mandibular division [Vc]
has exact synonym: mandibular division of fifth cranial nerve
has exact synonym: mandibular division of trigeminal nerve [Vc; V3]
has exact synonym: mandibular nerve [V3]
has exact synonym: mandibular nerve [Vc]
has exact synonym: nervus mandibularis [Vc; V3]
has exact synonym: nervus mandibularis [v3]
has exact synonym: nervus mandibularis [vc]
has exact synonym: ramus mandibularis (ramus V3)
has exact synonym: third division of fifth cranial nerve
has exact synonym: third division of trigeminal nerve
has exact synonym: trigeminal V nerve mandibular division
has OBO namespace: uberon
has related synonym: n. mandibularis
has related synonym: nervus mandibularis
has related synonym: trigeminal nerve mandibular division
id: UBERON:0000375
in subset: human reference atlas
in subset: pheno slim

Axiom
annotated source: mandibular nerve
annotated property: IAO_0000115
annotated target: The motor and sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the auricle, the external acoustic meatus, tympanic membrane, temporal region, the cheek, the skin overlying the mandible, the anterior portion of the tongue, the floor of the mouth, lower teeth and gingiva and transmits motor information from the muscles of mastication, the mylohyoid muscle and digastric muscle and the muscles tensor tympani and tensor veli palatini.
has db xref: MP:0009800
has db xref: Wikipedia:Mandibular_nerve

Axiom
annotated source: mandibular nerve
annotated property: hasDbXref
annotated target: UMLS:C0024695
source: ncithesaurus:Inferior_Maxillary_Nerve

Axiom
annotated source: mandibular nerve
annotated property: hasExactSynonym
annotated target: inferior maxillary nerve
has db xref: FMA:52996

Axiom
annotated source: mandibular nerve
annotated property: hasExactSynonym
annotated target: mandibular division [V3]
has db xref: FMA:52996

Axiom
annotated source: mandibular nerve
annotated property: hasExactSynonym
annotated target: mandibular division [Vc]
has db xref: FMA:52996

Axiom
annotated source: mandibular nerve
annotated property: hasExactSynonym
annotated target: mandibular division of fifth cranial nerve
has db xref: FMA:52996

Axiom
annotated source: mandibular nerve
annotated property: hasExactSynonym
annotated target: mandibular division of trigeminal nerve [Vc; V3]
has db xref: FMA:52996

Axiom
annotated source: mandibular nerve
annotated property: hasExactSynonym
annotated target: mandibular nerve [V3]
has db xref: FMA:52996

Axiom
annotated source: mandibular nerve
annotated property: hasExactSynonym
annotated target: mandibular nerve [Vc]
has db xref: FMA:52996

Axiom
annotated source: mandibular nerve
annotated property: hasExactSynonym
annotated target: nervus mandibularis [Vc; V3]
has db xref: FMA:52996

Axiom
annotated source: mandibular nerve
annotated property: hasExactSynonym
annotated target: nervus mandibularis [v3]
has db xref: FMA:52996
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: mandibular nerve
annotated property: hasExactSynonym
annotated target: nervus mandibularis [vc]
has db xref: FMA:52996
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: mandibular nerve
annotated property: hasExactSynonym
annotated target: ramus mandibularis (ramus V3)
has db xref: AAO:0010688

Axiom
annotated source: mandibular nerve
annotated property: hasExactSynonym
annotated target: third division of fifth cranial nerve
has db xref: FMA:52996

Axiom
annotated source: mandibular nerve
annotated property: hasExactSynonym
annotated target: third division of trigeminal nerve
has db xref: FMA:52996

Axiom
annotated source: mandibular nerve
annotated property: hasExactSynonym
annotated target: trigeminal V nerve mandibular division
has db xref: MA:0001101

Axiom
annotated source: mandibular nerve
annotated property: hasRelatedSynonym
annotated target: n. mandibularis
has db xref: Wikipedia:Mandibular_nerve
has synonym type: OMO_0003011

Axiom
annotated source: mandibular nerve
annotated property: hasRelatedSynonym
annotated target: nervus mandibularis
has db xref: BTO:0001375

Axiom
annotated source: mandibular nerve
annotated property: hasRelatedSynonym
annotated target: trigeminal nerve mandibular division
has db xref: EMAPA:17798

hindlimb stylopod
type: Class
equivalent class: Class
  intersection of: UBERON_0002472
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002103
subclass of: UBERON_0002472
subclass of: UBERON_0008784
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0002103
subclass of: Restriction
  on property: RO_0002551
  some values from: UBERON_0015052
IAO_0000115: The part of the hindlimb between pelvis and the knee, corresponding to the femur.
UBPROP_0000003: Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
UBPROP_0000013: Naming conventions for pod terms under discussion within phenoscape group.
has db xref: BTO:0001376
has db xref: CALOHA:TS-2039
has db xref: EFO:0001943
has db xref: EHDAA2:0002130
has db xref: EHDAA:5171
has db xref: EHDAA:6200
has db xref: EMAPA:17499
has db xref: FMA:24967
has db xref: GAID:50
has db xref: MA:0000052
has db xref: MESH:D013848
has db xref: NCIT:C33763
has db xref: SCTID:302544002
has db xref: UMLS:C0039866
has db xref: VHOG:0000349
has db xref: Wikipedia:Thigh
has db xref: galen:Thigh
has exact synonym: hind limb stylopod
has exact synonym: hind limb stylopodium
has exact synonym: hind propodium
has exact synonym: hindlimb propodium
has exact synonym: hindlimb stylopod
has exact synonym: hindlimb stylopodium
has exact synonym: proximal segment of free lower limb
has exact synonym: stylopod of hind limb
has exact synonym: stylopod of hindlimb
has exact synonym: stylopod of lower limb
has exact synonym: thigh
has exact synonym: upper leg
has OBO namespace: uberon
has related synonym: femur
id: UBERON:0000376
in subset: efo slim
in subset: pheno slim

Axiom
annotated source: hindlimb stylopod
annotated property: subClassOf
annotated target: Restriction
source: MA

Axiom
annotated source: hindlimb stylopod
annotated property: IAO_0000115
annotated target: The part of the hindlimb between pelvis and the knee, corresponding to the femur.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: hindlimb stylopod
annotated property: UBPROP_0000003
annotated target: Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000349
ontology: VHOG
source: ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268
source: http://bgee.unil.ch/

Axiom
annotated source: hindlimb stylopod
annotated property: UBPROP_0000013
annotated target: Naming conventions for pod terms under discussion within phenoscape group.

Axiom
annotated source: hindlimb stylopod
annotated property: hasDbXref
annotated target: UMLS:C0039866
source: ncithesaurus:Thigh

Axiom
annotated source: hindlimb stylopod
annotated property: hasExactSynonym
annotated target: hind limb stylopod
has db xref: OBOL:automatic

Axiom
annotated source: hindlimb stylopod
annotated property: hasExactSynonym
annotated target: hind limb stylopodium
has db xref: VHOG:0000349

Axiom
annotated source: hindlimb stylopod
annotated property: hasExactSynonym
annotated target: hind propodium
has db xref: AAO:0000887

Axiom
annotated source: hindlimb stylopod
annotated property: hasExactSynonym
annotated target: hindlimb propodium
has db xref: AAO:0000887

Axiom
annotated source: hindlimb stylopod
annotated property: hasExactSynonym
annotated target: hindlimb stylopod
has db xref: OBOL:automatic

Axiom
annotated source: hindlimb stylopod
annotated property: hasExactSynonym
annotated target: hindlimb stylopodium
has db xref: OBOL:automatic

Axiom
annotated source: hindlimb stylopod
annotated property: hasExactSynonym
annotated target: proximal segment of free lower limb
has db xref: FMA:24967

Axiom
annotated source: hindlimb stylopod
annotated property: hasExactSynonym
annotated target: stylopod of hind limb
has db xref: OBOL:automatic

Axiom
annotated source: hindlimb stylopod
annotated property: hasExactSynonym
annotated target: stylopod of hindlimb
has db xref: OBOL:automatic

Axiom
annotated source: hindlimb stylopod
annotated property: hasExactSynonym
annotated target: upper leg
has db xref: MA:0000052
has synonym type: HUMAN PREFERRED

Axiom
annotated source: hindlimb stylopod
annotated property: hasRelatedSynonym
annotated target: femur
has db xref: Wikipedia:Thigh
has synonym type: OMO_0003011

maxillary nerve
type: Class
subclass of: UBERON_0011779
subclass of: Restriction
  on property: RO_0002380
  some values from: UBERON_0001645
IAO_0000115: The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Medial ramus (sensory) of the trigeminal nerve.[AAO]
UBPROP_0000002: relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO]
has db xref: AAO:0010670
has db xref: BTO:0001378
has db xref: EHDAA2:0002087
has db xref: EMAPA:17799
has db xref: FMA:52724
has db xref: GAID:836
has db xref: MA:0001103
has db xref: MESH:D008442
has db xref: SCTID:280211001
has db xref: VHOG:0001346
has db xref: Wikipedia:Maxillary_nerve
has exact synonym: maxillary division [V2]
has exact synonym: maxillary division [Vb]
has exact synonym: maxillary division of fifth cranial nerve
has exact synonym: maxillary division of trigeminal nerve (Vb; V2)
has exact synonym: maxillary nerve [V2]
has exact synonym: maxillary nerve [Vb]
has exact synonym: nervus maxillaris (Vb; V2)
has exact synonym: nervus maxillaris [v2]
has exact synonym: nervus maxillaris [vb]
has exact synonym: ramus maxillaris (ramus V2)
has exact synonym: second division of fifth cranial nerve
has exact synonym: second division of trigeminal nerve
has exact synonym: trigeminal V nerve maxillary division
has OBO namespace: uberon
has related synonym: n. maxillaris
has related synonym: nervus maxillaris
has related synonym: trigeminal nerve maxillary division
id: UBERON:0000377
in subset: human reference atlas
in subset: pheno slim

Axiom
annotated source: maxillary nerve
annotated property: IAO_0000115
annotated target: The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses.
has db xref: MP:0009799
has db xref: Wikipedia:Maxillary_nerve

Axiom
annotated source: maxillary nerve
annotated property: UBPROP_0000001
annotated target: Medial ramus (sensory) of the trigeminal nerve.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010670
ontology: AAO
source: AAO:EJS

Axiom
annotated source: maxillary nerve
annotated property: UBPROP_0000002
annotated target: relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO]
date retrieved: 2012-06-20
external class: AAO:0010670
ontology: AAO

Axiom
annotated source: maxillary nerve
annotated property: hasExactSynonym
annotated target: maxillary division [V2]
has db xref: FMA:52724

Axiom
annotated source: maxillary nerve
annotated property: hasExactSynonym
annotated target: maxillary division [Vb]
has db xref: FMA:52724

Axiom
annotated source: maxillary nerve
annotated property: hasExactSynonym
annotated target: maxillary division of fifth cranial nerve
has db xref: FMA:52724

Axiom
annotated source: maxillary nerve
annotated property: hasExactSynonym
annotated target: maxillary division of trigeminal nerve (Vb; V2)
has db xref: FMA:52724

Axiom
annotated source: maxillary nerve
annotated property: hasExactSynonym
annotated target: maxillary nerve [V2]
has db xref: FMA:52724

Axiom
annotated source: maxillary nerve
annotated property: hasExactSynonym
annotated target: maxillary nerve [Vb]
has db xref: FMA:52724

Axiom
annotated source: maxillary nerve
annotated property: hasExactSynonym
annotated target: nervus maxillaris (Vb; V2)
has db xref: FMA:52724

Axiom
annotated source: maxillary nerve
annotated property: hasExactSynonym
annotated target: nervus maxillaris [v2]
has db xref: FMA:52724
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: maxillary nerve
annotated property: hasExactSynonym
annotated target: nervus maxillaris [vb]
has db xref: FMA:52724
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: maxillary nerve
annotated property: hasExactSynonym
annotated target: ramus maxillaris (ramus V2)
has db xref: AAO:0010670

Axiom
annotated source: maxillary nerve
annotated property: hasExactSynonym
annotated target: second division of fifth cranial nerve
has db xref: FMA:52724

Axiom
annotated source: maxillary nerve
annotated property: hasExactSynonym
annotated target: second division of trigeminal nerve
has db xref: FMA:52724

Axiom
annotated source: maxillary nerve
annotated property: hasExactSynonym
annotated target: trigeminal V nerve maxillary division
has db xref: MA:0001103

Axiom
annotated source: maxillary nerve
annotated property: hasRelatedSynonym
annotated target: n. maxillaris
has db xref: Wikipedia:Maxillary_nerve
has synonym type: OMO_0003011

Axiom
annotated source: maxillary nerve
annotated property: hasRelatedSynonym
annotated target: nervus maxillaris
has db xref: BTO:0001378

Axiom
annotated source: maxillary nerve
annotated property: hasRelatedSynonym
annotated target: trigeminal nerve maxillary division
has db xref: EMAPA:17799

tongue muscle
type: Class
equivalent class: Class
  intersection of: UBERON_0014892
  intersection of: Restriction
    on property: RO_0002177
    some values from: UBERON_0001723
equivalent class: Class
  union of: UBERON_0001575
  union of: UBERON_0001576
subclass of: UBERON_0013765
subclass of: UBERON_0014892
subclass of: Restriction
  on property: BFO_0000050
  some values from: mouth
subclass of: Restriction
  on property: RO_0002177
  some values from: UBERON_0001723
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0001723
IAO_0000115: The muscular portion of the tongue.
UBPROP_0000003: The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG]
has db xref: BTO:0001386
has db xref: EHDAA2:0002065
has db xref: EHDAA:9146
has db xref: EMAPA:17883
has db xref: FMA:46689
has db xref: MA:0001596
has db xref: NCIT:C49301
has db xref: NCIT:C52707
has db xref: SCTID:244781004
has db xref: UMLS:C0448325
has db xref: UMLS:C1710437
has db xref: VHOG:0001390
has db xref: Wikipedia:Muscles_of_tongue
has exact synonym: muscle of tongue
has exact synonym: muscle organ of tongue
has exact synonym: skeletal muscle tissue of tongue
has exact synonym: tongue skeletal muscle
has exact synonym: tongue skeletal muscle tissue
has OBO namespace: uberon
has related synonym: musculi linguae
id: UBERON:0000378
in subset: pheno slim

Axiom
annotated source: tongue muscle
annotated property: subClassOf
annotated target: UBERON_0014892
source: FEED:rd

Axiom
annotated source: tongue muscle
annotated property: subClassOf
annotated target: Restriction
source: FEED:rd
source: ISBN:1607950324

Axiom
annotated source: tongue muscle
annotated property: IAO_0000115
annotated target: The muscular portion of the tongue.
has db xref: MP:0004136
has db xref: Wikipedia:Muscles_of_tongue

Axiom
annotated source: tongue muscle
annotated property: UBPROP_0000003
annotated target: The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001390
ontology: VHOG
source: DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005)
source: http://bgee.unil.ch/

Axiom
annotated source: tongue muscle
annotated property: hasDbXref
annotated target: UMLS:C0448325
source: ncithesaurus:Tongue_Muscle

Axiom
annotated source: tongue muscle
annotated property: hasDbXref
annotated target: UMLS:C1710437
source: ncithesaurus:Tongue_Skeletal_Muscle_Tissue

Axiom
annotated source: tongue muscle
annotated property: hasExactSynonym
annotated target: muscle of tongue
has db xref: FMA:46689

Axiom
annotated source: tongue muscle
annotated property: hasExactSynonym
annotated target: muscle organ of tongue
has db xref: OBOL:accepted

Axiom
annotated source: tongue muscle
annotated property: hasExactSynonym
annotated target: skeletal muscle tissue of tongue
has db xref: OBOL:automatic

Axiom
annotated source: tongue muscle
annotated property: hasExactSynonym
annotated target: tongue skeletal muscle
has db xref: OBOL:automatic

Axiom
annotated source: tongue muscle
annotated property: hasExactSynonym
annotated target: tongue skeletal muscle tissue
has db xref: OBOL:automatic

Axiom
annotated source: tongue muscle
annotated property: hasRelatedSynonym
annotated target: musculi linguae
has db xref: Wikipedia:Muscles_of_tongue
has synonym type: OMO_0003011

tracheal mucosa
type: Class
equivalent class: Class
  intersection of: mucosa
  intersection of: Restriction
    on property: BFO_0000050
    some values from: respiratory airway
subclass of: UBERON_0004785
subclass of: Restriction
  on property: BFO_0000050
  some values from: respiratory airway
IAO_0000115: A mucosa that is part of a respiratory airway.
has db xref: BTO:0001390
has db xref: FMA:7471
has db xref: SCTID:660006
has exact synonym: mucosa of organ of trachea
has exact synonym: mucosa of organ of windpipe
has exact synonym: mucosa of trachea
has exact synonym: mucosa of windpipe
has exact synonym: mucous membrane of trachea
has exact synonym: mucous membrane of windpipe
has exact synonym: organ mucosa of trachea
has exact synonym: organ mucosa of windpipe
has exact synonym: trachea mucosa
has exact synonym: trachea mucosa of organ
has exact synonym: trachea mucous membrane
has exact synonym: trachea organ mucosa
has exact synonym: tracheal mucous membrane
has exact synonym: tunica mucosa (tracheae)
has exact synonym: tunica mucosa tracheae
has exact synonym: windpipe mucosa
has exact synonym: windpipe mucosa of organ
has exact synonym: windpipe mucous membrane
has exact synonym: windpipe organ mucosa
has OBO namespace: uberon
id: UBERON:0000379

Axiom
annotated source: tracheal mucosa
annotated property: IAO_0000115
annotated target: A mucosa that is part of a respiratory airway.
has db xref: OBOL:automatic

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: mucosa of organ of trachea
has db xref: OBOL:automatic

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: mucosa of organ of windpipe
has db xref: OBOL:automatic

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: mucosa of trachea
has db xref: OBOL:automatic

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: mucosa of windpipe
has db xref: OBOL:automatic

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: mucous membrane of trachea
has db xref: FMA:7471
has db xref: OBOL:automatic

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: mucous membrane of windpipe
has db xref: OBOL:automatic

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: organ mucosa of trachea
has db xref: OBOL:automatic

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: organ mucosa of windpipe
has db xref: OBOL:automatic

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: trachea mucosa
has db xref: OBOL:automatic

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: trachea mucosa of organ
has db xref: OBOL:automatic

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: trachea mucous membrane
has db xref: OBOL:automatic

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: trachea organ mucosa
has db xref: OBOL:automatic

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: tracheal mucous membrane
has db xref: FMA:7471

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: tunica mucosa (tracheae)
has db xref: FMA:7471

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: tunica mucosa tracheae
has db xref: FMA:7471
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: windpipe mucosa
has db xref: OBOL:automatic

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: windpipe mucosa of organ
has db xref: OBOL:automatic

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: windpipe mucous membrane
has db xref: OBOL:automatic

Axiom
annotated source: tracheal mucosa
annotated property: hasExactSynonym
annotated target: windpipe organ mucosa
has db xref: OBOL:automatic

apocrine sweat gland
type: Class
subclass of: UBERON_0001820
subclass of: UBERON_0012177
IAO_0000115: Apocrine sweat glands are sweat glands composed of a coiled secretory portion located at the junction of the dermis and subcutaneous fat, from which a straight portion inserts and secretes into the infundibular portion of the hair follicle. The ducts of apocrine glands open into the canals of hair follicles. The stimulus for the secretion of apocrine sweat glands is adrenaline, which is a hormone carried in the blood[WP].
RO_0002161: NCBITaxon 9822
UBPROP_0000008: In humans, apocrine sweat glands are found only in certain locations of the body: the axillae (armpits), the areola of the nipples, and the genitoanal region.
has db xref: BTO:0001458
has db xref: EMAPA:37426
has db xref: FMA:59155
has db xref: MESH:D001050
has db xref: NCIT:C32132
has db xref: SCTID:399916008
has db xref: UMLS:C0930083
has db xref: Wikipedia:Apocrine_sweat_gland
has exact synonym: glandula sudorifera apocrina
has OBO namespace: uberon
id: UBERON:0000382
in subset: organ slim
in subset: pheno slim

Axiom
annotated source: apocrine sweat gland
annotated property: subClassOf
annotated target: UBERON_0001820
source: FMA

Axiom
annotated source: apocrine sweat gland
annotated property: IAO_0000115
annotated target: Apocrine sweat glands are sweat glands composed of a coiled secretory portion located at the junction of the dermis and subcutaneous fat, from which a straight portion inserts and secretes into the infundibular portion of the hair follicle. The ducts of apocrine glands open into the canals of hair follicles. The stimulus for the secretion of apocrine sweat glands is adrenaline, which is a hormone carried in the blood[WP].
has db xref: PMID:18489347
has db xref: Wikipedia:Apocrine_sweat_gland

Axiom
annotated source: apocrine sweat gland
annotated property: hasDbXref
annotated target: EMAPA:37426
source: MA:th

Axiom
annotated source: apocrine sweat gland
annotated property: hasDbXref
annotated target: UMLS:C0930083
source: ncithesaurus:Apocrine_Sweat_Gland

Axiom
annotated source: apocrine sweat gland
annotated property: hasExactSynonym
annotated target: glandula sudorifera apocrina
has db xref: Wikipedia:Apocrine_sweat_gland
has synonym type: OMO_0003011

musculature of body
type: Class
equivalent class: Class
  intersection of: UBERON_0011216
  intersection of: Restriction
    on property: RO_0002473
    some values from: musculature
subclass of: UBERON_0011216
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6072
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0003012
subclass of: Restriction
  on property: RO_0002473
  some values from: musculature
IAO_0000115: The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].
IAO_0000116: consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77
RO_0002161: NCBITaxon 6040
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Anatomical system that consists of the muscles of the body.[VSAO]
UBPROP_0000012: we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA
has db xref: AAO:0000307
has db xref: BILA:0000088
has db xref: BTO:0001369
has db xref: BTO:0001485
has db xref: EFO:0000801
has db xref: FMA:72954
has db xref: MA:0002888
has db xref: MAT:0000025
has db xref: MIAA:0000025
has db xref: VSAO:0000033
has db xref: XAO:0004042
has exact synonym: muscle system
has exact synonym: muscle system of body
has exact synonym: muscular system
has exact synonym: musculature system
has exact synonym: set of all muscles
has exact synonym: set of muscles of body
has exact synonym: vertebrate muscular system
has OBO namespace: uberon
has related synonym: muskelsystem
id: UBERON:0000383
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim

Axiom
annotated source: musculature of body
annotated property: IAO_0000115
annotated target: The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].
has db xref: VSAO:0000033

Axiom
annotated source: musculature of body
annotated property: UBPROP_0000001
annotated target: Anatomical system that consists of the muscles of the body.[VSAO]
date retrieved: 2012-08-14
external class: VSAO:0000033
ontology: VSAO
source: VSAO:curator

Axiom
annotated source: musculature of body
annotated property: UBPROP_0000012
annotated target: we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA
external ontology: MA

Axiom
annotated source: musculature of body
annotated property: hasExactSynonym
annotated target: muscular system
has db xref: FMA:72954

Axiom
annotated source: musculature of body
annotated property: hasExactSynonym
annotated target: musculature system
has db xref: BILA:0000088

Axiom
annotated source: musculature of body
annotated property: hasExactSynonym
annotated target: set of all muscles
has db xref: FMA:72954

Axiom
annotated source: musculature of body
annotated property: hasExactSynonym
annotated target: set of muscles of body
has db xref: FMA:72954

Axiom
annotated source: musculature of body
annotated property: hasExactSynonym
annotated target: vertebrate muscular system
has db xref: BTO:0001369

Axiom
annotated source: musculature of body
annotated property: hasRelatedSynonym
annotated target: muskelsystem
has db xref: BTO:0001485

lens cortex
type: Class
equivalent class: Class
  intersection of: tissue
  intersection of: Restriction
    on property: RO_0002221
    some values from: lens nucleus
subclass of: tissue
subclass of: UBERON_0004121
subclass of: Restriction
  on property: BFO_0000050
  some values from: lens of camera-type eye
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0005614
subclass of: Restriction
  on property: RO_0002221
  some values from: lens nucleus
IAO_0000115: Tissue that surrounds the lens nucleus.
RO_0002175: NCBITaxon 9606
has db xref: BTO:0001632
has db xref: CALOHA:TS-0542
has db xref: FMA:58970
has db xref: MESH:D007904
has db xref: SCTID:280626006
has exact synonym: cortex of lens
has OBO namespace: uberon
id: UBERON:0000389
in subset: human reference atlas

Axiom
annotated source: lens cortex
annotated property: IAO_0000115
annotated target: Tissue that surrounds the lens nucleus.
has db xref: http://www.thefreedictionary.com/lens+cortex

Axiom
annotated source: lens cortex
annotated property: hasExactSynonym
annotated target: cortex of lens
has db xref: FMA:58970

lens nucleus
type: Class
equivalent class: Class
  intersection of: UBERON_0034944
  intersection of: Restriction
    on property: RO_0002219
    some values from: lens cortex
subclass of: UBERON_0004121
subclass of: UBERON_0034944
subclass of: Restriction
  on property: BFO_0000050
  some values from: lens of camera-type eye
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0005614
subclass of: Restriction
  on property: RO_0002219
  some values from: lens cortex
IAO_0000115: The core of the crystalline lens, surrounded by the cortex.
RO_0002175: NCBITaxon 9606
has db xref: BTO:0001633
has db xref: FMA:58971
has db xref: MESH:D007907
has db xref: SCTID:280628007
has exact synonym: nucleus of lens
has OBO namespace: uberon
id: UBERON:0000390
in subset: human reference atlas

Axiom
annotated source: lens nucleus
annotated property: IAO_0000115
annotated target: The core of the crystalline lens, surrounded by the cortex.
has db xref: BTO:0001633

Axiom
annotated source: lens nucleus
annotated property: hasExactSynonym
annotated target: nucleus of lens
has db xref: FMA:58971

leptomeninx
type: Class
subclass of: UBERON_0002360
subclass of: Restriction
  on property: RO_0002495
  some values from: UBERON_0007646
IAO_0000115: Pia mater or arachnoid mater.
IAO_0000116: check relationship to secondary meninx
UBPROP_0000012: in FMA/NIF this is a superclass of PM/AM - in BTO it is the mereological sum. We go with superclass here, as we are naming the class in the singular
has db xref: BTO:0001634
has db xref: CALOHA:TS-0546
has db xref: FMA:231515
has db xref: NCIT:C32979
has db xref: NLXANAT:090207
has db xref: SCTID:362303006
has db xref: UMLS:C0228126
has db xref: Wikipedia:Leptomeninges
has db xref: neuronames:2347
has exact synonym: leptomeninges
has OBO namespace: uberon
has related synonym: arachnoid mater and pia mater
has related synonym: arachnoidea mater et pia mater
has related synonym: pia-arachnoid
has related synonym: pia-arachnoid of neuraxis
id: UBERON:0000391
in subset: organ slim

Axiom
annotated source: leptomeninx
annotated property: IAO_0000115
annotated target: Pia mater or arachnoid mater.
has db xref: Wikipedia:Leptomeninges
has db xref: https://github.com/obophenotype/uberon/issues/300

Axiom
annotated source: leptomeninx
annotated property: UBPROP_0000012
annotated target: in FMA/NIF this is a superclass of PM/AM - in BTO it is the mereological sum. We go with superclass here, as we are naming the class in the singular
external ontology: FMA

Axiom
annotated source: leptomeninx
annotated property: hasDbXref
annotated target: UMLS:C0228126
source: ncithesaurus:Leptomeninges

Axiom
annotated source: leptomeninx
annotated property: hasExactSynonym
annotated target: leptomeninges
has db xref: NLXANAT:090207
has synonym type: OMO_0003004

Axiom
annotated source: leptomeninx
annotated property: hasRelatedSynonym
annotated target: arachnoid mater and pia mater
has db xref: FMA:231515

Axiom
annotated source: leptomeninx
annotated property: hasRelatedSynonym
annotated target: arachnoidea mater et pia mater
has db xref: BTO:0001634

Axiom
annotated source: leptomeninx
annotated property: hasRelatedSynonym
annotated target: pia-arachnoid
has db xref: BTO:0001634

Axiom
annotated source: leptomeninx
annotated property: hasRelatedSynonym
annotated target: pia-arachnoid of neuraxis
has db xref: FMA:231515

cochlear ganglion
type: Class
equivalent class: Class
  intersection of: UBERON_0001714
  intersection of: Restriction
    on property: extends fibers into
    some values from: UBERON_0004727
subclass of: UBERON_0001714
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002827
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0016490
subclass of: Restriction
  on property: extends fibers into
  some values from: UBERON_0004727
IAO_0000115: The group of nerve cell bodies that conveys auditory sensation from the organ of Corti to the hindbrain and resides on the cochlear part of the vestibulocochlear nerve (eighth cranial nerve)[MP]. distributed to the hair cells of the spiral organ. The cochlear fibers arise in bipolar cells in the spiral ganglion in the modiolus.
IAO_0000116: in BTO this is part of the cochlear modiolus, but this leads to the CG being in both the nervous and skeletal systems
has db xref: BAMS:GcVIII
has db xref: BTO:0001688
has db xref: EHDAA2:0002198
has db xref: EMAPA:17572
has db xref: FMA:53445
has db xref: GAID:722
has db xref: MA:0001085
has db xref: MESH:D013136
has db xref: SCTID:368955007
has db xref: VHOG:0001183
has db xref: Wikipedia:Spiral_ganglion
has db xref: neuronames:1405
has exact synonym: Corti's ganglion
has exact synonym: cochlear part of vestibulocochlear ganglion
has exact synonym: ganglion of Corti
has exact synonym: spiral ganglion
has exact synonym: vestibulocochlear VIII ganglion cochlear component
has OBO namespace: uberon
has related synonym: ganglion cochlearis
has related synonym: ganglion spirale
has related synonym: ganglion spirale cochleae
has related synonym: spiral ganglion of cochlea
has related synonym: vestibulocochlear ganglion cochlear component
id: UBERON:0000395
in subset: pheno slim

Axiom
annotated source: cochlear ganglion
annotated property: subClassOf
annotated target: Restriction
notes: cell bodies
source: BTO-modified
source: Wikipedia

Axiom
annotated source: cochlear ganglion
annotated property: IAO_0000115
annotated target: The group of nerve cell bodies that conveys auditory sensation from the organ of Corti to the hindbrain and resides on the cochlear part of the vestibulocochlear nerve (eighth cranial nerve)[MP]. distributed to the hair cells of the spiral organ. The cochlear fibers arise in bipolar cells in the spiral ganglion in the modiolus.
has db xref: MP:0002855
has db xref: http://www.dartmouth.edu/~humananatomy/part_8/chapter_44.html

Axiom
annotated source: cochlear ganglion
annotated property: hasExactSynonym
annotated target: Corti's ganglion
has db xref: FMA:53445

Axiom
annotated source: cochlear ganglion
annotated property: hasExactSynonym
annotated target: cochlear part of vestibulocochlear ganglion
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: cochlear ganglion
annotated property: hasExactSynonym
annotated target: ganglion of Corti
has db xref: FMA:53445

Axiom
annotated source: cochlear ganglion
annotated property: hasExactSynonym
annotated target: spiral ganglion
has db xref: FMA:53445

Axiom
annotated source: cochlear ganglion
annotated property: hasExactSynonym
annotated target: vestibulocochlear VIII ganglion cochlear component
has db xref: MA:0001085

Axiom
annotated source: cochlear ganglion
annotated property: hasRelatedSynonym
annotated target: ganglion cochlearis
has db xref: BTO:0001688

Axiom
annotated source: cochlear ganglion
annotated property: hasRelatedSynonym
annotated target: ganglion spirale
has db xref: Wikipedia:Spiral_ganglion
has synonym type: OMO_0003011

Axiom
annotated source: cochlear ganglion
annotated property: hasRelatedSynonym
annotated target: ganglion spirale cochleae
has db xref: BTO:0001688

Axiom
annotated source: cochlear ganglion
annotated property: hasRelatedSynonym
annotated target: spiral ganglion of cochlea
has db xref: BTO:0001688

Axiom
annotated source: cochlear ganglion
annotated property: hasRelatedSynonym
annotated target: vestibulocochlear ganglion cochlear component
has db xref: EMAPA:17572

colonic epithelium
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: BFO_0000050
    some values from: colon
subclass of: UBERON_0001278
subclass of: Restriction
  on property: BFO_0000050
  some values from: colon
IAO_0000115: An epithelium that is part of a colon [Automatically generated definition].
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Intestinal epithelium which lines the lumen of the posterior intestine.[TAO]
has db xref: BTO:0001709
has db xref: CALOHA:TS-0163
has db xref: EMAPA:18941
has db xref: FMA:17302
has db xref: MA:0003195
has db xref: SCTID:42978003
has db xref: TAO:0005128
has db xref: ZFA:0005128
has exact synonym: colon epithelial tissue
has exact synonym: colon epithelium
has exact synonym: epithelial tissue of colon
has exact synonym: epithelial tissue of large bowel
has exact synonym: epithelium of colon
has exact synonym: epithelium of large bowel
has exact synonym: large bowel epithelial tissue
has exact synonym: large bowel epithelium
has exact synonym: posterior intestine epithelium
has OBO namespace: uberon
id: UBERON:0000397
in subset: human reference atlas
in subset: vertebrate core

Axiom
annotated source: colonic epithelium
annotated property: IAO_0000115
annotated target: An epithelium that is part of a colon [Automatically generated definition].
has db xref: OBOL:automatic

Axiom
annotated source: colonic epithelium
annotated property: UBPROP_0000001
annotated target: Intestinal epithelium which lines the lumen of the posterior intestine.[TAO]
date retrieved: 2012-08-14
external class: TAO:0005128
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: colonic epithelium
annotated property: hasExactSynonym
annotated target: colon epithelial tissue
has db xref: OBOL:automatic

Axiom
annotated source: colonic epithelium
annotated property: hasExactSynonym
annotated target: colon epithelium
has db xref: FMA:17302
has db xref: OBOL:automatic

Axiom
annotated source: colonic epithelium
annotated property: hasExactSynonym
annotated target: epithelial tissue of colon
has db xref: OBOL:automatic

Axiom
annotated source: colonic epithelium
annotated property: hasExactSynonym
annotated target: epithelial tissue of large bowel
has db xref: OBOL:automatic

Axiom
annotated source: colonic epithelium
annotated property: hasExactSynonym
annotated target: epithelium of colon
has db xref: OBOL:automatic

Axiom
annotated source: colonic epithelium
annotated property: hasExactSynonym
annotated target: epithelium of large bowel
has db xref: OBOL:automatic

Axiom
annotated source: colonic epithelium
annotated property: hasExactSynonym
annotated target: large bowel epithelial tissue
has db xref: OBOL:automatic

Axiom
annotated source: colonic epithelium
annotated property: hasExactSynonym
annotated target: large bowel epithelium
has db xref: OBOL:automatic

Axiom
annotated source: colonic epithelium
annotated property: hasExactSynonym
annotated target: posterior intestine epithelium
has db xref: ZFA:0005128

cartilage tissue of sternum
type: Class
equivalent class: Class
  intersection of: UBERON_0002418
  intersection of: Restriction
    on property: BFO_0000050
    some values from: sternum
subclass of: UBERON_0002418
subclass of: UBERON_0003837
subclass of: Restriction
  on property: BFO_0000050
  some values from: sternum
IAO_0000115: Any portion of cartilage tissue that is part of the sternum.
has db xref: FMA:32567
has exact synonym: cartilage of sternum
has OBO namespace: uberon
id: UBERON:0000398
comment: Examples: cartilage of manubrium, cartilage of xiphoid process

Axiom
annotated source: cartilage tissue of sternum
annotated property: IAO_0000115
annotated target: Any portion of cartilage tissue that is part of the sternum.
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: cartilage tissue of sternum
annotated property: hasExactSynonym
annotated target: cartilage of sternum
has db xref: FMA:32567

nasal vestibule
type: Class
subclass of: UBERON_0002553
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001707
IAO_0000115: The nasal vestibule is the most anterior part of the nasal cavity. It's enclosed by the cartilages of nose and lined by the same epithelium of the skin. The other part of the nasal cavity, which is lined by the respiratory epithelium, is called nasal cavity proper. [WP,unvetted].
has db xref: BTO:0001761
has db xref: CALOHA:TS-0660
has db xref: FMA:59644
has db xref: SCTID:278940000
has db xref: Wikipedia:Nasal_vestibule
has exact synonym: vestibular part of nasal cavity
has OBO namespace: uberon
has related synonym: vestibulum nasale
has related synonym: vestibulum nasi
id: UBERON:0000402

Axiom
annotated source: nasal vestibule
annotated property: IAO_0000115
annotated target: The nasal vestibule is the most anterior part of the nasal cavity. It's enclosed by the cartilages of nose and lined by the same epithelium of the skin. The other part of the nasal cavity, which is lined by the respiratory epithelium, is called nasal cavity proper. [WP,unvetted].
has db xref: Wikipedia:Nasal_vestibule

Axiom
annotated source: nasal vestibule
annotated property: hasExactSynonym
annotated target: vestibular part of nasal cavity
has db xref: FMA:59644

Axiom
annotated source: nasal vestibule
annotated property: hasRelatedSynonym
annotated target: vestibulum nasale
has db xref: BTO:0001761

Axiom
annotated source: nasal vestibule
annotated property: hasRelatedSynonym
annotated target: vestibulum nasi
has db xref: BTO:0001761
has db xref: Wikipedia:Nasal_vestibule
has synonym type: OMO_0003011

serous gland
type: Class
equivalent class: Class
  intersection of: UBERON_0002365
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0000313
subclass of: UBERON_0002365
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0000313
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0013232
subclass of: Restriction
  on property: RO_0003000
  some values from: UBERON_0007794
IAO_0000115: A gland in which the principal secretory cells are serous secreting cells.
UBPROP_0000001: glands that secrete watery albuminous material that often contains enzymes[MP:0008052].
has db xref: BTO:0001837
has db xref: EMAPA:37950
has db xref: FMA:62889
has db xref: Wikipedia:Serous_gland
has OBO namespace: uberon
id: UBERON:0000409
in subset: organ slim
in subset: pheno slim

Axiom
annotated source: serous gland
annotated property: IAO_0000115
annotated target: A gland in which the principal secretory cells are serous secreting cells.
has db xref: http://orcid.org/0000-0002-6601-2165
has db xref: http://www.siumed.edu/~dking2/intro/glands.htm

Axiom
annotated source: serous gland
annotated property: UBPROP_0000001
annotated target: glands that secrete watery albuminous material that often contains enzymes[MP:0008052].
source: MP:0008052

Axiom
annotated source: serous gland
annotated property: hasDbXref
annotated target: EMAPA:37950
source: MA:th

bronchial mucosa
type: Class
equivalent class: Class
  intersection of: mucosa
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002185
subclass of: tracheal mucosa
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002185
IAO_0000115: A mucosa that is part of a bronchus [Automatically generated definition].
has db xref: BTO:0001846
has db xref: FMA:62652
has db xref: SCTID:30802009
has exact synonym: bronchi mucosa
has exact synonym: bronchi mucosa of organ
has exact synonym: bronchi mucous membrane
has exact synonym: bronchi organ mucosa
has exact synonym: bronchial trunk mucosa
has exact synonym: bronchial trunk mucosa of organ
has exact synonym: bronchial trunk mucous membrane
has exact synonym: bronchial trunk organ mucosa
has exact synonym: bronchus mucosa
has exact synonym: bronchus mucosa of organ
has exact synonym: bronchus mucous membrane
has exact synonym: bronchus organ mucosa
has exact synonym: mucosa of bronchi
has exact synonym: mucosa of bronchial trunk
has exact synonym: mucosa of bronchus
has exact synonym: mucosa of organ of bronchi
has exact synonym: mucosa of organ of bronchial trunk
has exact synonym: mucosa of organ of bronchus
has exact synonym: mucous membrane of bronchi
has exact synonym: mucous membrane of bronchial trunk
has exact synonym: mucous membrane of bronchus
has exact synonym: organ mucosa of bronchi
has exact synonym: organ mucosa of bronchial trunk
has exact synonym: organ mucosa of bronchus
has exact synonym: tunica mucosa bronchi
has OBO namespace: uberon
id: UBERON:0000410

Axiom
annotated source: bronchial mucosa
annotated property: IAO_0000115
annotated target: A mucosa that is part of a bronchus [Automatically generated definition].
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: bronchi mucosa
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: bronchi mucosa of organ
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: bronchi mucous membrane
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: bronchi organ mucosa
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: bronchial trunk mucosa
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: bronchial trunk mucosa of organ
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: bronchial trunk mucous membrane
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: bronchial trunk organ mucosa
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: bronchus mucosa
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: bronchus mucosa of organ
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: bronchus mucous membrane
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: bronchus organ mucosa
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: mucosa of bronchi
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: mucosa of bronchial trunk
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: mucosa of bronchus
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: mucosa of organ of bronchi
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: mucosa of organ of bronchial trunk
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: mucosa of organ of bronchus
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: mucous membrane of bronchi
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: mucous membrane of bronchial trunk
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: mucous membrane of bronchus
has db xref: FMA:62652
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: organ mucosa of bronchi
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: organ mucosa of bronchial trunk
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: organ mucosa of bronchus
has db xref: OBOL:automatic

Axiom
annotated source: bronchial mucosa
annotated property: hasExactSynonym
annotated target: tunica mucosa bronchi
has db xref: FMA:62652
has db xref: FMA:TA
has synonym type: OMO_0003011

mucous gland
type: Class
equivalent class: Class
  intersection of: UBERON_0002365
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0000319
subclass of: UBERON_0002365
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0000319
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0070254
subclass of: Restriction
  on property: RO_0003000
  some values from: mucus
IAO_0000115: A gland in which the principal secretory cells are mucus secreting cells.
UBPROP_0000008: In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong]
has db xref: AAO:0010601
has db xref: BTO:0001979
has db xref: EMAPA:37913
has db xref: FMA:62888
has db xref: Wikipedia:Mucous_gland
has exact synonym: glandula mucosa
has OBO namespace: uberon
has related synonym: muciparous gland
has related synonym: mucous secreting gland
has related synonym: mucus gland
has related synonym: mucus-secreting gland
id: UBERON:0000414
in subset: organ slim

Axiom
annotated source: mucous gland
annotated property: IAO_0000115
annotated target: A gland in which the principal secretory cells are mucus secreting cells.
has db xref: http://orcid.org/0000-0002-6601-2165
has db xref: http://www.siumed.edu/~dking2/intro/glands.htm

Axiom
annotated source: mucous gland
annotated property: UBPROP_0000008
annotated target: In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong]
has scope: NCBITaxon:8292
source: ISBN:0073040584

Axiom
annotated source: mucous gland
annotated property: hasDbXref
annotated target: EMAPA:37913
source: MA:th

Axiom
annotated source: mucous gland
annotated property: hasExactSynonym
annotated target: glandula mucosa
has db xref: Wikipedia:Mucous_gland
has synonym type: OMO_0003011

Axiom
annotated source: mucous gland
annotated property: hasRelatedSynonym
annotated target: muciparous gland
has db xref: BTO:0001979

artery wall
type: Class
equivalent class: Class
  intersection of: anatomical wall
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001637
subclass of: UBERON_0035965
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001637
IAO_0000115: An anatomical wall that is part of an artery [Automatically generated definition].
has db xref: BTO:0002009
has db xref: FMA:14155
has db xref: galen:ArterialWall
has exact synonym: arterial wall
has exact synonym: wall of artery
has OBO namespace: uberon
id: UBERON:0000415

Axiom
annotated source: artery wall
annotated property: IAO_0000115
annotated target: An anatomical wall that is part of an artery [Automatically generated definition].
has db xref: OBOL:automatic

Axiom
annotated source: artery wall
annotated property: hasExactSynonym
annotated target: arterial wall
has db xref: FMA:14155

Axiom
annotated source: artery wall
annotated property: hasExactSynonym
annotated target: wall of artery
has db xref: FMA:14155

prostate epithelium
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002367
subclass of: simple columnar epithelium
subclass of: UBERON_0005156
subclass of: UBERON_0005911
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002367
IAO_0000115: The prostate epithelium.
IAO_0000116: TODO - check 2 FMA IDs
RO_0002175: NCBITaxon 9606
has alternative id: UBERON:0002452
has db xref: BTO:0002397
has db xref: CALOHA:TS-2065
has db xref: EMAPA:35711
has db xref: FMA:66812
has db xref: FMA:79643
has db xref: MA:0001737
has db xref: NCIT:C13103
has db xref: UMLS:C1179826
has exact synonym: epithelial tissue of prostate
has exact synonym: epithelial tissue of prostate gland
has exact synonym: epithelium of prostate
has exact synonym: epithelium of prostate gland
has exact synonym: epithelium of prostatic gland
has exact synonym: prostate epithelial tissue
has exact synonym: prostate gland epithelial tissue
has exact synonym: prostate gland epithelium
has exact synonym: prostatic epithelium
has exact synonym: prostatic gland epithelium
has OBO namespace: uberon
id: UBERON:0000428
in subset: human reference atlas
in subset: pheno slim

Axiom
annotated source: prostate epithelium
annotated property: IAO_0000115
annotated target: The prostate epithelium.
has db xref: MP:0001168

Axiom
annotated source: prostate epithelium
annotated property: hasDbXref
annotated target: UMLS:C1179826
source: ncithesaurus:Prostatic_Epithelium

Axiom
annotated source: prostate epithelium
annotated property: hasExactSynonym
annotated target: epithelial tissue of prostate
has db xref: OBOL:automatic

Axiom
annotated source: prostate epithelium
annotated property: hasExactSynonym
annotated target: epithelial tissue of prostate gland
has db xref: OBOL:automatic

Axiom
annotated source: prostate epithelium
annotated property: hasExactSynonym
annotated target: epithelium of prostate
has db xref: OBOL:automatic

Axiom
annotated source: prostate epithelium
annotated property: hasExactSynonym
annotated target: epithelium of prostate gland
has db xref: OBOL:automatic

Axiom
annotated source: prostate epithelium
annotated property: hasExactSynonym
annotated target: epithelium of prostatic gland
has db xref: FMA:79643

Axiom
annotated source: prostate epithelium
annotated property: hasExactSynonym
annotated target: prostate epithelial tissue
has db xref: OBOL:automatic

Axiom
annotated source: prostate epithelium
annotated property: hasExactSynonym
annotated target: prostate gland epithelial tissue
has db xref: OBOL:automatic

Axiom
annotated source: prostate epithelium
annotated property: hasExactSynonym
annotated target: prostatic epithelium
has db xref: FMA:66812

enteric plexus
type: Class
equivalent class: Class
  intersection of: UBERON_0001810
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002005
subclass of: UBERON_0001816
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002005
IAO_0000115: A plexus of autonomic nerve fibers within the wall of the digestive tube, and made up of the submucosal, myenteric, and subserosal plexuses; it contains visceral afferent fibers, sympathetic postganglionic fibers, parasympathetic preganglionic and postganglionic fibers, and parasympathetic postganglionic cell bodies.
RO_0002175: NCBITaxon 9606
has alternative id: UBERON:0012372
has db xref: BTO:0002437
has db xref: EMAPA:35446
has db xref: FMA:77597
has db xref: MA:0001147
has exact synonym: enteric nerve plexus
has exact synonym: intrinsic nerve plexus
has exact synonym: plexus entericus
has exact synonym: plexus nervosus entericus
has exact synonym: sympathetic enteric nerve plexus
has OBO namespace: uberon
id: UBERON:0000429
in subset: human reference atlas

Axiom
annotated source: enteric plexus
annotated property: IAO_0000115
annotated target: A plexus of autonomic nerve fibers within the wall of the digestive tube, and made up of the submucosal, myenteric, and subserosal plexuses; it contains visceral afferent fibers, sympathetic postganglionic fibers, parasympathetic preganglionic and postganglionic fibers, and parasympathetic postganglionic cell bodies.
has db xref: BTO:0002437

Axiom
annotated source: enteric plexus
annotated property: hasExactSynonym
annotated target: enteric nerve plexus
has db xref: FMA:77597

Axiom
annotated source: enteric plexus
annotated property: hasExactSynonym
annotated target: intrinsic nerve plexus
has db xref: MA:0001147

Axiom
annotated source: enteric plexus
annotated property: hasExactSynonym
annotated target: plexus entericus
has db xref: BTO:0002437

Axiom
annotated source: enteric plexus
annotated property: hasExactSynonym
annotated target: plexus nervosus entericus
has db xref: FMA:77597
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: enteric plexus
annotated property: hasExactSynonym
annotated target: sympathetic enteric nerve plexus
has db xref: FMA:77597

arachnoid trabecula
type: Class
equivalent class: Class
  intersection of: trabecula
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002362
subclass of: trabecula
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002362
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0005581
IAO_0000115: The arachnoid trabeculae are delicate strands of connective tissue that loosely connect the two innermost layers of the meninges -- the arachnoid mater and the pia mater. They are found within the subarachnoid space where cerebrospinal fluid is also found. Embryologically, the trabeculae are the remnants of the common precursor that forms both the arachnoid and pial layers of the meninges.
has db xref: BTO:0002500
has db xref: FMA:83979
has db xref: Wikipedia:Arachnoid_trabeculae
has OBO namespace: uberon
has related synonym: arachnoid trabeculae
has related synonym: trabecula arachnoideum
id: UBERON:0000439

Axiom
annotated source: arachnoid trabecula
annotated property: IAO_0000115
annotated target: The arachnoid trabeculae are delicate strands of connective tissue that loosely connect the two innermost layers of the meninges -- the arachnoid mater and the pia mater. They are found within the subarachnoid space where cerebrospinal fluid is also found. Embryologically, the trabeculae are the remnants of the common precursor that forms both the arachnoid and pial layers of the meninges.
has db xref: Wikipedia:Arachnoid_trabeculae

Axiom
annotated source: arachnoid trabecula
annotated property: hasRelatedSynonym
annotated target: arachnoid trabeculae
has synonym type: OMO_0003004

Axiom
annotated source: arachnoid trabecula
annotated property: hasRelatedSynonym
annotated target: trabecula arachnoideum
has synonym type: OMO_0003011

trabecula
type: Class
subclass of: organ part
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0002384
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0001873
IAO_0000115: A small, often microscopic, tissue element in the form of a small beam, strut or rod, generally having a mechanical function, and usually but not necessarily composed of dense collagenous tissue. On histological section, a trabecula can look like a septum, but in three dimensions they are topologically distinct, with trabeculae being roughly rod or pillar-shaped and septa being sheet-like. Trabeculae are usually composed of dense fibrous tissue, i.e. mainly of collagen, and in most cases provide mechanical strengthening or stiffening to a soft solid organ, such as the spleen. They can be composed of other materials, such as bone or muscle[WP].
UBPROP_0000007: trabecular
has db xref: BTO:0002501
has db xref: FMA:85273
has db xref: Wikipedia:Trabecula
has exact synonym: trabeculae
has OBO namespace: uberon
id: UBERON:0000440
in subset: grouping class
in subset: pheno slim

Axiom
annotated source: trabecula
annotated property: IAO_0000115
annotated target: A small, often microscopic, tissue element in the form of a small beam, strut or rod, generally having a mechanical function, and usually but not necessarily composed of dense collagenous tissue. On histological section, a trabecula can look like a septum, but in three dimensions they are topologically distinct, with trabeculae being roughly rod or pillar-shaped and septa being sheet-like. Trabeculae are usually composed of dense fibrous tissue, i.e. mainly of collagen, and in most cases provide mechanical strengthening or stiffening to a soft solid organ, such as the spleen. They can be composed of other materials, such as bone or muscle[WP].
has db xref: GO:0060343
has db xref: Wikipedia:Trabecula

Axiom
annotated source: trabecula
annotated property: hasExactSynonym
annotated target: trabeculae
has synonym type: OMO_0003004

right testicular vein
type: Class
equivalent class: Class
  intersection of: testicular vein
  intersection of: Restriction
    on property: RO_0020102
    some values from: UBERON_0004534
subclass of: testicular vein
subclass of: Restriction
  on property: BSPO_0000120
  some values from: multicellular organism
subclass of: Restriction
  on property: RO_0002170
  some values from: left renal vein
subclass of: Restriction
  on property: RO_0020102
  some values from: UBERON_0004534
IAO_0000115: A vein that drains the left pampiniform plexus and empties into the left renal vein.
RO_0002175: NCBITaxon 9606
has db xref: BTO:0002679
has db xref: EMAPA:37383
has db xref: FMA:14341
has db xref: MA:0002220
has db xref: NCIT:C52697
has db xref: SCTID:53500001
has exact synonym: right spermatic vein
has exact synonym: vena testicularis (adrenalis) dextra
has OBO namespace: uberon
has related synonym: vena testicularis dextra
has related synonym: vena testicularis sinistra
id: UBERON:0000442
in subset: human reference atlas

Axiom
annotated source: right testicular vein
annotated property: IAO_0000115
annotated target: A vein that drains the left pampiniform plexus and empties into the left renal vein.
has db xref: Dorlands_Medical_Dictionary:MerckSource

Axiom
annotated source: right testicular vein
annotated property: hasDbXref
annotated target: EMAPA:37383
source: MA:th

Axiom
annotated source: right testicular vein
annotated property: hasExactSynonym
annotated target: right spermatic vein
has db xref: MA:0002220

Axiom
annotated source: right testicular vein
annotated property: hasExactSynonym
annotated target: vena testicularis (adrenalis) dextra
has db xref: FMA:14341

Axiom
annotated source: right testicular vein
annotated property: hasRelatedSynonym
annotated target: vena testicularis dextra
has db xref: BTO:0002679

Axiom
annotated source: right testicular vein
annotated property: hasRelatedSynonym
annotated target: vena testicularis sinistra
has db xref: BTO:0002680

left testicular vein
type: Class
equivalent class: Class
  intersection of: testicular vein
  intersection of: Restriction
    on property: RO_0020102
    some values from: UBERON_0004533
subclass of: testicular vein
subclass of: Restriction
  on property: BSPO_0000120
  some values from: multicellular organism
subclass of: Restriction
  on property: RO_0002170
  some values from: left renal vein
subclass of: Restriction
  on property: RO_0020102
  some values from: UBERON_0004533
IAO_0000115: A vein that drains the right pampiniform plexus and empties into the inferior vena cava.
RO_0002175: NCBITaxon 9606
has db xref: BTO:0002680
has db xref: EMAPA:37167
has db xref: FMA:14345
has db xref: MA:0002219
has db xref: NCIT:C52696
has db xref: SCTID:90988008
has exact synonym: left spermatic vein
has OBO namespace: uberon
has related synonym: vena testicularis dextra
has related synonym: vena testicularis sinistra
id: UBERON:0000443
in subset: human reference atlas

Axiom
annotated source: left testicular vein
annotated property: IAO_0000115
annotated target: A vein that drains the right pampiniform plexus and empties into the inferior vena cava.
has db xref: Dorlands_Medical_Dictionary:MerckSource

Axiom
annotated source: left testicular vein
annotated property: hasDbXref
annotated target: EMAPA:37167
source: MA:th

Axiom
annotated source: left testicular vein
annotated property: hasExactSynonym
annotated target: left spermatic vein
has db xref: MA:0002219

Axiom
annotated source: left testicular vein
annotated property: hasRelatedSynonym
annotated target: vena testicularis dextra
has db xref: BTO:0002679

Axiom
annotated source: left testicular vein
annotated property: hasRelatedSynonym
annotated target: vena testicularis sinistra
has db xref: BTO:0002680

lymphoid follicle
type: Class
subclass of: UBERON_0001744
IAO_0000116: introducing part_of to 'cortex of lymph node' as in issue 7 introduces equivalencies; the part_of has instead been added to 'lymph node follicle'
has db xref: BTO:0002684
has db xref: FMA:55222
has db xref: NCIT:C33040
has db xref: SCTID:64626006
has db xref: UMLS:C0229654
has exact synonym: nodular lymphoid tissue
has OBO namespace: uberon
has related synonym: folliculus lymphaticus
has related synonym: lymphatic follicle
has related synonym: lymphatic nodule
has related synonym: lymphoid nodule
has related synonym: nodulus lymphaticus
has related synonym: nodulus lymphoideus
id: UBERON:0000444

Axiom
annotated source: lymphoid follicle
annotated property: subClassOf
annotated target: UBERON_0001744
source: FMA

Axiom
annotated source: lymphoid follicle
annotated property: hasDbXref
annotated target: UMLS:C0229654
source: ncithesaurus:Lymphoid_Follicle

Axiom
annotated source: lymphoid follicle
annotated property: hasExactSynonym
annotated target: nodular lymphoid tissue
has db xref: FMA:55222

Axiom
annotated source: lymphoid follicle
annotated property: hasRelatedSynonym
annotated target: folliculus lymphaticus
has db xref: BTO:0002684

Axiom
annotated source: lymphoid follicle
annotated property: hasRelatedSynonym
annotated target: lymphatic follicle
has db xref: BTO:0002684

Axiom
annotated source: lymphoid follicle
annotated property: hasRelatedSynonym
annotated target: lymphatic nodule
has db xref: BTO:0002684

Axiom
annotated source: lymphoid follicle
annotated property: hasRelatedSynonym
annotated target: lymphoid nodule
has db xref: FMA:55222

Axiom
annotated source: lymphoid follicle
annotated property: hasRelatedSynonym
annotated target: nodulus lymphaticus
has db xref: BTO:0002684

Axiom
annotated source: lymphoid follicle
annotated property: hasRelatedSynonym
annotated target: nodulus lymphoideus
has db xref: BTO:0002684

cerebral subcortex
type: Class
subclass of: organ part
subclass of: Restriction
  on property: BFO_0000050
  some values from: brain
IAO_0000115: The layer located below the cerebral cortex that includes the forebrain, midbrain and hindbrain.
has db xref: BTO:0002858
has db xref: FMA:242188
has db xref: NCIT:C98712
has db xref: UMLS:C0815008
has exact synonym: cerebral medulla
has OBO namespace: uberon
has related synonym: subcortex
id: UBERON:0000454
in subset: pheno slim

Axiom
annotated source: cerebral subcortex
annotated property: IAO_0000115
annotated target: The layer located below the cerebral cortex that includes the forebrain, midbrain and hindbrain.
has db xref: ncithesaurus:Cerebral_Subcortex

Axiom
annotated source: cerebral subcortex
annotated property: hasDbXref
annotated target: UMLS:C0815008
source: ncithesaurus:Cerebral_Subcortex

Axiom
annotated source: cerebral subcortex
annotated property: hasExactSynonym
annotated target: cerebral medulla
has db xref: FMA:242188

Axiom
annotated source: cerebral subcortex
annotated property: hasRelatedSynonym
annotated target: subcortex
has db xref: BTO:0002858

secretion of exocrine gland
type: Class
equivalent class: Class
  intersection of: organism substance
  intersection of: Restriction
    on property: RO_0003001
    some values from: UBERON_0002365
subclass of: organism substance
subclass of: Restriction
  on property: RO_0003001
  some values from: UBERON_0002365
IAO_0000115: A portion of organism substance that is produced by exocrine glands.
UBPROP_0000012: BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
has alternative id: UBERON:0006540
has broad synonym: secretion
has db xref: AEO:0001005
has db xref: BTO:0002977
has db xref: BTO:0002979
has db xref: EMAPA:36535
has db xref: FMA:9675
has db xref: MA:0002504
has db xref: MESH:D012634
has db xref: NCIT:C34062
has db xref: UMLS:C1516992
has db xref: galen:Secretion
has exact synonym: bodily secretion
has exact synonym: exocrine gland fluid/secretion
has exact synonym: secreted substance
has OBO namespace: uberon
has related synonym: exocrine gland fluid
has related synonym: exocrine gland fluid or secretion
has related synonym: exocrine gland secretion
has related synonym: external secretion
id: UBERON:0000456

Axiom
annotated source: secretion of exocrine gland
annotated property: IAO_0000115
annotated target: A portion of organism substance that is produced by exocrine glands.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: secretion of exocrine gland
annotated property: UBPROP_0000012
annotated target: BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
external ontology: BTO

Axiom
annotated source: secretion of exocrine gland
annotated property: hasBroadSynonym
annotated target: secretion
has db xref: FMA:9675

Axiom
annotated source: secretion of exocrine gland
annotated property: hasDbXref
annotated target: UMLS:C1516992
source: ncithesaurus:Exocrine_Gland_Fluid_or_Secretion

Axiom
annotated source: secretion of exocrine gland
annotated property: hasExactSynonym
annotated target: bodily secretion
has db xref: MESH:D012634

Axiom
annotated source: secretion of exocrine gland
annotated property: hasExactSynonym
annotated target: exocrine gland fluid/secretion
has db xref: MA:0002504

Axiom
annotated source: secretion of exocrine gland
annotated property: hasRelatedSynonym
annotated target: external secretion
has db xref: BTO:0002977

cavernous artery
type: Class
equivalent class: Class
  intersection of: UBERON_0001637
  intersection of: Restriction
    on property: RO_0002252
    some values from: UBERON_0001532
  intersection of: Restriction
    on property: RO_0020101
    some values from: UBERON_0001675
subclass of: UBERON_0001637
subclass of: Restriction
  on property: RO_0002252
  some values from: UBERON_0001532
subclass of: Restriction
  on property: RO_0020101
  some values from: UBERON_0001675
IAO_0000115: Any of several small branches of the internal carotid artery that supply the trigeminal ganglion and the walls of the cavernous and petrosal sinuses.
has db xref: BTO:0002996
has db xref: FMA:70527
has exact synonym: cavernous branch of cavernous part of internal carotid artery
has exact synonym: ramus sinus cavernosi (pars cavernosa) (arteria carotis interna)
has OBO namespace: uberon
id: UBERON:0000457

Axiom
annotated source: cavernous artery
annotated property: IAO_0000115
annotated target: Any of several small branches of the internal carotid artery that supply the trigeminal ganglion and the walls of the cavernous and petrosal sinuses.
has db xref: BTO:0002996

Axiom
annotated source: cavernous artery
annotated property: hasExactSynonym
annotated target: cavernous branch of cavernous part of internal carotid artery
has db xref: FMA:70527

Axiom
annotated source: cavernous artery
annotated property: hasExactSynonym
annotated target: ramus sinus cavernosi (pars cavernosa) (arteria carotis interna)
has db xref: FMA:70527
has db xref: FMA:TA
has synonym type: OMO_0003011

endocervix
type: Class
equivalent class: Class
  intersection of: organ part
  intersection of: Restriction
    on property: BSPO_0001106
    some values from: uterine cervix
subclass of: organ part
subclass of: UBERON_0005156
subclass of: Restriction
  on property: BFO_0000051
  some values from: simple columnar epithelium
subclass of: Restriction
  on property: BSPO_0001106
  some values from: uterine cervix
IAO_0000115: The region of the opening of the uterine cervix into the uterine cavity.
RO_0002175: NCBITaxon 9606
has db xref: BTO:0003002
has db xref: FMA:86485
has db xref: NCIT:C12309
has db xref: SCTID:264460007
has db xref: UMLS:C0227837
has OBO namespace: uberon
id: UBERON:0000458
in subset: human reference atlas

Axiom
annotated source: endocervix
annotated property: IAO_0000115
annotated target: The region of the opening of the uterine cervix into the uterine cavity.
has db xref: BTO:0003002

Axiom
annotated source: endocervix
annotated property: hasDbXref
annotated target: UMLS:C0227837
source: ncithesaurus:Endocervix

uterine wall
type: Class
equivalent class: Class
  intersection of: anatomical wall
  intersection of: Restriction
    on property: BFO_0000050
    some values from: uterus
subclass of: anatomical wall
subclass of: UBERON_0005156
subclass of: Restriction
  on property: BFO_0000050
  some values from: uterus
IAO_0000115: An anatomical wall that is part of a uterus [Automatically generated definition].
has db xref: BTO:0003083
has db xref: FMA:17560
has db xref: SCTID:245485002
has exact synonym: anatomical wall of uterus
has exact synonym: uterus anatomical wall
has exact synonym: uterus wall
has exact synonym: wall of uterus
has OBO namespace: uberon
id: UBERON:0000459

Axiom
annotated source: uterine wall
annotated property: IAO_0000115
annotated target: An anatomical wall that is part of a uterus [Automatically generated definition].
has db xref: OBOL:automatic

Axiom
annotated source: uterine wall
annotated property: hasExactSynonym
annotated target: anatomical wall of uterus
has db xref: OBOL:automatic

Axiom
annotated source: uterine wall
annotated property: hasExactSynonym
annotated target: uterus anatomical wall
has db xref: OBOL:automatic

Axiom
annotated source: uterine wall
annotated property: hasExactSynonym
annotated target: uterus wall
has db xref: OBOL:automatic

Axiom
annotated source: uterine wall
annotated property: hasExactSynonym
annotated target: wall of uterus
has db xref: OBOL:automatic

organism substance
type: Class
subclass of: material anatomical entity
subclass of: Restriction
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0002198
IAO_0000115: Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: AAO:0010839
has db xref: AEO:0000004
has db xref: BILA:0000004
has db xref: CALOHA:TS-2101
has db xref: CARO:0000004
has db xref: EHDAA2:0003004
has db xref: EMAPA:35178
has db xref: FBbt:00007019
has db xref: FMA:9669
has db xref: HAO:0000004
has db xref: MA:0002450
has db xref: NCIT:C13236
has db xref: SPD:0000008
has db xref: TAO:0001487
has db xref: TGMA:0001824
has db xref: VHOG:0001726
has db xref: XAO:0004001
has db xref: ZFA:0001487
has db xref: galen:BodySubstance
has exact synonym: body fluid or substance
has exact synonym: body substance
has exact synonym: organism substance
has exact synonym: portion of body substance
has exact synonym: portion of organism substance
has OBO namespace: uberon
id: UBERON:0000463
in subset: common anatomy
in subset: pheno slim
in subset: upper level

Axiom
annotated source: organism substance
annotated property: subClassOf
annotated target: Restriction
notes: this relationship may be too strong and may be weakened in future

Axiom
annotated source: organism substance
annotated property: IAO_0000115
annotated target: Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: organism substance
annotated property: hasDbXref
annotated target: FBbt:00007019
mapping justification: ManualMappingCuration

Axiom
annotated source: organism substance
annotated property: hasExactSynonym
annotated target: body fluid or substance
has db xref: MA:0002450

Axiom
annotated source: organism substance
annotated property: hasExactSynonym
annotated target: body substance
has db xref: FMA:9669

Axiom
annotated source: organism substance
annotated property: hasExactSynonym
annotated target: organism substance
has db xref: CARO:0000004

Axiom
annotated source: organism substance
annotated property: hasExactSynonym
annotated target: portion of body substance
has db xref: FMA:9669

Axiom
annotated source: organism substance
annotated property: hasExactSynonym
annotated target: portion of organism substance
has db xref: ZFA:0001487

anatomical space
type: Class
subclass of: immaterial anatomical entity
subclass of: Restriction
  on property: RO_0002219
  some values from: anatomical structure
IAO_0000115: Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has broad synonym: lumen
has broad synonym: space
has db xref: AAO:0010110
has db xref: AEO:0000005
has db xref: BILA:0000005
has db xref: CARO:0000005
has db xref: EHDAA2:0003005
has db xref: FBbt:00007017
has db xref: FMA:5897
has db xref: HAO:0000005
has db xref: NCIT:C94478
has db xref: TAO:0001668
has db xref: TGMA:0001825
has db xref: UMLS:C0524461
has db xref: VHOG:0001728
has db xref: XAO:0003190
has db xref: ZFA:0001643
has exact synonym: lumen space
has OBO namespace: uberon
has related synonym: anatomical spaces
id: UBERON:0000464
in subset: common anatomy
in subset: upper level

Axiom
annotated source: anatomical space
annotated property: IAO_0000115
annotated target: Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: anatomical space
annotated property: hasDbXref
annotated target: FBbt:00007017
mapping justification: ManualMappingCuration

Axiom
annotated source: anatomical space
annotated property: hasDbXref
annotated target: UMLS:C0524461
source: ncithesaurus:Lumen_Space

Axiom
annotated source: anatomical space
annotated property: hasRelatedSynonym
annotated target: anatomical spaces
has db xref: ZFA:0001643
has synonym type: OMO_0003004

material anatomical entity
type: Class
subclass of: BFO_0000040
subclass of: anatomical entity
disjoint with: immaterial anatomical entity
IAO_0000115: Anatomical entity that has mass.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: AAO:0010264
has db xref: AEO:0000006
has db xref: BILA:0000006
has db xref: CARO:0000006
has db xref: EHDAA2:0003006
has db xref: FBbt:00007016
has db xref: FMA:67165
has db xref: HAO:0000006
has db xref: TAO:0001836
has db xref: TGMA:0001826
has db xref: VHOG:0001721
has OBO namespace: uberon
id: UBERON:0000465
in subset: common anatomy
in subset: upper level

Axiom
annotated source: material anatomical entity
annotated property: IAO_0000115
annotated target: Anatomical entity that has mass.
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: material anatomical entity
annotated property: hasDbXref
annotated target: FBbt:00007016
mapping justification: ManualMappingCuration

immaterial anatomical entity
type: Class
subclass of: BFO_0000141
subclass of: anatomical entity
IAO_0000115: Anatomical entity that has no mass.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: AAO:0010265
has db xref: AEO:0000007
has db xref: BILA:0000007
has db xref: CARO:0000007
has db xref: EHDAA2:0003007
has db xref: FBbt:00007015
has db xref: FMA:67112
has db xref: HAO:0000007
has db xref: TAO:0001835
has db xref: TGMA:0001827
has db xref: VHOG:0001727
has exact synonym: immaterial physical anatomical entity
has OBO namespace: uberon
id: UBERON:0000466
in subset: common anatomy
in subset: upper level

Axiom
annotated source: immaterial anatomical entity
annotated property: IAO_0000115
annotated target: Anatomical entity that has no mass.
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: immaterial anatomical entity
annotated property: hasDbXref
annotated target: FBbt:00007015
mapping justification: ManualMappingCuration

Axiom
annotated source: immaterial anatomical entity
annotated property: hasExactSynonym
annotated target: immaterial physical anatomical entity
has db xref: FMA:67112

anatomical system
type: Class
subclass of: anatomical structure
subclass of: Restriction
  on property: BFO_0000050
  some values from: multicellular organism
subclass of: Restriction
  on property: BFO_0000051
  some values from: organ
IAO_0000115: Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
RO_0002175: NCBITaxon 9606
has broad synonym: system
has db xref: AAO:0000007
has db xref: AEO:0000011
has db xref: BILA:0000011
has db xref: BIRNLEX:14
has db xref: BSA:0000049
has db xref: CALOHA:TS-2088
has db xref: CARO:0000011
has db xref: EHDAA2:0003011
has db xref: EHDAA:392
has db xref: EMAPA:16103
has db xref: EV:0100000
has db xref: FBbt:00004856
has db xref: FMA:7149
has db xref: HAO:0000011
has db xref: IDOMAL:0002460
has db xref: MA:0000003
has db xref: NCIT:C12919
has db xref: SCTID:278195005
has db xref: TAO:0001439
has db xref: TGMA:0001831
has db xref: UMLS:C0460002
has db xref: VHOG:0001725
has db xref: WBbt:0005746
has db xref: WBbt:0005763
has db xref: Wikipedia:Organ_system
has db xref: XAO:0003002
has db xref: ZFA:0001439
has db xref: galen:AnatomicalSystem
has exact synonym: body system
has exact synonym: connected anatomical system
has exact synonym: organ system
has OBO namespace: uberon
has related synonym: anatomical systems
id: UBERON:0000467
in subset: common anatomy
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: upper level

Axiom
annotated source: anatomical system
annotated property: IAO_0000115
annotated target: Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
has db xref: CARO:0000011

Axiom
annotated source: anatomical system
annotated property: hasBroadSynonym
annotated target: system
has db xref: GO:0048731

Axiom
annotated source: anatomical system
annotated property: hasDbXref
annotated target: FBbt:00004856
mapping justification: ManualMappingCuration

Axiom
annotated source: anatomical system
annotated property: hasDbXref
annotated target: IDOMAL:0002460
author id: https://orcid.org/0000-0003-4423-4370
mapping justification: ManualMappingCuration
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: anatomical system
annotated property: hasDbXref
annotated target: UMLS:C0460002
source: ncithesaurus:Organ_System

Axiom
annotated source: anatomical system
annotated property: hasExactSynonym
annotated target: body system
has db xref: BIRNLEX:14

Axiom
annotated source: anatomical system
annotated property: hasExactSynonym
annotated target: connected anatomical system
has db xref: CARO:0000011

Axiom
annotated source: anatomical system
annotated property: hasRelatedSynonym
annotated target: anatomical systems
has db xref: ZFA:0001439
has synonym type: OMO_0003004

multicellular organism
type: Class
subclass of: UBERON_0010000
IAO_0000115: Anatomical structure that is an individual member of a species and consists of more than one cell.
IAO_0000116: TODO - split body and mc organism? body continues after death stage
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
UBPROP_0000007: organismal
has broad synonym: organism
has db xref: AAO:0010026
has db xref: AEO:0000191
has db xref: BILA:0000012
has db xref: BIRNLEX:18
has db xref: BSA:0000038
has db xref: BTO:0000042
has db xref: CARO:0000012
has db xref: EFO:0002906
has db xref: EHDAA2:0003103
has db xref: EHDAA2:0003191
has db xref: EHDAA:1
has db xref: EMAPA:25765
has db xref: EV:0100016
has db xref: FBbt:00000001
has db xref: FMA:256135
has db xref: HAO:0000012
has db xref: NCIT:C13041
has db xref: SCTID:243928005
has db xref: TADS:0000001
has db xref: TAO:0001094
has db xref: TGMA:0001832
has db xref: VHOG:0000671
has db xref: WBbt:0007833
has db xref: Wikipedia:Multi-cellular_organism
has db xref: XAO:0003004
has db xref: ZFA:0001094
has db xref: galen:Organism
has db xref: ncithesaurus:Whole_Organism
has exact synonym: multi-cellular organism
has OBO namespace: uberon
has related synonym: Koerper
has related synonym: body
has related synonym: whole body
has related synonym: whole organism
id: UBERON:0000468
in subset: common anatomy
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: upper level

Axiom
annotated source: multicellular organism
annotated property: IAO_0000115
annotated target: Anatomical structure that is an individual member of a species and consists of more than one cell.
has db xref: CARO:0000012
has db xref: Wikipedia:Multi-cellular_organism
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: multicellular organism
annotated property: hasBroadSynonym
annotated target: organism
has db xref: FBbt:00000001
has db xref: VHOG:0000671
has db xref: WBbt:0007833

Axiom
annotated source: multicellular organism
annotated property: hasDbXref
annotated target: FBbt:00000001
mapping justification: ManualMappingCuration

Axiom
annotated source: multicellular organism
annotated property: hasExactSynonym
annotated target: multi-cellular organism
has db xref: CARO:0000012

Axiom
annotated source: multicellular organism
annotated property: hasRelatedSynonym
annotated target: Koerper
has db xref: BTO:0001489

Axiom
annotated source: multicellular organism
annotated property: hasRelatedSynonym
annotated target: body
has db xref: AEO:0000103
has db xref: BIRNLEX:18
has db xref: FMA:256135
has db xref: NCIT:C13041

Axiom
annotated source: multicellular organism
annotated property: hasRelatedSynonym
annotated target: whole body
has db xref: BTO:0001489

Axiom
annotated source: multicellular organism
annotated property: hasRelatedSynonym
annotated target: whole organism
has db xref: FBbt:00000001

compound organ component
type: Class
subclass of: multi-tissue structure
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0003103
IAO_0000115: Multi-tissue structure that is part of a compound organ.
IAO_0000232: this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future
has db xref: AAO:0010017
has db xref: AEO:0000019
has db xref: BILA:0000019
has db xref: CARO:0000019
has db xref: EHDAA2:0003019
has db xref: HAO:0000019
has db xref: TAO:0001489
has db xref: TGMA:0001835
has db xref: XAO:0003039
has db xref: ZFA:0001489
has OBO namespace: uberon
has related synonym: compound organ components
id: UBERON:0000471
in subset: upper level

Axiom
annotated source: compound organ component
annotated property: IAO_0000115
annotated target: Multi-tissue structure that is part of a compound organ.
has db xref: CARO:0000019
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: compound organ component
annotated property: hasRelatedSynonym
annotated target: compound organ components
has db xref: ZFA:0001489
has synonym type: OMO_0003004

testis
type: Class
equivalent class: Class
  intersection of: gonad
  intersection of: Restriction
    on property: BFO_0000050
    some values from: male reproductive system
subclass of: gonad
subclass of: UBERON_0003135
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0009117
disjoint with: ovary
disjoint with: UBERON_0009117
IAO_0000115: A gonad of a male animal. A gonad produces and releases sperm.
UBPROP_0000001: Male reproductive organ.[TAO]
UBPROP_0000003: (...) 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]
UBPROP_0000007: testicular
UBPROP_0000008: The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally
has alternative id: UBERON:0002117
has db xref: AAO:0000606
has db xref: BILA:0000124
has db xref: BSA:0000085
has db xref: BTO:0001363
has db xref: CALOHA:TS-1030
has db xref: EFO:0000984
has db xref: EHDAA2:0002007
has db xref: EHDAA:8146
has db xref: EMAPA:17972
has db xref: EV:0100102
has db xref: FBbt:00004928
has db xref: FMA:7210
has db xref: GAID:396
has db xref: HAO:0001007
has db xref: MA:0000411
has db xref: MAT:0000132
has db xref: MESH:D013737
has db xref: MIAA:0000132
has db xref: NCIT:C12412
has db xref: SCTID:181431007
has db xref: TAO:0000598
has db xref: UMLS:C0039597
has db xref: VHOG:0000252
has db xref: WBbt:0006794
has db xref: Wikipedia:Testis
has db xref: XAO:0000157
has db xref: ZFA:0000598
has db xref: galen:Testis
has exact synonym: gonad of male genitalia
has exact synonym: gonad of male reproductive system
has exact synonym: male gonad
has exact synonym: testicle
has OBO namespace: uberon
has related synonym: orchis
has related synonym: testes
has related synonym: testiculus
id: UBERON:0000473
in subset: efo slim
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: testis
annotated property: IAO_0000115
annotated target: A gonad of a male animal. A gonad produces and releases sperm.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: testis
annotated property: UBPROP_0000001
annotated target: Male reproductive organ.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000598
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: testis
annotated property: UBPROP_0000003
annotated target: (...) 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]
date retrieved: 2012-09-17
external class: VHOG:0000252
ontology: VHOG
source: DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)
source: http://bgee.unil.ch/

Axiom
annotated source: testis
annotated property: UBPROP_0000008
annotated target: The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally
source: ISBN:0123971756
taxon: NCBITaxon:40674

Axiom
annotated source: testis
annotated property: hasDbXref
annotated target: FBbt:00004928
mapping justification: ManualMappingCuration

Axiom
annotated source: testis
annotated property: hasDbXref
annotated target: UMLS:C0039597
source: ncithesaurus:Testis

Axiom
annotated source: testis
annotated property: hasExactSynonym
annotated target: gonad of male genitalia
has db xref: OBOL:automatic

Axiom
annotated source: testis
annotated property: hasExactSynonym
annotated target: gonad of male reproductive system
has db xref: OBOL:automatic

Axiom
annotated source: testis
annotated property: hasExactSynonym
annotated target: male gonad
has db xref: OBOL:automatic

Axiom
annotated source: testis
annotated property: hasExactSynonym
annotated target: testicle
has db xref: FMA:7210

Axiom
annotated source: testis
annotated property: hasRelatedSynonym
annotated target: orchis
has db xref: BTO:0001363

Axiom
annotated source: testis
annotated property: hasRelatedSynonym
annotated target: testes
has synonym type: OMO_0003004

Axiom
annotated source: testis
annotated property: hasRelatedSynonym
annotated target: testiculus
has db xref: BTO:0001363
has synonym type: OMO_0003011

female reproductive system
type: Class
equivalent class: Class
  intersection of: reproductive system
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0003100
subclass of: reproductive system
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0003100
IAO_0000115: The organs and associated structures associated with bearing offspring in a female animal.
RO_0002175: NCBITaxon 9606
UBPROP_0000003: By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]
has db xref: BTO:0000083
has db xref: CALOHA:TS-1303
has db xref: EFO:0000969
has db xref: EHDAA2:0000506
has db xref: EHDAA:8116
has db xref: EMAPA:17959
has db xref: EV:0100110
has db xref: FBbt:00004864
has db xref: FMA:45663
has db xref: GAID:364
has db xref: HAO:0000324
has db xref: MA:0000381
has db xref: MESH:D005836
has db xref: MIAA:0000028
has db xref: NCIT:C12402
has db xref: SCTID:361386004
has db xref: TGMA:0000635
has db xref: UMLS:C0700038
has db xref: VHOG:0000726
has db xref: Wikipedia:Female_genitalia
has db xref: WikipediaCategory:Female_reproductive_system
has db xref: XAO:0000156
has exact synonym: female organism genitalia
has exact synonym: female organism reproductive system
has exact synonym: genitalia of female organism
has exact synonym: reproductive system of female organism
has OBO namespace: uberon
has related synonym: female genital system
has related synonym: female genital tract
has related synonym: female genitalia
has related synonym: female genitals
has related synonym: female reproductive tract
has related synonym: gynaecological tissue
has related synonym: systema genitale femininum
id: UBERON:0000474
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: female reproductive system
annotated property: IAO_0000115
annotated target: The organs and associated structures associated with bearing offspring in a female animal.
has db xref: MP:0001119
has db xref: Wikipedia:Female_genitalia
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: female reproductive system
annotated property: UBPROP_0000003
annotated target: By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000726
ontology: VHOG
source: ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43
source: http://bgee.unil.ch/

Axiom
annotated source: female reproductive system
annotated property: hasDbXref
annotated target: FBbt:00004864
mapping justification: ManualMappingCuration

Axiom
annotated source: female reproductive system
annotated property: hasDbXref
annotated target: UMLS:C0700038
source: ncithesaurus:Female_Reproductive_System

Axiom
annotated source: female reproductive system
annotated property: hasExactSynonym
annotated target: female organism genitalia
has db xref: OBOL:automatic

Axiom
annotated source: female reproductive system
annotated property: hasExactSynonym
annotated target: female organism reproductive system
has db xref: OBOL:automatic

Axiom
annotated source: female reproductive system
annotated property: hasExactSynonym
annotated target: genitalia of female organism
has db xref: OBOL:automatic

Axiom
annotated source: female reproductive system
annotated property: hasExactSynonym
annotated target: reproductive system of female organism
has db xref: OBOL:automatic

Axiom
annotated source: female reproductive system
annotated property: hasRelatedSynonym
annotated target: female genitals
has db xref: XAO:0000156
has synonym type: OMO_0003004

Axiom
annotated source: female reproductive system
annotated property: hasRelatedSynonym
annotated target: female reproductive tract
has db xref: MA:0000381

Axiom
annotated source: female reproductive system
annotated property: hasRelatedSynonym
annotated target: gynaecological tissue
has db xref: BTO:0000083

Axiom
annotated source: female reproductive system
annotated property: hasRelatedSynonym
annotated target: systema genitale femininum
has db xref: BTO:0000083

organism subdivision
type: Class
subclass of: UBERON_0010000
subclass of: Restriction
  on property: BFO_0000050
  some values from: multicellular organism
IAO_0000115: Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
IAO_0000116: Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: AAO:0010053
has db xref: AEO:0000032
has db xref: BILA:0000032
has db xref: BIRNLEX:7
has db xref: CALOHA:TS-2084
has db xref: CARO:0000032
has db xref: EFO:0000808
has db xref: EHDAA2:0003032
has db xref: EMAPA:36031
has db xref: FBbt:00007009
has db xref: FMA:7153
has db xref: HAO:0000032
has db xref: MA:0002433
has db xref: MAT:0000293
has db xref: MESH:D001829
has db xref: MIAA:0000293
has db xref: NCIT:C32221
has db xref: TAO:0001308
has db xref: TGMA:0001840
has db xref: UMLS:C0229962
has db xref: VHOG:0001758
has db xref: Wikipedia:Body_part
has db xref: XAO:0003013
has db xref: ZFA:0001308
has db xref: galen:BodyPart
has exact synonym: anatomic region
has OBO namespace: uberon
has related synonym: body part
has related synonym: body region
has related synonym: cardinal body part
id: UBERON:0000475
in subset: common anatomy
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: upper level

Axiom
annotated source: organism subdivision
annotated property: subClassOf
annotated target: UBERON_0010000
source: CARO

Axiom
annotated source: organism subdivision
annotated property: IAO_0000115
annotated target: Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
has db xref: CARO:0000032
has db xref: CARO:DOS
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: organism subdivision
annotated property: hasDbXref
annotated target: FBbt:00007009
mapping justification: ManualMappingCuration

Axiom
annotated source: organism subdivision
annotated property: hasDbXref
annotated target: UMLS:C0229962
source: ncithesaurus:Body_Part

Axiom
annotated source: organism subdivision
annotated property: hasExactSynonym
annotated target: anatomic region
has db xref: MA:0002433

Axiom
annotated source: organism subdivision
annotated property: hasRelatedSynonym
annotated target: body region
has db xref: FMA:7153

Axiom
annotated source: organism subdivision
annotated property: hasRelatedSynonym
annotated target: cardinal body part
has db xref: FMA:7153

acellular anatomical structure
type: Class
subclass of: anatomical structure
disjoint with: UBERON_0010000
IAO_0000115: Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: AAO:0010268
has db xref: AEO:0000040
has db xref: BILA:0000040
has db xref: CARO:0000040
has db xref: EHDAA2:0003040
has db xref: FBbt:00007013
has db xref: FMA:63863
has db xref: HAO:0000040
has db xref: TAO:0000382
has db xref: TGMA:0001841
has db xref: XAO:0003162
has db xref: ZFA:0000382
has OBO namespace: uberon
has related synonym: acellular anatomical structures
id: UBERON:0000476
in subset: common anatomy
in subset: vertebrate core

Axiom
annotated source: acellular anatomical structure
annotated property: disjointWith
annotated target: UBERON_0010000
source: CARO

Axiom
annotated source: acellular anatomical structure
annotated property: IAO_0000115
annotated target: Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: acellular anatomical structure
annotated property: hasDbXref
annotated target: FBbt:00007013
mapping justification: ManualMappingCuration

Axiom
annotated source: acellular anatomical structure
annotated property: hasRelatedSynonym
annotated target: acellular anatomical structures
has db xref: ZFA:0000382
has synonym type: OMO_0003004

anatomical cluster
type: Class
subclass of: UBERON_0034923
IAO_0000115: Anatomical group whose component anatomical structures lie in close proximity to each other.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: FBbt:00007277
has db xref: VHOG:0001737
has OBO namespace: uberon
id: UBERON:0000477
in subset: common anatomy
in subset: upper level

Axiom
annotated source: anatomical cluster
annotated property: IAO_0000115
annotated target: Anatomical group whose component anatomical structures lie in close proximity to each other.
has db xref: FBbt:00007277

Axiom
annotated source: anatomical cluster
annotated property: hasDbXref
annotated target: FBbt:00007277
mapping justification: ManualMappingCuration

extraembryonic structure
type: Class
equivalent class: Class
  intersection of: UBERON_0005423
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0016887
subclass of: UBERON_0005423
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0016887
IAO_0000115: A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
has db xref: AAO:0010020
has db xref: AEO:0000042
has db xref: BILA:0000042
has db xref: CALOHA:TS-2119
has db xref: CARO:0000042
has db xref: EHDAA2:0003042
has db xref: EHDAA:46
has db xref: FBbt:00005835
has db xref: FMA:85537
has db xref: HAO:0000042
has db xref: NCIT:C34055
has db xref: SCTID:314908006
has db xref: TAO:0000020
has db xref: TGMA:0001843
has db xref: UMLS:C1282438
has db xref: VHOG:0000292
has db xref: XAO:0004005
has db xref: ZFA:0000020
has exact synonym: extra-embryonic structure
has OBO namespace: uberon
has related synonym: extraembryonic structures
has related synonym: extraembryonic tissue
id: UBERON:0000478
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core
comment: see also conceptus extraembryonic component in EHDAA2.

Axiom
annotated source: extraembryonic structure
annotated property: IAO_0000115
annotated target: A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
has db xref: CARO:DOS
has db xref: http://orcid.org/0000-0001-9114-8737
has db xref: https://cedar.bio.indiana.edu/trac/env/ontologies/ticket/279

Axiom
annotated source: extraembryonic structure
annotated property: hasDbXref
annotated target: FBbt:00005835
mapping justification: ManualMappingCuration

Axiom
annotated source: extraembryonic structure
annotated property: hasDbXref
annotated target: UMLS:C1282438
source: ncithesaurus:Extraembryonic_Structure

Axiom
annotated source: extraembryonic structure
annotated property: hasRelatedSynonym
annotated target: extraembryonic structures
has db xref: ZFA:0000020
has synonym type: OMO_0003004

tissue
type: Class
subclass of: UBERON_0010000
subclass of: Restriction
  on property: BFO_0000050
  some values from: multicellular organism
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0031012
IAO_0000115: Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
IAO_0000116: changed label and definition to reflect CARO2
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: AAO:0000607
has db xref: AAO:0010054
has db xref: AEO:0000043
has db xref: BILA:0000043
has db xref: BIRNLEX:19
has db xref: CALOHA:TS-2090
has db xref: CARO:0000043
has db xref: EHDAA2:0003043
has db xref: EMAPA:35868
has db xref: FBbt:00007003
has db xref: FMA:9637
has db xref: HAO:0000043
has db xref: MA:0003002
has db xref: MESH:D014024
has db xref: NCIT:C12801
has db xref: TAO:0001477
has db xref: TGMA:0001844
has db xref: UMLS:C0040300
has db xref: VHOG:0001757
has db xref: WBbt:0005729
has db xref: XAO:0003040
has db xref: ZFA:0001477
has db xref: galen:Tissue
has exact synonym: portion of tissue
has exact synonym: tissue portion
has narrow synonym: simple tissue
has OBO namespace: uberon
id: UBERON:0000479
in subset: common anatomy
in subset: pheno slim
in subset: upper level

Axiom
annotated source: tissue
annotated property: subClassOf
annotated target: UBERON_0010000
source: CARO

Axiom
annotated source: tissue
annotated property: IAO_0000115
annotated target: Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
has db xref: CARO:0000043

Axiom
annotated source: tissue
annotated property: hasDbXref
annotated target: FBbt:00007003
mapping justification: ManualMappingCuration

Axiom
annotated source: tissue
annotated property: hasDbXref
annotated target: UMLS:C0040300
source: ncithesaurus:Tissue

Axiom
annotated source: tissue
annotated property: hasExactSynonym
annotated target: portion of tissue
has db xref: CARO:0000043

Axiom
annotated source: tissue
annotated property: hasNarrowSynonym
annotated target: simple tissue
has db xref: AEO:0000043

multi-tissue structure
type: Class
subclass of: UBERON_0010000
subclass of: Restriction
  on property: BFO_0000051
  some values from: tissue
IAO_0000115: Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: AAO:0010048
has db xref: AEO:0000055
has db xref: BILA:0000055
has db xref: CARO:0000055
has db xref: EHDAA2:0003055
has db xref: FBbt:00007010
has db xref: HAO:0000055
has db xref: TAO:0001488
has db xref: TGMA:0001847
has db xref: VHOG:0001762
has db xref: XAO:0003037
has db xref: ZFA:0001488
has OBO namespace: uberon
has related synonym: multi-tissue structures
id: UBERON:0000481
in subset: common anatomy
in subset: upper level

Axiom
annotated source: multi-tissue structure
annotated property: subClassOf
annotated target: UBERON_0010000
source: CARO

Axiom
annotated source: multi-tissue structure
annotated property: IAO_0000115
annotated target: Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
has db xref: CARO:0000055
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: multi-tissue structure
annotated property: hasDbXref
annotated target: FBbt:00007010
mapping justification: ManualMappingCuration

Axiom
annotated source: multi-tissue structure
annotated property: hasRelatedSynonym
annotated target: multi-tissue structures
has db xref: ZFA:0001488
has synonym type: OMO_0003004

epithelium
type: Class
equivalent class: Class
  intersection of: tissue
  intersection of: Restriction
    on property: RO_0002473
    some values from: CL_0000066
equivalent class: Class
  union of: multilaminar epithelium
  union of: unilaminar epithelium
subclass of: tissue
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0005911
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0005769
subclass of: Restriction
  on property: RO_0002473
  some values from: CL_0000066
IAO_0000115: Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
UBPROP_0000003: The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]
UBPROP_0000007: epithelial
has db xref: AAO:0000144
has db xref: AAO:0010055
has db xref: AEO:0000066
has db xref: BILA:0000066
has db xref: BTO:0000416
has db xref: CALOHA:TS-0288
has db xref: CARO:0000066
has db xref: EHDAA2:0003066
has db xref: EMAPA:32738
has db xref: FBbt:00007005
has db xref: FMA:9639
has db xref: GAID:402
has db xref: HAO:0000066
has db xref: MA:0003060
has db xref: MESH:D004848
has db xref: NCIT:C12710
has db xref: SCTID:31610004
has db xref: TAO:0001486
has db xref: UMLS:C0014609
has db xref: VHOG:0000387
has db xref: Wikipedia:Epithelium
has db xref: XAO:0003045
has db xref: ZFA:0001486
has exact synonym: epithelial tissue
has exact synonym: portion of epithelium
has OBO namespace: uberon
id: UBERON:0000483
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core
comment: Editor note: surface epithelium may contain non-epithelial cells, such as melanocytes, lymphocytes and dendritic cells, within the sheet of epithelial cells. Do we consider these part of the epithelium, or located-in it?

Axiom
annotated source: epithelium
annotated property: IAO_0000115
annotated target: Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
has db xref: Wikipedia:Epithelium
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: epithelium
annotated property: UBPROP_0000003
annotated target: The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000387
ontology: VHOG
source: ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59
source: http://bgee.unil.ch/

Axiom
annotated source: epithelium
annotated property: hasDbXref
annotated target: FBbt:00007005
mapping justification: ManualMappingCuration

Axiom
annotated source: epithelium
annotated property: hasDbXref
annotated target: UMLS:C0014609
source: ncithesaurus:Epithelium

Axiom
annotated source: epithelium
annotated property: hasExactSynonym
annotated target: portion of epithelium
has db xref: FMA:9639

simple cuboidal epithelium
type: Class
subclass of: unilaminar epithelium
subclass of: UBERON_0010077
IAO_0000115: Unilaminar epithelium that consists of a single layer of cuboidal cells.
IAO_0000116: needs to be synchronized with CL - there is no distinct cuboidal cell in CL
has db xref: AAO:0010064
has db xref: AEO:0000067
has db xref: BILA:0000067
has db xref: CARO:0000067
has db xref: EHDAA2:0003067
has db xref: FMA:45566
has db xref: HAO:0000067
has db xref: NCIT:C33553
has db xref: TAO:0001497
has db xref: UMLS:C0836134
has db xref: Wikipedia:Simple_cuboidal_epithelium
has db xref: XAO:0004009
has db xref: ZFA:0001497
has exact synonym: epithelium simplex cuboideum
has OBO namespace: uberon
has related synonym: simple cuboidal epithelia
id: UBERON:0000484
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: simple cuboidal epithelium
annotated property: IAO_0000115
annotated target: Unilaminar epithelium that consists of a single layer of cuboidal cells.
has db xref: Wikipedia:Simple_cuboidal_epithelium
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: simple cuboidal epithelium
annotated property: hasDbXref
annotated target: UMLS:C0836134
source: ncithesaurus:Simple_Cuboidal_Epithelium

Axiom
annotated source: simple cuboidal epithelium
annotated property: hasRelatedSynonym
annotated target: simple cuboidal epithelia
has db xref: ZFA:0001497
has synonym type: OMO_0003004

simple columnar epithelium
type: Class
subclass of: unilaminar epithelium
subclass of: UBERON_0012274
IAO_0000115: Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA].
has broad synonym: columnar epithelium
has broad synonym: columnar epithlium
has db xref: AAO:0010063
has db xref: AEO:0000068
has db xref: BILA:0000068
has db xref: CARO:0000068
has db xref: EHDAA2_RETIRED:0003068
has db xref: FBbt:00007027
has db xref: FMA:45567
has db xref: HAO:0000068
has db xref: NCIT:C33552
has db xref: SCTID:32210007
has db xref: TAO:0001496
has db xref: UMLS:C0836135
has db xref: Wikipedia:Simple_columnar_epithelium
has db xref: XAO:0004008
has db xref: ZFA:0001496
has exact synonym: epithelium simplex columnare
has exact synonym: simple columnar epithelium
has OBO namespace: uberon
has related synonym: simple columnar epithelia
id: UBERON:0000485
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: simple columnar epithelium
annotated property: IAO_0000115
annotated target: Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA].
has db xref: FMA:FMA
has db xref: Wikipedia:Simple_columnar_epithelium
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: simple columnar epithelium
annotated property: hasBroadSynonym
annotated target: columnar epithelium
has db xref: EHDAA2:0003068

Axiom
annotated source: simple columnar epithelium
annotated property: hasBroadSynonym
annotated target: columnar epithlium
has db xref: AEO:0000068

Axiom
annotated source: simple columnar epithelium
annotated property: hasDbXref
annotated target: FBbt:00007027
mapping justification: ManualMappingCuration

Axiom
annotated source: simple columnar epithelium
annotated property: hasDbXref
annotated target: UMLS:C0836135
source: ncithesaurus:Simple_Columnar_Epithelium

Axiom
annotated source: simple columnar epithelium
annotated property: hasRelatedSynonym
annotated target: simple columnar epithelia
has db xref: ZFA:0001496
has synonym type: OMO_0003004

multilaminar epithelium
type: Class
subclass of: epithelium
IAO_0000115: Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA].
UBPROP_0000001: Epithelium that consists of more than one layer of epithelial cells.[CARO]
has db xref: AAO:0010059
has db xref: AEO:0000069
has db xref: BILA:0000069
has db xref: BTO:0002074
has db xref: CARO:0000069
has db xref: EHDAA2:0003069
has db xref: FMA:45562
has db xref: HAO:0000069
has db xref: NCIT:C33622
has db xref: SCTID:309044005
has db xref: TAO:0001494
has db xref: UMLS:C0682575
has db xref: Wikipedia:Stratified_epithelium
has db xref: XAO:0004006
has db xref: ZFA:0001494
has exact synonym: stratified epithelium
has OBO namespace: uberon
has related synonym: laminated epithelium
id: UBERON:0000486
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: multilaminar epithelium
annotated property: IAO_0000115
annotated target: Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA].
has db xref: FMA:FMA
has db xref: Wikipedia:Stratified_epithelium
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: multilaminar epithelium
annotated property: UBPROP_0000001
annotated target: Epithelium that consists of more than one layer of epithelial cells.[CARO]
date retrieved: 2012-06-20
external class: CARO:0000069
ontology: CARO
source: FMA:45562
source: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: multilaminar epithelium
annotated property: hasDbXref
annotated target: UMLS:C0682575
source: ncithesaurus:Stratified_Epithelium

Axiom
annotated source: multilaminar epithelium
annotated property: hasRelatedSynonym
annotated target: laminated epithelium
has db xref: BTO:0002074

simple squamous epithelium
type: Class
equivalent class: Class
  intersection of: unilaminar epithelium
  intersection of: Restriction
    on property: RO_0002473
    some values from: CL_0000076
subclass of: unilaminar epithelium
subclass of: UBERON_0006914
IAO_0000115: Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA].
UBPROP_0000001: Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]
has db xref: AAO:0010066
has db xref: AEO:0000070
has db xref: BILA:0000070
has db xref: BTO:0002073
has db xref: CARO:0000070
has db xref: EHDAA2:0003070
has db xref: FMA:45565
has db xref: HAO:0000070
has db xref: NCIT:C13178
has db xref: TAO:0001498
has db xref: UMLS:C0836133
has db xref: Wikipedia:Simple_squamous_epithelium
has db xref: XAO:0004010
has db xref: ZFA:0001498
has exact synonym: epithelium simplex squamosum
has OBO namespace: uberon
has related synonym: simple squamous epithelia
id: UBERON:0000487
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: simple squamous epithelium
annotated property: IAO_0000115
annotated target: Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA].
has db xref: FMA:45565
has db xref: Wikipedia:Simple_squamous_epithelium
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: simple squamous epithelium
annotated property: UBPROP_0000001
annotated target: Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]
date retrieved: 2012-06-20
external class: CARO:0000070
ontology: CARO
source: FMA:45565
source: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: simple squamous epithelium
annotated property: hasDbXref
annotated target: UMLS:C0836133
source: ncithesaurus:Simple_Squamous_Epithelium

Axiom
annotated source: simple squamous epithelium
annotated property: hasRelatedSynonym
annotated target: simple squamous epithelia
has db xref: ZFA:0001498
has synonym type: OMO_0003004

atypical epithelium
type: Class
subclass of: epithelium
IAO_0000115: Epithelium that consists of epithelial cells not arranged in one ore more layers.
has db xref: AAO:0010057
has db xref: AEO:0000071
has db xref: BILA:0000071
has db xref: CARO:0000071
has db xref: EHDAA2:0003071
has db xref: FMA:61741
has db xref: HAO:0000071
has db xref: TAO:0001493
has db xref: XAO:0004004
has db xref: ZFA:0001493
has exact synonym: heterogenous epithelium
has OBO namespace: uberon
has related synonym: atypical epithelia
id: UBERON:0000488
in subset: vertebrate core

Axiom
annotated source: atypical epithelium
annotated property: IAO_0000115
annotated target: Epithelium that consists of epithelial cells not arranged in one ore more layers.
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: atypical epithelium
annotated property: hasRelatedSynonym
annotated target: atypical epithelia
has db xref: ZFA:0001493
has synonym type: OMO_0003004

cavitated compound organ
type: Class
equivalent class: Class
  intersection of: UBERON_0003103
  intersection of: Restriction
    on property: BFO_0000051
    some values from: UBERON_0002553
subclass of: UBERON_0003103
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0002553
IAO_0000115: Compound organ that contains one or more macroscopic anatomical spaces.
IAO_0000232: this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future
has db xref: AAO:0010016
has db xref: AEO:0000072
has db xref: BILA:0000072
has db xref: CARO:0000072
has db xref: EHDAA2:0003072
has db xref: FMA:55671
has db xref: HAO:0000072
has db xref: TAO:0001490
has db xref: TGMA:0001857
has db xref: VHOG:0001730
has db xref: XAO:0003165
has db xref: ZFA:0001490
has exact synonym: cavitated organ
has OBO namespace: uberon
has related synonym: cavitated compound organs
id: UBERON:0000489
in subset: organ slim
in subset: upper level

Axiom
annotated source: cavitated compound organ
annotated property: IAO_0000115
annotated target: Compound organ that contains one or more macroscopic anatomical spaces.
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: cavitated compound organ
annotated property: hasExactSynonym
annotated target: cavitated organ
has db xref: FMA:55671

Axiom
annotated source: cavitated compound organ
annotated property: hasRelatedSynonym
annotated target: cavitated compound organs
has db xref: ZFA:0001490
has synonym type: OMO_0003004

unilaminar epithelium
type: Class
subclass of: epithelium
IAO_0000115: Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA].
IAO_0000116: consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable
UBPROP_0000001: Epithelium that consists of a single layer of epithelial cells.[CARO]
has db xref: AAO:0010062
has db xref: AEO:0000073
has db xref: BILA:0000073
has db xref: BTO:0002073
has db xref: CARO:0000073
has db xref: EHDAA2:0003073
has db xref: FMA:45561
has db xref: HAO:0000073
has db xref: NCIT:C33554
has db xref: SCTID:309043004
has db xref: TAO:0001495
has db xref: UMLS:C0682574
has db xref: XAO:0004007
has db xref: ZFA:0001495
has exact synonym: simple epithelium
has OBO namespace: uberon
has related synonym: unilaminar epithelia
id: UBERON:0000490
in subset: vertebrate core

Axiom
annotated source: unilaminar epithelium
annotated property: IAO_0000115
annotated target: Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA].
has db xref: FMA:45561
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: unilaminar epithelium
annotated property: UBPROP_0000001
annotated target: Epithelium that consists of a single layer of epithelial cells.[CARO]
date retrieved: 2012-06-20
external class: CARO:0000073
ontology: CARO
source: FMA:45561
source: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: unilaminar epithelium
annotated property: hasDbXref
annotated target: UMLS:C0682574
source: ncithesaurus:Simple_Epithelium

Axiom
annotated source: unilaminar epithelium
annotated property: hasExactSynonym
annotated target: simple epithelium
has db xref: FMA:45561

Axiom
annotated source: unilaminar epithelium
annotated property: hasRelatedSynonym
annotated target: unilaminar epithelia
has db xref: ZFA:0001495
has synonym type: OMO_0003004

mucus
type: Class
subclass of: secretion of exocrine gland
subclass of: UBERON_0006314
subclass of: Restriction
  on property: BFO_0000051
  some values from: CHEBI_37395
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0000998
subclass of: Restriction
  on property: RO_0003001
  some values from: mucosa
IAO_0000115: Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water.
UBPROP_0000007: mucoid
UBPROP_0000007: mucous
has db xref: CALOHA:TS-2144
has db xref: ENVO:02000040
has db xref: FMA:66938
has db xref: GAID:1164
has db xref: MESH:D009093
has db xref: NCIT:C13259
has db xref: UMLS:C0026727
has db xref: Wikipedia:Mucus
has db xref: galen:Mucus
has OBO namespace: uberon
id: UBERON:0000912

Axiom
annotated source: mucus
annotated property: IAO_0000115
annotated target: Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water.
has db xref: Wikipedia:Mucus

Axiom
annotated source: mucus
annotated property: hasDbXref
annotated target: UMLS:C0026727
source: ncithesaurus:Mucus

interstitial fluid
type: Class
subclass of: organism substance
subclass of: Restriction
  on property: BFO_0000050
  some values from: tissue
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6072
subclass of: Restriction
  on property: RO_0002221
  some values from: CL_0000000
IAO_0000115: Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid.
RO_0002171: UBERON_0001969
has db xref: ENVO:02000042
has db xref: FMA:9673
has db xref: NCIT:C120839
has db xref: Wikipedia:Interstitial_fluid
has exact synonym: intercellular fluid
has exact synonym: tissue fluid
has OBO namespace: uberon
id: UBERON:0000913
in subset: pheno slim

Axiom
annotated source: interstitial fluid
annotated property: IAO_0000115
annotated target: Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid.
has db xref: Wikipedia:Interstitial_fluid

Axiom
annotated source: interstitial fluid
annotated property: hasExactSynonym
annotated target: intercellular fluid
has db xref: ENVO:02000042

Axiom
annotated source: interstitial fluid
annotated property: hasExactSynonym
annotated target: tissue fluid
has db xref: ENVO:02000042

organismal segment
type: Class
subclass of: organism subdivision
IAO_0000115: One of the repeated divisions of the whole organism.
IAO_0000116: review this post-CARO2
has db xref: FBbt:00000003
has db xref: HAO:0000929
has db xref: MAT:0000271
has db xref: MIAA:0000271
has db xref: Wikipedia:Segmentation_(biology)
has exact synonym: segment
has exact synonym: serial element
has OBO namespace: uberon
id: UBERON:0000914
in subset: uberon slim
in subset: upper level

Axiom
annotated source: organismal segment
annotated property: IAO_0000115
annotated target: One of the repeated divisions of the whole organism.
has db xref: FB:gg
has db xref: Wikipedia:Segmentation_(biology)

Axiom
annotated source: organismal segment
annotated property: hasDbXref
annotated target: FBbt:00000003
mapping justification: ManualMappingCuration

Axiom
annotated source: organismal segment
annotated property: hasExactSynonym
annotated target: segment
has db xref: FBbt:00000003

thoracic segment of trunk
type: Class
equivalent class: Class
  intersection of: UBERON_0011676
  intersection of: Restriction
    on property: RO_0002551
    some values from: UBERON_0014477
subclass of: UBERON_0009569
subclass of: UBERON_0011676
subclass of: Restriction
  on property: RO_0002551
  some values from: UBERON_0014477
IAO_0000115: Subdivision of trunk that lies between the head and the abdomen.
IAO_0000232: note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest
RO_0002171: appendage
RO_0002171: head
RO_0002171: UBERON_0002417
has db xref: EMAPA:35862
has db xref: FMA:259209
has db xref: MA:0000022
has db xref: SCTID:302551006
has db xref: Wikipedia:Thorax
has exact synonym: thorax
has OBO namespace: uberon
has related synonym: anterior subdivision of trunk
has related synonym: upper body
has related synonym: upper trunk
id: UBERON:0000915
in subset: uberon slim

Axiom
annotated source: thoracic segment of trunk
annotated property: subClassOf
annotated target: UBERON_0009569
source: FMA

Axiom
annotated source: thoracic segment of trunk
annotated property: IAO_0000115
annotated target: Subdivision of trunk that lies between the head and the abdomen.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: thoracic segment of trunk
annotated property: hasExactSynonym
annotated target: thorax
has db xref: MA:0000022

Axiom
annotated source: thoracic segment of trunk
annotated property: hasRelatedSynonym
annotated target: upper trunk
has db xref: FMA:259209

abdomen
type: Class
subclass of: UBERON_0009569
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7742
IAO_0000115: The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.
IAO_0000116: Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class
UBPROP_0000007: abdominal
UBPROP_0000007: celiac
has db xref: BTO:0000020
has db xref: CALOHA:TS-0001
has db xref: EFO:0000968
has db xref: EMAPA:35102
has db xref: EV:0100011
has db xref: FMA:9577
has db xref: GAID:16
has db xref: MA:0000029
has db xref: MAT:0000298
has db xref: MESH:D000005
has db xref: MIAA:0000298
has db xref: SCTID:302553009
has db xref: Wikipedia:Abdomen
has db xref: galen:Abdomen
has exact synonym: abdominopelvic region
has exact synonym: abdominopelvis
has OBO namespace: uberon
has related synonym: adult abdomen
has related synonym: belly
has related synonym: celiac region
id: UBERON:0000916
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: abdomen
annotated property: subClassOf
annotated target: Restriction
source: MA

Axiom
annotated source: abdomen
annotated property: IAO_0000115
annotated target: The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: abdomen
annotated property: hasExactSynonym
annotated target: abdominopelvic region
has db xref: FMA:9577

Axiom
annotated source: abdomen
annotated property: hasExactSynonym
annotated target: abdominopelvis
has db xref: FMA:9577

egg chorion
type: Class
subclass of: acellular anatomical structure
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0016887
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6072
subclass of: Restriction
  on property: RO_0002221
  some values from: UBERON_0003125
disjoint with: UBERON_0003124
IAO_0000115: A protective, noncellular membrane that surrounds the eggs of various animals including insects and fish [GO].
UBPROP_0000001: The egg shell. Kimmel et al, 1995.[TAO]
has db xref: FBbt:00000038
has db xref: TAO:0000329
has db xref: TGMA:0000681
has db xref: Wikipedia:Chorion_(egg)
has db xref: ZFA:0000329
has exact synonym: chorion (egg)
has OBO namespace: uberon
has related synonym: chorion
id: UBERON:0000920
in subset: dubious grouping
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: egg chorion
annotated property: IAO_0000115
annotated target: A protective, noncellular membrane that surrounds the eggs of various animals including insects and fish [GO].
has db xref: GO:0042600
has db xref: Wikipedia:Chorion_(egg)

Axiom
annotated source: egg chorion
annotated property: UBPROP_0000001
annotated target: The egg shell. Kimmel et al, 1995.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000329
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: egg chorion
annotated property: hasDbXref
annotated target: FBbt:00000038
mapping justification: ManualMappingCuration

embryo
type: Class
equivalent class: Class
  intersection of: multicellular organism
  intersection of: Restriction
    on property: RO_0002489
    some values from: embryo stage
  intersection of: Restriction
    on property: RO_0002493
    some values from: embryo stage
subclass of: multicellular organism
subclass of: Restriction
  on property: RO_0002489
  some values from: embryo stage
subclass of: Restriction
  on property: RO_0002493
  some values from: embryo stage
IAO_0000115: Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
UBPROP_0000007: embryonic
UBPROP_0000012: Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
has db xref: AAO:0011035
has db xref: AEO:0000169
has db xref: BILA:0000056
has db xref: BSA:0000039
has db xref: BTO:0000379
has db xref: CALOHA:TS-0229
has db xref: EFO:0001367
has db xref: EHDAA2:0000002
has db xref: EHDAA2_RETIRED:0003236
has db xref: EHDAA:38
has db xref: EMAPA:16039
has db xref: FBbt:00000052
has db xref: FMA:69068
has db xref: GAID:963
has db xref: IDOMAL:0000646
has db xref: MAT:0000226
has db xref: MESH:D004622
has db xref: MIAA:0000019
has db xref: NCIT:C28147
has db xref: OGEM:000001
has db xref: SCTID:57991002
has db xref: UMLS:C0013935
has db xref: VHOG:0001766
has db xref: Wikipedia:Embryo
has db xref: XAO:0000113
has db xref: ZFA:0000103
has db xref: http://neurolex.org/wiki/Category:Embryonic_organism
has exact synonym: embryonic organism
has OBO namespace: uberon
has related synonym: developing organism
has related synonym: developmental tissue
id: UBERON:0000922
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: embryo
annotated property: IAO_0000115
annotated target: Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
has db xref: BTO:0000379
has db xref: FB:FBrf0039741
has db xref: FB:FBrf0041814
has db xref: GO:0009790
has db xref: Wikipedia:Embryo

Axiom
annotated source: embryo
annotated property: UBPROP_0000012
annotated target: Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
external ontology: ZFA

Axiom
annotated source: embryo
annotated property: hasDbXref
annotated target: FBbt:00000052
mapping justification: ManualMappingCuration

Axiom
annotated source: embryo
annotated property: hasDbXref
annotated target: IDOMAL:0000646
author id: https://orcid.org/0000-0003-4423-4370
mapping justification: ManualMappingCuration
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: embryo
annotated property: hasDbXref
annotated target: UMLS:C0013935
source: ncithesaurus:Embryo

Axiom
annotated source: embryo
annotated property: hasExactSynonym
annotated target: embryonic organism
has db xref: BILA:0000056

Axiom
annotated source: embryo
annotated property: hasRelatedSynonym
annotated target: developing organism
has db xref: BILA:0000056

germ layer
type: Class
subclass of: UBERON_0010316
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6072
IAO_0000115: A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
UBPROP_0000003: The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
has broad synonym: embryonic tissue
has db xref: AAO:0000480
has db xref: BILA:0000035
has db xref: BTO:0000556
has db xref: EMAPA:36033
has db xref: FBbt:00000110
has db xref: FMA:69069
has db xref: GAID:1303
has db xref: MESH:D005855
has db xref: NCIT:C12950
has db xref: NCIT:C54105
has db xref: TAO:0001122
has db xref: UMLS:C0920502
has db xref: UMLS:C1708239
has db xref: VHOG:0001223
has db xref: Wikipedia:Germ_layer
has db xref: XAO:0003011
has db xref: ZFA:0001122
has exact synonym: germinal layer
has narrow synonym: primary germ layer
has OBO namespace: uberon
has related synonym: embryonic germ layer
has related synonym: embryonic germ layers
id: UBERON:0000923
in subset: uberon slim
in subset: vertebrate core
comment: Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]

Axiom
annotated source: germ layer
annotated property: IAO_0000115
annotated target: A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
has db xref: Wikipedia:Germ_layer
has db xref: https://github.com/obophenotype/uberon/issues/203

Axiom
annotated source: germ layer
annotated property: UBPROP_0000003
annotated target: The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001223
ontology: VHOG
source: ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722
source: http://bgee.unil.ch/

Axiom
annotated source: germ layer
annotated property: hasBroadSynonym
annotated target: embryonic tissue
has db xref: FMA:69069

Axiom
annotated source: germ layer
annotated property: hasDbXref
annotated target: FBbt:00000110
mapping justification: ManualMappingCuration

Axiom
annotated source: germ layer
annotated property: hasDbXref
annotated target: UMLS:C0920502
source: ncithesaurus:Embryonic_Tissue

Axiom
annotated source: germ layer
annotated property: hasDbXref
annotated target: UMLS:C1708239
source: ncithesaurus:Germinal_Layer

Axiom
annotated source: germ layer
annotated property: hasExactSynonym
annotated target: germinal layer
has db xref: ncithesaurus:Germinal_Layer

Axiom
annotated source: germ layer
annotated property: hasNarrowSynonym
annotated target: primary germ layer
has db xref: GO:0001704
has db xref: ZFA:0001122

ectoderm
type: Class
subclass of: germ layer
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0000221
IAO_0000115: Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
UBPROP_0000001: Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]
UBPROP_0000003: The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
UBPROP_0000007: ectodermal
has db xref: AAO:0000137
has db xref: BILA:0000036
has db xref: BTO:0000315
has db xref: CALOHA:TS-0216
has db xref: EFO:0000414
has db xref: EHDAA2:0000428
has db xref: EMAPA:16069
has db xref: EV:0100003
has db xref: FBbt:00000111
has db xref: FMA:69070
has db xref: GAID:1304
has db xref: MAT:0000155
has db xref: MAT:0000173
has db xref: MESH:D004475
has db xref: MIAA:0000173
has db xref: NCIT:C12703
has db xref: SCTID:362851007
has db xref: TAO:0000016
has db xref: UMLS:C0013574
has db xref: VHOG:0000153
has db xref: Wikipedia:Ectoderm
has db xref: XAO:0000001
has db xref: ZFA:0000016
has exact synonym: embryonic ectoderm
has OBO namespace: uberon
id: UBERON:0000924
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: ectoderm
annotated property: subClassOf
annotated target: Restriction
source: Bgee:AN

Axiom
annotated source: ectoderm
annotated property: IAO_0000115
annotated target: Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
has db xref: Wikipedia:Ectoderm

Axiom
annotated source: ectoderm
annotated property: UBPROP_0000001
annotated target: Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000137
ontology: AAO
source: AAO:EJS

Axiom
annotated source: ectoderm
annotated property: UBPROP_0000003
annotated target: The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000153
ontology: VHOG
source: ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722
source: http://bgee.unil.ch/

Axiom
annotated source: ectoderm
annotated property: hasDbXref
annotated target: FBbt:00000111
mapping justification: ManualMappingCuration

Axiom
annotated source: ectoderm
annotated property: hasDbXref
annotated target: UMLS:C0013574
source: ncithesaurus:Ectoderm

Axiom
annotated source: ectoderm
annotated property: hasExactSynonym
annotated target: embryonic ectoderm
has db xref: VHOG:0000153

endoderm
type: Class
subclass of: germ layer
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0000223
IAO_0000115: Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
UBPROP_0000003: The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
UBPROP_0000007: endodermal
has db xref: AAO:0000139
has db xref: BILA:0000038
has db xref: BTO:0000800
has db xref: CALOHA:TS-0273
has db xref: EFO:0002545
has db xref: EHDAA2:0000436
has db xref: EMAPA:16062
has db xref: EV:0100005
has db xref: FBbt:00000125
has db xref: FMA:69071
has db xref: GAID:1305
has db xref: MAT:0000175
has db xref: MESH:D004707
has db xref: MIAA:0000175
has db xref: NCIT:C12706
has db xref: SCTID:362855003
has db xref: TAO:0000017
has db xref: UMLS:C0014144
has db xref: VHOG:0000154
has db xref: Wikipedia:Endoderm
has db xref: XAO:0000090
has db xref: ZFA:0000017
has OBO namespace: uberon
has related synonym: entoderm
id: UBERON:0000925
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: endoderm
annotated property: subClassOf
annotated target: Restriction
source: Bgee:AN

Axiom
annotated source: endoderm
annotated property: IAO_0000115
annotated target: Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
has db xref: Wikipedia:Endoderm

Axiom
annotated source: endoderm
annotated property: UBPROP_0000003
annotated target: The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000154
ontology: VHOG
source: ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722
source: http://bgee.unil.ch/

Axiom
annotated source: endoderm
annotated property: hasDbXref
annotated target: FBbt:00000125
mapping justification: ManualMappingCuration

Axiom
annotated source: endoderm
annotated property: hasDbXref
annotated target: UMLS:C0014144
source: ncithesaurus:Endoderm

Axiom
annotated source: endoderm
annotated property: hasRelatedSynonym
annotated target: entoderm
has db xref: DOI:10.5962/bhl.title.1013
has synonym type: DEPRECATED

mesoderm
type: Class
subclass of: germ layer
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0000222
IAO_0000115: The middle germ layer of the embryo, between the endoderm and ectoderm.
RO_0002161: NCBITaxon 6040
UBPROP_0000001: Primary germ layer that is the middle of the embryonic germ layers.[AAO]
UBPROP_0000003: The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
UBPROP_0000007: mesodermal
UBPROP_0000008: sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates
has alternative id: UBERON:0003263
has db xref: AAO:0000304
has db xref: BILA:0000037
has db xref: BTO:0000839
has db xref: CALOHA:TS-0623
has db xref: EFO:0001981
has db xref: EHDAA2:0001128
has db xref: EHDAA:124
has db xref: EHDAA:160
has db xref: EHDAA:183
has db xref: EMAPA:16083
has db xref: EV:0100006
has db xref: FBbt:00000126
has db xref: FMA:69072
has db xref: GAID:522
has db xref: MAT:0000174
has db xref: MESH:D008648
has db xref: MIAA:0000174
has db xref: NCIT:C12750
has db xref: SCTID:362854004
has db xref: TAO:0000041
has db xref: UMLS:C0025485
has db xref: VHOG:0000152
has db xref: Wikipedia:Mesoderm
has db xref: XAO:0000050
has db xref: ZFA:0000041
has OBO namespace: uberon
has related synonym: embryonic mesoderm
has related synonym: entire mesoderm
has related synonym: mesodermal mantle
id: UBERON:0000926
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: mesoderm
annotated property: subClassOf
annotated target: germ layer
notes: sometimes not considered primary

Axiom
annotated source: mesoderm
annotated property: subClassOf
annotated target: Restriction
source: Bgee:AN

Axiom
annotated source: mesoderm
annotated property: IAO_0000115
annotated target: The middle germ layer of the embryo, between the endoderm and ectoderm.
has db xref: Wikipedia:Mesoderm

Axiom
annotated source: mesoderm
annotated property: UBPROP_0000001
annotated target: Primary germ layer that is the middle of the embryonic germ layers.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000304
ontology: AAO
source: AAO:EJS

Axiom
annotated source: mesoderm
annotated property: UBPROP_0000003
annotated target: The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000152
ontology: VHOG
source: ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722
source: http://bgee.unil.ch/

Axiom
annotated source: mesoderm
annotated property: UBPROP_0000008
annotated target: sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates
source: https://github.com/obophenotype/uberon/wiki/The-neural-crest

Axiom
annotated source: mesoderm
annotated property: hasDbXref
annotated target: FBbt:00000126
mapping justification: ManualMappingCuration

Axiom
annotated source: mesoderm
annotated property: hasDbXref
annotated target: UMLS:C0025485
source: ncithesaurus:Mesoderm

Axiom
annotated source: mesoderm
annotated property: hasRelatedSynonym
annotated target: embryonic mesoderm
has db xref: VHOG:0000152

Axiom
annotated source: mesoderm
annotated property: hasRelatedSynonym
annotated target: entire mesoderm
has db xref: SCTID:362854004
has db xref: https://orcid.org/0000-0002-6601-2165

mesectoderm
type: Class
subclass of: germ layer
subclass of: Restriction
  on property: RO_0002220
  some values from: ectoderm
IAO_0000115: A double row of cells which are located at the midline from the end of gastrulations. The morphology of these cells is distinct from adjacent ectodermal cells - they are elongated such that one end remains exposed to the outside of the embryo at the mideline while the other end bissects the internalised mesoderm.
UBPROP_0000007: mesectodermal
has db xref: EFO:0003336
has db xref: FBbt:00000136
has db xref: MAT:0000243
has db xref: MIAA:0000243
has OBO namespace: uberon
has related synonym: MesEc
id: UBERON:0000927
in subset: efo slim
in subset: uberon slim
comment: Split term? The part of the mesenchyme derived from ectoderm, especially from the embryonic neural crest from which the pigment cells, meninges, and most of the branchial cartilages develop.[TFD]

Axiom
annotated source: mesectoderm
annotated property: IAO_0000115
annotated target: A double row of cells which are located at the midline from the end of gastrulations. The morphology of these cells is distinct from adjacent ectodermal cells - they are elongated such that one end remains exposed to the outside of the embryo at the mideline while the other end bissects the internalised mesoderm.
has db xref: FB:FBrf0089570

Axiom
annotated source: mesectoderm
annotated property: hasDbXref
annotated target: FBbt:00000136
mapping justification: ManualMappingCuration

stomodeum
type: Class
subclass of: UBERON_0013522
subclass of: Restriction
  on property: BFO_0000050
  some values from: ectoderm
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0035804
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6072
IAO_0000115: Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity.
IAO_0000116: consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence
UBPROP_0000001: Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]
UBPROP_0000001: the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx
UBPROP_0000007: stomodeal
UBPROP_0000008: This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity.
has broad synonym: stomodeal-hypophyseal primordium
has db xref: BTO:0004224
has db xref: EHDAA2:0001929
has db xref: EMAPA:16263
has db xref: FBbt:00000439
has db xref: FMA:295846
has db xref: NCIT:C34306
has db xref: TAO:0001290
has db xref: TGMA:0000135
has db xref: UMLS:C1514977
has db xref: Wikipedia:Stomodeum
has db xref: XAO:0000269
has db xref: ZFA:0001290
has exact synonym: mouth primordium
has exact synonym: primitive oral cavity
has exact synonym: stomatodeum
has exact synonym: stomodaeum
has OBO namespace: uberon
has related synonym: mouth pit
has related synonym: oral ectoderm
has related synonym: oral pit
id: UBERON:0000930
in subset: grouping class
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: stomodeum
annotated property: IAO_0000115
annotated target: Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity.
has db xref: Wikipedia:Stomodeum
has db xref: http://orcid.org/0000-0002-6601-2165
has db xref: https://github.com/obophenotype/uberon/issues/326

Axiom
annotated source: stomodeum
annotated property: UBPROP_0000001
annotated target: Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]
date retrieved: 2012-08-14
external class: TAO:0001290
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: stomodeum
annotated property: UBPROP_0000001
annotated target: the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx
source: MP:0012522
taxon: NCBITaxon:40674

Axiom
annotated source: stomodeum
annotated property: hasBroadSynonym
annotated target: stomodeal-hypophyseal primordium
has db xref: XAO:0000269

Axiom
annotated source: stomodeum
annotated property: hasDbXref
annotated target: FBbt:00000439
mapping justification: ManualMappingCuration

Axiom
annotated source: stomodeum
annotated property: hasDbXref
annotated target: UMLS:C1514977
source: ncithesaurus:Stomodeum

Axiom
annotated source: stomodeum
annotated property: hasExactSynonym
annotated target: mouth primordium
has db xref: XAO:0000269

Axiom
annotated source: stomodeum
annotated property: hasExactSynonym
annotated target: primitive oral cavity
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: stomodeum
annotated property: hasExactSynonym
annotated target: stomatodeum
has db xref: Wikipedia:Stomodeum

Axiom
annotated source: stomodeum
annotated property: hasRelatedSynonym
annotated target: mouth pit
has db xref: EMAPA:16263

Axiom
annotated source: stomodeum
annotated property: hasRelatedSynonym
annotated target: oral ectoderm
has db xref: ZFA:0001290
has db xref: ZFIN:ZDB-PUB-100726-23

Axiom
annotated source: stomodeum
annotated property: hasRelatedSynonym
annotated target: oral pit
has db xref: EMAPA:16263

proctodeum
type: Class
subclass of: UBERON_0016566
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0007026
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6072
subclass of: Restriction
  on property: RO_0002202
  some values from: ectoderm
subclass of: Restriction
  on property: RO_0002387
  some values from: UBERON_0001353
IAO_0000115: Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract.
IAO_0000116: removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male.
UBPROP_0000001: An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO]
UBPROP_0000001: Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO]
UBPROP_0000007: proctodeal
has db xref: AAO:0011087
has db xref: EHDAA2:0000121
has db xref: EMAPA:25038
has db xref: FBbt:00000123
has db xref: NCIT:C34278
has db xref: TAO:0000066
has db xref: UMLS:C0231054
has db xref: VHOG:0000139
has db xref: Wikipedia:Proctodeum
has db xref: XAO:0001019
has db xref: ZFA:0000066
has exact synonym: embryonic proctodaeum
has exact synonym: proctodaeum
has narrow synonym: amnioproctodeal invagination
has OBO namespace: uberon
has related synonym: anal pit
has related synonym: anus porus
id: UBERON:0000931
in subset: uberon slim

Axiom
annotated source: proctodeum
annotated property: subClassOf
annotated target: UBERON_0016566
source: EHDAA2

Axiom
annotated source: proctodeum
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: proctodeum
annotated property: IAO_0000115
annotated target: Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract.
has db xref: ZFA:0000066
has db xref: https://github.com/obophenotype/uberon/issues/685
has db xref: https://sourceforge.net/p/fbbtdv/tickets/52

Axiom
annotated source: proctodeum
annotated property: UBPROP_0000001
annotated target: An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000066
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: proctodeum
annotated property: UBPROP_0000001
annotated target: Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO]
date retrieved: 2012-06-20
external class: AAO:0011087
ontology: AAO
source: ZFA:0000066

Axiom
annotated source: proctodeum
annotated property: hasDbXref
annotated target: FBbt:00000123
mapping justification: ManualMappingCuration

Axiom
annotated source: proctodeum
annotated property: hasDbXref
annotated target: UMLS:C0231054
source: ncithesaurus:Proctodeum

Axiom
annotated source: proctodeum
annotated property: hasNarrowSynonym
annotated target: amnioproctodeal invagination
has db xref: FBbt:00000123

Axiom
annotated source: proctodeum
annotated property: hasRelatedSynonym
annotated target: anal pit
has db xref: VHOG:0000139

Axiom
annotated source: proctodeum
annotated property: hasRelatedSynonym
annotated target: anus porus
has db xref: XAO:0001019

chordate pharyngeal muscle
type: Class
equivalent class: Class
  intersection of: UBERON_0001630
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0004467
subclass of: UBERON_0001630
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0004467
subclass of: Restriction
  on property: RO_0002433
  some values from: musculature
IAO_0000115: A muscle that acts on the pharynx[WP, vetted].
UBPROP_0000001: A pharyngeal muscle is any muscle that forms part of the pharynx[GO].
UBPROP_0000202: FMA_67169
has db xref: BTO:0001048
has db xref: EFO:0003504
has db xref: FMA:46619
has db xref: GAID:154
has db xref: MA:0001797
has db xref: MESH:D010609
has db xref: NCIT:C13075
has db xref: SCTID:244798004
has db xref: TAO:0000172
has db xref: UMLS:C0031346
has db xref: Wikipedia:Pharyngeal_muscles
has db xref: ZFA:0000172
has exact synonym: branchial muscle
has exact synonym: muscle of pharynx
has exact synonym: muscle organ of pharynx
has exact synonym: pharyngeal muscle
has exact synonym: pharynx muscle
has exact synonym: pharynx muscle organ
has OBO namespace: uberon
has related synonym: branchial muscles
has related synonym: musculi pharyngis
has related synonym: musculus pharyngis
has related synonym: tunica muscularis pharyngis
id: UBERON:0000933
in subset: efo slim
in subset: pheno slim
comment: Innervation notes: They are innervated by the pharyngeal branch of the Vagus nerve (CN X) with the exception of the stylopharyngeus muscle which is innervated by the glossopharyngeal nerve (CN IX).[WP]

Axiom
annotated source: chordate pharyngeal muscle
annotated property: IAO_0000115
annotated target: A muscle that acts on the pharynx[WP, vetted].
has db xref: Wikipedia:Pharyngeal_muscles
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: chordate pharyngeal muscle
annotated property: UBPROP_0000001
annotated target: A pharyngeal muscle is any muscle that forms part of the pharynx[GO].
date retrieved: 2012-06-30
external class: GO:0043282
notes: does not quite work for some muscles such as stylopharyngeus
ontology: GO
source: GOC:go_curators

Axiom
annotated source: chordate pharyngeal muscle
annotated property: hasDbXref
annotated target: UMLS:C0031346
source: ncithesaurus:Pharyngeal_Muscle

Axiom
annotated source: chordate pharyngeal muscle
annotated property: hasExactSynonym
annotated target: branchial muscle
has db xref: ZFA:0000172

Axiom
annotated source: chordate pharyngeal muscle
annotated property: hasExactSynonym
annotated target: muscle organ of pharynx
has db xref: OBOL:automatic

Axiom
annotated source: chordate pharyngeal muscle
annotated property: hasExactSynonym
annotated target: pharynx muscle organ
has db xref: OBOL:automatic

Axiom
annotated source: chordate pharyngeal muscle
annotated property: hasRelatedSynonym
annotated target: branchial muscles
has db xref: TAO:0000172
has synonym type: OMO_0003004

Axiom
annotated source: chordate pharyngeal muscle
annotated property: hasRelatedSynonym
annotated target: musculi pharyngis
has db xref: Wikipedia:Pharyngeal_muscles
has synonym type: OMO_0003011

Axiom
annotated source: chordate pharyngeal muscle
annotated property: hasRelatedSynonym
annotated target: musculus pharyngis
has db xref: BTO:0001048

Axiom
annotated source: chordate pharyngeal muscle
annotated property: hasRelatedSynonym
annotated target: tunica muscularis pharyngis
has db xref: Wikipedia:Pharyngeal_muscles
has synonym type: OMO_0003011

ventral nerve cord
type: Class
equivalent class: Class
  intersection of: UBERON_0005053
  intersection of: Restriction
    on property: BSPO_0005001
    some values from: UBERON_0013235
subclass of: UBERON_0005053
subclass of: Restriction
  on property: BSPO_0005001
  some values from: UBERON_0013235
IAO_0000115: The pair of closely united ventral longitudinal nerves with their segmental ganglia that is characteristic of many elongate invertebrates (as earthworms)[BTO]. A large process bundle that runs along the vental mid-line extending from the ventral region of the nerve ring[WB]. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms[GO].
RO_0002161: NCBITaxon 7711
UBPROP_0000001: A cluster of neurons that extends posteriorly from the embryonic and larval brain and is surrounded by a connective tissue sheath.
UBPROP_0000008: The ventral nerve cords make up the nervous system of some phyla of the invertebrates, particularly within the nematodes, annelids and the arthropods. It usually consists of cerebral ganglia anteriorly with the nerve cords running down the ventral ('belly', as opposed to back) plane of the organism. This characteristic is important in qualifying the difference compared to the chordates, which have a dorsal nerve cord. Ventral nerve cords from anterior to posterior (the thoracic and abdominal tagma in the arthropods) are made up of segmented ganglia that are connected by a tract of nerve fibers passing from one side to the other of the nerve cord called commissures. The complete system bears some likeness to a rope ladder. In some animals the bilateral ganglia are fused into a single large ganglion per segment. This characteristic is found mostly in the insects.
has db xref: BTO:0002328
has db xref: EFO:0000896
has db xref: FBbt:00005097
has db xref: MAT:0000339
has db xref: MIAA:0000339
has db xref: NLX:146329
has db xref: WBbt:0005829
has db xref: Wikipedia:Ventral_nerve_cord
has exact synonym: ventral cord
has OBO namespace: uberon
id: UBERON:0000934
in subset: efo slim
in subset: uberon slim

Axiom
annotated source: ventral nerve cord
annotated property: IAO_0000115
annotated target: The pair of closely united ventral longitudinal nerves with their segmental ganglia that is characteristic of many elongate invertebrates (as earthworms)[BTO]. A large process bundle that runs along the vental mid-line extending from the ventral region of the nerve ring[WB]. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms[GO].
has db xref: BTO:0002328
has db xref: GO:0007419
has db xref: WB:Paper00000938
has db xref: Wikipedia:Ventral_nerve_cord

Axiom
annotated source: ventral nerve cord
annotated property: UBPROP_0000001
annotated target: A cluster of neurons that extends posteriorly from the embryonic and larval brain and is surrounded by a connective tissue sheath.
source: FBbt:00001102

Axiom
annotated source: ventral nerve cord
annotated property: hasDbXref
annotated target: FBbt:00005097
mapping justification: ManualMappingCuration

Axiom
annotated source: ventral nerve cord
annotated property: hasExactSynonym
annotated target: ventral cord
has db xref: GO:0007419

anterior commissure
type: Class
subclass of: UBERON_0002473
subclass of: UBERON_0005341
disjoint with: posterior commissure
IAO_0000115: A bundle of myelinated nerve fibers passing transversely through the lamina terminalis and connecting symmetrical parts of the two cerebral hemispheres; it consists of a smaller anterior part (pars anterior commissurae anterioris) and a larger posterior part (pars posterior commissurae anterioris).
RO_0002175: NCBITaxon 9606
UBPROP_0000003: In all vertebrates the thin structure that connects the two halves of the telencephalon shows a ridge-like thickening at the basal side known as the anterior commissure.[well established][VHOG]
has db xref: BAMS:AC
has db xref: BAMS:AG
has db xref: BAMS:Ac
has db xref: BAMS:ac
has db xref: BIRNLEX:1557
has db xref: BM:Tel-AC
has db xref: BTO:0002169
has db xref: DHBA:10559
has db xref: DMBA:17751
has db xref: EMAPA:19038
has db xref: FMA:61961
has db xref: HBA:9221
has db xref: MA:0002722
has db xref: NCIT:C32086
has db xref: NLX:144088
has db xref: SCTID:279313001
has db xref: SCTID:369119009
has db xref: TAO:0001108
has db xref: UMLS:C0152335
has db xref: VHOG:0001558
has db xref: Wikipedia:Anterior_commissure
has db xref: ZFA:0001108
has db xref: neuronames:205
has exact synonym: anterior cerebral commissure
has exact synonym: commissura anterior cerebri
has exact synonym: commissura rostralis
has OBO namespace: uberon
has related synonym: AC
has related synonym: anterior commissural nucleus
has related synonym: commissura anterior
has related synonym: commissura rostral
has related synonym: paleocortical commissure
has related synonym: precommisure
has related synonym: rostral commissure
id: UBERON:0000935
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: anterior commissure
annotated property: subClassOf
annotated target: UBERON_0002473
source: FMA
source: MA

Axiom
annotated source: anterior commissure
annotated property: subClassOf
annotated target: UBERON_0005341
source: MP

Axiom
annotated source: anterior commissure
annotated property: disjointWith
annotated target: posterior commissure
source: lexical

Axiom
annotated source: anterior commissure
annotated property: IAO_0000115
annotated target: A bundle of myelinated nerve fibers passing transversely through the lamina terminalis and connecting symmetrical parts of the two cerebral hemispheres; it consists of a smaller anterior part (pars anterior commissurae anterioris) and a larger posterior part (pars posterior commissurae anterioris).
has db xref: BTO:0002169

Axiom
annotated source: anterior commissure
annotated property: UBPROP_0000003
annotated target: In all vertebrates the thin structure that connects the two halves of the telencephalon shows a ridge-like thickening at the basal side known as the anterior commissure.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001558
ontology: VHOG
source: DOI:10.1111/j.1749-6632.1969.tb20432.x
source: http://bgee.unil.ch/

Axiom
annotated source: anterior commissure
annotated property: hasDbXref
annotated target: UMLS:C0152335
source: BIRNLEX:1557
source: ncithesaurus:Anterior_Commissure

Axiom
annotated source: anterior commissure
annotated property: hasExactSynonym
annotated target: anterior cerebral commissure
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: anterior commissure
annotated property: hasExactSynonym
annotated target: commissura anterior cerebri
has db xref: NeuroNames:205
has synonym type: OMO_0003011

Axiom
annotated source: anterior commissure
annotated property: hasRelatedSynonym
annotated target: AC
has db xref: NLX:144088
has synonym type: OMO_0003000

Axiom
annotated source: anterior commissure
annotated property: hasRelatedSynonym
annotated target: anterior commissural nucleus
has db xref: BAMS:AC

Axiom
annotated source: anterior commissure
annotated property: hasRelatedSynonym
annotated target: commissura anterior
has db xref: Wikipedia:Anterior_commissure
has synonym type: OMO_0003011

Axiom
annotated source: anterior commissure
annotated property: hasRelatedSynonym
annotated target: paleocortical commissure
has db xref: NeuroNames:205

Axiom
annotated source: anterior commissure
annotated property: hasRelatedSynonym
annotated target: precommisure
has db xref: Wikipedia:Anterior_commisure

Axiom
annotated source: anterior commissure
annotated property: hasRelatedSynonym
annotated target: rostral commissure
has db xref: NeuroNames:205

posterior commissure
type: Class
equivalent class: Class
  intersection of: nervous system commissure
  intersection of: Restriction
    on property: RO_0002176
    some values from: UBERON_0014450
subclass of: UBERON_0011590
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7742
subclass of: Restriction
  on property: RO_0002176
  some values from: UBERON_0014450
IAO_0000115: Rounded band of white fibers crossing the middle line on the dorsal aspect of the upper end of the cerebral aqueduct. It is important in the bilateral pupillary light reflex. Its fibers acquire their medullary sheaths early, but their connections have not been definitely determined. Most of them have their origin in a nucleus, the nucleus of the posterior commissure (nucleus of Darkschewitsch), which lies in the central gray substance of the upper end of the cerebral aqueduct, in front of the nucleus of the oculomotor nerve. Some are probably derived from the posterior part of the thalamus and from the superior colliculus, whereas others are believed to be continued downward into the medial longitudinal fasciculus. The posterior commissure interconnects the pretectal nuclei, mediating the consensual pupillary light reflex[WP]. Diencephalic tract which is located in the vicinity of the dorsal diencephalon and mesencephalon and connects the pretectal nuclei. From Neuroanatomy of the Zebrafish Brain[ZFA].
IAO_0000116: add connects relationships and check these outside mammalia
UBPROP_0000012: part_of brainstem in MA; midbrain tectum in NIF
has db xref: BAMS:PC
has db xref: BAMS:pc
has db xref: BIRNLEX:1026
has db xref: BM:MB-Tec-PC
has db xref: DHBA:10567
has db xref: DMBA:17787
has db xref: EMAPA:35695
has db xref: FMA:62072
has db xref: HBA:9229
has db xref: MA:0002743
has db xref: MBA:158
has db xref: NCIT:C33356
has db xref: TAO:0000320
has db xref: UMLS:C0152327
has db xref: Wikipedia:Posterior_commissure
has db xref: ZFA:0000320
has db xref: neuronames:484
has exact synonym: caudal commissure
has exact synonym: epithalamic commissure
has OBO namespace: uberon
has related synonym: commissura epithalami
has related synonym: commissura epithalamica
has related synonym: commissura posterior
has related synonym: posterior commissure (Lieutaud)
id: UBERON:0000936
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: posterior commissure
annotated property: subClassOf
annotated target: Restriction
source: FMA

Axiom
annotated source: posterior commissure
annotated property: IAO_0000115
annotated target: Rounded band of white fibers crossing the middle line on the dorsal aspect of the upper end of the cerebral aqueduct. It is important in the bilateral pupillary light reflex. Its fibers acquire their medullary sheaths early, but their connections have not been definitely determined. Most of them have their origin in a nucleus, the nucleus of the posterior commissure (nucleus of Darkschewitsch), which lies in the central gray substance of the upper end of the cerebral aqueduct, in front of the nucleus of the oculomotor nerve. Some are probably derived from the posterior part of the thalamus and from the superior colliculus, whereas others are believed to be continued downward into the medial longitudinal fasciculus. The posterior commissure interconnects the pretectal nuclei, mediating the consensual pupillary light reflex[WP]. Diencephalic tract which is located in the vicinity of the dorsal diencephalon and mesencephalon and connects the pretectal nuclei. From Neuroanatomy of the Zebrafish Brain[ZFA].
has db xref: Wikipedia:Posterior_commissure
has db xref: ZFA:0000320

Axiom
annotated source: posterior commissure
annotated property: UBPROP_0000012
annotated target: part_of brainstem in MA; midbrain tectum in NIF
external ontology: MA

Axiom
annotated source: posterior commissure
annotated property: hasDbXref
annotated target: UMLS:C0152327
source: BIRNLEX:1026
source: ncithesaurus:Posterior_Commissure

Axiom
annotated source: posterior commissure
annotated property: hasDbXref
annotated target: neuronames:484
source: BIRNLEX:1026

Axiom
annotated source: posterior commissure
annotated property: hasExactSynonym
annotated target: caudal commissure
has db xref: FMA:62072
has db xref: ZFA:0000320

Axiom
annotated source: posterior commissure
annotated property: hasExactSynonym
annotated target: epithalamic commissure
has db xref: FMA:62072

Axiom
annotated source: posterior commissure
annotated property: hasRelatedSynonym
annotated target: commissura epithalami
has db xref: NeuroNames:484
has synonym type: OMO_0003011

Axiom
annotated source: posterior commissure
annotated property: hasRelatedSynonym
annotated target: commissura epithalamica
has db xref: NeuroNames:484
has synonym type: OMO_0003011

Axiom
annotated source: posterior commissure
annotated property: hasRelatedSynonym
annotated target: commissura posterior
has db xref: Wikipedia:Posterior_commissure
has synonym type: OMO_0003011

Axiom
annotated source: posterior commissure
annotated property: hasRelatedSynonym
annotated target: posterior commissure (Lieutaud)
has db xref: NeuroNames:484

imaginal disc
type: Class
subclass of: multi-tissue structure
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002548
IAO_0000115: One of the parts of a holometabolous insect larva that will become a portion of the outside of the adult insect during the pupal transformation.
has db xref: BTO:0004658
has db xref: FBbt:00001761
has db xref: MAT:0000064
has db xref: MESH:D060227
has db xref: MIAA:0000064
has db xref: Wikipedia:Imaginal_disc
has OBO namespace: uberon
has related synonym: imaginal disk
id: UBERON:0000939
in subset: uberon slim
comment: Though inaginal discs are sometimes described as “epithelial sacs”, we do not classify them as such, because an “epithelial sac” is defined in Uberon as being a single epithelium, whereas imaginal discs are made of several epithelia with distinct properties.

Axiom
annotated source: imaginal disc
annotated property: subClassOf
annotated target: multi-tissue structure
source: FBbt text definition

Axiom
annotated source: imaginal disc
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: imaginal disc
annotated property: IAO_0000115
annotated target: One of the parts of a holometabolous insect larva that will become a portion of the outside of the adult insect during the pupal transformation.
has db xref: Wikipedia:Imaginal_disc

Axiom
annotated source: imaginal disc
annotated property: hasDbXref
annotated target: FBbt:00001761
mapping justification: ManualMappingCuration

Axiom
annotated source: imaginal disc
annotated property: hasDbXref
annotated target: MESH:D060227
author id: https://orcid.org/0000-0001-9439-5346
mapping justification: ManualMappingCuration
mapping provider: https://github.com/biopragmatics/biomappings

cranial nerve II
type: Class
equivalent class: Class
  intersection of: UBERON_0034713
  intersection of: Restriction
    on property: RO_0002134
    some values from: retina
  intersection of: Restriction
    on property: extends fibers into
    some values from: optic chiasma
subclass of: UBERON_0004121
subclass of: UBERON_0011215
subclass of: UBERON_0034713
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002104
subclass of: Restriction
  on property: RO_0002134
  some values from: retina
subclass of: Restriction
  on property: extends fibers into
  some values from: optic chiasma
subclass of: Restriction
  on property: extends fibers into
  some values from: UBERON_0003098
IAO_0000115: Cranial nerve fiber tract which is comprised of retinal ganglion cell axons running posterior medially towards the optic chiasm, at which some of the axons cross the midline and after which the structure is termed the optic tract. Transmits visual information from the retina to the brain[ZFA].
IAO_0000116: Do not classify under 'cranial nerve', as this is not a true nerve - should be classified as evaginated sensory afferent[ISBN:0471888893]
RO_0002175: NCBITaxon 9606
UBPROP_0000001: A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO]
UBPROP_0000001: Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO]
UBPROP_0000003: (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG]
UBPROP_0000012: (relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon
has broad synonym: 2n
has broad synonym: optic nerve
has db xref: AAO:0010345
has db xref: BAMS:2n
has db xref: BAMS:IIn
has db xref: BAMS:nII
has db xref: BIRNLEX:1640
has db xref: CALOHA:TS-0713
has db xref: DHBA:15544
has db xref: EFO:0004258
has db xref: EHDAA2:0001313
has db xref: EHDAA:6788
has db xref: EMAPA:17575
has db xref: FMA:50863
has db xref: GAID:831
has db xref: HBA:9307
has db xref: MA:0001097
has db xref: MBA:848
has db xref: MESH:D009900
has db xref: NCIT:C12761
has db xref: SCTID:180938001
has db xref: TAO:0000435
has db xref: UMLS:C0029130
has db xref: VHOG:0000543
has db xref: Wikipedia:Optic_nerve
has db xref: XAO:0000188
has db xref: ZFA:0000435
has db xref: neuronames:289
has exact synonym: 02 optic nerve
has exact synonym: cranial II
has exact synonym: nervus opticus
has exact synonym: nervus opticus [II]
has exact synonym: optic II
has exact synonym: optic II nerve
has exact synonym: optic nerve [II]
has exact synonym: second cranial nerve
has OBO namespace: uberon
has related synonym: CN-II
has related synonym: nerve II
has related synonym: optic
id: UBERON:0000941
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: cranial nerve II
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: cranial nerve II
annotated property: IAO_0000115
annotated target: Cranial nerve fiber tract which is comprised of retinal ganglion cell axons running posterior medially towards the optic chiasm, at which some of the axons cross the midline and after which the structure is termed the optic tract. Transmits visual information from the retina to the brain[ZFA].
has db xref: ISBN:0471209627
has db xref: ISBN:0471888893

Axiom
annotated source: cranial nerve II
annotated property: UBPROP_0000001
annotated target: A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO]
date retrieved: 2012-08-14
external class: TAO:0000435
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: cranial nerve II
annotated property: UBPROP_0000001
annotated target: Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010345
ontology: AAO
source: AAO:EJS

Axiom
annotated source: cranial nerve II
annotated property: UBPROP_0000003
annotated target: (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000543
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429, http://medical-dictionary.thefreedictionary.com/optic+stalk
source: http://bgee.unil.ch/

Axiom
annotated source: cranial nerve II
annotated property: UBPROP_0000012
annotated target: (relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon
external ontology: MA

Axiom
annotated source: cranial nerve II
annotated property: hasBroadSynonym
annotated target: 2n
has db xref: BIRNLEX:1640
has db xref: NIFSTD:NeuroNames_abbrevSource
has synonym type: OMO_0003000

Axiom
annotated source: cranial nerve II
annotated property: hasBroadSynonym
annotated target: optic nerve
has db xref: FMA:50863
has db xref: ZFA:0000435
has synonym type: SENSU

Axiom
annotated source: cranial nerve II
annotated property: hasDbXref
annotated target: UMLS:C0029130
source: BIRNLEX:1640
source: ncithesaurus:Optic_Nerve

Axiom
annotated source: cranial nerve II
annotated property: hasDbXref
annotated target: neuronames:289
source: BIRNLEX:1640

Axiom
annotated source: cranial nerve II
annotated property: hasExactSynonym
annotated target: 02 optic nerve
has db xref: AAO:0010345

Axiom
annotated source: cranial nerve II
annotated property: hasExactSynonym
annotated target: nervus opticus
has synonym type: OMO_0003011

Axiom
annotated source: cranial nerve II
annotated property: hasExactSynonym
annotated target: nervus opticus [II]
has db xref: FMA:50863
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: cranial nerve II
annotated property: hasExactSynonym
annotated target: optic II
has db xref: EHDAA2:0001313

Axiom
annotated source: cranial nerve II
annotated property: hasExactSynonym
annotated target: optic II nerve
has db xref: EHDAA2:0001313

Axiom
annotated source: cranial nerve II
annotated property: hasRelatedSynonym
annotated target: CN-II
has db xref: ZFA:0000435

Axiom
annotated source: cranial nerve II
annotated property: hasRelatedSynonym
annotated target: nerve II
has db xref: NeuroNames:289

Axiom
annotated source: cranial nerve II
annotated property: hasRelatedSynonym
annotated target: optic
has db xref: TAO:0000435

stomach
type: Class
subclass of: UBERON_0004921
subclass of: UBERON_0010039
subclass of: Restriction
  on property: BFO_0000050
  some values from: foregut
subclass of: Restriction
  on property: RO_0002433
  some values from: digestive system
IAO_0000115: 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.
RO_0002161: NCBITaxon 7864
RO_0002161: NCBITaxon 7878
RO_0002161: NCBITaxon 7955
RO_0002161: NCBITaxon 9259
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
UBPROP_0000003: 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]
UBPROP_0000008: 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
has db xref: AAO:0000579
has db xref: ANISEED:1235297
has db xref: BTO:0001307
has db xref: CALOHA:TS-0980
has db xref: EFO:0000837
has db xref: EHDAA2:0001915
has db xref: EHDAA:2993
has db xref: EMAPA:17021
has db xref: EV:0100070
has db xref: FMA:7148
has db xref: GAID:293
has db xref: MA:0000353
has db xref: MAT:0000051
has db xref: MESH:D013270
has db xref: MIAA:0000051
has db xref: NCIT:C12391
has db xref: SCTID:181246003
has db xref: TAO:0002121
has db xref: UMLS:C0038351
has db xref: VHOG:0000408
has db xref: Wikipedia:Stomach
has db xref: XAO:0000128
has db xref: galen:Stomach
has narrow synonym: stomach chamber
has OBO namespace: uberon
has related synonym: anterior intestine
has related synonym: gaster
has related synonym: mesenteron
has related synonym: ventriculus
id: UBERON:0000945
in subset: efo slim
in subset: human reference atlas
in subset: major organ
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: stomach
annotated property: subClassOf
annotated target: UBERON_0004921
source: cjm

Axiom
annotated source: stomach
annotated property: subClassOf
annotated target: UBERON_0010039
source: cjm

Axiom
annotated source: stomach
annotated property: subClassOf
annotated target: Restriction
notes: absent in lampreys and hagfishes
source: ISBN:0073040584

Axiom
annotated source: stomach
annotated property: subClassOf
annotated target: Restriction
evidence: ISBN:0486692132

Axiom
annotated source: stomach
annotated property: IAO_0000115
annotated target: An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
has db xref: ISBN:0073040584
has db xref: Wikipedia:Stomach
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: stomach
annotated property: RO_0002161
annotated target: NCBITaxon 7864
source: Wikipedia

Axiom
annotated source: stomach
annotated property: RO_0002161
annotated target: NCBITaxon 7878
source: Wikipedia

Axiom
annotated source: stomach
annotated property: RO_0002161
annotated target: NCBITaxon 7955
source: ZFA

Axiom
annotated source: stomach
annotated property: RO_0002161
annotated target: NCBITaxon 9259
source: Wikipedia

Axiom
annotated source: stomach
annotated property: UBPROP_0000001
annotated target: Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000579
ontology: AAO
source: AAO:EJS

Axiom
annotated source: stomach
annotated property: UBPROP_0000003
annotated target: 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]
date retrieved: 2012-09-17
external class: VHOG:0000408
ontology: VHOG
source: DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000)
source: http://bgee.unil.ch/

Axiom
annotated source: stomach
annotated property: UBPROP_0000008
annotated target: 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
source: WP:Stomach#In_other_animals

Axiom
annotated source: stomach
annotated property: hasDbXref
annotated target: UMLS:C0038351
source: ncithesaurus:Stomach

Axiom
annotated source: stomach
annotated property: hasRelatedSynonym
annotated target: gaster
has db xref: BTO:0001307

Axiom
annotated source: stomach
annotated property: hasRelatedSynonym
annotated target: ventriculus
has db xref: Wikipedia:Stomach
has synonym type: OMO_0003011

cardiac valve
type: Class
subclass of: UBERON_0003978
subclass of: UBERON_0010313
subclass of: Restriction
  on property: BFO_0000050
  some values from: heart
IAO_0000115: A membranous fold of the heart that prevents reflux of fluid.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: One of the four structures within the heart that prevent backflow of blood by opening and closing with each heartbeat. The valves include two semilunar valves, the aortic and pulmonary; the mitral or bicuspid valve; and the tricuspid valve. The valves permit blood flow in only one direction. [TFD][VHOG]
UBPROP_0000003: Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human.[well established][VHOG]
UBPROP_0000013: Rector et al: One might be tempted to define 'heart valve' equivalently to 'valve in the heart', and 'valve' as a 'structure which functions as a valve'. But this combination results in the 'foramen ovale' being classified as a kind of 'heart valve', since it is undoubtedly located in the heart and functions as a valve
has db xref: BTO:0000564
has db xref: EMAPA:17869
has db xref: EV:0100024
has db xref: FMA:7110
has db xref: GAID:176
has db xref: MA:0000086
has db xref: MESH:D006351
has db xref: NCIT:C12729
has db xref: SCTID:181285005
has db xref: TAO:0005065
has db xref: UMLS:C0018826
has db xref: VHOG:0000818
has db xref: Wikipedia:Cardiac_valve
has db xref: XAO:0004126
has db xref: ZFA:0005065
has db xref: galen:HeartValve
has exact synonym: heart valve
has exact synonym: valve of heart
has OBO namespace: uberon
has related synonym: heart valve
has related synonym: heart valves
has related synonym: stomodaeal valve
has related synonym: valvule
id: UBERON:0000946
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: cardiac valve
annotated property: subClassOf
annotated target: Restriction
source: PMID:15797462

Axiom
annotated source: cardiac valve
annotated property: IAO_0000115
annotated target: A membranous fold of the heart that prevents reflux of fluid.
has db xref: MESH:A07.541.510
has db xref: MP:0000285
has db xref: PMID:7926784

Axiom
annotated source: cardiac valve
annotated property: UBPROP_0000001
annotated target: One of the four structures within the heart that prevent backflow of blood by opening and closing with each heartbeat. The valves include two semilunar valves, the aortic and pulmonary; the mitral or bicuspid valve; and the tricuspid valve. The valves permit blood flow in only one direction. [TFD][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000818
ontology: VHOG
source: http://bgee.unil.ch/
source: http://medical-dictionary.thefreedictionary.com/heart+valve

Axiom
annotated source: cardiac valve
annotated property: UBPROP_0000003
annotated target: Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000818
ontology: VHOG
source: DOI:10.1161/CIRCRESAHA.109.201566 Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)
source: http://bgee.unil.ch/

Axiom
annotated source: cardiac valve
annotated property: hasDbXref
annotated target: UMLS:C0018826
source: ncithesaurus:Cardiac_Valve

Axiom
annotated source: cardiac valve
annotated property: hasRelatedSynonym
annotated target: heart valve
has db xref: XAO:0004126

aorta
type: Class
subclass of: UBERON_0003509
subclass of: UBERON_0003519
subclass of: UBERON_0013768
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002170
  some values from: UBERON_0002084
IAO_0000115: The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation.
IAO_0000116: This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO]
UBPROP_0000003: When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]
UBPROP_0000007: aortic
UBPROP_0000008: All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches
has db xref: AAO:0010213
has db xref: BTO:0000135
has db xref: CALOHA:TS-0046
has db xref: EFO:0000265
has db xref: EMAPA:18601
has db xref: EV:0100027
has db xref: FMA:3734
has db xref: GAID:469
has db xref: MA:0000062
has db xref: MAT:0000035
has db xref: MESH:D001011
has db xref: MIAA:0000035
has db xref: NCIT:C12669
has db xref: SCTID:181298001
has db xref: UMLS:C0003483
has db xref: VHOG:0001523
has db xref: Wikipedia:Aorta
has db xref: XAO:0003010
has db xref: galen:Aorta
has exact synonym: trunk of aortic tree
has exact synonym: trunk of systemic arterial tree
has narrow synonym: dorsal aorta
has OBO namespace: uberon
has related synonym: arteria maxima
id: UBERON:0000947
in subset: efo slim
in subset: grouping class
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: aorta
annotated property: subClassOf
annotated target: UBERON_0003509
source: MA

Axiom
annotated source: aorta
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: aorta
annotated property: IAO_0000115
annotated target: The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation.
has db xref: ISBN:0-683-40008-8
has db xref: MESH:A07.231.114.056
has db xref: MP:0000272
has db xref: Wikipedia:Aorta
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: aorta
annotated property: IAO_0000116
annotated target: This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae.
source: WP

Axiom
annotated source: aorta
annotated property: UBPROP_0000001
annotated target: The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010213
ontology: AAO
source: AAO:BJB

Axiom
annotated source: aorta
annotated property: UBPROP_0000003
annotated target: When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001523
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620
source: http://bgee.unil.ch/

Axiom
annotated source: aorta
annotated property: hasDbXref
annotated target: UMLS:C0003483
source: ncithesaurus:Aorta

Axiom
annotated source: aorta
annotated property: hasNarrowSynonym
annotated target: dorsal aorta
has db xref: Wikipedia:Aorta#In_other_animals
has db xref: ZFA:0000014
has synonym type: SENSU

Axiom
annotated source: aorta
annotated property: hasRelatedSynonym
annotated target: arteria maxima
has db xref: Wikipedia:Aorta
has synonym type: OMO_0003011

heart
type: Class
equivalent class: Class
  intersection of: UBERON_0007100
  intersection of: Restriction
    on property: BFO_0000051
    some values from: UBERON_0004151
subclass of: UBERON_0004120
subclass of: UBERON_0005181
subclass of: UBERON_0007100
subclass of: UBERON_0010314
subclass of: Restriction
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0004151
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7742
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0004141
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0004535
IAO_0000115: A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
RO_0002161: NCBITaxon 6239
RO_0002161: NCBITaxon 7227
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]
UBPROP_0000001: Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]
UBPROP_0000002: relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
UBPROP_0000003: As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]
UBPROP_0000007: cardiac
has db xref: AAO:0010210
has db xref: BILA:0000020
has db xref: BTO:0000562
has db xref: CALOHA:TS-0445
has db xref: EFO:0000815
has db xref: EHDAA2:0000738
has db xref: EHDAA:420
has db xref: EMAPA:16105
has db xref: EV:0100018
has db xref: FMA:7088
has db xref: GAID:174
has db xref: MA:0000072
has db xref: MAT:0000036
has db xref: MESH:D006321
has db xref: MIAA:0000036
has db xref: NCIT:C12727
has db xref: SCTID:302509004
has db xref: TAO:0000114
has db xref: UMLS:C0018787
has db xref: VHOG:0000276
has db xref: Wikipedia:Heart
has db xref: XAO:0000064
has db xref: ZFA:0000114
has db xref: galen:Heart
has exact synonym: chambered heart
has exact synonym: vertebrate heart
has narrow synonym: branchial heart
has OBO namespace: uberon
has related synonym: cardium
id: UBERON:0000948
in subset: efo slim
in subset: human reference atlas
in subset: major organ
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core
comment: Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706

Axiom
annotated source: heart
annotated property: subClassOf
annotated target: Restriction
source: MA

Axiom
annotated source: heart
annotated property: IAO_0000115
annotated target: A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
has db xref: Wikipedia:Heart
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: heart
annotated property: UBPROP_0000001
annotated target: Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000114
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: heart
annotated property: UBPROP_0000001
annotated target: Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010210
ontology: AAO
source: AAO:BJB

Axiom
annotated source: heart
annotated property: UBPROP_0000002
annotated target: relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
date retrieved: 2012-06-20
external class: AAO:0010210
ontology: AAO

Axiom
annotated source: heart
annotated property: UBPROP_0000003
annotated target: As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000276
ontology: VHOG
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481
source: http://bgee.unil.ch/

Axiom
annotated source: heart
annotated property: hasDbXref
annotated target: UMLS:C0018787
source: ncithesaurus:Heart

Axiom
annotated source: heart
annotated property: hasExactSynonym
annotated target: chambered heart
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: heart
annotated property: hasNarrowSynonym
annotated target: branchial heart
has synonym type: SENSU

Axiom
annotated source: heart
annotated property: hasRelatedSynonym
annotated target: cardium
has db xref: EMAPA:16105

endocrine system
type: Class
subclass of: UBERON_0015204
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6072
subclass of: Restriction
  on property: RO_0002473
  some values from: UBERON_0002368
subclass of: Restriction
  on property: RO_0002492
  some values from: fully formed stage
disjoint with: reproductive system
disjoint with: respiratory system
disjoint with: digestive system
disjoint with: circulatory system
disjoint with: nervous system
disjoint with: gustatory system
disjoint with: UBERON_0001434
disjoint with: UBERON_0002204
disjoint with: UBERON_0002294
disjoint with: UBERON_0002330
disjoint with: UBERON_0002390
disjoint with: UBERON_0002405
disjoint with: UBERON_0002416
disjoint with: UBERON_0002423
disjoint with: UBERON_0004456
disjoint with: UBERON_8450002
IAO_0000115: Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.
UBPROP_0000001: Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]
UBPROP_0000003: Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]
UBPROP_0000007: endocrine
has db xref: AAO:0010279
has db xref: CALOHA:TS-1301
has db xref: EFO:0002969
has db xref: EHDAA2:0002224
has db xref: EMAPA:35306
has db xref: EV:0100128
has db xref: FBbt:00005068
has db xref: FMA:9668
has db xref: GAID:439
has db xref: MA:0000012
has db xref: MESH:D004703
has db xref: NCIT:C12705
has db xref: SCTID:278876000
has db xref: TAO:0001158
has db xref: UMLS:C0014136
has db xref: VHOG:0000098
has db xref: Wikipedia:Endocrine_system
has db xref: XAO:0000158
has db xref: ZFA:0001158
has exact synonym: endocrine glandular system
has exact synonym: endocrine system
has exact synonym: systema endocrinum
has OBO namespace: uberon
id: UBERON:0000949
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: endocrine system
annotated property: IAO_0000115
annotated target: Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.
has db xref: NLM:endocrine+system
has db xref: Wikipedia:Endocrine_system

Axiom
annotated source: endocrine system
annotated property: UBPROP_0000001
annotated target: Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010279
ontology: AAO
source: AAO:BJB

Axiom
annotated source: endocrine system
annotated property: UBPROP_0000003
annotated target: Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000098
ontology: VHOG
source: DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009)
source: http://bgee.unil.ch/

Axiom
annotated source: endocrine system
annotated property: hasDbXref
annotated target: FBbt:00005068
mapping justification: ManualMappingCuration

Axiom
annotated source: endocrine system
annotated property: hasDbXref
annotated target: UMLS:C0014136
source: ncithesaurus:Endocrine_System

Axiom
annotated source: endocrine system
annotated property: hasExactSynonym
annotated target: endocrine glandular system
has db xref: EHDAA2:0002224

rotator muscle of the vertebral column
type: Class
equivalent class: Class
  intersection of: UBERON_0001630
  intersection of: Restriction
    on property: BFO_0000050
    some values from: dorsum
  intersection of: Restriction
    on property: RO_0002372
    some values from: transverse process of vertebra
  intersection of: Restriction
    on property: RO_0002373
    some values from: neural spine
subclass of: UBERON_0001630
subclass of: UBERON_0005174
subclass of: Restriction
  on property: RO_0002372
  some values from: transverse process of vertebra
subclass of: Restriction
  on property: RO_0002373
  some values from: neural spine
IAO_0000115: Any of a number of short transversospinal muscles chiefly developed in cervical, lumbar, and thoracic regions, arising from the transverse process of one vertebra and inserted into the root of the spinous process of the next two or three vertebrae above, with nerve supply from the dorsal branches of the spinal nerve, and whose actions rotate the vertebral column.
has broad synonym: rotator muscle
has db xref: FMA:23081
has db xref: SCTID:244872002
has OBO namespace: uberon
id: UBERON:0000951

Axiom
annotated source: rotator muscle of the vertebral column
annotated property: IAO_0000115
annotated target: Any of a number of short transversospinal muscles chiefly developed in cervical, lumbar, and thoracic regions, arising from the transverse process of one vertebra and inserted into the root of the spinous process of the next two or three vertebrae above, with nerve supply from the dorsal branches of the spinal nerve, and whose actions rotate the vertebral column.
has db xref: http://medical-dictionary.thefreedictionary.com/rotator+muscle

Axiom
annotated source: rotator muscle of the vertebral column
annotated property: hasBroadSynonym
annotated target: rotator muscle
has db xref: FMA:23081

brain
type: Class
subclass of: organ
subclass of: UBERON_0004121
subclass of: Restriction
subclass of: Restriction
  on property: BSPO_0000123
  some values from: multicellular organism
subclass of: Restriction
  on property: RO_0002433
  some values from: nervous system
subclass of: Restriction
  on property: RO_0002473
  some values from: CL_0002319
subclass of: Restriction
  on property: RO_0002492
  some values from: fully formed stage
IAO_0000115: 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].
IAO_0000116: requires review for applicability to invertebrate structures, e.g. synganglion
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
UBPROP_0000001: Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
UBPROP_0000001: 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)
UBPROP_0000003: (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
has db xref: AAO:0010478
has db xref: ABA:Brain
has db xref: BAMS:Br
has db xref: BAMS:Brain
has db xref: BILA:0000135
has db xref: BIRNLEX:796
has db xref: BTO:0000142
has db xref: CALOHA:TS-0095
has db xref: DHBA:10155
has db xref: EFO:0000302
has db xref: EHDAA2:0000183
has db xref: EHDAA:2641
has db xref: EHDAA:6485
has db xref: EMAPA:16894
has db xref: EV:0100164
has db xref: FBbt:00005095
has db xref: FMA:50801
has db xref: GAID:571
has db xref: HBA:4005
has db xref: MA:0000168
has db xref: MAT:0000098
has db xref: MBA:8
has db xref: MBA:997
has db xref: MESH:D001921
has db xref: MIAA:0000098
has db xref: NCIT:C12439
has db xref: PBA:3999
has db xref: SCTID:258335003
has db xref: TAO:0000008
has db xref: UMLS:C0006104
has db xref: UMLS:C1269537
has db xref: VHOG:0000157
has db xref: Wikipedia:Brain
has db xref: XAO:0000010
has db xref: ZFA:0000008
has db xref: galen:Brain
has db xref: neuronames:21
has OBO namespace: uberon
has related synonym: encephalon
has related synonym: suprasegmental levels of nervous system
has related synonym: suprasegmental structures
has related synonym: synganglion
has related synonym: the brain
id: UBERON:0000955
in subset: cumbo
in subset: efo slim
in subset: human reference atlas
in subset: major organ
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: brain
annotated property: subClassOf
annotated target: organ
source: GO

Axiom
annotated source: brain
annotated property: subClassOf
annotated target: Restriction
source: FMA

Axiom
annotated source: brain
annotated property: subClassOf
annotated target: Restriction
source: Bgee:AN

Axiom
annotated source: brain
annotated property: IAO_0000115
annotated target: The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
has db xref: Wikipedia:Brain
has db xref: https://github.com/obophenotype/uberon/issues/300

Axiom
annotated source: brain
annotated property: UBPROP_0000001
annotated target: Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000008
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: brain
annotated property: UBPROP_0000001
annotated target: Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010478
ontology: AAO
source: AAO:BJB

Axiom
annotated source: brain
annotated property: UBPROP_0000001
annotated target: 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)
source: http://neurolex.org/wiki/Cumbo_terms

Axiom
annotated source: brain
annotated property: UBPROP_0000003
annotated target: (...) 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]
date retrieved: 2012-09-17
external class: VHOG:0000157
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165
source: http://bgee.unil.ch/

Axiom
annotated source: brain
annotated property: hasDbXref
annotated target: FBbt:00005095
mapping justification: ManualMappingCuration

Axiom
annotated source: brain
annotated property: hasDbXref
annotated target: UMLS:C0006104
source: BIRNLEX:796
source: ncithesaurus:Brain

Axiom
annotated source: brain
annotated property: hasDbXref
annotated target: UMLS:C1269537
source: BIRNLEX:796

Axiom
annotated source: brain
annotated property: hasDbXref
annotated target: neuronames:21
source: BIRNLEX:796

Axiom
annotated source: brain
annotated property: hasRelatedSynonym
annotated target: encephalon
has db xref: BTO:0000142

Axiom
annotated source: brain
annotated property: hasRelatedSynonym
annotated target: suprasegmental levels of nervous system
has db xref: NeuroNames:21

Axiom
annotated source: brain
annotated property: hasRelatedSynonym
annotated target: suprasegmental structures
has db xref: NeuroNames:21

Axiom
annotated source: brain
annotated property: hasRelatedSynonym
annotated target: the brain
has db xref: NeuroNames:21

cerebral cortex
type: Class
subclass of: UBERON_0011215
subclass of: UBERON_0016548
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002254
  some values from: UBERON_0004035
subclass of: Restriction
  on property: RO_0002254
  some values from: UBERON_0005343
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0001893
IAO_0000115: 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.
IAO_0000232: We follow NIFSTD in defining cerebral cortex and including both neocortex and hippocampal formation (DG+hippocampus).
RO_0002175: NCBITaxon_117569
RO_0002175: NCBITaxon 9606
UBPROP_0000001: 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].
UBPROP_0000003: 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]
UBPROP_0000008: hagfishes have independently evolved a highly laminated cerebral cortex, comparable in many ways to the cerebral cortex of mammals [http://icb.oxfordjournals.org/content/42/4/743]
has db xref: BAMS:C
has db xref: BAMS:CTX
has db xref: BAMS:Cerebral_cortex
has db xref: BAMS:Cx
has db xref: BIRNLEX:1494
has db xref: BM:Tel-Cx
has db xref: BTO:0000233
has db xref: CALOHA:TS-0091
has db xref: DHBA:10159
has db xref: EFO:0000328
has db xref: EHDAA2:0000234
has db xref: EHDAA:5464
has db xref: EMAPA:17544
has db xref: EV:0100166
has db xref: FMA:61830
has db xref: GAID:629
has db xref: HBA:4008
has db xref: MA:0000185
has db xref: MAT:0000108
has db xref: MBA:688
has db xref: MESH:D002540
has db xref: MIAA:0000108
has db xref: NCIT:C12443
has db xref: PBA:128011354
has db xref: SCTID:362880003
has db xref: UMLS:C0007776
has db xref: VHOG:0000722
has db xref: Wikipedia:Cerebral_cortex
has db xref: neuronames:39
has exact synonym: cortex of cerebral hemisphere
has OBO namespace: uberon
has related synonym: brain cortex
has related synonym: cortex cerebralis
has related synonym: cortex cerebri
has related synonym: cortical plate (CTXpl)
has related synonym: cortical plate (areas)
has related synonym: pallium of the brain
id: UBERON:0000956
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: cerebral cortex
annotated property: subClassOf
annotated target: UBERON_0016548
source: FMA

Axiom
annotated source: cerebral cortex
annotated property: subClassOf
annotated target: Restriction
source: GO
source: ISBN:0471888893

Axiom
annotated source: cerebral cortex
annotated property: subClassOf
annotated target: Restriction
source: FMA
source: MA

Axiom
annotated source: cerebral cortex
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: cerebral cortex
annotated property: IAO_0000115
annotated target: 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.
has db xref: BIRNLEX:1494

Axiom
annotated source: cerebral cortex
annotated property: UBPROP_0000001
annotated target: 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].
source: Wikipedia:Cerebral_cortex

Axiom
annotated source: cerebral cortex
annotated property: UBPROP_0000003
annotated target: 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]
date retrieved: 2012-09-17
external class: VHOG:0000722
ontology: VHOG
source: DOI:10.1111/j.1749-6632.1969.tb20437.x Kruger L, Experimental analyses of the reptilian nervous system. Annals of the New York Academy of Sciences (1969)
source: http://bgee.unil.ch/

Axiom
annotated source: cerebral cortex
annotated property: hasDbXref
annotated target: UMLS:C0007776
source: BIRNLEX:1494
source: ncithesaurus:Cortex

Axiom
annotated source: cerebral cortex
annotated property: hasDbXref
annotated target: neuronames:39
source: BIRNLEX:1494

Axiom
annotated source: cerebral cortex
annotated property: hasExactSynonym
annotated target: cortex of cerebral hemisphere
has db xref: BTO:0000233
has db xref: FMA:61830

Axiom
annotated source: cerebral cortex
annotated property: hasRelatedSynonym
annotated target: brain cortex
has db xref: BTO:0000233

Axiom
annotated source: cerebral cortex
annotated property: hasRelatedSynonym
annotated target: cortex cerebralis
has db xref: NeuroNames:39
has synonym type: OMO_0003011

Axiom
annotated source: cerebral cortex
annotated property: hasRelatedSynonym
annotated target: cortex cerebri
has db xref: Wikipedia:Cerebral_cortex
has synonym type: OMO_0003011

Axiom
annotated source: cerebral cortex
annotated property: hasRelatedSynonym
annotated target: cortical plate (CTXpl)
has db xref: NeuroNames:39

Axiom
annotated source: cerebral cortex
annotated property: hasRelatedSynonym
annotated target: cortical plate (areas)
has db xref: NeuroNames:39

Axiom
annotated source: cerebral cortex
annotated property: hasRelatedSynonym
annotated target: pallium of the brain
has db xref: BTO:0000233

lamina
type: Class
equivalent class: Class
  intersection of: tissue
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002124
subclass of: tissue
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0002124
IAO_0000115: Any thin layer or plate.
IAO_0000116: TODO - merge with cell layer?
UBPROP_0000007: laminar
has db xref: Wikipedia:Lamina_of_the_vertebral_arch
has exact synonym: laminar tissue
has OBO namespace: uberon
id: UBERON:0000957
in subset: non informative
in subset: uberon slim
in subset: upper level

Axiom
annotated source: lamina
annotated property: IAO_0000115
annotated target: Any thin layer or plate.
has db xref: Wikipedia:Lamina_of_the_vertebral_arch

medulla of organ
type: Class
subclass of: compound organ component
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6072
subclass of: Restriction
  on property: RO_0002219
  some values from: UBERON_0001851
IAO_0000115: Middle part of an organ, surrounded by the cortex.
IAO_0000232: this class is used in a very general sense
UBPROP_0000007: medullary
has db xref: FMA:61108
has db xref: galen:Medulla
has exact synonym: medulla
has OBO namespace: uberon
id: UBERON:0000958
in subset: upper level

Axiom
annotated source: medulla of organ
annotated property: IAO_0000115
annotated target: Middle part of an organ, surrounded by the cortex.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: medulla of organ
annotated property: hasExactSynonym
annotated target: medulla
has db xref: FMA:61108

optic chiasma
type: Class
equivalent class: Class
  intersection of: UBERON_0007418
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001894
  intersection of: Restriction
    on property: extends fibers into
    some values from: cranial nerve II
  intersection of: Restriction
    on property: extends fibers into
    some values from: UBERON_0001908
subclass of: UBERON_0007425
subclass of: Restriction
  on property: extends fibers into
  some values from: cranial nerve II
subclass of: Restriction
  on property: extends fibers into
  some values from: UBERON_0001908
IAO_0000115: A decussation of the diencephalon where the fibers of the optic nerve cross.
UBPROP_0000001: The point at which fibers of the optic nerves cross.[AAO]
UBPROP_0000003: The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG]
has db xref: AAO:0010622
has db xref: BAMS:DC
has db xref: BAMS:OC
has db xref: BAMS:och
has db xref: BAMS:ox
has db xref: BIRNLEX:1416
has db xref: BM:Tel-OCX
has db xref: DHBA:10644
has db xref: DMBA:17783
has db xref: EHDAA2:0001302
has db xref: EHDAA:10227
has db xref: EMAPA:17603
has db xref: FMA:62045
has db xref: GAID:832
has db xref: HBA:9310
has db xref: MA:0001098
has db xref: MBA:117
has db xref: MESH:D009897
has db xref: NCIT:C90609
has db xref: SCTID:244453006
has db xref: TAO:0000556
has db xref: UMLS:C0029126
has db xref: VHOG:0000190
has db xref: Wikipedia:Optic_chiasm
has db xref: XAO:0004071
has db xref: ZFA:0000556
has db xref: neuronames:459
has exact synonym: chiasma opticum
has exact synonym: decussation of optic nerve fibers
has exact synonym: optic chiasm
has OBO namespace: uberon
has related synonym: chiasma
has related synonym: chiasma nervorum opticorum
has related synonym: optic chiasm (Rufus of Ephesus)
id: UBERON:0000959
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: optic chiasma
annotated property: IAO_0000115
annotated target: A decussation of the diencephalon where the fibers of the optic nerve cross.
has db xref: MGI:llw2
has db xref: MP:0009770
has db xref: Wikipedia:Optic_chiasm
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: optic chiasma
annotated property: UBPROP_0000001
annotated target: The point at which fibers of the optic nerves cross.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010622
ontology: AAO
source: AAO:DSM

Axiom
annotated source: optic chiasma
annotated property: UBPROP_0000003
annotated target: The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000190
ontology: VHOG
source: DOI:10.1016/j.preteyeres.2005.04.005 Jeffery G, Erskine L, Variations in the architecture and development of the vertebrate optic chiasm. Progress in retinal and eye research (2005)
source: http://bgee.unil.ch/

Axiom
annotated source: optic chiasma
annotated property: hasDbXref
annotated target: UMLS:C0029126
source: BIRNLEX:1416
source: ncithesaurus:Optic_Chiasm

Axiom
annotated source: optic chiasma
annotated property: hasDbXref
annotated target: neuronames:459
source: BIRNLEX:1416

Axiom
annotated source: optic chiasma
annotated property: hasExactSynonym
annotated target: chiasma opticum
has db xref: Wikipedia:Optic_chiasm
has synonym type: OMO_0003011

Axiom
annotated source: optic chiasma
annotated property: hasExactSynonym
annotated target: decussation of optic nerve fibers
has db xref: FMA:62045

Axiom
annotated source: optic chiasma
annotated property: hasExactSynonym
annotated target: optic chiasm
has db xref: Wikipedia:Optic_chiasm

Axiom
annotated source: optic chiasma
annotated property: hasRelatedSynonym
annotated target: chiasma
has db xref: NeuroNames:459
has synonym type: OMO_0003011

Axiom
annotated source: optic chiasma
annotated property: hasRelatedSynonym
annotated target: chiasma nervorum opticorum
has db xref: NeuroNames:459
has synonym type: OMO_0003011

Axiom
annotated source: optic chiasma
annotated property: hasRelatedSynonym
annotated target: optic chiasm (Rufus of Ephesus)
has db xref: NeuroNames:459

nerve of cervical vertebra
type: Class
equivalent class: Class
  intersection of: UBERON_0001780
  intersection of: Restriction
    on property: extends fibers into
    some values from: UBERON_0002726
subclass of: UBERON_0001780
subclass of: Restriction
  on property: extends fibers into
  some values from: UBERON_0002726
IAO_0000115: The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted].
RO_0002175: NCBITaxon 9606
has db xref: BAMS:cern
has db xref: FMA:5859
has db xref: NCIT:C32299
has db xref: NLXANAT:20090207
has db xref: SCTID:360497008
has db xref: UMLS:C0228815
has db xref: Wikipedia:Cervical_nerves
has db xref: neuronames:2351
has exact synonym: cervical nerve
has exact synonym: cervical nerve tree
has exact synonym: cervical spinal nerve
has exact synonym: nervus cervicalis
has OBO namespace: uberon
id: UBERON:0000962
in subset: human reference atlas
in subset: uberon slim
comment: Innervates: sternohyoid muscle, sternothyroid muscle, omohyoid muscle[WP]

Axiom
annotated source: nerve of cervical vertebra
annotated property: IAO_0000115
annotated target: The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted].
has db xref: Wikipedia:Cervical_nerves

Axiom
annotated source: nerve of cervical vertebra
annotated property: hasDbXref
annotated target: UMLS:C0228815
source: ncithesaurus:Cervical_Nerve

Axiom
annotated source: nerve of cervical vertebra
annotated property: hasExactSynonym
annotated target: cervical nerve
has db xref: FMA:5859

Axiom
annotated source: nerve of cervical vertebra
annotated property: hasExactSynonym
annotated target: nervus cervicalis
has db xref: FMA:5859
has db xref: FMA:TA
has synonym type: OMO_0003011

head sensillum
type: Class
equivalent class: Class
  intersection of: UBERON_0002536
  intersection of: Restriction
    on property: BFO_0000050
    some values from: head
subclass of: UBERON_0002536
subclass of: Restriction
  on property: BFO_0000050
  some values from: head
IAO_0000116: this term should be ceded to the arthropod anatomy ontology
has db xref: FBbt:00004114
has db xref: MAT:0000204
has db xref: MIAA:0000204
has OBO namespace: uberon
id: UBERON:0000963

Axiom
annotated source: head sensillum
annotated property: hasDbXref
annotated target: FBbt:00004114
mapping justification: ManualMappingCuration

cornea
type: Class
subclass of: UBERON_0010000
subclass of: UBERON_0010313
subclass of: Restriction
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0001772
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0004370
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0000964
subclass of: Restriction
  on property: RO_0002150
  some values from: UBERON_0001773
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0005427
subclass of: Restriction
  on property: RO_0002256
  some values from: UBERON_0005426
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0001801
IAO_0000115: The transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure.
RO_0002175: NCBITaxon 9606
UBPROP_0000007: corneal
UBPROP_0000008: Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water
has db xref: AAO:0010344
has db xref: BTO:0000286
has db xref: CALOHA:TS-0171
has db xref: EFO:0000377
has db xref: EHDAA2:0000316
has db xref: EHDAA:10199
has db xref: EMAPA:17161
has db xref: EV:0100341
has db xref: FMA:58238
has db xref: GAID:892
has db xref: MA:0000266
has db xref: MESH:D003315
has db xref: NCIT:C12342
has db xref: SCTID:181162001
has db xref: TAO:0000640
has db xref: UMLS:C0010031
has db xref: VHOG:0000164
has db xref: Wikipedia:Cornea
has db xref: XAO:0000180
has db xref: ZFA:0000640
has exact synonym: cornea of camera-type eye
has OBO namespace: uberon
has related synonym: corneas
has related synonym: tunica cornea
id: UBERON:0000964
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: cornea
annotated property: subClassOf
annotated target: Restriction
source: MA

Axiom
annotated source: cornea
annotated property: subClassOf
annotated target: Restriction
source: MA

Axiom
annotated source: cornea
annotated property: subClassOf
annotated target: Restriction
source: FMA-isa

Axiom
annotated source: cornea
annotated property: subClassOf
annotated target: Restriction
evidence: definitional

Axiom
annotated source: cornea
annotated property: IAO_0000115
annotated target: The transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure.
has db xref: ISBN:0-683-40008-8
has db xref: MESH:A09.371.060.217
has db xref: MP:0001312

Axiom
annotated source: cornea
annotated property: hasDbXref
annotated target: UMLS:C0010031
source: ncithesaurus:Cornea

Axiom
annotated source: cornea
annotated property: hasExactSynonym
annotated target: cornea of camera-type eye
has db xref: GO:0061303

Axiom
annotated source: cornea
annotated property: hasRelatedSynonym
annotated target: corneas
has db xref: ZFA:0000640
has synonym type: OMO_0003004

lens of camera-type eye
type: Class
subclass of: UBERON_0005389
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001801
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0005426
subclass of: Restriction
  on property: RO_0002256
  some values from: UBERON_0003902
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0001801
IAO_0000115: A transparent and refractive lens located posterior to the iris. The lens of camera-type eye refracts light to be focused on the retina.
RO_0002171: UBERON_0002049
RO_0002175: NCBITaxon 9606
UBPROP_0000003: The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
UBPROP_0000008: This class excludes compound eye corneal lenses.
has db xref: AAO:0010348
has db xref: BTO:0000723
has db xref: CALOHA:TS-0545
has db xref: EHDAA:9057
has db xref: EMAPA:17838
has db xref: EV:0100343
has db xref: FMA:58241
has db xref: MA:0000275
has db xref: MAT:0000141
has db xref: MESH:D007908
has db xref: MIAA:0000141
has db xref: NCIT:C12743
has db xref: RETIRED_EHDAA2:0000975
has db xref: SCTID:181169005
has db xref: TAO:0000035
has db xref: UMLS:C0023317
has db xref: VHOG:0000169
has db xref: Wikipedia:Lens_(anatomy)
has db xref: XAO:0000008
has db xref: ZFA:0000035
has exact synonym: camera-type eye lens
has exact synonym: eye lens
has exact synonym: lens
has exact synonym: lens crystallina
has OBO namespace: uberon
has related synonym: crystalline lens
has related synonym: lenses
has related synonym: ocular lens
id: UBERON:0000965
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core
comment: The lens is avascular and nourished by diffusion from the aqueous and vitreous humors.

Axiom
annotated source: lens of camera-type eye
annotated property: IAO_0000115
annotated target: A transparent and refractive lens located posterior to the iris. The lens of camera-type eye refracts light to be focused on the retina.
has db xref: Wikipedia:Lens_(anatomy)
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: lens of camera-type eye
annotated property: UBPROP_0000003
annotated target: The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000169
ontology: VHOG
source: DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
source: http://bgee.unil.ch/

Axiom
annotated source: lens of camera-type eye
annotated property: hasDbXref
annotated target: UMLS:C0023317
source: ncithesaurus:Crystalline_Lens

Axiom
annotated source: lens of camera-type eye
annotated property: hasExactSynonym
annotated target: camera-type eye lens
has db xref: GO:0002088

Axiom
annotated source: lens of camera-type eye
annotated property: hasExactSynonym
annotated target: eye lens
has synonym type: SENSU

Axiom
annotated source: lens of camera-type eye
annotated property: hasExactSynonym
annotated target: lens
has synonym type: SENSU

Axiom
annotated source: lens of camera-type eye
annotated property: hasExactSynonym
annotated target: lens crystallina
has db xref: Wikipedia:Lens_(anatomy)

Axiom
annotated source: lens of camera-type eye
annotated property: hasRelatedSynonym
annotated target: crystalline lens
has db xref: BTO:0000723
has db xref: PMID:36055924

Axiom
annotated source: lens of camera-type eye
annotated property: hasRelatedSynonym
annotated target: lenses
has db xref: ZFA:0000035
has synonym type: OMO_0003004

Axiom
annotated source: lens of camera-type eye
annotated property: hasRelatedSynonym
annotated target: ocular lens
has db xref: BTO:0000723

retina
type: Class
subclass of: UBERON_0004121
subclass of: UBERON_0005388
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001802
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0019207
IAO_0000115: The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
RO_0002161: NCBITaxon 6656
RO_0002175: NCBITaxon 9606
UBPROP_0000001: The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]
UBPROP_0000003: The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
UBPROP_0000007: retinal
has db xref: AAO:0010352
has db xref: BAMS:R
has db xref: BIRNLEX:1153
has db xref: BTO:0001175
has db xref: CALOHA:TS-0865
has db xref: EFO:0000832
has db xref: EHDAA2:0001627
has db xref: EHDAA:4757
has db xref: EMAPA:17168
has db xref: EV:0100348
has db xref: FMA:58301
has db xref: GAID:755
has db xref: MA:0000276
has db xref: MAT:0000142
has db xref: MBA:304325711
has db xref: MESH:D012160
has db xref: MIAA:0000142
has db xref: NCIT:C12343
has db xref: NIFSTD_RETIRED:birnlex_1156
has db xref: SCTID:181171005
has db xref: TAO:0000152
has db xref: UMLS:C0035298
has db xref: UMLS:C1278894
has db xref: VHOG:0000229
has db xref: Wikipedia:Retina
has db xref: XAO:0000009
has db xref: ZFA:0000152
has db xref: neuronames:1862
has exact synonym: inner layer of eyeball
has exact synonym: retina of camera-type eye
has exact synonym: tunica interna of eyeball
has OBO namespace: uberon
has related synonym: Netzhaut
has related synonym: retinas
id: UBERON:0000966
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core
comment: Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. Use the parent class photoreceptor array / light-sensitive tissue for arthropods

Axiom
annotated source: retina
annotated property: subClassOf
annotated target: Restriction
source: FMA

Axiom
annotated source: retina
annotated property: subClassOf
annotated target: Restriction
source: FMA

Axiom
annotated source: retina
annotated property: subClassOf
annotated target: Restriction
source: FMA

Axiom
annotated source: retina
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: retina
annotated property: IAO_0000115
annotated target: The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
has db xref: Wikipedia:Retina
has db xref: ZFIN:curator

Axiom
annotated source: retina
annotated property: UBPROP_0000001
annotated target: The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000152
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: retina
annotated property: UBPROP_0000003
annotated target: The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000229
ontology: VHOG
source: DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
source: http://bgee.unil.ch/

Axiom
annotated source: retina
annotated property: hasDbXref
annotated target: UMLS:C0035298
source: BIRNLEX:1153
source: ncithesaurus:Retina

Axiom
annotated source: retina
annotated property: hasDbXref
annotated target: UMLS:C1278894
source: BIRNLEX:1153

Axiom
annotated source: retina
annotated property: hasExactSynonym
annotated target: retina of camera-type eye
has db xref: GO:0060041

Axiom
annotated source: retina
annotated property: hasRelatedSynonym
annotated target: Netzhaut
has db xref: BTO:0001175

Axiom
annotated source: retina
annotated property: hasRelatedSynonym
annotated target: retinas
has db xref: ZFA:0000152
has synonym type: OMO_0003004

eye
type: Class
subclass of: sense organ
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002104
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0009584
IAO_0000115: An organ that detects light.
IAO_0000232: This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)
RO_0002175: NCBITaxon 9606
UBPROP_0000007: ocular
UBPROP_0000007: optic
UBPROP_0000010: Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva,
has db xref: BILA:0000017
has db xref: BTO:0000439
has db xref: CALOHA:TS-0309
has db xref: EFO:0000827
has db xref: EV:0100336
has db xref: FBbt:00005162
has db xref: GAID:69
has db xref: MAT:0000140
has db xref: MESH:D005123
has db xref: MIAA:0000140
has db xref: Wikipedia:Eye
has OBO namespace: uberon
has related synonym: light-detecting organ
has related synonym: visual apparatus
id: UBERON:0000970
in subset: efo slim
in subset: functional classification
in subset: human reference atlas
in subset: major organ
in subset: organ slim
in subset: uberon slim

Axiom
annotated source: eye
annotated property: subClassOf
annotated target: Restriction
source: PMID:21062451

Axiom
annotated source: eye
annotated property: subClassOf
annotated target: Restriction
source: PMID:21062451

Axiom
annotated source: eye
annotated property: IAO_0000115
annotated target: An organ that detects light.
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: eye
annotated property: hasDbXref
annotated target: FBbt:00005162
mapping justification: ManualMappingCuration

Axiom
annotated source: eye
annotated property: hasRelatedSynonym
annotated target: visual apparatus
has db xref: EV:0100336

ommatidium
type: Class
subclass of: eye
subclass of: UBERON_0002536
subclass of: Restriction
  on property: BFO_0000050
  some values from: compound eye
IAO_0000115: The smallest morphological and functional unit of the compound eye that consists of a usually limited and often constant number of rhabdomeric photoreceptor cells, cornea-secreting epithelial cells, and interommatidial pigment cells, and may additionally contain crystalline cone cells.
UBPROP_0000007: ommatidial
has db xref: BTO:0001922
has db xref: FBbt:00004510
has db xref: HAO:0000666
has db xref: MAT:0000143
has db xref: MIAA:0000143
has db xref: Wikipedia:Ommatidium
has exact synonym: omatidium
has OBO namespace: uberon
has related synonym: omatidia
id: UBERON:0000971
in subset: uberon slim

Axiom
annotated source: ommatidium
annotated property: subClassOf
annotated target: eye
source: PMID:21062451

Axiom
annotated source: ommatidium
annotated property: IAO_0000115
annotated target: The smallest morphological and functional unit of the compound eye that consists of a usually limited and often constant number of rhabdomeric photoreceptor cells, cornea-secreting epithelial cells, and interommatidial pigment cells, and may additionally contain crystalline cone cells.
has db xref: PMID:21062451

Axiom
annotated source: ommatidium
annotated property: hasDbXref
annotated target: FBbt:00004510
mapping justification: ManualMappingCuration

Axiom
annotated source: ommatidium
annotated property: hasRelatedSynonym
annotated target: omatidia
has synonym type: OMO_0003004

antenna
type: Class
subclass of: appendage
subclass of: UBERON_0015212
subclass of: Restriction
  on property: BFO_0000050
  some values from: head
subclass of: Restriction
  on property: BSPO_0000126
  some values from: head
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6656
IAO_0000115: The paired, usually multiple jointed, sensory organs articulating on the procephalic region of the head capsule; its highly versatile sensory structures are capable to detect the various environmental stimuli. In the context of Drosophila refers to they are the most anterior segmented sensory appendage of the head.
IAO_0000116: this term should be ceded to the arthropod anatomy ontology
RO_0002161: NCBITaxon 6843
UBPROP_0000007: antennal
UBPROP_0000007: antenno
has db xref: AEO:0000198
has db xref: BTO:0000074
has db xref: EFO:0000874
has db xref: FBbt:00004511
has db xref: HAO:0000101
has db xref: MAT:0000086
has db xref: MIAA:0000086
has db xref: TGMA:0000007
has db xref: Wikipedia:Antenna_(biology)
has OBO namespace: uberon
has related synonym: feeler
id: UBERON:0000972
in subset: efo slim
in subset: uberon slim

Axiom
annotated source: antenna
annotated property: subClassOf
annotated target: appendage
source: FBbt

Axiom
annotated source: antenna
annotated property: IAO_0000115
annotated target: The paired, usually multiple jointed, sensory organs articulating on the procephalic region of the head capsule; its highly versatile sensory structures are capable to detect the various environmental stimuli. In the context of Drosophila refers to they are the most anterior segmented sensory appendage of the head.
has db xref: FB:gg
has db xref: ISBN:3110148986
has db xref: Wikipedia:Antenna_(biology)

Axiom
annotated source: antenna
annotated property: hasDbXref
annotated target: FBbt:00004511
mapping justification: ManualMappingCuration

Axiom
annotated source: antenna
annotated property: hasRelatedSynonym
annotated target: feeler
has db xref: BTO:0000074

neck
type: Class
subclass of: organism subdivision
subclass of: Restriction
  on property: BFO_0000050
  some values from: anterior region of body
subclass of: Restriction
  on property: anteriorly connected to
  some values from: head
subclass of: Restriction
  on property: posteriorly connected to
  some values from: UBERON_0002100
IAO_0000115: An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.
IAO_0000232: true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck.
RO_0002174: NCBITaxon_32443
UBPROP_0000007: cervical
has db xref: AEO:0000108
has db xref: BTO:0000420
has db xref: CALOHA:TS-2045
has db xref: EFO:0000967
has db xref: EHDAA2:0003108
has db xref: EMAPA:35587
has db xref: FMA:7155
has db xref: GAID:86
has db xref: MA:0000024
has db xref: MAT:0000297
has db xref: MESH:D009333
has db xref: MIAA:0000297
has db xref: NCIT:C13063
has db xref: SCTID:302550007
has db xref: UMLS:C0027530
has db xref: Wikipedia:Neck
has db xref: galen:Neck
has OBO namespace: uberon
has related synonym: collum
has related synonym: neck (volume)
id: UBERON:0000974
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: neck
annotated property: IAO_0000115
annotated target: An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: neck
annotated property: RO_0002174
annotated target: NCBITaxon_32443
source: ISBN:9780674021839

Axiom
annotated source: neck
annotated property: hasDbXref
annotated target: UMLS:C0027530
source: ncithesaurus:Neck

Axiom
annotated source: neck
annotated property: hasRelatedSynonym
annotated target: collum
has db xref: Wikipedia:Neck
has synonym type: OMO_0003011

Axiom
annotated source: neck
annotated property: hasRelatedSynonym
annotated target: neck (volume)
has db xref: FMA:7155

sternum
type: Class
subclass of: UBERON_0005181
subclass of: UBERON_0010363
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002170
  some values from: UBERON_0002228
subclass of: Restriction
  on property: RO_0002170
  some values from: UBERON_0007831
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0003252
IAO_0000115: A midventral endochondral skeletal element which represents the origin site of the pectoral muscles[PHENOSCAPE:ad].
IAO_0000116: in EMAPA and EHDAA2 this is part of the skeleton of pectoral girdle; the classic def of pectoral girdle (see WP) excludes the rib cage and sternum
RO_0002161: NCBITaxon 8570
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Single element that constitutes the postzonal area of the pectoral girdle.[AAO]
UBPROP_0000002: relationship loss: part_of postzonal element (AAO:0000938)[AAO]
UBPROP_0000003: Fishes lack a sternum. (...) A sternum is absent in the first fossil tetrapods, but it is present in modern amphibians. (...) Thus, a sternum occurs in some modern amphibians, birds, mammals and archosaurs. However, its absence in the common ancestors to these groups means that it has arisen independently several times within the field of the midventral connective tissue.[well established][VHOG]
UBPROP_0000007: sternal
UBPROP_0000008: It probably first evolved in early tetrapods as an extension of the pectoral girdle; it is not found in fish. In amphibians and reptiles it is typically a shield-shaped structure, often composed entirely of cartilage. It is absent in both turtles and snakes. In birds it is a relatively large bone and typically bears an enormous projecting keel to which the flight muscles are attached. Only in mammals does the sternum take on the elongated, segmented form seen in humans. In some mammals, such as opossums, the individual segments never fuse and remain separated by cartilagenous plates throughout life
UBPROP_0000008: in birds, either ratite (no keel or carina) or carinate (keel and carina present)
UBPROP_0000011: While its developmental origins are similar to the ribs (from the myospetum and septum of the trunk region), it is often associated with the pectoral skeleton, due to both function and physical connections (i.e. the coracoid of archosaurs). It may be a single element or a series of smaller structure (sternebrae). Based on Kardong 2012. [PHENOSCAPE:ad].
has db xref: AAO:0000765
has db xref: BTO:0001302
has db xref: CALOHA:TS-0972
has db xref: EHDAA2:0001914
has db xref: EHDAA:9561
has db xref: EMAPA:18344
has db xref: FMA:7485
has db xref: GAID:246
has db xref: MA:0001331
has db xref: MESH:D013249
has db xref: NCIT:C12793
has db xref: SCTID:302522007
has db xref: UMLS:C0038293
has db xref: VHOG:0000856
has db xref: Wikipedia:Sternum
has db xref: galen:Sternum
has exact synonym: vertebrate sternum
has OBO namespace: uberon
has related synonym: breastbone
id: UBERON:0000975
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: sternum
annotated property: subClassOf
annotated target: UBERON_0010363
source: ISBN:0073040584

Axiom
annotated source: sternum
annotated property: subClassOf
annotated target: Restriction
source: FMA

Axiom
annotated source: sternum
annotated property: subClassOf
annotated target: Restriction
source: ISBN:0073040584

Axiom
annotated source: sternum
annotated property: IAO_0000115
annotated target: A midventral endochondral skeletal element which represents the origin site of the pectoral muscles[PHENOSCAPE:ad].
has db xref: PHENOSCAPE:ad
has db xref: https://github.com/obophenotype/uberon/issues/67

Axiom
annotated source: sternum
annotated property: RO_0002161
annotated target: NCBITaxon 8570
source: Wikipedia

Axiom
annotated source: sternum
annotated property: UBPROP_0000001
annotated target: Single element that constitutes the postzonal area of the pectoral girdle.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000765
ontology: AAO
source: AAO:LAP

Axiom
annotated source: sternum
annotated property: UBPROP_0000002
annotated target: relationship loss: part_of postzonal element (AAO:0000938)[AAO]
date retrieved: 2012-06-20
external class: AAO:0000765
ontology: AAO

Axiom
annotated source: sternum
annotated property: UBPROP_0000003
annotated target: Fishes lack a sternum. (...) A sternum is absent in the first fossil tetrapods, but it is present in modern amphibians. (...) Thus, a sternum occurs in some modern amphibians, birds, mammals and archosaurs. However, its absence in the common ancestors to these groups means that it has arisen independently several times within the field of the midventral connective tissue.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000856
ontology: VHOG
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.294
source: http://bgee.unil.ch/

Axiom
annotated source: sternum
annotated property: UBPROP_0000011
annotated target: While its developmental origins are similar to the ribs (from the myospetum and septum of the trunk region), it is often associated with the pectoral skeleton, due to both function and physical connections (i.e. the coracoid of archosaurs). It may be a single element or a series of smaller structure (sternebrae). Based on Kardong 2012. [PHENOSCAPE:ad].
source: WP

Axiom
annotated source: sternum
annotated property: hasDbXref
annotated target: UMLS:C0038293
source: ncithesaurus:Sternum

Axiom
annotated source: sternum
annotated property: hasRelatedSynonym
annotated target: breastbone
has db xref: BTO:0001302

humerus
type: Class
equivalent class: Class
  intersection of: UBERON_0015053
  intersection of: Restriction
    on property: RO_0002473
    some values from: UBERON_0002481
subclass of: UBERON_0003461
subclass of: UBERON_0003607
subclass of: UBERON_0004250
subclass of: UBERON_0015053
subclass of: Restriction
  on property: RO_0002131
  some values from: UBERON_0001470
subclass of: Restriction
  on property: proximally connected to
  some values from: UBERON_0007831
IAO_0000115: Paired endochondral long bone that extends between the pectoral girdle and the skeletal parts of the forelimb. [PHENOSCAPE:mah].
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Paired, elongate, cylindrical bones of endochondral origin that extend from the pectoral girdle to the elbows.[AAO]
UBPROP_0000003: Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
UBPROP_0000007: humeral
has db xref: AAO:0000679
has db xref: CALOHA:TS-2202
has db xref: EFO:0001398
has db xref: EMAPA:19106
has db xref: FMA:13303
has db xref: GAID:183
has db xref: MA:0001356
has db xref: MESH:D006811
has db xref: NCIT:C12731
has db xref: SCTID:181923006
has db xref: UMLS:C0020164
has db xref: VHOG:0001158
has db xref: Wikipedia:Humerus
has db xref: XAO:0003210
has db xref: galen:Humerus
has exact synonym: humeri
has exact synonym: humerus bone
has OBO namespace: uberon
has related synonym: mesomere 1 of pectoral appendage
has related synonym: proximal metapterygial mesomere of pectoral appendage
has related synonym: proximal metapterygial mesomere of pectoral fin
id: UBERON:0000976
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: humerus
annotated property: subClassOf
annotated target: Restriction
evidence: definitional

Axiom
annotated source: humerus
annotated property: IAO_0000115
annotated target: Paired endochondral long bone that extends between the pectoral girdle and the skeletal parts of the forelimb. [PHENOSCAPE:mah].
has db xref: AAO:0000679
has db xref: PHENOSCAPE:mah
has db xref: https://github.com/obophenotype/uberon/issues/106

Axiom
annotated source: humerus
annotated property: UBPROP_0000001
annotated target: Paired, elongate, cylindrical bones of endochondral origin that extend from the pectoral girdle to the elbows.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000679
ontology: AAO
source: AAO:LAP

Axiom
annotated source: humerus
annotated property: UBPROP_0000003
annotated target: Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001158
ontology: VHOG
source: ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268
source: http://bgee.unil.ch/

Axiom
annotated source: humerus
annotated property: hasDbXref
annotated target: UMLS:C0020164
source: ncithesaurus:Humerus

Axiom
annotated source: humerus
annotated property: hasExactSynonym
annotated target: humeri
has db xref: PHENOSCAPE:ad
has synonym type: OMO_0003004

Axiom
annotated source: humerus
annotated property: hasRelatedSynonym
annotated target: mesomere 1 of pectoral appendage
has db xref: ISBN:0226313409
has synonym type: HOMOLOGY

Axiom
annotated source: humerus
annotated property: hasRelatedSynonym
annotated target: proximal metapterygial mesomere of pectoral appendage
has db xref: ISBN:0226313409
has synonym type: HOMOLOGY

Axiom
annotated source: humerus
annotated property: hasRelatedSynonym
annotated target: proximal metapterygial mesomere of pectoral fin
has db xref: ISBN:0226313409
has synonym type: HOMOLOGY

pleura
type: Class
equivalent class: Class
  intersection of: serous membrane
  intersection of: Restriction
  intersection of: Restriction
    on property: BFO_0000051
    some values from: UBERON_0002400
  intersection of: Restriction
    on property: BFO_0000051
    some values from: UBERON_0002401
subclass of: serous membrane
subclass of: Restriction
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0002400
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0002401
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0001748
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_32524
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0003081
subclass of: Restriction
  on property: RO_0002433
  some values from: respiratory system
IAO_0000115: The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion).
RO_0002175: NCBITaxon 8782
UBPROP_0000001: The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG]
UBPROP_0000007: pleural
UBPROP_0000012: In MA, is_a cavity lining (which we equate to parietal). In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See https://github.com/obophenotype/uberon/issues/86
has db xref: BTO:0001791
has db xref: CALOHA:TS-2081
has db xref: EFO:0001980
has db xref: EV:0100044
has db xref: FMA:9583
has db xref: GAID:360
has db xref: MA:0000433
has db xref: MESH:D010994
has db xref: NCIT:C12469
has db xref: SCTID:181609007
has db xref: UMLS:C0032225
has db xref: VHOG:0000394
has db xref: Wikipedia:Pleura
has exact synonym: wall of pleural sac
has OBO namespace: uberon
has related synonym: pleura
has related synonym: pleural tissue
id: UBERON:0000977
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: pleura
annotated property: IAO_0000115
annotated target: The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion).
has db xref: ISBN:0-683-40008-8
has db xref: MP:0010820
has db xref: UBERON:cjm
has db xref: Wikipedia:Pulmonary_pleurae
has db xref: https://github.com/obophenotype/uberon/issues/1231

Axiom
annotated source: pleura
annotated property: RO_0002175
annotated target: NCBITaxon 8782
source: ISBN:978-0030223693
source: https://orcid.org/0000-0003-3308-6245

Axiom
annotated source: pleura
annotated property: UBPROP_0000001
annotated target: The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000394
ontology: VHOG
source: ISBN:0124020607
source: http://bgee.unil.ch/

Axiom
annotated source: pleura
annotated property: hasDbXref
annotated target: UMLS:C0032225
source: ncithesaurus:Pleural_Tissue

Axiom
annotated source: pleura
annotated property: hasRelatedSynonym
annotated target: pleural tissue
has db xref: BTO:0001791
has db xref: NCIT:C12469

leg
type: Class
subclass of: UBERON_0006058
subclass of: UBERON_0008784
subclass of: Restriction
  on property: distally connected to
  some values from: UBERON_0002387
subclass of: Restriction
  on property: proximally connected to
  some values from: UBERON_0001464
IAO_0000115: The portion of the hindlimb that contains both the stylopod and zeugopod.
RO_0002175: NCBITaxon 9606
UBPROP_0000003: Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
UBPROP_0000013: The term leg can mean: [1] an appendage on which an animal walks [2] the entire hindlimb of a tetrapod [3] the segment of a human leg between knee and ankle (cf FMA) [4] the region of a hindlimb include the stylopod and zeugopod, but excluding the autopod. We define this class as [4], and thus 'leg' is compltely analagous to 'arm'. For [1], see the class 'locomotive weight-bearing appendage'. For [2] we use 'hindlimb'. For
has db xref: BTO:0000721
has db xref: CALOHA:TS-2206
has db xref: EFO:0001411
has db xref: EHDAA2:0000972
has db xref: EHDAA:5151
has db xref: EHDAA:6176
has db xref: EHDAA:8289
has db xref: EMAPA:17489
has db xref: GAID:49
has db xref: MA:0000047
has db xref: MESH:D035002
has db xref: VHOG:0000345
has db xref: Wikipedia:Leg#Limb
has exact synonym: tetrapod leg
has OBO namespace: uberon
has related synonym: lower extremity
id: UBERON:0000978
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
comment: we use the less open to misinterpretation 'hindlimb zeugopod'. Editor note: currently declared as overlapping foot, as AOs disagree over whether some ankle parts are in the leg or foot

Axiom
annotated source: leg
annotated property: IAO_0000115
annotated target: The portion of the hindlimb that contains both the stylopod and zeugopod.
has db xref: Wikipedia:Leg#Limb

Axiom
annotated source: leg
annotated property: UBPROP_0000003
annotated target: Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000345
ontology: VHOG
source: ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268
source: http://bgee.unil.ch/

Axiom
annotated source: leg
annotated property: UBPROP_0000013
annotated target: The term leg can mean: [1] an appendage on which an animal walks [2] the entire hindlimb of a tetrapod [3] the segment of a human leg between knee and ankle (cf FMA) [4] the region of a hindlimb include the stylopod and zeugopod, but excluding the autopod. We define this class as [4], and thus 'leg' is compltely analagous to 'arm'. For [1], see the class 'locomotive weight-bearing appendage'. For [2] we use 'hindlimb'. For
source: 3

Axiom
annotated source: leg
annotated property: hasRelatedSynonym
annotated target: lower extremity
has db xref: MESH:A01.378.610

tibia
type: Class
equivalent class: Class
  intersection of: UBERON_0015004
  intersection of: Restriction
    on property: RO_0002473
    some values from: UBERON_0002481
subclass of: UBERON_0003608
subclass of: UBERON_0004251
subclass of: UBERON_0015004
subclass of: Restriction
  on property: BSPO_0001113
  some values from: UBERON_0010720
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0010849
IAO_0000115: The major preaxial endochondral bone in the posterior zeugopod[Phenoscape].
RO_0002175: NCBITaxon 9606
UBPROP_0000001: One of the two long bones of endochondral origin of the hind-epipodium; it is a straight, simple bone whose section is more or less rectangular at the ends and circular at its central portion.[AAO]
has db xref: AAO:0000890
has db xref: BTO:0001252
has db xref: CALOHA:TS-1048
has db xref: EFO:0003054
has db xref: EMAPA:19142
has db xref: FMA:24476
has db xref: GAID:204
has db xref: MA:0001361
has db xref: MESH:D013977
has db xref: NCIT:C12800
has db xref: SCTID:182061009
has db xref: UMLS:C0040184
has db xref: Wikipedia:Tibia
has db xref: galen:Tibia
has exact synonym: shankbone
has exact synonym: shinbone
has OBO namespace: uberon
id: UBERON:0000979
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: tibia
annotated property: IAO_0000115
annotated target: The major preaxial endochondral bone in the posterior zeugopod[Phenoscape].
has db xref: PHENOSCAPE:mah

Axiom
annotated source: tibia
annotated property: UBPROP_0000001
annotated target: One of the two long bones of endochondral origin of the hind-epipodium; it is a straight, simple bone whose section is more or less rectangular at the ends and circular at its central portion.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000890
ontology: AAO
source: AAO:LAP

Axiom
annotated source: tibia
annotated property: hasDbXref
annotated target: UMLS:C0040184
source: ncithesaurus:Tibia

Axiom
annotated source: tibia
annotated property: hasExactSynonym
annotated target: shankbone
has db xref: Wikipedia:Tibia

Axiom
annotated source: tibia
annotated property: hasExactSynonym
annotated target: shinbone
has db xref: Wikipedia:Tibia

femur
type: Class
equivalent class: Class
  intersection of: UBERON_0015052
  intersection of: Restriction
    on property: RO_0002473
    some values from: UBERON_0002481
subclass of: UBERON_0003608
subclass of: UBERON_0003826
subclass of: UBERON_0008202
subclass of: UBERON_0015052
subclass of: Restriction
subclass of: Restriction
  on property: proximally connected to
  some values from: UBERON_0007832
IAO_0000115: Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified].
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Endochondral longbone connecting the pelvic girdle with posterior zeugopodium.[VSAO]
UBPROP_0000001: Paired, elongate, cylindrical bones of endochondral origin that form the thighs, extending from the pelvic girdles to the knees.[AAO]
UBPROP_0000003: Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
UBPROP_0000007: femoral
has db xref: AAO:0000887
has db xref: AAO:0000889
has db xref: BTO:0001284
has db xref: CALOHA:TS-0322
has db xref: EFO:0001396
has db xref: EMAPA:19143
has db xref: FMA:9611
has db xref: GAID:199
has db xref: MA:0001359
has db xref: MESH:D005269
has db xref: NCIT:C12717
has db xref: SCTID:182046008
has db xref: UMLS:C0015811
has db xref: VHOG:0001159
has db xref: VSAO:0000186
has db xref: Wikipedia:Femur
has db xref: XAO:0003214
has db xref: galen:Femur
has exact synonym: thigh bone
has OBO namespace: uberon
has related synonym: femoral bone
has related synonym: mesomere 1 of pevlic appendage
has related synonym: os femorale
has related synonym: os femoris
has related synonym: os longissimum
has related synonym: proximal metapterygial mesomere of pelvic appendage
has related synonym: proximal metapterygial mesomere of pelvic fin
id: UBERON:0000981
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: femur
annotated property: subClassOf
annotated target: UBERON_0008202
source: MA

Axiom
annotated source: femur
annotated property: subClassOf
annotated target: Restriction
evidence: definitional

Axiom
annotated source: femur
annotated property: IAO_0000115
annotated target: Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified].
has db xref: VSAO:0000186
has db xref: Wikipedia:Femur

Axiom
annotated source: femur
annotated property: UBPROP_0000001
annotated target: Endochondral longbone connecting the pelvic girdle with posterior zeugopodium.[VSAO]
date retrieved: 2012-08-14
external class: VSAO:0000186
ontology: VSAO
source: VSAO:NI

Axiom
annotated source: femur
annotated property: UBPROP_0000001
annotated target: Paired, elongate, cylindrical bones of endochondral origin that form the thighs, extending from the pelvic girdles to the knees.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000889
ontology: AAO
source: AAO:LAP

Axiom
annotated source: femur
annotated property: UBPROP_0000003
annotated target: Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001159
ontology: VHOG
source: ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268
source: http://bgee.unil.ch/

Axiom
annotated source: femur
annotated property: hasDbXref
annotated target: UMLS:C0015811
source: ncithesaurus:Femur

Axiom
annotated source: femur
annotated property: hasRelatedSynonym
annotated target: femoral bone
has db xref: BTO:0001284

Axiom
annotated source: femur
annotated property: hasRelatedSynonym
annotated target: mesomere 1 of pevlic appendage
has db xref: ISBN:0226313409
has synonym type: HOMOLOGY

Axiom
annotated source: femur
annotated property: hasRelatedSynonym
annotated target: os femorale
has db xref: BTO:0001284
has synonym type: OMO_0003011

Axiom
annotated source: femur
annotated property: hasRelatedSynonym
annotated target: os femoris
has db xref: BTO:0001284
has synonym type: OMO_0003011

Axiom
annotated source: femur
annotated property: hasRelatedSynonym
annotated target: os longissimum
has db xref: Wikipedia:Femur
has synonym type: OMO_0003011

Axiom
annotated source: femur
annotated property: hasRelatedSynonym
annotated target: proximal metapterygial mesomere of pelvic appendage
has db xref: ISBN:0226313409
has synonym type: HOMOLOGY

Axiom
annotated source: femur
annotated property: hasRelatedSynonym
annotated target: proximal metapterygial mesomere of pelvic fin
has db xref: ISBN:0226313409
has synonym type: HOMOLOGY

skeletal joint
type: Class
equivalent class: Class
  union of: UBERON_0002217
  union of: UBERON_0011134
subclass of: UBERON_0004905
subclass of: Restriction
  on property: RO_0002176
  some values from: UBERON_0004765
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0001434
disjoint with: UBERON_0001474
IAO_0000115: Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
UBPROP_0000001: Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
UBPROP_0000001: Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
has broad synonym: articulation
has broad synonym: joint
has db xref: AEO:0000182
has db xref: BTO:0001686
has db xref: CALOHA:TS-2023
has db xref: EFO:0000948
has db xref: EMAPA:35456
has db xref: FMA:7490
has db xref: GAID:102
has db xref: MA:0000319
has db xref: MAT:0000188
has db xref: MESH:D007596
has db xref: MIAA:0000188
has db xref: NCIT:C13044
has db xref: RETIRED_EHDAA2:0003182
has db xref: SCTID:302536002
has db xref: TAO:0000367
has db xref: UMLS:C0022417
has db xref: VHOG:0001276
has db xref: VSAO:0000101
has db xref: Wikipedia:Joint
has db xref: XAO:0000171
has db xref: ZFA:0001596
has db xref: galen:Joint
has OBO namespace: uberon
has related synonym: articular joint
has related synonym: joints
id: UBERON:0000982
in subset: efo slim
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: skeletal joint
annotated property: IAO_0000115
annotated target: Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
has db xref: GO_REF:0000034
has db xref: VSAO:0000101
has db xref: Wikipedia:Joint
has db xref: http://dx.plos.org/10.1371/journal.pone.0051070

Axiom
annotated source: skeletal joint
annotated property: UBPROP_0000001
annotated target: Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
date retrieved: 2012-08-14
external class: VSAO:0000101
ontology: VSAO
source: PSPUB:0000170

Axiom
annotated source: skeletal joint
annotated property: UBPROP_0000001
annotated target: Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000367
ontology: TAO
source: TAO:pem

Axiom
annotated source: skeletal joint
annotated property: hasBroadSynonym
annotated target: articulation
has db xref: VSAO:0000101

Axiom
annotated source: skeletal joint
annotated property: hasBroadSynonym
annotated target: joint
has db xref: FMA:7490
has db xref: VSAO:0000101

Axiom
annotated source: skeletal joint
annotated property: hasDbXref
annotated target: UMLS:C0022417
source: ncithesaurus:Joint

Axiom
annotated source: skeletal joint
annotated property: hasRelatedSynonym
annotated target: articular joint
has db xref: BTO:0001686

Axiom
annotated source: skeletal joint
annotated property: hasRelatedSynonym
annotated target: joints
has db xref: ZFA:0001596
has synonym type: OMO_0003004

metatarsus region
type: Class
equivalent class: Class
  intersection of: UBERON_0009877
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002387
subclass of: UBERON_0008784
subclass of: UBERON_0009877
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002551
  some values from: UBERON_0010545
IAO_0000115: A metapodium region that is part of a pes.
UBPROP_0000012: mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton
has db xref: CALOHA:TS-2221
has db xref: FMA:24997
has db xref: MA:0000049
has db xref: SCTID:280711000
has db xref: SCTID:370639003
has exact synonym: hind metapodium
has exact synonym: metatarsal part of foot
has exact synonym: metatarsal region
has exact synonym: regio metatarsalis
has narrow synonym: hindlimb cannon region
has narrow synonym: hindlimb equine cannon region
has OBO namespace: uberon
has related synonym: metatarsus
id: UBERON:0000983
in subset: uberon slim

Axiom
annotated source: metatarsus region
annotated property: subClassOf
annotated target: Restriction
source: PHENOSCAPE:ni

Axiom
annotated source: metatarsus region
annotated property: IAO_0000115
annotated target: A metapodium region that is part of a pes.
has db xref: OBOL:automatic

Axiom
annotated source: metatarsus region
annotated property: hasExactSynonym
annotated target: hind metapodium
has db xref: AAO:0000221
has db xref: MA:th
has db xref: http://en.wiktionary.org/wiki/metapodial

Axiom
annotated source: metatarsus region
annotated property: hasExactSynonym
annotated target: metatarsal part of foot
has db xref: FMA:24997

Axiom
annotated source: metatarsus region
annotated property: hasExactSynonym
annotated target: metatarsal region
has db xref: FMA:24997

Axiom
annotated source: metatarsus region
annotated property: hasExactSynonym
annotated target: regio metatarsalis
has db xref: FMA:24997
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: metatarsus region
annotated property: hasNarrowSynonym
annotated target: hindlimb cannon region
has db xref: NCBITaxon:9788
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: metatarsus region
annotated property: hasNarrowSynonym
annotated target: hindlimb equine cannon region
has db xref: NCBITaxon:9788
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: metatarsus region
annotated property: hasRelatedSynonym
annotated target: metatarsus
has db xref: MA:0000049

imaginal disc-derived wing
type: Class
equivalent class: Class
  intersection of: wing
  intersection of: Restriction
    on property: RO_0002202
    some values from: imaginal disc
subclass of: wing
subclass of: Restriction
  on property: RO_0002202
  some values from: imaginal disc
IAO_0000115: A flight organ of the adult external thorax that is derived from a dorsal mesothoracic disc.
IAO_0000116: TODO - review. hymenoptera thorax = fusion of thorax and mesosoma/metasoma
has broad synonym: wing
has db xref: FBbt:00004729
has db xref: HAO:0001089
has db xref: TGMA:0000196
has OBO namespace: uberon
has related synonym: adult mesothoracic wing
has related synonym: adult metathoracic wing
has related synonym: thoracic wing
has related synonym: thorax wing
has related synonym: wing of thorax
id: UBERON:0000984
in subset: uberon slim

Axiom
annotated source: imaginal disc-derived wing
annotated property: IAO_0000115
annotated target: A flight organ of the adult external thorax that is derived from a dorsal mesothoracic disc.
has db xref: FB:gg

Axiom
annotated source: imaginal disc-derived wing
annotated property: hasBroadSynonym
annotated target: wing
has db xref: FBbt:00004729
has synonym type: SENSU

Axiom
annotated source: imaginal disc-derived wing
annotated property: hasDbXref
annotated target: FBbt:00004729
mapping justification: ManualMappingCuration

Axiom
annotated source: imaginal disc-derived wing
annotated property: hasRelatedSynonym
annotated target: thorax wing
has db xref: OBOL:automatic

Axiom
annotated source: imaginal disc-derived wing
annotated property: hasRelatedSynonym
annotated target: wing of thorax
has db xref: OBOL:automatic

axillary vein
type: Class
equivalent class: Class
  intersection of: UBERON_0001638
  intersection of: Restriction
    on property: RO_0020102
    some values from: UBERON_0009472
subclass of: UBERON_0001638
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001467
subclass of: Restriction
  on property: RO_0002170
  some values from: UBERON_0001587
subclass of: Restriction
  on property: RO_0020102
  some values from: UBERON_0009472
IAO_0000115: Vein that drains the axilla.
RO_0002175: NCBITaxon 9606
UBPROP_0000008: In human anatomy, the axillary vein is a large blood vessel that conveys blood from the lateral aspect of the thorax, axilla (armpit) and upper limb toward the heart. There is one axillary vein on each side of the body. Its origin is at the lower margin of the teres major muscle and a continuation of the brachial vein. Its tributaries include the basilic vein and cephalic vein, which are both superficial veins. It terminates at the lateral margin of the first rib, at which it becomes the subclavian vein. It is accompanied along its course by a similarly named artery, the axillary artery
has db xref: EMAPA:18758
has db xref: FMA:13329
has db xref: GAID:527
has db xref: MA:0002084
has db xref: MESH:D001367
has db xref: NCIT:C32171
has db xref: SCTID:181389002
has db xref: UMLS:C0004456
has db xref: Wikipedia:Axillary_vein
has db xref: galen:AxillaryVein
has exact synonym: vena axillaris
has OBO namespace: uberon
has related synonym: subcostal vein
id: UBERON:0000985
in subset: human reference atlas
in subset: uberon slim

Axiom
annotated source: axillary vein
annotated property: IAO_0000115
annotated target: Vein that drains the axilla.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: axillary vein
annotated property: UBPROP_0000008
annotated target: In human anatomy, the axillary vein is a large blood vessel that conveys blood from the lateral aspect of the thorax, axilla (armpit) and upper limb toward the heart. There is one axillary vein on each side of the body. Its origin is at the lower margin of the teres major muscle and a continuation of the brachial vein. Its tributaries include the basilic vein and cephalic vein, which are both superficial veins. It terminates at the lateral margin of the first rib, at which it becomes the subclavian vein. It is accompanied along its course by a similarly named artery, the axillary artery
source: WP

Axiom
annotated source: axillary vein
annotated property: hasDbXref
annotated target: UMLS:C0004456
source: ncithesaurus:Axillary_Vein

Axiom
annotated source: axillary vein
annotated property: hasExactSynonym
annotated target: vena axillaris
has db xref: Wikipedia:Axillary_vein
has synonym type: OMO_0003011

haltere
type: Class
subclass of: appendage
subclass of: Restriction
  on property: BFO_0000050
  some values from: organismal segment
subclass of: Restriction
  on property: RO_0002202
  some values from: imaginal disc
IAO_0000115: The capitate stalk on both sides of the thorax having developed from the dorsal metathoracic wing-buds, it is freely movable and capable of vibration, representing the hind wing of Diptera; used for flight balance.
IAO_0000116: this term should be ceded to the arthropod anatomy ontology
has db xref: EFO:0000886
has db xref: FBbt:00004783
has db xref: MAT:0000203
has db xref: MIAA:0000203
has db xref: Wikipedia:Haltere
has OBO namespace: uberon
has related synonym: balancer organ
id: UBERON:0000987
in subset: efo slim
in subset: uberon slim

Axiom
annotated source: haltere
annotated property: subClassOf
annotated target: appendage
source: FBbt

Axiom
annotated source: haltere
annotated property: IAO_0000115
annotated target: The capitate stalk on both sides of the thorax having developed from the dorsal metathoracic wing-buds, it is freely movable and capable of vibration, representing the hind wing of Diptera; used for flight balance.
has db xref: FB:gg
has db xref: ISBN:3110148986
has db xref: Wikipedia:Haltere

Axiom
annotated source: haltere
annotated property: hasDbXref
annotated target: FBbt:00004783
mapping justification: ManualMappingCuration

pons
type: Class
subclass of: UBERON_0002616
subclass of: Restriction
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002298
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7742
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0001895
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0002298
IAO_0000115: The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum.
IAO_0000116: The pons is not present in zebrafish. In this ontology we currently have some structures which are applicable to zebrafish appearing as parts of the pons. Currently we only include the weaker dubious_for_taxon relationship ubtil this is resolved
RO_0002174: NCBITaxon 7955
RO_0002175: NCBITaxon 9606
UBPROP_0000001: The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG]
UBPROP_0000003: During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG]
has db xref: BAMS:PONS
has db xref: BAMS:Pons
has db xref: BIRNLEX:733
has db xref: BM:Pons
has db xref: BTO:0001101
has db xref: CALOHA:TS-0813
has db xref: DHBA:10661
has db xref: EFO:0001394
has db xref: EHDAA2:0004394
has db xref: EMAPA:17563
has db xref: EV:0100253
has db xref: FMA:67943
has db xref: GAID:578
has db xref: HBA:9131
has db xref: MA:0000204
has db xref: MAT:0000115
has db xref: MBA:771
has db xref: MESH:D011149
has db xref: MIAA:0000115
has db xref: NCIT:C12511
has db xref: SCTID:279103004
has db xref: UMLS:C0032639
has db xref: UMLS:C1280999
has db xref: VHOG:0001176
has db xref: Wikipedia:Pons
has db xref: neuronames:547
has exact synonym: pons Varolii
has exact synonym: pons of Varolius
has OBO namespace: uberon
has related synonym: pons cerebri
id: UBERON:0000988
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: pons
annotated property: subClassOf
annotated target: Restriction
source: neuronames

Axiom
annotated source: pons
annotated property: IAO_0000115
annotated target: The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum.
has db xref: VHOG:0001176

Axiom
annotated source: pons
annotated property: UBPROP_0000001
annotated target: The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001176
ontology: VHOG
source: http://bgee.unil.ch/
source: http://medical-dictionary.thefreedictionary.com/pons

Axiom
annotated source: pons
annotated property: UBPROP_0000003
annotated target: During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001176
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.474
source: http://bgee.unil.ch/

Axiom
annotated source: pons
annotated property: hasDbXref
annotated target: UMLS:C0032639
source: BIRNLEX:733
source: ncithesaurus:Pons_Varolii

Axiom
annotated source: pons
annotated property: hasDbXref
annotated target: UMLS:C1280999
source: BIRNLEX:733

Axiom
annotated source: pons
annotated property: hasDbXref
annotated target: neuronames:547
source: BIRNLEX:733

Axiom
annotated source: pons
annotated property: hasExactSynonym
annotated target: pons Varolii
has db xref: ncithesaurus:Pons_Varolii

Axiom
annotated source: pons
annotated property: hasRelatedSynonym
annotated target: pons cerebri
has db xref: NeuroNames:547
has synonym type: OMO_0003011

penis
type: Class
subclass of: UBERON_0004120
subclass of: UBERON_0008811
subclass of: Restriction
IAO_0000115: An intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination.
UBPROP_0000007: penile
UBPROP_0000007: phallic
UBPROP_0000008: Most male birds (e.g., roosters and turkeys) have a cloaca (also present on the female), but not a penis. Among bird species with a penis are paleognathes (tinamous and ratites), Anatidae (ducks, geese and swans), and a very few other species (such as flamingoes). A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood. It is usually partially feathered and in some species features spines and brush-like filaments, and in flaccid state curls up inside the cloaca
has db xref: BTO:0000405
has db xref: CALOHA:TS-0758
has db xref: EFO:0000987
has db xref: EHDAA2:0001433
has db xref: EHDAA:9380
has db xref: EMAPA:18682
has db xref: EMAPA_RETIRED:18996
has db xref: EV:0100107
has db xref: FMA:9707
has db xref: GAID:389
has db xref: MA:0000408
has db xref: MAT:0000186
has db xref: MESH:D010413
has db xref: MIAA:0000186
has db xref: NCIT:C12409
has db xref: SCTID:265793009
has db xref: UMLS:C0030851
has db xref: VHOG:0000727
has db xref: Wikipedia:Penis
has db xref: galen:Penis
has OBO namespace: uberon
has related synonym: penes
has related synonym: phallus
id: UBERON:0000989
in subset: efo slim
in subset: organ slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: penis
annotated property: subClassOf
annotated target: UBERON_0008811
source: Wikipedia

Axiom
annotated source: penis
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: penis
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: penis
annotated property: IAO_0000115
annotated target: An intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination.
has db xref: ISBN:0-683-40008-8
has db xref: MP:0005187
has db xref: Wikipedia:Penis
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: penis
annotated property: UBPROP_0000008
annotated target: Most male birds (e.g., roosters and turkeys) have a cloaca (also present on the female), but not a penis. Among bird species with a penis are paleognathes (tinamous and ratites), Anatidae (ducks, geese and swans), and a very few other species (such as flamingoes). A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood. It is usually partially feathered and in some species features spines and brush-like filaments, and in flaccid state curls up inside the cloaca
source: WP

Axiom
annotated source: penis
annotated property: hasDbXref
annotated target: UMLS:C0030851
source: ncithesaurus:Penis

Axiom
annotated source: penis
annotated property: hasRelatedSynonym
annotated target: penes
has synonym type: OMO_0003004

reproductive system
type: Class
equivalent class: Class
  intersection of: anatomical system
  intersection of: Restriction
    on property: RO_0002216
    some values from: GO_0022414
subclass of: anatomical system
subclass of: Restriction
  on property: BFO_0000051
  some values from: gonad
subclass of: Restriction
  on property: RO_0002216
  some values from: GO_0022414
subclass of: Restriction
  on property: RO_0002492
  some values from: fully formed stage
disjoint with: respiratory system
disjoint with: digestive system
disjoint with: circulatory system
disjoint with: nervous system
disjoint with: gustatory system
disjoint with: UBERON_0001434
disjoint with: UBERON_0002204
disjoint with: UBERON_0002294
disjoint with: UBERON_0002330
disjoint with: UBERON_0002390
disjoint with: UBERON_0002405
disjoint with: UBERON_0002416
disjoint with: UBERON_0002423
disjoint with: UBERON_0004456
disjoint with: UBERON_8450002
IAO_0000115: Anatomical system that has as its parts the organs concerned with reproduction.
IAO_0000116: consider splitting genitalia from reproductive system
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]
UBPROP_0000003: Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]
UBPROP_0000202: FMA_75572
date: 2022-06-10T18:22:34Z
has db xref: AAO:0010258
has db xref: BILA:0000103
has db xref: BTO:0000081
has db xref: CALOHA:TS-1318
has db xref: EFO:0000809
has db xref: EHDAA2:0001603
has db xref: EHDAA:5923
has db xref: EMAPA:17381
has db xref: EV:0100100
has db xref: FBbt:00004857
has db xref: FMA:7160
has db xref: GAID:363
has db xref: HAO:0000374
has db xref: HAO:0000895
has db xref: MA:0000326
has db xref: MESH:D005835
has db xref: MIAA:0000305
has db xref: NCIT:C12841
has db xref: SCTID:278875001
has db xref: TAO:0000632
has db xref: UMLS:C1261210
has db xref: VHOG:0000182
has db xref: WBbt:0005747
has db xref: Wikipedia:Reproductive_system
has db xref: XAO:0000142
has db xref: ZFA:0000632
has narrow synonym: genital system
has narrow synonym: genitalia
has OBO namespace: uberon
has related synonym: Geschlechtsorgan
has related synonym: animal reproductive system
has related synonym: genital tract
has related synonym: organa genitalia
has related synonym: reproductive tissue
has related synonym: reproductive tract
has related synonym: systemata genitalia
id: UBERON:0000990
in subset: efo slim
in subset: functional classification
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: reproductive system
annotated property: IAO_0000115
annotated target: Anatomical system that has as its parts the organs concerned with reproduction.
has db xref: Wikipedia:Reproductive_system

Axiom
annotated source: reproductive system
annotated property: UBPROP_0000001
annotated target: Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010258
ontology: AAO
source: AAO:BJB

Axiom
annotated source: reproductive system
annotated property: UBPROP_0000003
annotated target: Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000182
ontology: VHOG
source: PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)
source: http://bgee.unil.ch/

Axiom
annotated source: reproductive system
annotated property: hasDbXref
annotated target: FBbt:00004857
mapping justification: ManualMappingCuration

Axiom
annotated source: reproductive system
annotated property: hasDbXref
annotated target: MESH:D005835
mapping justification: LexicalMatching
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: reproductive system
annotated property: hasDbXref
annotated target: UMLS:C1261210
source: ncithesaurus:Reproductive_System

Axiom
annotated source: reproductive system
annotated property: hasNarrowSynonym
annotated target: genitalia
has synonym type: OMO_0003004

Axiom
annotated source: reproductive system
annotated property: hasRelatedSynonym
annotated target: Geschlechtsorgan
has db xref: BTO:0000081

Axiom
annotated source: reproductive system
annotated property: hasRelatedSynonym
annotated target: animal reproductive system
has db xref: BTO:0000081

Axiom
annotated source: reproductive system
annotated property: hasRelatedSynonym
annotated target: organa genitalia
has db xref: BTO:0000081

Axiom
annotated source: reproductive system
annotated property: hasRelatedSynonym
annotated target: reproductive tissue
has db xref: BTO:0000081

Axiom
annotated source: reproductive system
annotated property: hasRelatedSynonym
annotated target: systemata genitalia
has db xref: Wikipedia:Reproductive_system
has synonym type: OMO_0003011

gonad
type: Class
equivalent class: Class
  intersection of: UBERON_0003133
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0000586
subclass of: UBERON_0003133
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0000586
subclass of: Restriction
  on property: BFO_0000067
  some values from: GO_0007276
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0005564
IAO_0000115: Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
UBPROP_0000001: Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]
UBPROP_0000001: The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]
UBPROP_0000003: Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]
UBPROP_0000007: gonadal
UBPROP_0000012: FMA xref is a 'general anatomical term'
has db xref: AAO:0000213
has db xref: BILA:0000123
has db xref: BSA:0000079
has db xref: BTO:0000534
has db xref: EMAPA:17383
has db xref: FMA:18250
has db xref: GAID:368
has db xref: HAO:0000379
has db xref: MA:0002420
has db xref: MESH:D006066
has db xref: NCIT:C12725
has db xref: SCTID:304623008
has db xref: TAO:0000413
has db xref: UMLS:C0018067
has db xref: VHOG:0000397
has db xref: WBbt:0005175
has db xref: Wikipedia:Gonad
has db xref: XAO:0003146
has db xref: ZFA:0000413
has exact synonym: gonada
has OBO namespace: uberon
has related synonym: gonads
id: UBERON:0000991
in subset: major organ
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: gonad
annotated property: IAO_0000115
annotated target: Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
has db xref: ISBN:0140512888
has db xref: Wikipedia:Gonad
has db xref: ZFA:0000413
has db xref: ZFIN:curator

Axiom
annotated source: gonad
annotated property: UBPROP_0000001
annotated target: Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000213
ontology: AAO
source: AAO:BJB

Axiom
annotated source: gonad
annotated property: UBPROP_0000001
annotated target: The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]
date retrieved: 2012-08-14
external class: TAO:0000413
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: gonad
annotated property: UBPROP_0000003
annotated target: Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000397
ontology: VHOG
source: DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)
source: http://bgee.unil.ch/

Axiom
annotated source: gonad
annotated property: UBPROP_0000012
annotated target: FMA xref is a 'general anatomical term'
external ontology: FMA

Axiom
annotated source: gonad
annotated property: hasDbXref
annotated target: UMLS:C0018067
source: ncithesaurus:Gonad

Axiom
annotated source: gonad
annotated property: hasRelatedSynonym
annotated target: gonads
has db xref: ZFA:0000413
has synonym type: OMO_0003004

ovary
type: Class
equivalent class: Class
  intersection of: gonad
  intersection of: Restriction
    on property: BFO_0000050
    some values from: female reproductive system
subclass of: gonad
subclass of: UBERON_0003134
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_33208
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0009117
disjoint with: UBERON_0009117
IAO_0000115: The gonad of a female organism which contains germ cells.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]
UBPROP_0000001: Female reproductive organ.[TAO]
UBPROP_0000003: (...) 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]
UBPROP_0000007: ovarian
UBPROP_0000008: Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo
has db xref: AAO:0000371
has db xref: BILA:0000125
has db xref: BSA:0000080
has db xref: BTO:0000975
has db xref: CALOHA:TS-0730
has db xref: EFO:0000973
has db xref: EHDAA2:0001360
has db xref: EHDAA:8124
has db xref: EMAPA:17962
has db xref: EV:0100111
has db xref: FBbt:00004865
has db xref: FMA:7209
has db xref: GAID:367
has db xref: MA:0000384
has db xref: MESH:D010053
has db xref: MIAA:0000125
has db xref: NCIT:C12404
has db xref: SCTID:181464007
has db xref: TAO:0000403
has db xref: UMLS:C0029939
has db xref: VHOG:0000251
has db xref: Wikipedia:Ovary
has db xref: XAO:0000258
has db xref: ZFA:0000403
has exact synonym: animal ovary
has exact synonym: female gonad
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
has exact synonym: ovum-producing ovary
has exact synonym: reproductive system of female organism gonad
has exact synonym: reproductive system of female organism gonada
has OBO namespace: uberon
has related synonym: ovaries
has related synonym: ovarium
id: UBERON:0000992
in subset: efo slim
in subset: human reference atlas
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: ovary
annotated property: IAO_0000115
annotated target: The gonad of a female organism which contains germ cells.
has db xref: ISBN:0-683-40008-8
has db xref: MP:0001126
has db xref: Wikipedia:Ovary

Axiom
annotated source: ovary
annotated property: UBPROP_0000001
annotated target: Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000371
ontology: AAO
source: AAO:BJB

Axiom
annotated source: ovary
annotated property: UBPROP_0000001
annotated target: Female reproductive organ.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000403
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: ovary
annotated property: UBPROP_0000003
annotated target: (...) 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]
date retrieved: 2012-09-17
external class: VHOG:0000251
ontology: VHOG
source: DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)
source: http://bgee.unil.ch/

Axiom
annotated source: ovary
annotated property: UBPROP_0000008
annotated target: 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
source: WP

Axiom
annotated source: ovary
annotated property: hasDbXref
annotated target: FBbt:00004865
mapping justification: ManualMappingCuration

Axiom
annotated source: ovary
annotated property: hasDbXref
annotated target: UMLS:C0029939
source: ncithesaurus:Ovary

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: animal ovary
has db xref: EFO:0000973

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: female organism genitalia gonad
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: female organism genitalia gonada
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: female organism reproductive system gonad
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: female organism reproductive system gonada
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: female reproductive system gonad
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: female reproductive system gonada
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: genitalia of female organism gonad
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: genitalia of female organism gonada
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: gonad of female organism genitalia
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: gonad of female organism reproductive system
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: gonad of female reproductive system
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: gonad of genitalia of female organism
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: gonad of reproductive system of female organism
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: gonada of female organism genitalia
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: gonada of female organism reproductive system
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: gonada of female reproductive system
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: gonada of genitalia of female organism
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: gonada of reproductive system of female organism
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: ovum-producing ovary
has db xref: GO:0061039
has synonym type: SENSU

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: reproductive system of female organism gonad
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasExactSynonym
annotated target: reproductive system of female organism gonada
has db xref: OBOL:automatic

Axiom
annotated source: ovary
annotated property: hasRelatedSynonym
annotated target: ovaries
has synonym type: OMO_0003004

Axiom
annotated source: ovary
annotated property: hasRelatedSynonym
annotated target: ovarium
has db xref: Wikipedia:Ovary
has synonym type: OMO_0003011

oviduct
type: Class
subclass of: tube
subclass of: UBERON_0005156
subclass of: Restriction
  on property: BFO_0000050
  some values from: female reproductive system
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6072
subclass of: Restriction
  on property: RO_0002176
  some values from: ovary
subclass of: Restriction
  on property: RO_0002176
  some values from: UBERON_0013514
IAO_0000115: A tube or collection of tubes in an animal from the ovaries to the outside of the body.
IAO_0000232: sometimes oviduct is used interchangeably with follaopian tube. Here they are different - the oviduct connects the gonad to the outside in a variety of animals. The mammal-class fallopian tube is derived from the mullerian duct and connects the gonads/infubdibulum to the uterus
UBPROP_0000001: A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG]
UBPROP_0000003: In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG]
UBPROP_0000008: The only female vertebrates to lack oviducts are the jawless fishes. In these species, the single fused ovary releases eggs directly into the body cavity. The fish eventually extrudes the eggs through small genital pores towards the rear of the body[WP]
UBPROP_0000008: in birds divided into infundibulum, magnum, isthmus, uterus, and vagina
has db xref: AAO:0010533
has db xref: BSA:0000083
has db xref: BTO:0000980
has db xref: EFO:0000974
has db xref: EMAPA:18984
has db xref: GAID:366
has db xref: MAT:0000126
has db xref: MESH:D010057
has db xref: MIAA:0000126
has db xref: NCIT:C77957
has db xref: TAO:0000560
has db xref: UMLS:C0029954
has db xref: VHOG:0001136
has db xref: Wikipedia:Oviduct
has db xref: XAO:0003052
has db xref: ZFA:0000560
has exact synonym: ovarian duct
has exact synonym: ovarian tube
has narrow synonym: uterine tube
has OBO namespace: uberon
has related synonym: female reproductive tracts
has related synonym: oviducts
has related synonym: tuba uterina
has related synonym: tuba uterinae
has related synonym: tubular parts of female reproductive system
id: UBERON:0000993
in subset: efo slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: oviduct
annotated property: IAO_0000115
annotated target: A tube or collection of tubes in an animal from the ovaries to the outside of the body.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: oviduct
annotated property: UBPROP_0000001
annotated target: A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001136
ontology: VHOG
source: http://bgee.unil.ch/
source: http://medical-dictionary.thefreedictionary.com/oviduct

Axiom
annotated source: oviduct
annotated property: UBPROP_0000003
annotated target: In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001136
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.687-688
source: http://bgee.unil.ch/

Axiom
annotated source: oviduct
annotated property: hasDbXref
annotated target: UMLS:C0029954
source: ncithesaurus:Oviduct

Axiom
annotated source: oviduct
annotated property: hasExactSynonym
annotated target: ovarian duct
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: oviduct
annotated property: hasExactSynonym
annotated target: ovarian tube
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: oviduct
annotated property: hasRelatedSynonym
annotated target: female reproductive tracts
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: oviduct
annotated property: hasRelatedSynonym
annotated target: oviducts
has db xref: ZFA:0000560
has synonym type: OMO_0003004

Axiom
annotated source: oviduct
annotated property: hasRelatedSynonym
annotated target: tuba uterina
has db xref: BTO:0000980

Axiom
annotated source: oviduct
annotated property: hasRelatedSynonym
annotated target: tuba uterinae
has db xref: BTO:0000980

Axiom
annotated source: oviduct
annotated property: hasRelatedSynonym
annotated target: tubular parts of female reproductive system
has db xref: http://orcid.org/0000-0002-6601-2165

spermathecum
type: Class
subclass of: organ
subclass of: UBERON_0005156
subclass of: Restriction
  on property: BFO_0000050
  some values from: gonad
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_33213
IAO_0000115: An organ of the female reproductive tract that functions to receive and store sperm from the male, and can sometimes be the site of fertilization when the oocytes are ready.
RO_0002161: NCBITaxon_314146
UBPROP_0000008: Some species have multiple spermathecae, as seen in earthworms, where four pairs of spermathecae are present. One pair in 6,7,8 and 9 segments. They receive and store the spermatozoa of another earthworm during copulation
has db xref: BTO:0001273
has db xref: EFO:0000977
has db xref: FBbt:00004921
has db xref: HAO:0000945
has db xref: MAT:0000168
has db xref: MIAA:0000168
has db xref: TGMA:0000560
has db xref: WBbt:0005319
has db xref: Wikipedia:Spermatheca
has OBO namespace: uberon
has related synonym: receptaculum seminis
has related synonym: seminal receptacle
has related synonym: spermatheca
has related synonym: spermathecae
id: UBERON:0000994
in subset: dubious grouping
in subset: efo slim
in subset: uberon slim

Axiom
annotated source: spermathecum
annotated property: IAO_0000115
annotated target: An organ of the female reproductive tract that functions to receive and store sperm from the male, and can sometimes be the site of fertilization when the oocytes are ready.
has db xref: Wikipedia:Spermatheca
has db xref: https://github.com/obophenotype/uberon/issues/1405

Axiom
annotated source: spermathecum
annotated property: hasDbXref
annotated target: FBbt:00004921
mapping justification: ManualMappingCuration

Axiom
annotated source: spermathecum
annotated property: hasRelatedSynonym
annotated target: receptaculum seminis
has db xref: BTO:0001273

Axiom
annotated source: spermathecum
annotated property: hasRelatedSynonym
annotated target: spermatheca
has synonym type: OMO_0003004

Axiom
annotated source: spermathecum
annotated property: hasRelatedSynonym
annotated target: spermathecae
has synonym type: OMO_0003004

uterus
type: Class
subclass of: UBERON_0013515
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0004175
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_32525
subclass of: Restriction
  on property: RO_0002495
  some values from: UBERON_0005795
IAO_0000115: The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: 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]
UBPROP_0000003: An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]
UBPROP_0000007: uterine
UBPROP_0000008: 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.
UBPROP_0000011: Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus]
has db xref: BTO:0001424
has db xref: CALOHA:TS-1102
has db xref: EFO:0000975
has db xref: EMAPA:29915
has db xref: EV:0100113
has db xref: FMA:17558
has db xref: GAID:172
has db xref: MA:0000389
has db xref: MAT:0000127
has db xref: MESH:D014599
has db xref: MIAA:0000127
has db xref: NCIT:C12405
has db xref: SCTID:181452004
has db xref: UMLS:C0042149
has db xref: VHOG:0001137
has db xref: Wikipedia:Uterus
has db xref: galen:Uterus
has OBO namespace: uberon
id: UBERON:0000995
in subset: efo slim
in subset: human reference atlas
in subset: organ slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: uterus
annotated property: subClassOf
annotated target: UBERON_0013515
source: cjm

Axiom
annotated source: uterus
annotated property: IAO_0000115
annotated target: The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth.
has db xref: MGI:csmith
has db xref: MP:0001120

Axiom
annotated source: uterus
annotated property: UBPROP_0000001
annotated target: 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]
date retrieved: 2012-09-17
external class: VHOG:0001137
ontology: VHOG
source: http://bgee.unil.ch/
source: http://medical-dictionary.thefreedictionary.com/uterus

Axiom
annotated source: uterus
annotated property: UBPROP_0000003
annotated target: An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001137
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.678
source: http://bgee.unil.ch/

Axiom
annotated source: uterus
annotated property: hasDbXref
annotated target: UMLS:C0042149
source: ncithesaurus:Uterus

vagina
type: Class
subclass of: UBERON_0004120
subclass of: UBERON_0013515
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0003975
IAO_0000115: A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP].
UBPROP_0000001: Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA]
UBPROP_0000001: The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG]
UBPROP_0000003: The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG]
UBPROP_0000007: vaginal
UBPROP_0000011: 'The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.' Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688
has db xref: BTO:0000243
has db xref: CALOHA:TS-1103
has db xref: EFO:0000976
has db xref: EMAPA:18986
has db xref: EV:0100117
has db xref: FMA:19949
has db xref: GAID:381
has db xref: MA:0000394
has db xref: MAT:0000128
has db xref: MESH:D014621
has db xref: MIAA:0000128
has db xref: NCIT:C12407
has db xref: SCTID:181441005
has db xref: UMLS:C0042232
has db xref: VHOG:0001138
has db xref: Wikipedia:Vagina
has db xref: galen:Vagina
has OBO namespace: uberon
has related synonym: distal oviductal region
has related synonym: distal portion of oviduct
has related synonym: vaginae
id: UBERON:0000996
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: vagina
annotated property: subClassOf
annotated target: UBERON_0013515
source: cjm

Axiom
annotated source: vagina
annotated property: subClassOf
annotated target: Restriction
source: FMA

Axiom
annotated source: vagina
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: vagina
annotated property: IAO_0000115
annotated target: A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP].
has db xref: Wikipedia:Vagina
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: vagina
annotated property: UBPROP_0000001
annotated target: Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA]
date retrieved: 2012-11-29
external class: FMA:19949
ontology: FMA

Axiom
annotated source: vagina
annotated property: UBPROP_0000001
annotated target: The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001138
ontology: VHOG
source: http://bgee.unil.ch/
source: http://medical-dictionary.thefreedictionary.com/vagina

Axiom
annotated source: vagina
annotated property: UBPROP_0000003
annotated target: The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001138
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688
source: http://bgee.unil.ch/

Axiom
annotated source: vagina
annotated property: hasDbXref
annotated target: UMLS:C0042232
source: ncithesaurus:Vagina

Axiom
annotated source: vagina
annotated property: hasRelatedSynonym
annotated target: vaginae
has synonym type: OMO_0003004

mammalian vulva
type: Class
subclass of: organ
subclass of: UBERON_0005156
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0005056
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_40674
IAO_0000115: External genital organs of the female mammal[WP].
UBPROP_0000001: The external genital organs of the female, including the labia majora, labia minora, clitoris, and vestibule of the vagina. [TFD][VHOG]
UBPROP_0000007: vulval
has db xref: BTO:0003101
has db xref: CALOHA:TS-1168
has db xref: EFO:0000978
has db xref: EMAPA:36631
has db xref: EV:0100118
has db xref: FMA:20462
has db xref: GAID:383
has db xref: MA:0000395
has db xref: MAT:0000169
has db xref: MESH:D014844
has db xref: MIAA:0000169
has db xref: NCIT:C12408
has db xref: SCTID:265796001
has db xref: UMLS:C0042993
has db xref: VHOG:0001458
has db xref: Wikipedia:Vulva
has db xref: galen:Vulva
has exact synonym: female pudendum
has exact synonym: mammalian vulva
has exact synonym: puboperineal region
has exact synonym: pudendum femininum
has exact synonym: vulva
has OBO namespace: uberon
has related synonym: pudendum
has related synonym: pudendum femininum
has related synonym: pudendum muliebre
id: UBERON:0000997
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: mammalian vulva
annotated property: IAO_0000115
annotated target: External genital organs of the female mammal[WP].
has db xref: Wikipedia:Vulva

Axiom
annotated source: mammalian vulva
annotated property: UBPROP_0000001
annotated target: The external genital organs of the female, including the labia majora, labia minora, clitoris, and vestibule of the vagina. [TFD][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001458
ontology: VHOG
source: http://bgee.unil.ch/
source: http://medical-dictionary.thefreedictionary.com/vulva

Axiom
annotated source: mammalian vulva
annotated property: hasDbXref
annotated target: UMLS:C0042993
source: ncithesaurus:Vulva

Axiom
annotated source: mammalian vulva
annotated property: hasExactSynonym
annotated target: female pudendum
has db xref: BTO:0003101
has db xref: FMA:20462
has db xref: doi:10.1002/ca.23705
has synonym type: DEPRECATED

Axiom
annotated source: mammalian vulva
annotated property: hasExactSynonym
annotated target: puboperineal region
has db xref: FMA:20462

Axiom
annotated source: mammalian vulva
annotated property: hasExactSynonym
annotated target: pudendum femininum
has db xref: FMA:20462
has db xref: FMA:TA
has db xref: doi:10.1002/ca.23705
has synonym type: DEPRECATED

Axiom
annotated source: mammalian vulva
annotated property: hasExactSynonym
annotated target: vulva
has db xref: MA:0000395

Axiom
annotated source: mammalian vulva
annotated property: hasRelatedSynonym
annotated target: pudendum
has db xref: BTO:0003101
has db xref: doi:10.1002/ca.23705
has synonym type: DEPRECATED

Axiom
annotated source: mammalian vulva
annotated property: hasRelatedSynonym
annotated target: pudendum femininum
has db xref: Wikipedia:Vulva
has db xref: doi:10.1002/ca.23705
has synonym type: DEPRECATED

Axiom
annotated source: mammalian vulva
annotated property: hasRelatedSynonym
annotated target: pudendum muliebre
has db xref: BTO:0003101
has db xref: doi:10.1002/ca.23705
has synonym type: DEPRECATED

seminal vesicle
type: Class
subclass of: UBERON_0004120
subclass of: UBERON_0006868
subclass of: Restriction
  on property: BFO_0000050
  some values from: testis
subclass of: Restriction
  on property: RO_0002202
  some values from: mesonephros
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0004054
subclass of: Restriction
  on property: RO_0003000
  some values from: UBERON_0010143
IAO_0000115: Either of a pair of glandular pouches that lie one on either side of the male reproductive tract posterolateral to the urinary bladder and in the human male secrete a sugar- and protein-containing fluid into the ejaculatory duct.
UBPROP_0000001: Either of a pair of pouchlike glands situated on each side of the male urinary bladder that secrete seminal fluid and nourish and promote the movement of spermatozoa through the urethra. [TFD][VHOG]
UBPROP_0000003: (In mammalian testis) Along the way (the sperm travel), three accessory sex glands, the seminal vesicle, prostate, and bulbourethral (Cowper's) gland, respectively, add their secretions as sperm move from the testes to the urethra.[well established][VHOG]
UBPROP_0000009: The seminal vesicles secrete a significant proportion of the fluid that ultimately becomes semen. Lipofuscin granules from dead epithelial cells give the secretion its yellowish color. About 50-70% of the seminal fluid in humans originates from the seminal vesicles, but is not expelled in the first ejaculate fractions which are dominated by spermatozoa and zinc-rich prostatic fluid.
has broad synonym: seminal gland
has db xref: AAO:0010788
has db xref: BTO:0001234
has db xref: CALOHA:TS-0919
has db xref: EFO:0000986
has db xref: EMAPA:19180
has db xref: EV:0100106
has db xref: FMA:19386
has db xref: GAID:394
has db xref: MA:0000410
has db xref: MAT:0000171
has db xref: MESH:D012669
has db xref: MIAA:0000171
has db xref: NCIT:C12787
has db xref: SCTID:181434004
has db xref: UMLS:C0036628
has db xref: VHOG:0001379
has db xref: Wikipedia:Seminal_vesicle
has OBO namespace: uberon
has related synonym: glandula seminalis
has related synonym: glandula vesiculosa
has related synonym: gonecyst
has related synonym: vas efferens
has related synonym: vesicula seminalis
has related synonym: vesiculae seminales
has related synonym: vesicular gland
has related synonym: vesicular glands
has related synonym: vesicular seminalis
has related synonym: vesiculæ seminales
id: UBERON:0000998
in subset: efo slim
in subset: organ slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: seminal vesicle
annotated property: IAO_0000115
annotated target: Either of a pair of glandular pouches that lie one on either side of the male reproductive tract posterolateral to the urinary bladder and in the human male secrete a sugar- and protein-containing fluid into the ejaculatory duct.
has db xref: BTO:0001234
has db xref: Wikipedia:Seminal_vesicle

Axiom
annotated source: seminal vesicle
annotated property: UBPROP_0000001
annotated target: Either of a pair of pouchlike glands situated on each side of the male urinary bladder that secrete seminal fluid and nourish and promote the movement of spermatozoa through the urethra. [TFD][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001379
ontology: VHOG
source: http://bgee.unil.ch/
source: http://medical-dictionary.thefreedictionary.com/prominence

Axiom
annotated source: seminal vesicle
annotated property: UBPROP_0000003
annotated target: (In mammalian testis) Along the way (the sperm travel), three accessory sex glands, the seminal vesicle, prostate, and bulbourethral (Cowper's) gland, respectively, add their secretions as sperm move from the testes to the urethra.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001379
ontology: VHOG
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.556
source: http://bgee.unil.ch/

Axiom
annotated source: seminal vesicle
annotated property: hasDbXref
annotated target: UMLS:C0036628
source: ncithesaurus:Seminal_Vesicle

Axiom
annotated source: seminal vesicle
annotated property: hasRelatedSynonym
annotated target: glandula seminalis
has db xref: BTO:0001234

Axiom
annotated source: seminal vesicle
annotated property: hasRelatedSynonym
annotated target: glandula vesiculosa
has db xref: BTO:0001234

Axiom
annotated source: seminal vesicle
annotated property: hasRelatedSynonym
annotated target: vesicula seminalis
has db xref: BTO:0001234
has db xref: Wikipedia:Seminal_vesicle

Axiom
annotated source: seminal vesicle
annotated property: hasRelatedSynonym
annotated target: vesiculae seminales
has db xref: Wikipedia:Seminal_vesicle
has synonym type: OMO_0003011

Axiom
annotated source: seminal vesicle
annotated property: hasRelatedSynonym
annotated target: vesicular gland
has db xref: Wikipedia:Seminal_vesicle

Axiom
annotated source: seminal vesicle
annotated property: hasRelatedSynonym
annotated target: vesicular glands
has db xref: Wikipedia:Seminal_vesicle

Axiom
annotated source: seminal vesicle
annotated property: hasRelatedSynonym
annotated target: vesicular seminalis
has db xref: Wikipedia:Seminal_vesicle

Axiom
annotated source: seminal vesicle
annotated property: hasRelatedSynonym
annotated target: vesiculæ seminales
has db xref: Wikipedia:Seminal_vesicle

ejaculatory duct
type: Class
subclass of: tube
subclass of: UBERON_0005904
subclass of: UBERON_0015212
subclass of: Restriction
  on property: BSPO_0000126
  some values from: male reproductive system
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7742
subclass of: Restriction
  on property: RO_0002216
  some values from: GO_0042713
subclass of: Restriction
  on property: channel for
  some values from: UBERON_0001968
subclass of: Restriction
  on property: channel for
  some values from: UBERON_0010143
subclass of: Restriction
  on property: channels from
  some values from: seminal vesicle
subclass of: Restriction
  on property: channels from
  some values from: vas deferens
subclass of: Restriction
  on property: channels into
  some values from: urethra
IAO_0000115: The Ejaculatory ducts (ductus ejaculatorii) are paired structures in male anatomy, about 2 cm in length. Each ejaculatory duct is formed by the union of the vas deferens with the duct of the seminal vesicle. They pass through the prostate, and empty into the urethra at the Colliculus seminalis. During ejaculation, semen passes through the ducts and exits the body via the penis[WP,unvetted].
has db xref: BTO:0001580
has db xref: CALOHA:TS-0211
has db xref: EFO:0000985
has db xref: EMAPA:19088
has db xref: FMA:19325
has db xref: GAID:388
has db xref: MA:0003247
has db xref: MAT:0000170
has db xref: MESH:D004543
has db xref: MIAA:0000170
has db xref: NCIT:C32493
has db xref: SCTID:279665005
has db xref: UMLS:C0013747
has db xref: Wikipedia:Ejaculatory_duct
has exact synonym: ductus ejaculatorii
has exact synonym: ductus ejaculatorius
has OBO namespace: uberon
has related synonym: ductus ejaculatorii
id: UBERON:0000999
in subset: efo slim
in subset: uberon slim

Axiom
annotated source: ejaculatory duct
annotated property: IAO_0000115
annotated target: The Ejaculatory ducts (ductus ejaculatorii) are paired structures in male anatomy, about 2 cm in length. Each ejaculatory duct is formed by the union of the vas deferens with the duct of the seminal vesicle. They pass through the prostate, and empty into the urethra at the Colliculus seminalis. During ejaculation, semen passes through the ducts and exits the body via the penis[WP,unvetted].
has db xref: Wikipedia:Ejaculatory_duct

Axiom
annotated source: ejaculatory duct
annotated property: hasDbXref
annotated target: UMLS:C0013747
source: ncithesaurus:Ejaculatory_Duct

Axiom
annotated source: ejaculatory duct
annotated property: hasExactSynonym
annotated target: ductus ejaculatorii
has db xref: BTO:0001580
has synonym type: OMO_0003004

Axiom
annotated source: ejaculatory duct
annotated property: hasExactSynonym
annotated target: ductus ejaculatorius
has db xref: BTO:0001580

Axiom
annotated source: ejaculatory duct
annotated property: hasRelatedSynonym
annotated target: ductus ejaculatorii
has db xref: Wikipedia:Ejaculatory_duct
has synonym type: OMO_0003011

vas deferens
type: Class
subclass of: tube
subclass of: UBERON_0005904
subclass of: Restriction
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0006947
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_32524
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0004054
subclass of: Restriction
  on property: channel for
  some values from: UBERON_0001968
subclass of: Restriction
  on property: channels from
  some values from: UBERON_0001301
subclass of: Restriction
  on property: channels into
  some values from: ejaculatory duct
IAO_0000115: A secretory duct that transports sperm from the testis. In mammals this is a continuation of the epididymis and ends in the prostatic urethra where it terminates to form ejaculatory duct.
UBPROP_0000003: The continuation of the archinephric duct, now called the deferent duct, extends caudally to the cloaca or to the part of the mammalian urethra that is derived from the cloaca.[well established][VHOG]
UBPROP_0000008: Most vertebrates have some form of duct to transfer the sperm from the testes to the urethra. In cartilaginous fish and amphibians, sperm is carried through the archinephric duct, which also partially helps to transport urine from the kidneys. In teleosts, there is a distinct sperm duct, separate from the ureters, and often called the vas deferens, although probably not truly homologous with that in humans. In cartilaginous fishes, the part of the archinephric duct closest to the testis is coiled up to form an epididymis. Below this are a number of small glands secreting components of the seminal fluid. The final portion of the duct also receives ducts from the kidneys in most species. In amniotes, however, the archinephric duct has become a true vas deferens, and is used only for conducting sperm, never urine. As in cartilaginous fish, the upper part of the duct forms the epididymis. In many species, the vas deferens ends in a small sac for storing sperm. The only vertebrates to lack any structure resembling a vas deferens are the primitive jawless fishes, which release sperm directly into the body cavity, and then into the surrounding water through a simple opening in the body wall.
has db xref: BTO:0001427
has db xref: CALOHA:TS-1105
has db xref: EFO:0000981
has db xref: EMAPA:18681
has db xref: EV:0100105
has db xref: FMA:19234
has db xref: GAID:404
has db xref: MA:0000413
has db xref: MESH:D014649
has db xref: MIAA:0000129
has db xref: NCIT:C12813
has db xref: SCTID:245467009
has db xref: UMLS:C0042360
has db xref: VHOG:0001135
has db xref: Wikipedia:Vas_deferens
has db xref: galen:VasDeferens
has exact synonym: deferent duct
has exact synonym: ductus deferens
has exact synonym: vas deferen
has OBO namespace: uberon
has related synonym: sperm duct
has related synonym: vasa deferentia
id: UBERON:0001000
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: vas deferens
annotated property: subClassOf
annotated target: Restriction
source: FMA

Axiom
annotated source: vas deferens
annotated property: IAO_0000115
annotated target: A secretory duct that transports sperm from the testis. In mammals this is a continuation of the epididymis and ends in the prostatic urethra where it terminates to form ejaculatory duct.
has db xref: ISBN:0-683-40008-8
has db xref: MGI:pvb
has db xref: MP:0002769
has db xref: Wikipedia:Vas_deferens
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: vas deferens
annotated property: UBPROP_0000003
annotated target: The continuation of the archinephric duct, now called the deferent duct, extends caudally to the cloaca or to the part of the mammalian urethra that is derived from the cloaca.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001135
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.670
source: http://bgee.unil.ch/

Axiom
annotated source: vas deferens
annotated property: UBPROP_0000008
annotated target: Most vertebrates have some form of duct to transfer the sperm from the testes to the urethra. In cartilaginous fish and amphibians, sperm is carried through the archinephric duct, which also partially helps to transport urine from the kidneys. In teleosts, there is a distinct sperm duct, separate from the ureters, and often called the vas deferens, although probably not truly homologous with that in humans. In cartilaginous fishes, the part of the archinephric duct closest to the testis is coiled up to form an epididymis. Below this are a number of small glands secreting components of the seminal fluid. The final portion of the duct also receives ducts from the kidneys in most species. In amniotes, however, the archinephric duct has become a true vas deferens, and is used only for conducting sperm, never urine. As in cartilaginous fish, the upper part of the duct forms the epididymis. In many species, the vas deferens ends in a small sac for storing sperm. The only vertebrates to lack any structure resembling a vas deferens are the primitive jawless fishes, which release sperm directly into the body cavity, and then into the surrounding water through a simple opening in the body wall.
source: WP

Axiom
annotated source: vas deferens
annotated property: hasDbXref
annotated target: UMLS:C0042360
source: ncithesaurus:Vas_Deferens

Axiom
annotated source: vas deferens
annotated property: hasExactSynonym
annotated target: ductus deferens
has db xref: Wikipedia:Vas_deferens

chitin-based cuticle
type: Class
equivalent class: Class
  intersection of: cuticle
  intersection of: Restriction
    on property: RO_0002473
    some values from: CHEBI_17029
subclass of: cuticle
subclass of: UBERON_0007491
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002416
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6656
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0007376
IAO_0000115: A cuticular covering that is composed primarily of chitin. The main structural component of arthropod cuticle is a polysaccharide, chitin, composed of N-acetylglucosamine units, together with proteins and lipids[WP].
has broad synonym: exoskeleton
has db xref: EFO:0000944
has db xref: FBbt:00004970
has db xref: HAO:0000240
has db xref: MAT:0000150
has db xref: MIAA:0000150
has db xref: Wikipedia:Arthropod_exoskeleton
has narrow synonym: cuticle
has OBO namespace: uberon
has related synonym: arthropod cuticle
has related synonym: arthropod exoskeleton
has related synonym: insect cuticle
id: UBERON:0001001
in subset: efo slim
in subset: uberon slim
comment: EDITOR_NOTE TODO - split from exoskeleton? Also: See above sf item to see if this belongs in GO

Axiom
annotated source: chitin-based cuticle
annotated property: IAO_0000115
annotated target: A cuticular covering that is composed primarily of chitin. The main structural component of arthropod cuticle is a polysaccharide, chitin, composed of N-acetylglucosamine units, together with proteins and lipids[WP].
has db xref: Wikipedia:Arthropod_exoskeleton
has db xref: Wikipedia:Cuticle#Invertebrate_zoology
has db xref: https://orcid.org/0000-0002-6601-2165
has db xref: https://sourceforge.net/tracker/index.php

Axiom
annotated source: chitin-based cuticle
annotated property: hasDbXref
annotated target: FBbt:00004970
mapping justification: ManualMappingCuration

Axiom
annotated source: chitin-based cuticle
annotated property: hasNarrowSynonym
annotated target: cuticle
has db xref: FBbt:00004970

Axiom
annotated source: chitin-based cuticle
annotated property: hasRelatedSynonym
annotated target: arthropod exoskeleton
has db xref: Wikipedia:Arthropod_exoskeleton

cuticle
type: Class
subclass of: acellular anatomical structure
subclass of: Restriction
IAO_0000115: Tough but flexible, non-mineral outer coverings of an organism, or parts of an organism, that provide protection. Cuticles are non-homologous, differing in their origin, structure and chemical composition[WP].
UBPROP_0000007: cuticular
has db xref: BTO:0001600
has db xref: Wikipedia:Cuticle
has OBO namespace: uberon
has related synonym: cuticula
has related synonym: cuticular exoskeleton
id: UBERON:0001002
in subset: grouping class
in subset: non informative
in subset: uberon slim
comment: EDITOR_NOTE TODO - check cuticle vs exoskeleton. Note that GO has a very generic definition of cuticle. See also arthropod-anatomy ontology. Note in ncit Cuticle is a plant part

Axiom
annotated source: cuticle
annotated property: subClassOf
annotated target: Restriction
source: Rieger - Evolution of the Cuticle in the Lower Eumetazoa

Axiom
annotated source: cuticle
annotated property: IAO_0000115
annotated target: Tough but flexible, non-mineral outer coverings of an organism, or parts of an organism, that provide protection. Cuticles are non-homologous, differing in their origin, structure and chemical composition[WP].
has db xref: Wikipedia:Cuticle
has db xref: http://sourceforge.net/tracker/

Axiom
annotated source: cuticle
annotated property: hasRelatedSynonym
annotated target: cuticula
has db xref: BTO:0001600

skin epidermis
type: Class
equivalent class: Class
  intersection of: UBERON_0007376
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002097
subclass of: UBERON_0007376
subclass of: UBERON_3000961
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002097
subclass of: Restriction
  on property: RO_0002220
  some values from: UBERON_0002067
subclass of: Restriction
  on property: RO_0002285
  some values from: UBERON_0003055
IAO_0000115: The outer epithelial layer of the skin that is superficial to the dermis.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]
UBPROP_0000001: The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]
UBPROP_0000002: relationship loss: subclass external integument structures (AAO:0000961)[AAO]
UBPROP_0000003: (...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]
UBPROP_0000007: epidermal
UBPROP_0000008: Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes).
has broad synonym: epidermis
has broad synonym: skin
has db xref: AAO:0000143
has db xref: BTO:0000404
has db xref: CALOHA:TS-0283
has db xref: EFO:0000954
has db xref: EMAPA:17528
has db xref: EV:0100153
has db xref: FMA:70596
has db xref: GAID:932
has db xref: MA:0000153
has db xref: MAT:0000154
has db xref: MESH:D004817
has db xref: MIAA:0000154
has db xref: NCIT:C12708
has db xref: SCTID:361694003
has db xref: TAO:0000105
has db xref: UMLS:C0014520
has db xref: VHOG:0000077
has db xref: Wikipedia:Epidermis_(skin)
has db xref: XAO:0000028
has db xref: ZFA:0000105
has exact synonym: vertebrate epidermis
has OBO namespace: uberon
id: UBERON:0001003
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: skin epidermis
annotated property: IAO_0000115
annotated target: The outer epithelial layer of the skin that is superficial to the dermis.
has db xref: ISBN:0073040584
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: skin epidermis
annotated property: UBPROP_0000001
annotated target: A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000105
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: skin epidermis
annotated property: UBPROP_0000001
annotated target: The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000143
ontology: AAO
source: AAO:BJB

Axiom
annotated source: skin epidermis
annotated property: UBPROP_0000002
annotated target: relationship loss: subclass external integument structures (AAO:0000961)[AAO]
date retrieved: 2012-06-20
external class: AAO:0000143
ontology: AAO

Axiom
annotated source: skin epidermis
annotated property: UBPROP_0000003
annotated target: (...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000077
ontology: VHOG
source: ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72
source: http://bgee.unil.ch/

Axiom
annotated source: skin epidermis
annotated property: hasDbXref
annotated target: UMLS:C0014520
source: ncithesaurus:Epidermis

respiratory system
type: Class
equivalent class: Class
  intersection of: anatomical system
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0007585
subclass of: anatomical system
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_33213
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0003016
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0007585
subclass of: Restriction
  on property: RO_0002492
  some values from: fully formed stage
disjoint with: digestive system
disjoint with: circulatory system
disjoint with: nervous system
disjoint with: gustatory system
disjoint with: UBERON_0001434
disjoint with: UBERON_0002204
disjoint with: UBERON_0002294
disjoint with: UBERON_0002330
disjoint with: UBERON_0002390
disjoint with: UBERON_0002405
disjoint with: UBERON_0002416
disjoint with: UBERON_0002423
disjoint with: UBERON_0004456
disjoint with: UBERON_8450002
IAO_0000115: Functional system which consists of structures involved in respiration.
RO_0002161: NCBITaxon_147099
RO_0002175: NCBITaxon 9606
UBPROP_0000001: The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]
UBPROP_0000003: There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]
has db xref: AAO:0000541
has db xref: BTO:0000203
has db xref: CALOHA:TS-1319
has db xref: EFO:0000804
has db xref: EHDAA2:0001604
has db xref: EHDAA:2203
has db xref: EMAPA:16727
has db xref: EV:0100036
has db xref: FMA:7158
has db xref: GAID:78
has db xref: MA:0000327
has db xref: MAT:0000030
has db xref: MESH:D012137
has db xref: MIAA:0000030
has db xref: NCIT:C12779
has db xref: SCTID:278197002
has db xref: TAO:0000272
has db xref: UMLS:C0035237
has db xref: VHOG:0000202
has db xref: Wikipedia:Respiratory_system
has db xref: XAO:0000117
has db xref: ZFA:0000272
has exact synonym: apparatus respiratorius
has exact synonym: respiratory system
has OBO namespace: uberon
has related synonym: Atmungssystem
has related synonym: apparatus respiratorius
has related synonym: systema respiratorium
id: UBERON:0001004
in subset: efo slim
in subset: functional classification
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: respiratory system
annotated property: IAO_0000115
annotated target: Functional system which consists of structures involved in respiration.
has db xref: Wikipedia:Respiratory_system
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: respiratory system
annotated property: RO_0002161
annotated target: NCBITaxon_147099
source: Wikipedia:Acoelomorpha

Axiom
annotated source: respiratory system
annotated property: UBPROP_0000001
annotated target: The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000541
ontology: AAO
source: AAO:BJB

Axiom
annotated source: respiratory system
annotated property: UBPROP_0000003
annotated target: There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000202
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23
source: http://bgee.unil.ch/

Axiom
annotated source: respiratory system
annotated property: hasDbXref
annotated target: UMLS:C0035237
source: ncithesaurus:Respiratory_System

Axiom
annotated source: respiratory system
annotated property: hasRelatedSynonym
annotated target: Atmungssystem
has db xref: BTO:0000203

Axiom
annotated source: respiratory system
annotated property: hasRelatedSynonym
annotated target: apparatus respiratorius
has db xref: BTO:0000203

Axiom
annotated source: respiratory system
annotated property: hasRelatedSynonym
annotated target: systema respiratorium
has db xref: Wikipedia:Respiratory_system
has synonym type: OMO_0003011

respiratory airway
type: Class
subclass of: UBERON_0003103
subclass of: UBERON_0004111
subclass of: Restriction
  on property: BFO_0000050
  some values from: respiratory system
subclass of: Restriction
  on property: channel for
  some values from: UBERON_0034874
IAO_0000115: An airway through which respiratory air passes in organisms.
IAO_0000232: This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends
has broad synonym: airway
has broad synonym: airways
has db xref: SCTID:361380005
has db xref: Wikipedia:Trachea
has OBO namespace: uberon
id: UBERON:0001005
in subset: grouping class
in subset: uberon slim

Axiom
annotated source: respiratory airway
annotated property: IAO_0000115
annotated target: An airway through which respiratory air passes in organisms.
has db xref: Wikipedia:Trachea

Axiom
annotated source: respiratory airway
annotated property: hasBroadSynonym
annotated target: airway
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: respiratory airway
annotated property: hasBroadSynonym
annotated target: airways
has db xref: http://orcid.org/0000-0002-6601-2165
has synonym type: OMO_0003004

digestive system
type: Class
equivalent class: Class
  intersection of: anatomical system
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0022600
subclass of: anatomical system
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0022600
subclass of: Restriction
  on property: RO_0002492
  some values from: fully formed stage
disjoint with: circulatory system
disjoint with: nervous system
disjoint with: gustatory system
disjoint with: UBERON_0001434
disjoint with: UBERON_0002204
disjoint with: UBERON_0002294
disjoint with: UBERON_0002330
disjoint with: UBERON_0002390
disjoint with: UBERON_0002405
disjoint with: UBERON_0002416
disjoint with: UBERON_0002423
disjoint with: UBERON_0004456
disjoint with: UBERON_8450002
IAO_0000115: Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
UBPROP_0000007: digestive
UBPROP_0000012: many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class
has db xref: AAO:0000129
has db xref: BILA:0000082
has db xref: BTO:0000058
has db xref: CALOHA:TS-1293
has db xref: EFO:0000793
has db xref: FBbt:00005055
has db xref: FMA:7152
has db xref: GAID:278
has db xref: MA:0002431
has db xref: MAT:0000018
has db xref: MESH:D004064
has db xref: MIAA:0000018
has db xref: SCTID:278859004
has db xref: TADS:0000170
has db xref: TAO:0000339
has db xref: WBbt:0005748
has db xref: Wikipedia:Digestive_system
has db xref: XAO:0000125
has db xref: ZFA:0000339
has db xref: galen:DigestiveSystem
has db xref: ncithesaurus:Digestive_System
has OBO namespace: uberon
has related synonym: alimentary system
has related synonym: alimentary tract
has related synonym: gastrointestinal system
has related synonym: gut
id: UBERON:0001007
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: digestive system
annotated property: IAO_0000115
annotated target: Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
has db xref: FB:gg
has db xref: NLM:alimentary+system
has db xref: Wikipedia:Digestive_system

Axiom
annotated source: digestive system
annotated property: UBPROP_0000001
annotated target: An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000129
ontology: AAO
source: AAO:BJB

Axiom
annotated source: digestive system
annotated property: UBPROP_0000012
annotated target: many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class
external ontology: MA

Axiom
annotated source: digestive system
annotated property: hasDbXref
annotated target: FBbt:00005055
mapping justification: ManualMappingCuration

renal system
type: Class
equivalent class: Class
  intersection of: UBERON_8450002
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0097254
subclass of: UBERON_8450002
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6072
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0097254
subclass of: Restriction
  on property: RO_0002492
  some values from: fully formed stage
IAO_0000115: The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.
RO_0002161: NCBITaxon_110815
RO_0002161: NCBITaxon_147099
RO_0002175: NCBITaxon 9606
UBPROP_0000001: An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]
UBPROP_0000003: Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]
UBPROP_0000008: In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels
UBPROP_0000008: This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans
has broad synonym: excretory system
has db xref: AAO:0010257
has db xref: BILA:0000015
has db xref: BTO:0001244
has db xref: BTO:0003092
has db xref: CALOHA:TS-1323
has db xref: EFO:0000803
has db xref: EHDAA2:0001601
has db xref: EHDAA:5901
has db xref: EMAPA:17366
has db xref: EV:0100095
has db xref: FBbt:00005056
has db xref: FMA:7159
has db xref: GAID:391
has db xref: MA:0000325
has db xref: MAT:0000027
has db xref: MESH:D014551
has db xref: MIAA:0000027
has db xref: NCIT:C12413
has db xref: SCTID:362204003
has db xref: TADS:0000162
has db xref: TAO:0000163
has db xref: UMLS:C1508753
has db xref: VHOG:0000723
has db xref: WBbt:0005736
has db xref: Wikipedia:Excretory_system
has db xref: XAO:0000143
has db xref: ZFA:0000163
has db xref: galen:UrinaryTract
has exact synonym: systema urinaria
has exact synonym: systema urinarium
has exact synonym: urinary system
has exact synonym: urinary tract
has OBO namespace: uberon
has related synonym: renal or urinary system
has related synonym: renal/urinary system
id: UBERON:0001008
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core
comment: EDITOR_NOTE In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here

Axiom
annotated source: renal system
annotated property: IAO_0000115
annotated target: The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.
has db xref: DOI:10.1371/journal.pone.0099864
has db xref: GO:0072001

Axiom
annotated source: renal system
annotated property: RO_0002161
annotated target: NCBITaxon_110815
source: Wikipedia

Axiom
annotated source: renal system
annotated property: RO_0002161
annotated target: NCBITaxon_147099
source: Wikipedia:Acoelomorpha

Axiom
annotated source: renal system
annotated property: UBPROP_0000001
annotated target: An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010257
ontology: AAO
source: AAO:BJB

Axiom
annotated source: renal system
annotated property: UBPROP_0000003
annotated target: Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000723
ontology: VHOG
source: ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406
source: http://bgee.unil.ch/

Axiom
annotated source: renal system
annotated property: UBPROP_0000008
annotated target: In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels
source: GO

Axiom
annotated source: renal system
annotated property: UBPROP_0000008
annotated target: This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans
source: DOI:10.1371/journal.pone.0099864

Axiom
annotated source: renal system
annotated property: hasDbXref
annotated target: FBbt:00005056
mapping justification: ManualMappingCuration

Axiom
annotated source: renal system
annotated property: hasDbXref
annotated target: UMLS:C1508753
source: ncithesaurus:Urinary_System

Axiom
annotated source: renal system
annotated property: hasExactSynonym
annotated target: systema urinaria
has db xref: FMA:7159

Axiom
annotated source: renal system
annotated property: hasExactSynonym
annotated target: systema urinarium
has db xref: BTO:0003092

Axiom
annotated source: renal system
annotated property: hasRelatedSynonym
annotated target: renal or urinary system
has db xref: EHDAA:5901

circulatory system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_33213
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0003013
subclass of: Restriction
  on property: RO_0002492
  some values from: fully formed stage
disjoint with: nervous system
disjoint with: gustatory system
disjoint with: UBERON_0001434
disjoint with: UBERON_0002204
disjoint with: UBERON_0002294
disjoint with: UBERON_0002330
disjoint with: UBERON_0002390
disjoint with: UBERON_0002405
disjoint with: UBERON_0002416
disjoint with: UBERON_0002423
disjoint with: UBERON_0004456
disjoint with: UBERON_8450002
IAO_0000115: Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
IAO_0000232: the cardiovascular system and the lymphatic system are parts of the circulatory system
RO_0002161: NCBITaxon_147099
RO_0002161: NCBITaxon 6073
RO_0002161: NCBITaxon 6157
RO_0002174: NCBITaxon 6231
UBPROP_0000001: Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]
UBPROP_0000003: We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]
has db xref: AAO:0000959
has db xref: CALOHA:TS-2103
has db xref: MESH:D002319
has db xref: VHOG:0001248
has db xref: Wikipedia:Circulatory_system
has OBO namespace: uberon
has related synonym: systema cardiovasculare
id: UBERON:0001009
in subset: uberon slim

Axiom
annotated source: circulatory system
annotated property: IAO_0000115
annotated target: Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
has db xref: Wikipedia:Circulatory_system

Axiom
annotated source: circulatory system
annotated property: RO_0002161
annotated target: NCBITaxon_147099
source: Wikipedia:Acoelomorpha

Axiom
annotated source: circulatory system
annotated property: RO_0002174
annotated target: NCBITaxon 6231
notes: WBbt coelomocyte currently classified as circulating cell

Axiom
annotated source: circulatory system
annotated property: UBPROP_0000001
annotated target: Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000959
ontology: AAO
source: AAO:BJB

Axiom
annotated source: circulatory system
annotated property: UBPROP_0000003
annotated target: We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001248
ontology: VHOG
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493
source: http://bgee.unil.ch/

Axiom
annotated source: circulatory system
annotated property: hasDbXref
annotated target: MESH:D002319
mapping justification: LexicalMatching
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: circulatory system
annotated property: hasRelatedSynonym
annotated target: systema cardiovasculare
has db xref: Wikipedia:Circulatory_system
has synonym type: OMO_0003011

adipose tissue
type: Class
equivalent class: Class
  intersection of: UBERON_0002384
  intersection of: Restriction
    on property: RO_0002473
    some values from: CL_0000136
subclass of: UBERON_0011822
subclass of: Restriction
  on property: RO_0002473
  some values from: CL_0000136
disjoint with: UBERON_0003714
IAO_0000115: Portion of connective tissue composed of adipocytes enmeshed in areolar tissue.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Connective tissue in which fat is stored.[TAO]
UBPROP_0000001: Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]
UBPROP_0000002: relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]
UBPROP_0000003: Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]
UBPROP_0000007: adipose
UBPROP_0000008: In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen.
UBPROP_0000012: in FMA this is dense irregular connective tissue
has db xref: AAO:0000001
has db xref: AEO:000020
has db xref: BTO:0001487
has db xref: CALOHA:TS-0013
has db xref: EFO:0000790
has db xref: EHDAA2:0003120
has db xref: EMAPA:35112
has db xref: EV:0100381
has db xref: FMA:20110
has db xref: GAID:920
has db xref: MA:0000009
has db xref: MAT:0000015
has db xref: MESH:D000273
has db xref: MIAA:0000015
has db xref: NCIT:C12472
has db xref: SCTID:55603005
has db xref: TAO:0002134
has db xref: UMLS:C0001527
has db xref: VHOG:0001284
has db xref: Wikipedia:Adipose_tissue
has db xref: XAO:0003049
has db xref: ZFA:0005345
has db xref: galen:FattyTissue
has exact synonym: fat
has exact synonym: fat tissue
has exact synonym: fatty tissue
has OBO namespace: uberon
has related synonym: adipose
has related synonym: bodyfat
has related synonym: fatty depot
id: UBERON:0001013
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: adipose tissue
annotated property: subClassOf
annotated target: UBERON_0011822
source: FMA

Axiom
annotated source: adipose tissue
annotated property: IAO_0000115
annotated target: Portion of connective tissue composed of adipocytes enmeshed in areolar tissue.
has db xref: MESH:A10.165.114
has db xref: MGI:cwg
has db xref: MP:0000003
has db xref: Wikipedia:Adipose_tissue
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: adipose tissue
annotated property: UBPROP_0000001
annotated target: Connective tissue in which fat is stored.[TAO]
date retrieved: 2012-08-14
external class: TAO:0002134
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: adipose tissue
annotated property: UBPROP_0000001
annotated target: Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000001
ontology: AAO
source: AAO:LAP

Axiom
annotated source: adipose tissue
annotated property: UBPROP_0000002
annotated target: relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]
date retrieved: 2012-06-20
external class: AAO:0000001
ontology: AAO

Axiom
annotated source: adipose tissue
annotated property: UBPROP_0000003
annotated target: Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001284
ontology: VHOG
source: DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007)
source: http://bgee.unil.ch/

Axiom
annotated source: adipose tissue
annotated property: UBPROP_0000012
annotated target: in FMA this is dense irregular connective tissue
external ontology: FMA

Axiom
annotated source: adipose tissue
annotated property: hasDbXref
annotated target: UMLS:C0001527
source: ncithesaurus:Adipose_Tissue

Axiom
annotated source: adipose tissue
annotated property: hasExactSynonym
annotated target: fat
has db xref: MA:0000009

Axiom
annotated source: adipose tissue
annotated property: hasRelatedSynonym
annotated target: adipose
has db xref: BTO:0001487

Axiom
annotated source: adipose tissue
annotated property: hasRelatedSynonym
annotated target: bodyfat
has db xref: BTO:0001487

musculature
type: Class
subclass of: UBERON_0011216
subclass of: Restriction
  on property: BFO_0000050
  some values from: musculature of body
subclass of: Restriction
  on property: RO_0002473
  some values from: UBERON_0001630
IAO_0000115: A subdivision of the muscular system corresponding to a subdisivision of an organism.
RO_0002171: UBERON_0001474
UBPROP_0000012: In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here.
has db xref: BTO:0000887
has db xref: EFO:0001949
has db xref: EMAPA:35577
has db xref: FMA:32558
has db xref: MA:0000165
has db xref: NCIT:C13056
has db xref: TAO:0000548
has db xref: UMLS:C0026845
has db xref: VSAO:0005038
has db xref: WBbt:0005737
has db xref: Wikipedia:Muscular_system
has db xref: ZFA:0000548
has exact synonym: muscle group
has exact synonym: muscles set
has exact synonym: musculature
has exact synonym: musculi
has exact synonym: set of muscles
has exact synonym: set of skeletal muscles
has OBO namespace: uberon
has related synonym: muscle system
has related synonym: muscles
has related synonym: musculature system
id: UBERON:0001015
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: musculature
annotated property: IAO_0000115
annotated target: A subdivision of the muscular system corresponding to a subdisivision of an organism.
has db xref: Wikipedia:Muscular_system
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: musculature
annotated property: UBPROP_0000012
annotated target: In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here.
external ontology: FMA

Axiom
annotated source: musculature
annotated property: hasDbXref
annotated target: UMLS:C0026845
source: ncithesaurus:Muscle

Axiom
annotated source: musculature
annotated property: hasExactSynonym
annotated target: musculi
has db xref: FMA:32558
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: musculature
annotated property: hasExactSynonym
annotated target: set of muscles
has db xref: FMA:32558

Axiom
annotated source: musculature
annotated property: hasExactSynonym
annotated target: set of skeletal muscles
has db xref: MA:0000165

nervous system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0000540
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6072
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0050877
subclass of: Restriction
  on property: RO_0002473
  some values from: CL_0002319
subclass of: Restriction
  on property: RO_0002492
  some values from: fully formed stage
disjoint with: gustatory system
disjoint with: UBERON_0001434
disjoint with: UBERON_0002204
disjoint with: UBERON_0002294
disjoint with: UBERON_0002330
disjoint with: UBERON_0002390
disjoint with: UBERON_0002405
disjoint with: UBERON_0002416
disjoint with: UBERON_0002423
disjoint with: UBERON_0004456
disjoint with: UBERON_8450002
IAO_0000115: 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].
RO_0002161: NCBITaxon 6040
RO_0002175: NCBITaxon 9606
UBPROP_0000001: 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]
UBPROP_0000001: Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
UBPROP_0000003: Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
UBPROP_0000007: nervous
UBPROP_0000007: neural
has db xref: AAO:0000324
has db xref: BILA:0000079
has db xref: BIRNLEX:844
has db xref: BTO:0001484
has db xref: CALOHA:TS-1313
has db xref: EFO:0000802
has db xref: EHDAA2:0001246
has db xref: EHDAA:826
has db xref: EMAPA:16469
has db xref: EV:0100162
has db xref: FBbt:00005093
has db xref: FMA:7157
has db xref: GAID:466
has db xref: MA:0000016
has db xref: MAT:0000026
has db xref: MESH:D009420
has db xref: MIAA:0000026
has db xref: NCIT:C12755
has db xref: SCTID:278196006
has db xref: TAO:0000396
has db xref: UMLS:C0027763
has db xref: VHOG:0000402
has db xref: WBbt:0005735
has db xref: Wikipedia:Nervous_system
has db xref: XAO:0000177
has db xref: ZFA:0000396
has db xref: neuronames:3236
has exact synonym: neurological system
has narrow synonym: nerve net
has OBO namespace: uberon
has related synonym: systema nervosum
id: UBERON:0001016
in subset: cumbo
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: nervous system
annotated property: subClassOf
annotated target: Restriction
source: Bgee:AN

Axiom
annotated source: nervous system
annotated property: IAO_0000115
annotated target: The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
has db xref: BIRNLEX:844
has db xref: ISBN:0-14-051288-8
has db xref: ISBN:3110148986
has db xref: NLM:nervous+system
has db xref: WB:rynl
has db xref: Wikipedia:Nervous_system
has db xref: ZFIN:curator

Axiom
annotated source: nervous system
annotated property: UBPROP_0000001
annotated target: 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]
date retrieved: 2012-08-14
external class: TAO:0000396
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: nervous system
annotated property: UBPROP_0000001
annotated target: Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000324
ontology: AAO
source: AAO:BJB

Axiom
annotated source: nervous system
annotated property: UBPROP_0000003
annotated target: Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000402
ontology: VHOG
source: ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117
source: http://bgee.unil.ch/

Axiom
annotated source: nervous system
annotated property: hasDbXref
annotated target: FBbt:00005093
mapping justification: ManualMappingCuration

Axiom
annotated source: nervous system
annotated property: hasDbXref
annotated target: UMLS:C0027763
source: ncithesaurus:Nervous_System

Axiom
annotated source: nervous system
annotated property: hasExactSynonym
annotated target: neurological system
has db xref: GO:0050877

Axiom
annotated source: nervous system
annotated property: hasNarrowSynonym
annotated target: nerve net
has db xref: Wikipedia:Nerve_net

Axiom
annotated source: nervous system
annotated property: hasRelatedSynonym
annotated target: systema nervosum
has db xref: Wikipedia:Nervous_system
has synonym type: OMO_0003011

central nervous system
type: Class
subclass of: UBERON_0004121
subclass of: UBERON_0011216
subclass of: Restriction
  on property: BFO_0000050
  some values from: nervous system
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_33213
IAO_0000115: The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
RO_0002161: NCBITaxon_147099
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Part of the nervous system which includes the brain and spinal cord.[AAO]
UBPROP_0000001: The brain and spinal cord. Kimmel et al, 1995.[TAO]
UBPROP_0000001: The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO).
UBPROP_0000003: (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]
has db xref: AAO:0000090
has db xref: BAMS:CNS
has db xref: BILA:0000080
has db xref: BIRNLEX:1099
has db xref: BTO:0000227
has db xref: CALOHA:TS-0150
has db xref: EFO:0000908
has db xref: EHDAA2:0000225
has db xref: EHDAA:828
has db xref: EMAPA:16470
has db xref: EMAPA:16754
has db xref: EV:0100163
has db xref: FBbt:00005094
has db xref: FMA:55675
has db xref: GAID:570
has db xref: MA:0000167
has db xref: MAT:0000457
has db xref: MESH:D002490
has db xref: NCIT:C12438
has db xref: SCTID:278199004
has db xref: TAO:0000012
has db xref: UMLS:C0927232
has db xref: VHOG:0000293
has db xref: Wikipedia:Central_nervous_system
has db xref: XAO:0000215
has db xref: ZFA:0000012
has db xref: neuronames:854
has exact synonym: CNS
has exact synonym: systema nervosum centrale
has narrow synonym: cerebrospinal axis
has OBO namespace: uberon
has related synonym: neuraxis
id: UBERON:0001017
in subset: cumbo
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: central nervous system
annotated property: subClassOf
annotated target: UBERON_0011216
source: FBbt
source: cjm

Axiom
annotated source: central nervous system
annotated property: subClassOf
annotated target: Restriction
source: Bgee:AN

Axiom
annotated source: central nervous system
annotated property: IAO_0000115
annotated target: The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
has db xref: GO:0021551
has db xref: http://www.frontiersinzoology.com/content/7/1/29
has db xref: https://sourceforge.net/p/geneontology/ontology-requests/11422/

Axiom
annotated source: central nervous system
annotated property: RO_0002161
annotated target: NCBITaxon_147099
source: Wikipedia:Acoelomorpha

Axiom
annotated source: central nervous system
annotated property: UBPROP_0000001
annotated target: Part of the nervous system which includes the brain and spinal cord.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000090
ontology: AAO
source: AAO:BJB

Axiom
annotated source: central nervous system
annotated property: UBPROP_0000001
annotated target: The brain and spinal cord. Kimmel et al, 1995.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000012
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: central nervous system
annotated property: UBPROP_0000001
annotated target: The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO).
source: BIRNLEX:1099

Axiom
annotated source: central nervous system
annotated property: UBPROP_0000003
annotated target: (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000293
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)
source: http://bgee.unil.ch/

Axiom
annotated source: central nervous system
annotated property: hasDbXref
annotated target: FBbt:00005094
mapping justification: ManualMappingCuration

Axiom
annotated source: central nervous system
annotated property: hasDbXref
annotated target: UMLS:C0927232
source: BIRNLEX:1099
source: ncithesaurus:Central_Nervous_System

Axiom
annotated source: central nervous system
annotated property: hasExactSynonym
annotated target: CNS
has synonym type: OMO_0003000

Axiom
annotated source: central nervous system
annotated property: hasExactSynonym
annotated target: systema nervosum centrale
has db xref: FMA:55675
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: central nervous system
annotated property: hasNarrowSynonym
annotated target: cerebrospinal axis
has db xref: FMA:55675

Axiom
annotated source: central nervous system
annotated property: hasRelatedSynonym
annotated target: neuraxis
has db xref: FMA:55675

axon tract
type: Class
subclass of: neuron projection bundle
subclass of: UBERON_0011215
IAO_0000115: A group of axons linking two or more neuropils and having a common origin, termination[FBbt].
UBPROP_0000001: White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO)
has db xref: BIRNLEX:1649
has db xref: EV:0100304
has db xref: FBbt:00005100
has db xref: FMA:83847
has db xref: NLX:147822
has exact synonym: axonal tract
has exact synonym: neuraxis tract
has exact synonym: tract of neuraxis
has narrow synonym: nerve tract
has OBO namespace: uberon
has related synonym: nerve tract
has related synonym: tract
id: UBERON:0001018
in subset: cumbo
in subset: pheno slim
comment: WP says this is the analog of peripheral nerves in CNS.

Axiom
annotated source: axon tract
annotated property: IAO_0000115
annotated target: A group of axons linking two or more neuropils and having a common origin, termination[FBbt].
has db xref: http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html
has db xref: https://github.com/obophenotype/uberon/issues/286

Axiom
annotated source: axon tract
annotated property: UBPROP_0000001
annotated target: White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO)
source: http://neurolex.org/wiki/Cumbo_terms

Axiom
annotated source: axon tract
annotated property: hasDbXref
annotated target: FBbt:00005100
mapping justification: ManualMappingCuration

Axiom
annotated source: axon tract
annotated property: hasExactSynonym
annotated target: neuraxis tract
has db xref: FMA:83847

Axiom
annotated source: axon tract
annotated property: hasExactSynonym
annotated target: tract of neuraxis
has db xref: FMA:83847

Axiom
annotated source: axon tract
annotated property: hasNarrowSynonym
annotated target: nerve tract
has db xref: BIRNLEX:1649

nerve fasciculus
type: Class
subclass of: neuron projection bundle
IAO_0000115: A slender neuron projection bundle[FBbt]; A bundle of anatomical fibers, as of muscle or nerve (American Heritage Dictionary 4th ed).
has broad synonym: fascicle
has db xref: BIRNLEX:872
has db xref: BTO:0002191
has db xref: EMAPA:36605
has db xref: FMA:12235
has db xref: NCIT:C32586
has db xref: TGMA:0000088
has db xref: UMLS:C1185741
has db xref: Wikipedia:Nervous_system_fascicle
has exact synonym: fasciculus
has exact synonym: nerve bundle
has exact synonym: nerve fasciculus
has exact synonym: neural fasciculus
has OBO namespace: uberon
has related synonym: nerve fiber tract
id: UBERON:0001019
in subset: uberon slim
comment: EDITOR_NOTE note FBbt class not disjoint from tract. Consider merging with 'neuron projection bundle'

Axiom
annotated source: nerve fasciculus
annotated property: IAO_0000115
annotated target: A slender neuron projection bundle[FBbt]; A bundle of anatomical fibers, as of muscle or nerve (American Heritage Dictionary 4th ed).
has db xref: BIRNLEX:872
has db xref: FBbt:00005101

Axiom
annotated source: nerve fasciculus
annotated property: hasBroadSynonym
annotated target: fascicle
has db xref: FBbt:00005101

Axiom
annotated source: nerve fasciculus
annotated property: hasDbXref
annotated target: UMLS:C1185741
source: ncithesaurus:Fascicle

Axiom
annotated source: nerve fasciculus
annotated property: hasExactSynonym
annotated target: fasciculus
has synonym type: OMO_0003011

Axiom
annotated source: nerve fasciculus
annotated property: hasExactSynonym
annotated target: nerve bundle
has db xref: FMA:12235

Axiom
annotated source: nerve fasciculus
annotated property: hasExactSynonym
annotated target: nerve fasciculus
has db xref: FMA:12235

Axiom
annotated source: nerve fasciculus
annotated property: hasExactSynonym
annotated target: neural fasciculus
has db xref: FMA:12235

Axiom
annotated source: nerve fasciculus
annotated property: hasRelatedSynonym
annotated target: nerve fiber tract
has db xref: BTO:0002191

nervous system commissure
type: Class
subclass of: axon tract
subclass of: Restriction
  on property: BSPO_0005001
  some values from: nervous system
IAO_0000115: Axon tract that crosses the midline of the central nervous system[NIF, modified]. In the context of Drosophila refers to a broad band of axons connecting equivalent neuropils each side of the brain[FBbt].
UBPROP_0000001: White matter fiber bundle that crosses the midline of the brain or spinal cord, that connects similar structures on both sides. (CUMBO; Heimer, L. The Human Brain, 2nd ed., 1995, pg 6)
UBPROP_0000007: commissural
has broad synonym: commissure
has db xref: FMA:83906
has db xref: NCIT:C32349
has db xref: NLX:110
has db xref: NLXANAT:20090513
has db xref: TADS:0000201
has db xref: UMLS:C1185742
has db xref: Wikipedia:Commissure
has exact synonym: commissure of neuraxis
has exact synonym: neuraxis commissure
has narrow synonym: white matter commissure
has OBO namespace: uberon
id: UBERON:0001020
in subset: cumbo
in subset: uberon slim
comment: *not* the same as FMA:76741 Commissure

Axiom
annotated source: nervous system commissure
annotated property: IAO_0000115
annotated target: Axon tract that crosses the midline of the central nervous system[NIF, modified]. In the context of Drosophila refers to a broad band of axons connecting equivalent neuropils each side of the brain[FBbt].
has db xref: NLXANAT:20090513
has db xref: https://github.com/obophenotype/uberon/issues/300
has db xref: https://github.com/obophenotype/uberon/issues/325

Axiom
annotated source: nervous system commissure
annotated property: UBPROP_0000001
annotated target: White matter fiber bundle that crosses the midline of the brain or spinal cord, that connects similar structures on both sides. (CUMBO; Heimer, L. The Human Brain, 2nd ed., 1995, pg 6)
source: http://neurolex.org/wiki/Cumbo_terms

Axiom
annotated source: nervous system commissure
annotated property: hasDbXref
annotated target: UMLS:C1185742
source: ncithesaurus:Commissure

Axiom
annotated source: nervous system commissure
annotated property: hasExactSynonym
annotated target: commissure of neuraxis
has db xref: FMA:83906

Axiom
annotated source: nervous system commissure
annotated property: hasExactSynonym
annotated target: neuraxis commissure
has db xref: FMA:83906

Axiom
annotated source: nervous system commissure
annotated property: hasNarrowSynonym
annotated target: white matter commissure
has db xref: CUMBO:CUMBO

nerve
type: Class
subclass of: neuron projection bundle
subclass of: Restriction
  on property: BFO_0000050
  some values from: peripheral nervous system
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0002045
IAO_0000115: An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: A portion of tissue which is a fasiculated group of axons.[TAO]
UBPROP_0000007: nervous
has db xref: AAO:0011070
has db xref: AEO:0000137
has db xref: BAMS:n
has db xref: BIRNLEX:1615
has db xref: BSA:0000098
has db xref: BTO:0000925
has db xref: BTO:0001027
has db xref: CALOHA:TS-0772
has db xref: EHDAA2:0003137
has db xref: EHDAA:2851
has db xref: EHDAA:3776
has db xref: EHDAA:4657
has db xref: EMAPA:32808
has db xref: EMAPA:32815
has db xref: EV:0100371
has db xref: FBbt:00005105
has db xref: FMA:65132
has db xref: FMA:65239
has db xref: GAID:747
has db xref: GAID:758
has db xref: MA:0000217
has db xref: MA:0000228
has db xref: MESH:D010525
has db xref: NCIT:C12466
has db xref: NCIT:C12768
has db xref: NLX:147826
has db xref: SCTID:244457007
has db xref: SCTID:256864008
has db xref: TAO:0007009
has db xref: UMLS:C0027740
has db xref: UMLS:C0031119
has db xref: VHOG:0000901
has db xref: Wikipedia:Nervous_system
has db xref: XAO:0000204
has db xref: XAO:0003047
has db xref: ZFA:0007009
has db xref: galen:Nerve
has exact synonym: nerves
has exact synonym: peripheral nerve
has OBO namespace: uberon
has related synonym: neural subtree
id: UBERON:0001021
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: nerve
annotated property: subClassOf
annotated target: neuron projection bundle
source: FBbt

Axiom
annotated source: nerve
annotated property: IAO_0000115
annotated target: An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures.
has db xref: FBbt:00005105
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: nerve
annotated property: UBPROP_0000001
annotated target: A portion of tissue which is a fasiculated group of axons.[TAO]
date retrieved: 2012-08-14
external class: TAO:0007009
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: nerve
annotated property: hasDbXref
annotated target: FBbt:00005105
mapping justification: ManualMappingCuration

Axiom
annotated source: nerve
annotated property: hasDbXref
annotated target: UMLS:C0027740
source: ncithesaurus:Nerve

Axiom
annotated source: nerve
annotated property: hasDbXref
annotated target: UMLS:C0031119
source: ncithesaurus:Peripheral_Nerve

Axiom
annotated source: nerve
annotated property: hasExactSynonym
annotated target: nerves
has db xref: TAO:0007009
has synonym type: OMO_0003004

Axiom
annotated source: nerve
annotated property: hasExactSynonym
annotated target: peripheral nerve
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: nerve
annotated property: hasRelatedSynonym
annotated target: neural subtree
has db xref: FMA:65132

sensory nerve
type: Class
subclass of: nerve
subclass of: Restriction
IAO_0000115: A nerve that transmits from sensory receptors on the surface of the body to the central nervous system.
has db xref: AEO:0000201
has db xref: EHDAA2:0003200
has db xref: FBbt:00005136
has db xref: FMA:5868
has db xref: Wikipedia:Sensory_nerve
has exact synonym: nervus sensorius
has OBO namespace: uberon
has related synonym: afferent nerve
id: UBERON:0001027
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: sensory nerve
annotated property: subClassOf
annotated target: Restriction
source: AEO

Axiom
annotated source: sensory nerve
annotated property: IAO_0000115
annotated target: A nerve that transmits from sensory receptors on the surface of the body to the central nervous system.
has db xref: UBERON:cjm
has db xref: Wikipedia:Sensory_nerve

Axiom
annotated source: sensory nerve
annotated property: hasDbXref
annotated target: FBbt:00005136
mapping justification: ManualMappingCuration

Axiom
annotated source: sensory nerve
annotated property: hasExactSynonym
annotated target: nervus sensorius
has db xref: Wikipedia:Sensory_nerve
has synonym type: OMO_0003011

sensory system
type: Class
subclass of: UBERON_0015203
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0004456
subclass of: Restriction
  on property: RO_0002131
  some values from: nervous system
subclass of: Restriction
  on property: RO_0002216
  some values from: GO_0007600
IAO_0000115: Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
RO_0002175: NCBITaxon 9606
UBPROP_0000003: An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]
UBPROP_0000012: note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
has db xref: AAO:0000555
has db xref: BAMS:SEN
has db xref: BILA:0000099
has db xref: EFO:0000805
has db xref: EHDAA2:0003094
has db xref: EMAPA:16192
has db xref: FBbt:00007692
has db xref: FMA:75259
has db xref: MA:0002442
has db xref: MAT:0000031
has db xref: MIAA:0000031
has db xref: NLXANAT:090816
has db xref: TAO:0000282
has db xref: VHOG:0001674
has db xref: Wikipedia:Sensory_system
has db xref: XAO:0003194
has db xref: ZFA:0000282
has exact synonym: organa sensuum
has exact synonym: sense organ subsystem
has exact synonym: sense organs
has exact synonym: sense organs set
has exact synonym: sensory subsystem
has exact synonym: sensory systems
has OBO namespace: uberon
has related synonym: organa sensuum
has related synonym: sensory organ system
has related synonym: set of sense organs
id: UBERON:0001032
in subset: efo slim
in subset: human reference atlas
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: sensory system
annotated property: IAO_0000115
annotated target: Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
has db xref: Wikipedia:Sensory_system

Axiom
annotated source: sensory system
annotated property: UBPROP_0000003
annotated target: An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001674
ontology: VHOG
source: DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)
source: http://bgee.unil.ch/

Axiom
annotated source: sensory system
annotated property: hasDbXref
annotated target: FBbt:00007692
mapping justification: ManualMappingCuration

Axiom
annotated source: sensory system
annotated property: hasExactSynonym
annotated target: organa sensuum
has db xref: FMA:75259
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: sensory system
annotated property: hasExactSynonym
annotated target: sense organs
has db xref: FMA:75259

Axiom
annotated source: sensory system
annotated property: hasExactSynonym
annotated target: sense organs set
has db xref: FMA:75259

Axiom
annotated source: sensory system
annotated property: hasExactSynonym
annotated target: sensory systems
has db xref: TAO:0000282
has synonym type: OMO_0003004

Axiom
annotated source: sensory system
annotated property: hasRelatedSynonym
annotated target: organa sensuum
has db xref: Wikipedia:Sensory_system
has synonym type: OMO_0003011

Axiom
annotated source: sensory system
annotated property: hasRelatedSynonym
annotated target: set of sense organs
has db xref: FMA:75259

gustatory system
type: Class
equivalent class: Class
  intersection of: anatomical system
  intersection of: Restriction
    on property: RO_0002216
    some values from: GO_0050912
subclass of: anatomical system
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6072
subclass of: Restriction
  on property: RO_0002216
  some values from: GO_0050912
subclass of: Restriction
  on property: RO_0002492
  some values from: fully formed stage
disjoint with: UBERON_0001434
disjoint with: UBERON_0002204
disjoint with: UBERON_0002294
disjoint with: UBERON_0002330
disjoint with: UBERON_0002390
disjoint with: UBERON_0002405
disjoint with: UBERON_0002416
disjoint with: UBERON_0002423
disjoint with: UBERON_0004456
disjoint with: UBERON_8450002
IAO_0000115: The sensory system for the sense of taste.
UBPROP_0000001: The sensory system for the sense of taste[NLXANAT:090803].
UBPROP_0000001: The sensory system used for the sense of taste.[AAO]
UBPROP_0000007: gustatory
UBPROP_0000012: in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes
has db xref: AAO:0010577
has db xref: BILA:0000143
has db xref: EFO:0000830
has db xref: FMA:7194
has db xref: MA:0002446
has db xref: MAT:0000275
has db xref: MIAA:0000275
has db xref: NLXANAT:090803
has db xref: SCTID:423940004
has db xref: TAO:0001101
has db xref: Wikipedia:Gustatory_system
has db xref: XAO:0003197
has db xref: ZFA:0001101
has db xref: neuronames:2889
has exact synonym: gustatory organ system
has exact synonym: taste system
has OBO namespace: uberon
id: UBERON:0001033
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: gustatory system
annotated property: IAO_0000115
annotated target: The sensory system for the sense of taste.
has db xref: NLXANAT:090803

Axiom
annotated source: gustatory system
annotated property: UBPROP_0000001
annotated target: The sensory system for the sense of taste[NLXANAT:090803].
source: NLXANAT:090803

Axiom
annotated source: gustatory system
annotated property: UBPROP_0000001
annotated target: The sensory system used for the sense of taste.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010577
ontology: AAO
source: AAO:EJS

Axiom
annotated source: gustatory system
annotated property: UBPROP_0000012
annotated target: in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes
external ontology: ZFA

strand of hair
type: Class
subclass of: cutaneous appendage
subclass of: Restriction
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0045095
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_40674
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0002073
IAO_0000115: A filament, mostly protein, that grows from follicles found in the dermis[WP].
IAO_0000116: TODO for now we treat vibrissa/whisker as a syonym, but these have different follicles. We could introduce subclasses (see also: Pangolin scales)
IAO_0000232: this class defines an individual hair
has db xref: BTO:0001501
has db xref: CALOHA:TS-0430
has db xref: EFO:0000958
has db xref: EMAPA:18769
has db xref: EV:0100157
has db xref: FMA:53667
has db xref: GAID:71
has db xref: MA:0000155
has db xref: MAT:0000160
has db xref: MESH:D006197
has db xref: MIAA:0000160
has db xref: NCIT:C32705
has db xref: SCTID:361702001
has db xref: UMLS:C0018494
has db xref: VHOG:0001191
has db xref: Wikipedia:Hair
has exact synonym: hair
has OBO namespace: uberon
has related synonym: coat hair
has related synonym: coat/ hair
has related synonym: fur
has related synonym: microchaeta
has related synonym: quill
has related synonym: setulae
has related synonym: vibrissa
has related synonym: whisker
id: UBERON:0001037
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: strand of hair
annotated property: subClassOf
annotated target: cutaneous appendage
source: FMA

Axiom
annotated source: strand of hair
annotated property: subClassOf
annotated target: Restriction
source: FMA

Axiom
annotated source: strand of hair
annotated property: subClassOf
annotated target: Restriction
source: FMA

Axiom
annotated source: strand of hair
annotated property: IAO_0000115
annotated target: A filament, mostly protein, that grows from follicles found in the dermis[WP].
has db xref: Wikipedia:Hair

Axiom
annotated source: strand of hair
annotated property: hasDbXref
annotated target: UMLS:C0018494
source: ncithesaurus:Hair

Axiom
annotated source: strand of hair
annotated property: hasRelatedSynonym
annotated target: quill
has synonym type: SENSU

Axiom
annotated source: strand of hair
annotated property: hasRelatedSynonym
annotated target: vibrissa
has synonym type: SENSU

Axiom
annotated source: strand of hair
annotated property: hasRelatedSynonym
annotated target: whisker
has synonym type: SENSU

yolk sac
type: Class
subclass of: UBERON_0005292
subclass of: UBERON_0005631
subclass of: UBERON_0007499
subclass of: Restriction
IAO_0000115: A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP].
IAO_0000116: consider splitting class
UBPROP_0000001: One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG]
UBPROP_0000001: the extraembryonic tissue membrane, formed from the visceral endoderm and the extraembryonic mesoderm, which is located ventral to the embryonic disc and is connected to the presumptive midgut of the embryo; the yolk that it contains is the site of embryonic hematopoiesis and vitelline circulation is involved in early embryonic circulation; it is the origin of the primordial germ cells
UBPROP_0000003: Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]
UBPROP_0000008: In therians, a structure homologous to the yolk sac is is present, but contains no yolk platelets. Instead it is filled with fluid [ISBN:0073040584 (Vertebrates, Kardong)]
has db xref: BTO:0001471
has db xref: CALOHA:TS-1130
has db xref: EFO:0003078
has db xref: EHDAA2:0002212
has db xref: EHDAA:164
has db xref: EMAPA:16085
has db xref: FMA:87180
has db xref: GAID:1301
has db xref: MESH:D015017
has db xref: NCIT:C14128
has db xref: SCTID:362845002
has db xref: UMLS:C0043425
has db xref: VHOG:0000830
has db xref: Wikipedia:Yolk_sac
has OBO namespace: uberon
has related synonym: saccus vitellinus
has related synonym: vesicula umbilicalis
id: UBERON:0001040
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: yolk sac
annotated property: subClassOf
annotated target: UBERON_0007499
source: EHDAA2

Axiom
annotated source: yolk sac
annotated property: subClassOf
annotated target: Restriction
source: ISBN:0073040584

Axiom
annotated source: yolk sac
annotated property: subClassOf
annotated target: Restriction
source: ISBN:0073040584

Axiom
annotated source: yolk sac
annotated property: IAO_0000115
annotated target: A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP].
has db xref: Wikipedia:Yolk_sac

Axiom
annotated source: yolk sac
annotated property: UBPROP_0000001
annotated target: One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000830
ontology: VHOG
source: http://bgee.unil.ch/
source: http://medical-dictionary.thefreedictionary.com/yolk+sac

Axiom
annotated source: yolk sac
annotated property: UBPROP_0000001
annotated target: the extraembryonic tissue membrane, formed from the visceral endoderm and the extraembryonic mesoderm, which is located ventral to the embryonic disc and is connected to the presumptive midgut of the embryo; the yolk that it contains is the site of embryonic hematopoiesis and vitelline circulation is involved in early embryonic circulation; it is the origin of the primordial germ cells
source: MP:0001718

Axiom
annotated source: yolk sac
annotated property: UBPROP_0000003
annotated target: Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000830
ontology: VHOG
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187
source: http://bgee.unil.ch/

Axiom
annotated source: yolk sac
annotated property: hasDbXref
annotated target: UMLS:C0043425
source: ncithesaurus:Yolk_Sac

Axiom
annotated source: yolk sac
annotated property: hasRelatedSynonym
annotated target: saccus vitellinus
has db xref: Wikipedia:Yolk_sac
has synonym type: OMO_0003011

Axiom
annotated source: yolk sac
annotated property: hasRelatedSynonym
annotated target: vesicula umbilicalis
has db xref: Wikipedia:Yolk_sac
has synonym type: OMO_0003011

foregut
type: Class
subclass of: UBERON_0004921
IAO_0000115: Anterior subdivision of a digestive tract.
IAO_0000116: Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure
UBPROP_0000001: The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder.
UBPROP_0000003: The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
has db xref: AAO:0011042
has db xref: BILA:0000085
has db xref: BTO:0000507
has db xref: EHDAA2:0000557
has db xref: EHDAA:520
has db xref: EMAPA:16548
has db xref: FBbt:00005379
has db xref: FMA:45616
has db xref: MA:0001526
has db xref: NCIT:C34180
has db xref: SCTID:361409009
has db xref: TGMA:0001014
has db xref: UMLS:C0231051
has db xref: VHOG:0000285
has db xref: Wikipedia:Foregut
has db xref: XAO:0000232
has OBO namespace: uberon
has related synonym: praeenteron
has related synonym: proenteron
id: UBERON:0001041
in subset: developmental classification
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: foregut
annotated property: IAO_0000115
annotated target: Anterior subdivision of a digestive tract.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: foregut
annotated property: UBPROP_0000001
annotated target: The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder.
source: MP:0000474

Axiom
annotated source: foregut
annotated property: UBPROP_0000003
annotated target: The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000285
ontology: VHOG
source: ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
source: http://bgee.unil.ch/

Axiom
annotated source: foregut
annotated property: hasDbXref
annotated target: FBbt:00005379
mapping justification: ManualMappingCuration

Axiom
annotated source: foregut
annotated property: hasDbXref
annotated target: UMLS:C0231051
source: ncithesaurus:Foregut

Axiom
annotated source: foregut
annotated property: hasRelatedSynonym
annotated target: praeenteron
has db xref: Wikipedia:Foregut
has synonym type: OMO_0003011

Axiom
annotated source: foregut
annotated property: hasRelatedSynonym
annotated target: proenteron
has db xref: Wikipedia:Foregut
has synonym type: OMO_0003011

chordate pharynx
type: Class
subclass of: UBERON_0006562
subclass of: Restriction
  on property: BFO_0000050
  some values from: respiratory system
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7711
IAO_0000115: A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED].
UBPROP_0000001: A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867].
UBPROP_0000001: Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]
UBPROP_0000001: Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]
UBPROP_0000001: Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576].
UBPROP_0000001: The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
UBPROP_0000002: relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]
UBPROP_0000002: relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]
UBPROP_0000003: (...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]
UBPROP_0000012: MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme
has broad synonym: pharynx
has db xref: AAO:0000967
has db xref: BTO:0001049
has db xref: CALOHA:TS-0785
has db xref: EFO:0000836
has db xref: EHDAA2:0001458
has db xref: EHDAA:2947
has db xref: EMAPA:16706
has db xref: EV:0100065
has db xref: FMA:46688
has db xref: GAID:155
has db xref: MA:0000432
has db xref: MESH:D010614
has db xref: NCIT:C12425
has db xref: SCTID:181211006
has db xref: TAO:0000056
has db xref: UMLS:C0031354
has db xref: VHOG:0000462
has db xref: Wikipedia:Pharynx
has db xref: XAO:0003227
has db xref: ZFA:0000056
has db xref: galen:Pharynx
has OBO namespace: uberon
id: UBERON:0001042
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core
comment: Consider generalizing to deuterostome pharynx

Axiom
annotated source: chordate pharynx
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: chordate pharynx
annotated property: IAO_0000115
annotated target: A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED].
has db xref: http://www.feedexp.org

Axiom
annotated source: chordate pharynx
annotated property: UBPROP_0000001
annotated target: A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867].
source: MESH:A03.867

Axiom
annotated source: chordate pharynx
annotated property: UBPROP_0000001
annotated target: Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000967
ontology: AAO
source: AAO:EJS

Axiom
annotated source: chordate pharynx
annotated property: UBPROP_0000001
annotated target: Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000056
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: chordate pharynx
annotated property: UBPROP_0000001
annotated target: Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576].
source: ZFIN:ZDB-PUB-961014-576

Axiom
annotated source: chordate pharynx
annotated property: UBPROP_0000001
annotated target: The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000462
ontology: VHOG
source: http://bgee.unil.ch/

Axiom
annotated source: chordate pharynx
annotated property: UBPROP_0000002
annotated target: relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]
date retrieved: 2012-06-20
external class: AAO:0000967
ontology: AAO

Axiom
annotated source: chordate pharynx
annotated property: UBPROP_0000002
annotated target: relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]
date retrieved: 2012-06-20
external class: AAO:0000967
ontology: AAO

Axiom
annotated source: chordate pharynx
annotated property: UBPROP_0000003
annotated target: (...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000462
ontology: VHOG
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503
source: http://bgee.unil.ch/

Axiom
annotated source: chordate pharynx
annotated property: UBPROP_0000012
annotated target: MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme
external ontology: MA

Axiom
annotated source: chordate pharynx
annotated property: hasBroadSynonym
annotated target: pharynx
has db xref: FMA:46688
has synonym type: SENSU

Axiom
annotated source: chordate pharynx
annotated property: hasDbXref
annotated target: UMLS:C0031354
source: ncithesaurus:Pharynx

esophagus
type: Class
subclass of: UBERON_0004921
subclass of: UBERON_0005178
subclass of: UBERON_0013765
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0004908
subclass of: Restriction
  on property: RO_0002202
  some values from: foregut
subclass of: Restriction
  on property: proximally connected to
  some values from: chordate pharynx
IAO_0000115: 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).
RO_0002175: NCBITaxon 9606
UBPROP_0000001: 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]
UBPROP_0000003: 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]
UBPROP_0000007: esophageal
UBPROP_0000012: 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)
has db xref: AAO:0000145
has db xref: ANISEED:1235301
has db xref: BTO:0000959
has db xref: CALOHA:TS-0700
has db xref: EFO:0000835
has db xref: EHDAA2:0001285
has db xref: EHDAA:2937
has db xref: EMAPA:16833
has db xref: EV:0100069
has db xref: FMA:7131
has db xref: GAID:291
has db xref: MA:0000352
has db xref: MAT:0000048
has db xref: MESH:D004947
has db xref: MIAA:0000048
has db xref: NCIT:C12389
has db xref: SCTID:181245004
has db xref: TAO:0000204
has db xref: UMLS:C0014876
has db xref: VHOG:0000450
has db xref: Wikipedia:Esophagus
has db xref: XAO:0000127
has db xref: ZFA:0000204
has db xref: galen:Esophagus
has exact synonym: gullet
has exact synonym: oesophagus
has OBO namespace: uberon
id: UBERON:0001043
in subset: efo slim
in subset: human reference atlas
in subset: major organ
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: esophagus
annotated property: IAO_0000115
annotated target: 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).
has db xref: Wikipedia:Esophagus
has db xref: http://www.rivm.nl/interspeciesinfo/inter/oesophagus/

Axiom
annotated source: esophagus
annotated property: UBPROP_0000001
annotated target: 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]
date retrieved: 2012-06-20
external class: AAO:0000145
ontology: AAO
source: AAO:EJS

Axiom
annotated source: esophagus
annotated property: UBPROP_0000003
annotated target: 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]
date retrieved: 2012-09-17
external class: VHOG:0000450
ontology: VHOG
source: DOI:10.1111/j.1096-3642.1996.tb01658.x Mallatt J, Ventilation and the origin of jawed vertebrates: a new mouth. Zoological Journal of the Linnean Society (1996)
source: http://bgee.unil.ch/

Axiom
annotated source: esophagus
annotated property: UBPROP_0000012
annotated target: 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 ontology: MA

Axiom
annotated source: esophagus
annotated property: hasDbXref
annotated target: UMLS:C0014876
source: ncithesaurus:Esophagus

saliva-secreting gland
type: Class
equivalent class: Class
  intersection of: UBERON_0002530
  intersection of: Restriction
    on property: RO_0003000
    some values from: UBERON_0001836
subclass of: UBERON_0010047
subclass of: Restriction
  on property: RO_0001025
  some values from: oral cavity
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_33213
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0046541
subclass of: Restriction
  on property: RO_0002433
  some values from: digestive system
subclass of: Restriction
  on property: RO_0003000
  some values from: UBERON_0001836
IAO_0000115: Saliva-secreting exocrine glands of the oral cavity[GO].
IAO_0000232: currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: A gland that produces the saliva. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
UBPROP_0000003: In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system.[well established][VHOG]
UBPROP_0000008: The salivary glands in mammals are exocrine glands, glands with ducts, that produce saliva. They also secrete amylase, an enzyme that breaks down starch into maltose. In other organisms such as insects, salivary glands are often used to produce biologically important proteins like silk or glues, and fly salivary glands contain polytene chromosomes that have been useful in genetic research. The salivary glands of some species are modified to produce enzymes; salivary amylase is found in many, but by no means all, bird and mammal species (including humans, as noted above). Furthermore, the venom glands of poisonous snakes, Gila monsters, and some shrews, are modified salivary glands
has db xref: BTO:0001203
has db xref: CALOHA:TS-0892
has db xref: EFO:0000859
has db xref: EHDAA2:0001775
has db xref: EHDAA:7987
has db xref: EMAPA:17751
has db xref: EV:0100059
has db xref: FBbt:00005382
has db xref: FMA:9597
has db xref: GAID:937
has db xref: MA:0000346
has db xref: MAT:0000079
has db xref: MESH:D012469
has db xref: MIAA:0000079
has db xref: NCIT:C12426
has db xref: SCTID:181236000
has db xref: UMLS:C0036098
has db xref: VHOG:0000376
has db xref: Wikipedia:Salivary_gland
has db xref: galen:SalivaryGland
has exact synonym: salivary gland
has OBO namespace: uberon
has related synonym: glandulae salivariae
id: UBERON:0001044
in subset: efo slim
in subset: functional classification
in subset: human reference atlas
in subset: organ slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: saliva-secreting gland
annotated property: IAO_0000115
annotated target: Saliva-secreting exocrine glands of the oral cavity[GO].
has db xref: GO:0007431
has db xref: Wikipedia:Salivary_gland

Axiom
annotated source: saliva-secreting gland
annotated property: IAO_0000232
annotated target: currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals.
source: 3

Axiom
annotated source: saliva-secreting gland
annotated property: UBPROP_0000001
annotated target: A gland that produces the saliva. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000376
ontology: VHOG
source: http://bgee.unil.ch/

Axiom
annotated source: saliva-secreting gland
annotated property: UBPROP_0000003
annotated target: In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000376
ontology: VHOG
source: ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptationm(2005) p.211
source: http://bgee.unil.ch/

Axiom
annotated source: saliva-secreting gland
annotated property: hasDbXref
annotated target: FBbt:00005382
mapping justification: ManualMappingCuration

Axiom
annotated source: saliva-secreting gland
annotated property: hasDbXref
annotated target: UMLS:C0036098
source: ncithesaurus:Salivary_Gland

Axiom
annotated source: saliva-secreting gland
annotated property: hasExactSynonym
annotated target: salivary gland
has db xref: MA:0000346

Axiom
annotated source: saliva-secreting gland
annotated property: hasRelatedSynonym
annotated target: glandulae salivariae
has db xref: Wikipedia:Salivary_gland
has synonym type: OMO_0003011

midgut
type: Class
subclass of: UBERON_0004921
subclass of: Restriction
  on property: proximally connected to
  some values from: foregut
IAO_0000115: Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO].
IAO_0000116: Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class
UBPROP_0000003: The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
UBPROP_0000008: In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon
UBPROP_0000012: in FMA this represents an embryonic region.
has db xref: BILA:0000086
has db xref: BTO:0000863
has db xref: EFO:0001950
has db xref: EHDAA2:0001185
has db xref: EHDAA:983
has db xref: EMAPA:16255
has db xref: FBbt:00005383
has db xref: FMA:45617
has db xref: MA:0001564
has db xref: NCIT:C34210
has db xref: SCTID:361410004
has db xref: TGMA:0001036
has db xref: UMLS:C0231052
has db xref: VHOG:0000290
has db xref: Wikipedia:Midgut
has db xref: XAO:0000103
has OBO namespace: uberon
has related synonym: mesenteron
id: UBERON:0001045
in subset: developmental classification
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: midgut
annotated property: IAO_0000115
annotated target: Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO].
has db xref: GO:0007494
has db xref: Wikipedia:Midgut

Axiom
annotated source: midgut
annotated property: UBPROP_0000003
annotated target: The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000290
ontology: VHOG
source: ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
source: http://bgee.unil.ch/

Axiom
annotated source: midgut
annotated property: UBPROP_0000008
annotated target: In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon
source: WP

Axiom
annotated source: midgut
annotated property: UBPROP_0000012
annotated target: in FMA this represents an embryonic region.
external ontology: FMA

Axiom
annotated source: midgut
annotated property: hasDbXref
annotated target: FBbt:00005383
mapping justification: ManualMappingCuration

Axiom
annotated source: midgut
annotated property: hasDbXref
annotated target: UMLS:C0231052
source: ncithesaurus:Midgut

Axiom
annotated source: midgut
annotated property: hasRelatedSynonym
annotated target: mesenteron
has db xref: Wikipedia:Midgut
has synonym type: OMO_0003011

hindgut
type: Class
subclass of: UBERON_0004921
subclass of: Restriction
subclass of: Restriction
  on property: proximally connected to
  some values from: midgut
IAO_0000115: The caudalmost subdivision of a digestive tract.
IAO_0000116: Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class
UBPROP_0000001: the caudal portion of the primitive digestive tube of the embryo
UBPROP_0000003: The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
UBPROP_0000012: in FMA this class has no children. In MA it has a single child hindgut epithelium
has db xref: AAO:0011052
has db xref: BILA:0000087
has db xref: BTO:0000510
has db xref: EHDAA2:0000779
has db xref: EHDAA:975
has db xref: EMAPA:16715
has db xref: FBbt:00005384
has db xref: FMA:45618
has db xref: MA:0001527
has db xref: NCIT:C34188
has db xref: SCTID:362856002
has db xref: TGMA:0001020
has db xref: UMLS:C0231053
has db xref: VHOG:0000459
has db xref: Wikipedia:Hindgut
has db xref: XAO:0000104
has OBO namespace: uberon
has related synonym: metenteron
id: UBERON:0001046
in subset: developmental classification
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: hindgut
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: hindgut
annotated property: IAO_0000115
annotated target: The caudalmost subdivision of a digestive tract.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: hindgut
annotated property: UBPROP_0000001
annotated target: the caudal portion of the primitive digestive tube of the embryo
source: MP:0008786

Axiom
annotated source: hindgut
annotated property: UBPROP_0000003
annotated target: The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000459
ontology: VHOG
source: ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
source: http://bgee.unil.ch/

Axiom
annotated source: hindgut
annotated property: UBPROP_0000012
annotated target: in FMA this class has no children. In MA it has a single child hindgut epithelium
external ontology: FMA

Axiom
annotated source: hindgut
annotated property: hasDbXref
annotated target: FBbt:00005384
mapping justification: ManualMappingCuration

Axiom
annotated source: hindgut
annotated property: hasDbXref
annotated target: UMLS:C0231053
source: ncithesaurus:Hindgut

Axiom
annotated source: hindgut
annotated property: hasRelatedSynonym
annotated target: metenteron
has db xref: Wikipedia:Hindgut
has synonym type: OMO_0003011

primordium
type: Class
subclass of: UBERON_0005423
subclass of: Restriction
  on property: BFO_0000050
  some values from: multicellular organism
IAO_0000115: Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].
has db xref: AEO:0000171
has db xref: BTO:0001886
has db xref: EFO:0001652
has db xref: EHDAA2:0003171
has db xref: FBbt:00005495
has db xref: FMA:86589
has db xref: MAT:0000482
has db xref: NCIT:C34275
has db xref: UMLS:C0678727
has db xref: Wikipedia:Primordium
has db xref: XAO:0003043
has OBO namespace: uberon
has related synonym: bud
has related synonym: future organ
has related synonym: placode
has related synonym: primordia
has related synonym: rudiment
id: UBERON:0001048
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: primordium
annotated property: subClassOf
annotated target: UBERON_0005423
source: EHDAA2

Axiom
annotated source: primordium
annotated property: IAO_0000115
annotated target: Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].
has db xref: BTO:0001886
has db xref: FB:DJS
has db xref: FB:FBrf0089570
has db xref: http://flybase.org/reports/FBrf0178740.html

Axiom
annotated source: primordium
annotated property: hasDbXref
annotated target: FBbt:00005495
mapping justification: ManualMappingCuration

Axiom
annotated source: primordium
annotated property: hasDbXref
annotated target: UMLS:C0678727
source: ncithesaurus:Primordium

Axiom
annotated source: primordium
annotated property: hasRelatedSynonym
annotated target: placode
has db xref: FBbt:00005495

Axiom
annotated source: primordium
annotated property: hasRelatedSynonym
annotated target: primordia
has db xref: XAO:0003043
has synonym type: OMO_0003004

neural tube
type: Class
subclass of: UBERON_0003914
subclass of: UBERON_0005291
subclass of: UBERON_0010371
subclass of: UBERON_0016879
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0005068
IAO_0000115: In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].
UBPROP_0000001: Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]
UBPROP_0000001: The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]
UBPROP_0000003: (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
UBPROP_0000011: The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium
has db xref: AAO:0010617
has db xref: BTO:0001057
has db xref: CALOHA:TS-2371
has db xref: DHBA:10154
has db xref: EHDAA2:0001254
has db xref: EHDAA:2869
has db xref: EHDAA:908
has db xref: EMAPA:16164
has db xref: EMAPA:16757
has db xref: FMA:293882
has db xref: MAT:0000069
has db xref: MESH:D054259
has db xref: MIAA:0000069
has db xref: NCIT:C34226
has db xref: SCTID:362852000
has db xref: TAO:0001135
has db xref: UMLS:C0231024
has db xref: VHOG:0000307
has db xref: Wikipedia:Neural_tube
has db xref: XAO:0003204
has db xref: ZFA:0001135
has db xref: neuronames:1365
has OBO namespace: uberon
has related synonym: neural primordium
has related synonym: presumptive central nervous system
has related synonym: tubus neuralis
id: UBERON:0001049
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: neural tube
annotated property: subClassOf
annotated target: UBERON_0003914
source: EHDAA2

Axiom
annotated source: neural tube
annotated property: IAO_0000115
annotated target: In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].
has db xref: Wikipedia:Neural_tube

Axiom
annotated source: neural tube
annotated property: UBPROP_0000001
annotated target: Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010617
ontology: AAO
source: AAO:JOR

Axiom
annotated source: neural tube
annotated property: UBPROP_0000001
annotated target: The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000307
ontology: VHOG
source: http://bgee.unil.ch/
source: http://medical-dictionary.thefreedictionary.com/neural+tube

Axiom
annotated source: neural tube
annotated property: UBPROP_0000003
annotated target: (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000307
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
source: http://bgee.unil.ch/

Axiom
annotated source: neural tube
annotated property: UBPROP_0000011
annotated target: The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium
source: GO:0021915

Axiom
annotated source: neural tube
annotated property: hasDbXref
annotated target: MESH:D054259
author id: https://orcid.org/0000-0001-9439-5346
mapping justification: ManualMappingCuration
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: neural tube
annotated property: hasDbXref
annotated target: UMLS:C0231024
source: ncithesaurus:Neural_Tube

Axiom
annotated source: neural tube
annotated property: hasRelatedSynonym
annotated target: tubus neuralis
has db xref: Wikipedia:Neural_tube
has synonym type: OMO_0003011

rectum
type: Class
subclass of: UBERON_0004921
subclass of: Restriction
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0006866
subclass of: Restriction
  on property: RO_0002150
  some values from: sigmoid colon
subclass of: Restriction
  on property: RO_0002433
  some values from: large intestine
IAO_0000115: The terminal portion of the intestinal tube, terminating with the anus.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
UBPROP_0000007: rectal
UBPROP_0000008: In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html
has db xref: AAO:0010401
has db xref: BTO:0001158
has db xref: CALOHA:TS-1180
has db xref: EFO:0000848
has db xref: EHDAA2:0001592
has db xref: EHDAA:5836
has db xref: EMAPA:17896
has db xref: EV:0100081
has db xref: FMA:14544
has db xref: GAID:311
has db xref: MA:0000336
has db xref: MAT:0000050
has db xref: MESH:D012007
has db xref: MIAA:0000050
has db xref: NCIT:C12390
has db xref: SCTID:181261002
has db xref: UMLS:C0034896
has db xref: VHOG:0001751
has db xref: Wikipedia:Rectum
has db xref: XAO:0000238
has db xref: galen:Rectum
has exact synonym: terminal portion of intestine
has OBO namespace: uberon
has related synonym: intestinum rectum
has related synonym: rectal sac
has related synonym: terminal portion of large intestine
id: UBERON:0001052
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: rectum
annotated property: subClassOf
annotated target: UBERON_0004921
order: 4
source: cjm

Axiom
annotated source: rectum
annotated property: subClassOf
annotated target: Restriction
source: MA

Axiom
annotated source: rectum
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: rectum
annotated property: subClassOf
annotated target: Restriction
source: ISBN:0073040584

Axiom
annotated source: rectum
annotated property: IAO_0000115
annotated target: The terminal portion of the intestinal tube, terminating with the anus.
has db xref: ISBN:0-683-40008-8
has db xref: MP:0000492
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: rectum
annotated property: UBPROP_0000001
annotated target: The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001751
ontology: VHOG
source: http://bgee.unil.ch/

Axiom
annotated source: rectum
annotated property: hasDbXref
annotated target: UMLS:C0034896
source: ncithesaurus:Rectum

Axiom
annotated source: rectum
annotated property: hasRelatedSynonym
annotated target: intestinum rectum
has db xref: BTO:0001158

Malpighian tubule
type: Class
subclass of: UBERON_0009773
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6656
IAO_0000115: A tubule that extends from the posterior part of the digestive tract which absorbs solutes, water, and wastes from the surrounding hemolymph. Each tubule consists of a single layer of cells that is closed off at the distal end with the proximal end joining the alimentary canal at the junction between the midgut and hindgut[WP,modified].
UBPROP_0000008: It is unclear as to whether the Malpighian tubules of arachnids and those of the Uniramia are homologous or the result of convergent evolution.[Wikipedia:Malpighian_tubule_system]
has db xref: BTO:0000810
has db xref: EFO:0000243
has db xref: FBbt:00005786
has db xref: GAID:1228
has db xref: MAT:0000123
has db xref: MESH:D008317
has db xref: MIAA:0000123
has db xref: SCTID:41055008
has db xref: TADS:0000163
has db xref: TGMA:0001038
has db xref: Wikipedia:Malpighian_tubule
has OBO namespace: uberon
has related synonym: Malphigian tube
has related synonym: Malpighian tube
has related synonym: tuba Malpighii
id: UBERON:0001054
in subset: efo slim
in subset: uberon slim
comment: EDITOR_NOTE this will be ceded to the Arthropod Anatomy Ontology

Axiom
annotated source: Malpighian tubule
annotated property: subClassOf
annotated target: UBERON_0009773
source: GO

Axiom
annotated source: Malpighian tubule
annotated property: IAO_0000115
annotated target: A tubule that extends from the posterior part of the digestive tract which absorbs solutes, water, and wastes from the surrounding hemolymph. Each tubule consists of a single layer of cells that is closed off at the distal end with the proximal end joining the alimentary canal at the junction between the midgut and hindgut[WP,modified].
has db xref: Wikipedia:Malpighian_tubule_system

Axiom
annotated source: Malpighian tubule
annotated property: hasDbXref
annotated target: FBbt:00005786
mapping justification: ManualMappingCuration

Axiom
annotated source: Malpighian tubule
annotated property: hasRelatedSynonym
annotated target: Malphigian tube
has db xref: BTO:0000810
has synonym type: MISSPELLING

Axiom
annotated source: Malpighian tubule
annotated property: hasRelatedSynonym
annotated target: Malpighian tube
has db xref: UBERON:cjm

Axiom
annotated source: Malpighian tubule
annotated property: hasRelatedSynonym
annotated target: tuba Malpighii
has db xref: BTO:0000810

mushroom body
type: Class
subclass of: anatomical cluster
subclass of: Restriction
  on property: BFO_0000050
  some values from: brain
IAO_0000115: Prominent lobed neuropils found in annelids and all arthropods except crustaceans. They are thought to be involved in olfactory associative learning and memory[MESH] Mushroom body neuropils are divided into calyces, pedunculus, and its subsequent lobes. In Drosophila these are the alpha, beta, and gamma lobes.
RO_0002161: NCBITaxon 6217
RO_0002175: NCBITaxon 6340
RO_0002175: NCBITaxon 6656
UBPROP_0000008: Also in annelids. 'Comparison to the vertebrate pallium reveals that the annelid mushroom bodies develop from similar molecular coordinates within a conserved overall molecular brain topology and that their development involves conserved patterning mechanisms and produces conserved neuron types that existed already in the proto- stome-deuterostome ancestors. These data indicate deep homology of pallium and mushroom bodies and date back the origin of higher brain centers to prebilaterian times'
has db xref: BTO:0002675
has db xref: EFO:0000925
has db xref: FBbt:00005801
has db xref: GAID:1231
has db xref: MAT:0000336
has db xref: MESH:D024521
has db xref: MIAA:0000336
has db xref: Wikipedia:Mushroom_body
has exact synonym: mushroom bodies
has OBO namespace: uberon
has related synonym: corpora pedunculata
id: UBERON:0001058
in subset: efo slim
in subset: uberon slim

Axiom
annotated source: mushroom body
annotated property: subClassOf
annotated target: Restriction
notes: annelids and arthropods

Axiom
annotated source: mushroom body
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: mushroom body
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: mushroom body
annotated property: IAO_0000115
annotated target: Prominent lobed neuropils found in annelids and all arthropods except crustaceans. They are thought to be involved in olfactory associative learning and memory[MESH] Mushroom body neuropils are divided into calyces, pedunculus, and its subsequent lobes. In Drosophila these are the alpha, beta, and gamma lobes.
has db xref: MESH:A13.641
has db xref: Wikipedia:Mushroom_body
has db xref: http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html

Axiom
annotated source: mushroom body
annotated property: UBPROP_0000008
annotated target: Also in annelids. 'Comparison to the vertebrate pallium reveals that the annelid mushroom bodies develop from similar molecular coordinates within a conserved overall molecular brain topology and that their development involves conserved patterning mechanisms and produces conserved neuron types that existed already in the proto- stome-deuterostome ancestors. These data indicate deep homology of pallium and mushroom bodies and date back the origin of higher brain centers to prebilaterian times'
source: PMID:20813265

Axiom
annotated source: mushroom body
annotated property: hasDbXref
annotated target: FBbt:00005801
mapping justification: ManualMappingCuration

Axiom
annotated source: mushroom body
annotated property: hasExactSynonym
annotated target: mushroom bodies
has synonym type: OMO_0003004

Axiom
annotated source: mushroom body
annotated property: hasRelatedSynonym
annotated target: corpora pedunculata
has db xref: FBbt:00005801
has db xref: PMID:21062451

anatomical entity
type: Class
IAO_0000115: 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.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: AAO:0010841
has db xref: AEO:0000000
has db xref: BFO:0000004
has db xref: BILA:0000000
has db xref: BIRNLEX:6
has db xref: CARO:0000000
has db xref: EHDAA2:0002229
has db xref: FBbt:10000000
has db xref: FMA:62955
has db xref: HAO:0000000
has db xref: MA:0000001
has db xref: NCIT:C12219
has db xref: TAO:0100000
has db xref: TGMA:0001822
has db xref: UMLS:C1515976
has db xref: WBbt:0000100
has db xref: XAO:0000000
has db xref: ZFA:0100000
has OBO namespace: uberon
id: UBERON:0001062
in subset: common anatomy
in subset: upper level

Axiom
annotated source: anatomical entity
annotated property: IAO_0000115
annotated target: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
has db xref: FMA:62955
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: anatomical entity
annotated property: hasDbXref
annotated target: FBbt:10000000
mapping justification: ManualMappingCuration

Axiom
annotated source: anatomical entity
annotated property: hasDbXref
annotated target: UMLS:C1515976
source: ncithesaurus:Anatomic_Structure_System_or_Substance

ventral pancreatic duct
type: Class
subclass of: tube
subclass of: UBERON_0007329
subclass of: Restriction
  on property: RO_0002150
  some values from: UBERON_0001174
subclass of: Restriction
  on property: channel for
  some values from: UBERON_0001970
subclass of: Restriction
  on property: channels into
  some values from: UBERON_0004913
IAO_0000115: A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla.
RO_0002175: NCBITaxon 9606
UBPROP_0000003: These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG]
UBPROP_0000011: Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct.
has alternative id: UBERON:0005627
has broad synonym: pancreatic duct
has db xref: BTO:0002362
has db xref: EHDAA2:0001396
has db xref: EHDAA:6905
has db xref: EMAPA:17510
has db xref: FMA:16003
has db xref: GAID:337
has db xref: MA:0000126
has db xref: MESH:D010183
has db xref: NCIT:C12272
has db xref: RETIRED_EHDAA2:0002177
has db xref: SCTID:245385001
has db xref: UMLS:C0030288
has db xref: VHOG:0000256
has db xref: Wikipedia:Pancreatic_duct
has exact synonym: chief pancreatic duct
has exact synonym: duct of Wirsung
has exact synonym: main pancreatic duct
has OBO namespace: uberon
has related synonym: canal of Wirsung
has related synonym: ductus pancreatis ventralis
has related synonym: hepaticopancreatic duct
id: UBERON:0001064
in subset: human reference atlas
in subset: uberon slim
comment: EDITOR_NOTE in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue

Axiom
annotated source: ventral pancreatic duct
annotated property: subClassOf
annotated target: UBERON_0007329
source: FMA

Axiom
annotated source: ventral pancreatic duct
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: ventral pancreatic duct
annotated property: IAO_0000115
annotated target: A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla.
has db xref: Wikipedia:Pancreatic_duct

Axiom
annotated source: ventral pancreatic duct
annotated property: UBPROP_0000003
annotated target: These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000256
ontology: VHOG
source: DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005)
source: http://bgee.unil.ch/

Axiom
annotated source: ventral pancreatic duct
annotated property: UBPROP_0000011
annotated target: Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct.
source: WP

Axiom
annotated source: ventral pancreatic duct
annotated property: hasBroadSynonym
annotated target: pancreatic duct
has db xref: MESH:A03.734.667

Axiom
annotated source: ventral pancreatic duct
annotated property: hasDbXref
annotated target: UMLS:C0030288
source: ncithesaurus:Pancreatic_Duct

Axiom
annotated source: ventral pancreatic duct
annotated property: hasExactSynonym
annotated target: chief pancreatic duct
has db xref: FMA:16003

Axiom
annotated source: ventral pancreatic duct
annotated property: hasExactSynonym
annotated target: duct of Wirsung
has db xref: Wikipedia:Pancreatic_duct

Axiom
annotated source: ventral pancreatic duct
annotated property: hasExactSynonym
annotated target: main pancreatic duct
has db xref: MA:0000126

Axiom
annotated source: ventral pancreatic duct
annotated property: hasRelatedSynonym
annotated target: canal of Wirsung
has db xref: BTO:0002362

Axiom
annotated source: ventral pancreatic duct
annotated property: hasRelatedSynonym
annotated target: hepaticopancreatic duct
has db xref: BTO:0002362

skin of back
type: Class
equivalent class: Class
  intersection of: zone of skin
  intersection of: Restriction
    on property: BFO_0000050
    some values from: dorsum
subclass of: skin of trunk
subclass of: Restriction
IAO_0000115: A zone of skin that is part of a back [Automatically generated definition].
has db xref: EMAPA:36392
has db xref: FMA:10462
has db xref: FMA:22985
has db xref: MA:0000498
has db xref: SCTID:181492002
has exact synonym: back skin
has exact synonym: back zone of skin
has exact synonym: skin, dorsal region
has exact synonym: zone of skin of back
has OBO namespace: uberon
id: UBERON:0001068
in subset: pheno slim
comment: EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region

Axiom
annotated source: skin of back
annotated property: subClassOf
annotated target: skin of trunk
source: MA

Axiom
annotated source: skin of back
annotated property: subClassOf
annotated target: Restriction
source: MA

Axiom
annotated source: skin of back
annotated property: IAO_0000115
annotated target: A zone of skin that is part of a back [Automatically generated definition].
has db xref: OBOL:automatic

Axiom
annotated source: skin of back
annotated property: hasExactSynonym
annotated target: back zone of skin
has db xref: OBOL:automatic

Axiom
annotated source: skin of back
annotated property: hasExactSynonym
annotated target: skin, dorsal region
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: skin of back
annotated property: hasExactSynonym
annotated target: zone of skin of back
has db xref: OBOL:automatic

external carotid artery
type: Class
subclass of: UBERON_0005396
subclass of: Restriction
IAO_0000115: A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP].
RO_0002175: NCBITaxon 9606
UBPROP_0000008: not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO
has db xref: AAO:0010218
has db xref: AAO:0010416
has db xref: BTO:0004696
has db xref: EFO:0001953
has db xref: EHDAA2:0000461
has db xref: EMAPA:18611
has db xref: FMA:10635
has db xref: GAID:480
has db xref: MA:0001929
has db xref: MESH:D002342
has db xref: NCIT:C32551
has db xref: SCTID:362044002
has db xref: UMLS:C0007275
has db xref: VHOG:0000265
has db xref: Wikipedia:External_carotid_artery
has db xref: XAO:0000345
has exact synonym: external carotid
has OBO namespace: uberon
has related synonym: arteria carotis externa
id: UBERON:0001070
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: external carotid artery
annotated property: subClassOf
annotated target: UBERON_0005396
source: MA

Axiom
annotated source: external carotid artery
annotated property: subClassOf
annotated target: Restriction
source: FMA

Axiom
annotated source: external carotid artery
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: external carotid artery
annotated property: subClassOf
annotated target: Restriction
source: FMA

Axiom
annotated source: external carotid artery
annotated property: IAO_0000115
annotated target: A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP].
has db xref: MGI:anna

Axiom
annotated source: external carotid artery
annotated property: hasDbXref
annotated target: UMLS:C0007275
source: ncithesaurus:External_Carotid_Artery

Axiom
annotated source: external carotid artery
annotated property: hasExactSynonym
annotated target: external carotid
has db xref: AAO:0010218

Axiom
annotated source: external carotid artery
annotated property: hasRelatedSynonym
annotated target: arteria carotis externa
has db xref: Wikipedia:External_carotid_artery
has synonym type: OMO_0003011

superficial cervical artery
type: Class
equivalent class: Class
  intersection of: UBERON_0012320
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0035549
subclass of: UBERON_0012320
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0035549
subclass of: Restriction
  on property: RO_0002170
  some values from: UBERON_0012324
IAO_0000115: It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery.
RO_0002175: NCBITaxon 9606
has db xref: EMAPA:37117
has db xref: FMA:10665
has db xref: MA:0002052
has db xref: NCIT:C53005
has db xref: SCTID:161746006
has db xref: UMLS:C0226271
has db xref: Wikipedia:Superficial_part_of_transverse_cervical_artery
has exact synonym: superficial branch of transverse cervical artery
has OBO namespace: uberon
id: UBERON:0001071
in subset: human reference atlas
in subset: uberon slim
comment: The transverse cervical artery splits into two branches, a superficial one and a deep one[WP]

Axiom
annotated source: superficial cervical artery
annotated property: IAO_0000115
annotated target: It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery.
has db xref: Wikipedia:Superficial_part_of_transverse_cervical_artery

Axiom
annotated source: superficial cervical artery
annotated property: hasDbXref
annotated target: EMAPA:37117
source: MA:th

Axiom
annotated source: superficial cervical artery
annotated property: hasDbXref
annotated target: UMLS:C0226271
source: ncithesaurus:Superficial_Cervical_Artery

Axiom
annotated source: superficial cervical artery
annotated property: hasExactSynonym
annotated target: superficial branch of transverse cervical artery
has db xref: Wikipedia:Superficial_part_of_transverse_cervical_artery

inferior vena cava
type: Class
equivalent class: Class
  intersection of: UBERON_0004087
  intersection of: Restriction
    on property: RO_0020102
    some values from: posterior region of body
subclass of: UBERON_0004087
subclass of: Restriction
  on property: RO_0002170
  some values from: UBERON_0002078
subclass of: Restriction
  on property: RO_0020102
  some values from: posterior region of body
disjoint with: UBERON_0001585
IAO_0000115: A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA].
UBPROP_0000003: Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG]
has db xref: AAO:0011083
has db xref: BTO:0002682
has db xref: EHDAA2:0000611
has db xref: EMAPA:18416
has db xref: FMA:10951
has db xref: GAID:548
has db xref: MA:0000480
has db xref: MESH:D014682
has db xref: NCIT:C12815
has db xref: SCTID:181369003
has db xref: UMLS:C0042458
has db xref: VHOG:0001194
has db xref: Wikipedia:Inferior_vena_cava
has db xref: XAO:0000388
has db xref: galen:InferiorVenaCava
has exact synonym: inferior caval vein
has exact synonym: posterior vena cava
has OBO namespace: uberon
has related synonym: caudal vena cava
has related synonym: postcava
has related synonym: vena cava inferior
id: UBERON:0001072
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: inferior vena cava
annotated property: disjointWith
annotated target: UBERON_0001585
source: lexical

Axiom
annotated source: inferior vena cava
annotated property: IAO_0000115
annotated target: A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart.
has db xref: Wikipedia:Inferior_vena_cava
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: inferior vena cava
annotated property: UBPROP_0000001
annotated target: Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA].
source: FMA:10951

Axiom
annotated source: inferior vena cava
annotated property: UBPROP_0000003
annotated target: Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001194
ontology: VHOG
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455
source: http://bgee.unil.ch/

Axiom
annotated source: inferior vena cava
annotated property: hasDbXref
annotated target: UMLS:C0042458
source: ncithesaurus:Inferior_Vena_Cava

Axiom
annotated source: inferior vena cava
annotated property: hasExactSynonym
annotated target: inferior caval vein
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: inferior vena cava
annotated property: hasExactSynonym
annotated target: posterior vena cava
has db xref: PMID:21154280

Axiom
annotated source: inferior vena cava
annotated property: hasRelatedSynonym
annotated target: caudal vena cava
has db xref: VHOG:0001194

Axiom
annotated source: inferior vena cava
annotated property: hasRelatedSynonym
annotated target: vena cava inferior
has db xref: BTO:0002682
has db xref: Wikipedia:Inferior_vena_cava
has synonym type: OMO_0003011

ileocecal junction
type: Class
equivalent class: Class
  intersection of: UBERON_0007651
  intersection of: Restriction
    on property: RO_0002176
    some values from: large intestine
  intersection of: Restriction
    on property: RO_0002176
    some values from: UBERON_0002108
subclass of: UBERON_8410024
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7742
subclass of: Restriction
  on property: RO_0002176
  some values from: large intestine
subclass of: Restriction
  on property: RO_0002176
  some values from: UBERON_0002108
IAO_0000115: A point along the course of the gastrointestinal tract where the small intestine (ileum) ends as it opens into the cecal portion of the large intestine; occurs usually within the iliac fossa, demarcated internally as the ileocecal orifice.
has db xref: EMAPA:37601
has db xref: FMA:11338
has db xref: MA:0000332
has db xref: SCTID:264021000
has exact synonym: ileocaecal junction
has OBO namespace: uberon
id: UBERON:0001073

Axiom
annotated source: ileocecal junction
annotated property: IAO_0000115
annotated target: A point along the course of the gastrointestinal tract where the small intestine (ileum) ends as it opens into the cecal portion of the large intestine; occurs usually within the iliac fossa, demarcated internally as the ileocecal orifice.
has db xref: http://www.medilexicon.com/medicaldictionary.php

Axiom
annotated source: ileocecal junction
annotated property: hasDbXref
annotated target: EMAPA:37601
source: MA:th

pericardial cavity
type: Class
equivalent class: Class
  intersection of: UBERON_0002553
  intersection of: Restriction
    on property: RO_0002572
    some values from: UBERON_0002406
subclass of: UBERON_0002323
subclass of: UBERON_0035809
subclass of: Restriction
subclass of: Restriction
  on property: RO_0001015
  some values from: UBERON_0002409
subclass of: Restriction
  on property: RO_0002219
  some values from: UBERON_0002357
subclass of: Restriction
  on property: RO_0002572
  some values from: UBERON_0002406
IAO_0000115: A potential space between the visceral and parietal layers of the pericardium.
UBPROP_0000001: Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO]
UBPROP_0000003: In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
UBPROP_0000012: check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal)
has db xref: BSA:0000091
has db xref: EHDAA2:0001434
has db xref: EMAPA:16131
has db xref: EMAPA:16132
has db xref: FMA:11350
has db xref: MA:0000053
has db xref: NCIT:C38662
has db xref: SCTID:362027001
has db xref: TAO:0002220
has db xref: UMLS:C0225972
has db xref: VHOG:0000556
has db xref: Wikipedia:Pericardial_cavity
has db xref: ZFA:0001655
has db xref: galen:PericardialSpace
has exact synonym: cavity of pericardial sac
has exact synonym: pericardial space
has OBO namespace: uberon
has related synonym: cavitas pericardiaca
id: UBERON:0001074
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: pericardial cavity
annotated property: subClassOf
annotated target: UBERON_0002323
source: MA

Axiom
annotated source: pericardial cavity
annotated property: subClassOf
annotated target: Restriction
source: FMA

Axiom
annotated source: pericardial cavity
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: pericardial cavity
annotated property: IAO_0000115
annotated target: A potential space between the visceral and parietal layers of the pericardium.
has db xref: Wikipedia:Pericardium

Axiom
annotated source: pericardial cavity
annotated property: UBPROP_0000001
annotated target: Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO]
date retrieved: 2012-08-14
external class: TAO:0002220
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: pericardial cavity
annotated property: UBPROP_0000003
annotated target: In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000556
ontology: VHOG
source: ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206
source: http://bgee.unil.ch/

Axiom
annotated source: pericardial cavity
annotated property: UBPROP_0000012
annotated target: check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal)
external ontology: ZFA

Axiom
annotated source: pericardial cavity
annotated property: hasDbXref
annotated target: UMLS:C0225972
source: ncithesaurus:Pericardial_Cavity

Axiom
annotated source: pericardial cavity
annotated property: hasExactSynonym
annotated target: pericardial space
has db xref: Wikipedia:Pericardial_cavity

Axiom
annotated source: pericardial cavity
annotated property: hasRelatedSynonym
annotated target: cavitas pericardiaca
has db xref: Wikipedia:Pericardial_cavity
has synonym type: OMO_0003011

neural spine
type: Class
subclass of: UBERON_0006061
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0003861
IAO_0000115: An extension of a neural arches dorsal to the neural canal[TAO,modified].
UBPROP_0000001: Elaboration of the mid-dorsal keel into a posterior or posterolateral process.[AAO]
UBPROP_0000001: Neural spines are extensions of neural arches dorsal to the neural canal in the median skeletogenous septum. Neural spines are typically unpaired median structures but can be paired in some instances, e.g., in the abdominal region of basal teleosts such as Leptolepis, Elops, Megalops, and Hiodon).[TAO]
UBPROP_0000001: Small, posteriorly directed process at the posterior margin of each neural arch lamina; it is not a neural spine.[AAO]
UBPROP_0000002: relationship loss: part_of mid-dorsal keel (AAO:0000735)[AAO]
UBPROP_0000008: The spinous process of a vertebra is directed backward and downward from the junction of the laminae (in humans), and serves for the attachment of muscles and ligaments. In animals without an erect stance, the process points upward and may slant forward or backward. Spinous processes are exaggerated in some animals, such as the extinct Dimetrodon and Spinosaurus, where they form a sail- or finback. [Wikipedia:Spinous_process]
has broad synonym: spinous process
has db xref: AAO:0000705
has db xref: EMAPA:25107
has db xref: FMA:11948
has db xref: MA:0001455
has db xref: NCIT:C116112
has db xref: SCTID:264259004
has db xref: TAO:0001336
has db xref: Wikipedia:Spinous_process
has db xref: ZFA:0001336
has exact synonym: processus spinosus
has exact synonym: processus spinosus vertebrae
has exact synonym: spinous process of vertebra
has exact synonym: vertebra spinous process
has OBO namespace: uberon
has related synonym: neural spine
has related synonym: neural spines
has related synonym: spine of verterba
id: UBERON:0001076
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: neural spine
annotated property: IAO_0000115
annotated target: An extension of a neural arches dorsal to the neural canal[TAO,modified].
has db xref: TAO:0001336
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: neural spine
annotated property: UBPROP_0000001
annotated target: Elaboration of the mid-dorsal keel into a posterior or posterolateral process.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000705
ontology: AAO
source: AAO:Pugener_and_Maglia_2008

Axiom
annotated source: neural spine
annotated property: UBPROP_0000001
annotated target: Neural spines are extensions of neural arches dorsal to the neural canal in the median skeletogenous septum. Neural spines are typically unpaired median structures but can be paired in some instances, e.g., in the abdominal region of basal teleosts such as Leptolepis, Elops, Megalops, and Hiodon).[TAO]
date retrieved: 2012-08-14
external class: TAO:0001336
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: neural spine
annotated property: UBPROP_0000001
annotated target: Small, posteriorly directed process at the posterior margin of each neural arch lamina; it is not a neural spine.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000739
ontology: AAO
source: AAO:Pugener_2002

Axiom
annotated source: neural spine
annotated property: UBPROP_0000002
annotated target: relationship loss: part_of mid-dorsal keel (AAO:0000735)[AAO]
date retrieved: 2012-06-20
external class: AAO:0000705
ontology: AAO

Axiom
annotated source: neural spine
annotated property: hasExactSynonym
annotated target: spinous process of vertebra
has db xref: FMA:11948
has synonym type: HUMAN PREFERRED

Axiom
annotated source: neural spine
annotated property: hasExactSynonym
annotated target: vertebra spinous process
has db xref: MA:0001455

Axiom
annotated source: neural spine
annotated property: hasRelatedSynonym
annotated target: neural spines
has db xref: ZFA:0001336
has synonym type: OMO_0003004

Axiom
annotated source: neural spine
annotated property: hasRelatedSynonym
annotated target: spine of verterba
has db xref: FMA:11948

transverse process of vertebra
type: Class
subclass of: UBERON_0006061
IAO_0000115: The transverse or costal processes of a vertebra, two in number, project one at either side from the point where the lamina joins the pedicle, between the superior and inferior articular processes. They serve for the attachment of muscles and ligaments. [WP,unvetted].
UBPROP_0000001: Projections on each side of the vertebra from the point where the neural arch lamina joins the pedicel for the articulation with the head of a single-headed rib or the upper head of a double-headed rib. Also called diapophyses. They provide surfaces for the attachment of muscles. In anurans, the term transverse process is used in reference to the processes associated with the presacral and postsacral vertebrae.
has db xref: AAO:0000698
has db xref: FMA:11949
has db xref: MA:0001456
has db xref: SCTID:264238006
has db xref: Wikipedia:Transverse_process
has db xref: XAO:0003102
has exact synonym: processus transversus
has exact synonym: processus transversus vertebrae
has exact synonym: transverse process
has exact synonym: vertebra transverse process
has OBO namespace: uberon
has related synonym: diapophyses
has related synonym: diapophysis
id: UBERON:0001077
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: transverse process of vertebra
annotated property: IAO_0000115
annotated target: The transverse or costal processes of a vertebra, two in number, project one at either side from the point where the lamina joins the pedicle, between the superior and inferior articular processes. They serve for the attachment of muscles and ligaments. [WP,unvetted].
has db xref: Wikipedia:Transverse_process

Axiom
annotated source: transverse process of vertebra
annotated property: UBPROP_0000001
annotated target: Projections on each side of the vertebra from the point where the neural arch lamina joins the pedicel for the articulation with the head of a single-headed rib or the upper head of a double-headed rib. Also called diapophyses. They provide surfaces for the attachment of muscles. In anurans, the term transverse process is used in reference to the processes associated with the presacral and postsacral vertebrae.
source: AAO:0000698

endocardium of ventricle
type: Class
equivalent class: Class
  intersection of: UBERON_0002165
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002082
subclass of: UBERON_0002165
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0002082
IAO_0000115: Endocardium that is part of the cardiac ventricle.
has db xref: EMAPA:32747
has db xref: FMA:12148
has db xref: MA:0000079
has db xref: SCTID:192172004
has db xref: TAO:0002247
has db xref: VHOG:0000607
has db xref: ZFA:0001615
has exact synonym: cardiac ventricle endocardium
has exact synonym: endocardium of cardiac ventricle
has exact synonym: endocardium of heart ventricle
has exact synonym: endocardium of lower chamber of heart
has exact synonym: endocardium of ventricle of heart
has exact synonym: heart ventricle endocardium
has exact synonym: lower chamber of heart endocardium
has exact synonym: ventricle endocardium
has exact synonym: ventricle of heart endocardium
has exact synonym: ventricular endocardium
has OBO namespace: uberon
has related synonym: ventricle endocardial tissue
id: UBERON:0001081
in subset: pheno slim
in subset: vertebrate core

Axiom
annotated source: endocardium of ventricle
annotated property: IAO_0000115
annotated target: Endocardium that is part of the cardiac ventricle.
has db xref: ZFIN:curator

Axiom
annotated source: endocardium of ventricle
annotated property: hasExactSynonym
annotated target: cardiac ventricle endocardium
has db xref: OBOL:automatic

Axiom
annotated source: endocardium of ventricle
annotated property: hasExactSynonym
annotated target: endocardium of cardiac ventricle
has db xref: OBOL:automatic

Axiom
annotated source: endocardium of ventricle
annotated property: hasExactSynonym
annotated target: endocardium of heart ventricle
has db xref: OBOL:automatic

Axiom
annotated source: endocardium of ventricle
annotated property: hasExactSynonym
annotated target: endocardium of lower chamber of heart
has db xref: OBOL:automatic

Axiom
annotated source: endocardium of ventricle
annotated property: hasExactSynonym
annotated target: endocardium of ventricle of heart
has db xref: OBOL:automatic

Axiom
annotated source: endocardium of ventricle
annotated property: hasExactSynonym
annotated target: heart ventricle endocardium
has db xref: OBOL:automatic

Axiom
annotated source: endocardium of ventricle
annotated property: hasExactSynonym
annotated target: lower chamber of heart endocardium
has db xref: OBOL:automatic

Axiom
annotated source: endocardium of ventricle
annotated property: hasExactSynonym
annotated target: ventricle of heart endocardium
has db xref: OBOL:automatic

Axiom
annotated source: endocardium of ventricle
annotated property: hasRelatedSynonym
annotated target: ventricle endocardial tissue
has db xref: VHOG:0000607

epicardium of ventricle
type: Class
equivalent class: Class
  intersection of: UBERON_0002348
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002082
subclass of: UBERON_0002348
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002082
IAO_0000115: An epicardial layer that lines a cardiac ventricle.
UBPROP_0000001: The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO]
has db xref: FMA:12150
has db xref: TAO:0005058
has db xref: ZFA:0005058
has exact synonym: cardiac ventricle epicardium
has exact synonym: ventricular epicardium
has OBO namespace: uberon
id: UBERON:0001082
in subset: vertebrate core

Axiom
annotated source: epicardium of ventricle
annotated property: IAO_0000115
annotated target: An epicardial layer that lines a cardiac ventricle.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: epicardium of ventricle
annotated property: UBPROP_0000001
annotated target: The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO]
date retrieved: 2012-08-14
external class: TAO:0005058
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: epicardium of ventricle
annotated property: hasExactSynonym
annotated target: cardiac ventricle epicardium
has db xref: OBOL:automatic

myocardium of ventricle
type: Class
equivalent class: Class
  intersection of: UBERON_0002349
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002082
subclass of: UBERON_0002349
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0002082
IAO_0000115: Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer.
UBPROP_0000001: Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO]
UBPROP_0000003: As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]
has db xref: EFO:0003088
has db xref: EMAPA:32748
has db xref: FMA:12151
has db xref: MA:0000082
has db xref: SCTID:192084000
has db xref: TAO:0005061
has db xref: VHOG:0000604
has db xref: ZFA:0005061
has exact synonym: ventricle myocardium
has exact synonym: ventricular myocardium
has OBO namespace: uberon
has related synonym: ventricle cardiac muscle
id: UBERON:0001083
in subset: efo slim
in subset: pheno slim
in subset: vertebrate core

Axiom
annotated source: myocardium of ventricle
annotated property: IAO_0000115
annotated target: Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer.
has db xref: ZFIN:curator

Axiom
annotated source: myocardium of ventricle
annotated property: UBPROP_0000001
annotated target: Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO]
date retrieved: 2012-08-14
external class: TAO:0005061
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: myocardium of ventricle
annotated property: UBPROP_0000003
annotated target: As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000604
ontology: VHOG
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481
source: http://bgee.unil.ch/

Axiom
annotated source: myocardium of ventricle
annotated property: hasRelatedSynonym
annotated target: ventricle cardiac muscle
has db xref: VHOG:0000604

skin of head
type: Class
equivalent class: Class
  intersection of: zone of skin
  intersection of: Restriction
    on property: BFO_0000050
    some values from: head
subclass of: UBERON_0012180
subclass of: Restriction
  on property: BFO_0000050
  some values from: head
IAO_0000115: A zone of skin that is part of a head [Automatically generated definition].
has db xref: FMA:12166
has db xref: FMA:24756
has db xref: MA:0000582
has db xref: NCIT:C52757
has db xref: SCTID:181484006
has db xref: UMLS:C0205029
has exact synonym: adult head zone of skin
has exact synonym: head skin
has exact synonym: head zone of skin
has exact synonym: zone of skin of adult head
has exact synonym: zone of skin of head
has OBO namespace: uberon
id: UBERON:0001084
comment: EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region

Axiom
annotated source: skin of head
annotated property: IAO_0000115
annotated target: A zone of skin that is part of a head [Automatically generated definition].
has db xref: OBOL:automatic

Axiom
annotated source: skin of head
annotated property: hasDbXref
annotated target: UMLS:C0205029
source: ncithesaurus:Head_Skin

Axiom
annotated source: skin of head
annotated property: hasExactSynonym
annotated target: adult head zone of skin
has db xref: OBOL:automatic

Axiom
annotated source: skin of head
annotated property: hasExactSynonym
annotated target: head zone of skin
has db xref: OBOL:automatic

Axiom
annotated source: skin of head
annotated property: hasExactSynonym
annotated target: zone of skin of adult head
has db xref: OBOL:automatic

Axiom
annotated source: skin of head
annotated property: hasExactSynonym
annotated target: zone of skin of head
has db xref: OBOL:automatic

skin of trunk
type: Class
equivalent class: Class
  intersection of: zone of skin
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002100
subclass of: zone of skin
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002100
IAO_0000115: A zone of skin that is part of a trunk [Automatically generated definition].
has db xref: EMAPA:37278
has db xref: FMA:12167
has db xref: FMA:23093
has db xref: MA:0000517
has db xref: NCIT:C12295
has db xref: SCTID:181489001
has db xref: UMLS:C0205031
has exact synonym: torso zone of skin
has exact synonym: trunk skin
has exact synonym: trunk zone of skin
has exact synonym: zone of skin of torso
has exact synonym: zone of skin of trunk
has OBO namespace: uberon
id: UBERON:0001085
comment: EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region

Axiom
annotated source: skin of trunk
annotated property: IAO_0000115
annotated target: A zone of skin that is part of a trunk [Automatically generated definition].
has db xref: OBOL:automatic

Axiom
annotated source: skin of trunk
annotated property: hasDbXref
annotated target: EMAPA:37278
source: MA:th

Axiom
annotated source: skin of trunk
annotated property: hasDbXref
annotated target: UMLS:C0205031
source: ncithesaurus:Skin_of_the_Trunk

Axiom
annotated source: skin of trunk
annotated property: hasExactSynonym
annotated target: torso zone of skin
has db xref: OBOL:automatic

Axiom
annotated source: skin of trunk
annotated property: hasExactSynonym
annotated target: trunk zone of skin
has db xref: OBOL:automatic

Axiom
annotated source: skin of trunk
annotated property: hasExactSynonym
annotated target: zone of skin of torso
has db xref: OBOL:automatic

Axiom
annotated source: skin of trunk
annotated property: hasExactSynonym
annotated target: zone of skin of trunk
has db xref: OBOL:automatic

pleural fluid
type: Class
equivalent class: Class
  intersection of: UBERON_0007779
  intersection of: Restriction
    on property: RO_0001025
    some values from: UBERON_0002402
subclass of: UBERON_0036244
subclass of: Restriction
  on property: RO_0001025
  some values from: UBERON_0002402
IAO_0000115: Transudate contained in the pleural cavity.
has db xref: BTO:0003080
has db xref: FMA:12273
has db xref: MA:0002532
has db xref: MAT:0000500
has db xref: Wikipedia:Pleural_fluid
has db xref: ncithesaurus:Pleural_Fluid
has OBO namespace: uberon
id: UBERON:0001087
in subset: uberon slim

Axiom
annotated source: pleural fluid
annotated property: IAO_0000115
annotated target: Transudate contained in the pleural cavity.
has db xref: FMA:12273

urine
type: Class
equivalent class: Class
  intersection of: excreta
  intersection of: Restriction
    on property: RO_0003001
    some values from: UBERON_0002113
subclass of: excreta
subclass of: Restriction
  on property: RO_0003001
  some values from: UBERON_0002113
IAO_0000115: Excretion that is the output of a kidney.
UBPROP_0000008: kidney excreta from some taxa (e.g. in aves) may not be liquid
has db xref: BTO:0001419
has db xref: CALOHA:TS-1092
has db xref: EFO:0001939
has db xref: EMAPA:36554
has db xref: ENVO:00002047
has db xref: FMA:12274
has db xref: GAID:1189
has db xref: MA:0002545
has db xref: MAT:0000058
has db xref: MESH:D014556
has db xref: MIAA:0000058
has db xref: NCIT:C13283
has db xref: UMLS:C0042036
has db xref: Wikipedia:Urine
has db xref: galen:Urine
has OBO namespace: uberon
id: UBERON:0001088
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: urine
annotated property: IAO_0000115
annotated target: Excretion that is the output of a kidney.
has db xref: Wikipedia:Urine
has db xref: https://github.com/geneontology/go-ontology/issues/11025

Axiom
annotated source: urine
annotated property: hasDbXref
annotated target: UMLS:C0042036
source: ncithesaurus:Urine

sweat
type: Class
equivalent class: Class
  intersection of: secretion of exocrine gland
  intersection of: Restriction
    on property: RO_0003001
    some values from: UBERON_0001820
subclass of: secretion of exocrine gland
subclass of: UBERON_0006314
subclass of: Restriction
  on property: RO_0003001
  some values from: UBERON_0001820
IAO_0000115: Secretion produced by a sweat gland.
has db xref: BTO:0001254
has db xref: ENVO:02000025
has db xref: FMA:12275
has db xref: GAID:1172
has db xref: MA:0002539
has db xref: MESH:D013542
has db xref: NCIT:C13280
has db xref: UMLS:C0038984
has db xref: Wikipedia:Sweat
has OBO namespace: uberon
has related synonym: skin exudate
id: UBERON:0001089
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: sweat
annotated property: IAO_0000115
annotated target: Secretion produced by a sweat gland.
has db xref: FMA:12275

Axiom
annotated source: sweat
annotated property: hasDbXref
annotated target: UMLS:C0038984
source: ncithesaurus:Sweat

Axiom
annotated source: sweat
annotated property: hasRelatedSynonym
annotated target: skin exudate
has db xref: BTO:0001254

synovial fluid
type: Class
equivalent class: Class
  intersection of: UBERON_0007779
  intersection of: Restriction
    on property: RO_0003001
    some values from: CL_0000214
subclass of: UBERON_0007779
subclass of: UBERON_0007794
subclass of: Restriction
  on property: BFO_0000051
  some values from: CHEBI_16336
subclass of: Restriction
  on property: RO_0001025
  some values from: UBERON_0007617
subclass of: Restriction
  on property: RO_0003001
  some values from: CL_0000214
IAO_0000115: Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
UBPROP_0000001: Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]
UBPROP_0000009: It provides nutrients and lubrication for articular cartilage
UBPROP_0000010: The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma
has db xref: BTO:0001339
has db xref: CALOHA:TS-0996
has db xref: ENVO:02000039
has db xref: FMA:12277
has db xref: GAID:265
has db xref: MA:0002544
has db xref: MESH:D013582
has db xref: NCIT:C33718
has db xref: TAO:0005154
has db xref: UMLS:C0039097
has db xref: Wikipedia:Synovial_fluid
has db xref: ZFA:0005154
has db xref: galen:SynovialFluid
has exact synonym: joint fluid
has OBO namespace: uberon
id: UBERON:0001090
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: synovial fluid
annotated property: subClassOf
annotated target: UBERON_0007794
source: FMA

Axiom
annotated source: synovial fluid
annotated property: IAO_0000115
annotated target: Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK274/

Axiom
annotated source: synovial fluid
annotated property: UBPROP_0000001
annotated target: Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]
date retrieved: 2012-08-14
external class: TAO:0005154
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: synovial fluid
annotated property: hasDbXref
annotated target: UMLS:C0039097
source: ncithesaurus:Synovial_Fluid

Axiom
annotated source: synovial fluid
annotated property: hasExactSynonym
annotated target: joint fluid
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK274/

calcareous tooth
type: Class
subclass of: UBERON_0003913
subclass of: UBERON_0010314
subclass of: Restriction
  on property: BFO_0000051
  some values from: UBERON_0001751
IAO_0000115: Skeletal element within the mouth (or in some species, upper part of the digestive tract) that is composed of dentine and is used in procuring or masticating food.
RO_0002161: NCBITaxon_189497
RO_0002161: NCBITaxon 8782
RO_0002161: NCBITaxon 9257
RO_0002161: NCBITaxon 9761
UBPROP_0000003: The ancestor of recent vertebrate teeth was a tooth-like structure on the outer body surface of jawless fishes.[well established][VHOG]
UBPROP_0000007: dental
UBPROP_0000008: absent in living platypus, present in toothed Miocene platypus Obduron dicksoni
has db xref: AEO:0000220
has db xref: BTO:0000397
has db xref: CALOHA:TS-1055
has db xref: EFO:0000839
has db xref: EHDAA2:0004605
has db xref: EMAPA:32906
has db xref: EV:0100063
has db xref: FMA:12516
has db xref: GAID:1260
has db xref: MA:0000348
has db xref: MAT:0000041
has db xref: MESH:D014070
has db xref: MIAA:0000041
has db xref: NCIT:C12506
has db xref: SCTID:302214001
has db xref: TAO:0001625
has db xref: UMLS:C0040426
has db xref: VHOG:0001733
has db xref: Wikipedia:Tooth
has db xref: XAO:0000431
has exact synonym: dental element
has exact synonym: dentine containing tooth
has exact synonym: tooth
has exact synonym: vertebrate tooth
has OBO namespace: uberon
id: UBERON:0001091
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core
comment: EDITOR_NOTE we place ZFA ctb 5 tooth here for now. Consider changing name from calcaeeous tooth. Note that sea cucumbers develop calcareous tooth-like structures

Axiom
annotated source: calcareous tooth
annotated property: subClassOf
annotated target: Restriction
source: XAO-modified

Axiom
annotated source: calcareous tooth
annotated property: subClassOf
annotated target: Restriction
source: ZFA-modified

Axiom
annotated source: calcareous tooth
annotated property: subClassOf
annotated target: Restriction
source: cjm

Axiom
annotated source: calcareous tooth
annotated property: IAO_0000115
annotated target: Skeletal element within the mouth (or in some species, upper part of the digestive tract) that is composed of dentine and is used in procuring or masticating food.
has db xref: Wikipedia:Tooth_(animal)
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: calcareous tooth
annotated property: RO_0002161
annotated target: NCBITaxon_189497
source: Wikipedia

Axiom
annotated source: calcareous tooth
annotated property: RO_0002161
annotated target: NCBITaxon 9257
source: PMID:10210685

Axiom
annotated source: calcareous tooth
annotated property: UBPROP_0000003
annotated target: The ancestor of recent vertebrate teeth was a tooth-like structure on the outer body surface of jawless fishes.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001733
ontology: VHOG
source: PMID:19266065 Koussoulakou DS, Margaritis LH, Koussoulakos SL, A curriculum vitae of teeth: evolution, generation, regeneration. International Journal of Biological Sciences (2009)
source: http://bgee.unil.ch/

Axiom
annotated source: calcareous tooth
annotated property: UBPROP_0000008
annotated target: absent in living platypus, present in toothed Miocene platypus Obduron dicksoni
source: PMID:10210685

Axiom
annotated source: calcareous tooth
annotated property: hasDbXref
annotated target: UMLS:C0040426
source: ncithesaurus:Tooth

Axiom
annotated source: calcareous tooth
annotated property: hasExactSynonym
annotated target: dental element
has db xref: http://orcid.org/0000-0002-6601-2165

vertebral bone 1
type: Class
subclass of: UBERON_0002412
subclass of: Restriction
  on property: BSPO_0000096
  some values from: vertebral bone 2
IAO_0000115: The first vertebral bone in the vertebral column.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: First postcranial vertebra, which is modified anteriorly to articulate with the skull.[AAO]
UBPROP_0000001: Vertebra that is posteriorly adjacent to the neurocranium.[TAO]
UBPROP_0000107: 1
has broad synonym: C1
has db xref: AAO:0000709
has db xref: EHDAA:10606
has db xref: EMAPA:19431
has db xref: FMA:12519
has db xref: GAID:236
has db xref: MA:0001421
has db xref: MESH:D001270
has db xref: NCIT:C32239
has db xref: SCTID:181818007
has db xref: TAO:0001167
has db xref: UMLS:C0004170
has db xref: Wikipedia:Atlas_(anatomy)
has db xref: ZFA:0001167
has exact synonym: C1 vertebra
has exact synonym: atlas
has exact synonym: atlas (CI)
has exact synonym: atlas [C I]
has exact synonym: atlas vertebra
has exact synonym: cervical atlas
has exact synonym: cervical vertebra 1
has exact synonym: first cervical vertebra
has exact synonym: vertebra 1
has OBO namespace: uberon
id: UBERON:0001092
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: vertebral bone 1
annotated property: IAO_0000115
annotated target: The first vertebral bone in the vertebral column.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: vertebral bone 1
annotated property: UBPROP_0000001
annotated target: First postcranial vertebra, which is modified anteriorly to articulate with the skull.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000709
ontology: AAO
source: AAO:Duellman_and_Trueb_1994

Axiom
annotated source: vertebral bone 1
annotated property: UBPROP_0000001
annotated target: Vertebra that is posteriorly adjacent to the neurocranium.[TAO]
date retrieved: 2012-08-14
external class: TAO:0001167
ontology: TAO
source: TAO:wd

Axiom
annotated source: vertebral bone 1
annotated property: hasDbXref
annotated target: UMLS:C0004170
source: ncithesaurus:C1_Vertebra

Axiom
annotated source: vertebral bone 1
annotated property: hasExactSynonym
annotated target: atlas [C I]
has db xref: FMA:12519
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: vertebral bone 1
annotated property: hasExactSynonym
annotated target: cervical atlas
has db xref: MP:0011576

Axiom
annotated source: vertebral bone 1
annotated property: hasExactSynonym
annotated target: cervical vertebra 1
has db xref: MA:0001421
has synonym type: HUMAN PREFERRED

Axiom
annotated source: vertebral bone 1
annotated property: hasExactSynonym
annotated target: vertebra 1
has db xref: TAO:0001167

vertebral bone 2
type: Class
subclass of: UBERON_0002412
subclass of: Restriction
IAO_0000115: The second vertebral bone in the vertebral column.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Vertebra that is posteriorly adjacent to vertebra 1.[TAO]
UBPROP_0000013: not the same as ZFA term 'axis'
UBPROP_0000107: 2
has db xref: EHDAA:10608
has db xref: EMAPA:19432
has db xref: FMA:12520
has db xref: GAID:237
has db xref: MA:0001422
has db xref: MESH:D001368
has db xref: NCIT:C32240
has db xref: SCTID:181819004
has db xref: TAO:0001168
has db xref: UMLS:C0004457
has db xref: Wikipedia:Axis_(anatomy)
has db xref: ZFA:0001168
has exact synonym: axis (CII)
has exact synonym: axis [C II]
has exact synonym: axis vertebra
has exact synonym: cervical axis
has exact synonym: vertebra 2
has narrow synonym: C2 vertebra
has narrow synonym: cervical vertebra 2
has narrow synonym: second cervical vertebra
has OBO namespace: uberon
has related synonym: C2
has related synonym: axis
id: UBERON:0001093
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: vertebral bone 2
annotated property: subClassOf
annotated target: Restriction
source: FMA

Axiom
annotated source: vertebral bone 2
annotated property: IAO_0000115
annotated target: The second vertebral bone in the vertebral column.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: vertebral bone 2
annotated property: UBPROP_0000001
annotated target: Vertebra that is posteriorly adjacent to vertebra 1.[TAO]
date retrieved: 2012-08-14
external class: TAO:0001168
ontology: TAO
source: TAO:wd

Axiom
annotated source: vertebral bone 2
annotated property: hasDbXref
annotated target: UMLS:C0004457
source: ncithesaurus:C2_Vertebra

Axiom
annotated source: vertebral bone 2
annotated property: hasExactSynonym
annotated target: axis [C II]
has db xref: FMA:12520
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: vertebral bone 2
annotated property: hasExactSynonym
annotated target: cervical axis
has db xref: MP:0004608

Axiom
annotated source: vertebral bone 2
annotated property: hasExactSynonym
annotated target: vertebra 2
has db xref: ZFA:0001168

Axiom
annotated source: vertebral bone 2
annotated property: hasNarrowSynonym
annotated target: cervical vertebra 2
has db xref: MA:0001422
has synonym type: HUMAN PREFERRED

Axiom
annotated source: vertebral bone 2
annotated property: hasRelatedSynonym
annotated target: axis
has db xref: MA:0001422
has synonym type: INCONSISTENT

caudal vertebra
type: Class
equivalent class: Class
  intersection of: UBERON_0018142
  intersection of: Restriction
    on property: RO_0002473
    some values from: UBERON_0002481
subclass of: UBERON_0002412
subclass of: UBERON_0004247
subclass of: UBERON_0018142
IAO_0000115: Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx).
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO]
UBPROP_0000012: we deliberately merge the MA classes as we believe them equivalent
has alternative id: UBERON:0006070
has broad synonym: caudal vertebra
has db xref: EMAPA:18374
has db xref: FMA:12527
has db xref: MA:0000310
has db xref: MA:0001420
has db xref: NCIT:C32334
has db xref: SCTID:361774004
has db xref: TAO:0000326
has db xref: UMLS:C0223616
has db xref: Wikipedia:Caudal_vertebra
has db xref: XAO:0003079
has db xref: ZFA:0000326
has db xref: galen:CoccygealVertebra
has exact synonym: caudal vertebrae
has exact synonym: caudal vertebral bone
has exact synonym: caudal vertebral bone element
has exact synonym: coccygeal segment
has exact synonym: coccygeal vertebra
has exact synonym: fused tail vertebra
has OBO namespace: uberon
has related synonym: coccygea
has related synonym: tail vertebra
id: UBERON:0001095
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core
comment: Taxon notes In zebrafish, Vertebra bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae

Axiom
annotated source: caudal vertebra
annotated property: IAO_0000115
annotated target: Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx).
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: caudal vertebra
annotated property: UBPROP_0000001
annotated target: Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000326
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: caudal vertebra
annotated property: UBPROP_0000012
annotated target: we deliberately merge the MA classes as we believe them equivalent
external ontology: MA

Axiom
annotated source: caudal vertebra
annotated property: hasBroadSynonym
annotated target: caudal vertebra
has db xref: FMA:12527
has synonym type: SENSU

Axiom
annotated source: caudal vertebra
annotated property: hasDbXref
annotated target: UMLS:C0223616
source: ncithesaurus:Coccygeal_Vertebra

Axiom
annotated source: caudal vertebra
annotated property: hasExactSynonym
annotated target: caudal vertebrae
has synonym type: OMO_0003004

Axiom
annotated source: caudal vertebra
annotated property: hasExactSynonym
annotated target: coccygeal vertebra
has db xref: FMA:12527

Axiom
annotated source: caudal vertebra
annotated property: hasExactSynonym
annotated target: fused tail vertebra
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: caudal vertebra
annotated property: hasRelatedSynonym
annotated target: coccygea
has db xref: MA:0001420

Axiom
annotated source: caudal vertebra
annotated property: hasRelatedSynonym
annotated target: tail vertebra
has db xref: MA:0000310

wall of esophagus
type: Class
equivalent class: Class
  intersection of: anatomical wall
  intersection of: Restriction
    on property: BFO_0000050
    some values from: esophagus
subclass of: gut wall
subclass of: Restriction
  on property: BFO_0000050
  some values from: esophagus
IAO_0000115: An anatomical wall that is part of a esophagus [Automatically generated definition].
has db xref: EMAPA:35326
has db xref: FMA:12611
has db xref: MA:0002691
has exact synonym: anatomical wall of esophagus
has exact synonym: anatomical wall of gullet
has exact synonym: anatomical wall of oesophagus
has exact synonym: esophageal wall
has exact synonym: esophagus anatomical wall
has exact synonym: esophagus wall
has exact synonym: gullet anatomical wall
has exact synonym: gullet wall
has exact synonym: oesophagus anatomical wall
has exact synonym: oesophagus wall
has exact synonym: wall of gullet
has exact synonym: wall of oesophagus
has OBO namespace: uberon
id: UBERON:0001096

Axiom
annotated source: wall of esophagus
annotated property: IAO_0000115
annotated target: An anatomical wall that is part of a esophagus [Automatically generated definition].
has db xref: OBOL:automatic

Axiom
annotated source: wall of esophagus
annotated property: hasExactSynonym
annotated target: anatomical wall of esophagus
has db xref: OBOL:automatic

Axiom
annotated source: wall of esophagus
annotated property: hasExactSynonym
annotated target: anatomical wall of gullet
has db xref: OBOL:automatic

Axiom
annotated source: wall of esophagus
annotated property: hasExactSynonym
annotated target: anatomical wall of oesophagus
has db xref: OBOL:automatic

Axiom
annotated source: wall of esophagus
annotated property: hasExactSynonym
annotated target: esophagus anatomical wall
has db xref: OBOL:automatic

Axiom
annotated source: wall of esophagus
annotated property: hasExactSynonym
annotated target: gullet anatomical wall
has db xref: OBOL:automatic

Axiom
annotated source: wall of esophagus
annotated property: hasExactSynonym
annotated target: gullet wall
has db xref: OBOL:automatic

Axiom
annotated source: wall of esophagus
annotated property: hasExactSynonym
annotated target: oesophagus anatomical wall
has db xref: OBOL:automatic

Axiom
annotated source: wall of esophagus
annotated property: hasExactSynonym
annotated target: oesophagus wall
has db xref: OBOL:automatic

Axiom
annotated source: wall of esophagus
annotated property: hasExactSynonym
annotated target: wall of gullet
has db xref: OBOL:automatic

Axiom
annotated source: wall of esophagus
annotated property: hasExactSynonym
annotated target: wall of oesophagus
has db xref: OBOL:automatic

diaphragm
type: Class
subclass of: UBERON_0003830
subclass of: UBERON_0003831
subclass of: Restriction
  on property: RO_0002005
  some values from: UBERON_0001884
IAO_0000115: A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control.
RO_0002161: NCBITaxon 8782
UBPROP_0000001: The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO].
UBPROP_0000003: The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG]
UBPROP_0000007: phrenic
UBPROP_0000008: The existence of some membrane separating the pharynx from the stomach can be traced widely among the chordates. Thus amphioxus possesses an atrium by which water exits the pharynx, which has been argued (and disputed) to be homologous to structures in ascidians and hagfishes.[3]
UBPROP_0000008: The urochordate epicardium separates digestive organs from the pharynx and heart, but the anus returns to the upper compartment to discharge wastes through an outgoing siphon (Thoracic_diaphragm#Comparative_anatomy_and_evolution)
UBPROP_0000009: barrier between thoracic and abdominal cavities; stop gastric contents from refluxing into the oesophagus
UBPROP_0000009: breathing control
UBPROP_0000011: originate from the cervical somites, likely C3-C5[PMID:23586979]
has db xref: BTO:0000341
has db xref: CALOHA:TS-0198
has db xref: EFO:0000937
has db xref: EHDAA2:0003495
has db xref: EMAPA:17701
has db xref: EV:0100376
has db xref: FMA:13295
has db xref: GAID:158
has db xref: MA:0001904
has db xref: MAT:0000502
has db xref: MESH:D003964
has db xref: NCIT:C12702
has db xref: SCTID:181614006
has db xref: UMLS:C0011980
has db xref: VHOG:0000713
has db xref: Wikipedia:Thoracid_diaphragm
has exact synonym: diaphragm muscle
has exact synonym: diaphragm of thorax
has exact synonym: thoracic diaphragm
has OBO namespace: uberon
has related synonym: midriff
has related synonym: phren
id: UBERON:0001103
in subset: efo slim
in subset: organ slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: diaphragm
annotated property: subClassOf
annotated target: Restriction
source: PMID:23586979

Axiom
annotated source: diaphragm
annotated property: subClassOf
annotated target: Restriction
evidence: definitional

Axiom
annotated source: diaphragm
annotated property: IAO_0000115
annotated target: A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control.
has db xref: MP:0002279

Axiom
annotated source: diaphragm
annotated property: RO_0002161
annotated target: NCBITaxon 8782
source: Wikipedia:Thoracic_diaphragm#Comparative_anatomy_and_evolution

Axiom
annotated source: diaphragm
annotated property: UBPROP_0000001
annotated target: The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO].
source: GO:0060539

Axiom
annotated source: diaphragm
annotated property: UBPROP_0000003
annotated target: The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000713
ontology: VHOG
source: ISBN:978-0471384618 Colbert EH, Evolution of the vertebrates: a history of the backboned animals through time (2001) p.278
source: http://bgee.unil.ch/

Axiom
annotated source: diaphragm
annotated property: hasDbXref
annotated target: UMLS:C0011980
source: ncithesaurus:Diaphragm

Axiom
annotated source: diaphragm
annotated property: hasExactSynonym
annotated target: diaphragm muscle
has db xref: BTO:0000341

Axiom
annotated source: diaphragm
annotated property: hasRelatedSynonym
annotated target: midriff
has db xref: BTO:0000341

Axiom
annotated source: diaphragm
annotated property: hasRelatedSynonym
annotated target: phren
has db xref: BTO:0000341

clavicle bone
type: Class
subclass of: UBERON_0002495
subclass of: UBERON_0007829
subclass of: UBERON_0015212
subclass of: Restriction
  on property: BSPO_0000126
  some values from: UBERON_0002091
IAO_0000115: A paired dermal or endochondral bone that is part of the pectoral girdle. The clavicle may be in contact with the interclavicle or coracoid and forms an attachment site for pectoral musculature. [PHENOSCAPE:ad].
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Slender, paired bones of intramembranous origin that invest the anterior margins of the procoracoids.[AAO]
UBPROP_0000002: relationship loss: part_of zonal element (AAO:0000936)[AAO]
UBPROP_0000003: In early tetrapods, the connecting skull bone, the posttemporal, and adjoining shoulder bones, supracleithrum and postcleithrum (=anocleithrum), are absent, leaving a dermal shoulder girdle composed of the remaining ventral elements: the paired cleithrum and clavicle, and an unpaired midventral interclavicle that joins both halves of the girdle across the midline. (...) Several dermal elements of the shoulder persist in early synapsids. The clavicle and interclavicle are present in therapsids and monotremes, but in marsupials and placentals, the interclavicle is absent, the clavicle often is reduced in size, and the scapula becomes the predominant shoulder element.[well established][VHOG]
UBPROP_0000007: clavicular
UBPROP_0000008: The clavicle first appears as part of the skeleton in primitive bony fish, where it is associated with the pectoral fin; they also have a bone called the cleithrum. In such fish, the paired clavicles run behind and below the gills on each side, and are joined by a solid symphysis on the fish's underside. They are, however, absent in cartilagenous fish and in the vast majority of living bony fish, including all of the teleosts[ISBN 0-03-910284-X].
UBPROP_0000011: In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal.
UBPROP_0000012: FMA and MA differ in whether they consider this part of the shoulder
has db xref: AAO:0000761
has db xref: EMAPA:18721
has db xref: FMA:13321
has db xref: GAID:182
has db xref: MA:0001329
has db xref: MESH:D002968
has db xref: MFMO:0000047
has db xref: NCIT:C12695
has db xref: SCTID:181910004
has db xref: UMLS:C0008913
has db xref: VHOG:0000849
has db xref: VSAO:0005031
has db xref: Wikipedia:Clavicle
has db xref: galen:Clavicle
has exact synonym: clavicle
has exact synonym: clavicula
has exact synonym: collar bone
has exact synonym: collarbone
has OBO namespace: uberon
id: UBERON:0001105
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: clavicle bone
annotated property: subClassOf
annotated target: UBERON_0002495
source: FMA

Axiom
annotated source: clavicle bone
annotated property: subClassOf
annotated target: Restriction
editor: mah
source: ISBN:978-0-12-319060-4

Axiom
annotated source: clavicle bone
annotated property: subClassOf
annotated target: Restriction
notes: from secondary cartilage of fusion
source: ISBN:978-0-12-319060-4

Axiom
annotated source: clavicle bone
annotated property: IAO_0000115
annotated target: A paired dermal or endochondral bone that is part of the pectoral girdle. The clavicle may be in contact with the interclavicle or coracoid and forms an attachment site for pectoral musculature. [PHENOSCAPE:ad].
has db xref: PHENOSCAPE:ad
has db xref: https://github.com/obophenotype/uberon/issues/103

Axiom
annotated source: clavicle bone
annotated property: UBPROP_0000001
annotated target: Slender, paired bones of intramembranous origin that invest the anterior margins of the procoracoids.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000761
ontology: AAO
source: AAO:LAP

Axiom
annotated source: clavicle bone
annotated property: UBPROP_0000002
annotated target: relationship loss: part_of zonal element (AAO:0000936)[AAO]
date retrieved: 2012-06-20
external class: AAO:0000761
ontology: AAO

Axiom
annotated source: clavicle bone
annotated property: UBPROP_0000003
annotated target: In early tetrapods, the connecting skull bone, the posttemporal, and adjoining shoulder bones, supracleithrum and postcleithrum (=anocleithrum), are absent, leaving a dermal shoulder girdle composed of the remaining ventral elements: the paired cleithrum and clavicle, and an unpaired midventral interclavicle that joins both halves of the girdle across the midline. (...) Several dermal elements of the shoulder persist in early synapsids. The clavicle and interclavicle are present in therapsids and monotremes, but in marsupials and placentals, the interclavicle is absent, the clavicle often is reduced in size, and the scapula becomes the predominant shoulder element.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000849
ontology: VHOG
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.330-333 and Figure 9.18
source: http://bgee.unil.ch/

Axiom
annotated source: clavicle bone
annotated property: UBPROP_0000011
annotated target: In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal.
source: ISBN:978-0-12-319060-4

Axiom
annotated source: clavicle bone
annotated property: UBPROP_0000012
annotated target: FMA and MA differ in whether they consider this part of the shoulder
external ontology: FMA

Axiom
annotated source: clavicle bone
annotated property: hasDbXref
annotated target: UMLS:C0008913
source: ncithesaurus:Clavicle

Axiom
annotated source: clavicle bone
annotated property: hasExactSynonym
annotated target: clavicle
has db xref: VSAO:0005031

Axiom
annotated source: clavicle bone
annotated property: hasExactSynonym
annotated target: clavicula
has db xref: VSAO:0005031

latissimus dorsi muscle
type: Class
subclass of: UBERON_0001482
subclass of: UBERON_0034908
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002372
  some values from: UBERON_0006849
IAO_0000115: The latissimus dorsi is the larger, flat, dorso-lateral muscle on the trunk, posterior to the arm, and partly covered by the trapezius on its median dorsal region. [WP,unvetted].
RO_0002175: NCBITaxon 9606
UBPROP_0000008: In humans it inserts along a roughened line deep in the groove. In other mammals (most, I believe) it is an actual projection, the latissimus dorsi process [FEED:rd] [https://github.com/obophenotype/uberon/issues/1192]
has db xref: EFO:0003067
has db xref: EHDAA2:0000932
has db xref: EHDAA:8307
has db xref: EMAPA:18178
has db xref: FMA:13357
has db xref: MA:0002331
has db xref: NCIT:C33150
has db xref: SCTID:181747008
has db xref: UMLS:C0224362
has db xref: VHOG:0000930
has db xref: Wikipedia:Latissimus_dorsi_muscle
has exact synonym: dorsal latissimus muscle
has exact synonym: latissimi dorsi
has exact synonym: latissimus dorsi
has exact synonym: musculus latissimus dorsi
has OBO namespace: uberon
has related synonym: musculus latissimus dorsi
id: UBERON:0001112
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
comment: Dorsal group[Kardong]

Axiom
annotated source: latissimus dorsi muscle
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: latissimus dorsi muscle
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: latissimus dorsi muscle
annotated property: subClassOf
annotated target: Restriction
notes: spinous processes of thoracic T7-T12 thoracolumbar fascia iliac crest and inferior 3 or 4 ribs inferior angle of scapula
source: dbpedia

Axiom
annotated source: latissimus dorsi muscle
annotated property: subClassOf
annotated target: Restriction
notes: floor of intertubercular groove of the humerus
source: dbpedia

Axiom
annotated source: latissimus dorsi muscle
annotated property: subClassOf
annotated target: Restriction
source: dbpedia

Axiom
annotated source: latissimus dorsi muscle
annotated property: subClassOf
annotated target: Restriction
source: dbpedia

Axiom
annotated source: latissimus dorsi muscle
annotated property: IAO_0000115
annotated target: The latissimus dorsi is the larger, flat, dorso-lateral muscle on the trunk, posterior to the arm, and partly covered by the trapezius on its median dorsal region. [WP,unvetted].
has db xref: Wikipedia:Latissimus_dorsi_muscle

Axiom
annotated source: latissimus dorsi muscle
annotated property: hasDbXref
annotated target: UMLS:C0224362
source: ncithesaurus:Musculus_Latissimus_Dorsi

Axiom
annotated source: latissimus dorsi muscle
annotated property: hasExactSynonym
annotated target: latissimi dorsi
has synonym type: OMO_0003004

Axiom
annotated source: latissimus dorsi muscle
annotated property: hasRelatedSynonym
annotated target: musculus latissimus dorsi
has db xref: Wikipedia:Latissimus_dorsi_muscle
has synonym type: OMO_0003011

lobe of liver
type: Class
subclass of: UBERON_0009912
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002107
IAO_0000115: Traditional gross anatomy divided the liver into four lobes based on surface features. The falciform ligament is visible on the front (anterior side) of the liver. This divides the liver into a left anatomical lobe, and a right anatomical lobe.
IAO_0000116: some work needs to be done to ensure the child terms of this class have correct isa/partof placement. in MA they are subclasses, in FMA they are parts
has db xref: EMAPA:18306
has db xref: FMA:13361
has db xref: MA:0000360
has db xref: NCIT:C49579
has db xref: SCTID:245378000
has db xref: UMLS:C0447541
has db xref: Wikipedia:Liver#Lobes
has exact synonym: hepatic lobe
has exact synonym: liver lobe
has exact synonym: lobus hepatis
has OBO namespace: uberon
id: UBERON:0001113

Axiom
annotated source: lobe of liver
annotated property: subClassOf
annotated target: UBERON_0009912
source: FMA

Axiom
annotated source: lobe of liver
annotated property: IAO_0000115
annotated target: Traditional gross anatomy divided the liver into four lobes based on surface features. The falciform ligament is visible on the front (anterior side) of the liver. This divides the liver into a left anatomical lobe, and a right anatomical lobe.
has db xref: Wikipedia:Liver#Lobes

Axiom
annotated source: lobe of liver
annotated property: hasDbXref
annotated target: UMLS:C0447541
source: ncithesaurus:Liver_Lobe

right lobe of liver
type: Class
subclass of: lobe of liver
IAO_0000115: The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted].
UBPROP_0000001: Portion of the liver which develops on the fish's right side adjacent to the gall bladder.[TAO]
has db xref: EHDAA2:0001008
has db xref: EHDAA:4001
has db xref: EMAPA:18311
has db xref: FMA:13362
has db xref: MA:0000363
has db xref: NCIT:C33481
has db xref: SCTID:362182008
has db xref: TAO:0005173
has db xref: UMLS:C0227481
has db xref: VHOG:0001424
has db xref: Wikipedia:Right_lobe_of_liver
has db xref: ZFA:0005173
has exact synonym: liver right lobe
has exact synonym: lobus hepaticus dexter
has exact synonym: right liver lobe
has OBO namespace: uberon
has related synonym: 2nd lobe
has related synonym: gall bladder lobe
has related synonym: lobus hepatis dexter
has related synonym: right hepatic lobe
has related synonym: second lobe
id: UBERON:0001114
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: right lobe of liver
annotated property: IAO_0000115
annotated target: The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted].
has db xref: Wikipedia:Right_lobe_of_liver

Axiom
annotated source: right lobe of liver
annotated property: UBPROP_0000001
annotated target: Portion of the liver which develops on the fish's right side adjacent to the gall bladder.[TAO]
date retrieved: 2012-08-14
external class: TAO:0005173
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: right lobe of liver
annotated property: hasDbXref
annotated target: UMLS:C0227481
source: ncithesaurus:Right_Lobe_of_the_Liver

Axiom
annotated source: right lobe of liver
annotated property: hasExactSynonym
annotated target: lobus hepaticus dexter
has synonym type: OMO_0003011

Axiom
annotated source: right lobe of liver
annotated property: hasExactSynonym
annotated target: right liver lobe
has db xref: ZFA:0005173

Axiom
annotated source: right lobe of liver
annotated property: hasRelatedSynonym
annotated target: 2nd lobe
has db xref: TAO:0005173

Axiom
annotated source: right lobe of liver
annotated property: hasRelatedSynonym
annotated target: gall bladder lobe
has db xref: ZFA:0005173
has synonym type: SENSU

Axiom
annotated source: right lobe of liver
annotated property: hasRelatedSynonym
annotated target: lobus hepatis dexter
has db xref: Wikipedia:Right_lobe_of_liver
has synonym type: OMO_0003011

Axiom
annotated source: right lobe of liver
annotated property: hasRelatedSynonym
annotated target: right hepatic lobe
has db xref: EMAPA:18311

Axiom
annotated source: right lobe of liver
annotated property: hasRelatedSynonym
annotated target: second lobe
has db xref: TAO:0005173

left lobe of liver
type: Class
subclass of: lobe of liver
IAO_0000115: The left lobe is smaller and more flattened than the right. It is situated in the epigastric and left hypochondriac regions. Its upper surface is slightly convex and is moulded on to the diaphragm; its under surface presents the gastric impression and omental tuberosity. [WP,unvetted].
UBPROP_0000001: Portion of the liver which develops on the fish's left side.[TAO]
has db xref: EHDAA2:0001000
has db xref: EHDAA:3995
has db xref: EMAPA:18307
has db xref: FMA:13363
has db xref: MA:0000361
has db xref: NCIT:C32965
has db xref: SCTID:362183003
has db xref: TAO:0005172
has db xref: UMLS:C0227486
has db xref: VHOG:0001423
has db xref: Wikipedia:Left_lobe_of_liver
has db xref: ZFA:0005172
has exact synonym: left liver lobe
has exact synonym: liver left lobe
has exact synonym: lobus hepaticus sinister
has OBO namespace: uberon
has related synonym: left hepatic lobe
has related synonym: lobus hepatis sinister
id: UBERON:0001115
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: left lobe of liver
annotated property: IAO_0000115
annotated target: The left lobe is smaller and more flattened than the right. It is situated in the epigastric and left hypochondriac regions. Its upper surface is slightly convex and is moulded on to the diaphragm; its under surface presents the gastric impression and omental tuberosity. [WP,unvetted].
has db xref: Wikipedia:Left_lobe_of_liver

Axiom
annotated source: left lobe of liver
annotated property: UBPROP_0000001
annotated target: Portion of the liver which develops on the fish's left side.[TAO]
date retrieved: 2012-08-14
external class: TAO:0005172
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: left lobe of liver
annotated property: hasDbXref
annotated target: UMLS:C0227486
source: ncithesaurus:Left_Lobe_of_the_Liver

Axiom
annotated source: left lobe of liver
annotated property: hasExactSynonym
annotated target: lobus hepaticus sinister
has synonym type: OMO_0003011

Axiom
annotated source: left lobe of liver
annotated property: hasRelatedSynonym
annotated target: left hepatic lobe
has db xref: EMAPA:18307

Axiom
annotated source: left lobe of liver
annotated property: hasRelatedSynonym
annotated target: lobus hepatis sinister
has db xref: Wikipedia:Left_lobe_of_liver
has synonym type: OMO_0003011

lobe of thyroid gland
type: Class
equivalent class: Class
  intersection of: UBERON_0009912
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002046
subclass of: UBERON_0009912
subclass of: UBERON_0015212
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002046
IAO_0000115: A lobe of tissue that is part of a thyroid gland.
UBPROP_0000003: Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG]
has db xref: EHDAA2:0002032
has db xref: EMAPA:18196
has db xref: FMA:13367
has db xref: MA:0000131
has db xref: NCIT:C33784
has db xref: SCTID:245537001
has db xref: UMLS:C0447647
has db xref: VHOG:0000732
has db xref: Wikipedia:Lobes_of_thyroid_gland
has exact synonym: lobus (glandula thyroidea)
has exact synonym: lobus glandulae thyroideae
has exact synonym: thyroid gland lobe
has exact synonym: thyroid lobe
has OBO namespace: uberon
has related synonym: lobuli glandulae thyroideae
id: UBERON:0001118
comment: The lobes of the thyroid gland are conical in shape, the apex of each being directed upward and lateralward as far as the junction of the middle with the lower third of the thyroid cartilage; the base looks downward, and is on a level with the fifth or sixth tracheal ring. Each lobe is about 5 cm. long; its greatest width is about 3 cm. , and its thickness about 2 cm. The lateral or superficial surface is convex, and covered by the skin, the superficial and deep fasciæ, the Sternocleidomastoideus, the superior belly of the Omohyoideus, the Sternohyoideus and Sternothyreoideus, and beneath the last muscle by the pretracheal layer of the deep fascia, which forms a capsule for the gland. The deep or medial surface is moulded over the underlying structures, viz. , the thyroid and cricoid cartilages, the trachea, the Constrictor pharyngis inferior and posterior part of the Cricothyreoideus, the esophagus (particularly on the left side of the neck), the superior and inferior thyroid arteries, and the recurrent nerves. The anterior border is thin, and inclines obliquely from above downward toward the middle line of the neck, while the posterior border is thick and overlaps the common carotid artery, and, as a rule, the parathyroids

Axiom
annotated source: lobe of thyroid gland
annotated property: subClassOf
annotated target: Restriction
source: FMA-abduced-lr

Axiom
annotated source: lobe of thyroid gland
annotated property: IAO_0000115
annotated target: A lobe of tissue that is part of a thyroid gland.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: lobe of thyroid gland
annotated property: UBPROP_0000003
annotated target: Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000732
ontology: VHOG
source: http://bgee.unil.ch/
source: http://www.thyroidmanager.org/Chapter1/chapter01.htm

Axiom
annotated source: lobe of thyroid gland
annotated property: hasDbXref
annotated target: UMLS:C0447647
source: ncithesaurus:Thyroid_Gland_Lobe

Axiom
annotated source: lobe of thyroid gland
annotated property: hasExactSynonym
annotated target: lobus glandulae thyroideae
has db xref: FMA:13367
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: lobe of thyroid gland
annotated property: hasRelatedSynonym
annotated target: lobuli glandulae thyroideae
has db xref: Wikipedia:Lobes_of_thyroid_gland
has synonym type: OMO_0003011

right lobe of thyroid gland
type: Class
equivalent class: Class
  intersection of: lobe of thyroid gland
  intersection of: Restriction
    on property: BSPO_0000121
    some values from: UBERON_0002046
subclass of: lobe of thyroid gland
subclass of: Restriction
  on property: BSPO_0000121
  some values from: UBERON_0002046
IAO_0000115: A lobe of thyroid gland that is in the right side of a thyroid gland.
UBPROP_0000003: Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG]
UBPROP_0000006: https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
has db xref: EHDAA2:0001759
has db xref: EMAPA:18198
has db xref: FMA:13368
has db xref: MA:0000729
has db xref: NCIT:C33491
has db xref: SCTID:170482008
has db xref: UMLS:C0229581
has db xref: VHOG:0000733
has exact synonym: lobus dexter (glandula thyroidea)
has exact synonym: right thyroid lobe
has exact synonym: thyroid gland right lobe
has OBO namespace: uberon
id: UBERON:0001119

Axiom
annotated source: right lobe of thyroid gland
annotated property: IAO_0000115
annotated target: A lobe of thyroid gland that is in the right side of a thyroid gland.
has db xref: OBOL:automatic

Axiom
annotated source: right lobe of thyroid gland
annotated property: UBPROP_0000003
annotated target: Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000733
ontology: VHOG
source: http://bgee.unil.ch/
source: http://www.thyroidmanager.org/Chapter1/chapter01.htm

Axiom
annotated source: right lobe of thyroid gland
annotated property: hasDbXref
annotated target: UMLS:C0229581
source: ncithesaurus:Right_Thyroid_Gland_Lobe

left lobe of thyroid gland
type: Class
equivalent class: Class
  intersection of: lobe of thyroid gland
  intersection of: Restriction
    on property: BSPO_0000120
    some values from: UBERON_0002046
subclass of: lobe of thyroid gland
subclass of: Restriction
  on property: BSPO_0000120
  some values from: UBERON_0002046
IAO_0000115: A lobe of thyroid gland that is in the left side of a thyroid gland.
UBPROP_0000003: Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG]
UBPROP_0000006: https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
has db xref: EHDAA2:0000965
has db xref: EMAPA:18197
has db xref: FMA:13369
has db xref: MA:0000728
has db xref: NCIT:C32973
has db xref: SCTID:170784008
has db xref: UMLS:C0229582
has db xref: VHOG:0000734
has exact synonym: left thyroid lobe
has exact synonym: lobus sinister (glandula thyroidea)
has exact synonym: thyroid gland left lobe
has OBO namespace: uberon
id: UBERON:0001120

Axiom
annotated source: left lobe of thyroid gland
annotated property: IAO_0000115
annotated target: A lobe of thyroid gland that is in the left side of a thyroid gland.
has db xref: OBOL:automatic

Axiom
annotated source: left lobe of thyroid gland
annotated property: UBPROP_0000003
annotated target: Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000734
ontology: VHOG
source: http://bgee.unil.ch/
source: http://www.thyroidmanager.org/Chapter1/chapter01.htm

Axiom
annotated source: left lobe of thyroid gland
annotated property: hasDbXref
annotated target: UMLS:C0229582
source: ncithesaurus:Left_Thyroid_Gland_Lobe

serratus ventralis
type: Class
subclass of: UBERON_0001482
subclass of: UBERON_0034908
subclass of: Restriction
IAO_0000115: The serratus ventralis is a muscle that originates on the surface of the upper eight or nine ribs at the side of the chest and inserts along the entire anterior length of the medial border of the scapula. [WP,unvetted].
RO_0002175: NCBITaxon 9606
has db xref: EHDAA2:0001832
has db xref: EHDAA:9463
has db xref: EMAPA:18525
has db xref: FMA:13397
has db xref: MA:0002378
has db xref: NCIT:C53014
has db xref: SCTID:181748003
has db xref: UMLS:C1710059
has db xref: VHOG:0000679
has db xref: Wikipedia:Serratus_anterior_muscle
has exact synonym: Boxer's muscle
has exact synonym: serratus anterior
has exact synonym: serratus anterior muscle
has exact synonym: serratus ventralis muscle
has OBO namespace: uberon
has related synonym: musculus serratus anterior
has related synonym: serratus lateralis
id: UBERON:0001125
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: serratus ventralis
annotated property: subClassOf
annotated target: Restriction
notes: long thoracic nerve
source: dbpedia

Axiom
annotated source: serratus ventralis
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: serratus ventralis
annotated property: subClassOf
annotated target: Restriction
notes: fleshy slips from the outer surface of upper 8 or 9 ribs
source: dbpedia

Axiom
annotated source: serratus ventralis
annotated property: subClassOf
annotated target: Restriction
notes: costal aspect of medial margin of the scapula
source: dbpedia

Axiom
annotated source: serratus ventralis
annotated property: subClassOf
annotated target: Restriction
source: dbpedia

Axiom
annotated source: serratus ventralis
annotated property: IAO_0000115
annotated target: The serratus ventralis is a muscle that originates on the surface of the upper eight or nine ribs at the side of the chest and inserts along the entire anterior length of the medial border of the scapula. [WP,unvetted].
has db xref: Wikipedia:Serratus_anterior_muscle

Axiom
annotated source: serratus ventralis
annotated property: hasDbXref
annotated target: UMLS:C1710059
source: ncithesaurus:Serratus_Ventralis

Axiom
annotated source: serratus ventralis
annotated property: hasExactSynonym
annotated target: serratus anterior
has db xref: VHOG:0000679

Axiom
annotated source: serratus ventralis
annotated property: hasRelatedSynonym
annotated target: musculus serratus anterior
has db xref: Wikipedia:Serratus_anterior_muscle
has synonym type: OMO_0003011

Axiom
annotated source: serratus ventralis
annotated property: hasRelatedSynonym
annotated target: serratus lateralis
has db xref: Wikipedia:Serratus_anterior_muscle
has synonym type: OMO_0003011

vertebral column
type: Class
equivalent class: Class
  intersection of: subdivision of skeletal system
  intersection of: Restriction
    on property: RO_0002473
    some values from: UBERON_0010913
subclass of: subdivision of skeletal system
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7742
subclass of: Restriction
  on property: RO_0002473
  some values from: UBERON_0010913
subclass of: Restriction
  on property: protects
  some values from: UBERON_0002240
IAO_0000115: Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO].
IAO_0000116: Note that in contrast to VSAO, this is a subset of the skeletal system, and thus includes intervertebral joints, cartilage and ligaments etc. Some ontologies such as AAO seem to purely refer to the skeleton
RO_0002161: NCBITaxon 7762
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Anatomical cluster that consists of all the vertebra in the body.[VSAO]
UBPROP_0000001: The vertebral column consists of a series of vertebrae connected by ligaments. It provides a supporting axis for the body and protects the spinal cord. [TFD][VHOG]
UBPROP_0000003: Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...).[well established][VHOG]
has broad synonym: spine
has db xref: AAO:0000699
has db xref: AAO:0000734
has db xref: BTO:0000818
has db xref: EFO:0001369
has db xref: EHDA:10119
has db xref: EMAPA:35919
has db xref: FMA:13478
has db xref: GAID:106
has db xref: MA:0002416
has db xref: MESH:D013131
has db xref: NCIT:C12998
has db xref: NCIT:C33588
has db xref: NIF_Subcellular:sao1145756102
has db xref: SCTID:44300000
has db xref: TAO:0001559
has db xref: UMLS:C0037949
has db xref: UMLS:C1519455
has db xref: VHOG:0001142
has db xref: VSAO:0000185
has db xref: Wikipedia:Vertebral_column
has db xref: XAO:0003074
has db xref: ZFA:0001559
has db xref: galen:SpinalColumn
has narrow synonym: backbone
has narrow synonym: vertebral column skeleton
has OBO namespace: uberon
has related synonym: columna vertebralis
has related synonym: dorsal spine
has related synonym: spinal column
has related synonym: vertebral region
id: UBERON:0001130
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: vertebral column
annotated property: subClassOf
annotated target: Restriction
source: cjm

Axiom
annotated source: vertebral column
annotated property: IAO_0000115
annotated target: Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO].
has db xref: VSAO:0000185
has db xref: https://orcid.org/0000-0002-6601-2165
has db xref: https://sourceforge.net/tracker/

Axiom
annotated source: vertebral column
annotated property: UBPROP_0000001
annotated target: Anatomical cluster that consists of all the vertebra in the body.[VSAO]
date retrieved: 2012-08-14
external class: VSAO:0000185
ontology: VSAO
source: VSAO:curator

Axiom
annotated source: vertebral column
annotated property: UBPROP_0000001
annotated target: The vertebral column consists of a series of vertebrae connected by ligaments. It provides a supporting axis for the body and protects the spinal cord. [TFD][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001142
ontology: VHOG
source: http://bgee.unil.ch/
source: http://medical-dictionary.thefreedictionary.com/vertebral+column

Axiom
annotated source: vertebral column
annotated property: UBPROP_0000003
annotated target: Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001142
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.53
source: http://bgee.unil.ch/

Axiom
annotated source: vertebral column
annotated property: hasBroadSynonym
annotated target: spine
has db xref: FMA:13478

Axiom
annotated source: vertebral column
annotated property: hasDbXref
annotated target: UMLS:C0037949
source: ncithesaurus:Vertebral_Column

Axiom
annotated source: vertebral column
annotated property: hasDbXref
annotated target: UMLS:C1519455
source: ncithesaurus:Spinal_Cord_Column

Axiom
annotated source: vertebral column
annotated property: hasNarrowSynonym
annotated target: backbone
has db xref: FMA:13478

Axiom
annotated source: vertebral column
annotated property: hasNarrowSynonym
annotated target: vertebral column skeleton
has db xref: AAO:0000699

Axiom
annotated source: vertebral column
annotated property: hasRelatedSynonym
annotated target: columna vertebralis
has db xref: BTO:0000818

Axiom
annotated source: vertebral column
annotated property: hasRelatedSynonym
annotated target: dorsal spine
has db xref: BTO:0000818

Axiom
annotated source: vertebral column
annotated property: hasRelatedSynonym
annotated target: spinal column
has db xref: MESH:A02.835.232.834

parathyroid gland
type: Class
subclass of: UBERON_0002368
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0035898
IAO_0000115: The parathyroid gland is an endocrine gland for secretion of parathyroid hormone, usually found as a pair, embedded in the connective tissue capsule on the posterior surface of the thyroid gland. Parathyroid regulates calcium and phosphorous metabolism.
UBPROP_0000001: Any one of several small structures, usually four, attached to the dorsal surfaces of the lateral lobes of the thyroid gland. [TFD][VHOG]
UBPROP_0000001: Either of the two pairs of small, spherical, encapsulated glands which develop from ventral growths of the third and fourth pharyngeal pouches and are closely associated with the external jugular veins. Calcitonin and parathyroid hormone are secreted by these glands.[AAO]
UBPROP_0000003: The evolution of the tetrapods, and the shift from an aquatic to a terrestrial environment, was believed to have required new controls for regulating calcium homeostasis, and thus the evolution of parathyroid glands (...) both the tetrapod parathyroid and the gills of fish contribute to the regulation of extracellular calcium levels. It is therefore reasonable to suggest that the parathyroid gland evolved as a result of the transformation of the gills into the parathyroid glands of tetrapods and the transition from an aquatic to a terrestrial environment. This interpretation would also explain the positioning of the parathyroid gland within the pharynx in the tetrapod body. Were the parathyroid gland to have emerged de novo with the evolution of the tetrapods it could, as an endocrine organ, have been placed anywhere in the body and still exert its effect.[well established][VHOG]
UBPROP_0000008: Parathyroid glands are found in all adult tetrapods, although they vary in their number, and in their exact position. Mammals typically have four parathyroids, while other groups typically have six. Fish do not possess parathyroid glands, although the ultimobranchial glands, which are found close to the oesophagus, may have a similar function and could even be homologous with the tetrapod parathyroids. Even these glands are absent in the most primitive vertebrates, the jawless fish, but as these species have no bone in their skeletons, only cartilage, it may be that they have less need to regulate calcium metabolism. The conserved homology of genes and calcium-sensing receptors in fish gills with those in the parathryroid glands of birds and mammals is recognized by evolutionary developmental biology as evolution-using genes and gene networks in novel ways to generate new structures with some similar functions and novel functions[WP]
UBPROP_0000011: In humans and chick it emerges from pouches 3 and 4, but in mice it is exclusively generated by the third pouch
UBPROP_0000011: table 13.1 of Kardong is used to create the taxon-specific developmental relationships here, although some omissions are made for simplicity.
has db xref: AAO:0010545
has db xref: BTO:0000997
has db xref: CALOHA:TS-0745
has db xref: EFO:0000862
has db xref: EMAPA:32812
has db xref: EV:0100134
has db xref: FMA:13890
has db xref: GAID:452
has db xref: MA:0000128
has db xref: MAT:0000082
has db xref: MESH:D010280
has db xref: MIAA:0000082
has db xref: NCIT:C12765
has db xref: SCTID:181121007
has db xref: UMLS:C0030518
has db xref: VHOG:0001188
has db xref: Wikipedia:Parathyroid_gland
has db xref: XAO:0000167
has exact synonym: parathyroid
has OBO namespace: uberon
has related synonym: epithelial body
has related synonym: parathyroid secreting cell
id: UBERON:0001132
in subset: organ slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: parathyroid gland
annotated property: subClassOf
annotated target: Restriction
source: PMID:16313389

Axiom
annotated source: parathyroid gland
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: parathyroid gland
annotated property: IAO_0000115
annotated target: The parathyroid gland is an endocrine gland for secretion of parathyroid hormone, usually found as a pair, embedded in the connective tissue capsule on the posterior surface of the thyroid gland. Parathyroid regulates calcium and phosphorous metabolism.
has db xref: ISBN:0-683-40008-8
has db xref: MP:0000678
has db xref: Wikipedia:Parathyroid_gland

Axiom
annotated source: parathyroid gland
annotated property: UBPROP_0000001
annotated target: Any one of several small structures, usually four, attached to the dorsal surfaces of the lateral lobes of the thyroid gland. [TFD][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001188
ontology: VHOG
source: http://bgee.unil.ch/
source: http://medical-dictionary.thefreedictionary.com/parathyroid+gland

Axiom
annotated source: parathyroid gland
annotated property: UBPROP_0000001
annotated target: Either of the two pairs of small, spherical, encapsulated glands which develop from ventral growths of the third and fourth pharyngeal pouches and are closely associated with the external jugular veins. Calcitonin and parathyroid hormone are secreted by these glands.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010545
ontology: AAO
source: AAO:BJB

Axiom
annotated source: parathyroid gland
annotated property: UBPROP_0000003
annotated target: The evolution of the tetrapods, and the shift from an aquatic to a terrestrial environment, was believed to have required new controls for regulating calcium homeostasis, and thus the evolution of parathyroid glands (...) both the tetrapod parathyroid and the gills of fish contribute to the regulation of extracellular calcium levels. It is therefore reasonable to suggest that the parathyroid gland evolved as a result of the transformation of the gills into the parathyroid glands of tetrapods and the transition from an aquatic to a terrestrial environment. This interpretation would also explain the positioning of the parathyroid gland within the pharynx in the tetrapod body. Were the parathyroid gland to have emerged de novo with the evolution of the tetrapods it could, as an endocrine organ, have been placed anywhere in the body and still exert its effect.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001188
ontology: VHOG
source: DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)
source: http://bgee.unil.ch/

Axiom
annotated source: parathyroid gland
annotated property: UBPROP_0000011
annotated target: table 13.1 of Kardong is used to create the taxon-specific developmental relationships here, although some omissions are made for simplicity.
source: PMID:16313389

Axiom
annotated source: parathyroid gland
annotated property: hasDbXref
annotated target: UMLS:C0030518
source: ncithesaurus:Parathyroid_Gland

Axiom
annotated source: parathyroid gland
annotated property: hasRelatedSynonym
annotated target: epithelial body
has db xref: XAO:0000167

cardiac muscle tissue
type: Class
equivalent class: Class
  intersection of: UBERON_0002036
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0000746
subclass of: UBERON_8600006
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0007100
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0000746
subclass of: Restriction
  on property: RO_0002473
  some values from: CL_0000746
disjoint with: skeletal muscle tissue
IAO_0000115: Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified].
IAO_0000116: check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit
has alternative id: UBERON:0007096
has db xref: AAO:0010245
has db xref: AEO:0000142
has db xref: BILA:0000134
has db xref: BTO:0000199
has db xref: CALOHA:TS-0440
has db xref: EHDAA2:0003142
has db xref: EMAPA:32688
has db xref: FMA:14068
has db xref: TAO:0005280
has db xref: Wikipedia:Cardiac_muscle
has db xref: ZFA:0005280
has db xref: galen:CardiacMuscle
has db xref: galen:CardiacMuscleTissue
has db xref: ncithesaurus:Heart_Muscle
has exact synonym: cardiac muscle
has exact synonym: cardiac muscle muscle tissue
has exact synonym: cardiac muscle textus muscularis
has exact synonym: heart muscle muscle tissue
has exact synonym: heart muscle textus muscularis
has exact synonym: heart myocardium muscle tissue
has exact synonym: heart myocardium textus muscularis
has exact synonym: muscle of heart muscle tissue
has exact synonym: muscle of heart textus muscularis
has exact synonym: muscle tissue of cardiac muscle
has exact synonym: muscle tissue of heart muscle
has exact synonym: muscle tissue of heart myocardium
has exact synonym: muscle tissue of muscle of heart
has exact synonym: muscle tissue of myocardium
has exact synonym: myocardium muscle tissue
has exact synonym: myocardium textus muscularis
has exact synonym: textus muscularis of cardiac muscle
has exact synonym: textus muscularis of heart muscle
has exact synonym: textus muscularis of heart myocardium
has exact synonym: textus muscularis of muscle of heart
has exact synonym: textus muscularis of myocardium
has OBO namespace: uberon
has related synonym: cardiac musculature
id: UBERON:0001133
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: cardiac muscle tissue
annotated property: IAO_0000115
annotated target: Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified].
has db xref: ZFA:0005280

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: cardiac muscle muscle tissue
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: cardiac muscle textus muscularis
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: heart muscle muscle tissue
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: heart muscle textus muscularis
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: heart myocardium muscle tissue
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: heart myocardium textus muscularis
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: muscle of heart muscle tissue
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: muscle of heart textus muscularis
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: muscle tissue of cardiac muscle
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: muscle tissue of heart muscle
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: muscle tissue of heart myocardium
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: muscle tissue of muscle of heart
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: muscle tissue of myocardium
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: myocardium muscle tissue
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: myocardium textus muscularis
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: textus muscularis of cardiac muscle
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: textus muscularis of heart muscle
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: textus muscularis of heart myocardium
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: textus muscularis of muscle of heart
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasExactSynonym
annotated target: textus muscularis of myocardium
has db xref: OBOL:automatic

Axiom
annotated source: cardiac muscle tissue
annotated property: hasRelatedSynonym
annotated target: cardiac musculature
has db xref: BILA:0000134

skeletal muscle tissue
type: Class
equivalent class: Class
  intersection of: UBERON_0002385
  intersection of: Restriction
    on property: RO_0002473
    some values from: CL_0008002
subclass of: UBERON_0002036
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0014892
subclass of: Restriction
  on property: RO_0002202
  some values from: UBERON_0003082
subclass of: Restriction
  on property: RO_0002473
  some values from: CL_0008002
IAO_0000115: Muscle tissue that consists primarily of skeletal muscle fibers.
IAO_0000116: TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle.
UBPROP_0000001: Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]
UBPROP_0000001: Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]
UBPROP_0000003: This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]
has broad synonym: skeletal muscle
has db xref: EMAPA:32716
has db xref: FMA:14069
has db xref: MA:0002439
has db xref: NCIT:C13050
has db xref: SCTID:426215008
has db xref: UMLS:C0242692
has db xref: Wikipedia:Skeletal_striated_muscle
has OBO namespace: uberon
has related synonym: skeletal muscle system
has related synonym: somatic muscle
id: UBERON:0001134
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: skeletal muscle tissue
annotated property: IAO_0000115
annotated target: Muscle tissue that consists primarily of skeletal muscle fibers.
has db xref: https://github.com/obophenotype/uberon/issues/324

Axiom
annotated source: skeletal muscle tissue
annotated property: UBPROP_0000001
annotated target: Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]
date retrieved: 2012-08-14
external class: TAO:0005277
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: skeletal muscle tissue
annotated property: UBPROP_0000001
annotated target: Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]
external class: FMA:14069
ontology: FMA

Axiom
annotated source: skeletal muscle tissue
annotated property: UBPROP_0000003
annotated target: This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000319
ontology: VHOG
source: PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999)
source: http://bgee.unil.ch/

Axiom
annotated source: skeletal muscle tissue
annotated property: hasDbXref
annotated target: UMLS:C0242692
source: ncithesaurus:Skeletal_Muscle_Tissue

Axiom
annotated source: skeletal muscle tissue
annotated property: hasRelatedSynonym
annotated target: skeletal muscle system
has db xref: BTO:0001103

Axiom
annotated source: skeletal muscle tissue
annotated property: hasRelatedSynonym
annotated target: somatic muscle
has db xref: BTO:0001103

smooth muscle tissue
type: Class
equivalent class: Class
  intersection of: UBERON_0002385
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0000192
subclass of: UBERON_0002385
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0000192
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0071953
subclass of: Restriction
  on property: RO_0002473
  some values from: CL_0000192
disjoint with: UBERON_0002036
IAO_0000115: Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO].
UBPROP_0000001: A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]
UBPROP_0000001: Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]
UBPROP_0000003: (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]
UBPROP_0000013: GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells.
has db xref: AAO:0010244
has db xref: AEO:0000141
has db xref: BTO:0001260
has db xref: CALOHA:TS-0943
has db xref: EFO:0000889
has db xref: EHDAA2:0003141
has db xref: EMAPA:32717
has db xref: EV:0100378
has db xref: FMA:14070
has db xref: GAID:167
has db xref: MA:0000166
has db xref: MAT:0000303
has db xref: MESH:D009130
has db xref: MIAA:0000303
has db xref: NCIT:C12437
has db xref: TAO:0005274
has db xref: UMLS:C1267092
has db xref: VHOG:0001246
has db xref: WBbt:0005781
has db xref: Wikipedia:Smooth_muscle_tissue
has db xref: XAO:0000175
has db xref: ZFA:0005274
has db xref: galen:SmoothMuscle
has db xref: galen:SmoothMuscleTissue
has exact synonym: involuntary muscle
has exact synonym: non-striated muscle
has exact synonym: smooth muscle
has exact synonym: textus muscularis nonstriatus
has narrow synonym: visceral muscle
has narrow synonym: visceral muscle tissue
has OBO namespace: uberon
has related synonym: textus muscularis levis; textus muscularis nonstriatus
id: UBERON:0001135
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: smooth muscle tissue
annotated property: IAO_0000115
annotated target: Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO].
has db xref: GO:0006939
has db xref: Wikipedia:Smooth_muscle_tissue

Axiom
annotated source: smooth muscle tissue
annotated property: UBPROP_0000001
annotated target: A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]
date retrieved: 2012-08-14
external class: TAO:0005274
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: smooth muscle tissue
annotated property: UBPROP_0000001
annotated target: Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010244
ontology: AAO
source: AAO:CAM

Axiom
annotated source: smooth muscle tissue
annotated property: UBPROP_0000003
annotated target: (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001246
ontology: VHOG
source: DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011)
source: http://bgee.unil.ch/

Axiom
annotated source: smooth muscle tissue
annotated property: hasDbXref
annotated target: UMLS:C1267092
source: ncithesaurus:Smooth_Muscle_Tissue

Axiom
annotated source: smooth muscle tissue
annotated property: hasExactSynonym
annotated target: textus muscularis nonstriatus
has db xref: FMA:14070
has db xref: FMA:TA
has synonym type: OMO_0003011

Axiom
annotated source: smooth muscle tissue
annotated property: hasNarrowSynonym
annotated target: visceral muscle
has synonym type: SENSU

Axiom
annotated source: smooth muscle tissue
annotated property: hasNarrowSynonym
annotated target: visceral muscle tissue
has synonym type: SENSU

Axiom
annotated source: smooth muscle tissue
annotated property: hasRelatedSynonym
annotated target: textus muscularis levis; textus muscularis nonstriatus
has db xref: Wikipedia:Smooth_muscle_tissue
has synonym type: OMO_0003011

mesothelium
type: Class
equivalent class: Class
  intersection of: simple squamous epithelium
  intersection of: Restriction
    on property: BFO_0000050
    some values from: serous membrane
  intersection of: Restriction
    on property: RO_0002202
    some values from: mesoderm
subclass of: simple squamous epithelium
subclass of: UBERON_0012275
subclass of: Restriction
  on property: BFO_0000050
  some values from: serous membrane
IAO_0000115: Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri).
has db xref: AEO:0000111
has db xref: BTO:0002422
has db xref: CALOHA:TS-1183
has db xref: EHDAA2_RETIRED:0003111
has db xref: EHDAA:2331
has db xref: EHDAA:2349
has db xref: EHDAA:295
has db xref: EHDAA:6073
has db xref: EHDAA:640
has db xref: EHDAA:646
has db xref: EMAPA:32856
has db xref: FMA:14074
has db xref: MA:0000565
has db xref: NCIT:C33105
has db xref: SCTID:361918002
has db xref: UMLS:C0086610
has db xref: Wikipedia:Mesothelium
has OBO namespace: uberon
id: UBERON:0001136
in subset: uberon slim

Axiom
annotated source: mesothelium
annotated property: subClassOf
annotated target: Restriction
source: FMA

Axiom
annotated source: mesothelium
annotated property: IAO_0000115
annotated target: Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri).
has db xref: FMA:14074
has db xref: Wikipedia:Mesothelium

Axiom
annotated source: mesothelium
annotated property: hasDbXref
annotated target: UMLS:C0086610
source: ncithesaurus:Mesothelium

dorsum
type: Class
subclass of: organism subdivision
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_33213
IAO_0000115: A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column..
UBPROP_0000007: dorsal
UBPROP_0000008: In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body
has db xref: BTO:0001713
has db xref: CALOHA:TS-2223
has db xref: EFO:0001405
has db xref: FMA:14181
has db xref: GAID:30
has db xref: MESH:D001415
has db xref: NCIT:C13062
has db xref: SCTID:123961009
has db xref: UMLS:C0004600
has db xref: Wikipedia:Dorsum_(anatomy)
has db xref: galen:Back
has exact synonym: back
has exact synonym: back of body proper
has exact synonym: dorsal part of organism
has OBO namespace: uberon
id: UBERON:0001137
in subset: efo slim
in subset: uberon slim

Axiom
annotated source: dorsum
annotated property: IAO_0000115
annotated target: A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column..
has db xref: BSPO:0000063
has db xref: UBERONREF:0000006
has db xref: Wikipedia:Dorsum_(anatomy)

Axiom
annotated source: dorsum
annotated property: hasDbXref
annotated target: UMLS:C0004600
source: ncithesaurus:Back

Axiom
annotated source: dorsum
annotated property: hasExactSynonym
annotated target: back
has db xref: FMA:14181

Axiom
annotated source: dorsum
annotated property: hasExactSynonym
annotated target: back of body proper
has db xref: FMA:14181

superior mesenteric vein
type: Class
equivalent class: Class
  intersection of: UBERON_0005617
  intersection of: Restriction
    on property: RO_0020102
    some values from: UBERON_0002108
subclass of: UBERON_0005617
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0005806
subclass of: Restriction
  on property: RO_0002170
  some values from: UBERON_0001639
subclass of: Restriction
  on property: RO_0020102
  some values from: UBERON_0002108
IAO_0000115: In anatomy, the superior mesenteric vein (SMV) is a blood vessel that drains blood from the small intestine. At its termination behind the neck of the pancreas, the SMV combines with the splenic vein to form the hepatic portal vein. The SMV lies to the right of the similarly named artery, the superior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted].
RO_0002175: NCBITaxon 9606
has db xref: BTO:0002783
has db xref: EHDAA2:0001951
has db xref: EHDAA:5414
has db xref: EMAPA:18643
has db xref: FMA:14332
has db xref: MA:0002179
has db xref: NCIT:C33687
has db xref: SCTID:278031001
has db xref: UMLS:C0226742
has db xref: VHOG:0000552
has db xref: Wikipedia:Superior_mesenteric_vein
has OBO namespace: uberon
has related synonym: upper mesenteric vein
has related synonym: vena mesenterica superior
id: UBERON:0001138
in subset: human reference atlas
in subset: uberon slim

Axiom
annotated source: superior mesenteric vein
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia:Vitelline_vein

Axiom
annotated source: superior mesenteric vein
annotated property: IAO_0000115
annotated target: In anatomy, the superior mesenteric vein (SMV) is a blood vessel that drains blood from the small intestine. At its termination behind the neck of the pancreas, the SMV combines with the splenic vein to form the hepatic portal vein. The SMV lies to the right of the similarly named artery, the superior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted].
has db xref: Wikipedia:Superior_mesenteric_vein

Axiom
annotated source: superior mesenteric vein
annotated property: hasDbXref
annotated target: UMLS:C0226742
source: ncithesaurus:Superior_Mesenteric_Vein

Axiom
annotated source: superior mesenteric vein
annotated property: hasRelatedSynonym
annotated target: upper mesenteric vein
has db xref: BTO:0002783

Axiom
annotated source: superior mesenteric vein
annotated property: hasRelatedSynonym
annotated target: vena mesenterica superior
has db xref: Wikipedia:Superior_mesenteric_vein
has synonym type: OMO_0003011

common iliac vein
type: Class
subclass of: UBERON_0005610
subclass of: UBERON_0015212
subclass of: Restriction
IAO_0000115: A vein that drains the pelvis and lower limbs into the inferior vena cava.
RO_0002175: NCBITaxon 9606
UBPROP_0000008: In human anatomy, the common iliac veins are formed by the external iliac veins and internal iliac veins and together, in the abdomen at the level of the fifth lumbar vertebrae, form the inferior vena cava. They drain blood from the pelvis and lower limbs. Both common iliac veins are accompanied along their course by common iliac arteries.
has db xref: EMAPA:17874
has db xref: FMA:14333
has db xref: MA:0002143
has db xref: NCIT:C32359
has db xref: SCTID:181398004
has db xref: UMLS:C0226758
has db xref: Wikipedia:Common_iliac_vein
has db xref: galen:CommonIliacVein
has exact synonym: common iliac venous tree
has OBO namespace: uberon
has related synonym: vena iliaca communis
id: UBERON:0001139
in subset: human reference atlas
in subset: uberon slim

Axiom
annotated source: common iliac vein
annotated property: subClassOf
annotated target: UBERON_0005610
source: MA

Axiom
annotated source: common iliac vein
annotated property: subClassOf
annotated target: Restriction
source: FMA-abduced-lr

Axiom
annotated source: common iliac vein
annotated property: IAO_0000115
annotated target: A vein that drains the pelvis and lower limbs into the inferior vena cava.
has db xref: MURDOCH:403
has db xref: Wikipedia:Common_iliac_vein

Axiom
annotated source: common iliac vein
annotated property: UBPROP_0000008
annotated target: In human anatomy, the common iliac veins are formed by the external iliac veins and internal iliac veins and together, in the abdomen at the level of the fifth lumbar vertebrae, form the inferior vena cava. They drain blood from the pelvis and lower limbs. Both common iliac veins are accompanied along their course by common iliac arteries.
source: Wikipedia:Common_iliac_vein

Axiom
annotated source: common iliac vein
annotated property: hasDbXref
annotated target: UMLS:C0226758
source: ncithesaurus:Common_Iliac_Vein

Axiom
annotated source: common iliac vein
annotated property: hasRelatedSynonym
annotated target: vena iliaca communis
has db xref: Wikipedia:Common_iliac_vein
has synonym type: OMO_0003011

renal vein
type: Class
equivalent class: Class
  intersection of: UBERON_0001638
  intersection of: Restriction
    on property: RO_0020102
    some values from: UBERON_0002113
subclass of: UBERON_0001638
subclass of: Restriction
  on property: RO_0002376
  some values from: inferior vena cava
subclass of: Restriction
  on property: RO_0020102
  some values from: UBERON_0002113
IAO_0000115: Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein].
UBPROP_0000012: in EHDAA2, the renal vein is part of the kidney
has db xref: BTO:0002681
has db xref: EHDAA2:0001602
has db xref: EHDAA:8722
has db xref: EMAPA:28376
has db xref: FMA:14334
has db xref: GAID:544
has db xref: MA:0002210
has db xref: MESH:D012082
has db xref: NCIT:C33462
has db xref: SCTID:116358006
has db xref: UMLS:C0035092
has db xref: Wikipedia:Renal_vein
has db xref: galen:RenalVein
has exact synonym: kidney vein
has exact synonym: renal venous tree
has exact synonym: vein of kidney
has OBO namespace: uberon
has related synonym: venae renales
id: UBERON:0001140
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: renal vein
annotated property: IAO_0000115
annotated target: Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava.
has db xref: ISBN:0-683-40008-8
has db xref: MGI:csmith
has db xref: MP:0011323

Axiom
annotated source: renal vein
annotated property: UBPROP_0000001
annotated target: The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein].
source: Wikipedia:Renal_vein

Axiom
annotated source: renal vein
annotated property: UBPROP_0000012
annotated target: in EHDAA2, the renal vein is part of the kidney
external ontology: EHDAA2

Axiom
annotated source: renal vein
annotated property: hasDbXref
annotated target: UMLS:C0035092
source: ncithesaurus:Renal_Vein

Axiom
annotated source: renal vein
annotated property: hasExactSynonym
annotated target: kidney vein
has db xref: OBOL:automatic

Axiom
annotated source: renal vein
annotated property: hasExactSynonym
annotated target: vein of kidney
has db xref: OBOL:automatic

Axiom
annotated source: renal vein
annotated property: hasRelatedSynonym
annotated target: venae renales
has db xref: Wikipedia:Renal_vein
has synonym type: OMO_0003011

right renal vein
type: Class
equivalent class: Class
  intersection of: renal vein
  intersection of: Restriction
    on property: RO_0020102
    some values from: UBERON_0004539
subclass of: renal vein
subclass of: Restriction
  on property: RO_0020102
  some values from: UBERON_0004539
IAO_0000115: A renal vein that drains the right kidney.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: A vein that drains blood from the right kidney into the inferior vena cava[ncithesaurus].
has db xref: EMAPA:37381
has db xref: FMA:14335
has db xref: MA:0002212
has db xref: NCIT:C52695
has db xref: SCTID:116357001
has db xref: UMLS:C0508000
has OBO namespace: uberon
id: UBERON:0001141
in subset: human reference atlas
in subset: pheno slim

Axiom
annotated source: right renal vein
annotated property: IAO_0000115
annotated target: A renal vein that drains the right kidney.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: right renal vein
annotated property: UBPROP_0000001
annotated target: A vein that drains blood from the right kidney into the inferior vena cava[ncithesaurus].
source: ncithesaurus:Right_Renal_Vein

Axiom
annotated source: right renal vein
annotated property: hasDbXref
annotated target: EMAPA:37381
source: MA:th

Axiom
annotated source: right renal vein
annotated property: hasDbXref
annotated target: UMLS:C0508000
source: ncithesaurus:Right_Renal_Vein

left renal vein
type: Class
equivalent class: Class
  intersection of: renal vein
  intersection of: Restriction
    on property: RO_0020102
    some values from: UBERON_0004538
subclass of: renal vein
subclass of: Restriction
  on property: RO_0020102
  some values from: UBERON_0004538
IAO_0000115: A renal vein that drains the left kidney.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: A vein that drains blood from the left kidney into the inferior vena cava[ncithesaurus].
has db xref: EMAPA:37166
has db xref: FMA:14336
has db xref: MA:0002211
has db xref: NCIT:C52693
has db xref: SCTID:116356005
has db xref: UMLS:C0508001
has OBO namespace: uberon
id: UBERON:0001142
in subset: human reference atlas
in subset: pheno slim

Axiom
annotated source: left renal vein
annotated property: IAO_0000115
annotated target: A renal vein that drains the left kidney.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: left renal vein
annotated property: UBPROP_0000001
annotated target: A vein that drains blood from the left kidney into the inferior vena cava[ncithesaurus].
source: ncithesaurus:Left_Renal_Vein

Axiom
annotated source: left renal vein
annotated property: hasDbXref
annotated target: EMAPA:37166
source: MA:th

Axiom
annotated source: left renal vein
annotated property: hasDbXref
annotated target: UMLS:C0508001
source: ncithesaurus:Left_Renal_Vein

hepatic vein
type: Class
equivalent class: Class
  intersection of: UBERON_0001638
  intersection of: Restriction
    on property: RO_0020102
    some values from: UBERON_0002107
subclass of: UBERON_0013126
subclass of: UBERON_0015796
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0006877
subclass of: Restriction
  on property: RO_0020102
  some values from: UBERON_0002107
disjoint with: UBERON_0001639
IAO_0000115: Vein that carries blood away from the liver[ZFA].
IAO_0000116: todo - add developmental relationships for other taxa
has db xref: AAO:0010216
has db xref: EMAPA:19221
has db xref: FMA:14337
has db xref: GAID:534
has db xref: MA:0003015
has db xref: MESH:D006503
has db xref: NCIT:C32736
has db xref: SCTID:278191001
has db xref: TAO:0000670
has db xref: UMLS:C0019155
has db xref: Wikipedia:Hepatic_vein
has db xref: XAO:0000387
has db xref: ZFA:0000670
has db xref: galen:HepaticVein
has exact synonym: liver vein
has exact synonym: vein of liver
has exact synonym: vena hepatica
has OBO namespace: uberon
has related synonym: hepatic veins
has related synonym: venae hepaticae
id: UBERON:0001143
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: hepatic vein
annotated property: subClassOf
annotated target: Restriction
source: FMA-abduced-lr

Axiom
annotated source: hepatic vein
annotated property: IAO_0000115
annotated target: Vein that carries blood away from the liver[ZFA].
has db xref: Wikipedia:Hepatic_vein
has db xref: ZFA:0000670
has db xref: https://sourceforge.net/tracker/

Axiom
annotated source: hepatic vein
annotated property: hasDbXref
annotated target: UMLS:C0019155
source: ncithesaurus:Hepatic_Vein

Axiom
annotated source: hepatic vein
annotated property: hasExactSynonym
annotated target: liver vein
has db xref: OBOL:automatic

Axiom
annotated source: hepatic vein
annotated property: hasExactSynonym
annotated target: vein of liver
has db xref: OBOL:automatic

Axiom
annotated source: hepatic vein
annotated property: hasExactSynonym
annotated target: vena hepatica
has synonym type: OMO_0003011

Axiom
annotated source: hepatic vein
annotated property: hasRelatedSynonym
annotated target: hepatic veins
has synonym type: OMO_0003004

Axiom
annotated source: hepatic vein
annotated property: hasRelatedSynonym
annotated target: venae hepaticae
has db xref: Wikipedia:Hepatic_vein
has synonym type: OMO_0003011

testicular vein
type: Class
equivalent class: Class
  intersection of: UBERON_0001638
  intersection of: Restriction
    on property: RO_0020102
    some values from: testis
subclass of: UBERON_0001638
subclass of: UBERON_0015212
subclass of: Restriction
  on property: BSPO_0000126
  some values from: multicellular organism
subclass of: Restriction
  on property: RO_0002170
  some values from: inferior vena cava
subclass of: Restriction
  on property: RO_0002170
  some values from: UBERON_0001330
subclass of: Restriction
  on property: RO_0020102
  some values from: testis
subclass of: Restriction
  on property: sexually homologous to
  some values from: ovarian vein
IAO_0000115: A vein that carries deoxygenated blood from a single male gonad. It is the male equivalent of the ovarian vein, and is the venous counterpart of the testicular artery. It is a paired vein, with one supplying each testis.
IAO_0000116: TODO - check testicular vs spermatic vein (MA:0002218)
UBPROP_0000008: In humans, the right testicular vein generally joins the inferior vena cava; the left testicular vein, unlike the right, often joins the left renal vein instead of the inferior vena cava. The veins emerge from the back of the testis, and receive tributaries from the epididymis; they unite and form a convoluted plexus, called the pampiniform plexus, which constitutes the greater mass of the spermatic cord; the vessels composing this plexus are very numerous, and ascend along the cord, in front of the ductus deferens. Below the subcutaneous inguinal ring, they unite to form three or four veins, which pass along the inguinal canal, and, entering the abdomen through the abdominal inguinal ring, coalesce to form two veins, which ascend on the Psoas major, behind the peritoneum, lying one on either side of the internal spermatic artery. These unite to form a single vein, which opens, on the right side, into the inferior vena cava (at an acute angle), on the left side into the left renal vein (at a right angle). The spermatic veins are provided with valves. The left spermatic vein passes behind the iliac colon and is thus exposed to pressure from the contents of that part of the bowel
has db xref: BTO:0002678
has db xref: EMAPA:18647
has db xref: FMA:14344
has db xref: MA:0002218
has db xref: MA:0002234
has db xref: NCIT:C53050
has db xref: SCTID:264496006
has db xref: UMLS:C0226718
has db xref: Wikipedia:Testicular_vein
has exact synonym: male gonadal vein
has exact synonym: spermatic vein
has exact synonym: testicle vein
has exact synonym: testicular venous tree
has exact synonym: vein of testicle
has OBO namespace: uberon
has related synonym: vena tesicularis
has related synonym: vena testicularis dextra
has related synonym: vena testicularis sinistra
has related synonym: venae spermaticae
id: UBERON:0001144
in subset: uberon slim

Axiom
annotated source: testicular vein
annotated property: IAO_0000115
annotated target: A vein that carries deoxygenated blood from a single male gonad. It is the male equivalent of the ovarian vein, and is the venous counterpart of the testicular artery. It is a paired vein, with one supplying each testis.
has db xref: Wikipedia:Testicular_vein
has db xref: http://orcid.org/0000-0002-6601-2165
has db xref: https://sourceforge.net/tracker/

Axiom
annotated source: testicular vein
annotated property: hasDbXref
annotated target: UMLS:C0226718
source: ncithesaurus:Spermatic_Vein

Axiom
annotated source: testicular vein
annotated property: hasExactSynonym
annotated target: male gonadal vein
has db xref: Wikipedia:Testicular_vein

Axiom
annotated source: testicular vein
annotated property: hasExactSynonym
annotated target: spermatic vein
has db xref: Wikipedia:Testicular_vein

Axiom
annotated source: testicular vein
annotated property: hasExactSynonym
annotated target: testicle vein
has db xref: OBOL:automatic

Axiom
annotated source: testicular vein
annotated property: hasExactSynonym
annotated target: testicular venous tree
has db xref: Wikipedia:Testicular_vein

Axiom
annotated source: testicular vein
annotated property: hasExactSynonym
annotated target: vein of testicle
has db xref: OBOL:automatic

Axiom
annotated source: testicular vein
annotated property: hasRelatedSynonym
annotated target: vena tesicularis
has db xref: BTO:0002678

Axiom
annotated source: testicular vein
annotated property: hasRelatedSynonym
annotated target: vena testicularis dextra
has db xref: Wikipedia:Testicular_vein
has synonym type: OMO_0003011

Axiom
annotated source: testicular vein
annotated property: hasRelatedSynonym
annotated target: vena testicularis sinistra
has db xref: Wikipedia:Testicular_vein
has synonym type: OMO_0003011

Axiom
annotated source: testicular vein
annotated property: hasRelatedSynonym
annotated target: venae spermaticae
has db xref: Wikipedia:Testicular_vein
has synonym type: OMO_0003011

ovarian vein
type: Class
equivalent class: Class
  intersection of: UBERON_0001638
  intersection of: Restriction
    on property: RO_0020102
    some values from: ovary
subclass of: UBERON_0001638
subclass of: UBERON_0015212
subclass of: Restriction
  on property: BSPO_0000126
  some values from: multicellular organism
subclass of: Restriction
  on property: RO_0020102
  some values from: ovary
IAO_0000115: A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries.
has db xref: EMAPA:18644
has db xref: FMA:14346
has db xref: MA:0002186
has db xref: NCIT:C53058
has db xref: SCTID:278193003
has db xref: UMLS:C0226720
has db xref: Wikipedia:Ovarian_vein
has exact synonym: female reproductive system gonad vein
has exact synonym: female reproductive system gonada vein
has exact synonym: gonad of female reproductive system vein
has exact synonym: gonada of female reproductive system vein
has exact synonym: ovary vein
has exact synonym: vein of female reproductive system gonad
has exact synonym: vein of female reproductive system gonada
has exact synonym: vein of gonad of female reproductive system
has exact synonym: vein of gonada of female reproductive system
has exact synonym: vein of ovary
has OBO namespace: uberon
has related synonym: vena ovarica dextra
has related synonym: vena ovarica sinistra
id: UBERON:0001145
in subset: uberon slim

Axiom
annotated source: ovarian vein
annotated property: IAO_0000115
annotated target: A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries.
has db xref: Wikipedia:Ovarian_vein

Axiom
annotated source: ovarian vein
annotated property: hasDbXref
annotated target: UMLS:C0226720
source: ncithesaurus:Ovarian_Vein

Axiom
annotated source: ovarian vein
annotated property: hasExactSynonym
annotated target: female reproductive system gonad vein
has db xref: OBOL:automatic

Axiom
annotated source: ovarian vein
annotated property: hasExactSynonym
annotated target: female reproductive system gonada vein
has db xref: OBOL:automatic

Axiom
annotated source: ovarian vein
annotated property: hasExactSynonym
annotated target: gonad of female reproductive system vein
has db xref: OBOL:automatic

Axiom
annotated source: ovarian vein
annotated property: hasExactSynonym
annotated target: gonada of female reproductive system vein
has db xref: OBOL:automatic

Axiom
annotated source: ovarian vein
annotated property: hasExactSynonym
annotated target: ovary vein
has db xref: OBOL:automatic

Axiom
annotated source: ovarian vein
annotated property: hasExactSynonym
annotated target: vein of female reproductive system gonad
has db xref: OBOL:automatic

Axiom
annotated source: ovarian vein
annotated property: hasExactSynonym
annotated target: vein of female reproductive system gonada
has db xref: OBOL:automatic

Axiom
annotated source: ovarian vein
annotated property: hasExactSynonym
annotated target: vein of gonad of female reproductive system
has db xref: OBOL:automatic

Axiom
annotated source: ovarian vein
annotated property: hasExactSynonym
annotated target: vein of gonada of female reproductive system
has db xref: OBOL:automatic

Axiom
annotated source: ovarian vein
annotated property: hasExactSynonym
annotated target: vein of ovary
has db xref: OBOL:automatic

Axiom
annotated source: ovarian vein
annotated property: hasRelatedSynonym
annotated target: vena ovarica dextra
has db xref: Wikipedia:Ovarian_vein
has synonym type: OMO_0003011

Axiom
annotated source: ovarian vein
annotated property: hasRelatedSynonym
annotated target: vena ovarica sinistra
has db xref: Wikipedia:Ovarian_vein
has synonym type: OMO_0003011

suprarenal vein
type: Class
equivalent class: Class
  intersection of: UBERON_0001638
  intersection of: Restriction
    on property: RO_0020102
    some values from: UBERON_0002369
subclass of: UBERON_0001638
subclass of: Restriction
  on property: RO_0020102
  some values from: UBERON_0002369
IAO_0000115: A vein that drains the adrenal gland.
has db xref: EHDAA2:0001966
has db xref: EHDAA:8731
has db xref: FMA:14348
has db xref: MA:0002081
has db xref: MA:0002229
has db xref: NCIT:C53129
has db xref: SCTID:278194009
has db xref: UMLS:C0226717
has db xref: Wikipedia:Suprarenal_vein
has OBO namespace: uberon
has related synonym: adrenal vein
id: UBERON:0001146
in subset: uberon slim

Axiom
annotated source: suprarenal vein
annotated property: IAO_0000115
annotated target: A vein that drains the adrenal gland.
has db xref: http://orcid.org/0000-0002-6601-2165
has db xref: https://github.com/obophenotype/mouse-anatomy-ontology/issues/110

Axiom
annotated source: suprarenal vein
annotated property: hasDbXref
annotated target: UMLS:C0226717
source: ncithesaurus:Suprarenal_Vein

Axiom
annotated source: suprarenal vein
annotated property: hasRelatedSynonym
annotated target: adrenal vein
has db xref: MA:0002081

cystic duct
type: Class
equivalent class: Class
  intersection of: duct
  intersection of: Restriction
    on property: RO_0002150
    some values from: UBERON_0001174
  intersection of: Restriction
    on property: RO_0002150
    some values from: UBERON_0002110
subclass of: UBERON_0003703
subclass of: Restriction
  on property: RO_0002150
  some values from: UBERON_0001174
subclass of: Restriction
  on property: RO_0002150
  some values from: UBERON_0002110
subclass of: Restriction
  on property: channels into
  some values from: UBERON_0001174
disjoint with: UBERON_0005171
IAO_0000115: The tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct.
UBPROP_0000001: Duct that connects the gall bladder and the common bile duct.[TAO]
UBPROP_0000001: The duct of the gallbladder which joins the common hepatic duct, thus forming the common biliary duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
has db xref: EHDAA2:0000333
has db xref: EHDAA:3045
has db xref: EMAPA:16841
has db xref: FMA:14539
has db xref: GAID:290
has db xref: MA:0000355
has db xref: MESH:D003549
has db xref: NCIT:C32421
has db xref: SCTID:245398005
has db xref: TAO:0005166
has db xref: UMLS:C0010672
has db xref: VHOG:0000213
has db xref: Wikipedia:Cystic_duct
has db xref: ZFA:0005166
has db xref: galen:CysticDuct
has OBO namespace: uberon
has related synonym: ductus cysticus
id: UBERON:0001152
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: cystic duct
annotated property: subClassOf
annotated target: UBERON_0003703
source: FMA

Axiom
annotated source: cystic duct
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: cystic duct
annotated property: IAO_0000115
annotated target: The tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct.
has db xref: ISBN:0-683-40008-8
has db xref: MP:0009493

Axiom
annotated source: cystic duct
annotated property: UBPROP_0000001
annotated target: Duct that connects the gall bladder and the common bile duct.[TAO]
date retrieved: 2012-08-14
external class: TAO:0005166
ontology: TAO
source: ZFIN:Curator

Axiom
annotated source: cystic duct
annotated property: UBPROP_0000001
annotated target: The duct of the gallbladder which joins the common hepatic duct, thus forming the common biliary duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000213
ontology: VHOG
source: http://bgee.unil.ch/

Axiom
annotated source: cystic duct
annotated property: hasDbXref
annotated target: UMLS:C0010672
source: ncithesaurus:Cystic_Duct

Axiom
annotated source: cystic duct
annotated property: hasRelatedSynonym
annotated target: ductus cysticus
has db xref: Wikipedia:Cystic_duct
has synonym type: OMO_0003011

caecum
type: Class
subclass of: UBERON_0009854
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7776
subclass of: Restriction
  on property: RO_0002433
  some values from: large intestine
IAO_0000115: A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.
RO_0002161: NCBITaxon_32443
RO_0002175: NCBITaxon 9606
UBPROP_0000007: caecal
UBPROP_0000008: A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates.
has db xref: BTO:0000166
has db xref: CALOHA:TS-0122
has db xref: EFO:0000850
has db xref: EHDAA2:0000206
has db xref: EHDAA:3913
has db xref: EMAPA:35197
has db xref: EV:0100397
has db xref: FMA:14541
has db xref: GAID:307
has db xref: MA:0000334
has db xref: MESH:D002432
has db xref: MIAA:0000288
has db xref: NCIT:C12381
has db xref: SCTID:181256004
has db xref: UMLS:C0007531
has db xref: VHOG:0001559
has db xref: Wikipedia:Cecum
has db xref: galen:Cecum
has exact synonym: caecum
has exact synonym: cecum
has exact synonym: intestinum crassum caecum
has narrow synonym: caeca
has narrow synonym: ceca
has OBO namespace: uberon
has related synonym: blind intestine
has related synonym: blindgut
has related synonym: intestinum caecum
has related synonym: intestinum crassum cecum
id: UBERON:0001153
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
comment: Taxon notes: in some herbivorous lizards, a cecum is present between small and large intestines[Kardong]

Axiom
annotated source: caecum
annotated property: subClassOf
annotated target: Restriction
source: EHDAA2

Axiom
annotated source: caecum
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: caecum
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: caecum
annotated property: IAO_0000115
annotated target: A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.
has db xref: Wikipedia:Cecum

Axiom
annotated source: caecum
annotated property: RO_0002161
annotated target: NCBITaxon_32443
source: Wikipedia

Axiom
annotated source: caecum
annotated property: UBPROP_0000008
annotated target: A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates.
source: WP

Axiom
annotated source: caecum
annotated property: hasDbXref
annotated target: UMLS:C0007531
source: ncithesaurus:Cecum

Axiom
annotated source: caecum
annotated property: hasExactSynonym
annotated target: caecum
has db xref: VHOG:0001559

Axiom
annotated source: caecum
annotated property: hasExactSynonym
annotated target: cecum
has db xref: FMA:14541

Axiom
annotated source: caecum
annotated property: hasNarrowSynonym
annotated target: caeca
has db xref: NCBITaxon:8782
has synonym type: OMO_0003004

Axiom
annotated source: caecum
annotated property: hasNarrowSynonym
annotated target: ceca
has db xref: NCBITaxon:8782
has synonym type: OMO_0003004

Axiom
annotated source: caecum
annotated property: hasRelatedSynonym
annotated target: blind intestine
has db xref: BTO:0000166

Axiom
annotated source: caecum
annotated property: hasRelatedSynonym
annotated target: blindgut
has db xref: BTO:0000166

Axiom
annotated source: caecum
annotated property: hasRelatedSynonym
annotated target: intestinum caecum
has db xref: BTO:0000166

Axiom
annotated source: caecum
annotated property: hasRelatedSynonym
annotated target: intestinum crassum cecum
has db xref: BTO:0000166

colon
type: Class
subclass of: UBERON_0004921
subclass of: Restriction
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7742
subclass of: Restriction
  on property: RO_0002433
  some values from: large intestine
IAO_0000115: A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal.
IAO_0000116: Some references do not consider the caecum to be part of the colon.
IAO_0000116: TODO - abstract this such that it legitimately covers all vertebrates
UBPROP_0000001: The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]
UBPROP_0000001: The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]
UBPROP_0000003: Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
UBPROP_0000007: colonic
UBPROP_0000008: In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]
UBPROP_0000008: In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN]
UBPROP_0000009: it extracts water and salt from solid wastes before they are eliminated from the body[WP]
has db xref: AAO:0010400
has db xref: BTO:0000269
has db xref: CALOHA:TS-0158
has db xref: EFO:0000361
has db xref: EMAPA:18939
has db xref: EV:0100079
has db xref: FMA:14543
has db xref: GAID:309
has db xref: MA:0000335
has db xref: MAP:0000001
has db xref: MAT:0000526
has db xref: MESH:D003106
has db xref: NCIT:C12382
has db xref: SCTID:302508007
has db xref: TAO:0000706
has db xref: UMLS:C0009368
has db xref: VHOG:0000648
has db xref: Wikipedia:Colon_(anatomy)
has db xref: XAO:0000243
has db xref: ZFA:0000706
has db xref: galen:Colon
has exact synonym: large bowel
has narrow synonym: posterior intestine
has OBO namespace: uberon
has related synonym: hindgut
id: UBERON:0001155
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: colon
annotated property: subClassOf
annotated target: UBERON_0004921
order: 3
source: cjm

Axiom
annotated source: colon
annotated property: subClassOf
annotated target: Restriction
source: FMA

Axiom
annotated source: colon
annotated property: IAO_0000115
annotated target: A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal.
has db xref: Wikipedia:Colon_(anatomy)
has db xref: ZFIN:curator
has db xref: http://orcid.org/0000-0002-2825-0621
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: colon
annotated property: IAO_0000116
annotated target: Some references do not consider the caecum to be part of the colon.
has db xref: http://orcid.org/0000-0002-1572-1316

Axiom
annotated source: colon
annotated property: UBPROP_0000001
annotated target: The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010400
ontology: AAO
source: UBERON:0001155

Axiom
annotated source: colon
annotated property: UBPROP_0000001
annotated target: The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000706
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: colon
annotated property: UBPROP_0000003
annotated target: Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000648
ontology: VHOG
source: ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
source: http://bgee.unil.ch/

Axiom
annotated source: colon
annotated property: hasDbXref
annotated target: UMLS:C0009368
source: ncithesaurus:Colon

ascending colon
type: Class
subclass of: proximal-distal subdivision of colon
subclass of: Restriction
  on property: RO_0002150
  some values from: transverse colon
IAO_0000115: Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified].
RO_0002175: NCBITaxon 9606
UBPROP_0000012: in MA, this is a subclass of colon
has db xref: BTO:0000270
has db xref: CALOHA:TS-0057
has db xref: EFO:0000843
has db xref: EMAPA:35151
has db xref: FMA:14545
has db xref: MA:0001541
has db xref: MAT:0000311
has db xref: MESH:D044682
has db xref: MIAA:0000311
has db xref: NCIT:C12265
has db xref: SCTID:362162009
has db xref: UMLS:C0227375
has db xref: Wikipedia:Ascending_colon
has db xref: galen:AscendingColon
has exact synonym: colon ascendens
has OBO namespace: uberon
has related synonym: spiral colon
id: UBERON:0001156
in subset: efo slim
in subset: human reference atlas
in subset: uberon slim

Axiom
annotated source: ascending colon
annotated property: subClassOf
annotated target: proximal-distal subdivision of colon
source: FMA

Axiom
annotated source: ascending colon
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: ascending colon
annotated property: IAO_0000115
annotated target: Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified].
has db xref: FMA:14545
has db xref: Wikipedia:Ascending_colon

Axiom
annotated source: ascending colon
annotated property: UBPROP_0000012
annotated target: in MA, this is a subclass of colon
external ontology: MA

Axiom
annotated source: ascending colon
annotated property: hasDbXref
annotated target: MESH:D044682
author id: https://orcid.org/0000-0001-9439-5346
mapping justification: ManualMappingCuration
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: ascending colon
annotated property: hasDbXref
annotated target: UMLS:C0227375
source: ncithesaurus:Ascending_Colon

Axiom
annotated source: ascending colon
annotated property: hasExactSynonym
annotated target: colon ascendens
has db xref: Wikipedia:Ascending_colon
has synonym type: OMO_0003011

Axiom
annotated source: ascending colon
annotated property: hasRelatedSynonym
annotated target: spiral colon
has db xref: Wikipedia:Spiral_colon
has synonym type: SENSU

transverse colon
type: Class
subclass of: proximal-distal subdivision of colon
subclass of: Restriction
  on property: RO_0002150
  some values from: descending colon
IAO_0000115: The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon[BTO,modified].
RO_0002175: NCBITaxon 9606
has db xref: BTO:0000272
has db xref: CALOHA:TS-2052
has db xref: EFO:0000844
has db xref: EMAPA:35880
has db xref: FMA:14546
has db xref: MA:0001543
has db xref: MAT:0000312
has db xref: MESH:D044684
has db xref: MIAA:0000312
has db xref: NCIT:C12385
has db xref: SCTID:362163004
has db xref: UMLS:C0227386
has db xref: Wikipedia:Transverse_colon
has db xref: galen:TransverseColon
has exact synonym: colon transversum
has OBO namespace: uberon
id: UBERON:0001157
in subset: efo slim
in subset: human reference atlas
in subset: uberon slim

Axiom
annotated source: transverse colon
annotated property: subClassOf
annotated target: proximal-distal subdivision of colon
source: FMA

Axiom
annotated source: transverse colon
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: transverse colon
annotated property: IAO_0000115
annotated target: The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon[BTO,modified].
has db xref: BTO:0000272
has db xref: Wikipedia:Transverse_colon

Axiom
annotated source: transverse colon
annotated property: hasDbXref
annotated target: MESH:D044684
author id: https://orcid.org/0000-0001-9439-5346
mapping justification: ManualMappingCuration
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: transverse colon
annotated property: hasDbXref
annotated target: UMLS:C0227386
source: ncithesaurus:Transverse_Colon

Axiom
annotated source: transverse colon
annotated property: hasExactSynonym
annotated target: colon transversum
has db xref: Wikipedia:Transverse_colon
has synonym type: OMO_0003011

descending colon
type: Class
subclass of: proximal-distal subdivision of colon
subclass of: Restriction
  on property: RO_0002150
  some values from: sigmoid colon
IAO_0000115: The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon.
RO_0002175: NCBITaxon 9606
has db xref: BTO:0000641
has db xref: CALOHA:TS-2010
has db xref: EFO:0000845
has db xref: EMAPA:35285
has db xref: FMA:14547
has db xref: MA:0001542
has db xref: MAT:0000313
has db xref: MESH:D044683
has db xref: MIAA:0000313
has db xref: NCIT:C12268
has db xref: SCTID:362165006
has db xref: UMLS:C0227389
has db xref: Wikipedia:Descending_colon
has db xref: galen:DescendingColon
has exact synonym: colon descendens
has OBO namespace: uberon
id: UBERON:0001158
in subset: efo slim
in subset: human reference atlas
in subset: uberon slim

Axiom
annotated source: descending colon
annotated property: subClassOf
annotated target: proximal-distal subdivision of colon
source: FMA

Axiom
annotated source: descending colon
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: descending colon
annotated property: IAO_0000115
annotated target: The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon.
has db xref: BTO:0000641

Axiom
annotated source: descending colon
annotated property: hasDbXref
annotated target: MESH:D044683
author id: https://orcid.org/0000-0001-9439-5346
mapping justification: ManualMappingCuration
mapping provider: https://github.com/biopragmatics/biomappings

Axiom
annotated source: descending colon
annotated property: hasDbXref
annotated target: UMLS:C0227389
source: ncithesaurus:Descending_Colon

Axiom
annotated source: descending colon
annotated property: hasExactSynonym
annotated target: colon descendens
has db xref: Wikipedia:Descending_colon
has synonym type: OMO_0003011

sigmoid colon
type: Class
subclass of: proximal-distal subdivision of colon
subclass of: Restriction
  on property: RO_0002150
  some values from: rectum
IAO_0000115: The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity.
RO_0002175: NCBITaxon 9606
has db xref: BTO:0000645
has db xref: CALOHA:TS-2044
has db xref: EFO:0000846
has db xref: EMAPA:36391
has db xref: FMA:14548
has db xref: MAT:0000314
has db xref: MESH:D012809
has db xref: MIAA:0000314
has db xref: NCIT:C12384
has db xref: NCIT:C33550
has db xref: SCTID:362166007
has db xref: UMLS:C0227391
has db xref: UMLS:C0682612
has db xref: Wikipedia:Sigmoid_colon
has db xref: galen:SigmoidColon
has OBO namespace: uberon
has related synonym: colon sigmoideum
has related synonym: pelvic colon
has related synonym: sigmoid colon
has related synonym: sigmoid flexure
id: UBERON:0001159
in subset: efo slim
in subset: human reference atlas
in subset: uberon slim

Axiom
annotated source: sigmoid colon
annotated property: subClassOf
annotated target: proximal-distal subdivision of colon
source: FMA

Axiom
annotated source: sigmoid colon
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: sigmoid colon
annotated property: IAO_0000115
annotated target: The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity.
has db xref: Wikipedia:Sigmoid_colon

Axiom
annotated source: sigmoid colon
annotated property: hasDbXref
annotated target: UMLS:C0227391
source: ncithesaurus:Sigmoid_Colon

Axiom
annotated source: sigmoid colon
annotated property: hasDbXref
annotated target: UMLS:C0682612
source: ncithesaurus:Sigmoid_Flexure

Axiom
annotated source: sigmoid colon
annotated property: hasRelatedSynonym
annotated target: colon sigmoideum
has db xref: Wikipedia:Sigmoid_colon
has synonym type: OMO_0003011

body of stomach
type: Class
subclass of: UBERON_0009870
IAO_0000115: The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO].
IAO_0000116: we include this as zone of stomach even though it is not distinguished by gland type
has db xref: BTO:0000505
has db xref: EMAPA:35810
has db xref: FMA:14560
has db xref: MA:0002559
has db xref: NCIT:C12258
has db xref: SCTID:362140009
has db xref: UMLS:C0227230
has db xref: Wikipedia:Body_of_stomach
has db xref: galen:GastricCorpus
has exact synonym: corpus gastricum (ventriculare)
has exact synonym: gastric body
has exact synonym: stomach body
has OBO namespace: uberon
has related synonym: corpus gastricum
has related synonym: corpus ventriculare
has related synonym: corpus ventriculi
has related synonym: gastric corpus
id: UBERON:0001161
in subset: uberon slim

Axiom
annotated source: body of stomach
annotated property: subClassOf
annotated target: UBERON_0009870
source: FMA

Axiom
annotated source: body of stomach
annotated property: IAO_0000115
annotated target: The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO].
has db xref: GO:0014845
has db xref: Wikipedia:Body_of_stomach

Axiom
annotated source: body of stomach
annotated property: hasDbXref
annotated target: UMLS:C0227230
source: ncithesaurus:Body_of_Stomach

Axiom
annotated source: body of stomach
annotated property: hasRelatedSynonym
annotated target: corpus gastricum
has db xref: BTO:0000505
has db xref: Wikipedia:Body_of_stomach
has synonym type: OMO_0003011

Axiom
annotated source: body of stomach
annotated property: hasRelatedSynonym
annotated target: corpus ventriculare
has db xref: BTO:0000505

Axiom
annotated source: body of stomach
annotated property: hasRelatedSynonym
annotated target: corpus ventriculi
has db xref: BTO:0000505

pyloric antrum
type: Class
subclass of: UBERON_0009870
subclass of: Restriction
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0000502
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0000508
subclass of: Restriction
  on property: RO_0002150
  some values from: body of stomach
subclass of: Restriction
  on property: RO_0002433
  some values from: UBERON_0001166
IAO_0000115: The area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells.
has broad synonym: antrum
has db xref: BTO:0001732
has db xref: EFO:0002555
has db xref: EMAPA:17891
has db xref: FMA:14579
has db xref: GAID:332
has db xref: MA:0001624
has db xref: MESH:D011706
has db xref: NCIT:C12259
has db xref: SCTID:362142001
has db xref: UMLS:C0034193
has db xref: Wikipedia:Pyloric_antrum
has db xref: galen:PyloricAntrum
has exact synonym: antrum of stomach
has exact synonym: stomach pyloric antrum
has OBO namespace: uberon
has related synonym: antrum of Willis
has related synonym: antrum pylori
has related synonym: antrum pyloricum
has related synonym: gastric antrum
has related synonym: stomach antrum
id: UBERON:0001165
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: pyloric antrum
annotated property: subClassOf
annotated target: UBERON_0009870
source: FMA

Axiom
annotated source: pyloric antrum
annotated property: subClassOf
annotated target: Restriction
source: Wikipedia

Axiom
annotated source: pyloric antrum
annotated property: IAO_0000115
annotated target: The area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells.
has db xref: ISBN:0-683-40008-8
has db xref: MP:0010790

Axiom
annotated source: pyloric antrum
annotated property: hasDbXref
annotated target: UMLS:C0034193
source: ncithesaurus:Antrum_Pylori

Axiom
annotated source: pyloric antrum
annotated property: hasRelatedSynonym
annotated target: antrum of Willis
has db xref: BTO:0001732

Axiom
annotated source: pyloric antrum
annotated property: hasRelatedSynonym
annotated target: antrum pylori
has db xref: BTO:0001732

Axiom
annotated source: pyloric antrum
annotated property: hasRelatedSynonym
annotated target: antrum pyloricum
has db xref: BTO:0001732
has db xref: Wikipedia:Pyloric_antrum
has synonym type: OMO_0003011

Axiom
annotated source: pyloric antrum
annotated property: hasRelatedSynonym
annotated target: gastric antrum
has db xref: BTO:0001732