format-version: 1.2 data-version: uberon/releases/2021-07-27/ext.owl subsetdef: added_for_HCA "Classes tagged with this subset property were added upon request from the Human Cell Atlas (HCA)." subsetdef: cumbo "CUMBO" subsetdef: cyclostome_subset "cyclostome structures" subsetdef: defined_by_cytoarchitecture "brain region defined by cyto-architecture" subsetdef: defined_by_ordinal_series "classes that are defined by relative position counting from first in a series of elements along an axis in an individual organism rather than by strict homology" subsetdef: developmental_classification "developmental_classification" subsetdef: dubious_grouping "Indicates that subclasses in AOs may be inappropriately linked" subsetdef: early_development "A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes." subsetdef: efo_slim "EFO slim" subsetdef: emapa_ehdaa2 "derived from the union of EHDAA2 and EMAPA - still to be checked" subsetdef: feed_aligned "subset of classes that have logical defs text defs and synonyms aligned with FEED" subsetdef: functional_classification "functional_classification" subsetdef: grouping_class "Subset consisting of classes creating for grouping purposes" subsetdef: homology_grouping "A grouping class that depends on an assumption of homology between subclasses" subsetdef: inconsistent_with_fma "classes that have some inconsistency with FMA" subsetdef: major_organ "somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads" subsetdef: metazoa_core "core classes typically found across metazoa. one purpose is to create a rough set of terms that could be used to start a new metazoan AO. Note this subset is not yet fully fleshed out" subsetdef: non_informative "abstract class brought in to group ontology classes but not informative" subsetdef: organ_slim "organs, excluding individual muscles and skeletal elements" subsetdef: pheno_slim "Phenotype slim" subsetdef: phenotype_rcn "A subset specifically created for the 2012 Phenotype RCN meeting. Includes some human-specific terms that may eventually be removed when they are adequately represented with part of relationships in FMA" subsetdef: uberon_slim "Uberon slim - subset that excludes obscure terms and deep compositional terms" subsetdef: unverified_taxonomic_grouping "Indicates that the class encompasses classes from other AOs that have not been verified" subsetdef: upper_level "abstract upper-level terms not directly useful for analysis" subsetdef: vertebrate_core "core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO" synonymtypedef: ABBREVIATION "abbreviation" synonymtypedef: BRAIN_NAME_ABV "brain name abbreviations (drosophila)" synonymtypedef: COMPARATIVE_PREFERRED "preferred term in the context of comparative anatomy" synonymtypedef: DEPRECATED "A historic synonym, no longer encouraged" synonymtypedef: DEVELOPMENTAL "developmental term" synonymtypedef: DUBIOUS "dubious or contested synonym" synonymtypedef: HOMOLOGY "a synonym made on the basis of a possibly homologous structure in another species" synonymtypedef: HUMAN_PREFERRED "preferred term when talking about an instance of this class in Homo sapiens" synonymtypedef: INCONSISTENT "indicates that a synonym is used in an inconsistent or confusing way, typically between species" synonymtypedef: LATIN "latin term" synonymtypedef: MISSPELLING "a mis-spelling that is in common use and thus recorded" synonymtypedef: NON_AMNIOTE "synonym that is inappropriate for amniotes" synonymtypedef: NON_MAMMAL "synonym that is inappropriate for mammals" synonymtypedef: PENDING_REVIEW "expert consultation and attribution required" synonymtypedef: PLURAL "plural term" synonymtypedef: SENSU "taxonomic disambiguation" synonymtypedef: SYSTEMATIC "a systematic synonym used as the base name for design patterns" default-namespace: uberon treat-xrefs-as-equivalent: AEO treat-xrefs-as-equivalent: BILA treat-xrefs-as-equivalent: BSPO treat-xrefs-as-equivalent: CARO treat-xrefs-as-equivalent: EFO treat-xrefs-as-equivalent: GO treat-xrefs-as-equivalent: OG treat-xrefs-as-equivalent: VSAO treat-xrefs-as-is_a: VHOG remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 437 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 20 Logical Axioms: 9] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 38 Logical Axioms: 38] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 2 Logical Axioms: 2] import: http://purl.obolibrary.org/obo/uberon/imports/chebi_import.owl import: http://purl.obolibrary.org/obo/uberon/imports/cl_import.owl import: http://purl.obolibrary.org/obo/uberon/imports/envo_import.owl import: http://purl.obolibrary.org/obo/uberon/imports/go_import.owl import: http://purl.obolibrary.org/obo/uberon/imports/nbo_import.owl import: http://purl.obolibrary.org/obo/uberon/imports/ncbitaxon_import.owl import: http://purl.obolibrary.org/obo/uberon/imports/pato_import.owl import: http://purl.obolibrary.org/obo/uberon/imports/pr_import.owl import: http://purl.obolibrary.org/obo/uberon/imports/ro_import.owl ontology: uberon/ext property_value: dc-contributor "Alan Ruttenberg" xsd:string property_value: dc-contributor "Alexander Diehl" xsd:string property_value: dc-contributor "Ann Maglia" xsd:string property_value: dc-contributor "Anna Anagnostopoulos" xsd:string property_value: dc-contributor "Bgee Project - http://bgee.unil.ch" xsd:string property_value: dc-contributor "Bill Bug" xsd:string property_value: dc-contributor "Brian K Hall" xsd:string property_value: dc-contributor "Carlo Torniai" xsd:string property_value: dc-contributor "Catherine Leroy" xsd:string property_value: dc-contributor "Ceri Van Slyke" xsd:string property_value: dc-contributor "Cynthia Smith" xsd:string property_value: dc-contributor "David Hill" xsd:string property_value: dc-contributor "David Osumi-Sutherland" xsd:string property_value: dc-contributor "Duncan Davidson" xsd:string property_value: dc-contributor "Frederic Bastian" xsd:string property_value: dc-contributor "Gene Ontology Consortium" xsd:string property_value: dc-contributor "George Gkoutos" xsd:string property_value: dc-contributor "Hilmar Lapp" xsd:string property_value: dc-contributor "James Balhoff" xsd:string property_value: dc-contributor "James Malone" xsd:string property_value: dc-contributor "Jonathan Bard" xsd:string property_value: dc-contributor "Lydie Lane" xsd:string property_value: dc-contributor "Marc Robinson-Rechavi" xsd:string property_value: dc-contributor "Mark Engelstad - https://orcid.org/0000-0001-5889-4463" xsd:string property_value: dc-contributor "Maryann Martone" xsd:string property_value: dc-contributor "neXtProt project" xsd:string property_value: dc-contributor "NIF Project - http://neuinfo.org/" xsd:string property_value: dc-contributor "Onard Mejino" xsd:string property_value: dc-contributor "PATO Project" xsd:string property_value: dc-contributor "Paul Schofield" xsd:string property_value: dc-contributor "Paul Sereno" xsd:string property_value: dc-contributor "Paula Duek Roggli" xsd:string property_value: dc-contributor "Paula Mabee" xsd:string property_value: dc-contributor "Phenoscape Project" xsd:string property_value: dc-contributor "Rebecca Foulger" xsd:string property_value: dc-contributor "Robert Druzinsky" xsd:string property_value: dc-contributor "Sarah Whitcher Kansa - https://orcid.org/0000-0001-7920-5321" xsd:string property_value: dc-contributor "Shahim Essaid" xsd:string property_value: dc-contributor "Suzanna Lewis" xsd:string property_value: dc-contributor "Terry Hayamizu" xsd:string property_value: dc-contributor "Terry Meehan" xsd:string property_value: dc-contributor "Trish Whetzel" xsd:string property_value: dc-contributor "Yvonne Bradford" xsd:string property_value: dc-creator "Alex Dececchi" xsd:string property_value: dc-creator "Anne Niknejad" xsd:string property_value: dc-creator "Aurelie Comte" xsd:string property_value: dc-creator "Chris Mungall - http://orcid.org/0000-0002-6601-2165 " xsd:string property_value: dc-creator "David Blackburn" xsd:string property_value: dc-creator "Erik Segerdell" xsd:string property_value: dc-creator "Melissa Haendel" xsd:string property_value: dc-creator "Nicolas Matentzoglu" xsd:string property_value: dc-creator "Nizar Ibrahim" xsd:string property_value: dc-creator "Wasila Dahdul" xsd:string property_value: dc-description "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data." xsd:string property_value: dc-publisher http://uberon.org xsd:anyURI property_value: dc-source "aggregates AAO from 13:04:2012" xsd:string property_value: dc-source "aggregates TAO from 09:08:2012" xsd:string property_value: dc-source "aggregates VSAO from 16:07:2012" xsd:string property_value: dc-source http://braininfo.rprc.washington.edu/ property_value: dc-source http://dbpedia.org property_value: dc-source http://en.wikipedia.org/wiki/ property_value: dc-source http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl property_value: dc-source http://palaeos.com property_value: dc-source http://pons.incf.org/wiki/Common_Upper_Mammalian_Brain_Ontology_%28Cumbo%29 property_value: dc-source http://purl.obolibrary.org/obo/aao.owl property_value: dc-source http://purl.obolibrary.org/obo/aba.owl property_value: dc-source http://purl.obolibrary.org/obo/aeo.owl property_value: dc-source http://purl.obolibrary.org/obo/bila.owl property_value: dc-source http://purl.obolibrary.org/obo/bto.owl property_value: dc-source http://purl.obolibrary.org/obo/caro.owl property_value: dc-source http://purl.obolibrary.org/obo/cl.owl property_value: dc-source http://purl.obolibrary.org/obo/ehdaa2.owl property_value: dc-source http://purl.obolibrary.org/obo/emapa.owl property_value: dc-source http://purl.obolibrary.org/obo/fbbt.owl property_value: dc-source http://purl.obolibrary.org/obo/fma.owl property_value: dc-source http://purl.obolibrary.org/obo/go.owl property_value: dc-source http://purl.obolibrary.org/obo/hp.owl property_value: dc-source http://purl.obolibrary.org/obo/ma.owl property_value: dc-source http://purl.obolibrary.org/obo/mp.owl property_value: dc-source http://purl.obolibrary.org/obo/tao.owl property_value: dc-source http://purl.obolibrary.org/obo/vhog.owl property_value: dc-source http://purl.obolibrary.org/obo/vsao.owl property_value: dc-source http://purl.obolibrary.org/obo/wbbt.owl property_value: dc-source http://purl.obolibrary.org/obo/xao.owl property_value: dc-source http://purl.obolibrary.org/obo/zfa.owl property_value: dc-source http://uri.neuinfo.org/nif/nifstd property_value: dc-source http://wiki.phenotypercn.org/wg/phenotypercn/index.php?title=Neural_Crest_Workshop xsd:anyURI property_value: dc-source http://wiki.phenotypercn.org/wiki/August_2012_Notes xsd:anyURI property_value: dc-source http://www.brain-map.org property_value: dc-source http://www.e-lico.eu/public/kupo/kupo.owl property_value: dc-source http://www.ebi.ac.uk/efo/efo.owl property_value: dc-source https://docs.google.com/document/d/16JZOuH9sh_a8uIXA4cqg0Q1H6MV5yCj3-rhuKsZoV_U/edit xsd:anyURI property_value: dc-source https://docs.google.com/document/d/1cPWBqrl_Qy7XHEWFqtR_PgQX61yRkgGuLaiDpnEXxkE/edit xsd:anyURI property_value: dc-source https://docs.google.com/document/d/1MnUgispgGfNQoezYzWzzGTnkAnI0gzRnJIwdip6MMtw/edit xsd:anyURI property_value: dc-source https://docs.google.com/document/d/1r9kNPpFYGdu0SpJDLyFAVQczBlG0wAZCBMd18gG3Ot8/edit# xsd:anyURI property_value: dc-source https://docs.google.com/spreadsheet/ccc?key=0Aj8NJdyb-leqdDM0R3hTVTRHRExDVjRCSkZEbDc5N1E#gid=0 xsd:anyURI property_value: dc-source "ISBN:0030229073 Invertebrate Zoology, Barnes" xsd:string property_value: dc-source "ISBN:0073040584 Vertebrates, Kardong" xsd:string property_value: dc-source "ISBN:0123813611 Comparative Anatomy and Histology: A Mouse and Human Atlas, Treuting and Dintzis" xsd:string property_value: dc-source "ISBN:0226313379 Fins into Limbs: Evolution, Development, and Transformation, Hall" xsd:string property_value: dc-source "ISBN:0443065837 Human embryology, Larsen" xsd:string property_value: dc-source "ISBN:0471888893 Comparative Vertebrate Neuroanatomy: Evolution and Adaptation by Butler and Hodos" xsd:string property_value: dc-source "ISBN:0683400088 Stedman's Medical Dictionary" xsd:string property_value: dc-source "ISBN:1588900649 Color Atlas and Textbook of Human Anatomy: Nervous system and sensory organs By Werner Kahle, Michael Frotscher" xsd:string property_value: dc-source "ISBN:1588903958 Principles and practice of pediatric neurosurgery By A. Leland Albright, P. David Adelson, Ian F. Pollack" xsd:string property_value: dc-source "ISBN:1607950324 Craniofacial Embryogenetics & Development, 2nd edition, Sperber" xsd:string property_value: dc-source "ISBN:978-0-12-369548-2 Principles of Developmental Genetics, Sally A Moody" xsd:string property_value: dc-source "ISBN:9780120749034 The laboratory rat" xsd:string property_value: dc-source "ISBN:9780397517251 Surgical anatomy of the hand and upper extremity. By James R. Doyle and Michael J. Botte" xsd:string property_value: dc-source "ISBN:9780674021839 The Tree of Life - Guillaume Lecointre, Herve Le Guyader" xsd:string property_value: dc-source "ISBN:9780878932504 Developmental Biology" xsd:string property_value: dc-source "MESH" xsd:string property_value: dc-source "PMID:11433360 Placental development: lessons from mouse mutants" xsd:string property_value: dc-source "PMID:16417468 Forgotten and novel aspects in pancreas development, Pieler and Chen" xsd:string property_value: dc-title "Uber-anatomy ontology" xsd:string property_value: dcterms-isReferencedBy http://genomebiology.com/2012/13/1/R5 xsd:anyURI property_value: dcterms-isReferencedBy http://www.ncbi.nlm.nih.gov/pubmed/22293552 xsd:anyURI property_value: dcterms-license http://creativecommons.org/licenses/by/3.0/ property_value: doap-bug-database https://github.com/obophenotype/uberon/issues/ xsd:anyURI property_value: doap-GitRepository https://github.com/cmungall/uberon/ xsd:anyURI property_value: doap-mailing-list https://lists.sourceforge.net/lists/listinfo/obo-anatomy xsd:anyURI property_value: doap-SVNRepository https://obo.svn.sourceforge.net/svnroot/obo/uberon/ xsd:anyURI property_value: foaf-homepage http://uberon.org xsd:anyURI treat-xrefs-as-has-subclass: EHDAA treat-xrefs-as-has-subclass: EV treat-xrefs-as-has-subclass: NCIT treat-xrefs-as-has-subclass: OGES treat-xrefs-as-has-subclass: SCTID treat-xrefs-as-reverse-genus-differentia: AAO part_of NCBITaxon:8292 treat-xrefs-as-reverse-genus-differentia: DHBA part_of NCBITaxon:9606 treat-xrefs-as-reverse-genus-differentia: DMBA part_of NCBITaxon:10090 treat-xrefs-as-reverse-genus-differentia: EHDAA2 part_of NCBITaxon:9606 treat-xrefs-as-reverse-genus-differentia: EMAPA part_of NCBITaxon:10090 treat-xrefs-as-reverse-genus-differentia: FBbt part_of NCBITaxon:7227 treat-xrefs-as-reverse-genus-differentia: FBdv part_of NCBITaxon:7227 treat-xrefs-as-reverse-genus-differentia: FMA part_of NCBITaxon:9606 treat-xrefs-as-reverse-genus-differentia: HAO part_of NCBITaxon:7399 treat-xrefs-as-reverse-genus-differentia: HBA part_of NCBITaxon:9606 treat-xrefs-as-reverse-genus-differentia: HsapDv part_of NCBITaxon:9606 treat-xrefs-as-reverse-genus-differentia: MA part_of NCBITaxon:10090 treat-xrefs-as-reverse-genus-differentia: MBA part_of NCBITaxon:10090 treat-xrefs-as-reverse-genus-differentia: MFO part_of NCBITaxon:8089 treat-xrefs-as-reverse-genus-differentia: MmusDv part_of NCBITaxon:10090 treat-xrefs-as-reverse-genus-differentia: OlatDv part_of NCBITaxon:8089 treat-xrefs-as-reverse-genus-differentia: PBA part_of NCBITaxon:9443 treat-xrefs-as-reverse-genus-differentia: SPD part_of NCBITaxon:6893 treat-xrefs-as-reverse-genus-differentia: TADS part_of NCBITaxon:6939 treat-xrefs-as-reverse-genus-differentia: TAO part_of NCBITaxon:32443 treat-xrefs-as-reverse-genus-differentia: TGMA part_of NCBITaxon:44484 treat-xrefs-as-reverse-genus-differentia: WBbt part_of NCBITaxon:6237 treat-xrefs-as-reverse-genus-differentia: WBls part_of NCBITaxon:6237 treat-xrefs-as-reverse-genus-differentia: XAO part_of NCBITaxon:8353 treat-xrefs-as-reverse-genus-differentia: ZFA part_of NCBITaxon:7954 treat-xrefs-as-reverse-genus-differentia: ZFS part_of NCBITaxon:7954 [Term] id: BFO:0000004 is_a: BFO:0000002 [Term] id: BFO:0000015 is_a: BFO:0000003 [Term] id: BFO:0000040 is_a: BFO:0000004 [Term] id: BFO:0000141 is_a: BFO:0000004 [Term] id: CL:1000359 is_a: UBERON:0000397 ! colonic epithelium [Term] id: GO:0008150 is_a: BFO:0000015 [Term] id: GO:0048520 is_a: GO:0048584 [Term] id: GO:0048521 is_a: GO:0048585 [Term] id: UBERON:0000000 name: processual entity def: "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity." [span:ProcessualEntity] subset: upper_level is_a: BFO:0000003 disjoint_from: UBERON:0001062 ! anatomical entity [Term] id: UBERON:0000002 name: uterine cervix def: "Lower, narrow portion of the uterus where it joins with the top end of the vagina." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Cervix] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "canalis cervicis uteri" EXACT LATIN [FMA:17740, FMA:TA] synonym: "caudal segment of uterus" EXACT [] synonym: "cervical canal" RELATED [FMA:17740] synonym: "cervical canal of uterus" EXACT [FMA:17740] synonym: "cervix" BROAD [EFO:0000979] synonym: "cervix of uterus" RELATED [BTO:0001421] synonym: "cervix uteri" EXACT LATIN [EMAPA:29927] synonym: "neck of uterus" EXACT [FMA:17740] synonym: "uterine cervix" EXACT [FMA:17740] xref: BTO:0001421 xref: BTO:0002249 xref: CALOHA:TS-0134 xref: EFO:0000979 xref: EMAPA:29927 xref: EV:0100114 xref: FMA:17740 xref: GAID:376 xref: galen:CervixUteri xref: MA:0000392 xref: MAT:0000292 xref: MESH:D002584 xref: NCIT:C12311 xref: OpenCyc:Mx4rvVipEJwpEbGdrcN5Y29ycA xref: SCTID:181453009 xref: UMLS:C0007874 {source="ncithesaurus:Cervix"} xref: VHOG:0001359 xref: Wikipedia:Cervix is_a: CARO:0000000 is_a: UBERON:0001560 ! neck of organ is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0001560 ! neck of organ intersection_of: continuous_with UBERON:0000996 ! vagina intersection_of: part_of UBERON:0000995 ! uterus relationship: continuous_with UBERON:0000996 ! vagina relationship: contributes_to_morphology_of UBERON:0000995 ! uterus relationship: part_of UBERON:0000995 ! uterus property_value: external_definition "The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001359", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/uterine+cervix"} property_value: has_relational_adjective "cervical" xsd:string property_value: homology_notes "The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0000003 name: naris def: "Orifice of the olfactory system. The naris is the route by which odorants enter the olfactory system[MAH]." [http://orcid.org/0000-0001-9114-8737] subset: uberon_slim subset: vertebrate_core xref: AAO:0000311 xref: EHDAA2:0001225 xref: EHDAA:9083 xref: EMAPA:17847 xref: galen:Naris xref: MA:0000282 xref: SCTID:272650008 xref: VHOG:0000663 is_a: UBERON:0000161 ! orifice intersection_of: UBERON:0000161 ! orifice intersection_of: connects UBERON:0001707 ! nasal cavity intersection_of: part_of UBERON:0005725 ! olfactory system relationship: connects UBERON:0001707 ! nasal cavity relationship: in_lateral_side_of UBERON:0000033 {gci_relation="part_of", gci_filler="NCBITaxon:7776", notes="hagfish have median nostril"} ! head relationship: only_in_taxon NCBITaxon:7711 relationship: part_of UBERON:0000033 {source="ZFA"} ! head relationship: part_of UBERON:0005725 ! olfactory system property_value: external_definition "One of paired external openings of the nasal chamber.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000311", ontology="AAO", source="AAO:EJS"} property_value: external_ontology_notes "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" xsd:string {external_ontology="FMA"} property_value: homology_notes "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]" xsd:string {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/"} property_value: taxon_notes "in actinopterygians, both pairs of nares are external. In tetrapods, the exhalant empties into the buccal cavity" xsd:string [Term] id: UBERON:0000004 name: nose def: "The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity." [UBERON:cjm] subset: efo_slim subset: major_organ subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "nasal sac" EXACT SENSU [ZFA:0000047] synonym: "nasus" RELATED LATIN [Wikipedia:Nose] synonym: "nose" EXACT HUMAN_PREFERRED [MA:0000281] synonym: "olfactory apparatus" RELATED [UBERON:cjm] synonym: "peripheral olfactory organ" EXACT [ZFA:0000047] synonym: "proboscis" RELATED [] xref: BTO:0000840 xref: CALOHA:TS-2037 xref: EHDAA2:0001274 xref: EHDAA:1502 xref: EMAPA:16542 xref: EV:0100037 xref: EV:0100370 xref: FMA:46472 xref: GAID:77 xref: galen:Nose xref: MA:0000281 xref: MAT:0000139 xref: MESH:D009666 xref: MIAA:0000139 xref: NCIT:C12756 xref: OpenCyc:Mx4rvViCbJwpEbGdrcN5Y29ycA xref: SCTID:181195007 xref: TAO:0000047 xref: UMLS:C0028429 {source="ncithesaurus:Nose"} xref: Wikipedia:Nose xref: ZFA:0000047 is_a: CARO:0000003 is_a: UBERON:0000475 ! organism subdivision is_a: UBERON:0002268 ! olfactory organ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: capable_of_part_of GO:0007608 relationship: contributes_to_morphology_of UBERON:0001004 ! respiratory system relationship: contributes_to_morphology_of UBERON:0001456 ! face relationship: develops_from UBERON:0003050 {source="ZFA"} ! olfactory placode relationship: has_skeleton UBERON:0006813 ! nasal skeleton relationship: only_in_taxon NCBITaxon:7742 relationship: part_of UBERON:0001004 {gci_relation="part_of", gci_filler="NCBITaxon:32523", source="PMID:25312359"} ! respiratory system relationship: part_of UBERON:0001456 {source="FMA", source="ZFA-def"} ! face relationship: part_of UBERON:0004089 {gci_relation="part_of", gci_filler="NCBITaxon:7776", notes="midface division only makes sense for gnathostomes"} ! midface property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/d/d0/Canine-nose.jpg xsd:anyURI property_value: external_definition "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]." xsd:string {source="Wikipedia:Nose"} property_value: external_definition "Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047]." xsd:string {source="ZFA:0000047"} property_value: external_definition "the organ that is specialized for smell and is part of the respiratory system" xsd:string {source="MP:0002233"} property_value: taxon_notes "the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359]" xsd:string [Term] id: UBERON:0000005 name: chemosensory organ subset: functional_classification subset: uberon_slim synonym: "chemosensory sensory organ" EXACT [FBbt:00005157] xref: FBbt:00005157 is_a: CARO:0000000 is_a: UBERON:0000020 ! sense organ intersection_of: UBERON:0000020 ! sense organ intersection_of: capable_of GO:0007606 relationship: capable_of GO:0007606 relationship: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0005726 ! chemosensory system [Term] id: UBERON:0000006 name: islet of Langerhans def: "the clusters of hormone-producing cells that are scattered throughout the pancreas" [MA:0000127, MESH:A03.734.414, MP:0005215] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "island of Langerhans" RELATED [BTO:0000991] synonym: "island of pancreas" RELATED [BTO:0000991] synonym: "islets of Langerhans" RELATED [] synonym: "pancreatic insula" EXACT [] synonym: "pancreatic islet" EXACT [] xref: AAO:0010406 xref: BTO:0000991 xref: CALOHA:TS-0741 xref: EFO:0000856 xref: EMAPA:32927 xref: EV:0100130 xref: FMA:16016 xref: GAID:324 xref: MA:0000127 xref: MAT:0000076 xref: MESH:D007515 xref: MIAA:0000076 xref: NCIT:C12608 xref: UMLS:C0022131 {source="ncithesaurus:Islet_of_Langerhans"} xref: VHOG:0000646 xref: Wikipedia:Islets_of_Langerhans xref: XAO:0000159 is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0034922 ! cell cluster relationship: contributes_to_morphology_of UBERON:0000016 ! endocrine pancreas relationship: fma_set_term FMA:76489 relationship: has_part CL:0000168 {source="PMID:16417468"} relationship: has_part CL:0000172 {source="PMID:16417468"} relationship: has_part CL:0000696 {gci_relation="part_of", gci_filler="NCBITaxon:7778", source="PMID:16417468"} relationship: has_part CL:0000696 {gci_filler="NCBITaxon:117570", gci_relation="part_of", source="PMID:16417468"} relationship: has_part CL:0002067 {source="PMID:16417468"} relationship: part_of UBERON:0000016 ! endocrine pancreas property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png xsd:anyURI property_value: external_definition "Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010406", ontology="AAO", source="AAO:BJB"} property_value: homology_notes "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]" xsd:string {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/"} property_value: taxon_notes "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)" xsd:string {source="PMID:16417468"} [Term] id: UBERON:0000007 name: pituitary gland def: "The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]." [Wikipedia:Pituitary_gland, ZFIN:curator] 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] subset: efo_slim subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "glandula pituitaria" EXACT LATIN [Wikipedia:Pituitary_gland] synonym: "Hp" BROAD ABBREVIATION [BIRNLEX:1353, NIFSTD:NeuroNames_abbrevSource] synonym: "hypophysis" RELATED [ZFA:0000118] synonym: "hypophysis cerebri" RELATED [MA:0000176] synonym: "pituitary" EXACT [BTO:0001073] synonym: "pituitary body" EXACT [BTO:0001073] xref: AAO:0010536 xref: BAMS:PIT xref: BAMS:Pit xref: BIRNLEX:1353 xref: BM:Die-Hy-HY xref: BTO:0001073 xref: CALOHA:TS-0798 xref: DHBA:10505 xref: EFO:0000857 xref: EHDAA2:0001471 xref: EHDAA:2183 xref: EHDAA:4477 xref: EMAPA:35998 xref: EV:0100132 xref: FMA:13889 xref: GAID:457 xref: HBA:4634 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=399 {source="BIRNLEX:1353"} xref: MA:0000176 xref: MAT:0000077 xref: MESH:D010902 xref: MIAA:0000077 xref: NCIT:C12399 xref: OpenCyc:Mx4rv6NQYJwpEbGdrcN5Y29ycA xref: SCTID:181125003 xref: TAO:0000118 xref: UMLS:C0032005 {source="BIRNLEX:1353"} xref: UMLS:C0032005 {source="ncithesaurus:Pituitary_Gland"} xref: VHOG:0000143 xref: Wikipedia:Pituitary_gland xref: XAO:0000017 xref: ZFA:0000118 is_a: UBERON:0002368 {source="BTO", source="EFO", source="VHOG"} ! endocrine gland is_a: UBERON:0003296 ! gland of diencephalon is_a: UBERON:0010133 ! neuroendocrine gland is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: capable_of_part_of GO:0007276 relationship: contributes_to_morphology_of UBERON:0001894 ! diencephalon relationship: develops_from UBERON:0034875 ! future pituitary gland relationship: has_part CL:0000440 {source="ZFA"} relationship: has_part CL:0000642 {source="ZFA"} relationship: has_part UBERON:0002196 ! adenohypophysis relationship: has_part UBERON:0002198 ! neurohypophysis relationship: immediate_transformation_of UBERON:0034875 {source="BGEE:ANN"} ! future pituitary gland relationship: only_in_taxon NCBITaxon:7742 {source="PMID:19084529"} relationship: part_of UBERON:0001894 {source="MA", source="ZFA"} ! diencephalon property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1180.png xsd:anyURI property_value: external_definition "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]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010536", ontology="AAO", source="AAO:BJB"} property_value: external_definition "An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000118", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "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]" xsd:string {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/"} property_value: taxon_notes "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]" xsd:string [Term] id: UBERON:0000009 name: submucosa def: "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]." [Wikipedia:Submucosa] subset: pheno_slim subset: uberon_slim synonym: "organ submucosa" EXACT [FMA:85391] synonym: "region of submucosa" EXACT [FMA:85392] synonym: "submucosa of organ" EXACT [FMA:85391] synonym: "submucosa of region of organ" EXACT [FMA:85392] synonym: "submucous layer" RELATED [BTO:0002107] synonym: "tela submucosa" RELATED [BTO:0002107] synonym: "tunica submucosa" RELATED [] xref: BTO:0002107 xref: FMA:85391 xref: FMA:85392 xref: NCIT:C13167 xref: SCTID:68439008 xref: UMLS:C0225344 {source="ncithesaurus:Submucosa"} xref: Wikipedia:Submucosa is_a: UBERON:0004923 ! organ component layer relationship: composed_primarily_of UBERON:0002384 ! connective tissue relationship: immediately_deep_to UBERON:0000344 ! mucosa relationship: only_in_taxon NCBITaxon:7711 property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png xsd:anyURI property_value: depicted_by http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png xsd:anyURI property_value: has_relational_adjective "submucosal" xsd:string [Term] id: UBERON:0000010 name: peripheral nervous system def: "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." [GO:0007422] subset: cumbo subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "pars peripherica" EXACT LATIN [FMA:9903, FMA:TA, Wikipedia:Peripheral_nervous_system] synonym: "PNS" BROAD ABBREVIATION [] synonym: "systema nervosum periphericum" EXACT LATIN [FMA:9903, FMA:TA, Wikipedia:Peripheral_nervous_system] xref: AAO:0000429 xref: BAMS:PNS xref: BILA:0000081 xref: BIRNLEX:1111 xref: BTO:0001028 xref: CALOHA:TS-0808 xref: EFO:0000891 xref: EHDAA2:0001445 xref: EHDAA:2893 xref: EMAPA:16665 xref: EV:0100335 xref: FBbt:00005098 xref: FMA:9903 xref: GAID:715 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=3232 xref: MA:0000218 xref: MAT:0000338 xref: MESH:D017933 xref: MIAA:0000338 xref: NCIT:C12465 xref: SCTID:362292005 xref: TAO:0000142 xref: UMLS:C0206417 {source="ncithesaurus:Peripheral_Nervous_System"} xref: UMLS:C0206417 {source="BIRNLEX:1111"} xref: UMLS:C1305921 {source="BIRNLEX:1111"} xref: VHOG:0000399 xref: Wikipedia:Peripheral_nervous_system xref: XAO:0000178 xref: ZFA:0000142 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001016 ! nervous system property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png xsd:anyURI property_value: external_definition "Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000142", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000429", ontology="AAO", source="AAO:BJB"} property_value: external_definition "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)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} property_value: homology_notes "(...) 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]" xsd:string {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/"} [Term] id: UBERON:0000011 name: parasympathetic nervous system def: "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]." [GO:0048486] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "parasympathetic part of autonomic division of nervous system" EXACT [] synonym: "pars parasympathica divisionis autonomici systematis nervosi" EXACT LATIN [FMA:9907, FMA:TA] synonym: "pars parasympathica divisionis autonomici systematis nervosi" RELATED LATIN [Wikipedia:Parasympathetic_nervous_system] synonym: "PNS - parasympathetic" EXACT [] xref: AAO:0010488 xref: BIRNLEX:2517 xref: BTO:0001833 xref: CALOHA:TS-2094 xref: EFO:0000894 xref: EHDA:10096 xref: EHDAA2:0001402 xref: EHDAA:4655 xref: EMAPA:17270 xref: FMA:9907 xref: GAID:708 xref: MA:0000223 xref: MAT:0000101 xref: MESH:D010275 xref: MIAA:0000101 xref: NCIT:C12764 xref: SCTID:362496006 xref: TAO:0001575 xref: UMLS:C0030510 {source="ncithesaurus:Parasympathetic_Nervous_System"} xref: UMLS:C0030510 {source="BIRNLEX:2517"} xref: UMLS:C1305770 {source="BIRNLEX:2517"} xref: VHOG:0000755 xref: Wikipedia:Parasympathetic_nervous_system xref: ZFA:0001575 is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: contributes_to_morphology_of UBERON:0002410 ! autonomic nervous system relationship: has_developmental_contribution_from UBERON:0002342 {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neural crest relationship: part_of UBERON:0002410 {source="FMA", source="MA", source="WP", source="ZFA-modified-from-isa"} ! autonomic nervous system property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png xsd:anyURI property_value: external_definition "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]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010488", ontology="AAO", source="AAO:BJB"} property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000012 name: somatic nervous system def: "Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors." [NLXANAT:100301] subset: pheno_slim subset: uberon_slim synonym: "PNS - somatic" EXACT [] synonym: "somatic nervous system, somatic division" EXACT [NLXANAT:100301] synonym: "somatic part of peripheral nervous system" EXACT [UBERON:cjm] synonym: "somatic peripheral nervous system" EXACT [NLXANAT:100301] xref: EFO:0000892 xref: FMA:9904 xref: MA:0002850 xref: MAT:0000099 xref: MIAA:0000099 xref: NLXANAT:100301 xref: Wikipedia:Somatic_nervous_system is_a: CARO:0000000 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: contributes_to_morphology_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0000010 ! peripheral nervous system [Term] id: UBERON:0000013 name: sympathetic nervous system def: "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]." [GO:0048485] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "pars sympathica divisionis autonomici systematis nervosi" EXACT LATIN [FMA:9906, FMA:TA] synonym: "pars sympathica divisionis autonomici systematis nervosi" RELATED LATIN [Wikipedia:Sympathetic_nervous_system] synonym: "sympathetic nervous system" EXACT [] synonym: "sympathetic part of autonomic division of nervous system" EXACT [] xref: AAO:0010487 xref: BIRNLEX:2516 xref: BTO:0001832 xref: CALOHA:TS-2050 xref: EFO:0000893 xref: EHDAA2:0001971 xref: EHDAA:3769 xref: EMAPA:16985 xref: FMA:9906 xref: GAID:710 xref: MA:0000225 xref: MESH:D013564 xref: MIAA:0000100 xref: NCIT:C12795 xref: SCTID:362484004 xref: TAO:0001576 xref: UMLS:C0039044 {source="ncithesaurus:Sympathetic_Nervous_System"} xref: UMLS:C0039044 {source="BIRNLEX:2516"} xref: UMLS:C1269646 {source="BIRNLEX:2516"} xref: VHOG:0000384 xref: Wikipedia:Sympathetic_nervous_system xref: ZFA:0001576 is_a: CARO:0000000 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: contributes_to_morphology_of UBERON:0002410 ! autonomic nervous system relationship: part_of UBERON:0002410 {source="FMA", source="MA", source="ZFA-modified-from-isa"} ! autonomic nervous system property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png xsd:anyURI property_value: development_notes "has developmental contribution from NC in verteberates (https://github.com/obophenotype/uberon/wiki/The-neural-crest)" xsd:string property_value: external_definition "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]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010487", ontology="AAO", source="AAO:BJB"} property_value: external_definition "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000384", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000014 name: zone of skin def: "Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Skin] subset: pheno_slim synonym: "portion of skin" EXACT [] synonym: "region of skin" EXACT [] synonym: "skin" EXACT [MA:0000151] synonym: "skin region" EXACT [] synonym: "skin zone" EXACT [] xref: EHDAA2:0001844 xref: EHDAA:6530 xref: EMAPA:17525 xref: EV:0100152 xref: FMA:86166 xref: GAID:933 xref: MA:0000151 xref: MAT:0000284 xref: MESH:D012867 xref: MIAA:0000284 xref: OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA xref: SCTID:20795001 xref: VHOG:0000860 xref: Wikipedia:Skin is_a: UBERON:0034944 {source="FMA"} ! zone of organ relationship: has_part UBERON:0001003 ! skin epidermis relationship: has_part UBERON:0002067 ! dermis relationship: part_of UBERON:0002097 ! skin of body property_value: curator_notes "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" xsd:string property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg xsd:anyURI property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg xsd:anyURI property_value: external_ontology_notes "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" xsd:string property_value: homology_notes "(...) 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]" xsd:string {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/"} [Term] id: UBERON:0000015 name: non-material anatomical boundary def: "A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures." [CARO:0000010] 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. subset: upper_level synonym: "anatomical boundary" EXACT [CARO:0000010] xref: AEO:0000192 xref: CARO:0000010 xref: FMA:50705 is_a: UBERON:0000466 {source="CARO"} ! immaterial anatomical entity [Term] id: UBERON:0000016 name: endocrine pancreas def: "The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin." [GO:GO, http://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "endocrine pancreas" EXACT [] synonym: "endocrine part of pancreas" RELATED [BTO:0000650] synonym: "islets of Langerhans part of pancreas" RELATED [] synonym: "pars endocrina pancreatis" EXACT [] xref: BTO:0000650 xref: CALOHA:TS-1302 xref: EFO:0002542 xref: EMAPA:35305 xref: EV:0100129 xref: FMA:16018 xref: MA:0001582 xref: NCIT:C32509 xref: SCTID:361339003 xref: TAO:0001260 xref: VHOG:0000049 xref: Wikipedia:Islets_of_Langerhans xref: ZFA:0001260 is_a: UBERON:0000471 {source="ZFA"} ! compound organ component is_a: UBERON:0004119 ! endoderm-derived structure relationship: capable_of GO:0030073 {source="GO"} relationship: capable_of GO:0070091 {source="GO"} relationship: capable_of GO:0070253 {source="GO"} relationship: composed_primarily_of UBERON:0000006 ! islet of Langerhans relationship: contributes_to_morphology_of UBERON:0001264 ! pancreas relationship: develops_from UBERON:0003923 ! dorsal pancreatic bud relationship: part_of UBERON:0000949 {source="AAO", source="FMA", source="XAO"} ! endocrine system relationship: part_of UBERON:0001264 ! pancreas property_value: editor_note "create a separate class for distributed pancreas, eg cyclostomes?" xsd:string property_value: external_definition "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000049", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/Pancreas"} property_value: external_definition "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]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001260", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]" xsd:string {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/"} property_value: taxon_notes "endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys" xsd:string {source="PMID:20959416"} [Term] id: UBERON:0000017 name: exocrine pancreas def: "The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO]." [GOC:GO, http://orcid.org/0000-0002-6601-2165] subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "exocrine component of pancreas" RELATED [] synonym: "exocrine pancreas" EXACT [] synonym: "exocrine part of pancreas" RELATED [BTO:0000434] synonym: "pars exocrina pancreatis" EXACT [] xref: AAO:0010407 xref: BTO:0000434 xref: CALOHA:TS-1241 xref: EMAPA:35328 xref: EV:0100093 xref: FMA:16017 xref: MA:0002415 xref: NCIT:C32546 xref: SCTID:248202004 xref: TAO:0001249 xref: UMLS:C0553695 {source="ncithesaurus:Exocrine_Pancreas"} xref: VHOG:0000048 xref: Wikipedia:Exocrine_component_of_pancreas xref: XAO:0000137 xref: ZFA:0001249 is_a: UBERON:0000409 ! serous gland is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0005177 ! trunk region element relationship: capable_of_part_of GO:0007586 relationship: contributes_to_morphology_of UBERON:0001264 ! pancreas relationship: develops_from UBERON:0003924 ! ventral pancreatic bud relationship: has_part UBERON:0001263 ! pancreatic acinus relationship: has_part UBERON:0007329 ! pancreatic duct relationship: part_of UBERON:0001264 ! pancreas relationship: part_of UBERON:0002330 ! exocrine system property_value: external_definition "The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001249", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000048", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/Pancreas"} property_value: homology_notes "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0000018 name: compound eye def: "A light sensing organ composed of ommatidia" [FB:gg, Wikipedia:Compound_eye] subset: organ_slim subset: uberon_slim synonym: "adult compound eye" RELATED [] synonym: "faceted eye" RELATED [] synonym: "Facettenauge" RELATED [BTO:0001921] synonym: "insect eye" RELATED [] synonym: "Komplexauge" RELATED [BTO:0001921] synonym: "zusammengesetztes Auge" RELATED [BTO:0001921] xref: BTO:0001921 xref: FBbt:00004508 xref: HAO:0000217 xref: TGMA:0000024 xref: Wikipedia:Compound_eye is_a: UBERON:0015165 ! multi-unit eye intersection_of: UBERON:0000970 ! eye intersection_of: composed_primarily_of UBERON:0000971 ! ommatidium relationship: composed_primarily_of UBERON:0000971 ! ommatidium relationship: only_in_taxon NCBITaxon:6656 {source="PMID:21062451"} property_value: seeAlso https://github.com/obophenotype/uberon/issues/457 xsd:anyURI property_value: taxon_notes "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" xsd:string {source="PMID:21062451"} [Term] id: UBERON:0000019 name: camera-type eye def: "An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid." [GO:0043010, https://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "camera-type eye plus associated structures" RELATED [] synonym: "eye" BROAD [FMA:54448] synonym: "eyes" RELATED PLURAL [TAO:0000107] synonym: "orbital part of face" RELATED [FMA:54448] synonym: "orbital region" RELATED [FMA:54448] synonym: "regio orbitalis" EXACT LATIN [FMA:54448, FMA:TA] synonym: "vertebrate eye" NARROW [] xref: AAO:0010340 xref: BIRNLEX:1169 xref: BTO:0004688 xref: EHDAA2:0000484 xref: EHDAA:936 xref: EMAPA:16198 xref: FMA:54448 xref: MA:0000261 xref: NCIT:C12401 xref: OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvVil5pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycA xref: SCTID:181143004 xref: TAO:0000107 xref: UMLS:C0015392 {source="BIRNLEX:1169"} xref: UMLS:C0015392 {source="ncithesaurus:Eye"} xref: UMLS:C1280202 {source="BIRNLEX:1169"} xref: VHOG:0000275 xref: XAO:0000179 xref: ZFA:0000107 is_a: UBERON:0000047 ! simple eye relationship: develops_from UBERON:0003072 {evidence="definitional"} ! optic cup relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_developmental_contribution_from UBERON:0002342 {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neural crest relationship: has_part UBERON:0000965 ! lens of camera-type eye relationship: has_part UBERON:0000966 ! retina relationship: in_lateral_side_of UBERON:0000033 ! head relationship: part_of UBERON:0004088 ! orbital region property_value: external_definition "A cavitated compound organ that transduces light waves into neural signals.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000107", ontology="TAO", source="TAO:wd"} property_value: external_ontology_notes "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" xsd:string {external_ontology="FMA"} property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000020 name: sense organ def: "An organ that is capable of transducing sensory stimulus to the nervous system." [https://github.com/obophenotype/uberon/issues/549, https://orcid.org/0000-0002-6601-2165] subset: uberon_slim synonym: "organ of sense organ system" EXACT [OBOL:accepted] synonym: "organ of sensory organ system" EXACT [OBOL:accepted] synonym: "organ of sensory system" EXACT [OBOL:accepted] synonym: "sense organ system organ" EXACT [OBOL:automatic] synonym: "sensillum" NARROW [WBbt:0006929] synonym: "sensor" RELATED [] synonym: "sensory organ" EXACT [] synonym: "sensory organ system organ" EXACT [OBOL:automatic] synonym: "sensory system organ" EXACT [OBOL:accepted] synonym: "Sinnesorgan" RELATED [BTO:0000202] xref: AEO:0000094 xref: BSA:0000121 xref: BTO:0000202 xref: CALOHA:TS-2043 xref: EHDAA2:0001824 xref: EHDAA:500 xref: EMAPA:35955 xref: FBbt:00005155 xref: GAID:63 xref: HAO:0000930 xref: MA:0000017 xref: MESH:D012679 xref: NCIT:C33224 xref: SCTID:244485009 xref: UMLS:C0935626 {source="ncithesaurus:Organ_of_the_Special_Sense"} xref: VHOG:0001407 xref: WBbt:0006929 is_a: UBERON:0000062 ! organ intersection_of: UBERON:0000062 ! organ intersection_of: capable_of GO:0050906 relationship: capable_of GO:0050906 relationship: dc-contributor https://github.com/cmungall relationship: part_of UBERON:0001032 ! sensory system property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png xsd:anyURI [Term] id: UBERON:0000021 name: cutaneous appendage def: "Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales." [https://orcid.org/0000-0002-6601-2165] subset: uberon_slim synonym: "epidermal appendage" NARROW [] synonym: "epidermal growth" RELATED [] synonym: "skin appendage" EXACT [FMA:71012] xref: CALOHA:TS-0051 xref: FMA:71012 xref: SCTID:276160000 is_a: CARO:0000003 relationship: attaches_to UBERON:0002097 ! skin of body relationship: part_of UBERON:0002416 ! integumental system property_value: editor_note "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." xsd:string [Term] id: UBERON:0000022 name: feather def: "one of the epidermal growths that form the distinctive outer covering, or plumage, on birds. Feathers are formed in tiny follicles in the epidermis, or outer skin layer, that produce keratin proteins." [Wikipedia:Feather] subset: efo_slim subset: uberon_slim xref: BTO:0000447 xref: EFO:0000955 xref: GAID:1214 xref: MAT:0000156 xref: MESH:D005241 xref: OpenCyc:Mx4rvVjW-5wpEbGdrcN5Y29ycA xref: SCTID:410027006 xref: Wikipedia:Feather is_a: UBERON:0000021 ! cutaneous appendage relationship: develops_from UBERON:0001003 ! skin epidermis relationship: has_part GO:0045095 relationship: only_in_taxon NCBITaxon:436491 property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/4/41/Parts_of_feather_modified.jpg xsd:anyURI property_value: seeAlso http://xkcd.com/1104/ xsd:anyURI property_value: structure_notes "The beta-keratins in feathers, beaks and claws - and the claws, scales and shells of reptiles - are composed of protein strands hydrogen-bonded into beta-pleated sheets, which are then further twisted and crosslinked by disulfide bridges into structures even tougher than the alpha-keratins of mammalian hair, horns and hoof." xsd:string property_value: taxon_notes "Among the characteristics that distinguish the extant Aves from other living groups. Feathers have also been noticed in those Theropoda which have been termed feathered dinosaurs. Although feathers cover most parts of the body of birds, they arise only from certain well-defined tracts on the skin. They aid in flight, thermal insulation, waterproofing and coloration that helps in communication and protection" xsd:string [Term] id: UBERON:0000023 name: wing def: "Appendage that is shaped in order to produce lift for flight through the air." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: grouping_class subset: uberon_slim synonym: "aliform appendage" EXACT [http://orcid.org/0000-0002-6601-2165] xref: BTO:0001463 xref: EFO:0000885 xref: GAID:1217 xref: MAT:0000202 xref: MESH:D014921 xref: MIAA:0000202 xref: Wikipedia:Wing is_a: UBERON:0000026 ! appendage intersection_of: UBERON:0000026 ! appendage intersection_of: has_quality PATO:0002236 relationship: capable_of_part_of GO:0060361 relationship: confers_advantage_in ENVO:00000568 relationship: has_quality PATO:0002236 relationship: never_in_taxon NCBITaxon:118072 {source="bgee"} relationship: never_in_taxon NCBITaxon:186634 {seeAlso="Wikipedia:Flying_fish", source="bgee"} relationship: never_in_taxon NCBITaxon:314147 {source="bgee"} relationship: never_in_taxon NCBITaxon:6231 {source="bgee"} relationship: never_in_taxon NCBITaxon:7878 {source="bgee"} relationship: never_in_taxon NCBITaxon:8292 {notes="we do not consider flying frogs to have wings", source="bgee"} relationship: never_in_taxon NCBITaxon:8457 {source="bgee"} relationship: never_in_taxon NCBITaxon:91561 {source="bgee"} relationship: never_in_taxon NCBITaxon:9254 {source="bgee"} relationship: never_in_taxon NCBITaxon:9263 {source="bgee"} relationship: never_in_taxon NCBITaxon:9443 {source="bgee"} relationship: never_in_taxon NCBITaxon:9606 relationship: only_in_taxon NCBITaxon:33213 property_value: has_relational_adjective "alar" xsd:string property_value: taxon_notes "This class is not monophyletic. See also: GO:0007629" xsd:string [Term] id: UBERON:0000024 name: forelimb wing def: "Forelimb that is used to produce lift for flight through the air." [http://orcid.org/0000-0002-6601-2165] comment: Examples: bat wing, bird wing is_a: UBERON:0000023 ! wing is_a: UBERON:0002102 ! forelimb intersection_of: UBERON:0002102 ! forelimb intersection_of: has_quality PATO:0002236 relationship: has_quality PATO:0002236 [Term] id: UBERON:0000025 name: tube def: "Any hollow cylindrical anatomical structure containing a lumen through which substances are transported." [http://orcid.org/0000-0002-6601-2165] synonym: "anatomical tube" EXACT [] synonym: "duct" NARROW [] xref: galen:Tube is_a: UBERON:0004111 ! anatomical conduit intersection_of: UBERON:0004111 ! anatomical conduit intersection_of: has_quality PATO:0002299 relationship: has_part UBERON:0013522 ! subdivision of tube relationship: has_quality PATO:0002299 property_value: curator_notes "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)" xsd:string property_value: has_relational_adjective "tubular" xsd:string [Term] id: UBERON:0000026 name: appendage def: "Major subdivision of an organism that protrudes from the body[DOS, CARO]." [CARO:DOS] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "appendages" RELATED PLURAL [XAO:0000218] synonym: "extremitaet" RELATED [BTO:0001492] synonym: "extremity" RELATED [] synonym: "limbs/digits/tail" RELATED [MP:0000001] xref: AEO:0000193 xref: BILA:0000018 xref: BTO:0001492 xref: CARO:0010003 xref: EFO:0000799 xref: EHDAA2:0003193 xref: EMAPA:37283 {source="MA:th"} xref: EV:0100155 xref: FBbt:00007000 xref: HAO:0000144 xref: MAT:0000023 xref: MESH:D005121 xref: MIAA:0000023 xref: NCIT:C61460 xref: OpenCyc:Mx4rvViC-JwpEbGdrcN5Y29ycA xref: UMLS:C0598782 {source="ncithesaurus:Appendage"} xref: VSAO:0000075 xref: Wikipedia:Appendage xref: XAO:0000218 is_a: UBERON:0000475 ! organism subdivision relationship: only_in_taxon NCBITaxon:6072 property_value: external_definition "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]." xsd:string {source="BILA:0000018"} property_value: external_definition "Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]." xsd:string {source="GO:0048736"} property_value: has_relational_adjective "appendicular" xsd:string property_value: taxon_notes "this is currently a subtype of organism subdivision - which would exclude feathers" xsd:string [Term] id: UBERON:0000029 name: lymph node def: "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." [BTO:0000784] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "lymph gland" RELATED [VHOG:0001273] synonym: "nodus lymphaticus" RELATED LATIN [Wikipedia:Lymph_node] xref: BTO:0000784 xref: CALOHA:TS-0579 xref: EFO:0000872 xref: EMAPA:35523 xref: EV:0100050 xref: FMA:5034 xref: GAID:947 xref: galen:Lymphnode xref: MA:0000139 xref: MAT:0000442 xref: MESH:D008198 xref: NCIT:C12745 xref: NCIT:C33027 xref: OpenCyc:Mx4rwLPqLpwpEbGdrcN5Y29ycA xref: SCTID:181756000 xref: TAO_RETIRED:0005318 xref: UMLS:C0024204 {source="ncithesaurus:Lymph_Node"} xref: VHOG:0001273 xref: Wikipedia:Lymph_node xref: ZFA_RETIRED:0005318 is_a: CARO:0000000 is_a: UBERON:0005057 ! immune organ intersection_of: UBERON:0000062 ! organ intersection_of: composed_primarily_of UBERON:0001744 ! lymphoid tissue intersection_of: continuous_with UBERON:0001473 ! lymphatic vessel relationship: composed_primarily_of UBERON:0001744 ! lymphoid tissue relationship: continuous_with UBERON:0001473 ! lymphatic vessel relationship: develops_from UBERON:0034953 ! embryonic lymph sac relationship: has_part UBERON:0002006 ! cortex of lymph node relationship: has_part UBERON:0002007 ! medulla of lymph node relationship: has_part UBERON:0002194 ! capsule of lymph node relationship: has_part UBERON:0002391 ! lymph relationship: never_in_taxon NCBITaxon:32443 {source="DOI:10.1177/0192623311409597", source="ZFA:0005318"} relationship: never_in_taxon NCBITaxon:8570 {source="Wikipedia"} relationship: only_in_taxon NCBITaxon:7776 relationship: part_of UBERON:0002465 ! lymphoid system property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/b/b8/Illu_lymph_node_structure.png xsd:anyURI property_value: homology_notes "Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG]" xsd:string {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/"} property_value: seeAlso https://github.com/obophenotype/uberon/issues/650 xsd:anyURI [Term] id: UBERON:0000030 name: lamina propria def: "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." [Wikipedia:Lamina_propria] subset: uberon_slim synonym: "lamina propria mucosa" EXACT [] synonym: "lamina propria mucosae" EXACT [] synonym: "tunica propria" RELATED [BTO:0002330] xref: BTO:0002330 xref: FMA:62517 xref: NCIT:C32918 xref: SCTID:298225002 xref: UMLS:C1179187 {source="ncithesaurus:Lamina_Propria"} xref: Wikipedia:Lamina_propria is_a: UBERON:0004923 ! organ component layer relationship: composed_primarily_of UBERON:0011825 ! loose connective tissue relationship: immediately_deep_to UBERON:0000483 ! epithelium relationship: part_of UBERON:0000344 ! mucosa property_value: depicted_by GI:Organization.svg xsd:anyURI [Term] id: UBERON:0000031 name: lamina propria of trachea def: "A lamina propria that is part of a respiratory airway." [OBOL:automatic] synonym: "lamina propria mucosa of trachea" EXACT [OBOL:automatic] synonym: "lamina propria mucosa of windpipe" EXACT [OBOL:automatic] synonym: "lamina propria mucosae of trachea" EXACT [OBOL:automatic] synonym: "lamina propria mucosae of windpipe" EXACT [OBOL:automatic] synonym: "lamina propria of windpipe" EXACT [OBOL:automatic] synonym: "trachea lamina propria" EXACT [] synonym: "trachea lamina propria mucosa" EXACT [OBOL:automatic] synonym: "trachea lamina propria mucosae" EXACT [OBOL:automatic] synonym: "tracheal lamina propria" EXACT [] synonym: "windpipe lamina propria" EXACT [OBOL:automatic] synonym: "windpipe lamina propria mucosa" EXACT [OBOL:automatic] synonym: "windpipe lamina propria mucosae" EXACT [OBOL:automatic] xref: EMAPA:35877 xref: FMA:265157 xref: MA:0001858 xref: NCIT:C49305 xref: UMLS:C1710457 {source="ncithesaurus:Trachea_Lamina_Propria"} is_a: UBERON:0004779 ! respiratory system lamina propria intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0001005 ! respiratory airway relationship: part_of UBERON:0000379 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! tracheal mucosa relationship: part_of UBERON:0001005 ! respiratory airway [Term] id: UBERON:0000032 name: obsolete cranial structure comment: obsoleted as it was a grouping class that served no purpose is_obsolete: true [Term] id: UBERON:0000033 name: head def: "The head is the anterior-most division of the body [GO]." [GO:0060322, Wikipedia:Head] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "adult head" NARROW [] synonym: "cephalic area" RELATED [SPD:0000016] synonym: "head (volume)" EXACT [FMA:7154] xref: AAO:0010335 xref: AEO:0000106 xref: BILA:0000115 xref: BIRNLEX:1230 xref: BTO:0000282 xref: CALOHA:TS-0436 xref: EFO:0000964 xref: EHDAA2:0003106 xref: EMAPA:31858 xref: FBbt:00000004 xref: FMA:7154 xref: GAID:61 xref: galen:Head xref: HAO:0000397 xref: MA:0000023 xref: MAT:0000294 xref: MESH:D006257 xref: MIAA:0000294 xref: NCIT:C12419 xref: OpenCyc:Mx4rEOLm4rgPEdmAAAACs6hRjg xref: OpenCyc:Mx4rvVi6YJwpEbGdrcN5Y29ycA xref: SCTID:302548004 xref: SPD:0000016 xref: TAO:0001114 xref: TGMA:0000002 xref: UMLS:C0018670 {source="ncithesaurus:Head"} xref: UMLS:C0018670 {source="BIRNLEX:1230"} xref: VHOG:0001644 xref: WBbt:0005739 xref: Wikipedia:Head xref: XAO:0003024 xref: ZFA:0001114 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: has_skeleton UBERON:0003129 {gci_relation="part_of", gci_filler="NCBITaxon:7776"} ! skull relationship: only_in_taxon NCBITaxon:33213 relationship: part_of UBERON:0000153 ! anterior region of body relationship: part_of UBERON:0007811 ! craniocervical region property_value: external_definition "Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010335", ontology="AAO", source="AAO:BJB"} property_value: external_definition "Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001114", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0000035 name: primary ovarian follicle def: "An ovarian follicle that has one layer of granulosa cells." [GO:0001545, GOC:mtg_mpo, http://ovary.stanford.edu] subset: pheno_slim synonym: "folliculus ovaricus primarius" EXACT LATIN [FMA:18634] synonym: "ovary primary follicle" EXACT [MA:0002907] synonym: "ovary primary follicle" EXACT [EMAPA:35631] synonym: "preantral follicle of ovary" RELATED [] synonym: "primary egg follicle" RELATED [] synonym: "primary follicle" RELATED [EMAPA:35631] synonym: "primary follicle of ovary" EXACT [FMA:18634] synonym: "primary ovarian follicle" EXACT [FMA:18634] xref: BTO:0000410 xref: EMAPA:35631 xref: FMA:18634 xref: MA:0002907 xref: SCTID:258665002 is_a: UBERON:0001305 ! ovarian follicle intersection_of: UBERON:0001305 ! ovarian follicle intersection_of: has_component UBERON:0005170 {minCardinality="1", maxCardinality="1"} ! granulosa cell layer relationship: develops_from UBERON:0003981 ! primordial ovarian follicle relationship: has_component UBERON:0005170 ! granulosa cell layer [Term] id: UBERON:0000036 name: secondary ovarian follicle def: "A maturing ovarian follicle that has two more more layers of granulosa cells, up to the onset of antrum formation." [GO:0001546, http://ovary.stanford.edu, http://www.repropedia.org/secondary-ovarian-follicle] subset: pheno_slim synonym: "antral follicle of ovary" RELATED [FMA:18637] synonym: "folliculus ovaricus secondarius" EXACT [] synonym: "ovary secondary follicle" EXACT [MA:0002908] synonym: "pre-antral follicle" EXACT [GO:0001546] synonym: "pre-ovulatory follicle" RELATED [EMAPA:30777] synonym: "preantral follicle" EXACT [GO:0001546] synonym: "secondary egg follicle" RELATED [] synonym: "secondary follicle" RELATED [EMAPA:35632] synonym: "secondary follicle of ovary" EXACT [] xref: EMAPA:35632 xref: FMA:18637 xref: MA:0002908 is_a: UBERON:0001305 ! ovarian follicle intersection_of: UBERON:0001305 ! ovarian follicle intersection_of: has_component UBERON:0005170 {minCardinality="2"} ! granulosa cell layer intersection_of: has_potential_to_develop_into UBERON:0000037 ! tertiary ovarian follicle relationship: develops_from UBERON:0000035 ! primary ovarian follicle relationship: has_component UBERON:0005170 ! granulosa cell layer relationship: has_potential_to_develop_into UBERON:0000037 ! tertiary ovarian follicle property_value: editor_note "consider adopting distinction in MA" xsd:string [Term] id: UBERON:0000037 name: tertiary ovarian follicle def: "A follicle that has reached the most mature stage of folliculogenesis, characterized by the presence of the antrum" [http://orcid.org/0000-0002-6601-2165, http://www.repropedia.org/antral-follicle] subset: pheno_slim subset: uberon_slim synonym: "antral follicle" BROAD [] synonym: "antral ovarian follicle" EXACT [GO:0001547] synonym: "folliculi ovarici vesiculosi" EXACT LATIN [FMA:18641, FMA:TA] synonym: "folliculus ovaricus tertiarius" EXACT [] synonym: "folliculus ovaricus tertiarius (vesiculosus)" EXACT [FMA:18641] synonym: "folliculus ovaricus tertiarius (vesiculous)" EXACT [] synonym: "Graafian follicle" EXACT [http://www.repropedia.org/antral-follicle] synonym: "ovary antral follicle" EXACT [http://www.repropedia.org/antral-follicle, MA:0002909] synonym: "tertiary egg follicle" RELATED [] synonym: "tertiary follicle of ovary" EXACT [FMA:18641, http://www.repropedia.org/antral-follicle] synonym: "vesicular follicle of ovary" EXACT [FMA:18641] synonym: "vesicular ovarian follicle" EXACT [FMA:18641] xref: EMAPA:30763 xref: FMA:18641 xref: MA:0002909 xref: NCIT:C32692 xref: SCTID:362261008 xref: UMLS:C0600225 {source="ncithesaurus:Graafian_Follicle"} is_a: UBERON:0001305 ! ovarian follicle intersection_of: UBERON:0001305 ! ovarian follicle intersection_of: has_component UBERON:0005170 {minCardinality="2"} ! granulosa cell layer intersection_of: has_part UBERON:0000039 ! follicular antrum relationship: develops_from UBERON:0000036 ! secondary ovarian follicle relationship: has_component UBERON:0005170 ! granulosa cell layer relationship: has_part UBERON:0000039 ! follicular antrum property_value: depicted_by Primary:follicle-4.JPG xsd:anyURI [Term] id: UBERON:0000038 name: follicular fluid def: "The fluid surrounding the ovum and granulosa cells in the ovarian follicle." [ISBN:145114847X, MESH:D015571, Wikipedia:Follicular_fluid] subset: uberon_slim synonym: "antral fluid, ovarian follicle" RELATED [] synonym: "liquor follicularis" EXACT [FMA:18665] synonym: "liquor folliculi" EXACT LATIN [] synonym: "liquor folliculi" RELATED LATIN [Wikipedia:Follicular_fluid] synonym: "ovarian follicular fluid" RELATED [BTO:0004383] synonym: "ovary follicle fluid" EXACT [MA:0002511] synonym: "ovary follicular fluid" RELATED [BTO:0004383] xref: BTO:0004383 xref: CALOHA:TS-0728 xref: FMA:18665 xref: GAID:372 xref: MA:0002511 xref: MESH:D015571 xref: NCIT:C52556 xref: UMLS:C1709369 {source="ncithesaurus:Ovarian_Follicle_Fluid"} xref: Wikipedia:Follicular_fluid is_a: CARO:0000000 is_a: UBERON:0000463 ! organism substance relationship: has_part CHEBI:17089 relationship: has_part UBERON:0000456 ! secretion of exocrine gland relationship: has_part UBERON:0007779 ! transudate relationship: located_in UBERON:0000039 ! follicular antrum relationship: part_of UBERON:0001305 ! ovarian follicle relationship: surrounds CL:0000025 property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png xsd:anyURI property_value: structure_notes "The follicular fluid contains sex steroids, glycoprotein hormones, plasma proteins, mucopolysaccharides, and enzymes and is rich in hyaluronic acid." xsd:string property_value: taxon_notes "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]" xsd:string [Term] id: UBERON:0000039 name: follicular antrum def: "Region of ovarian follicle filled with follicular fluid." [Wikipedia:Follicular_antrum] subset: uberon_slim synonym: "antral cavity" EXACT [FMA:18675] synonym: "antrum folliculare" EXACT [FMA:18675] synonym: "antrum follicularum" RELATED LATIN [Wikipedia:Follicular_antrum] synonym: "ovarian follicle antrum" EXACT [GO:0001548] xref: EMAPA:37867 {source="MA:th"} xref: FMA:18675 xref: Wikipedia:Follicular_antrum is_a: CARO:0000000 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: location_of UBERON:0000038 ! follicular fluid intersection_of: part_of UBERON:0001305 ! ovarian follicle relationship: location_of UBERON:0000038 ! follicular fluid relationship: part_of UBERON:0001305 ! ovarian follicle [Term] id: UBERON:0000040 name: Leydig's organ def: "A hemopoietic organ found in elasmobranchs. Along with the spleen and special tissue around the gonads, this structure produces red blood cells and it is nestled along the top and bottom of the esophagus." [http://www.elasmo-research.org/education/topics/p_blood_cells.htm, Wikipedia:Leydig's_organ] comment: Phenotype notes: Leydig's organ can be quite large - a 1.6-kilogram (3.5-pound) one was reported from a 1.8-metre (6-foot) long Bluntnose Sixgill Shark (Hexanchus griseus). Structure notes: divided into dorsal and ventral patches, gradation varies between species. Lacks erythroblasts and fat cells[Honma 1983] subset: uberon_slim xref: Wikipedia:Leydig's_organ is_a: UBERON:0004177 ! hemopoietic organ is_a: UBERON:0005057 ! immune organ is_a: UBERON:0005178 ! thoracic cavity element relationship: composed_primarily_of CL:0000738 {source="Honma1983"} relationship: located_in UBERON:0001096 ! wall of esophagus relationship: never_in_taxon NCBITaxon:7863 {source="Wikipedia"} relationship: only_in_taxon NCBITaxon:7778 {source="Wikipedia"} relationship: part_of UBERON:0002390 ! hematopoietic system relationship: part_of UBERON:0002405 ! immune system property_value: taxon_notes "Found in elasmobranchs (sharks and rays) but with some exceptions." xsd:string [Term] id: UBERON:0000041 name: odontode scale def: "Multi-tissue structure composed of enameloid, dentine surrounding a pulp cavity, and bone of attachment anchoring the element into the dermis[VSAO]." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000079] subset: uberon_slim synonym: "dermal denticle" EXACT [Wikipedia:Dermal_denticle] synonym: "odontode scale" EXACT [VSAO:0000079] synonym: "placoid scale" EXACT [VSAO:curator] xref: VSAO:0000079 xref: Wikipedia:Dermal_denticle is_a: UBERON:0007380 {source="VSAO"} ! dermal scale relationship: has_part UBERON:0001751 ! dentine relationship: has_part UBERON:0011692 ! enameloid relationship: present_in_taxon NCBITaxon:119203 relationship: present_in_taxon NCBITaxon:7777 property_value: editor_note "TODO check dentin def" xsd:string property_value: external_definition "Small outgrowths which cover the skin of many cartilaginous fish including sharks. They are similar in structure to teeth, and teeth may have evolved from denticle-like structures in primitive fish.[citation needed] The placoid scales in sharks are formed of dentine with dermal papillae located in the core. These scales develop from the dermal layer of the skin, which is in contrast to the epidermal development seen the in the elasmoid scales of tetrapods. The shape of denticle varies from species to species and can be used in identification. Studies have found that the denticles create tiny vortices that reduce drag to make swimming more efficient. Denticles also allow sharks to swim silently compared to other fish that generate considerable noise when they ply the water[WP][Wikipedia:Dermal_denticle]." xsd:string {source="Wikipedia:Dermal_denticle"} property_value: taxon_notes "Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone." xsd:string [Term] id: UBERON:0000042 name: serous membrane def: "multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer." [https://github.com/obophenotype/uberon/issues/86, Wikipedia:Serous_membrane] subset: uberon_slim subset: vertebrate_core synonym: "serosa" RELATED [Wikipedia:Serous_membrane] synonym: "tunica serosa" EXACT LATIN [FMA:9581] synonym: "wall of serous sac" EXACT [FMA:9581] xref: FMA:9581 xref: GAID:19 xref: MESH:D012704 xref: NCIT:C13169 xref: SCTID:362878009 xref: TAO:0005425 xref: UMLS:C0036760 {source="ncithesaurus:Serosa"} xref: Wikipedia:Serous_membrane xref: ZFA:0005425 is_a: UBERON:0000481 ! multi-tissue structure relationship: dc-contributor https://github.com/cmungall relationship: develops_from UBERON:0000926 {source="Wikipedia"} ! mesoderm relationship: has_part UBERON:0001136 ! mesothelium relationship: has_part UBERON:0002384 ! connective tissue relationship: part_of UBERON:0000060 ! anatomical wall property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png xsd:anyURI property_value: depicted_by http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png xsd:anyURI property_value: external_definition "A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005425", ontology="TAO", source="Wikipedia:Serous_membrane"} property_value: external_definition "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]" xsd:string {source="Wikipedia:Serous_membrane"} property_value: external_ontology_notes "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." xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000043 name: tendon def: "Dense regular connective tissue that connects muscle to bone[VSAO]." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000073, Wikipedia:Tendon] subset: pheno_slim subset: uberon_slim synonym: "sinew" RELATED [Wikipedia:Tendon] synonym: "tendo" RELATED LATIN [Wikipedia:Tendon] xref: AEO:0000091 xref: BTO:0001356 xref: CALOHA:TS-1021 xref: EHDAA2:0003091 xref: EMAPA:35854 xref: EV:0100149 xref: FMA:9721 xref: GAID:276 xref: galen:Tendon xref: MA:0000115 xref: MESH:D013710 xref: NCIT:C13045 xref: OpenCyc:Mx4rvVjefJwpEbGdrcN5Y29ycA xref: SCTID:256667004 xref: UMLS:C0039508 {source="ncithesaurus:Tendon"} xref: VHOG:0001286 xref: VSAO:0000073 xref: Wikipedia:Tendon xref: XAO:0000173 xref: ZFA:0005647 is_a: UBERON:0007846 {source="VSAO"} ! dense regular connective tissue relationship: connects UBERON:0001474 ! bone element relationship: connects UBERON:0001630 ! muscle organ relationship: has_part CL:0000057 {source="AEO"} relationship: has_part CL:0000327 {source="AEO"} relationship: only_in_taxon NCBITaxon:7742 relationship: part_of UBERON:0002204 {source="OG"} ! musculoskeletal system property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg xsd:anyURI property_value: external_definition "Dense regular connective tissue that connects muscle to bone.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000073", ontology="VSAO", source="PSPUB:0000170"} property_value: external_ontology_notes "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" xsd:string {external_ontology="FMA"} property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000044 name: dorsal root ganglion alt_id: UBERON:0026602 def: "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)" [BIRNLEX:2596] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "dorsal root ganglia" RELATED PLURAL [] synonym: "dorsal root ganglion" EXACT [BTO:0001264] synonym: "DRG" RELATED ABBREVIATION [] synonym: "ganglion of dorsal root" EXACT [OBOL:automatic] synonym: "ganglion sensorium nervi spinalis" RELATED [BTO:0001264] synonym: "ganglion sensorium nervi spinalis" RELATED LATIN [Wikipedia:Dorsal_root_ganglion] synonym: "ganglion spinale" RELATED [BTO:0001264] synonym: "ganglion spinalis" EXACT [FMA:5888] synonym: "posterior root ganglion" RELATED [EMAPA:16668] synonym: "spinal ganglion" EXACT [FMA:5888] synonym: "spinal ganglion part of peripheral nervous system" EXACT [BIRNLEX:2598] xref: AAO:0011032 xref: BIRNLEX:2596 xref: BIRNLEX:2598 xref: BTO:0001264 xref: CALOHA:TS-0954 xref: EFO:0000900 xref: EHDAA2:0000418 xref: EHDAA2:0001897 xref: EHDAA:2899 xref: EMAPA:16667 xref: EMAPA:16668 xref: EMAPA:18372 xref: EV:0100373 xref: FMA:5888 xref: MA:0000231 xref: MA:0000232 xref: MAT:0000162 xref: MIAA:0000162 xref: NCIT:C12462 xref: SCTID:244455004 xref: TAO:0000200 xref: UMLS:C0017070 {source="ncithesaurus:Dorsal_Root_Ganglion"} xref: UMLS:C0017070 {source="BIRNLEX:2596"} xref: VHOG:0000222 xref: Wikipedia:Dorsal_root_ganglion xref: XAO:0000210 xref: ZFA:0000200 is_a: UBERON:0001800 {source="MA"} ! sensory ganglion is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0000045 ! ganglion intersection_of: extends_fibers_into UBERON:0001780 ! spinal nerve intersection_of: extends_fibers_into UBERON:0002261 ! dorsal root of spinal cord relationship: develops_from UBERON:0003083 {source="DOI:10.1101/gr.157586.113", source="ZFA", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! trunk neural crest relationship: extends_fibers_into UBERON:0001780 ! spinal nerve relationship: extends_fibers_into UBERON:0002261 ! dorsal root of spinal cord relationship: located_in UBERON:0006692 ! vertebral canal property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/7/71/DRG_Chicken_e7.jpg xsd:anyURI property_value: development_notes "The sensory ganglia of spinal nerves arise only from the neural crest, whereas many sensory ganglia of the 'dorsal' cranial nerves arise from epibranchial placodes as well as the neural crest[DOI:10.1093/icb/icn065]" xsd:string property_value: external_definition "Trunk ganglion which is located adjacent to the spine on a dorsal root and contains the cell bodies of afferent sensory nerves.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000200", ontology="TAO", source="ZFIN:curator"} property_value: external_ontology_notes "MA and EMAPA introduce distinct classes for what appears to be the same thing" xsd:string {external_ontology="FMA"} property_value: homology_notes "From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0000045 name: ganglion def: "A biological tissue mass, most commonly a mass of nerve cell bodies." [https://github.com/obophenotype/uberon/issues/300, Wikipedia:Ganglion] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "ganglia" RELATED [] synonym: "neural ganglion" RELATED [BTO:0000497] xref: AAO:0010426 xref: AEO:0000135 xref: BAMS:G xref: BTO:0000497 xref: CALOHA:TS-0397 xref: EFO:0000899 xref: EHDAA2:0003135 xref: EHDAA:2897 xref: EHDAA:4662 xref: EHDAA:5621 xref: EHDAA:918 xref: EMAPA:32846 xref: EV:0100372 xref: FBbt:00005137 xref: FMA:5884 xref: MA:0002406 xref: MAT:0000207 xref: MAT:0000343 xref: MESH:D005724 xref: MIAA:0000207 xref: MIAA:0000343 xref: NCIT:C12719 xref: NLXANAT:100302 xref: TAO:0000190 xref: TGMA:0001016 xref: UMLS:C0017067 {source="ncithesaurus:Ganglion"} xref: VHOG:0000156 xref: WBbt:0005189 xref: Wikipedia:Ganglion xref: XAO:0000209 xref: ZFA:0000190 is_a: CARO:0000000 is_a: UBERON:0010001 {source="https://github.com/obophenotype/uberon/issues/702"} ! cell cluster organ disjoint_from: UBERON:0002420 {inconsistent_with="BTO"} ! basal ganglion relationship: composed_primarily_of UBERON:0003714 {source="EHDAA2"} ! neural tissue relationship: dc-contributor https://github.com/cmungall relationship: develops_from UBERON:0003869 ! presumptive ganglion relationship: immediate_transformation_of UBERON:0003869 {source="Bgee:AN"} ! presumptive ganglion relationship: part_of UBERON:0001016 ! nervous system property_value: editor_note "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." xsd:string property_value: external_definition "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" xsd:string {source="PMID:21062451"} property_value: external_definition "Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010426", ontology="AAO", source="AAO:EJS"} property_value: external_definition "Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000190", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "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]." xsd:string {source="NLXANAT:100302"} property_value: has_relational_adjective "ganglionic" xsd:string property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000046 name: stemma def: "eye-spots which may be set into a pit to reduce the angles of light that enters and affects the eyespot, to allow the organism to deduce the angle of incoming light" [Wikipedia:Eye#Pit_eyes, Wikipedia:Stemma] subset: uberon_slim synonym: "pit eye" EXACT [Wikipedia:Eye#Pit_eyes] xref: Wikipedia:Stemma is_a: UBERON:0000047 ! simple eye relationship: never_in_taxon NCBITaxon:7742 [Term] id: UBERON:0000047 name: simple eye def: "An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity." [Wikipedia:Eye#Simple_eyes] subset: grouping_class subset: uberon_slim xref: TGMA:0000729 xref: Wikipedia:Eye#Simple_eyes is_a: UBERON:0000970 ! eye [Term] id: UBERON:0000048 name: pinhole eye def: "Simple eye that has a small aperture (which may be adjustable) and deep pit. It is only found in the nautiloids." [DOI:10.1146/annurev.ne.15.030192.000245, Wikipedia:Pinhole_eye] subset: grouping_class subset: uberon_slim xref: Wikipedia:Pinhole_eye is_a: UBERON:0000047 ! simple eye relationship: only_in_taxon NCBITaxon:32577 [Term] id: UBERON:0000049 name: spherical lensed eye def: "simple eye that consists of a lens of one refractive index" [Wikipedia:Eye#Spherical_lensed_eye] subset: grouping_class is_a: UBERON:0000047 ! simple eye [Term] id: UBERON:0000050 name: simple eye with multiple lenses def: "simple eye that has two or more lenses. Some marine organisms bear more than one lens; for instance the copeopod Pontella has three. The outer has a parabolic surface, countering the effects of spherical aberration while allowing a sharp image to be formed. Copilla's eyes have two lenses, which move in and out like a telescope" [Wikipedia:Eye#Multiple_lenses] subset: grouping_class subset: uberon_slim xref: Wikipedia:Eye#Multiple_lenses is_a: UBERON:0000047 ! simple eye relationship: has_component UBERON:0005389 {min_cardinality="2"} ! transparent eye structure relationship: never_in_taxon NCBITaxon:7742 [Term] id: UBERON:0000051 name: fornix of vagina def: "The deepest portions of the vagina, extending into the recesses created by the vaginal portion of cervix[WP,unvetted]." [Wikipedia:Vaginal_fornix] subset: uberon_slim synonym: "fornix" BROAD [] synonym: "fornix vaginae" EXACT LATIN [FMA:19985, FMA:TA] synonym: "vaginal fornices" RELATED PLURAL [] synonym: "vaginal fornix" EXACT [] xref: FMA:19985 xref: NCIT:C33848 xref: SCTID:245475003 xref: UMLS:C0227794 {source="ncithesaurus:Vaginal_Fornix"} xref: Wikipedia:Vaginal_fornix is_a: CARO:0000000 is_a: UBERON:0002553 ! anatomical cavity disjoint_from: UBERON:0000052 ! fornix of brain relationship: part_of UBERON:0000996 ! vagina property_value: depicted_by Female:anatomy.png xsd:anyURI [Term] id: UBERON:0000052 name: fornix of brain def: "A C-shaped bundle of fibres (axons) in the brain, and carries signals from the hippocampus to the mammillary bodies and septal nuclei. It is typically divided into the columns (crus), body, commissure and the pre-commissural and post-commissural fornix (MM)." [BIRNLEX:705] subset: pheno_slim subset: uberon_slim synonym: "brain fornix" EXACT [] synonym: "cerebral fornix" EXACT [] synonym: "forebrain fornix" EXACT [FMA:61965] synonym: "fornix" BROAD [] synonym: "fornix (column and body of fornix)" RELATED [FMA:61965] synonym: "fornix cerebri" RELATED LATIN [NeuroNames:268] synonym: "fornix hippocampus" RELATED [] synonym: "fornix of neuraxis" EXACT [FMA:83865] synonym: "hippocampus fornix" RELATED [] synonym: "neuraxis fornix" EXACT [FMA:83865] xref: BAMS:f xref: BIRNLEX:705 xref: DHBA:10576 xref: DMBA:17767 xref: EMAPA:35352 xref: FMA:61965 {notes="inferred"} xref: FMA:83865 xref: HBA:9249 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=268 {source="BIRNLEX:705"} xref: MA:0002747 xref: NCIT:C32289 xref: SCTID:279302004 xref: UMLS:C0152334 {source="BIRNLEX:705"} xref: UMLS:C0458370 {source="ncithesaurus:Cerebral_Fornix"} xref: Wikipedia:fornix_of_brain is_a: UBERON:0007702 ! tract of brain relationship: extends_fibers_into UBERON:0002206 ! mammillary body relationship: extends_fibers_into UBERON:0002663 ! septal nuclear complex relationship: part_of UBERON:0002421 {source="NIFSTD"} ! hippocampal formation property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/2/21/Gray747.png xsd:anyURI [Term] id: UBERON:0000053 name: macula lutea def: "An oval area in the retina, usually located temporal to the posterior pole of the eye and slightly below the level of the optic disk. It is characterized by the presence of a yellow pigment diffusely permeating the inner layers, contains the fovea centralis in its center, and provides the best phototopic visual acuity. It is devoid of retinal blood vessels, except in its periphery, and receives nourishment from the choriocapillaris of the choroid. (From Cline et al., Dictionary of Visual Science, 4th ed)" [MESH:A09.371.729.522] subset: pheno_slim subset: uberon_slim synonym: "macula" RELATED [] synonym: "macula flava retinae" RELATED [BTO:0003015] synonym: "macula retinae" RELATED [BTO:0003015] synonym: "maculae" RELATED [] xref: BIRNLEX:2540 xref: BTO:0003015 xref: EMAPA:36516 xref: EV:0100349 xref: FMA:58637 xref: GAID:909 xref: MA:0001306 xref: MESH:D008266 xref: NCIT:C26464 xref: NCIT:C33044 xref: SCTID:362517001 xref: UMLS:C0450295 {source="ncithesaurus:Macula_Lutea"} xref: UMLS:C0450295 {source="BIRNLEX:2540"} xref: UMLS:C1284755 {source="BIRNLEX:2540"} xref: Wikipedia:Macula_of_retina is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure disjoint_from: UBERON:0000054 ! macula relationship: part_of UBERON:0000966 ! retina property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png xsd:anyURI [Term] id: UBERON:0000054 name: macula def: "Thickened areas of the saccule or utricle where the termination of the vestibular nerve occurs[MESH,modified]." [MESH:A09.246.631.909.625.125] subset: pheno_slim subset: uberon_slim synonym: "acoustic macula" RELATED [MESH:A09.246.631.909.625.125] synonym: "acoustic maculae" RELATED PLURAL [MESH:A09.246.631.909.625.125] synonym: "macula" EXACT [] synonym: "maculae" EXACT PLURAL [] synonym: "sensory macula" EXACT [ZFA:0000386] synonym: "sensory patch" EXACT [ZFA:0000386] xref: GAID:777 xref: MESH:D008267 xref: TAO:0000386 xref: ZFA:0000386 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part GO:0070451 relationship: part_of UBERON:0001846 ! internal ear property_value: curator_notes "this refers to the inner ear structure, not the macula of the retina. We follow ZFA in including a grouping class for the macula of utricle and sacule" xsd:string property_value: external_definition "Patches of thickened, pseudostratified epithelium of the inner ear, consisting of regular arrays of sensory hair cells interspersed with supporting cells. Each patch has its own charcteristic shape and polarity pattern. (See Anatomical Atlas entry for sensory patches of the ear by T. Whitfield.)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000386", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "macular" xsd:string [Term] id: UBERON:0000055 name: vessel def: "A tubular structure that contains, conveys body fluid, such as blood or lymph." [https://orcid.org/0000-0002-6601-2165] subset: grouping_class subset: pheno_slim is_a: UBERON:0004111 ! anatomical conduit relationship: channel_for UBERON:0006314 ! bodily fluid [Term] id: UBERON:0000056 name: ureter def: "Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs." [GO:0090189, Wikipedia:Ureter] subset: efo_slim subset: major_organ subset: organ_slim subset: pheno_slim subset: uberon_slim synonym: "metanephric duct" RELATED [ISBN:0073040584, VHOG:0000605] xref: AAO:0010254 xref: BTO:0001409 xref: CALOHA:TS-1084 xref: EFO:0000930 xref: EHDAA2:0002139 xref: EHDAA:9341 xref: EMAPA:17950 xref: EV:0100097 xref: FMA:9704 xref: GAID:438 xref: galen:Ureter xref: MA:0000378 xref: MAT:0000120 xref: MESH:D014513 xref: MIAA:0000120 xref: NCIT:C12416 xref: OpenCyc:Mx4rvhmm6JwpEbGdrcN5Y29ycA xref: SCTID:302511008 xref: UMLS:C0041951 {source="ncithesaurus:Ureter"} xref: VHOG:0000605 xref: Wikipedia:Ureter xref: XAO:0000144 relationship: channel_for UBERON:0001088 ! urine relationship: channels_from UBERON:0001224 ! renal pelvis relationship: channels_into UBERON:0001255 ! urinary bladder relationship: develops_from UBERON:0005081 {source="GO"} ! ureter ureteric bud relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism relationship: part_of UBERON:0002355 {xref="MA:0000378"} ! pelvic region of trunk relationship: part_of UBERON:0011143 {source="FMA"} ! upper urinary tract relationship: part_of UBERON:0036295 ! renal pelvis/ureter property_value: depicted_by Urinary:system.svg xsd:anyURI property_value: external_definition "Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010254", ontology="AAO", source="AAO:BJB"} property_value: external_definition "The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000605", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: has_relational_adjective "ureteral" xsd:string property_value: has_relational_adjective "ureteric" xsd:string property_value: homology_notes "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]" xsd:string {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/"} property_value: structure_notes "in humans, consists of adventitial, muscular and mucoa layers" xsd:string [Term] id: UBERON:0000057 name: urethra def: "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" [MGI:anna, MP:0000537] subset: efo_slim subset: major_organ subset: organ_slim subset: pheno_slim subset: uberon_slim xref: BTO:0001426 xref: CALOHA:TS-1132 xref: EFO:0000931 xref: EMAPA:30901 xref: EV:0100099 xref: FMA:19667 xref: GAID:390 xref: galen:Urethra xref: MA:0000379 xref: MAT:0000121 xref: MESH:D014521 xref: MIAA:0000121 xref: NCIT:C12417 xref: OpenCyc:Mx4rvVjkypwpEbGdrcN5Y29ycA xref: SCTID:302513006 xref: UMLS:C0041967 {source="ncithesaurus:Urethra"} xref: VHOG:0001264 xref: Wikipedia:Urethra xref: XAO:0000153 is_a: UBERON:0000062 ! organ relationship: capable_of_part_of GO:0060073 relationship: channel_for UBERON:0001088 ! urine relationship: channels_from UBERON:0001255 ! urinary bladder relationship: continuous_with UBERON:0001255 ! urinary bladder relationship: develops_from UBERON:0000164 {notes="pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra", source="Wikipedia"} ! primitive urogenital sinus relationship: develops_from UBERON:0013241 {source="Wikipedia"} ! embryonic urethral groove relationship: part_of UBERON:0001556 ! lower urinary tract property_value: depicted_by Female:anatomy.png xsd:anyURI property_value: has_relational_adjective "urethral" xsd:string property_value: taxon_notes "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." xsd:string [Term] id: UBERON:0000058 name: duct def: "A tubular structure that transports secreted or excreted substances." [http://orcid.org/0000-0002-6601-2165, http://www.siumed.edu/~dking2/intro/glands.htm#ducts] subset: grouping_class synonym: "anatomical duct" EXACT [] synonym: "ducts" RELATED PLURAL [XAO:0004000] synonym: "exocrine duct" NARROW [] synonym: "exocrine gland duct" NARROW [] xref: AAO:0011123 xref: FBbt:00100314 xref: FMA:30320 xref: galen:Duct xref: NCIT:C12948 xref: SCTID:91726008 xref: TAO:0005171 xref: UMLS:C0687028 {source="ncithesaurus:Duct"} xref: Wikipedia:Duct_(anatomy) xref: XAO:0004000 xref: ZFA:0005171 is_a: UBERON:0000063 ! organ subunit relationship: conduit_for UBERON:0000463 ! organism substance relationship: has_part UBERON:0013686 ! anatomical conduit space relationship: has_part UBERON:0034969 ! epithelial layer of duct relationship: has_quality PATO:0002299 property_value: external_definition "A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]." xsd:string {source="ZFA:0005171"} property_value: external_ontology_notes "Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here." xsd:string [Term] id: UBERON:0000059 name: large intestine def: "A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]." [ISBN:0073040584, Wikipedia:Large_intestine_(anatomy)] subset: efo_slim subset: major_organ subset: organ_slim subset: pheno_slim synonym: "intestinum crassum" RELATED [BTO:0000706] xref: AAO:0010396 xref: BTO:0000706 xref: CALOHA:TS-1306 xref: EFO:0000840 xref: EMAPA:19252 xref: EV:0100077 xref: FMA:7201 xref: GAID:306 xref: galen:LargeIntestine xref: MA:0000333 xref: MESH:A03.492.411.495 xref: MIAA:0000046 xref: NCIT:C12379 xref: OpenCyc:Mx4rvVkF5pwpEbGdrcN5Y29ycA xref: SCTID:181254001 xref: UMLS:C0021851 {source="ncithesaurus:Large_Intestine"} xref: VHOG:0000054 xref: Wikipedia:Large_intestine_(anatomy) xref: XAO:0000131 is_a: UBERON:0004921 {source="cjm"} ! subdivision of digestive tract relationship: contributes_to_morphology_of UBERON:0000160 ! intestine relationship: only_in_taxon NCBITaxon:7742 relationship: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0004907 ! lower digestive tract property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000060 name: anatomical wall alt_id: UBERON:0009915 def: "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers." [FMA:82482] subset: upper_level synonym: "organ wall" RELATED [FMA:82482] synonym: "wall" BROAD [] synonym: "wall of organ" EXACT [FMA:82482] xref: EMAPA:25036 xref: FMA:82482 xref: galen:Wall is_a: UBERON:0000064 ! organ part relationship: adjacent_to UBERON:0002553 ! anatomical cavity relationship: has_part UBERON:0004923 ! organ component layer property_value: external_ontology_notes "in FMA, serosa is a wall" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000061 name: anatomical structure def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [CARO:0000003] subset: upper_level synonym: "biological structure" EXACT [] synonym: "connected biological structure" EXACT [CARO:0000003] xref: AAO:0010825 xref: AEO:0000003 xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 xref: FBbt:00007001 xref: FMA:305751 xref: FMA:67135 xref: GAID:781 xref: HAO:0000003 xref: http://dbpedia.org/ontology/AnatomicalStructure xref: MA:0003000 xref: MESH:D000825 xref: SCTID:362889002 xref: TAO:0000037 xref: TGMA:0001823 xref: VHOG:0001759 xref: XAO:0003000 xref: ZFA:0000037 is_a: UBERON:0000465 ! material anatomical entity relationship: existence_ends_during_or_before UBERON:0000071 ! death stage relationship: existence_starts_during_or_after UBERON:0000106 ! zygote stage [Term] id: UBERON:0000062 name: organ def: "Anatomical structure that performs a specific function or group of functions [WP]." [Wikipedia:Organ_(anatomy)] subset: upper_level synonym: "anatomical unit" RELATED [] synonym: "body organ" RELATED [] synonym: "element" RELATED [http://orcid.org/0000-0002-6601-2165] xref: BIRNLEX:4 xref: CARO:0020004 xref: EFO:0000634 xref: EMAPA:35949 xref: ENVO:01000162 xref: FMA:67498 xref: MA:0003001 xref: NCIT:C13018 xref: OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA xref: OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA xref: SCTID:272625005 xref: UMLS:C0178784 {source="ncithesaurus:Organ"} xref: WBbt:0003760 xref: Wikipedia:Organ_(anatomy) is_a: UBERON:0010000 ! multicellular anatomical structure disjoint_from: UBERON:0002095 {source="PMID:28192867"} ! mesentery disjoint_from: UBERON:0034921 ! multi organ part structure relationship: capable_of GO:0008150 relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage relationship: has_boundary UBERON:0006984 ! anatomical surface relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} relationship: part_of UBERON:0000467 ! anatomical system property_value: external_definition "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." xsd:string {source="GO:0048513"} property_value: external_ontology_notes "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" xsd:string [Term] id: UBERON:0000063 name: organ subunit def: "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." [http://orcid.org/0000-0002-6601-2165] subset: upper_level synonym: "organ region with fixed fiat boundary" RELATED [FMA:86140] synonym: "organ segment" RELATED [FMA:86140] synonym: "segment of organ" RELATED [FMA:86140] xref: FMA:86140 is_a: UBERON:0000064 ! organ part property_value: editor_note "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" xsd:string property_value: external_definition "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." xsd:string {source="FMA:86140", version="3"} property_value: external_definition "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." xsd:string {source="FMA:86140", version="1"} [Term] id: UBERON:0000064 name: organ part def: "A multicellular structure that is a part of an organ." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: non_informative subset: upper_level synonym: "cardinal organ part" EXACT [FMA:82472] synonym: "regional part of organ" RELATED [BIRNLEX:16] xref: AAO:0011124 xref: BIRNLEX:16 xref: EFO:0000635 xref: FMA:82472 xref: SCTID:113343008 xref: SCTID:91717005 is_a: UBERON:0010000 ! multicellular anatomical structure relationship: part_of UBERON:0000062 ! organ property_value: curator_notes "currently defined in a very broad sense, may be replaced by more specific classes in the future" xsd:string [Term] id: UBERON:0000065 name: respiratory tract def: "Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts" [https://orcid.org/0000-0002-6601-2165] xref: EHDAA2:0001606 xref: EHDAA:1568 xref: EHDAA:2219 xref: EMAPA:16737 xref: FMA:265130 xref: OpenCyc:Mx4rvvM--pwpEbGdrcN5Y29ycA xref: SCTID:361110005 xref: VHOG:0000393 is_a: UBERON:0001005 ! respiratory airway is_a: UBERON:0004119 ! endoderm-derived structure relationship: develops_from UBERON:0007026 {source="NCBIBook:NBK10107"} ! presumptive gut relationship: develops_from UBERON:0008947 ! respiratory primordium relationship: part_of UBERON:0001004 ! respiratory system [Term] id: UBERON:0000066 name: fully formed stage def: "The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage." [https://orcid.org/0000-0002-6601-2165] subset: efo_slim synonym: "adult stage" BROAD [] synonym: "fully formed animal stage" EXACT [] synonym: "juvenile-adult stage" EXACT [] xref: BilaDO:0000004 xref: BTO:0001043 xref: EFO:0001272 xref: FBdv:00005369 xref: WBls:0000041 xref: XtroDO:0000084 is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000092 ! post-embryonic stage relationship: preceded_by UBERON:0000111 ! organogenesis stage relationship: preceded_by UBERON:0004729 {gci_relation="part_of", gci_filler="NCBITaxon:6239"} ! nematode larval stage relationship: precedes UBERON:0000071 ! death stage property_value: seeAlso https://github.com/obophenotype/uberon/issues/566 xsd:anyURI [Term] id: UBERON:0000067 name: obsolete embryo stage part def: "A stage that is part of the embryo stage." [https://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "embryonic stage part" EXACT [] is_obsolete: true [Term] id: UBERON:0000068 name: embryo stage def: "A life cycle stage that starts with fertilization and ends with the fully formed embryo." [http://orcid.org/0000-0002-6601-2165] synonym: "embryogenesis" RELATED [] synonym: "embryonic stage" EXACT [] xref: BilaDO:0000002 xref: EV:0300001 xref: FBdv:00005289 xref: FMA:72652 xref: HsapDv:0000002 xref: MmusDv:0000002 xref: OGES:000000 xref: OGES:000022 xref: SCTID:296280003 xref: WBls:0000003 xref: WBls:0000092 xref: WBls:0000102 xref: XAO:1000012 is_a: UBERON:0000105 ! life cycle stage disjoint_from: UBERON:0000092 ! post-embryonic stage relationship: part_of GO:0009790 relationship: part_of UBERON:0000104 ! life cycle relationship: precedes UBERON:0000066 ! fully formed stage relationship: precedes UBERON:0000092 ! post-embryonic stage relationship: simultaneous_with GO:0009790 [Term] id: UBERON:0000069 name: larval stage def: "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." [Wikipedia:Larva] subset: efo_slim synonym: "ammocoete" NARROW SENSU [Wikipedia:Larva] synonym: "ammocoete stage" NARROW SENSU [Wikipedia:Larva] synonym: "bipinnaria" NARROW SENSU [Wikipedia:Larva] synonym: "bipinnaria stage" NARROW SENSU [Wikipedia:Larva] synonym: "caterpillar" NARROW SENSU [Wikipedia:Larva] synonym: "caterpillar stage" NARROW SENSU [Wikipedia:Larva] synonym: "glochidium" NARROW SENSU [Wikipedia:Larva] synonym: "glochidium stage" NARROW SENSU [Wikipedia:Larva] synonym: "grub" NARROW SENSU [Wikipedia:Larva] synonym: "grub stage" NARROW SENSU [Wikipedia:Larva] synonym: "larva" RELATED [] synonym: "larva stage" EXACT [] synonym: "leptocephalus" NARROW SENSU [Wikipedia:Larva] synonym: "leptocephalus stage" NARROW SENSU [Wikipedia:Larva] synonym: "maggot" NARROW SENSU [Wikipedia:Larva] synonym: "maggot stage" NARROW SENSU [Wikipedia:Larva] synonym: "metacestode" NARROW SENSU [BTO:0000859] synonym: "naiad, nymph" NARROW SENSU [Wikipedia:Larva] synonym: "naiad, nymph stage" NARROW SENSU [Wikipedia:Larva] synonym: "nauplius" NARROW SENSU [Wikipedia:Larva] synonym: "nauplius stage" NARROW SENSU [Wikipedia:Larva] synonym: "nymph" NARROW SENSU [Wikipedia:Larva] synonym: "nymph stage" NARROW SENSU [Wikipedia:Larva] synonym: "planula" NARROW SENSU [Wikipedia:Larva] synonym: "planula stage" NARROW SENSU [Wikipedia:Larva] synonym: "tornaria" NARROW SENSU [NCBITaxon:10219] synonym: "trochophore" NARROW SENSU [Wikipedia:Larva] synonym: "trochophore stage" NARROW SENSU [Wikipedia:Larva] synonym: "veliger" NARROW SENSU [Wikipedia:Larva] synonym: "veliger stage" NARROW SENSU [Wikipedia:Larva] synonym: "wriggler" NARROW SENSU [Wikipedia:Larva] synonym: "wriggler stage" NARROW SENSU [Wikipedia:Larva] synonym: "zoea" NARROW SENSU [Wikipedia:Larva] synonym: "zoea stage" NARROW SENSU [Wikipedia:Larva] xref: BTO:0000915 xref: BTO:0000954 xref: EFO:0001303 xref: FBdv:00005336 xref: MIAA:0000400 xref: OGES:000008 xref: Wikipedia:Larva xref: ZFS:0000048 is_a: UBERON:0000105 ! life cycle stage relationship: immediately_preceded_by UBERON:0000068 ! embryo stage relationship: never_in_taxon NCBITaxon:32524 relationship: part_of GO:0002164 relationship: part_of UBERON:0000092 ! post-embryonic stage relationship: simultaneous_with GO:0002164 property_value: curator_notes "Uberon includes clade-specific subclasses, e.g. nematod larva" xsd:string property_value: taxon_notes "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" xsd:string {source="WP"} [Term] id: UBERON:0000070 name: pupal stage def: "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." [https://github.com/obophenotype/uberon/issues/562, Wikipedia:Pupa] synonym: "aurelia stage" NARROW [NCBITaxon:37572, Wikipedia:Pupa] synonym: "chrysalides stage" NARROW [NCBITaxon:37572, Wikipedia:Pupa] synonym: "chrysalis stage" NARROW [NCBITaxon:37572, Wikipedia:Pupa] synonym: "pupa stage" EXACT [] xref: FBdv:00005349 xref: Wikipedia:Pupa is_a: UBERON:0000105 ! life cycle stage relationship: dc-contributor https://github.com/ANiknejad relationship: dc-contributor https://github.com/cmungall relationship: dc-contributor https://github.com/dosumis relationship: dc-contributor https://github.com/fbastian relationship: dc-contributor https://github.com/mmc46 relationship: immediately_preceded_by UBERON:0000069 ! larval stage relationship: only_in_taxon NCBITaxon:33392 relationship: part_of GO:0035209 relationship: part_of UBERON:0000092 ! post-embryonic stage relationship: simultaneous_with GO:0035209 {notes="may be better to model pupal development as including the pre-pupal stage"} property_value: seeAlso https://github.com/obophenotype/uberon/issues/562 xsd:anyURI property_value: taxon_notes "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" xsd:string [Term] id: UBERON:0000071 name: death stage def: "End of the life of an organism." [XAO:0000437] synonym: "death" RELATED [] xref: XAO:0000437 xref: XtroDO:0000085 is_a: UBERON:0000105 ! life cycle stage relationship: ends UBERON:0000104 ! life cycle relationship: part_of UBERON:0000104 ! life cycle property_value: external_ontology_notes "ncit:Death is an outcome" xsd:string {external_ontology="ncit"} [Term] id: UBERON:0000072 name: proximo-distal subdivision of respiratory tract def: "An section of a respiratory tract." [http://orcid.org/0000-0002-6601-2165] subset: non_informative synonym: "respiratory tract" RELATED [MA:0000434] synonym: "subdivision of respiratory tract" RELATED [] xref: EMAPA:16737 xref: FMA:45660 xref: MA:0000434 is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: part_of UBERON:0000065 ! respiratory tract relationship: part_of UBERON:0000065 ! respiratory tract property_value: external_ontology_notes "MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole" xsd:string {external_ontology="MA"} [Term] id: UBERON:0000073 name: regional part of nervous system def: "Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS." [BIRNLEX:1157] subset: non_informative subset: upper_level synonym: "part of nervous system" EXACT [BIRNLEX:1157] xref: BIRNLEX:1157 xref: NCIT:C13040 xref: SCTID:25087005 xref: UMLS:C1518256 {source="ncithesaurus:Nervous_System_Part"} is_a: UBERON:0000481 ! multi-tissue structure intersection_of: UBERON:0000481 ! multi-tissue structure intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system created_by: Melissa Haendel creation_date: 2009-06-18T09:00:04Z [Term] id: UBERON:0000074 name: renal glomerulus def: "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]." [MP:0005325, Wikipedia:Glomerulus] subset: efo_slim subset: pheno_slim subset: vertebrate_core synonym: "glomerular capillary tuft" RELATED [ZFA:0001288] synonym: "glomerular tuft" RELATED INCONSISTENT [] synonym: "glomerulus" BROAD [] synonym: "glomerulus renis" RELATED LATIN [Wikipedia:Glomerulus] synonym: "Malphigian glomerulus" RELATED MISSPELLING [BTO:0000530] synonym: "Malpighian glomerulus" RELATED [http://medical-dictionary.thefreedictionary.com/malpighian+glomerulus] synonym: "Malpighian tuft" RELATED [http://medical-dictionary.thefreedictionary.com/malpighian+glomerulus] synonym: "renal corpuscle" RELATED INCONSISTENT [] synonym: "renal glomeruli" EXACT [TAO:0001288] xref: BTO:0000530 xref: CALOHA:TS-0862 xref: EFO:0003667 xref: EMAPA:28329 xref: EV:0100386 xref: FMA:15624 xref: MA:0001657 xref: MESH:D007678 xref: NCIT:C13250 xref: SCTID:362217000 xref: TAO:0001288 xref: UMLS:C0022663 {source="ncithesaurus:Glomerulus"} xref: Wikipedia:Glomerulus xref: ZFA:0001288 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:0001047 ! neural glomerulus relationship: develops_from UBERON:0005749 ! glomerular tuft relationship: part_of UBERON:0001229 {source="FMA", source="MA"} ! renal corpuscle relationship: surrounded_by UBERON:0001230 ! glomerular capsule property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg xsd:anyURI property_value: depicted_by Renal:corpuscle.svg xsd:anyURI property_value: external_ontology_notes "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?" xsd:string {external_ontology="ZFA"} created_by: Melissa Haendel creation_date: 2009-06-18T09:26:37Z [Term] id: UBERON:0000075 name: subdivision of skeletal system alt_id: UBERON:0010322 def: "Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] subset: non_informative synonym: "skeletal system part" RELATED [] synonym: "skeletal system subdivision" EXACT [FMA:85544] xref: FMA:85544 xref: galen:ComplexSkeletalStructure xref: NCIT:C34076 xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: composed_primarily_of UBERON:0004765 ! skeletal element relationship: only_in_taxon NCBITaxon:7711 relationship: part_of UBERON:0001434 ! skeletal system [Term] id: UBERON:0000076 name: external ectoderm def: "The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm." [MGI:anna, MP:0012532] subset: pheno_slim synonym: "surface (external) ectoderm" EXACT [] synonym: "surface ectoderm" EXACT [MP:0012532] xref: EHDAA2:0001968 xref: EHDAA:1494 xref: EHDAA:350 xref: EHDAA:4784 xref: EHDAA:4790 xref: EHDAA:4796 xref: EHDAA:7860 xref: EMAPA:16096 xref: FMA:87656 xref: NCIT:C34309 xref: UMLS:C1515087 {source="ncithesaurus:Surface_Ectoderm"} xref: Wikipedia:External_ectoderm is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000924 {source="EHDAA2"} ! ectoderm property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png xsd:anyURI property_value: development_notes "(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" xsd:string property_value: editor_note "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)" xsd:string [Term] id: UBERON:0000077 name: mixed endoderm/mesoderm-derived structure def: "An anatomical structure that develops from the endoderm and the mesoderm." [https://orcid.org/0000-0002-6601-2165] subset: grouping_class intersection_of: UBERON:0000061 ! anatomical structure intersection_of: develops_from UBERON:0000925 ! endoderm intersection_of: develops_from UBERON:0000926 ! mesoderm relationship: develops_from UBERON:0000925 ! endoderm relationship: develops_from UBERON:0000926 ! mesoderm property_value: curator_notes "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" xsd:string [Term] id: UBERON:0000078 name: mixed ectoderm/mesoderm/endoderm-derived structure def: "An anatomical structure that develops from the ectoderm, mesoderm and endoderm." [https://orcid.org/0000-0002-6601-2165] subset: grouping_class intersection_of: UBERON:0000061 ! anatomical structure intersection_of: develops_from UBERON:0000924 ! ectoderm intersection_of: develops_from UBERON:0000925 ! endoderm intersection_of: develops_from UBERON:0000926 ! mesoderm relationship: develops_from UBERON:0000924 ! ectoderm relationship: develops_from UBERON:0000925 ! endoderm relationship: develops_from UBERON:0000926 ! mesoderm property_value: curator_notes "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" xsd:string [Term] id: UBERON:0000079 name: male reproductive system def: "The organs associated with producing offspring in the gender that produces spermatozoa." [MP:0001145] subset: efo_slim subset: pheno_slim synonym: "genitalia of male organism" EXACT [OBOL:automatic] synonym: "male genital organ" RELATED [BTO:0000082] synonym: "male genital system" EXACT [FMA:45664] synonym: "male genital tract" RELATED [] synonym: "male genitalia" EXACT [] synonym: "male genitals" EXACT [] synonym: "male organism genitalia" EXACT [OBOL:automatic] synonym: "male organism reproductive system" EXACT [OBOL:automatic] synonym: "male reproductive tract" RELATED [MA:0000396] synonym: "reproductive system of male organism" EXACT [OBOL:automatic] synonym: "systema genitale masculinum" RELATED [BTO:0000082] xref: BTO:0000082 xref: CALOHA:TS-1310 xref: EFO:0000970 xref: EHDAA2:0001054 xref: EHDAA:8136 xref: EMAPA:17968 xref: EV:0100101 xref: FBbt:00004927 xref: FMA:45664 xref: GAID:386 xref: HAO:0000505 xref: MA:0000396 xref: MESH:D005837 xref: NCIT:C12722 xref: OpenCyc:Mx4rvViCepwpEbGdrcN5Y29ycA xref: SCTID:361340001 xref: TGMA:0000634 xref: UMLS:C0017422 {source="ncithesaurus:Male_Genitalia"} xref: UMLS:C1963704 {source="ncithesaurus:Male_Reproductive_System"} xref: VHOG:0000725 xref: Wikipedia:Male_reproductive_system_(human) xref: XAO:0000155 is_a: UBERON:0000990 ! reproductive system intersection_of: UBERON:0000990 ! reproductive system intersection_of: part_of UBERON:0003101 ! male organism disjoint_from: UBERON:0000474 ! female reproductive system relationship: part_of UBERON:0003101 ! male organism property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000080 name: mesonephros def: "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." [GO:0001823, Wikipedia:Mesonephros] subset: efo_slim subset: organ_slim subset: pheno_slim subset: vertebrate_core synonym: "amphibian adult kidney" RELATED [XAO:0000141] synonym: "corpus Wolffi" RELATED [BTO:0001542] synonym: "mesonephric kidney" EXACT [XAO:0000141] synonym: "mesonephroi" EXACT PLURAL [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron] synonym: "middle kidney" RELATED [BTO:0001542] synonym: "opisthonephros" RELATED [VHOG:0000038, XAO:0000141] synonym: "opisto nephros" RELATED [] synonym: "opistonephros" RELATED [http://www.usm.maine.edu/bio/courses/bio205/bio205_26_sex.html] synonym: "Wolffian body" EXACT [BTO:0001542, GOC:yaf, MESH:A16.254.500, Wikipedia:Mesonephros] xref: AAO:0010384 xref: BTO:0001542 xref: CALOHA:TS-0624 xref: EFO:0000928 xref: EHDAA2:0001130 xref: EHDAA:1581 xref: EHDAA:5903 xref: EMAPA:16744 xref: FMA:72171 xref: GAID:1308 xref: MESH:D001755 xref: NCIT:C26467 xref: SCTID:308799002 xref: TAO:0000529 xref: UMLS:C0025492 {source="ncithesaurus:Mesonephros"} xref: VHOG:0000038 xref: Wikipedia:Mesonephros xref: XAO:0000141 xref: ZFA:0000529 is_a: UBERON:0002113 ! kidney relationship: develops_from UBERON:0002120 ! pronephros property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png xsd:anyURI property_value: external_definition "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000038", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: external_definition "Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010384", ontology="AAO", source="AAO:BJB"} property_value: function_notes "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]" xsd:string property_value: has_relational_adjective "mesonephric" xsd:string property_value: homology_notes "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]" xsd:string {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/"} property_value: taxon_notes "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" xsd:string [Term] id: UBERON:0000081 name: metanephros def: "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]" [GO:0001656, Wikipedia:Metanephros#Metanephros] subset: organ_slim subset: pheno_slim synonym: "definite kidney" RELATED [BTO:0001543] synonym: "definitive kidney" RELATED [BTO:0001543] synonym: "hind kidney" RELATED [BTO:0001543] synonym: "metanephric kidney" RELATED [VHOG:0000039] synonym: "metanephron" EXACT [BTO:0001543] xref: BTO:0001543 xref: EHDAA2:0001137 xref: EHDAA:3089 xref: EHDAA:5911 xref: EMAPA:17373 xref: EMAPA_RETIRED:17207 xref: FMA:72172 xref: NCIT:C34209 xref: SCTID:308797000 xref: UMLS:C0231049 {source="ncithesaurus:Metanephros"} xref: VHOG:0000039 xref: Wikipedia:Metanephros#Metanephros is_a: UBERON:0002113 ! kidney relationship: developmentally_replaces UBERON:0000080 {source="ISBN:9780878932504"} ! mesonephros relationship: develops_from UBERON:0003220 {evidence="definitional"} ! metanephric mesenchyme relationship: develops_from UBERON:0005080 {source="GO"} ! metanephric ureteric bud relationship: develops_from UBERON:0005753 ! caudal part of nephrogenic cord relationship: existence_ends_during UBERON:0000066 ! fully formed stage property_value: development_notes "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" xsd:string property_value: editor_note "TODO check developmental relationships" xsd:string property_value: external_definition "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000039", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: has_relational_adjective "metanephric" xsd:string property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000082 name: adult mammalian kidney def: "A kidney at the most advanced stage of development in a mammal." [https://github.com/obophenotype/uberon/issues/1232, Wikipedia:Kidney_development] xref: BTO:0000671 xref: CALOHA:TS-0510 xref: EFO:0000929 xref: EV:0100096 xref: FMA:7203 xref: GAID:423 xref: galen:Kidney xref: MA:0000368 xref: MAT:0000119 xref: MESH:D007668 xref: MIAA:0000119 xref: NCIT:C12415 xref: OpenCyc:Mx4rvVjlYpwpEbGdrcN5Y29ycA xref: SCTID:181414000 is_a: UBERON:0002113 ! kidney is_a: UBERON:0004120 ! mesoderm-derived structure relationship: develops_from UBERON:0000081 ! metanephros [Term] id: UBERON:0000083 name: mesonephric tubule def: "A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]." [Wikipedia:Mesonephric_tubules] synonym: "renal tubules" RELATED PLURAL [VHOG:0000500] synonym: "tubuli mesonephrici" RELATED LATIN [Wikipedia:Mesonephric_tubules] xref: AAO:0010389 xref: EHDAA2:0001134 xref: EMAPA:16747 xref: VHOG:0000500 xref: Wikipedia:Mesonephric_tubules xref: XAO:0000148 is_a: UBERON:0003914 ! epithelial tube intersection_of: UBERON:0003914 ! epithelial tube intersection_of: part_of UBERON:0000080 ! mesonephros relationship: part_of UBERON:0000080 ! mesonephros property_value: editor_note "TODO check" xsd:string property_value: external_definition "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000500", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/mesonephric+tubule"} property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000084 name: ureteric bud def: "An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]" [MP:0010979, PMID:19828308] subset: pheno_slim synonym: "diverticulum" RELATED [BTO:0001646] synonym: "diverticulum metanephricum" RELATED LATIN [Wikipedia:Ureteric_bud] synonym: "gemma ureterica" RELATED LATIN [Wikipedia:Ureteric_bud] synonym: "metanephric bud" RELATED [BTO:0001646] synonym: "metanephric diverticulum" RELATED [Wikipedia:Metanephros#Metanephros] synonym: "ureteric ampulla" RELATED [] synonym: "ureteric diverticulum" RELATED [VHOG:0000541] xref: BTO:0001646 xref: EHDAA2:0002140 xref: EHDAA:3091 xref: EHDAA:5917 xref: EMAPA:17209 xref: NCIT:C34207 xref: SCTID:361528000 xref: UMLS:C1284058 {source="ncithesaurus:Metanephric_Diverticulum"} xref: VHOG:0000541 xref: Wikipedia:Ureteric_bud is_a: CARO:0000003 is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac relationship: developmentally_induced_by UBERON:0003220 {source="ISBN:9780878932504"} ! metanephric mesenchyme relationship: develops_from UBERON:0003074 {source="EHDAA2"} ! mesonephric duct relationship: part_of UBERON:0003074 ! mesonephric duct property_value: external_definition "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000541", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: external_definition "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]." xsd:string {source="VHOG:0000541"} property_value: homology_notes "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0000085 name: morula def: "A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum." [MP:0012130] subset: pheno_slim synonym: "morula (2-16 cells)" RELATED [EHDAA2:0000005] xref: BTO:0001508 xref: EHDAA2:0000005 xref: FMA:292334 xref: GAID:1295 xref: MESH:A16.254.270.550 xref: NCIT:C34212 xref: SCTID:361474003 xref: UMLS:C0026573 {source="ncithesaurus:Morula"} xref: Wikipedia:Morula is_a: CARO:0000000 is_a: UBERON:0000922 ! embryo relationship: existence_ends_during UBERON:0000107 ! cleavage stage relationship: existence_starts_during UBERON:0000107 ! cleavage stage relationship: has_part CL:0000353 relationship: part_of UBERON:0004716 {source="EHDAA2"} ! conceptus relationship: surrounded_by UBERON:0000086 ! zona pellucida property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png xsd:anyURI property_value: external_ontology_notes "EHDAA2 has embryo starting later" xsd:string {external_ontology="EHDAA2"} [Term] id: UBERON:0000086 name: zona pellucida def: "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." [Wikipedia:Zona_pellucida] subset: pheno_slim subset: vertebrate_core synonym: "oolemma" RELATED [BTO:0003135] synonym: "pellucid zone" RELATED [BTO:0003135] synonym: "striated membrane" RELATED [BTO:0003135] synonym: "vitelline envelope" RELATED [] synonym: "vitelline membrane" RELATED [] synonym: "zona pellucida - vitelline membrane" BROAD [VHOG:0000720] synonym: "zona radiata" RELATED [BTO:0003135] synonym: "zona striata" RELATED [BTO:0003135] xref: BTO:0003135 xref: EHDAA2:0002220 xref: EHDAA:31 xref: EHDAA:62 xref: EMAPA:16035 xref: FMA:18674 xref: GAID:410 xref: MA:0001715 xref: MESH:D015044 xref: NCIT:C33896 xref: TAO:0001111 xref: UMLS:C0043519 {source="ncithesaurus:Zona_Pellucida"} xref: VHOG:0000720 xref: Wikipedia:Zona_pellucida xref: ZFA:0001111 is_a: CARO:0000000 is_a: UBERON:0000476 ! acellular anatomical structure relationship: bounding_layer_of CL:0000023 relationship: has_part CHEBI:17089 relationship: part_of CL:0000023 relationship: part_of UBERON:0000992 ! ovary property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png xsd:anyURI property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000087 name: inner cell mass def: "A mass of cells that develop into the body of the embryo and some extraembryonic tissues" [ISBN:0-683-40008-8, MGI:pvb] subset: early_development subset: efo_slim subset: pheno_slim synonym: "early embryoblast" RELATED [FMA:86557] synonym: "embryoblast" RELATED [] synonym: "embryoblastus; massa cellularis interna; pluriblastus senior" RELATED LATIN [Wikipedia:Inner_cell_mass] synonym: "ICM" RELATED [VHOG:0000742] synonym: "pluriblast" RELATED [] xref: EFO:0000547 xref: EHDAA2:0000830 xref: EHDAA:40 xref: EMAPA:16041 xref: FMA:86557 xref: NCIT:C13740 xref: SCTID:361456007 xref: UMLS:C1283994 {source="ncithesaurus:Inner_Cell_Mass"} xref: VHOG:0000742 xref: Wikipedia:Inner_cell_mass is_a: CARO:0000000 is_a: UBERON:0002050 ! embryonic structure relationship: develops_from UBERON:0000085 {source="EHDAA2"} ! morula relationship: develops_from UBERON:0000358 {source="Wikipedia"} ! blastocyst relationship: part_of UBERON:0000922 {source="EHDAA2"} ! embryo relationship: surrounded_by UBERON:0000088 {source="Wikipedia"} ! trophoblast property_value: depicted_by Blastocyst:English.svg xsd:anyURI property_value: development_notes "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]" xsd:string property_value: external_definition "A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000742", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0000088 name: trophoblast def: "the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta" [ISBN:0-683-40008-8, MP:0005031] 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] subset: early_development subset: pheno_slim synonym: "massa cellularis externa" RELATED LATIN [Wikipedia:Trophoblast] synonym: "trophoblast layer" EXACT [MP:0005031] synonym: "trophoblastus" RELATED LATIN [Wikipedia:Trophoblast] synonym: "trophoderm" RELATED [BTO:0001079] xref: BTO:0001079 xref: CALOHA:TS-1070 xref: EV:0100120 xref: FMA:83029 xref: GAID:1152 xref: MESH:A11.936 xref: NCIT:C93292 xref: SCTID:362839005 xref: UMLS:C0041178 {source="ncithesaurus:Trophoblast"} xref: Wikipedia:Trophoblast is_a: CARO:0000000 is_a: UBERON:0002050 ! embryonic structure relationship: composed_primarily_of CL:0000351 relationship: develops_from UBERON:0004345 {source="MP-def", source="PMID:19829370"} ! trophectoderm relationship: part_of UBERON:0000358 ! blastocyst property_value: depicted_by Blastocyst:English.svg xsd:anyURI property_value: development_notes "The postimplantation derivatives of the trophectoderm, which make up most of the fetal part of the placenta" xsd:string {source="PMID:19829370"} property_value: external_definition "the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta[MP]" xsd:string {date_retrieved="2012-08-23", external_class="MP:0005031", external_class_label="trophoblast layer", ontology="MP", source="ISBN:0-683-40008-8"} property_value: has_relational_adjective "trophoblastic" xsd:string [Term] id: UBERON:0000089 name: hypoblast (generic) def: "." [GO:dph, https://sourceforge.net/p/geneontology/ontology-requests/9676/, Wikipedia:Hypoblast, ZFIN:cvs] subset: early_development subset: efo_slim subset: grouping_class subset: uberon_slim subset: vertebrate_core synonym: "endomesoderm" RELATED [ISBN:0073040584, VHOG:0001222] synonym: "future endoderm and mesoderm" RELATED [ISBN:0073040584] synonym: "hypoblast" EXACT [VHOG:0001222] synonym: "hypoblastus" RELATED LATIN [Wikipedia:Hypoblast] synonym: "mesendoderm" RELATED [ZFIN:ZDB-PUB-961014-576] xref: AAO:0000229 xref: AAO:0010619 xref: BTO:0003953 xref: EFO:0001930 xref: EMAPA:32762 xref: FMA:293873 xref: MAT:0000418 xref: MIAA:0000418 xref: NCIT:C34190 xref: TAO:0000117 xref: UMLS:C1512561 {source="ncithesaurus:Hypoblast"} xref: VHOG:0001222 xref: Wikipedia:Hypoblast xref: XAO:0003044 xref: ZFA:0000117 is_a: CARO:0000000 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0004750 ! blastoderm property_value: curator_notes "this term groups together disparate structures with different relationships." xsd:string property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png xsd:anyURI property_value: editor_note "TODO - consider relationship to UBERON:0000091 ! bilaminar disc" xsd:string property_value: external_definition "A primary germ layer that can give rise to both mesoderm and endoderm.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010619", ontology="AAO", source="AAO:EJS"} property_value: external_definition "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]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000117", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "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]" xsd:string {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/"} property_value: seeAlso https://github.com/obophenotype/uberon/issues/437 xsd:anyURI [Term] id: UBERON:0000090 name: blastocele def: "fluid-filled central region of a blastocyst." [Wikipedia:Blastocele] subset: early_development subset: pheno_slim synonym: "blastocelic cavity" RELATED [EMAPA:16044] synonym: "blastocoel" RELATED [VHOG:0000811] synonym: "blastocoele" EXACT [] synonym: "blastocoelic cavity" EXACT [EHDAA2:0000175] synonym: "blastocyst cavity" EXACT [] synonym: "cleavage cavity" EXACT [] synonym: "segmentation cavity" EXACT [] xref: AAO:0010433 xref: EHDAA2:0000175 xref: EHDAA:50 xref: EMAPA:16044 xref: FMA:293131 xref: SCTID:361455006 xref: VHOG:0000811 xref: Wikipedia:Blastocele xref: XAO:0000294 is_a: UBERON:0002553 ! anatomical cavity relationship: dubious_for_taxon NCBITaxon:7955 {source="http://zfin.org/zf_info/zfbook/stages/gast.html"} relationship: surrounded_by UBERON:0002532 ! epiblast (generic) property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/c/c3/Blastocyst.gif xsd:anyURI property_value: external_definition "A blastocoel forms during embryogenesis when a zygote (a fertilized ovum) divides into many cells through mitosis. The blastocoel is the cavity of the blastula, a closed space which is invaded by early mesenchyme and later obliterated by the enlarging archenteron.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010433", ontology="AAO", source="ISBN:0-02-377110-0", source="ISBN:0815318960"} property_value: external_definition "The cavity inside the blastula. [The_evolution_of_organ_systems_(2007)_Oxford:_Oxford_University_Press, p.150, see_Schmidt-Rhaesa_A][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000811", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "In the development of many animals, a hollow blastula stage is formed during early embryogenesis. Such a hollow blastula is even regarded as an autapomorphy of Metazoa and is present already in some sponges.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000811", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.150", source="http://bgee.unil.ch/"} property_value: seeAlso https://github.com/obophenotype/uberon/issues/475 xsd:anyURI [Term] id: UBERON:0000091 name: bilaminar disc def: "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." [MP:0003886] subset: early_development subset: pheno_slim synonym: "bilaminar disk" RELATED [Wikipedia:Bilaminar_disc] synonym: "bilaminary embryonic disc" EXACT [] synonym: "bilaminary germ disc" EXACT [ISBN:9780878932504] synonym: "embryonic disc" BROAD [MP:0003886] synonym: "embryonic shield" BROAD [MP:0003886] synonym: "germinal disc" BROAD [MP:0003886] synonym: "germinal disk" BROAD [MP:0003886] xref: FMA:293863 xref: NCIT:C34112 xref: UMLS:C1283997 {source="ncithesaurus:Bilaminar_Embryonic_Disc"} xref: Wikipedia:Bilaminar_disc is_a: CARO:0000000 is_a: UBERON:0002050 ! embryonic structure relationship: develops_from UBERON:0000087 {source="Wikipedia"} ! inner cell mass property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png xsd:anyURI [Term] id: UBERON:0000092 name: post-embryonic stage def: "stage succeeding embryo, including mature structure" [https://orcid.org/0000-0002-6601-2165] synonym: "post-hatching stage" NARROW [] synonym: "postembryonic" RELATED [] synonym: "postembryonic stage" EXACT [] xref: BilaDO:0000003 xref: OGES:000010 xref: OGES:000014 xref: OGES:000024 xref: WBls:0000022 xref: WBls:0000093 xref: WBls:0000103 is_a: UBERON:0000105 ! life cycle stage relationship: part_of GO:0009791 relationship: part_of UBERON:0000104 ! life cycle relationship: preceded_by UBERON:0000068 ! embryo stage relationship: simultaneous_with GO:0009791 property_value: seeAlso https://github.com/obophenotype/uberon/issues/344 xsd:anyURI property_value: taxon_notes "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" xsd:string [Term] id: UBERON:0000093 name: sulcus def: "A depression or fissure in the surface of an organ." [Wikipedia:Sulcus_(anatomy)] subset: grouping_class subset: non_informative xref: Wikipedia:Sulcus_(anatomy) is_a: UBERON:0000464 ! anatomical space created_by: cjm creation_date: 2009-04-09T06:23:22Z [Term] id: UBERON:0000094 name: membrane organ def: "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]" [FMA:7145] synonym: "membrane" BROAD [] synonym: "membrane of organ" EXACT [] xref: FMA:7145 is_a: UBERON:0000062 ! organ relationship: composed_primarily_of UBERON:0011823 {source="FMA-def"} ! dense connective tissue created_by: cjm creation_date: 2009-07-30T05:19:13Z [Term] id: UBERON:0000095 name: cardiac neural crest def: "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]" [Wikipedia:Cardiac_neural_crest] subset: vertebrate_core synonym: "cardiac neural crest complex" RELATED [Wikipedia:Cardiac_neural_crest] synonym: "complexus cristae neuralis cardiacus" RELATED [Wikipedia:Cardiac_neural_crest] xref: TAO:0002173 xref: Wikipedia:Cardiac_neural_crest xref: XAO:0004190 xref: ZFA:0001648 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0002342 ! neural crest property_value: external_definition "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]." xsd:string {source="DOI:10.1242/dev.091751"} property_value: external_ontology_notes "ZFA treats this as a subtype of NC." xsd:string {external_ontology="ZFA"} created_by: cjm creation_date: 2009-07-30T07:57:38Z [Term] id: UBERON:0000100 name: blastopore def: "the orifice of invagination of the endomesodermal cells during the embryonic stages of an organism." [BGEE:ANN, https://github.com/obophenotype/uberon/issues/660, PMID:23103190] subset: early_development subset: metazoa_core xref: AAO:0000045 xref: BTO:0001695 xref: Wikipedia:Blastopore xref: XAO:0000208 is_a: CARO:0000000 is_a: UBERON:0002050 ! embryonic structure relationship: dc-contributor https://github.com/ANiknejad relationship: dc-contributor https://github.com/cmungall relationship: dubious_for_taxon NCBITaxon:7955 {source="http://zfin.org/zf_info/zfbook/stages/gast.html"} relationship: part_of UBERON:0004735 {source="BGEE:ANN"} ! archenteron property_value: external_definition "A slit-like invagination on the dorsal side of the blastula surface of the embryo where the mesoderm and endoderm move inside the embryo at gatrulation.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000045", ontology="AAO", source="AAO:BJB"} property_value: seeAlso https://github.com/obophenotype/uberon/issues/660 xsd:anyURI property_value: taxon_notes "In protostome development, the first opening in development, the blastopore, becomes the animal's mouth; In deuterostome development, the blastopore becomes the animal's anus" xsd:string [Term] id: UBERON:0000101 name: lobe of lung def: "A lung lobe is one of the rounded projections that compose the lung[GO]." [GOC:GO] subset: pheno_slim synonym: "lung lobe" EXACT [] synonym: "pulminory lobe" EXACT [] synonym: "pulmonary lobe" EXACT [FMA:7311] xref: EMAPA:36281 xref: FMA:7311 xref: galen:LobeOfLung xref: MA:0003098 xref: NCIT:C34021 xref: OpenCyc:Mx4rvo6-vpwpEbGdrcN5Y29ycA xref: SCTID:245524004 xref: UMLS:C0225752 {source="ncithesaurus:Lung_Lobe"} is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0009912 {source="FMA"} ! anatomical lobe relationship: contributes_to_morphology_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung [Term] id: UBERON:0000102 name: lung vasculature def: "The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO]." [GOC:GO] subset: pheno_slim synonym: "lung vascular network" EXACT [OBOL:automatic] synonym: "pulmonary vasculature" EXACT [FMA:73750] synonym: "vascular network of lung" EXACT [OBOL:automatic] synonym: "vasculature of lung" EXACT [OBOL:automatic] xref: FMA:73750 is_a: CARO:0000000 is_a: UBERON:0002201 ! vasculature of trunk is_a: UBERON:0006876 ! vasculature of organ intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung [Term] id: UBERON:0000103 name: obsolete life cycle stage boundary def: "Instant starting or ending a life cycle stage. These can be arbitrary/fiat." [https://orcid.org/0000-0002-6601-2165] synonym: "life cycle stage transition event" EXACT [] synonym: "life cycle stage transition instant" EXACT [] xref: span:ProcessBoundary is_obsolete: true [Term] id: UBERON:0000104 name: life cycle def: "An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism." [https://orcid.org/0000-0002-6601-2165] subset: upper_level synonym: "entire life cycle" EXACT [] synonym: "entire lifespan" EXACT [] synonym: "life" EXACT [] synonym: "lifespan" EXACT [] xref: FBdv:00000000 xref: HsapDv:0000001 xref: MmusDv:0000001 xref: ncithesaurus:Life xref: OGES:000011 is_a: UBERON:0000000 ! processual entity relationship: ends_with UBERON:0000071 ! death stage relationship: has_part UBERON:0000105 ! life cycle stage relationship: starts_with UBERON:0000106 ! zygote stage property_value: seeAlso https://github.com/obophenotype/uberon/issues/532 xsd:anyURI [Term] id: UBERON:0000105 name: life cycle stage def: "A spatiotemporal region encompassing some part of the life cycle of an organism." [https://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: upper_level synonym: "developmental stage" NARROW [] synonym: "stage" NARROW [] xref: BILS:0000105 xref: EFO:0000399 xref: FBdv:00007012 xref: FMA:24120 xref: HsapDv:0000000 xref: MmusDv:0000000 xref: ncithesaurus:Developmental_Stage xref: OlatDv:0000010 xref: PdumDv:0000090 xref: WBls:0000002 xref: XAO:1000000 xref: ZFS:0000000 xref: ZFS:0100000 is_a: UBERON:0000000 ! processual entity relationship: part_of UBERON:0000104 ! life cycle property_value: editor_note "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string property_value: external_ontology_notes "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" xsd:string property_value: external_ontology_notes "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" xsd:string [Term] id: UBERON:0000106 name: zygote stage def: "A stage at which the organism is a single cell produced by means of sexual reproduction." [Wikipedia:Zygote] subset: efo_slim synonym: "1-cell stage" EXACT [] synonym: "fertilized egg stage" EXACT [BTO:0000854] synonym: "fertilized egg stage" RELATED [] synonym: "one cell stage" EXACT [] synonym: "one-cell stage" RELATED [VHOG:0000745] synonym: "zygote" RELATED [VHOG:0000745] synonym: "zygotum" RELATED LATIN [Wikipedia:Zygote] xref: BilaDO:0000005 xref: BILS:0000106 xref: EFO:0001322 xref: EHDAA:27 xref: FBdv:00005288 xref: NCIT:C12601 xref: PdumDv:0000100 xref: VHOG:0000745 xref: Wikipedia:Zygote xref: XAO:1000001 xref: ZFS:0000001 is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: seeAlso EMAPA:16033 relationship: starts UBERON:0000104 ! life cycle property_value: homology_notes "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0000107 name: cleavage stage def: "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." [GO:0040016, Wikipedia:Cleavage_(embryo)] subset: efo_slim xref: BilaDO:0000006 xref: BILS:0000107 xref: EFO:0001290 xref: FBdv:00000054 xref: MESH:A16.254.270 xref: MmusDv:0000004 xref: OGES:000015 xref: OGES:000020 xref: PdumDv:0000200 xref: Wikipedia:Cleavage_(embryo) xref: XAO:1000004 xref: ZFS:0000046 is_a: UBERON:0000105 ! life cycle stage intersection_of: UBERON:0000105 ! life cycle stage intersection_of: simultaneous_with GO:0040016 relationship: immediately_preceded_by UBERON:0000106 ! zygote stage relationship: part_of GO:0040016 relationship: part_of UBERON:0000068 ! embryo stage relationship: simultaneous_with GO:0040016 [Term] id: UBERON:0000108 name: blastula stage def: "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." [Wikipedia:Blastula] subset: efo_slim xref: BilaDO:0000007 xref: BILS:0000108 xref: EFO:0001282 xref: HsapDv:0000006 xref: MmusDv:0000007 xref: OGES:000003 xref: OGES:000016 xref: OGES:000021 xref: OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg xref: WBls:0000005 xref: Wikipedia:Blastula xref: XAO:1000003 xref: ZFS:0000045 is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png xsd:anyURI property_value: editor_note "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] id: UBERON:0000109 name: gastrula stage def: "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." [GO:0007369] subset: efo_slim synonym: "blastocystis trilaminaris stage" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar blastocyst stage" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar blastoderm stage" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar disk stage" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ stage" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar stage" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BilaDO:0000008 xref: BILS:0000109 xref: EFO:0001296 xref: FBdv:00005317 xref: HsapDv:0000010 xref: MmusDv:0000013 xref: OGES:000004 xref: OGES:000019 xref: WBls:0000010 xref: XAO:1000005 xref: ZFS:0000047 is_a: UBERON:0000105 ! life cycle stage relationship: only_in_taxon NCBITaxon:6072 relationship: part_of GO:0007369 relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage relationship: simultaneous_with GO:0007369 [Term] id: UBERON:0000110 name: neurula stage def: "Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system." [GO:0001841] xref: BilaDO:0000009 xref: BILS:0000110 xref: HsapDv:0000012 xref: MmusDv:0000017 xref: XAO:1000006 is_a: UBERON:0000105 ! life cycle stage relationship: only_in_taxon NCBITaxon:6072 relationship: part_of GO:0001841 relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage relationship: simultaneous_with GO:0001841 property_value: seeAlso https://github.com/obophenotype/uberon/issues/343 xsd:anyURI [Term] id: UBERON:0000111 name: organogenesis stage def: "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism." [Wikipedia:Organogenesis] synonym: "segmentation stage" RELATED [] xref: BilaDO:0000010 xref: BILS:0000111 xref: HsapDv:0000015 xref: MmusDv:0000018 xref: OGES:000005 xref: OGES:000032 xref: Wikipedia:Organogenesis is_a: UBERON:0000105 ! life cycle stage relationship: only_in_taxon NCBITaxon:6072 relationship: part_of GO:0048513 relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000110 ! neurula stage relationship: simultaneous_with GO:0048513 property_value: seeAlso https://github.com/obophenotype/uberon/issues/533 xsd:anyURI [Term] id: UBERON:0000112 name: sexually immature stage subset: efo_slim synonym: "immature stage" EXACT [VHOG:FB] synonym: "juvenile stage" NARROW [XAO:1000010] synonym: "subadult stage" RELATED [http://eol.org/schema/terms/subadult] xref: BILS:0000112 xref: BTO:0002168 xref: EFO:0001300 xref: EV:0300051 xref: MmusDv:0000043 xref: OGES:000009 xref: XAO:1000010 xref: XtroDO:0000083 xref: ZFS:0000051 is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000066 ! fully formed stage relationship: preceded_by UBERON:0000069 {gci_relation="part_of", gci_filler="NCBITaxon:7955", source="ZFS"} ! larval stage property_value: external_definition "The stage of being a sexually immature adult animal[XAO:1000010]." xsd:string {source="XAO:1000010"} property_value: seeAlso https://github.com/obophenotype/uberon/issues/427 xsd:anyURI property_value: taxon_notes "In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother)" xsd:string [Term] id: UBERON:0000113 name: post-juvenile adult stage def: "The stage of being a sexually mature adult animal." [https://orcid.org/0000-0002-6601-2165] synonym: "adult stage" BROAD [] xref: BILS:0000113 xref: EV:0300064 xref: EV:0300070 xref: MIAA:0000403 xref: MmusDv:0000110 xref: OGES:000026 xref: OGES:000027 xref: XAO:1000093 xref: ZFS:0000044 is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000066 ! fully formed stage relationship: preceded_by UBERON:0000112 ! sexually immature stage property_value: seeAlso https://github.com/obophenotype/uberon/issues/345 xsd:anyURI property_value: seeAlso https://github.com/obophenotype/uberon/issues/499 xsd:anyURI [Term] id: UBERON:0000114 name: lung connective tissue def: "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" [ISBN:0-683-40008-8, MGI:anna, MP:0002276, PMID:14635660] subset: pheno_slim synonym: "connective tissue of lung" EXACT [OBOL:automatic] synonym: "lung interstitial tissue" RELATED [MA:0001782] synonym: "lung interstitium" RELATED [] synonym: "pulmonary connective tissue" RELATED [EMAPA:35521] synonym: "pulmonary interstitial tissue" RELATED [] synonym: "pulmonary interstitium" EXACT [FMA:27533] xref: EMAPA:35521 xref: FMA:27533 xref: MA:0001782 xref: SCTID:201609008 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0003580 ! lower respiratory tract connective tissue is_a: UBERON:0003837 ! thoracic segment connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0002048 ! lung relationship: contributes_to_morphology_of UBERON:0002048 ! lung relationship: develops_from UBERON:0004883 ! lung mesenchyme relationship: part_of UBERON:0002048 ! lung relationship: transformation_of UBERON:0004883 ! lung mesenchyme property_value: function_notes "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" xsd:string [Term] id: UBERON:0000115 name: lung epithelium def: "The epithelial layer of the lung." [MP:0006382] subset: pheno_slim synonym: "epithelial tissue of lung" EXACT [OBOL:automatic] synonym: "epithelium of lung" EXACT [OBOL:automatic] synonym: "lung epithelial tissue" EXACT [OBOL:automatic] synonym: "pulmonary epithelium" RELATED [BTO:0001653] xref: BTO:0001653 xref: EMAPA:32860 xref: MA:0001783 is_a: UBERON:0004815 ! lower respiratory tract epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002048 ! lung relationship: contributes_to_morphology_of UBERON:0002048 ! lung relationship: develops_from UBERON:0001041 ! foregut relationship: part_of UBERON:0002048 ! lung property_value: taxon_notes "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]" xsd:string [Term] id: UBERON:0000116 name: lung saccule def: "Primitive gas exchange portion of the lung composed of type I and type II cells[GO]." [GO:0060430] subset: pheno_slim is_a: UBERON:0000064 ! organ part is_a: UBERON:0004119 ! endoderm-derived structure relationship: has_part CL:0000322 relationship: part_of UBERON:0002299 {source="GO"} ! alveolus of lung [Term] id: UBERON:0000117 name: respiratory tube def: "A tube in the respiratory system. Examples: bronchus, bronchiole, trachea." [GO:0030323, http://orcid.org/0000-0002-6601-2165] synonym: "airway" RELATED [] synonym: "respiratory conducting tube" NARROW [MP:0004391] synonym: "segment of tracheobronchial tree" EXACT [FMA:12224] synonym: "segment of tracheobronchial tree" NARROW [FMA:12224] synonym: "tracheobronchial tree segment" NARROW [FMA:12224] xref: EMAPA:37946 {source="MA:th"} xref: FMA:12224 is_a: UBERON:0000025 ! tube is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000025 ! tube intersection_of: part_of UBERON:0000065 ! respiratory tract relationship: has_part UBERON:0000483 ! epithelium relationship: part_of UBERON:0000065 ! respiratory tract property_value: external_ontology_notes "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)" xsd:string {external_ontology="GO"} [Term] id: UBERON:0000118 name: lung bud def: "Structure derived from foregut that becomes a lung[GO]." [GO:0060431, Wikipedia:Respiratory_bud] subset: pheno_slim synonym: "gemma pulmonalis" RELATED LATIN [Wikipedia:Lung_buds] synonym: "gemma respiratoria" RELATED LATIN [Wikipedia:Lung_buds] synonym: "lung bud" RELATED PLURAL [] synonym: "primary lung bud" RELATED [GO:0060572] synonym: "respiratory diverticulum" RELATED [Wikipedia:Lung_buds] xref: BTO:0001643 xref: EHDAA2:0004089 xref: NCIT:C34260 xref: NCIT:C34282 xref: SCTID:361427007 xref: UMLS:C1514420 {source="ncithesaurus:Primary_Bronchial_Bud"} xref: UMLS:C1514897 {source="ncithesaurus:Respiratory_Diverticulum"} xref: Wikipedia:Respiratory_bud is_a: UBERON:0005153 {source="GO:0060441"} ! epithelial bud is_a: UBERON:0005911 ! endo-epithelium relationship: adjacent_to UBERON:0004872 ! splanchnic layer of lateral plate mesoderm relationship: develops_from UBERON:0005597 ! lung primordium relationship: develops_from UBERON:0008947 {source="EHDAA2"} ! respiratory primordium property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/7/71/Gray948.png xsd:anyURI property_value: editor_note "clarify successors - include bronchi?" xsd:string [Term] id: UBERON:0000119 name: cell layer def: "Portion of tissue, that consists of single layer of cells connected to each other by cell junctions. Examples: layer of glial cells; epithelium." [https://orcid.org/0000-0002-6601-2165] subset: upper_level synonym: "cell sheath" RELATED [] synonym: "layer" BROAD [NCIT:C66831] synonym: "layer of cells" EXACT [] synonym: "sheath of cells" RELATED [] xref: NCIT:C66831 is_a: UBERON:0000957 ! lamina relationship: has_quality PATO:0002124 property_value: editor_note "consider adding to caro" xsd:string [Term] id: UBERON:0000120 name: blood brain barrier def: "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." [DOI:10.1002/glia.20642, Wikipedia:Blood-brain_barrier] synonym: "BBB" RELATED [] synonym: "blood-brain barrier" EXACT [] xref: http://uri.neuinfo.org/nif/nifstd/nlx_subcell_100205 xref: NCIT:C13194 xref: UMLS:C0005854 {source="ncithesaurus:Blood-Brain_Barrier"} xref: Wikipedia:Blood-brain_barrier is_a: CARO:0000000 is_a: UBERON:0000119 ! cell layer relationship: adjacent_to UBERON:0000179 ! haemolymphatic fluid relationship: adjacent_to UBERON:0000955 ! brain relationship: part_of UBERON:0001016 ! nervous system [Term] id: UBERON:0000121 name: perineurium def: "A layer of thin, concentrically arranged cells with interspersed collagen that lies within the epineurium. (Nolte, J., The Human Brain 3rd edition)" [NLXANAT:090205] xref: BTO:0003153 xref: EMAPA:37849 {source="MA:th"} xref: FMA:52585 xref: NCIT:C33302 xref: NCIT:C41407 xref: NLXANAT:090205 xref: SCTID:362299001 xref: UMLS:C0205890 {source="ncithesaurus:Perineurium"} xref: Wikipedia:Perineurium is_a: CARO:0000000 is_a: UBERON:0011822 {source="FMA"} ! dense irregular connective tissue relationship: bounding_layer_of UBERON:0001019 ! nerve fasciculus relationship: has_part GO:0005581 relationship: located_in UBERON:0000124 ! epineurium relationship: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001019 ! nerve fasciculus property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray636.png xsd:anyURI property_value: external_definition "Connective tissue surrounding a fascicle[Wikipedia:Perineurium]." xsd:string {source="Wikipedia:Perineurium"} property_value: external_ontology_notes "consider FBbt:00007090 (perineurium): The outer two layers of glial cells that cover the central nervous system and the nerves. The outer layer is the perineurial sheath (sometimes referred to as the perineurial sheath outer layer); the inner layer is the sub-perineural glial sheath (sometimes referred to as the perineurial sheath inner layer)" xsd:string {external_ontology="FBbt"} property_value: has_relational_adjective "perineurial" xsd:string [Term] id: UBERON:0000122 name: neuron projection bundle alt_id: UBERON:0005163 def: "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." [CARO:0001001, FBbt:00005099, FBC:DOS] synonym: "funiculus" EXACT [] synonym: "nerve fiber bundle" EXACT [FBbt:00005099] synonym: "neural fiber bundle" EXACT [] xref: CARO:0001001 xref: FBbt:00005099 xref: NLX:147821 is_a: CARO:0000000 is_a: UBERON:0005162 ! multi cell part structure relationship: has_part GO:0043005 relationship: part_of UBERON:0001016 ! nervous system [Term] id: UBERON:0000123 name: endoneurium def: "The loose connective tissue within the perineurium that continues into nerve fascicles and surrounds individual fibers. (Nolte, J. The Human Brain 3rd edition)" [NLXANAT:090202] xref: EMAPA:37847 {source="MA:th"} xref: FMA:52586 xref: NCIT:C32518 xref: NLXANAT:090202 xref: SCTID:15931004 xref: UMLS:C0205888 {source="ncithesaurus:Endoneurium"} xref: Wikipedia:Endodeurium is_a: CARO:0000000 is_a: UBERON:0006804 {source="FMA"} ! reticular tissue relationship: bounding_layer_of UBERON:0006134 ! nerve fiber relationship: located_in UBERON:0000121 ! perineurium relationship: part_of UBERON:0000010 ! peripheral nervous system relationship: part_of UBERON:0006134 ! nerve fiber relationship: surrounds GO:0043209 property_value: external_definition "a layer of delicate connective tissue that encloses the myelin sheath of a nerve fiber within a funiculus[Wikipedia:Endodeurium]." xsd:string {source="Wikipedia:Endodeurium"} [Term] id: UBERON:0000124 name: epineurium def: "A loose connective tissue sheath surrounding each peripheral nerve. Composed mainly of colagen and fibroblasts, it forms a substantial covering over nerve trunks, then thins to an incomplete layer around smaller branches near their terminations. The epineurium is continuous centrally with the dura. Peripherally, it usually ends near the termination of a nerve fiber, but it may continue as the capsule of Meissner corpuscles and a few other encapsulated endings. Nolte, J. The Human Brain 3rd edition" [NLXANAT:090203] xref: BTO:0003154 xref: EMAPA:37848 {source="MA:th"} xref: FMA:12234 xref: NCIT:C32528 xref: NLXANAT:090203 xref: SCTID:64482002 xref: UMLS:C0205889 {source="ncithesaurus:Epineurium"} xref: Wikipedia:Epineurium is_a: CARO:0000000 is_a: UBERON:0011822 {source="FMA"} ! dense irregular connective tissue relationship: part_of UBERON:0000010 ! peripheral nervous system relationship: surrounds UBERON:0001021 ! nerve property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray636.png xsd:anyURI property_value: external_definition "outermost layer of connective tissue surrounding a peripheral nerve. It includes the blood vessels supplying the nerve. It consists of adipose tissue and fibrocollagenous tissues[Wikipedia:Epineurium]." xsd:string {source="Wikipedia:Epineurium"} [Term] id: UBERON:0000125 name: neural nucleus def: "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)" [NLX:28443] subset: cumbo synonym: "nervous system nucleus" EXACT [] synonym: "neuraxis nucleus" EXACT [FMA:83686] synonym: "neuronal nucleus" EXACT [AEO:0000136] synonym: "nucleus" BROAD [] synonym: "nucleus of CNS" EXACT [NLX:28443] synonym: "nucleus of neuraxis" RELATED [] xref: AEO:0000136 xref: FMA:83686 xref: NCIT:C13197 xref: NLX:28443 xref: Wikipedia:Nucleus_(neuroanatomy) is_a: UBERON:0011215 ! central nervous system cell part cluster relationship: composed_primarily_of UBERON:0002020 ! gray matter relationship: only_in_taxon NCBITaxon:7711 {notes="we limit this structure by definition to chordate and vertebrate nervous systems"} relationship: part_of UBERON:0001017 {source="CUMBO"} ! central nervous system property_value: external_definition "Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021]." xsd:string {source="GO_REF:0000021"} property_value: external_ontology_notes "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." xsd:string [Term] id: UBERON:0000126 name: cranial nerve nucleus def: "Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves" [NLX:28532] synonym: "cranial neural nucleus" EXACT [FMA:54501] synonym: "nucleus nervi cranialis" RELATED LATIN [Wikipedia:Cranial_nerve_nucleus] synonym: "nucleus of cranial nerve" EXACT [] xref: EMAPA:37066 {source="MA:th"} xref: FMA:54501 xref: NLX:28532 xref: SCTID:280160003 xref: Wikipedia:Cranial_nerve_nucleus is_a: UBERON:0002308 ! nucleus of brain intersection_of: UBERON:0002308 ! nucleus of brain intersection_of: extends_fibers_into UBERON:0001785 ! cranial nerve relationship: extends_fibers_into UBERON:0001785 ! cranial nerve property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png xsd:anyURI [Term] id: UBERON:0000127 name: facial nucleus def: "the group of motor neurons residing in the pons that innervate the muscles of facial expression" [ISBN:0838580343, MP:0000909] subset: pheno_slim synonym: "facial nerve nucleus" EXACT [] synonym: "facial VII motor nucleus" RELATED [MA:0001014] synonym: "facial VII nucleus" EXACT [MA:0001014] synonym: "nucleus of facial nerve" EXACT [FMA:54572] xref: BAMS:7 xref: BAMS:7N xref: BAMS:VII xref: BM:Pons-VII xref: DHBA:12420 xref: EHDAA2:0004638 xref: EMAPA:35338 xref: EV:0100267 xref: FMA:54572 xref: MA:0001014 xref: NCIT:C12898 xref: SCTID:280166009 xref: UMLS:C0228740 {source="ncithesaurus:Facial_Nerve_Nucleus"} xref: VHOG:0001412 is_a: UBERON:0000126 ! cranial nerve nucleus is_a: UBERON:0006331 ! brainstem nucleus is_a: UBERON:0009662 ! hindbrain nucleus intersection_of: UBERON:0000126 ! cranial nerve nucleus intersection_of: extends_fibers_into UBERON:0001647 ! facial nerve relationship: contributes_to_morphology_of UBERON:0000988 ! pons relationship: develops_from UBERON:0010123 ! future facial nucleus relationship: extends_fibers_into UBERON:0001647 ! facial nerve relationship: immediate_transformation_of UBERON:0010123 {evidence="definitional"} ! future facial nucleus relationship: part_of UBERON:0000988 ! pons property_value: external_ontology_notes "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." xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000128 name: olivary body def: "prominent oval structure in the medulla oblongata, present in pairs, the lower portion of the brainstem. They contain the olivary nuclei" [Wikipedia:Olivary_body] subset: pheno_slim synonym: "oliva" RELATED LATIN [Wikipedia:Olivary_body] synonym: "olivary nucleus" RELATED [BTO:0002299] synonym: "olive" RELATED [] synonym: "olive body" EXACT [] xref: BTO:0002299 xref: SCTID:279293003 xref: Wikipedia:Olivary_body is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010000 ! multicellular anatomical structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001896 ! medulla oblongata property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray679.png xsd:anyURI [Term] id: UBERON:0000130 name: transverse foramen def: "Foramen that pierces the transverse processes of the seven cervical vertebrae. In the upper six vertebrae, the foramen gives passage to the vertebral artery, vertebral vein, and a plexus of sympathetic nerves. The seventh foramen lacks the artery, but contains the vein and sympathetic nerves." [Wikipedia:Transverse_foramen] synonym: "foramen transversarium" EXACT [Wikipedia:Transverse_foramen] synonym: "foramen transversarium" RELATED LATIN [Wikipedia:Transverse_foramen] synonym: "foramen transversarium of cervical vertebra" EXACT [FMA:23998] synonym: "foramen transversarium vertebrae cervicales" EXACT LATIN [FMA:23997, FMA:TA] synonym: "transverse foramen of cervical vertebra" EXACT [FMA:23997] xref: EMAPA:36272 xref: FMA:23997 xref: SCTID:280735005 xref: Wikipedia:Transverse_foramen is_a: UBERON:0004111 {source="FMA"} ! anatomical conduit is_a: UBERON:0005744 ! bone foramen is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: conduit_for UBERON:0001588 ! vertebral vein relationship: conduit_for UBERON:0012373 ! sympathetic nerve plexus relationship: part_of UBERON:0001077 ! transverse process of vertebra relationship: part_of UBERON:0002413 ! cervical vertebra property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/3c/Gray84.png xsd:anyURI [Term] id: UBERON:0000144 name: trochlea of humerus def: "The medial portion of the articular surface of the humerus is named the trochlea, and presents a deep depression between two well-marked borders; it is convex from before backward, concave from side to side, and occupies the anterior, lower, and posterior parts of the extremity. It is directly inferior to the most prominent anterior humeral fossia, the Coronoid fossia. It articulates with the ulna." [Wikipedia:Trochlea_of_humerus] synonym: "humeral trochlea" EXACT [FMA:23370] synonym: "trochlea humeri" EXACT [Wikipedia:Trochlea_of_humerus] xref: FMA:23370 xref: SCTID:282817004 xref: Wikipedia:Trochlea_of_humerus is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005055 ! zone of long bone is_a: UBERON:0005913 {source="FMA"} ! zone of bone organ is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0004404 ! distal epiphysis of humerus property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/4/4b/Trochleahumeri.png xsd:anyURI [Term] id: UBERON:0000151 name: pectoral fin def: "Paired fin that is located in the thoracic region of the body." [TAO:curator, VSAO:0000147] synonym: "forefin" EXACT [VSAO:0000147] synonym: "pectoral fins" RELATED PLURAL [ZFA:0001161] xref: BTO:0004653 xref: SCTID:416982006 xref: TAO:0001161 xref: VSAO:0000147 xref: Wikipedia:Pectoral_fin#Fins xref: ZFA:0001161 is_a: UBERON:0002534 ! paired fin is_a: UBERON:0004710 {is_entailed="true"} ! pectoral appendage intersection_of: UBERON:0002534 ! paired fin intersection_of: part_of UBERON:0010708 ! pectoral complex relationship: develops_from UBERON:0005419 ! pectoral appendage bud relationship: has_skeleton UBERON:0010710 ! pectoral fin skeleton relationship: part_of UBERON:0010708 ! pectoral complex property_value: external_definition "Paired fin that is located in the thoracic region of the body.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001161", ontology="TAO", source="TAO:wd"} property_value: external_definition "Paired fin that is located in the thoracic region of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000147", ontology="VSAO", source="TAO:curator"} [Term] id: UBERON:0000152 name: pelvic fin def: "Paired fin located in the abdominal position of the body." [TAO:curator, VSAO:0000129] subset: efo_slim synonym: "pelvic fins" RELATED PLURAL [ZFA:0001184] xref: BTO:0004651 xref: EFO:0003644 xref: TAO:0001184 xref: VSAO:0000129 xref: Wikipedia:Pectoral_fin#Fins xref: ZFA:0001184 is_a: UBERON:0002534 ! paired fin is_a: UBERON:0004709 {is_entailed="true"} ! pelvic appendage intersection_of: UBERON:0002534 ! paired fin intersection_of: part_of UBERON:0010709 ! pelvic complex relationship: develops_from UBERON:0005420 ! pelvic appendage bud relationship: has_skeleton UBERON:0010711 ! pelvic fin skeleton relationship: part_of UBERON:0010709 ! pelvic complex property_value: external_definition "Paired fin located in the abdominal position of the body.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001184", ontology="TAO", source="TAO:wd"} property_value: external_definition "Paired fin located in the abdominal position of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000129", ontology="VSAO", source="TAO:curator"} [Term] id: UBERON:0000153 name: anterior region of body is_a: UBERON:0000475 ! organism subdivision disjoint_from: UBERON:0000154 {source="lexical"} ! posterior region of body relationship: anterior_to UBERON:0000154 ! posterior region of body relationship: only_in_taxon NCBITaxon:33213 [Term] id: UBERON:0000154 name: posterior region of body is_a: UBERON:0000475 ! organism subdivision relationship: only_in_taxon NCBITaxon:33213 [Term] id: UBERON:0000155 name: theca cell layer def: "A layer of the ovarian follicle that consists of theca cells." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: pheno_slim subset: vertebrate_core synonym: "layer of theca cells" EXACT [] synonym: "ovarian theca" RELATED [EMAPA:35636] synonym: "ovary theca" EXACT [MA:0001712] synonym: "theca cell layer of ovarian follicle" EXACT [] synonym: "theca folliculi" RELATED LATIN [Wikipedia:Theca_of_follicle] synonym: "theca folliculi" RELATED LATIN [] synonym: "theca of follicle" EXACT [] synonym: "thecal cell layer" EXACT [ZFA:0001113] synonym: "thecal cell layers" RELATED PLURAL [ZFA:0001113] xref: BTO:0002853 xref: EFO:0003629 xref: EMAPA:35636 xref: FMA:18656 xref: MA:0001712 xref: SCTID:361385000 xref: TAO:0001113 xref: Wikipedia:Theca_of_follicle xref: ZFA:0001113 is_a: UBERON:0000119 ! cell layer is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000119 ! cell layer intersection_of: composed_primarily_of CL:0000503 intersection_of: part_of UBERON:0001305 ! ovarian follicle relationship: composed_primarily_of CL:0000503 relationship: part_of UBERON:0001305 ! ovarian follicle property_value: function_notes "The theca folliculi are responsible for the production of testosterone from androstenedione in females, and indirectly the production of estrogens by supplying the neighboring granulosa cells with androstenedione that can then be used as a substrate for aromatase. [Wikipedia:Theca_of_follicle]" xsd:string [Term] id: UBERON:0000156 name: theca externa alt_id: UBERON:0005182 def: "The theca externa is the outer layers of the theca folliculi. It contains abundant collagen and is mainly supportive." [Wikipedia:Theca_externa] subset: pheno_slim synonym: "external coat of theca folliculi" RELATED [BTO:0002852] synonym: "ovary theca externa" EXACT [MA:0001713] synonym: "theca externa (folliculus ovaricus tertiarius)" EXACT [FMA:18657] synonym: "tunica externa of theca folliculi" EXACT [FMA:18657] synonym: "tunica externa thecae folliculi" RELATED [BTO:0002852] synonym: "tunica externa thecae folliculi" RELATED LATIN [Wikipedia:Theca_externa] xref: BTO:0002852 xref: FMA:18657 xref: MA:0001713 xref: SCTID:258767003 xref: Wikipedia:Theca_externa is_a: UBERON:0000158 ! membranous layer is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure relationship: bounding_layer_of UBERON:0000155 ! theca cell layer relationship: has_part GO:0005581 relationship: part_of UBERON:0000155 ! theca cell layer relationship: surrounds UBERON:0000157 ! theca interna property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/5/50/Mature_Graffian_follicle.jpg xsd:anyURI [Term] id: UBERON:0000157 name: theca interna alt_id: UBERON:0005183 def: "Theca interna cells express receptors for luteinizing hormone, which when activated will stimulate the production of androstenedione from cholesterol by the enzyme desmolase. Androstenedione ultimately gives the granulosa cells the precursor substrate for estrogen manufacturing." [Wikipedia:Theca_externa#Theca_interna] subset: pheno_slim synonym: "internal coat of capsule of Graafian follicle" RELATED [BTO:0002851] synonym: "ovary theca interna" EXACT [MA:0001714] synonym: "theca interna (folliculus ovaricus tertiarius)" EXACT [FMA:18658] synonym: "tunica interna of theca folliculi" EXACT [FMA:18658] synonym: "tunica interna thecae folliculi" RELATED [BTO:0002851] xref: BTO:0002851 xref: FMA:18658 xref: MA:0001714 xref: SCTID:258869006 xref: Wikipedia:Theca_externa#Theca_interna is_a: UBERON:0000158 ! membranous layer is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure relationship: contributes_to_morphology_of UBERON:0000155 ! theca cell layer relationship: part_of UBERON:0000155 ! theca cell layer [Term] id: UBERON:0000158 name: membranous layer synonym: "membrane" BROAD [] synonym: "membranous organ component" EXACT [FMA:82500] xref: FMA:30322 xref: FMA:82500 xref: MESH:D008566 xref: NCIT:C12749 is_a: UBERON:0004923 ! organ component layer relationship: bounding_layer_of UBERON:0000064 ! organ part property_value: external_definition "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." xsd:string {source="ncithesaurus:Membrane"} [Term] id: UBERON:0000159 name: anal canal def: "The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus." [Wikipedia:Anal_canal] subset: pheno_slim subset: uberon_slim synonym: "anal canal" EXACT [] synonym: "anal canal viewed anatomically" EXACT [] synonym: "anal pad" RELATED [] synonym: "anatomical anal canal" EXACT [] synonym: "anus" RELATED [] synonym: "canalis analis" RELATED LATIN [Wikipedia:Anal_canal] synonym: "canalis analis" RELATED [BTO:0001978] synonym: "cloaca" RELATED [] synonym: "cloacal chamber" RELATED [] synonym: "mesenteron" RELATED [] synonym: "pars analis recti" RELATED [BTO:0001978] xref: BTO:0001978 xref: CALOHA:TS-2160 xref: EMAPA:18256 xref: FMA:15703 xref: galen:AnalCanal xref: MA:0000330 xref: NCIT:C12375 xref: SCTID:245438008 xref: UMLS:C0227411 {source="ncithesaurus:Anal_Canal"} xref: Wikipedia:Anal_canal is_a: UBERON:0004111 ! anatomical conduit relationship: channel_for UBERON:0001988 ! feces relationship: continuous_with UBERON:0001052 ! rectum relationship: continuous_with UBERON:0001245 ! anus relationship: develops_from UBERON:0011272 {source="Wikipathways:WP2062"} ! embryonic skin basal layer relationship: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0001353 ! anal region property_value: depicted_by https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png xsd:anyURI property_value: editor_note "requires alignment with EHDAA2 and complete developmental relationships" xsd:string [Term] id: UBERON:0000160 name: intestine def: "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." [GOC:GO, Wikipedia:Intestine] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "bowel" EXACT [] synonym: "intestinal tract" RELATED [] xref: AAO:0000246 xref: ANISEED:1235303 xref: BSA:0000093 xref: BTO:0000648 xref: CALOHA:TS-0490 xref: EFO:0000834 xref: EMAPA:32874 xref: EV:0100071 xref: FMA:7199 xref: GAID:295 xref: galen:Intestine xref: MA:0000328 xref: MA:0001524 xref: MESH:A03.492.411 xref: MIAA:0000043 xref: NCIT:C12736 xref: SCTID:256876008 xref: TAO:0001338 xref: UMLS:C0021853 {source="ncithesaurus:Intestine"} xref: VHOG:0000056 xref: WBbt:0005772 xref: Wikipedia:Intestine xref: XAO:0000129 xref: ZFA:0001338 is_a: UBERON:0004921 {source="cjm"} ! subdivision of digestive tract relationship: contributes_to_morphology_of UBERON:0001007 ! digestive system relationship: part_of UBERON:0005409 ! alimentary part of gastrointestinal system property_value: editor_note "This class is probably too inclusive" xsd:string property_value: external_definition "Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000246", ontology="AAO", source="AAO:EJS"} property_value: external_definition "The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000056", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: has_relational_adjective "intestinal" xsd:string property_value: taxon_notes "In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type." xsd:string [Term] id: UBERON:0000161 name: orifice def: "Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]." [FMA:3724] synonym: "anatomical orifice" EXACT [FMA:3724] synonym: "anatomical ostium" BROAD [FMA:3724] synonym: "hilum" NARROW [] synonym: "ostium" BROAD [] xref: FMA:3724 xref: SCTID:91837002 is_a: UBERON:0004111 ! anatomical conduit property_value: external_ontology_notes "in FMA, this is an anatomical conduit *space*, rather than anatomical conduit" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000162 name: cloaca def: "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" [ISBN:0073040584, Wikipedia:Cloaca] synonym: "cloacal chamber" RELATED [AAO:0000095] synonym: "vent" RELATED [XAO:0000244] xref: AAO:0000095 xref: GAID:1206 xref: MESH:D002988 xref: NCIT:C34127 xref: SCTID:362857006 xref: SCTID:370631000 xref: UMLS:C0008987 {source="ncithesaurus:Cloaca"} xref: VHOG:0001186 xref: Wikipedia:Cloaca xref: XAO:0000244 xref: ZFA:0005781 is_a: UBERON:0013522 ! subdivision of tube relationship: only_in_taxon NCBITaxon:7742 relationship: part_of UBERON:0001555 {source="ZFA"} ! digestive tract relationship: part_of UBERON:0004122 {source="AAO"} ! genitourinary system relationship: present_in_taxon 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."} property_value: development_notes "hindgut endoderm and proctodeal ectoderm." xsd:string {source="WP"} property_value: editor_note "adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca" xsd:string property_value: external_definition "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001186", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/cloaca"} property_value: external_definition "Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000095", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "cloacal" xsd:string property_value: homology_notes "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]" xsd:string {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/"} property_value: taxon_notes "Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs" xsd:string [Term] id: UBERON:0000163 name: embryonic cloaca def: "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]." [MP:0010115, Wikipedia:Cloaca_(embryology)] subset: pheno_slim synonym: "cloaca" RELATED SENSU [] xref: EHDAA2:0000256 xref: EHDAA:4895 xref: EMAPA:27573 xref: Wikipedia:Cloaca_(embryology) is_a: UBERON:0000162 ! cloaca relationship: has_developmental_contribution_from UBERON:0003064 ! intermediate mesoderm relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0001008 {source="EHDAA2"} ! renal system relationship: part_of UBERON:0012361 {source="EHDAA2"} ! internal anal region property_value: curator_notes "this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals." xsd:string [Term] id: UBERON:0000164 name: primitive urogenital sinus def: "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" [ISBN:0-683-40008-8, MP:0010116] subset: pheno_slim synonym: "fetal UGS" EXACT [PMID:18977204] synonym: "sinus urogenitalis" EXACT LATIN [] synonym: "UGS" EXACT [MP:0010116] synonym: "urogenital sinus" BROAD [MP:0010116] xref: EHDAA2:0004060 xref: EHDAA:5029 xref: EHDAA:5919 xref: EMAPA:17379 xref: NCIT:C34322 xref: SCTID:50961009 xref: UMLS:C0231057 {source="ncithesaurus:Urogenital_Sinus"} xref: VHOG:0000414 xref: Wikipedia:Definitive_urogenital_sinus relationship: contributes_to_morphology_of UBERON:0000163 ! embryonic cloaca relationship: develops_from UBERON:0003064 ! intermediate mesoderm relationship: only_in_taxon NCBITaxon:7742 relationship: part_of UBERON:0000163 {source="MP-def"} ! embryonic cloaca relationship: part_of UBERON:0001008 {source="EHDAA2"} ! renal system property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png xsd:anyURI property_value: external_definition "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000414", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/urogenital+sinus"} property_value: homology_notes "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]" xsd:string {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/"} property_value: terminology_notes "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" xsd:string {source="MP"} [Term] id: UBERON:0000165 name: mouth def: "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)." [https://github.com/obophenotype/uberon/wiki/The-digestive-tract, Wikipedia:Mouth] subset: efo_slim subset: major_organ subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "adult mouth" NARROW [] synonym: "cavital oralis" RELATED LATIN [Wikipedia:Mouth] synonym: "cavitas oris" RELATED [BTO:0001090] synonym: "cavum oris" RELATED [BTO:0001090] synonym: "mouth cavity" RELATED [BTO:0001090] synonym: "oral region" RELATED [EHDAA2:0001326] synonym: "oral vestibule" RELATED [BTO:0001090] synonym: "regio oralis" EXACT [BTO:0004698] synonym: "regio oralis" EXACT LATIN [FMA:49184, FMA:TA] synonym: "rima oris" RELATED [BTO:0001090] synonym: "stoma" RELATED [] synonym: "stomatodaeum" RELATED [VHOG:0000812] synonym: "trophic apparatus" RELATED [http://orcid.org/0000-0002-6601-2165] synonym: "vestibule of mouth" RELATED [BTO:0001090] synonym: "vestibulum oris" RELATED [BTO:0001090] xref: AAO:0010355 xref: BTO:0001090 xref: BTO:0004698 xref: CALOHA:TS-1315 xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 xref: FBbt:00003126 xref: FMA:49184 xref: GAID:75 xref: galen:Mouth xref: http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg xref: MA:0000341 xref: MA:0002474 xref: MAT:0000038 xref: MESH:D009055 xref: MIAA:0000038 xref: OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA xref: SCTID:21082005 xref: TADS:0000040 xref: TAO:0000547 xref: TAO:0000590 xref: TGMA:0000131 xref: VHOG:0000280 xref: VHOG:0000812 xref: Wikipedia:Mouth xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 is_a: UBERON:0004921 {notes="the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts"} ! subdivision of digestive tract intersection_of: UBERON:0004921 ! subdivision of digestive tract intersection_of: proximalmost_part_of UBERON:0001555 ! digestive tract relationship: develops_from UBERON:0035804 ! future mouth relationship: only_in_taxon NCBITaxon:6072 relationship: part_of UBERON:0000033 ! head relationship: proximalmost_part_of UBERON:0001555 ! digestive tract property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg xsd:anyURI property_value: development_notes "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" xsd:string property_value: external_definition "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010355", ontology="AAO", source="AAO:BJB"} property_value: external_ontology_notes "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" xsd:string {external_ontology="FMA"} property_value: has_relational_adjective "oral" xsd:string property_value: homology_notes "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]" xsd:string {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/"} property_value: seeAlso https://github.com/obophenotype/uberon/issues/661 xsd:anyURI [Term] id: UBERON:0000166 name: oral opening def: "The orifice that connects the mouth to the exterior of the body." [https://github.com/obophenotype/uberon/wiki/The-digestive-tract] subset: uberon_slim subset: vertebrate_core synonym: "mouth" RELATED INCONSISTENT [] synonym: "oral fissure" EXACT [FMA:59806] synonym: "oral orifice" EXACT [FMA:59806] synonym: "oral part of face" RELATED [] xref: FMA:59806 is_a: UBERON:0000161 {source="FMA"} ! orifice relationship: part_of UBERON:0000165 ! mouth property_value: homology_notes "(...) 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]" xsd:string {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/"} [Term] id: UBERON:0000167 name: oral cavity def: "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)" [https://github.com/obophenotype/uberon/wiki/The-digestive-tract, https://orcid.org/0000-0002-6601-2165, ISBN:0073040584] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "bucca" RELATED [] synonym: "buccal cavity" EXACT [FMA:20292, ISBN:0073040584] synonym: "cavity of mouth" EXACT [] xref: AAO:0000053 xref: AAO:0000960 xref: BSA:0000107 xref: CALOHA:TS-1315 xref: EFO:0001975 xref: EHDAA2:0001324 xref: EHDAA:6970 xref: EMAPA:17411 xref: EMAPA:18399 xref: EV:0100057 xref: FMA:20292 xref: HAO:0000669 xref: NCIT:C12421 xref: SCTID:181220002 xref: TAO:0001027 xref: TGMA:0000102 xref: UMLS:C0226896 {source="ncithesaurus:Oral_Cavity"} xref: VHOG:0000188 xref: WBbt:0005255 xref: XAO:0000126 xref: ZFA:0001027 is_a: UBERON:0002553 ! anatomical cavity intersection_of: UBERON:0000464 ! anatomical space intersection_of: luminal_space_of UBERON:0000165 ! mouth relationship: contributes_to_morphology_of UBERON:0000165 ! mouth relationship: luminal_space_of UBERON:0000165 ! mouth relationship: part_of UBERON:0000165 ! mouth property_value: external_definition "Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000960", ontology="AAO", source="AAO:EJS"} property_value: external_definition "The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000188", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/oral+cavity"} property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000168 name: proximal-distal subdivision of colon def: "A section dividing a colon along a proximal-distal axis." [http://orcid.org/0000-0002-6601-2165] subset: non_informative synonym: "segment of colon" RELATED [FMA:222905] xref: FMA:222905 is_a: UBERON:0004921 {order="4", source="cjm"} ! subdivision of digestive tract intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: subdivision_of UBERON:0001155 ! colon relationship: part_of UBERON:0001155 ! colon relationship: subdivision_of UBERON:0001155 ! colon [Term] id: UBERON:0000170 name: pair of lungs def: "The pair of anatomical structures comprised of a left lung and right lung." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "lungs" EXACT [] synonym: "lungs pair" EXACT [] synonym: "pulmones" EXACT LATIN [FMA:68877, FMA:TA] synonym: "set of lungs" EXACT [] xref: FMA:68877 xref: OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA is_a: CARO:0000000 is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection intersection_of: has_member UBERON:0002167 ! right lung intersection_of: has_member UBERON:0002168 ! left lung relationship: has_member UBERON:0002167 ! right lung relationship: has_member UBERON:0002167 {minCardinality="1", maxCardinality="1"} ! right lung relationship: has_member UBERON:0002168 ! left lung relationship: has_member UBERON:0002168 {minCardinality="1", maxCardinality="1"} ! left lung relationship: located_in UBERON:0002224 ! thoracic cavity relationship: part_of UBERON:0001558 {source="FMA-abduced"} ! lower respiratory tract [Term] id: UBERON:0000171 name: respiration organ def: "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." [GO:0007585] subset: functional_classification subset: organ_slim synonym: "apparatus respiratorius organ" EXACT [OBOL:automatic] synonym: "breathing organ" EXACT [] synonym: "gas exchange organ" RELATED [] synonym: "organ of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "organ of respiratory system" EXACT [OBOL:automatic] synonym: "respiratory organ" EXACT [] synonym: "respiratory system organ" EXACT [OBOL:automatic] xref: EMAPA:17607 xref: SCTID:272626006 xref: SPD:0000428 xref: TGMA:0001247 is_a: UBERON:0000062 ! organ intersection_of: UBERON:0000062 ! organ intersection_of: capable_of GO:0007585 relationship: capable_of GO:0007585 relationship: part_of UBERON:0001004 ! respiratory system [Term] id: UBERON:0000172 name: vomit def: "A bodily fluid consisting of the expulsed contents of the stomach disgorged through the mouth or nose that happens as a result of a vomit reflex." [ENVO:00000338, UBERON:cjm, Wikipedia:Vomiting] synonym: "vomitus" EXACT LATIN [] xref: ENVO:00000338 xref: galen:Vomitus xref: NCIT:C77666 xref: OpenCyc:Mx4rvViQTJwpEbGdrcN5Y29ycA is_a: UBERON:0036017 ! regurgitated substance [Term] id: UBERON:0000173 name: amniotic fluid def: "Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid." [ENVO:02000021, MP:MP] subset: pheno_slim synonym: "acqua amnii" RELATED LATIN [BTO:0000068] synonym: "liquor amnii" RELATED LATIN [BTO:0000068] xref: BTO:0000068 xref: CALOHA:TS-0034 xref: EMAPA:36771 xref: ENVO:02000021 xref: EV:0100123 xref: FMA:305905 xref: GAID:1155 xref: MA:0002893 xref: MESH:D000653 xref: NCIT:C13188 xref: UMLS:C0002638 {source="ncithesaurus:Amniotic_Fluid"} xref: VHOG:0001267 is_a: UBERON:0000463 ! organism substance relationship: functionally_related_to GO:0001701 relationship: located_in UBERON:0000305 ! amnion relationship: only_in_taxon NCBITaxon:32524 relationship: surrounds UBERON:0000922 ! embryo [Term] id: UBERON:0000174 name: excreta alt_id: UBERON:0000324 alt_id: UBERON:0007550 def: "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" [GO:0007588, http://orcid.org/0000-0002-6601-2165] synonym: "excreted substance" EXACT [] synonym: "excretion" RELATED [BTO:0000491] synonym: "portion of excreted substance" EXACT [FMA:9674] synonym: "waste substance" EXACT [AEO:0000184] xref: AEO:0000184 xref: BTO:0000491 xref: EHDAA2_RETIRED:0003184 xref: ENVO:02000022 xref: FMA:9674 xref: galen:Excretion is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance intersection_of: output_of GO:0007588 relationship: output_of GO:0007588 [Term] id: UBERON:0000175 name: pleural effusion def: "Pleural effusion is a bodily fluid that is produced in exess and accumulates in the pleural cavity, the fluid-filled space that surrounds the lungs. Excessive amounts of such fluid can impair breathing by limiting the expansion of the lungs during inhalation." [ENVO:02000033] xref: ENVO:02000033 xref: ncithesaurus:Pleural_Effusion xref: OpenCyc:Mx4rLaTGCK2TEduAAAAOpmP6tw is_a: UBERON:0001087 ! pleural fluid relationship: located_in UBERON:0002402 ! pleural cavity property_value: editor_note "cede to MPATH? Note the ncit class is under finding." xsd:string [Term] id: UBERON:0000176 name: oronasal secretion def: "A bodily fluid secreted from the body via the mouth or nose." [ENVO:02000035] synonym: "oronasal discharge" NARROW [] xref: ENVO:02000035 is_a: UBERON:0000463 ! organism substance relationship: only_in_taxon NCBITaxon:33213 relationship: produced_by UBERON:0001826 ! nasal cavity mucosa [Term] id: UBERON:0000177 name: pus def: "Pus is a bodily fluid consisting of a whitish-yellow or yellow substance produced during inflammatory responses of the body that can be found in regions of pyogenic bacterial infections. Pus is produced from the dead and living cells which travel into the intercellular spaces around the affected cells." [ENVO:02000038, Wikipedia:Pus] synonym: "purulent exudate" RELATED [] xref: ENVO:02000038 xref: galen:Pus xref: ncithesaurus:Pus xref: OpenCyc:Mx4rvVjG6ZwpEbGdrcN5Y29ycA xref: Wikipedia:Pus is_a: UBERON:0000463 ! organism substance relationship: only_in_taxon NCBITaxon:7742 relationship: output_of GO:0006954 property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/9/90/Swollen_eye_with_conjunctivitis.jpg xsd:anyURI property_value: external_ontology_notes "biospecimen in NCIT" xsd:string {external_ontology="NCIT"} [Term] id: UBERON:0000178 name: blood def: "A fluid that is composed of blood plasma and erythrocytes." [FMA:9670, http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/9, Wikipedia:Blood] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "portion of blood" EXACT [] synonym: "vertebrate blood" EXACT [] synonym: "whole blood" RELATED [BTO:0000089] xref: AAO:0000046 xref: BTO:0000089 xref: CALOHA:TS-0079 xref: EFO:0000296 xref: EHDAA2:0000176 xref: EHDAA:418 xref: EMAPA:16332 xref: ENVO:02000027 xref: EV:0100047 xref: FMA:9670 xref: GAID:965 xref: galen:Blood xref: MA:0000059 xref: MESH:D001769 xref: MIAA:0000315 xref: NCIT:C12434 xref: OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA xref: TAO:0000007 xref: UMLS:C0005767 {source="ncithesaurus:Blood"} xref: VHOG:0000224 xref: Wikipedia:Blood xref: XAO:0000124 xref: ZFA:0000007 is_a: UBERON:0000179 ! haemolymphatic fluid relationship: dc-contributor https://github.com/cmungall relationship: dc-contributor https://github.com/tmeehan relationship: develops_from UBERON:0006596 ! presumptive blood relationship: has_part CL:0000232 {source="CL:tm"} relationship: has_part UBERON:0001969 ! blood plasma relationship: immediate_transformation_of UBERON:0006596 {source="Bgee:AN"} ! presumptive blood relationship: located_in UBERON:0002049 {source="https://github.com/obophenotype/uberon/issues/1330"} ! vasculature relationship: part_of UBERON:0002390 ! hematopoietic system property_value: axiom_lost_from_external_ontology "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO"} property_value: curator_notes "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid." xsd:string property_value: external_definition "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000007", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO", source="AAO:LAP"} property_value: homology_notes "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0000179 name: haemolymphatic fluid def: "Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs." [http://orcid.org/0000-0002-6601-2165] synonym: "blood or blood analog" RELATED [] synonym: "circulating fluid" RELATED [] xref: CARO:0000081 is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system relationship: only_in_taxon NCBITaxon:6072 relationship: part_of UBERON:0002193 ! hemolymphoid system created_by: cjm creation_date: 2009-04-08T04:38:19Z [Term] id: UBERON:0000180 name: lateral lumbar region of abdomen def: "A region of the posterior torso (lower back) beneath the ribs and above the ilium." [Wikipedia:Abdomen#9-region_scheme, Wikipedia:Latus_(anatomy)] synonym: "flank" EXACT [Wikipedia:Latus_(anatomy)] synonym: "lateral region" EXACT [FMA:14603] synonym: "lateral region of abdomen" EXACT [FMA:14603] synonym: "latus" EXACT [FMA:14603] synonym: "regio lateralis" EXACT [FMA:14603] xref: CALOHA:TS-2336 xref: FMA:14603 xref: galen:Flank xref: NCIT:C93028 xref: SCTID:243329008 xref: UMLS:C0230171 {source="ncithesaurus:Flank"} xref: Wikipedia:Latus_(anatomy) is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0000916 ! abdomen property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray1220.png xsd:anyURI [Term] id: UBERON:0000199 name: neck of radius def: "The narrow part of the shaft of the radius just below the head." [http://www.medilexicon.com/medicaldictionary.php?t=58913] subset: pheno_slim synonym: "collum radii" EXACT [_rib] synonym: "radial neck" EXACT [FMA:23479] xref: FMA:23479 xref: galen:NeckOfRadius xref: SCTID:181942005 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005055 ! zone of long bone is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0018664 ! neck of bone element intersection_of: UBERON:0001560 ! neck of organ intersection_of: part_of UBERON:0001423 ! radius bone relationship: part_of UBERON:0001423 ! radius bone relationship: part_of UBERON:0004413 {source="FMA"} ! proximal epiphysis of radius [Term] id: UBERON:0000200 name: gyrus def: "A ridge on the cerebral cortex. It is generally surrounded by one or more sulci ." [https://github.com/obophenotype/uberon/issues/573, Wikipedia:Gyrus] subset: pheno_slim synonym: "cerebral gyrus" EXACT [BTO:0002495] synonym: "folia" RELATED PLURAL [] synonym: "folium" RELATED [PHENOSCAPE:wd] synonym: "folium of brain" RELATED [] synonym: "gyri" RELATED PLURAL [BTO:0002495] synonym: "gyri of cerebrum" RELATED PLURAL [BTO:0002495] synonym: "gyrus of cerebral hemisphere" RELATED [FMA:83874] synonym: "gyrus of cerebrum" RELATED [BTO:0002495] synonym: "gyrus of neuraxis" EXACT [FMA:83874] synonym: "neuraxis gyrus" EXACT [FMA:83874] xref: BTO:0002495 xref: FMA:83874 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1211 xref: NCIT:C32290 xref: SCTID:279165009 xref: UMLS:C0458308 {source="ncithesaurus:Cerebral_Gyrus"} xref: Wikipedia:Gyrus is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0034768 ! morphological feature relationship: dc-contributor https://github.com/cmungall relationship: dc-contributor https://github.com/RDruzinsky relationship: dc-contributor https://github.com/wdahdul relationship: dubious_for_taxon NCBITaxon:10088 relationship: fma_set_term FMA:72015 relationship: only_in_taxon NCBITaxon:40674 relationship: part_of UBERON:0001869 ! cerebral hemisphere relationship: surrounded_by UBERON:0013118 ! sulcus of brain property_value: seeAlso https://github.com/obophenotype/uberon/issues/573 xsd:anyURI [Term] id: UBERON:0000201 name: endothelial blood brain barrier def: "A blood brain barrier that is composed of endothelial cells." [https://orcid.org/0000-0002-6601-2165] xref: NIF_Subcellular:nlx_subcell_100205 is_a: UBERON:0000120 ! blood brain barrier is_a: UBERON:0001986 ! endothelium intersection_of: UBERON:0000120 ! blood brain barrier intersection_of: composed_primarily_of CL:0000115 relationship: composed_primarily_of CL:0000115 created_by: cjm creation_date: 2009-04-10T08:15:44Z [Term] id: UBERON:0000202 name: glial blood brain barrier def: "A blood brain barrier composed of glial cells." [https://orcid.org/0000-0002-6601-2165] xref: FBbt:00007091 is_a: UBERON:0000120 ! blood brain barrier intersection_of: UBERON:0000120 ! blood brain barrier intersection_of: composed_primarily_of CL:0000124 relationship: composed_primarily_of CL:0000124 created_by: cjm creation_date: 2009-04-10T08:42:24Z [Term] id: UBERON:0000203 name: pallium alt_id: UBERON:0007333 def: "Dorsal part (roof region) of the telencephalon[GO]." [GO:0021543, https://github.com/obophenotype/uberon/issues/287, ISBN:0471888893, Wikipedia:Pallium_(neuroanatomy)] subset: developmental_classification subset: efo_slim synonym: "area dorsalis telencephali" EXACT [ZFA:0000505] synonym: "dorsal part of telencephalon" EXACT [ISBN:0471888893] synonym: "dorsal telencephalic area" EXACT [ZFA:0000505] synonym: "dorsal telencephalon" EXACT [ZFA:0000505] xref: BTO:0003399 xref: DMBA:15903 xref: EFO:0003534 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=3240 xref: SCTID:369224000 xref: TAO:0000505 xref: TAO:0007007 xref: Wikipedia:Avian_pallium xref: Wikipedia:Pallium_(neuroanatomy) xref: ZFA:0000505 is_a: UBERON:0002616 ! regional part of brain is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001893 ! telencephalon relationship: present_in_taxon NCBITaxon:7762 {source="PMID:8932866"} property_value: homology_notes "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." xsd:string {source="Wikipedia:Avian_pallium", taxon="NCBITaxon:8782"} property_value: seeAlso https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/87 xsd:anyURI property_value: taxon_notes "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" xsd:string {source="WP"} created_by: cjm creation_date: 2009-04-18T12:03:09Z [Term] id: UBERON:0000204 name: ventral part of telencephalon def: "Ventral part (base region) of the telencephalon." [GO:0021544, GO_REF:0000021, ISBN:0471888893, PMID:12626695] subset: developmental_classification subset: efo_slim synonym: "area ventralis telencephali" EXACT [ZFA:0000304] synonym: "subpallium" EXACT [GO:0021544, ZFA:0000304] synonym: "subpallium" NARROW [BTO:0003401, NCBITaxon:8782] synonym: "ventral telencephalon" EXACT [ZFA:0000304] xref: BTO:0003401 xref: DMBA:15751 xref: EFO:0003522 xref: TAO:0000304 xref: ZFA:0000304 is_a: UBERON:0002616 ! regional part of brain is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: dorsal_to UBERON:0000203 {notes="separated by cell-free region"} ! pallium relationship: part_of UBERON:0001893 ! telencephalon property_value: external_ontology_notes "BTO term refers specifically to the avian structure" xsd:string {external_ontology="BTO"} created_by: cjm creation_date: 2009-04-18T12:12:27Z [Term] id: UBERON:0000205 name: papula def: "A thin protuberance on the surface of the body of an echinoderm containing diverticula of the water vascular system lined by ciliated peritoneum. Along with tube feet, provide the principle gas exchange surfaces.." [ISBN:0030229073] synonym: "papulae" EXACT PLURAL [ISBN:0030229073] synonym: "papulli" EXACT PLURAL [] xref: Wikipedia:Papula is_a: UBERON:0002535 ! gill relationship: only_in_taxon NCBITaxon:7586 created_by: cjm creation_date: 2009-04-18T01:13:57Z [Term] id: UBERON:0000206 name: pharyngeal gill def: "A gill that develops in the walls of the pharynx along a series of gill slits opening to the exterior. In fish, the gills are located on both sides of the pharynx." [Wikipedia:Gill#Vertebrate_gills] xref: ANISEED:1235300 xref: Wikipedia:Gill#Vertebrate_gills is_a: UBERON:0002535 ! gill relationship: adjacent_to UBERON:0001042 ! chordate pharynx property_value: function_notes "Gills are made of filaments which help increase surface area for oxygen exchange" xsd:string property_value: taxon_notes "In bony fish, the gills are covered by a bony cover called an operculum. When a fish breathes, it opens its mouth at regular times and draws in a mouthful of water. It then draws the sides of its throat together, forcing the water through the gill openings. The water passes over the gills on the outside. Valves inside the mouth keep the water from escaping through the mouth again. The operculum can be very important in adjusting the pressure of water inside of the pharynx to allow proper ventilation of the gills. Lampreys and sharks lack an operculum, they have multiple gill openings. Also, they must use different methods to force water over the gills. In sharks and rays, this ventilation of the gills is achieved either by the use of spiracles or ram ventilation (ventilation by constantly swimming). Although some animals use this method it is much better for animals to use a spiracle because they are less susceptible to injury" xsd:string created_by: cjm creation_date: 2009-04-18T01:18:17Z [Term] id: UBERON:0000207 name: compound eye corneal lens def: "A chitinous extracellular secretion of the four underlying cone cells and the pigment cells." [GO:0048058] synonym: "acellular lens" RELATED [] xref: FBbt:00004199 xref: TADS:0000304 is_a: UBERON:0000476 ! acellular anatomical structure is_a: UBERON:0005389 ! transparent eye structure disjoint_from: UBERON:0000965 ! lens of camera-type eye relationship: part_of UBERON:0000018 ! compound eye created_by: cjm creation_date: 2009-04-18T01:35:32Z [Term] id: UBERON:0000208 name: obsolete cellular lens is_obsolete: true replaced_by: UBERON:0000965 created_by: cjm creation_date: 2009-04-18T01:37:39Z [Term] id: UBERON:0000209 name: tetrapod frontal bone def: "the bone forming the forehead and roof of the eye orbit" [ISBN:0-683-40008-8, MP:0000107, PMID:7914451, Wikipedia:Frontal_bone] subset: pheno_slim synonym: "frontal" NARROW [AAO:0000206] synonym: "frontal bone" NARROW SENSU [FMA:52734, MA:0001466] synonym: "frontal bone" NARROW HUMAN_PREFERRED [FMA:52734, MA:0001466] synonym: "os frontal" NARROW SENSU [Wikipedia:Frontal_bone] synonym: "os frontale" RELATED LATIN [Wikipedia:Frontal_bone] xref: AAO:0000206 xref: EMAPA:19016 xref: FMA:52734 xref: GAID:226 xref: MA:0001466 xref: MESH:D005624 xref: NCIT:C32635 xref: SCTID:181793006 xref: UMLS:C0016732 {source="ncithesaurus:Frontal_Bone"} xref: VHOG:0001324 xref: VSAO:0000208 xref: Wikipedia:Frontal_bone is_a: UBERON:0002514 ! intramembranous bone is_a: UBERON:0008907 ! dermal bone is_a: UBERON:0010428 {source="FMA"} ! flat bone is_a: UBERON:0011164 ! neurocranium bone relationship: connected_to UBERON:0001677 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! sphenoid bone relationship: connected_to UBERON:0001679 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! ethmoid bone relationship: part_of UBERON:0001703 ! neurocranium relationship: part_of UBERON:0003113 {source="cjm"} ! dermatocranium property_value: depicted_by Frontal:bone.png xsd:anyURI property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/9/97/Gray136.png xsd:anyURI property_value: development_notes "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)." xsd:string property_value: taxon_notes "fused in humans, paired in other animals" xsd:string [Term] id: UBERON:0000210 name: tetrapod parietal bone def: "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." [Wikipedia:Parietal_bone, ZFA:0000514] subset: pheno_slim synonym: "actinopterygian frontal bone" NARROW [TAO:0000514] synonym: "frontal bone" NARROW [TAO:0000514] synonym: "os parietale" RELATED LATIN [Wikipedia:Parietal_bone] synonym: "os parietale" RELATED [Wikipedia:Parietal_bone] synonym: "parietal" NARROW SENSU [AAO:0000390] synonym: "parietal bone" NARROW SENSU [FMA:9613] xref: AAO:0000390 xref: EMAPA:18715 xref: FMA:9613 xref: GAID:229 xref: MA:0001469 xref: MESH:D010294 xref: NCIT:C12766 xref: SCTID:181794000 xref: UMLS:C0030558 {source="ncithesaurus:Parietal_Bone"} xref: VHOG:0001324 xref: VHOG:0001326 xref: Wikipedia:Parietal_bone is_a: UBERON:0002514 ! intramembranous bone is_a: UBERON:0010428 {source="FMA"} ! flat bone is_a: UBERON:0011164 ! neurocranium bone relationship: contributes_to_morphology_of UBERON:0004339 ! vault of skull relationship: part_of UBERON:0001703 ! neurocranium relationship: part_of UBERON:0004339 {source="PMID:11523816"} ! vault of skull property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/2/21/Gray132.png xsd:anyURI property_value: homology_notes "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]" xsd:string {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/"} property_value: taxon_notes "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" xsd:string {source="WP"} [Term] id: UBERON:0000211 name: ligament def: "Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000073] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "ligament organ" EXACT [FMA:21496] xref: CALOHA:TS-2145 xref: EFO:0001966 xref: EMAPA:35493 xref: FMA:21496 xref: FMA:30319 xref: galen:Ligament xref: MA:0000113 xref: MESH:D008022 xref: NCIT:C13046 xref: OpenCyc:Mx4rvVjqpZwpEbGdrcN5Y29ycA xref: SCTID:182358004 xref: TAO:0001682 xref: UMLS:C0023685 {source="ncithesaurus:Ligament"} xref: VHOG:0001272 xref: Wikipedia:Ligament xref: XAO:0004031 xref: ZFA:0001675 is_a: UBERON:0000062 ! organ relationship: has_part UBERON:0002384 ! connective tissue relationship: only_in_taxon NCBITaxon:33213 property_value: depicted_by Knee:diagram.svg xsd:anyURI property_value: external_definition "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]." xsd:string {source="FMA:21496"} property_value: external_definition "Portion of connective tissue that connects bone or cartilage.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001682", ontology="TAO", source="TAO:wd"} property_value: external_ontology_notes "this groups both skeletal and non-skeletal ligaments. What is called a 'ligament' in many AOs is actually a skeletal ligament" xsd:string property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000212 name: toilet claw def: "A specialized claw or nail on the foot of certain primates, used for personal grooming." [Wikipedia:Toilet-claw] xref: Wikipedia:Toilet-claw is_a: UBERON:0001705 ! nail relationship: capable_of_part_of GO:0007625 relationship: capable_of_part_of NBO:0000451 {source="Wikipedia"} created_by: cjm creation_date: 2009-05-19T08:19:58Z [Term] id: UBERON:0000218 name: vertebral arch of axis def: "A neural arch that is part of a vertebral bone 2." [OBOL:automatic] synonym: "vertebral foramen of cervical vertebra 2" EXACT [] xref: FMA:24053 is_a: UBERON:0003861 ! neural arch intersection_of: UBERON:0003861 ! neural arch intersection_of: part_of UBERON:0001093 ! vertebral bone 2 relationship: part_of UBERON:0001093 ! vertebral bone 2 [Term] id: UBERON:0000219 name: vertebral foramen of atlas def: "." [Wikipedia:Atlas_(anatomy)#Vertebral_foramen] synonym: "vertebral foramen of cervical vertebra 1" EXACT [] xref: FMA:24293 xref: SCTID:281228008 xref: Wikipedia:Atlas_(anatomy)#Vertebral_foramen is_a: UBERON:0001131 ! vertebral foramen is_a: UBERON:0005744 ! bone foramen is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0001131 ! vertebral foramen intersection_of: part_of UBERON:0001092 ! vertebral bone 1 relationship: part_of UBERON:0001092 ! vertebral bone 1 [Term] id: UBERON:0000220 name: atlanto-occipital joint def: "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" [Wikipedia:Atlanto-occipital_joint] synonym: "articulatio atlanto-occipitalis" EXACT [FMA:24939] synonym: "articulatio atlantooccipitalis" RELATED LATIN [Wikipedia:Atlanto-occipital_joint] synonym: "atlanto occipital joint" EXACT [] synonym: "atlantooccipital joint" EXACT [] synonym: "craniovertebral joint" EXACT [FMA:24939] synonym: "occipito atlantal joint" EXACT [] synonym: "occipito-atlantal joint" EXACT [] xref: FMA:24939 xref: NCIT:C32158 xref: ncithesaurus:Atlanto-occipital_Joint-Atlanto xref: SCTID:361831006 xref: UMLS:C0004169 {source="ncithesaurus:Atlanto-occipital_Joint"} xref: Wikipedia:Atlanto-occipital_joint is_a: CARO:0000000 is_a: UBERON:0002217 ! synovial joint is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0002217 ! synovial joint intersection_of: connects UBERON:0001092 ! vertebral bone 1 intersection_of: connects UBERON:0001676 ! occipital bone relationship: connects UBERON:0001092 ! vertebral bone 1 relationship: connects UBERON:0001676 ! occipital bone relationship: in_lateral_side_of UBERON:0006072 {source="FMA-abduced-lr"} ! cervical region of vertebral column relationship: part_of UBERON:0006072 ! cervical region of vertebral column relationship: part_of UBERON:0011138 ! postcranial axial skeletal system property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray304.png xsd:anyURI [Term] id: UBERON:0000221 name: supraauricular point def: "A craniometric point on the posterior root of the zygomatic process of the temporal bone directly above the auricular point." [http://www.medilexicon.com/medicaldictionary.php?t=70620] synonym: "supra-auricular part of head" EXACT [FMA:224222] xref: FMA:224222 is_a: CARO:0000000 is_a: UBERON:0006983 {source="FMA"} ! anatomical point relationship: part_of UBERON:0004655 ! zygomatic process of temporal bone [Term] id: UBERON:0000301 name: amniotic cavity def: "A closed space between the embryo and the amnion which contains the amniotic fluid and is formed by the fusion of the parts of the anterior and posterior amniotic folds." [MP:0011199] subset: pheno_slim synonym: "cavitas amniotica" RELATED LATIN [Wikipedia:Amniotic_cavity] xref: BTO:0000025 xref: EHDAA2:0000119 xref: EHDAA:83 xref: EMAPA:16079 xref: FMA:63941 xref: NCIT:C34102 xref: SCTID:280366002 xref: UMLS:C0230976 {source="ncithesaurus:Amniotic_Cavity"} xref: VHOG:0000855 xref: Wikipedia:Amniotic_cavity is_a: UBERON:0012466 ! extraembryonic cavity is_a: UBERON:0012467 ! enclosed anatomical space relationship: contains UBERON:0000173 ! amniotic fluid relationship: develops_from UBERON:0000087 {source="EHDAA2"} ! inner cell mass relationship: develops_from UBERON:0009742 {source="cjm"} ! proamniotic cavity relationship: has_quality PATO:0000608 relationship: part_of UBERON:0016887 ! entire extraembryonic component relationship: surrounded_by UBERON:0005971 {source="cjm"} ! amniotic fold property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/5/55/Gray31.png xsd:anyURI property_value: external_definition "The closed sac between the embryo and the amnion, containing the amniotic fluid. [Free_Online_Medical_Dictionary]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000855", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/amniotic+cavity"} [Term] id: UBERON:0000303 name: adductor longus def: "An adductor muscle that attaches to the hip and femur. In humans, it is a part of the adductor group of the thigh, that as the name suggests adducts the thigh. The adductor longus muscle forms the medial wall of the femoral triangle[WP, generalized]." [Wikipedia:Adductor_longus_muscle] subset: pheno_slim synonym: "adductor longus muscle" EXACT [] synonym: "long adductor muscle" RELATED [BTO:0000029] synonym: "musculus adductor longus" RELATED [BTO:0000029] synonym: "musculus adductor longus" RELATED LATIN [Wikipedia:Adductor_longus_muscle] xref: AAO:0010034 xref: BTO:0000029 xref: EMAPA:36220 xref: FMA:22441 xref: SCTID:181686003 xref: Wikipedia:Adductor_longus_muscle is_a: UBERON:0004252 ! hindlimb stylopod muscle is_a: UBERON:0011144 {source="Wikipedia"} ! adductor muscle of hip relationship: has_muscle_insertion UBERON:0000981 {notes="linea aspera", source="dbpedia"} ! femur relationship: has_muscle_origin UBERON:0001275 {notes="pubic body just below the pubic crest", source="dbpedia"} ! pubis relationship: part_of UBERON:0000376 ! hindlimb stylopod property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/e2/Anterior_Hip_Muscles_2.PNG xsd:anyURI property_value: external_definition "Originates on the iliac portion of the ventral iliac rim and inserts on the lateral surface of the M. adductor magnus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010034", ontology="AAO", source="AAO:EJS"} property_value: external_ontology_notes "definition generalized to accommodate AAO class - 'Originates on the iliac portion of the ventral iliac rim and inserts on the lateral surface of the M. adductor magnus.' [AAO:0010034]" xsd:string {external_ontology="AAO"} [Term] id: UBERON:0000304 name: tendon sheath def: "A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath" [Wikipedia:Tendon_sheath] synonym: "synovial tendon sheath" EXACT [FMA:45087] synonym: "vagina tendinis" RELATED LATIN [Wikipedia:Tendon_sheath] xref: BTO:0000051 xref: FMA:45087 xref: FMA:76715 xref: NCIT:C96299 xref: SCTID:361885006 xref: UMLS:C0224856 {source="ncithesaurus:Tendon_Sheath"} xref: Wikipedia:Tendon_sheath is_a: CARO:0000000 is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: bounding_layer_of UBERON:0000043 ! tendon relationship: bounding_layer_of UBERON:0000043 ! tendon relationship: has_part UBERON:0011233 ! synovial membrane of synovial tendon sheath relationship: has_part UBERON:0011234 ! fibrous membrane of synovial tendon sheath relationship: part_of UBERON:0000043 ! tendon property_value: editor_note "TODO - add layer relations. 'tendon sheath' GAT in FMA." xsd:string [Term] id: UBERON:0000305 name: amnion def: "the thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected" [MGI:csmith, MP:0005029] subset: pheno_slim synonym: "amnios" EXACT [http://placentation.ucsd.edu/glossfs.html] xref: BTO:0000065 xref: CALOHA:TS-0033 xref: EHDAA2:0000116 xref: EHDAA:136 xref: EMAPA:16109 xref: EV:0100122 xref: FMA:80223 xref: GAID:1298 xref: MESH:A16.254.403.277 xref: NCIT:C12365 xref: SCTID:181457005 xref: UMLS:C0002630 {source="ncithesaurus:Amnion"} xref: VHOG:0000721 xref: Wikipedia:Amnion is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005631 ! extraembryonic membrane relationship: develops_from UBERON:0005971 {source="ISBN:0073040584"} ! amniotic fold relationship: has_developmental_contribution_from UBERON:0000924 {source="ISBN:0073040584-table5.4"} ! ectoderm relationship: has_developmental_contribution_from UBERON:0004871 {source="ISBN:0073040584-table5.4"} ! somatic layer of lateral plate mesoderm relationship: has_part UBERON:0003254 ! amniotic ectoderm relationship: has_part UBERON:0003262 ! amniotic mesoderm relationship: only_in_taxon NCBITaxon:32524 {source="Hymans"} relationship: surrounds UBERON:0000922 ! embryo property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/e7/Gray14.png xsd:anyURI property_value: external_definition "A thin but tough extraembryonic membrane of reptiles, birds and mammals that lines the chorion and contains the fEtus and the amniotic fluid around it. [Biology_Online][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000721", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: has_relational_adjective "amniotic" xsd:string property_value: homology_notes "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000721", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187", source="http://bgee.unil.ch/"} [Term] id: UBERON:0000307 name: blastula alt_id: UBERON:0007011 def: "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." [Wikipedia:Blastula] subset: inconsistent_with_fma synonym: "blastosphere" RELATED [Wikipedia:Blastula] synonym: "blastula embryo" EXACT [BILA:0000059] xref: BILA:0000059 xref: BTO:0000128 xref: GAID:1294 xref: MESH:A16.254.270.274 xref: OGEM:000006 xref: OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg xref: Wikipedia:Blastula is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism intersection_of: existence_starts_and_ends_during UBERON:0000108 ! blastula stage relationship: develops_from UBERON:0007010 ! cleaving embryo relationship: existence_starts_and_ends_during UBERON:0000108 ! blastula stage property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png xsd:anyURI property_value: editor_note "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" xsd:string [Term] id: UBERON:0000309 name: body wall def: "The external portion of an animal body derived from ectoderm and mesoderm layers that encloses the body cavity." [MP:0003385] subset: pheno_slim synonym: "trunk wall" NARROW [FMA:10427] synonym: "wall fo trunk" EXACT [FMA:10427] synonym: "wall of trunk" NARROW [FMA:10427] xref: BTO:0000139 xref: EMAPA:32761 xref: FMA:10427 xref: galen:BodyWall xref: SCTID:281483004 is_a: UBERON:0000475 ! organism subdivision property_value: external_ontology_notes "the BTO class refers to earthworms." xsd:string {external_ontology="BTO"} property_value: taxon_notes "defined generically to encompass both vertebrates and invertebrates" xsd:string [Term] id: UBERON:0000310 name: breast def: "The upper ventral region of the torso of an organism." [Wikipedia:Breast] subset: pheno_slim synonym: "mamma" RELATED LATIN [Wikipedia:Breast] synonym: "mammary part of chest" EXACT [FMA:9601] synonym: "mammary region" EXACT [FMA:9601] xref: BTO:0000149 xref: CALOHA:TS-2083 xref: EV:0100124 xref: FMA:9601 xref: GAID:33 xref: galen:Breast xref: MESH:D001940 xref: NCIT:C12971 xref: OpenCyc:Mx4rvVjV7ZwpEbGdrcN5Y29ycA xref: SCTID:181131000 xref: UMLS:C0006141 {source="ncithesaurus:Breast"} xref: Wikipedia:Breast is_a: UBERON:0034929 ! external soft tissue zone relationship: part_of UBERON:0001443 ! chest property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/6e/Closeup_of_female_breast.jpg xsd:anyURI property_value: taxon_notes "The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's." xsd:string {source="WP,unvetted"} [Term] id: UBERON:0000311 name: extensor muscle def: "a skeletal muscle whose contraction extends or stretches a body part." [http://www.thefreedictionary.com/extensor+muscle, https://github.com/obophenotype/uberon/issues/57] comment: Any of the muscles that increase the angle between segments of a limb, E.g. straightening the elbow or knee or bending the wrist or spine backward. The movement is usually directed backward, with the notable exception of the knee joint. In humans, certain muscles of the hand and foot are named for this function. In the hand these include the extensor carpi radialis brevis, extensor carpi radialis longus, and extensor carpi ulnaris, which run from the humerus along the back of the forearm to the metacarpal bones at the back of the hand. [http://www.britannica.com/EBchecked/topic/198909/extensor-muscle] subset: pheno_slim synonym: "extensor" RELATED [] xref: BTO:0000151 xref: FMA:75000 is_a: UBERON:0014892 ! skeletal muscle organ relationship: dc-contributor https://github.com/cmungall relationship: develops_from UBERON:0010962 ! extensor pre-muscle mass relationship: part_of UBERON:0000026 ! appendage [Term] id: UBERON:0000312 name: inner cambium layer of periosteum synonym: "cambial layer" EXACT [FMA:234358] synonym: "cambial layer of periosteum" EXACT [FMA:234358] synonym: "cambium" EXACT [] synonym: "cambium layer of periosteum" EXACT [FMA:234358] synonym: "inner cambial layer of periosteum" EXACT [FMA:234358] synonym: "internal layer of periosteum" EXACT [] synonym: "internal periosteum" EXACT [] synonym: "osteogenic layer of periosteum" EXACT [Wikipedia:Periosteum] xref: FMA:234358 is_a: UBERON:0000158 ! membranous layer is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: composed_primarily_of UBERON:0011824 ! fibrous connective tissue relationship: has_part CL:0007010 {source="Wikipedia"} relationship: part_of UBERON:0002515 {source="FMA"} ! periosteum [Term] id: UBERON:0000313 name: portion of cartilage tissue in tibia def: "Cartilage pertaining to the tibia." [Dorlands_Medical_Dictionary:MerckSource] synonym: "cartilage of tibia" RELATED [FMA:33923] synonym: "tibial cartilage" EXACT [] xref: BTO:0000207 xref: FMA:33923 is_a: UBERON:0004270 ! lower leg connective tissue is_a: UBERON:0007391 ! pelvic appendage cartilage tissue is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0002418 ! cartilage tissue intersection_of: part_of UBERON:0000979 ! tibia relationship: part_of UBERON:0000979 ! tibia property_value: curator_notes "This class represents a portion of cartilage tissue located in the tibia, *not* the cartilaginous condensation of an emrbyonic tibia" xsd:string [Term] id: UBERON:0000314 name: cecum mucosa def: "A mucosa that is part of a cecum [Automatically generated definition]." [OBOL:automatic] synonym: "caecum mucosa" EXACT [OBOL:automatic] synonym: "caecum mucosa of organ" EXACT [OBOL:automatic] synonym: "caecum mucous membrane" EXACT [OBOL:automatic] synonym: "caecum organ mucosa" EXACT [OBOL:automatic] synonym: "cecal mucosa" EXACT [FMA:14998] synonym: "cecum mucosa of organ" EXACT [OBOL:automatic] synonym: "cecum mucous membrane" EXACT [OBOL:automatic] synonym: "cecum organ mucosa" EXACT [OBOL:automatic] synonym: "intestinum crassum caecum mucosa" EXACT [OBOL:automatic] synonym: "intestinum crassum caecum mucosa of organ" EXACT [OBOL:automatic] synonym: "intestinum crassum caecum mucous membrane" EXACT [OBOL:automatic] synonym: "intestinum crassum caecum organ mucosa" EXACT [OBOL:automatic] synonym: "mucosa of caecum" EXACT [OBOL:automatic] synonym: "mucosa of cecum" EXACT [OBOL:automatic] synonym: "mucosa of intestinum crassum caecum" EXACT [OBOL:automatic] synonym: "mucosa of organ of caecum" EXACT [OBOL:automatic] synonym: "mucosa of organ of cecum" EXACT [OBOL:automatic] synonym: "mucosa of organ of intestinum crassum caecum" EXACT [OBOL:automatic] synonym: "mucous membrane of caecum" EXACT [OBOL:automatic] synonym: "mucous membrane of cecum" EXACT [OBOL:automatic] synonym: "mucous membrane of intestinum crassum caecum" EXACT [OBOL:automatic] synonym: "organ mucosa of caecum" EXACT [OBOL:automatic] synonym: "organ mucosa of cecum" EXACT [OBOL:automatic] synonym: "organ mucosa of intestinum crassum caecum" EXACT [OBOL:automatic] xref: BTO:0000213 xref: FMA:14998 is_a: UBERON:0000317 ! colonic mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001153 ! caecum relationship: part_of UBERON:0001153 ! caecum [Term] id: UBERON:0000315 name: subarachnoid space def: "The space between the arachnoid and pia mater." [GOC:add, https://sourceforge.net/p/obo/mammalian-phenotype-requests/1168/, Wikipedia:Subarachnoid_space] subset: pheno_slim synonym: "cavitas subarachnoidea" RELATED LATIN [BTO:0000230] synonym: "cavum subarachnoideale" RELATED LATIN [Wikipedia:Subarachnoid_space] synonym: "spatium leptomeningeum" RELATED LATIN [BTO:0000230] synonym: "spatium subarachnoideum" RELATED LATIN [BTO:0000230] synonym: "spatium subarachnoideum" RELATED LATIN [Wikipedia:Subarachnoid_space] synonym: "subarachnoid cavity" RELATED [BTO:0000230] xref: BTO:0000230 xref: EMAPA:32666 xref: FMA:83716 xref: GAID:689 xref: MESH:D013346 xref: SCTID:362311001 xref: Wikipedia:Subarachnoid_space is_a: CARO:0000000 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: adjacent_to UBERON:0002361 ! pia mater intersection_of: adjacent_to UBERON:0002362 ! arachnoid mater relationship: adjacent_to UBERON:0002361 ! pia mater relationship: adjacent_to UBERON:0002362 ! arachnoid mater relationship: contains UBERON:0001359 ! cerebrospinal fluid relationship: contains UBERON:0001981 {source="ISBN:0471888893"} ! blood vessel relationship: part_of UBERON:0000955 ! brain property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray769-en.svg xsd:anyURI property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray769.png xsd:anyURI [Term] id: UBERON:0000316 name: cervical mucus def: "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." [BTO:0000242, Wikipedia:Cervix#Cervical_mucus, Wikipedia:Mucus#Reproductive_system] synonym: "cervix mucus" EXACT [OBOL:automatic] xref: BTO:0000242 xref: FMA:83689 xref: MESH:D002582 xref: Wikipedia:Mucus#Reproductive_system is_a: UBERON:0000912 ! mucus intersection_of: UBERON:0000912 ! mucus intersection_of: produced_by UBERON:0000002 ! uterine cervix relationship: produced_by UBERON:0000002 ! uterine cervix [Term] id: UBERON:0000317 name: colonic mucosa alt_id: UBERON:0003347 alt_id: UBERON:0004981 def: "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." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim synonym: "colon mucosa" EXACT [FMA:14984] synonym: "colon mucous membrane" EXACT [OBOL:automatic] synonym: "colonic mucosa" EXACT [] synonym: "colonic mucous membrane" EXACT [FMA:14984] synonym: "large bowel mucosa" EXACT [OBOL:automatic] synonym: "mucosa of colon" EXACT [FMA:14984] synonym: "mucosa of large bowel" EXACT [OBOL:automatic] xref: BTO:0000271 xref: CALOHA:TS-0164 xref: EFO:0003038 xref: EMAPA:27375 xref: FMA:14984 xref: FMA:85388 xref: MA:0003194 xref: SCTID:362157008 intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001155 ! colon relationship: part_of UBERON:0001155 ! colon [Term] id: UBERON:0000319 name: cytotrophoblast def: "The inner layer of the trophoblast, interior to the syncytiotrophoblast in an embryo. It serves to anchor the embryonic chorion to the maternal endometrium. Cytotrophoblasts are stem cells in the chorionic villi. During differentiation, mononuclear cytotrophoblast fuse together into the multinucleated syncytiotrophoblasts. The primary villi has only the cytotrophoblast as an axe. [WP,unvetted]." [http://placentation.ucsd.edu/glossfs.html, Wikipedia:Cytotrophoblast] synonym: "cellular trophoblast" EXACT [FMA:83039] synonym: "cytotrophoblastic cell" RELATED [FMA:83039] synonym: "cytotrophoblastic cell layer" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "cytotrophoblastus" RELATED LATIN [Wikipedia:Cytotrophoblast] synonym: "Langhans' layer" RELATED [Wikipedia:Cytotrophoblast] synonym: "layer of Langhans" RELATED [Wikipedia:Cytotrophoblast] xref: BTO:0000322 xref: EHDAA:127 xref: EHDAA:152 xref: EHDAA:89 xref: EMAPA:16067 xref: FMA:83039 xref: NCIT:C33919 xref: SCTID:308841008 xref: UMLS:C0230960 {source="ncithesaurus:Cytotrophoblast"} xref: VHOG:0000683 xref: Wikipedia:Cytotrophoblast is_a: CARO:0000000 is_a: UBERON:0002050 ! embryonic structure relationship: adjacent_to UBERON:0000371 ! syncytiotrophoblast relationship: adjacent_to UBERON:0000453 ! decidua basalis relationship: part_of UBERON:0000088 ! trophoblast property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/d/df/Gray36.png xsd:anyURI property_value: editor_note "todo - unify with EHDAA2, which distinguishes multiple types of cytotrophoblast" xsd:string property_value: external_definition "A derivative layer of the trophoblast, the cells of which retain their boundaries and contribute to the extraembryonic mesoderm [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.189, see_Kardong_KV][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000683", ontology="VHOG", source="http://bgee.unil.ch/"} [Term] id: UBERON:0000320 name: duodenal mucosa alt_id: UBERON:0003348 def: "A mucosa that is part of a duodenum [Automatically generated definition]." [OBOL:automatic] synonym: "doudenal mucosa" EXACT [FMA:14942] synonym: "duodenal mucous membrane" EXACT [FMA:14942] synonym: "duodenum mucosa" RELATED [BTO:0000367] synonym: "mucosa of duodenum" EXACT [OBOL:automatic] synonym: "mucous membrane of duodenum" EXACT [OBOL:automatic] xref: BTO:0000367 xref: CALOHA:TS-0213 xref: EMAPA:27235 xref: FMA:14942 xref: MA:0003207 xref: SCTID:362146003 is_a: UBERON:0001204 ! mucosa of small intestine intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0002114 ! duodenum relationship: part_of UBERON:0002114 ! duodenum [Term] id: UBERON:0000323 name: late embryo def: "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." [BGEE:ANiknejad] subset: efo_slim subset: pheno_slim synonym: "embryo late growth stage" RELATED [BTO:0000449] synonym: "embryo late stage" RELATED [BTO:0000449] synonym: "fetus" NARROW [BTO:0000449] xref: BTO:0000449 xref: CALOHA:TS-0360 xref: EFO:0001323 xref: FBbt:00005333 xref: FMA:63919 xref: GAID:552 xref: MESH:D005333 xref: NCIT:C13235 xref: OpenCyc:Mx4rvZfC2ZwpEbGdrcN5Y29ycA xref: SCTID:83418008 xref: UMLS:C0015965 {source="ncithesaurus:Fetus"} is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000922 ! embryo intersection_of: existence_starts_and_ends_during UBERON:0007220 ! late embryonic stage relationship: existence_starts_and_ends_during UBERON:0007220 ! late embryonic stage property_value: editor_note "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." xsd:string property_value: external_definition "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]." xsd:string {source="FMA:63919"} [Term] id: UBERON:0000325 name: gastric gland def: "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." [MGI:anna] subset: organ_slim subset: pheno_slim xref: BTO:0000503 xref: EMAPA:27181 xref: FMA:14919 is_a: UBERON:0002365 {source="cjm"} ! exocrine gland is_a: UBERON:0003294 ! gland of foregut relationship: part_of UBERON:0006924 {source="ISBN:0073040584"} ! stomach glandular epithelium [Term] id: UBERON:0000326 name: pancreatic juice def: "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." [GO:0030157] synonym: "pancreatic fluid" RELATED [] synonym: "pancreatic secretion" RELATED [] synonym: "succus pancreaticus" RELATED [BTO:0000504] xref: BTO:0000504 xref: CALOHA:TS-2235 xref: FMA:62973 xref: GAID:1166 xref: MESH:D010189 is_a: UBERON:0000456 ! secretion of exocrine gland intersection_of: UBERON:0000456 ! secretion of exocrine gland intersection_of: produced_by UBERON:0001264 ! pancreas relationship: produced_by UBERON:0001264 ! pancreas [Term] id: UBERON:0000328 name: gut wall def: "The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity)." [http://orcid.org/0000-0002-6601-2165] synonym: "digestive tract wall" EXACT [] synonym: "wall of alimentary tract" RELATED [] synonym: "wall of digestive tract" EXACT [] synonym: "wall of gut" EXACT [FMA:45653] xref: BTO:0000547 xref: FMA:45653 is_a: UBERON:0000060 ! anatomical wall intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract property_value: curator_notes "We model the digestive tract as consisting of two parts: the wall and the lumen." xsd:string [Term] id: UBERON:0000329 name: hair root def: "The enlarged basal part of a hair within the skin[BTO]. The root of the hair ends in an enlargement, the hair bulb, which is whiter in color and softer in texture than the shaft, and is lodged in a follicular involution of the epidermis called the hair follicle. [Wikipedia]." [BTO:0000555, Wikipedia:Hair_root] synonym: "root of hair" EXACT [FMA:70730] xref: BTO:0000555 xref: CALOHA:TS-0433 xref: FMA:70730 xref: NCIT:C32707 xref: NCIT:C32711 xref: UMLS:C1182707 {source="ncithesaurus:Hair_Root"} xref: Wikipedia:Hair_root is_a: UBERON:0000021 ! cutaneous appendage is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001037 ! strand of hair property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray944.png xsd:anyURI [Term] id: UBERON:0000331 name: ileal mucosa def: "A mucosa that is part of a ileum [Automatically generated definition]." [OBOL:automatic] synonym: "ileal mucous membrane" EXACT [FMA:14956] synonym: "ileum mucosa" EXACT [FMA:14956] synonym: "ileum mucosa" EXACT [OBOL:automatic] synonym: "ileum mucosa of organ" EXACT [OBOL:automatic] synonym: "ileum mucous membrane" EXACT [OBOL:automatic] synonym: "ileum organ mucosa" EXACT [OBOL:automatic] synonym: "mucosa of ileum" EXACT [OBOL:automatic] synonym: "mucosa of organ of ileum" EXACT [OBOL:automatic] synonym: "mucous membrane of ileum" EXACT [OBOL:automatic] synonym: "organ mucosa of ileum" EXACT [OBOL:automatic] xref: BTO:0000619 xref: CALOHA:TS-0470 xref: EMAPA:35424 xref: FMA:14956 xref: MA:0003216 xref: SCTID:85458007 is_a: UBERON:0001204 ! mucosa of small intestine intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0002116 ! ileum relationship: part_of UBERON:0002116 ! ileum [Term] id: UBERON:0000332 name: yellow bone marrow def: "bone marrow in which the fat cells predominate in the meshes of the reticular network." [http://medical-dictionary.thefreedictionary.com/Yellow+Marrow] synonym: "fat marrow" RELATED [BTO:0000635] synonym: "medulla ossium flava" EXACT LATIN [BTO:0000635] synonym: "yellow marrow" EXACT [BTO:0000635] xref: BTO:0000635 xref: FMA:74596 xref: SCTID:328639002 xref: SCTID:5023006 is_a: UBERON:0002371 ! bone marrow intersection_of: UBERON:0002371 ! bone marrow intersection_of: composed_primarily_of CL:0000136 relationship: composed_primarily_of CL:0000136 relationship: part_of UBERON:0007195 ! stroma of bone marrow [Term] id: UBERON:0000333 name: intestinal gland def: "A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm]." [https://orcid.org/0000-0002-6601-2165] subset: organ_slim synonym: "bowel mucosa gland" EXACT [OBOL:automatic] synonym: "bowel mucosa of organ gland" EXACT [OBOL:automatic] synonym: "bowel mucous membrane gland" EXACT [OBOL:automatic] synonym: "bowel organ mucosa gland" EXACT [OBOL:automatic] synonym: "gland of bowel mucosa" EXACT [OBOL:automatic] synonym: "gland of bowel mucosa of organ" EXACT [OBOL:automatic] synonym: "gland of bowel mucous membrane" EXACT [OBOL:automatic] synonym: "gland of bowel organ mucosa" EXACT [OBOL:automatic] synonym: "gland of intestinal mucosa" EXACT [OBOL:automatic] synonym: "gland of intestine mucosa" EXACT [OBOL:automatic] synonym: "gland of intestine mucosa of organ" EXACT [OBOL:automatic] synonym: "gland of intestine mucous membrane" EXACT [OBOL:automatic] synonym: "gland of intestine organ mucosa" EXACT [OBOL:automatic] synonym: "gland of mucosa of bowel" EXACT [OBOL:automatic] synonym: "gland of mucosa of intestine" EXACT [OBOL:automatic] synonym: "gland of mucosa of organ of bowel" EXACT [OBOL:automatic] synonym: "gland of mucosa of organ of intestine" EXACT [OBOL:automatic] synonym: "gland of mucous membrane of bowel" EXACT [OBOL:automatic] synonym: "gland of mucous membrane of intestine" EXACT [OBOL:automatic] synonym: "gland of organ mucosa of bowel" EXACT [OBOL:automatic] synonym: "gland of organ mucosa of intestine" EXACT [OBOL:automatic] synonym: "glandula intestinalis" EXACT [FMA:15052] synonym: "glandulae intestinales" RELATED [] synonym: "intestinal mucosa gland" EXACT [OBOL:automatic] synonym: "intestine mucosa gland" EXACT [OBOL:automatic] synonym: "intestine mucosa of organ gland" EXACT [OBOL:automatic] synonym: "intestine mucous membrane gland" EXACT [OBOL:automatic] synonym: "intestine organ mucosa gland" EXACT [OBOL:automatic] synonym: "mucosa of bowel gland" EXACT [OBOL:automatic] synonym: "mucosa of intestine gland" EXACT [OBOL:automatic] synonym: "mucosa of organ of bowel gland" EXACT [OBOL:automatic] synonym: "mucosa of organ of intestine gland" EXACT [OBOL:automatic] synonym: "mucous membrane of bowel gland" EXACT [OBOL:automatic] synonym: "mucous membrane of intestine gland" EXACT [OBOL:automatic] synonym: "organ mucosa of bowel gland" EXACT [OBOL:automatic] synonym: "organ mucosa of intestine gland" EXACT [OBOL:automatic] xref: BTO:0000640 xref: FMA:15052 xref: SCTID:266297002 intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0001242 ! intestinal mucosa relationship: part_of UBERON:0001242 ! intestinal mucosa property_value: external_ontology_notes "Note that some sources treat 'intestinal gland' as synonymous with crypts" xsd:string [Term] id: UBERON:0000341 name: throat def: "In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted]." [Wikipedia:Throat] subset: pheno_slim synonym: "gula" RELATED LATIN [] xref: BTO:0000828 xref: EMAPA:37973 {source="MA:th"} xref: FMA:228738 xref: NCIT:C54272 xref: OpenCyc:Mx4rwQtO_JwpEbGdrcN5Y29ycA xref: UMLS:C0230069 {source="ncithesaurus:Throat"} xref: Wikipedia:Throat is_a: UBERON:0034929 ! external soft tissue zone relationship: part_of UBERON:0000974 ! neck property_value: depicted_by Throat:Diagram.png xsd:anyURI property_value: has_relational_adjective "gular" xsd:string property_value: taxon_notes "The hyoid bone and the clavicle are the only bones located in the throat of mammals." xsd:string [Term] id: UBERON:0000344 name: mucosa def: "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]" [Wikipedia:Mucous_membrane] subset: pheno_slim synonym: "mucosa of organ" EXACT [FMA:85355] synonym: "mucosa of organ part" EXACT [FMA:85358] synonym: "mucosal region" EXACT [FMA:85358] synonym: "mucous membrane" EXACT [FMA:85355] synonym: "organ mucosa" EXACT [FMA:85355] synonym: "region of mucosa" RELATED [FMA:85358] synonym: "tunica mucosa" RELATED LATIN [Wikipedia:Mucous_membrane] synonym: "tunica mucosa" RELATED [BTO:0000886] xref: AEO:0000199 xref: BTO:0000886 xref: CALOHA:TS-2031 xref: EHDAA2_RETIRED:0003234 xref: EV:0100382 xref: FMA:85355 xref: FMA:85358 xref: GAID:297 xref: galen:Mucosa xref: MESH:D009092 xref: NCIT:C13166 xref: OpenCyc:Mx4rvmKNOpwpEbGdrcN5Y29ycA xref: SCTID:361693009 xref: UMLS:C0026724 {source="ncithesaurus:Mucosa"} xref: Wikipedia:Mucous_membrane is_a: UBERON:0004923 ! organ component layer relationship: has_part UBERON:0000483 ! epithelium relationship: has_part UBERON:0002384 ! connective tissue relationship: only_in_taxon NCBITaxon:7711 property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png xsd:anyURI property_value: depicted_by http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png xsd:anyURI property_value: external_ontology_notes "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" xsd:string {external_ontology="FMA"} property_value: has_relational_adjective "mucosal" xsd:string [Term] id: UBERON:0000345 name: myelin def: "A dielectric (electrically insulating) material consisting of protein and fat that forms a layer, the myelin sheath, usually around only the axon of a neuron. Myelin is about 40 % water; the dry mass of myelin is about 70 - 85 % lipids and about 15 - 30 % proteins. Some of the proteins that make up myelin are myelin basic protein (MBP), myelin oligodendrocyte glycoprotein (MOG), and proteolipid protein (PLP). The primary lipid of myelin is a glycolipid called galactocerebroside (GalC). The intertwining hydrocarbon chains of sphingomyelin serve to strengthen the myelin sheath." [Wikipedia:Myelin] subset: pheno_slim xref: BTO:0000894 xref: FMA:62977 xref: ncithesaurus:Myelin xref: Wikipedia:Myelin is_a: CARO:0000000 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CHEBI:36498 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} relationship: has_part CHEBI:64583 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} relationship: has_part PR:000010228 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} relationship: only_in_taxon NCBITaxon:33213 relationship: part_of UBERON:0001016 ! nervous system relationship: present_in_taxon NCBITaxon:6340 {source="http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html"} relationship: present_in_taxon NCBITaxon:6681 {source="http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html"} relationship: present_in_taxon NCBITaxon:7742 {source="http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html"} property_value: editor_note "cede to other ontology. Retired in ncit" xsd:string [Term] id: UBERON:0000346 name: obsolete myelin membrane synonym: "myelinated plasma membrane of Schwann cell" EXACT [FMA:73417] property_value: external_ontology_notes "BTO has def The multilamellar myelin membrane is a specisalised lipid-rich domain of the glial cell plasma membrane. FMA has primary term name Myelinated plasma membrane of Schwann cell" xsd:string {external_ontology="BTO"} is_obsolete: true consider: BTO:0000895 consider: FMA:73417 [Term] id: UBERON:0000347 name: entire myelin sheath def: "The insulating envelope that surrounds nerve fibers or axons." [MP:0003871] subset: pheno_slim synonym: "medullary sheath" RELATED [BTO:0000900] xref: BTO:0000900 xref: CALOHA:TS-2363 xref: FMA:62983 xref: GAID:731 xref: GO:0043209 xref: MESH:D009186 xref: NCIT:C13261 xref: UMLS:C0026973 {source="ncithesaurus:Myelin_Sheath"} is_a: CARO:0000000 is_a: UBERON:0005162 ! multi cell part structure relationship: composed_primarily_of GO:0043209 relationship: has_part UBERON:0000345 ! myelin property_value: editor_note "do not cede to GO until GO includes has_part link to myelin" xsd:string [Term] id: UBERON:0000348 name: ophthalmic nerve def: "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." [MP:0009798, Wikipedia:Ophthalmic_nerve] comment: Terminology notes. This nerve is known by a ridiculous number of names[http://palaeos.com/vertebrates/glossary/glossaryPo.html] subset: pheno_slim synonym: "ciliary nerve" RELATED [http://palaeos.com/vertebrates/glossary/glossaryPo.html] synonym: "cranial nerve V, branch V1" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "ethmoidal nerve" RELATED [Wikipedia:Ophthalmic_nerve] synonym: "first branch of fifth cranial nerve" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "first division of fifth cranial nerve" EXACT [FMA:52621] synonym: "first division of trigeminal nerve" EXACT [FMA:52621] synonym: "nervus ophthalmicus (V1)" EXACT [FMA:52621] synonym: "nervus ophthalmicus (Va)" EXACT [FMA:52621] synonym: "nervus ophthalmicus [v1]" EXACT LATIN [FMA:52621, FMA:TA] synonym: "nervus ophthalmicus [va]" EXACT LATIN [FMA:52621, FMA:TA] synonym: "ophthalmic division" RELATED [Wikipedia:Ophthalmic_nerve] synonym: "ophthalmic division" RELATED [BTO:0000926] synonym: "ophthalmic division [V1]" EXACT [FMA:52621] synonym: "ophthalmic division [Va]" EXACT [FMA:52621] synonym: "ophthalmic division of fifth cranial nerve" EXACT [FMA:52621] synonym: "ophthalmic division of trigeminal nerve (V1)" EXACT [FMA:52621] synonym: "ophthalmic division of trigeminal nerve (Va)" EXACT [FMA:52621] synonym: "ophthalmic nerve [V1]" EXACT [FMA:52621] synonym: "ophthalmic nerve [Va]" EXACT [FMA:52621] synonym: "opthalmic nerve" EXACT [Wikipedia:Ophthalmic_nerve] synonym: "profundal nerve" RELATED [http://orcid.org/0000-0002-6601-2165] synonym: "profundus" RELATED [http://palaeos.com/vertebrates/glossary/glossaryPo.html] synonym: "profundus nerve" RELATED [http://palaeos.com/vertebrates/glossary/glossaryPo.html] synonym: "ramus opthalmicus profundus (ramus V1)" EXACT [AAO:0010648] synonym: "rostral branch of trigeminal nerve" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "trigeminal nerve ophthalmic division" RELATED [EMAPA:17800] synonym: "trigeminal V nerve ophthalmic division" EXACT [MA:0001104] xref: AAO:0010648 xref: BTO:0000926 xref: EHDAA2:0002088 xref: EHDAA:3744 xref: EMAPA:17800 xref: FMA:52621 xref: GAID:837 xref: MA:0001104 xref: MESH:D009882 xref: NCIT:C33215 xref: OpenCyc:Mx4rwEs_K5wpEbGdrcN5Y29ycA xref: SCTID:280210000 xref: UMLS:C0029082 {source="ncithesaurus:Ophthalmic_Nerve"} xref: VHOG:0001349 xref: Wikipedia:Ophthalmic_nerve is_a: CARO:0001001 is_a: UBERON:0011779 ! nerve of head region relationship: branching_part_of UBERON:0001645 {notes="may be a distinct nerve in teleosts", source="multiple"} ! trigeminal nerve relationship: develops_from UBERON:0035597 ! profundal placode relationship: innervates UBERON:1000021 ! skin of face relationship: part_of UBERON:0001645 ! trigeminal nerve property_value: external_definition "Sensory medial ramus of the trigeminal nerve.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010648", ontology="AAO", source="AAO:EJS"} property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000349 name: limbic system def: "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]." [BIRNLEX:Limbic_system, Wikipedia:Limbic_system] 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] subset: non_informative subset: pheno_slim synonym: "visceral brain" RELATED [ISBN:0123813611] xref: BTO:0000928 xref: CALOHA:TS-1307 xref: FMA:242000 xref: GAID:615 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2055 xref: MESH:A08.186.211.577 xref: NCIT:C94541 xref: OpenCyc:Mx4rwAeba5wpEbGdrcN5Y29ycA xref: SCTID:361342009 xref: UMLS:C0023715 {source="ncithesaurus:Limbic_System"} xref: Wikipedia:Limbic_system is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:0001890 ! forebrain property_value: depicted_by Brain:limbicsystem.jpg xsd:anyURI property_value: editor_note "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." xsd:string [Term] id: UBERON:0000351 name: nuchal ligament def: "A fibrous membrane, which, in the neck, represents the supraspinal ligaments of the upper vertebrae." [Wikipedia:Nuchal_ligament] synonym: "ligament of neck" EXACT [FMA:13427] synonym: "ligamentum nuchae" EXACT LATIN [FMA:13427] synonym: "paddywhack" NARROW [NCBITaxon:9895, Wikipedia:Paddywhack] synonym: "paxwax" RELATED [] xref: BTO:0000952 xref: EMAPA:19207 xref: FMA:13427 xref: SCTID:166962007 xref: Wikipedia:Nuchal_ligament is_a: CARO:0000003 is_a: UBERON:0005174 ! dorsal region element is_a: UBERON:0008846 ! skeletal ligament relationship: attaches_to UBERON:0001676 ! occipital bone relationship: attaches_to UBERON:0002413 {notes="C7 in humans"} ! cervical vertebra relationship: never_in_taxon NCBITaxon:9596 relationship: part_of UBERON:0012477 {source="BTO"} ! dorsal part of neck relationship: present_in_taxon NCBITaxon:9606 relationship: present_in_taxon NCBITaxon:9608 relationship: present_in_taxon NCBITaxon:9788 relationship: present_in_taxon NCBITaxon:9895 property_value: function_notes "As it is required for running, not all animals have a nuchal ligament" xsd:string property_value: taxon_notes "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" xsd:string [Term] id: UBERON:0000353 name: parenchyma def: "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." [Wikipedia:Parenchyma] xref: EHDAA:3015 xref: EHDAA:3905 xref: EHDAA:3999 xref: EHDAA:4005 xref: EHDAA:6899 xref: EHDAA:6903 xref: EHDAA:6994 xref: EHDAA:8086 xref: EHDAA:9182 xref: EHDAA:9190 xref: EHDAA:9196 xref: EHDAA:9202 xref: FMA:45732 xref: NCIT:C74601 xref: UMLS:C0933845 {source="ncithesaurus:Parenchyma"} xref: Wikipedia:Parenchyma is_a: UBERON:0000064 ! organ part disjoint_from: UBERON:0003891 ! stroma relationship: capable_of GO:0032501 relationship: only_in_taxon NCBITaxon:6072 property_value: development_notes "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" xsd:string {source="WP"} property_value: external_ontology_notes "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" xsd:string {external_ontology="FMA"} property_value: has_relational_adjective "parenchymal" xsd:string [Term] id: UBERON:0000355 name: pharyngeal mucosa alt_id: UBERON:0003344 def: "A mucosa that is part of a pharynx [Automatically generated definition]." [OBOL:automatic] synonym: "mucosa of organ of pharynx" EXACT [OBOL:automatic] synonym: "mucosa of pharynx" EXACT [OBOL:automatic] synonym: "mucous membrane of pharynx" EXACT [OBOL:automatic] synonym: "mucous membrane of pharynx" EXACT [FMA:55031] synonym: "mucous membrane of the pharynx" RELATED [BTO:0001047] synonym: "organ mucosa of pharynx" EXACT [OBOL:automatic] synonym: "pharynx mucosa" EXACT [OBOL:automatic] synonym: "pharynx mucosa of organ" EXACT [OBOL:automatic] synonym: "pharynx mucous membrane" EXACT [OBOL:automatic] synonym: "pharynx organ mucosa" EXACT [OBOL:automatic] synonym: "tunica mucosa pharyngea" EXACT LATIN [FMA:55031, FMA:TA] synonym: "tunica mucosa pharyngis" EXACT [] xref: BTO:0001047 xref: EMAPA:26957 xref: FMA:55031 xref: MA:0003143 xref: SCTID:362121003 intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001042 ! chordate pharynx relationship: part_of UBERON:0001042 ! chordate pharynx [Term] id: UBERON:0000358 name: blastocyst def: "The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO]." [GO:0001824, Wikipedia:Blastocyst] subset: efo_slim synonym: "blastocystis" RELATED LATIN [Wikipedia:Blastocyst] synonym: "blastula" RELATED [FMA:83041] xref: BTO:0001099 xref: CALOHA:TS-0076 xref: EFO:0000295 xref: EMAPA:36035 xref: EV:0100394 xref: FMA:83041 xref: GAID:1153 xref: MESH:A16.254.085 xref: NCIT:C13739 xref: SCTID:308837009 xref: UMLS:C1281743 {source="ncithesaurus:Blastocyst"} xref: Wikipedia:Blastocyst is_a: CARO:0000000 is_a: UBERON:0002050 ! embryonic structure relationship: develops_from UBERON:0000085 ! morula relationship: existence_starts_and_ends_during UBERON:0000108 ! blastula stage relationship: has_part UBERON:0000087 ! inner cell mass relationship: has_part UBERON:0000088 ! trophoblast relationship: only_in_taxon NCBITaxon:32525 relationship: part_of UBERON:0000307 ! blastula property_value: depicted_by Blastocyst:English.svg xsd:anyURI property_value: editor_note "Gilbert fig11.32 has blastocyst has giving rise to ICM and trophoblast (which in this source is a synonym for trophectoderm)" xsd:string [Term] id: UBERON:0000359 name: preputial gland def: "A aired, lobulated, modified sebaceous glands located in the inguinal region adjacent to the penis and vagina, with pheromonal functions in male rodents; in males, the preputial gland empties into the preputial cavity and in females, the preputial (aka clitoral) gland duct empties into the clitoral fossa." [MP:0013329] subset: organ_slim subset: pheno_slim synonym: "clitoral/preputial gland" RELATED [MA:0003044] synonym: "glandulae preputiales" EXACT LATIN [FMA:71652, FMA:TA] synonym: "preputial glands" EXACT [FMA:71652] synonym: "preputial glands set" EXACT [FMA:71652] xref: CALOHA:TS-0824 xref: EMAPA:35701 xref: MA:0003044 xref: NCIT:C22174 xref: SCTID:278916008 xref: UMLS:C1947929 {source="ncithesaurus:Prepucial_Gland_MMHCC"} xref: Wikipedia:Preputial_gland is_a: UBERON:0003937 ! reproductive gland is_a: UBERON:0015251 {source="ISBN:0123813611", source="MA"} ! modified sebaceous gland relationship: fma_set_term FMA:71652 relationship: never_in_taxon NCBITaxon:9606 {source="ISBN:0123813611", source="MP:0013329"} relationship: only_in_taxon NCBITaxon:40674 relationship: part_of UBERON:0000990 ! reproductive system property_value: external_definition "the paired, lobulated, modified sebaceous glands of the corona, the neck of the glans penis, and the inner surface of the prepuce with pheromonal functions in male rodents; male preputial secretions strongly attract females, may accelerate estrus, and have been implicated in intermale aggression; homologous to the clitoral glands (aka female preputial glands) in female rodents; there is no true anatomical equivalent in humans." xsd:string {external_class="MP:0002717", ontology="MP"} property_value: homology_notes "There is debate about whether humans have functional homologues to preputial glands." xsd:string {source="Wikipedia:Preputial_gland#Human_homologoues"} [Term] id: UBERON:0000360 name: obsolete rectal gland is_obsolete: true consider: UBERON:0004757 consider: UBERON:0004758 consider: UBERON:0004759 consider: UBERON:0004760 [Term] id: UBERON:0000361 name: red bone marrow def: "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." [http://medical-dictionary.thefreedictionary.com/red+marrow] synonym: "medulla ossium rubra" EXACT LATIN [BTO:0001160] synonym: "parenchyma of none marrow marrow" RELATED [http://orcid.org/0000-0002-6601-2165] synonym: "parenchymal red marrow" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "red marrow" EXACT [BTO:0001160] xref: BTO:0001160 xref: FMA:74595 xref: SCTID:328538003 xref: SCTID:75330005 is_a: UBERON:0002371 ! bone marrow intersection_of: UBERON:0002371 ! bone marrow intersection_of: composed_primarily_of CL:0000988 relationship: composed_primarily_of CL:0000988 relationship: part_of UBERON:0012429 ! hematopoietic tissue [Term] id: UBERON:0000362 name: renal medulla def: "the inner portion of the kidney consisting of the renal pyramids" [ISBN:0-683-40008-8, MGI:smb, MP:0003014] subset: pheno_slim synonym: "kidney medulla" EXACT [OBOL:automatic] synonym: "medulla of kidney" EXACT [OBOL:automatic] synonym: "medulla renalis" EXACT LATIN [FMA:74268, FMA:TA] synonym: "medullary pyramids" RELATED PLURAL [FMA:74268] synonym: "pyramides renales" EXACT LATIN [FMA:74268, FMA:TA] synonym: "renal marrow" RELATED [BTO:0001167] synonym: "renal medullae" EXACT PLURAL [FMA:86327] synonym: "renal medullae set" EXACT PLURAL [FMA:86327] synonym: "renal pyramids" EXACT PLURAL [FMA:74268] synonym: "renal pyramids set" EXACT PLURAL [FMA:74268] xref: BTO:0001167 xref: CALOHA:TS-1157 xref: EMAPA:19279 xref: GAID:425 xref: galen:MedullaOfKidney xref: MA:0000373 xref: MESH:D007679 xref: NCIT:C12740 xref: SCTID:30737000 xref: UMLS:C0022664 {source="ncithesaurus:Renal_Medulla"} xref: Wikipedia:Renal_medulla is_a: CARO:0000000 is_a: UBERON:0000958 ! medulla of organ intersection_of: UBERON:0000958 ! medulla of organ intersection_of: part_of UBERON:0002113 ! kidney relationship: capable_of_part_of GO:0070295 relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: has_part UBERON:0004200 ! kidney pyramid relationship: part_of UBERON:0002113 ! kidney property_value: depicted_by Illu:kidney.jpg xsd:anyURI property_value: structure_notes "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" xsd:string [Term] id: UBERON:0000363 name: reticuloendothelial system def: "A part of the immune system that consists of the phagocytic cells located in reticular connective tissue. The cells are primarily monocytes and macrophages, and they accumulate in lymph nodes and the spleen. The Kupffer cells of the liver and tissue histiocytes are also part of the RES[WP]." [Wikipedia:Reticuloendothelial_system] synonym: "lymphoreticular" RELATED [BioMart:BioMart] synonym: "lymphoreticular system" EXACT [Wikipedia:Reticuloendothelial_system] synonym: "mononuclear phagocyte system" EXACT [FMA:84189] synonym: "RES" EXACT [Wikipedia:Reticuloendothelial_system] synonym: "reticuloendothelial system" EXACT [FMA:84189] xref: BTO:0001174 xref: EV:0100048 xref: FMA:84189 xref: GAID:1004 xref: MESH:D012157 xref: NCIT:C12780 xref: SCTID:278874002 xref: UMLS:C0035287 {source="ncithesaurus:Reticuloendothelial_System"} xref: Wikipedia:Reticuloendothelial_system is_a: UBERON:0000061 ! anatomical structure relationship: composed_primarily_of CL:0000234 relationship: only_in_taxon NCBITaxon:7742 relationship: part_of UBERON:0002405 ! immune system relationship: part_of UBERON:0006804 ! reticular tissue [Term] id: UBERON:0000364 name: obsolete rootlet synonym: "fila radicularia" EXACT LATIN [FMA:76787, FMA:TA] synonym: "Rootlets" EXACT [FMA:76787] synonym: "Rootlets set" EXACT [FMA:76787] xref: BTO:0001192 is_obsolete: true consider: FMA:76787 [Term] id: UBERON:0000365 name: urothelium def: "An epithelial tissue layer that lines much of the urinary tract, including the renal pelvis, the ureters, the bladder, and parts of the urethra." [https://github.com/obophenotype/uberon/issues/92, Wikipedia:Urothelium] subset: pheno_slim synonym: "epithelium transitionale" EXACT [FMA:63914] synonym: "transitional epithelium" BROAD INCONSISTENT [] synonym: "transitional epithelium" EXACT [FMA:63914, https://github.com/obophenotype/uberon/issues/92] synonym: "uroepithelium" EXACT [FMA:67695] xref: BTO:0003906 xref: CALOHA:TS-1096 xref: EMAPA:37978 {source="MA:th"} xref: FMA:63914 xref: FMA:67695 xref: GAID:935 xref: MESH:D019459 xref: NCIT:C12884 xref: NCIT:C13318 xref: SCTID:30117005 xref: SCTID:57789003 xref: UMLS:C0225339 {source="ncithesaurus:Transitional_Epithelium"} xref: UMLS:C0227598 {source="ncithesaurus:Urothelium"} xref: Wikipedia:Transitional_epithelium xref: Wikipedia:Urothelium is_a: UBERON:0000486 ! multilaminar epithelium is_a: UBERON:0005911 ! endo-epithelium relationship: part_of UBERON:0001008 ! renal system property_value: depicted_by Harnblase:Urothel.png xsd:anyURI property_value: has_relational_adjective "urothelial" xsd:string [Term] id: UBERON:0000366 name: flexor muscle def: "a skeletal muscle whose contraction bends a joint." [http://www.thefreedictionary.com/flexor+muscle, https://github.com/obophenotype/uberon/issues/57] subset: pheno_slim subset: vertebrate_core synonym: "flexor" RELATED [] xref: BTO:0001257 xref: FMA:74559 xref: FMA:74999 xref: TAO:0005271 xref: ZFA:0005271 is_a: UBERON:0014892 ! skeletal muscle organ relationship: dc-contributor https://github.com/cmungall relationship: develops_from UBERON:0010977 ! flexor pre-muscle mass relationship: part_of UBERON:0000026 ! appendage property_value: external_definition "A muscle that decreases the angle of a joint.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005271", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0000368 name: adductor brevis def: "The adductor brevis is a muscle in the thigh situated immediately behind the pectineus and adductor longus. It is somewhat triangular in form, and arises by a narrow origin from the outer surfaces of the superior and inferior rami of the pubis, between the gracilis and obturator externus. Its fibers, passing backward, lateralward, and downward, are inserted, by an aponeurosis, into the line leading from the lesser trochanter to the linea aspera and into the upper part of the linea aspera, immediately behind the pectineus and upper part of the adductor longus.[WP]." [Wikipedia:Adductor_brevis_muscle] synonym: "adductor brevis muscle" EXACT [] synonym: "musculus adductos brevis" EXACT [FMA:22442] xref: BTO:0001288 xref: EMAPA:36219 xref: FMA:22442 xref: OpenCyc:Mx4rv13lfJwpEbGdrcN5Y29ycA xref: SCTID:181687007 xref: Wikipedia:Adductor_brevis_muscle is_a: UBERON:0004252 ! hindlimb stylopod muscle is_a: UBERON:0011144 {source="Wikipedia"} ! adductor muscle of hip relationship: has_muscle_insertion UBERON:0002504 {notes="the lesser trochanter and linea aspera of the femur", source="dbpedia"} ! lesser trochanter relationship: has_muscle_origin UBERON:0001275 {notes="anterior surface of the inferior ramus and body of the pubis", source="dbpedia"} ! pubis relationship: innervated_by UBERON:0005465 {source="dbpedia"} ! obturator nerve relationship: part_of UBERON:0000376 ! hindlimb stylopod property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/e2/Anterior_Hip_Muscles_2.PNG xsd:anyURI [Term] id: UBERON:0000369 name: corpus striatum alt_id: UBERON:0010082 def: "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]." [Wikipedia:Corpus_striatum] 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 subset: efo_slim synonym: "striate body" RELATED [BTO:0001311] synonym: "striated body" RELATED [BTO:0001311] xref: BAMS:CSTR xref: BTO:0001311 xref: CALOHA:TS-0183 xref: EFO:0000381 xref: EHDAA2:0000596 xref: EMAPA:17549 xref: EV:0100184 xref: FMA:77616 xref: GAID:667 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2339 xref: MESH:A08.186.211.730.885.105.487 xref: NCIT:C12448 xref: SCTID:279318005 xref: UMLS:C0010097 {source="ncithesaurus:Corpus_Striatum"} xref: VHOG:0001175 xref: Wikipedia:Corpus_striatum is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0002420 {source="MA"} ! basal ganglion property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray656.png xsd:anyURI property_value: homology_notes "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]" xsd:string {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/"} property_value: terminology_notes "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]" xsd:string [Term] id: UBERON:0000370 name: adductor magnus def: "An adductor muscle that attaches to the pelvic bone and the femur. In humans, the adductor magnus is a large triangular muscle, situated on the medial side of the thigh. The portion which arises from the ischiopubic ramus (a small part of the inferior ramus of the pubis, and the inferior ramus of the ischium) is called the 'adductor magnesius portion', and the portion arising from the tuberosity of the ischium is called the 'hamstring portion'. The hamstring portion is not considered part of the hamstring group of muscles, but it is adjacent to it.[WP,generalized]." [Wikipedia:Adductor_magnus_muscle] synonym: "adductor magnus muscle" EXACT [] synonym: "musculus adductor magnus" RELATED LATIN [Wikipedia:Adductor_magnus_muscle] xref: AAO:0010040 xref: BTO:0001312 xref: EMAPA:36221 xref: FMA:22443 xref: galen:AdductorMagnus xref: OpenCyc:Mx4rvuSd6JwpEbGdrcN5Y29ycA xref: SCTID:181688002 xref: Wikipedia:Adductor_magnus_muscle is_a: UBERON:0004252 ! hindlimb stylopod muscle is_a: UBERON:0011144 {source="Wikipedia"} ! adductor muscle of hip relationship: has_muscle_insertion UBERON:0000981 {source="dbpedia"} ! femur relationship: has_muscle_origin UBERON:0001275 {notes="tuberosity of the ischium", source="dbpedia"} ! pubis relationship: innervated_by UBERON:0001322 {notes="posterior branch of obturator nerve and sciatic nerve", source="dbpedia"} ! sciatic nerve relationship: innervated_by UBERON:0005465 {notes="posterior branch of obturator nerve and sciatic nerve", source="dbpedia"} ! obturator nerve relationship: part_of UBERON:0000376 ! hindlimb stylopod property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/e2/Anterior_Hip_Muscles_2.PNG xsd:anyURI property_value: external_definition "Origin by two heads that are separated by a ventral tendon of the M. semitendinosus. One head originates from the ventral border of the pubic portion of the pelvic rim. The other head originates from the ischiatic border of the pelvic rim. The ventral head fuses with accessory head from the M. semitendinosus and inserts along the ventro-medial border of the femur. The dorsal belly merges with the ventral and accessory heads and inserts along the medial surface of the femur.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010040", ontology="AAO", source="AAO:EJS"} property_value: external_ontology_notes "Definition generalized to accommodate AAO class - 'Origin by two heads that are separated by a ventral tendon of the M. semitendinosus. One head originates from the ventral border of the pubic portion of the pelvic rim. The other head originates from the ischiatic border of the pelvic rim. The ventral head fuses with accessory head from the M. semitendinosus and inserts along the ventro-medial border of the femur. The dorsal belly merges with the ventral and accessory heads and inserts along the medial surface of the femur.' [AAO:0010040]" xsd:string {external_ontology="AAO"} [Term] id: UBERON:0000371 name: syncytiotrophoblast def: "extraembryonic cells of trophoblastic shell surrounding embryo, outside the cytotrophoblast layer, involved with implantation of the blastocyst by eroding extracellular matrix surrounding maternal endometrial cells at site of implantation, also contribute to villi. (dark staining, multinucleated)." [http://embryology.med.unsw.edu.au/Notes/placenta5.htm, Wikipedia:Syncytiotrophoblast] synonym: "syncitiotrophoblast" RELATED [] synonym: "syncitiotrophoblastus" RELATED LATIN [Wikipedia:Syncytiotrophoblast] synonym: "syncytial trophoblast" EXACT [FMA:83040] synonym: "syntrophoblast" RELATED [] synonym: "syntrophoblast layer" EXACT [ISBN:0073040584] xref: BTO:0001335 xref: EHDAA:129 xref: EHDAA:91 xref: EMAPA:16068 xref: FMA:83040 xref: NCIT:C33918 xref: SCTID:256965005 xref: UMLS:C1135936 {source="ncithesaurus:Syncytiotrophoblast"} xref: Wikipedia:Syncytiotrophoblast is_a: CARO:0000000 is_a: UBERON:0002050 {source="FMA"} ! embryonic structure relationship: composed_primarily_of CL:0000525 relationship: part_of UBERON:0000088 {source="BTO"} ! trophoblast relationship: part_of UBERON:0004364 {source="EMAPA"} ! ectoplacental cone property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/d/df/Gray36.png xsd:anyURI [Term] id: UBERON:0000372 name: extensor digitorum brevis pes def: "A muscle on the upper surface of the foot that helps extend digits 2 through 4." [Wikipedia:Extensor_digitorum_brevis_muscle] synonym: "extensor digitorum brevis" EXACT [FMA:51140] synonym: "extensor digitorum brevis muscle" EXACT [] synonym: "musculus extensor digitorum brevis" RELATED LATIN [Wikipedia:Extensor_digitorum_brevis_muscle] xref: BTO:0001337 xref: EMAPA:36258 xref: FMA:51140 xref: Wikipedia:Extensor_digitorum_brevis_muscle is_a: CARO:0000003 is_a: UBERON:0000311 ! extensor muscle is_a: UBERON:0001498 ! muscle of pes relationship: has_muscle_insertion UBERON:0003221 {notes="proximal dorsal region of middle phalanges 2 3 and 4", source="dbpedia"} ! phalanx relationship: has_muscle_origin UBERON:0001450 {notes="dorsal surface of calcaneus", source="dbpedia"} ! calcaneus relationship: part_of UBERON:0002387 ! pes property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1241.png xsd:anyURI property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray441.png xsd:anyURI [Term] id: UBERON:0000373 name: tapetum of corpus callosum def: "On either side of the corpus collosum, the fibers radiate in the white substance and pass to the various parts of the cerebral cortex; those curving forward from the genu into the frontal lobe constitute the forceps anterior, and those curving backward into the occipital lobe, the forceps posterior. Between these two parts is the main body of the fibers which constitute the tapetum and extend laterally on either side into the temporal lobe, and cover in the central part of the lateral ventricle. [Wikipedia via Greys]" [Wikipedia:Tapetum_of_corpus_callosum] synonym: "tapetum" BROAD INCONSISTENT [FMA:77208] synonym: "tapetum corporis callosi" RELATED LATIN [Wikipedia:Tapetum_of_corpus_callosum] xref: DHBA:12027 xref: FMA:77208 xref: HBA:265504966 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1596 xref: SCTID:279312006 xref: Wikipedia:Tapetum_of_corpus_callosum is_a: UBERON:0002437 ! cerebral hemisphere white matter relationship: part_of UBERON:0002336 ! corpus callosum property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/aa/Gray733.png xsd:anyURI property_value: external_ontology_notes "not to be confused with BTO:0001350 or GO:0048655-tapetal layer morphogenesis" xsd:string {external_ontology="BTO"} [Term] id: UBERON:0000375 name: mandibular nerve def: "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." [MP:0009800, Wikipedia:Mandibular_nerve] subset: pheno_slim synonym: "inferior maxillary nerve" EXACT [FMA:52996] synonym: "mandibular division [V3]" EXACT [FMA:52996] synonym: "mandibular division [Vc]" EXACT [FMA:52996] synonym: "mandibular division of fifth cranial nerve" EXACT [FMA:52996] synonym: "mandibular division of trigeminal nerve [Vc; V3]" EXACT [FMA:52996] synonym: "mandibular nerve [V3]" EXACT [FMA:52996] synonym: "mandibular nerve [Vc]" EXACT [FMA:52996] synonym: "n. mandibularis" RELATED LATIN [Wikipedia:Mandibular_nerve] synonym: "nervus mandibularis" RELATED [BTO:0001375] synonym: "nervus mandibularis [v3]" EXACT LATIN [FMA:52996, FMA:TA] synonym: "nervus mandibularis [Vc; V3]" EXACT [FMA:52996] synonym: "nervus mandibularis [vc]" EXACT LATIN [FMA:52996, FMA:TA] synonym: "ramus mandibularis (ramus V3)" EXACT [AAO:0010688] synonym: "third division of fifth cranial nerve" EXACT [FMA:52996] synonym: "third division of trigeminal nerve" EXACT [FMA:52996] synonym: "trigeminal nerve mandibular division" RELATED [EMAPA:17798] synonym: "trigeminal V nerve mandibular division" EXACT [MA:0001101] xref: AAO:0010688 xref: AAO:0010703 xref: BTO:0001375 xref: EHDAA2:0002086 xref: EMAPA:17798 xref: FMA:52996 xref: GAID:834 xref: MA:0001101 xref: MESH:D008340 xref: NCIT:C32779 xref: OpenCyc:Mx4rvcQKSpwpEbGdrcN5Y29ycA xref: SCTID:280212008 xref: UMLS:C0024695 {source="ncithesaurus:Inferior_Maxillary_Nerve"} xref: VHOG:0001345 xref: Wikipedia:Mandibular_nerve is_a: UBERON:0011779 ! nerve of head region relationship: branching_part_of UBERON:0001645 ! trigeminal nerve relationship: part_of UBERON:0001645 ! trigeminal nerve property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray781.png xsd:anyURI [Term] id: UBERON:0000376 name: hindlimb stylopod def: "The part of the hindlimb between pelvis and the knee, corresponding to the femur." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: pheno_slim synonym: "femur" RELATED LATIN [Wikipedia:Thigh] synonym: "hind limb stylopod" EXACT [OBOL:automatic] synonym: "hind limb stylopodium" EXACT [VHOG:0000349] synonym: "hind propodium" EXACT [AAO:0000887] synonym: "hindlimb propodium" EXACT [AAO:0000887] synonym: "hindlimb stylopod" EXACT [OBOL:automatic] synonym: "hindlimb stylopodium" EXACT [OBOL:automatic] synonym: "proximal segment of free lower limb" EXACT [FMA:24967] synonym: "stylopod of hind limb" EXACT [OBOL:automatic] synonym: "stylopod of hindlimb" EXACT [OBOL:automatic] synonym: "stylopod of lower limb" EXACT [] synonym: "thigh" EXACT [] synonym: "upper leg" EXACT HUMAN_PREFERRED [MA:0000052] xref: BTO:0001376 xref: CALOHA:TS-2039 xref: EFO:0001943 xref: EHDAA2:0002130 xref: EHDAA:5171 xref: EHDAA:6200 xref: EMAPA:17499 xref: FMA:24967 xref: GAID:50 xref: galen:Thigh xref: MA:0000052 xref: MESH:D013848 xref: NCIT:C33763 xref: OpenCyc:Mx4rvVjN7JwpEbGdrcN5Y29ycA xref: SCTID:302544002 xref: UMLS:C0039866 {source="ncithesaurus:Thigh"} xref: VHOG:0000349 xref: Wikipedia:Thigh is_a: UBERON:0002472 ! stylopod is_a: UBERON:0008784 ! lower limb segment intersection_of: UBERON:0002472 ! stylopod intersection_of: part_of UBERON:0002103 ! hindlimb relationship: contributes_to_morphology_of UBERON:0002103 ! hindlimb relationship: has_skeleton UBERON:0015052 ! femur endochondral element relationship: part_of UBERON:0000978 {source="MA"} ! leg relationship: part_of UBERON:0002103 ! hindlimb property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/4/4b/Gray1238.png xsd:anyURI property_value: homology_notes "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]" xsd:string {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/"} property_value: terminology_notes "Naming conventions for pod terms under discussion within phenoscape group." xsd:string {seeAlso="https://github.com/obophenotype/uberon/issues/61"} [Term] id: UBERON:0000377 name: maxillary nerve def: "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." [MP:0009799, Wikipedia:Maxillary_nerve] subset: pheno_slim synonym: "maxillary division [V2]" EXACT [FMA:52724] synonym: "maxillary division [Vb]" EXACT [FMA:52724] synonym: "maxillary division of fifth cranial nerve" EXACT [FMA:52724] synonym: "maxillary division of trigeminal nerve (Vb; V2)" EXACT [FMA:52724] synonym: "maxillary nerve [V2]" EXACT [FMA:52724] synonym: "maxillary nerve [Vb]" EXACT [FMA:52724] synonym: "n. maxillaris" RELATED LATIN [Wikipedia:Maxillary_nerve] synonym: "nervus maxillaris" RELATED [BTO:0001378] synonym: "nervus maxillaris (Vb; V2)" EXACT [FMA:52724] synonym: "nervus maxillaris [v2]" EXACT LATIN [FMA:52724, FMA:TA] synonym: "nervus maxillaris [vb]" EXACT LATIN [FMA:52724, FMA:TA] synonym: "ramus maxillaris (ramus V2)" EXACT [AAO:0010670] synonym: "second division of fifth cranial nerve" EXACT [FMA:52724] synonym: "second division of trigeminal nerve" EXACT [FMA:52724] synonym: "trigeminal nerve maxillary division" RELATED [EMAPA:17799] synonym: "trigeminal V nerve maxillary division" EXACT [MA:0001103] xref: AAO:0010670 xref: BTO:0001378 xref: EHDAA2:0002087 xref: EMAPA:17799 xref: FMA:52724 xref: GAID:836 xref: MA:0001103 xref: MESH:D008442 xref: OpenCyc:Mx4rvWNU9JwpEbGdrcN5Y29ycA xref: SCTID:280211001 xref: VHOG:0001346 xref: Wikipedia:Maxillary_nerve is_a: UBERON:0011779 ! nerve of head region relationship: branching_part_of UBERON:0001645 ! trigeminal nerve relationship: part_of UBERON:0001645 ! trigeminal nerve property_value: axiom_lost_from_external_ontology "relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010670", ontology="AAO"} property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/a9/Gray779.png xsd:anyURI property_value: external_definition "Medial ramus (sensory) of the trigeminal nerve.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010670", ontology="AAO", source="AAO:EJS"} [Term] id: UBERON:0000378 name: tongue muscle def: "The muscular portion of the tongue." [MP:0004136, Wikipedia:Muscles_of_tongue] subset: pheno_slim synonym: "muscle of tongue" EXACT [FMA:46689] synonym: "muscle organ of tongue" EXACT [OBOL:accepted] synonym: "musculi linguae" RELATED LATIN [Wikipedia:Muscles_of_tongue] synonym: "skeletal muscle tissue of tongue" EXACT [OBOL:automatic] synonym: "tongue skeletal muscle" EXACT [OBOL:automatic] synonym: "tongue skeletal muscle tissue" EXACT [OBOL:automatic] xref: BTO:0001386 xref: EHDAA2:0002065 xref: EHDAA:9146 xref: EMAPA:17883 xref: FMA:46689 xref: MA:0001596 xref: NCIT:C49301 xref: NCIT:C52707 xref: SCTID:244781004 xref: UMLS:C0448325 {source="ncithesaurus:Tongue_Muscle"} xref: UMLS:C1710437 {source="ncithesaurus:Tongue_Skeletal_Muscle_Tissue"} xref: VHOG:0001390 xref: Wikipedia:Muscles_of_tongue is_a: CARO:0000003 is_a: UBERON:0010959 ! craniocervical muscle is_a: UBERON:0013765 ! digestive system element is_a: UBERON:0014892 {source="FEED:rd"} ! skeletal muscle organ intersection_of: UBERON:0014892 ! skeletal muscle organ intersection_of: attaches_to_part_of UBERON:0001723 ! tongue union_of: UBERON:0001575 ! extrinsic muscle of tongue union_of: UBERON:0001576 ! intrinsic muscle of tongue relationship: attaches_to_part_of UBERON:0001723 ! tongue relationship: contributes_to_morphology_of UBERON:0001723 ! tongue relationship: develops_from UBERON:0005594 {source="FEED:rd", source="ISBN:1607950324"} ! head somite relationship: part_of UBERON:0000165 ! mouth property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/c/c6/Gray1019.png xsd:anyURI property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000379 name: tracheal mucosa def: "A mucosa that is part of a respiratory airway." [OBOL:automatic] synonym: "mucosa of organ of trachea" EXACT [OBOL:automatic] synonym: "mucosa of organ of windpipe" EXACT [OBOL:automatic] synonym: "mucosa of trachea" EXACT [OBOL:automatic] synonym: "mucosa of windpipe" EXACT [OBOL:automatic] synonym: "mucous membrane of trachea" EXACT [FMA:7471] synonym: "mucous membrane of trachea" EXACT [OBOL:automatic] synonym: "mucous membrane of windpipe" EXACT [OBOL:automatic] synonym: "organ mucosa of trachea" EXACT [OBOL:automatic] synonym: "organ mucosa of windpipe" EXACT [OBOL:automatic] synonym: "trachea mucosa" EXACT [OBOL:automatic] synonym: "trachea mucosa of organ" EXACT [OBOL:automatic] synonym: "trachea mucous membrane" EXACT [OBOL:automatic] synonym: "trachea organ mucosa" EXACT [OBOL:automatic] synonym: "tracheal mucous membrane" EXACT [FMA:7471] synonym: "tunica mucosa (tracheae)" EXACT [FMA:7471] synonym: "tunica mucosa tracheae" EXACT LATIN [FMA:7471, FMA:TA] synonym: "windpipe mucosa" EXACT [OBOL:automatic] synonym: "windpipe mucosa of organ" EXACT [OBOL:automatic] synonym: "windpipe mucous membrane" EXACT [OBOL:automatic] synonym: "windpipe organ mucosa" EXACT [OBOL:automatic] xref: BTO:0001390 xref: FMA:7471 xref: SCTID:660006 is_a: UBERON:0004785 ! respiratory system mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001005 ! respiratory airway relationship: part_of UBERON:0001005 ! respiratory airway [Term] id: UBERON:0000380 name: obsolete tuber xref: BTO:0001400 xref: OpenCyc:Mx4raeDj5Cw8QdiT7e8pb2JzAA is_obsolete: true consider: EFO:0001015 consider: FMA:75430 [Term] id: UBERON:0000381 name: urinary bladder detrusor smooth muscle def: "bundles of smooth muscle fibers forming the muscular wall of the urinary bladder, which are arranged in a longitudinal and a circular layer and, on contraction, serve to expel urine[MP]." [MP:0011774, Wikipedia:Detrusor_urinae_muscle] subset: pheno_slim synonym: "detrusor" EXACT [FMA:68018] synonym: "detrusor muscle" EXACT [BTO:0001453] synonym: "detrusor muscle of bladder" EXACT [EMAPA:28637] synonym: "detrusor smooth muscle" EXACT [] synonym: "detrusor urinae muscle" EXACT [Wikipedia:Detrusor_urinae_muscle] synonym: "muscularis propria" BROAD [ncithesaurus:Muscularis_Propria, Wikipedia:Detrusor_urinae_muscle] synonym: "muscularis propria of the urinary bladder" EXACT [Wikipedia:Detrusor_urinae_muscle] synonym: "musculus detrusor vesicae" EXACT LATIN [FMA:68018, FMA:TA] synonym: "musculus detrusor vesicae urinariae" RELATED LATIN [Wikipedia:Detrusor_urinae_muscle] synonym: "urinary bladder detrusor muscle" EXACT [MA:0001698] synonym: "urinary bladder detrussor smooth muscle" EXACT [MA:0001698] xref: BTO:0001453 xref: EMAPA:28637 xref: FMA:68018 xref: MA:0001698 xref: NCIT:C62404 xref: SCTID:279414008 xref: Wikipedia:Detrusor_urinae_muscle is_a: CARO:0000003 is_a: UBERON:0004228 ! urinary bladder smooth muscle relationship: capable_of_part_of GO:0060073 relationship: contributes_to_morphology_of UBERON:0001255 ! urinary bladder relationship: has_muscle_insertion UBERON:0000996 {gci_filler="UBERON:0003100", gci_relation="part_of", notes="female", source="dbpedia-modified"} ! vagina relationship: has_muscle_insertion UBERON:0002367 {gci_filler="UBERON:0003101", gci_relation="part_of", notes="male", source="dbpedia-modified"} ! prostate gland relationship: has_muscle_origin UBERON:0001275 {notes="posterior surface of the body of the pubis", source="dbpedia"} ! pubis relationship: part_of UBERON:0012378 {source="FMA"} ! muscle layer of urinary bladder property_value: depicted_by Illu:bladder.jpg xsd:anyURI [Term] id: UBERON:0000382 name: apocrine sweat gland def: "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]." [Wikipedia:Apocrine_sweat_gland] subset: organ_slim subset: pheno_slim synonym: "glandula sudorifera apocrina" EXACT LATIN [Wikipedia:Apocrine_sweat_gland] xref: BTO:0001458 xref: EMAPA:37426 {source="MA:th"} xref: FMA:59155 xref: MESH:D001050 xref: NCIT:C32132 xref: SCTID:399916008 xref: UMLS:C0930083 {source="ncithesaurus:Apocrine_Sweat_Gland"} xref: Wikipedia:Apocrine_sweat_gland is_a: UBERON:0001820 {source="FMA"} ! sweat gland is_a: UBERON:0010243 {notes="The term apocrine sweat gland is a misnomer. While it was once thought that apocrine sweat glands were true apocrine glands, it is now known that they use merocrine excretion. However, they have retained the original name", source="Wikipedia"} ! merocrine gland disjoint_from: UBERON:0000423 ! eccrine sweat gland relationship: never_in_taxon NCBITaxon:9822 {source="http://www.nal.usda.gov/awic/pubs/swine/swine.htm"} relationship: part_of UBERON:0001003 {source="FMA"} ! skin epidermis property_value: curator_notes "A note of confusion is the difference between apocrine secretion and apocrine sweat gland. Apocrine secretion refers to the apical loss of a cell's membrane to create cell blebs, thus creating a secretory product. Apocrine sweat gland refers to a structure, not a secretion process. Apocrine sweat glands actually use a merocrine type secretion, or that mediated by exocytosis of secretory granules. When 'apocrine gland' is used without the word sweat, it is often referring to the gland which uses merocrine secretion, and not the secretion method. The important difference in apocrine sweat gland structure is its larger lumen, compared to the more narrow lumen of the eccrine sweat gland." xsd:string property_value: taxon_notes "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." xsd:string [Term] id: UBERON:0000383 name: musculature of body def: "The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]." [VSAO:0000033] subset: efo_slim subset: pheno_slim synonym: "muscle system" EXACT [] synonym: "muscle system of body" EXACT [] synonym: "muscular system" EXACT [FMA:72954] synonym: "musculature system" EXACT [BILA:0000088] synonym: "muskelsystem" RELATED [BTO:0001485] synonym: "set of all muscles" EXACT [FMA:72954] synonym: "set of muscles of body" EXACT [FMA:72954] synonym: "vertebrate muscular system" EXACT [BTO:0001369] xref: AAO:0000307 xref: BILA:0000088 xref: BTO:0001369 xref: BTO:0001485 xref: EFO:0000801 xref: EMAPA:35578 xref: FBbt:00005069 xref: FMA:72954 xref: MA:0002888 xref: MAT:0000025 xref: MIAA:0000025 xref: VSAO:0000033 xref: XAO:0004042 is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision intersection_of: composed_primarily_of UBERON:0001015 ! musculature relationship: capable_of GO:0003012 relationship: composed_primarily_of UBERON:0001015 ! musculature relationship: never_in_taxon NCBITaxon:6040 relationship: only_in_taxon NCBITaxon:6072 relationship: part_of UBERON:0002204 ! musculoskeletal system property_value: editor_note "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string property_value: external_definition "Anatomical system that consists of the muscles of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000033", ontology="VSAO", source="VSAO:curator"} property_value: external_ontology_notes "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" xsd:string {external_ontology="MA"} [Term] id: UBERON:0000385 name: obsolete labial gland comment: the label 'labial gland' refers to two distinct classes. From the BTO def: 1. One of the small tubular mucous and serous glands lying beneath the mucous membrane of the lips.n2. A salivary gland, or modification thereof, opening at the base of the labium in certain insects. synonym: "glandulae labiales" EXACT LATIN [FMA:71613, FMA:TA] synonym: "Labial glands" EXACT [FMA:71613] synonym: "Labial glands set" EXACT [FMA:71613] xref: BTO:0001548 is_obsolete: true consider: FMA:71613 consider: HAO:0000449 [Term] id: UBERON:0000387 name: meniscus def: "crescent-shaped fibrocartilaginous structure present in the knee, acromioclavicular, sternoclavicular, and temporomandibular joints[2] that, in contrast to articular disks, only partly divides a joint cavity.[3] A small meniscus also occurs in the radio-carpal joint." [Wikipedia:Meniscus_(anatomy)] synonym: "articular disc" EXACT [FMA:76690] xref: BTO:0001592 xref: EV:0100145 xref: FMA:76690 xref: galen:Meniscus xref: NCIT:C33096 xref: UMLS:C0224498 {source="ncithesaurus:Meniscus"} xref: Wikipedia:Meniscus_(anatomy) is_a: CARO:0000000 is_a: UBERON:0010000 ! multicellular anatomical structure relationship: composed_primarily_of UBERON:0001995 ! fibrocartilage relationship: part_of UBERON:0000982 ! skeletal joint [Term] id: UBERON:0000388 name: epiglottis def: "A part of the pharynx that consists of a flap of elastic cartilage tissue plus a mucous membrane covering, attached to the entrance of the larynx. The epiglottis is found at the root of the tongue and folds back over the entrance to the larynx during swallowing, preventing inhalation of food or drink[MP,modified]" [http://orcid.org/0000-0002-6601-2165, MGI:llw2, MP:0010371, Wikipedia:Epiglottis] subset: pheno_slim xref: BTO:0001628 xref: EHDAA2:0004081 xref: EMAPA:18289 xref: FMA:55130 xref: GAID:111 xref: MESH:A02.165.507.411 xref: NCIT:C12709 xref: OpenCyc:Mx4rvVjxE5wpEbGdrcN5Y29ycA xref: SCTID:245502004 xref: UMLS:C0014540 {source="ncithesaurus:Epiglottis"} xref: Wikipedia:Epiglottis is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0013522 ! subdivision of tube relationship: develops_from UBERON:0003115 {source="EHDAA2"} ! pharyngeal arch 4 relationship: has_component UBERON:0001742 ! epiglottic cartilage relationship: has_component UBERON:0004982 ! mucosa of epiglottis relationship: never_in_taxon NCBITaxon:8782 relationship: part_of UBERON:0001051 ! hypopharynx property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/e2/Gray958.png xsd:anyURI property_value: has_relational_adjective "epiglottal" xsd:string [Term] id: UBERON:0000389 name: lens cortex def: "Tissue that surrounds the lens nucleus" [http://www.thefreedictionary.com/lens+cortex] synonym: "cortex of lens" EXACT [FMA:58970] xref: BTO:0001632 xref: CALOHA:TS-0542 xref: FMA:58970 xref: MESH:A09.371.509.225 xref: SCTID:280626006 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: surrounds UBERON:0000390 ! lens nucleus relationship: develops_from UBERON:0005614 ! lens anterior epithelium relationship: part_of UBERON:0000965 ! lens of camera-type eye relationship: surrounds UBERON:0000390 ! lens nucleus [Term] id: UBERON:0000390 name: lens nucleus def: "The core of the crystalline lens, surrounded by the cortex." [BTO:0001633] synonym: "nucleus of lens" EXACT [FMA:58971] xref: BTO:0001633 xref: FMA:58971 xref: MESH:A09.371.509.670 xref: SCTID:280628007 is_a: UBERON:0034944 ! zone of organ intersection_of: UBERON:0034944 ! zone of organ intersection_of: surrounded_by UBERON:0000389 ! lens cortex relationship: develops_from UBERON:0005614 ! lens anterior epithelium relationship: part_of UBERON:0000965 ! lens of camera-type eye relationship: surrounded_by UBERON:0000389 ! lens cortex [Term] id: UBERON:0000391 name: leptomeninx def: "pia mater or arachnoid mater." [https://github.com/obophenotype/uberon/issues/300, Wikipedia:Leptomeninges] subset: organ_slim synonym: "arachnoid mater and pia mater" RELATED [FMA:231515] synonym: "arachnoidea mater et pia mater" RELATED [BTO:0001634] synonym: "leptomeninges" EXACT PLURAL [NLXANAT:090207] synonym: "pia-arachnoid" RELATED [BTO:0001634] synonym: "pia-arachnoid of neuraxis" RELATED [FMA:231515] xref: BTO:0001634 xref: CALOHA:TS-0546 xref: FMA:231515 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2347 xref: NCIT:C32979 xref: NLXANAT:090207 xref: SCTID:362303006 xref: UMLS:C0228126 {source="ncithesaurus:Leptomeninges"} xref: Wikipedia:Leptomeninges is_a: UBERON:0002360 ! meninx is_a: UBERON:0010313 ! neural crest-derived structure relationship: dc-contributor https://github.com/cmungall relationship: develops_from UBERON:0007646 ! endomeninx relationship: immediate_transformation_of UBERON:0007646 ! endomeninx property_value: editor_note "check relationship to secondary meninx" xsd:string property_value: external_ontology_notes "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" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000392 name: longissimus muscle def: "The longissimus is the muscle lateral to the semispinalis. It is the longest subdivision of the sacrospinalis that extends forward into the transverse processes of the posterior cervical vertebrae. [WP,unvetted]." [Wikipedia:Longissimus] synonym: "intermediate column of erector spinae" RELATED [] synonym: "longissimus" EXACT [FMA:77178] synonym: "musculus longissimus" EXACT LATIN [Wikipedia:Longissimus] synonym: "musculus longissimus" EXACT [BTO:0001648] xref: BTO:0001648 xref: EMAPA:37648 {source="MA:th"} xref: FMA:77178 xref: SCTID:244858006 xref: Wikipedia:Longissimus is_a: UBERON:0004518 {source="FMA"} ! muscle of vertebral column relationship: has_muscle_insertion UBERON:0001077 {source="dbpedia"} ! transverse process of vertebra relationship: has_muscle_origin UBERON:0001077 {source="dbpedia"} ! transverse process of vertebra relationship: innervated_by UBERON:0006839 {source="dbpedia"} ! dorsal ramus of spinal nerve relationship: part_of UBERON:0002462 {source="BTO"} ! erector spinae muscle group property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/1/1f/Longissimus.png xsd:anyURI [Term] id: UBERON:0000395 name: cochlear ganglion def: "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." [http://www.dartmouth.edu/~humananatomy/part_8/chapter_44.html, MP:0002855] subset: pheno_slim synonym: "cochlear part of vestibulocochlear ganglion" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "Corti's ganglion" EXACT [FMA:53445] synonym: "ganglion cochlearis" RELATED [BTO:0001688] synonym: "ganglion of Corti" EXACT [FMA:53445] synonym: "ganglion spirale" RELATED LATIN [Wikipedia:Spiral_ganglion] synonym: "ganglion spirale cochleae" RELATED [BTO:0001688] synonym: "spiral ganglion" EXACT [FMA:53445] synonym: "spiral ganglion of cochlea" RELATED [BTO:0001688] synonym: "vestibulocochlear ganglion cochlear component" RELATED [EMAPA:17572] synonym: "vestibulocochlear VIII ganglion cochlear component" EXACT [MA:0001085] xref: BAMS:GcVIII xref: BTO:0001688 xref: EHDAA2:0002198 xref: EMAPA:17572 xref: FMA:53445 xref: GAID:722 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1405 xref: MA:0001085 xref: MESH:D013136 xref: SCTID:368955007 xref: VHOG:0001183 xref: Wikipedia:Spiral_ganglion is_a: UBERON:0001714 ! cranial ganglion is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001714 ! cranial ganglion intersection_of: extends_fibers_into UBERON:0004727 ! cochlear nerve relationship: extends_fibers_into UBERON:0004727 ! cochlear nerve relationship: located_in UBERON:0006723 {notes="cell bodies", source="BTO-modified", source="Wikipedia"} ! cochlear modiolus relationship: part_of UBERON:0002827 ! vestibulocochlear ganglion relationship: part_of UBERON:0016490 ! auditory system property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray903.png xsd:anyURI property_value: editor_note "in BTO this is part of the cochlear modiolus, but this leads to the CG being in both the nervous and skeletal systems" xsd:string [Term] id: UBERON:0000396 name: vallate papilla alt_id: UBERON:0002927 def: "Any of the large papillae, which have multiple taste buds in the trough surrounding the papillae, located near the base and on the dorsal side of the tongue" [MGI:smb, MP:0006258] subset: pheno_slim synonym: "circumvallate papilla" EXACT [MA:0001594] synonym: "circumvallate papilla of tongue" EXACT [FMA:54822] synonym: "circumvallate papillae" RELATED PLURAL [] synonym: "papilla vallatae" EXACT PLURAL [FMA:71449, FMA:TA] synonym: "vallate papilla of tongue" EXACT [] xref: BIRNLEX:4106_2 xref: BTO:0001705 xref: EMAPA:18271 xref: FMA:54822 xref: MA:0001594 xref: NCIT:C32322 xref: SCTID:69517000 xref: UMLS:C0226965 {source="BIRNLEX:4106_2"} xref: UMLS:C1182961 {source="BIRNLEX:4106_2"} xref: UMLS:C1182961 {source="ncithesaurus:Circumvallate_Papilla"} xref: UMLS:C1267555 {source="BIRNLEX:4106_2"} xref: Wikipedia:Vallate_papilla is_a: UBERON:0014389 ! gustatory papilla of tongue relationship: has_part UBERON:0001727 {source="MP-abduced"} ! taste bud property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray1015.png xsd:anyURI property_value: external_definition "Any one of the largest papilla of the tongue, 8 to 12 in number, arranged in the form of a V anterior to the sulcus terminalis of the tongu[BTO:0001705, Wikipedia:Vallate_papilla]e" xsd:string {source="BTO:0001705, Wikipedia:Vallate_papilla"} [Term] id: UBERON:0000397 name: colonic epithelium def: "An epithelium that is part of a colon [Automatically generated definition]." [OBOL:automatic] subset: vertebrate_core synonym: "colon epithelial tissue" EXACT [OBOL:automatic] synonym: "colon epithelium" EXACT [FMA:17302] synonym: "colon epithelium" EXACT [OBOL:automatic] synonym: "epithelial tissue of colon" EXACT [OBOL:automatic] synonym: "epithelial tissue of large bowel" EXACT [OBOL:automatic] synonym: "epithelium of colon" EXACT [OBOL:automatic] synonym: "epithelium of large bowel" EXACT [OBOL:automatic] synonym: "large bowel epithelial tissue" EXACT [OBOL:automatic] synonym: "large bowel epithelium" EXACT [OBOL:automatic] synonym: "posterior intestine epithelium" EXACT [ZFA:0005128] xref: BTO:0001709 xref: CALOHA:TS-0163 xref: EMAPA:18941 xref: FMA:17302 xref: MA:0003195 xref: SCTID:42978003 xref: TAO:0005128 xref: ZFA:0005128 intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001155 ! colon relationship: part_of UBERON:0001155 ! colon property_value: external_definition "Intestinal epithelium which lines the lumen of the posterior intestine.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005128", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0000398 name: cartilage tissue of sternum def: "Any portion of cartilage tissue that is part of the sternum" [https://orcid.org/0000-0002-6601-2165] comment: Examples: cartilage of manubrium, cartilage of xiphoid process synonym: "cartilage of sternum" EXACT [FMA:32567] xref: FMA:32567 is_a: UBERON:0002418 ! cartilage tissue is_a: UBERON:0003837 ! thoracic segment connective tissue intersection_of: UBERON:0002418 ! cartilage tissue intersection_of: part_of UBERON:0000975 ! sternum relationship: part_of UBERON:0000975 ! sternum [Term] id: UBERON:0000399 name: jejunal mucosa def: "A mucosa that is part of a jejunum [Automatically generated definition]." [OBOL:automatic] synonym: "jejunal mucous membrane" EXACT [FMA:14949] synonym: "jejunum mucosa" EXACT [FMA:14949] synonym: "jejunum mucosa of organ" EXACT [OBOL:automatic] synonym: "jejunum mucous membrane" EXACT [OBOL:automatic] synonym: "jejunum organ mucosa" EXACT [OBOL:automatic] synonym: "mucosa of jejunum" EXACT [FMA:14949] synonym: "mucosa of organ of jejunum" EXACT [OBOL:automatic] synonym: "mucous membrane of jejunum" EXACT [OBOL:automatic] synonym: "organ mucosa of jejunum" EXACT [OBOL:automatic] xref: BTO:0001742 xref: CALOHA:TS-0495 xref: EMAPA:27109 xref: FMA:14949 xref: MA:0003214 xref: SCTID:362151009 is_a: UBERON:0001204 ! mucosa of small intestine intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0002115 ! jejunum relationship: part_of UBERON:0002115 ! jejunum [Term] id: UBERON:0000400 name: jejunal epithelium def: "An epithelium that is part of a jejunum." [OBOL:automatic] synonym: "epithelium of jejunum" EXACT [] xref: BTO:0001743 xref: CALOHA:TS-0494 xref: EMAPA:18668 xref: FMA:17232 xref: MA:0003215 xref: SCTID:57300004 is_a: UBERON:0001902 {source="BTO"} ! epithelium of small intestine is_a: UBERON:0013636 ! epithelium of intestinal villus intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002115 ! jejunum relationship: part_of UBERON:0002115 ! jejunum relationship: part_of UBERON:0008343 {source="FMA"} ! intestinal villus of jejunum [Term] id: UBERON:0000401 name: mandibular ramus def: "the upturned perpendicular extremity of the mandible" [ISBN:0-683-40008-8, MP:0010150] subset: pheno_slim synonym: "lower ramus" RELATED [Wikipedia:Ramus_of_the_mandible] synonym: "mandible ramus" EXACT [MA:0002815] synonym: "rami mandibulae" RELATED PLURAL [Wikipedia:Ramus_of_the_mandible] synonym: "ramus mandibulae" RELATED PLURAL [Wikipedia:Ramus_of_the_mandible] synonym: "ramus mandibulae" RELATED LATIN [Wikipedia:Ramus_of_the_mandible] synonym: "ramus of mandible" EXACT [FMA:52828] xref: BTO:0001751 xref: EMAPA:25100 xref: FMA:52828 xref: MA:0002815 xref: SCTID:361739000 xref: Wikipedia:Ramus_of_the_mandible is_a: UBERON:0005913 ! zone of bone organ is_a: UBERON:0010313 ! neural crest-derived structure relationship: contributes_to_morphology_of UBERON:0001684 ! mandible relationship: part_of UBERON:0001684 ! mandible property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png xsd:anyURI [Term] id: UBERON:0000402 name: nasal vestibule def: "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]." [Wikipedia:Nasal_vestibule] synonym: "vestibular part of nasal cavity" EXACT [FMA:59644] synonym: "vestibulum nasale" RELATED [BTO:0001761] synonym: "vestibulum nasi" RELATED [BTO:0001761] synonym: "vestibulum nasi" RELATED LATIN [Wikipedia:Nasal_vestibule] xref: BTO:0001761 xref: CALOHA:TS-0660 xref: FMA:59644 xref: SCTID:278940000 xref: Wikipedia:Nasal_vestibule is_a: CARO:0000000 is_a: UBERON:0002553 ! anatomical cavity relationship: part_of UBERON:0001707 ! nasal cavity property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/7/7c/Gray994.png xsd:anyURI [Term] id: UBERON:0000403 name: scalp def: "The outer covering of the calvaria. It is composed of several layers: SKIN; subcutaneous connective tissue; the occipitofrontal muscle which includes the tendonous galea aponeurotica; Loose connective tissue; and the pericranium (the PERIOSTEUM of the SKULL)." [MESH:A01.456.810] subset: pheno_slim synonym: "scalpus" RELATED LATIN [Wikipedia:Scalp] xref: BTO:0001809 xref: CALOHA:TS-0896 xref: EMAPA:37949 {source="MA:th"} xref: FMA:46494 xref: GAID:80 xref: galen:Scalp xref: MESH:D012535 xref: NCIT:C89807 xref: OpenCyc:Mx4rwNtaz5wpEbGdrcN5Y29ycA xref: SCTID:181480002 xref: UMLS:C0036270 {source="ncithesaurus:Scalp"} xref: Wikipedia:Scalp is_a: CARO:0000000 is_a: UBERON:0034921 ! multi organ part structure relationship: has_part UBERON:0000014 ! zone of skin relationship: has_part UBERON:0002384 ! connective tissue relationship: has_part UBERON:0002515 ! periosteum relationship: part_of UBERON:0000033 {source="BTO"} ! head property_value: depicted_by Double:cowlick.jpg xsd:anyURI property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/5/55/Layers_of_the_scalp_and_meninges.png xsd:anyURI [Term] id: UBERON:0000407 name: sympathetic trunk def: "One of a a paired bundle of nerve fibers plus ganglia that run from the base of the skull to the coccyx." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Sympathetic_trunk] synonym: "gangliated cord" EXACT [Wikipedia:Sympathetic_trunk] synonym: "sympathetic chain" EXACT [FMA:6258] synonym: "sympathetic ganglionic chain" EXACT [Wikipedia:Sympathetic_trunk] synonym: "truncus sympathicus" RELATED LATIN [Wikipedia:Sympathetic_trunk] xref: AAO:0010791 xref: BAMS:S xref: BTO:0001834 xref: CALOHA:TS-2049 xref: EV:0100374 xref: FMA:6258 xref: SCTID:181099004 xref: Wikipedia:Sympathetic_trunk xref: XAO:0000211 is_a: CARO:0000000 is_a: UBERON:0000062 ! organ is_a: UBERON:0015212 ! lateral structure relationship: in_lateral_side_of UBERON:0000013 {source="FMA-abduced-lr"} ! sympathetic nervous system relationship: part_of UBERON:0000013 ! sympathetic nervous system property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray847.png xsd:anyURI [Term] id: UBERON:0000408 name: vertebral ganglion def: "Any of a group of sympathetic ganglia which form two chains extending from the base of the skull to the coccyx along the sides of the spinal column." [BTO:0001835] synonym: "intermediate ganglion" EXACT [FMA:6572] xref: BTO:0001835 xref: FMA:6572 xref: SCTID:176596009 is_a: UBERON:0001806 {source="BTO", source="Wikipedia"} ! sympathetic ganglion is_a: UBERON:0001807 ! paravertebral ganglion relationship: part_of UBERON:0001991 ! cervical ganglion [Term] id: UBERON:0000409 name: serous gland def: "A gland in which the principal secretory cells are serous secreting cells." [http://orcid.org/0000-0002-6601-2165, http://www.siumed.edu/~dking2/intro/glands.htm] subset: organ_slim subset: pheno_slim xref: BTO:0001837 xref: EMAPA:37950 {source="MA:th"} xref: FMA:62889 xref: Wikipedia:Serous_gland is_a: UBERON:0002365 ! exocrine gland intersection_of: UBERON:0002365 ! exocrine gland intersection_of: has_part CL:0000313 relationship: has_part CL:0000313 relationship: has_part UBERON:0013232 ! serous acinus relationship: produces UBERON:0007794 ! secretion of serous gland property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png xsd:anyURI property_value: external_definition "glands that secrete watery albuminous material that often contains enzymes[MP:0008052]." xsd:string {source="MP:0008052"} [Term] id: UBERON:0000410 name: bronchial mucosa def: "A mucosa that is part of a bronchus [Automatically generated definition]." [OBOL:automatic] synonym: "bronchi mucosa" EXACT [OBOL:automatic] synonym: "bronchi mucosa of organ" EXACT [OBOL:automatic] synonym: "bronchi mucous membrane" EXACT [OBOL:automatic] synonym: "bronchi organ mucosa" EXACT [OBOL:automatic] synonym: "bronchial trunk mucosa" EXACT [OBOL:automatic] synonym: "bronchial trunk mucosa of organ" EXACT [OBOL:automatic] synonym: "bronchial trunk mucous membrane" EXACT [OBOL:automatic] synonym: "bronchial trunk organ mucosa" EXACT [OBOL:automatic] synonym: "bronchus mucosa" EXACT [OBOL:automatic] synonym: "bronchus mucosa of organ" EXACT [OBOL:automatic] synonym: "bronchus mucous membrane" EXACT [OBOL:automatic] synonym: "bronchus organ mucosa" EXACT [OBOL:automatic] synonym: "mucosa of bronchi" EXACT [OBOL:automatic] synonym: "mucosa of bronchial trunk" EXACT [OBOL:automatic] synonym: "mucosa of bronchus" EXACT [OBOL:automatic] synonym: "mucosa of organ of bronchi" EXACT [OBOL:automatic] synonym: "mucosa of organ of bronchial trunk" EXACT [OBOL:automatic] synonym: "mucosa of organ of bronchus" EXACT [OBOL:automatic] synonym: "mucous membrane of bronchi" EXACT [OBOL:automatic] synonym: "mucous membrane of bronchial trunk" EXACT [OBOL:automatic] synonym: "mucous membrane of bronchus" EXACT [FMA:62652] synonym: "mucous membrane of bronchus" EXACT [OBOL:automatic] synonym: "organ mucosa of bronchi" EXACT [OBOL:automatic] synonym: "organ mucosa of bronchial trunk" EXACT [OBOL:automatic] synonym: "organ mucosa of bronchus" EXACT [OBOL:automatic] synonym: "tunica mucosa bronchi" EXACT LATIN [FMA:62652, FMA:TA] xref: BTO:0001846 xref: FMA:62652 xref: SCTID:30802009 is_a: UBERON:0000379 ! tracheal mucosa is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0002185 ! bronchus relationship: part_of UBERON:0002185 ! bronchus [Term] id: UBERON:0000411 name: visual cortex def: "the part of the cerebral cortex responsible for processing visual information." [Wikipedia:Visual_cortex] comment: The visual cortex is made up of Brodmann area 17 (the primary visual cortex), and Brodmann area 18 and Brodmann area 19, the extrastriate cortical areas. subset: efo_slim synonym: "higher-order visual cortex" RELATED [FMA:242644] synonym: "visual areas" RELATED [BAMS:VIS] xref: BAMS:VIS xref: BTO:0001857 xref: CALOHA:TS-1117 xref: EFO:0000916 xref: EMAPA:36446 xref: EV:0100171 xref: FMA:242644 xref: GAID:679 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1911 xref: MBA:669 xref: MESH:A08.186.211.730.885.213.571.735 xref: Wikipedia:Visual_cortex is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0035014 {source="cjm"} ! functional part of brain relationship: part_of UBERON:0000956 ! cerebral cortex relationship: part_of UBERON:0002021 {source="BTO"} ! occipital lobe relationship: part_of UBERON:0016540 {source="tgbugs"} ! occipital cortex property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/7/70/Brodmann_areas_17_18_19.png xsd:anyURI [Term] id: UBERON:0000412 name: dermal papilla def: "A mesodermal signaling center of the hair follicle consisting of closely packed specialized mesenchymal fibroblasts. Framed by the enlarged bulb matrix in anagen." [DOI:10.1016/j.cub.2008.12.005] subset: pheno_slim synonym: "dermal papilla cell" RELATED [BTO:0001858] synonym: "dermal papillae" EXACT PLURAL [] synonym: "follicular papilla" EXACT [FMA:70737] synonym: "hair follicle dermal papilla" RELATED [MP:0010687] synonym: "hair papilla" RELATED [] synonym: "papilla corii" RELATED [BTO:0001858] synonym: "papilla dermatis" RELATED [BTO:0001858] synonym: "papilla dermis" RELATED [BTO:0001858] synonym: "papilla of corium" RELATED [BTO:0001858] synonym: "papillae dermis" RELATED LATIN [Wikipedia:Dermal_papillae] synonym: "skin papilla" RELATED [BTO:0001858] xref: BTO:0001858 xref: CALOHA:TS-0431 xref: EMAPA:36484 xref: FMA:70737 xref: NCIT:C32710 xref: NCIT:C83189 xref: SCTID:320101005 xref: UMLS:C0221931 {source="ncithesaurus:Dermal_Papilla"} xref: Wikipedia:Dermal_papillae is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure relationship: composed_primarily_of CL:0000057 relationship: part_of UBERON:0001992 ! papillary layer of dermis property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/34/Skin.jpg xsd:anyURI property_value: editor_note "consider adding grouping class for TAO:0001995 ! papilla" xsd:string property_value: external_ontology_notes "ncit has 'hair papilla' as part of hypodermis" xsd:string {external_ontology="ncit"} property_value: function_notes "Blood vessels in the dermal papillae nourish all hair follicles and bring nutrients and oxygen to the lower layers of epidermal cells." xsd:string property_value: taxon_notes "In humans, at the surface of the skin in hands and feet, they appear as epidermal or papillary ridges (colloquially known as fingerprints)" xsd:string [Term] id: UBERON:0000414 name: mucous gland def: "A gland in which the principal secretory cells are mucus secreting cells." [http://orcid.org/0000-0002-6601-2165, http://www.siumed.edu/~dking2/intro/glands.htm] subset: organ_slim synonym: "glandula mucosa" EXACT LATIN [Wikipedia:Mucous_gland] synonym: "muciparous gland" RELATED [BTO:0001979] synonym: "mucous secreting gland" RELATED [] synonym: "mucus gland" RELATED [] synonym: "mucus-secreting gland" RELATED [] xref: AAO:0010601 xref: BTO:0001979 xref: EMAPA:37913 {source="MA:th"} xref: FMA:62888 xref: Wikipedia:Mucous_gland is_a: UBERON:0002365 ! exocrine gland intersection_of: UBERON:0002365 ! exocrine gland intersection_of: has_part CL:0000319 disjoint_from: UBERON:3010602 ! granular gland relationship: capable_of GO:0070254 relationship: has_part CL:0000319 relationship: produces UBERON:0000912 ! mucus property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png xsd:anyURI property_value: taxon_notes "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]" xsd:string {scope="NCBITaxon:8292", source="ISBN:0073040584"} [Term] id: UBERON:0000415 name: artery wall def: "An anatomical wall that is part of an artery [Automatically generated definition]." [OBOL:automatic] synonym: "arterial wall" EXACT [FMA:14155] synonym: "wall of artery" EXACT [FMA:14155] xref: BTO:0002009 xref: FMA:14155 xref: galen:ArterialWall intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001637 ! artery relationship: part_of UBERON:0001637 ! artery [Term] id: UBERON:0000416 name: subdural space def: "A narrow fluid-containing space, often only a potential space, between the dura mater and the arachnoid." [BTO:0002082, PMID:8421539, Wikipedia:Subdural_space] synonym: "cavum subdurale" RELATED LATIN [Wikipedia:Subdural_space] synonym: "cavum subdurale" RELATED [BTO:0002082] synonym: "spatium subdurale" RELATED LATIN [Wikipedia:Subdural_space] synonym: "spatium subdurale" RELATED [BTO:0002082] synonym: "subdural cavity" RELATED [BTO:0002082] synonym: "subdural cleavage" RELATED [BTO:0002082] synonym: "subdural cleft" RELATED [BTO:0002082] xref: BTO:0002082 xref: FMA:83803 xref: GAID:692 xref: MESH:D013355 xref: SCTID:362308002 xref: Wikipedia:Subdural_space is_a: CARO:0000000 is_a: UBERON:0000464 ! anatomical space relationship: adjacent_to UBERON:0002362 ! arachnoid mater relationship: adjacent_to UBERON:0002363 ! dura mater relationship: part_of UBERON:0010743 ! meningeal cluster property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray769-en.svg xsd:anyURI property_value: editor_note "consider obsoleting - see PMID:8421539" xsd:string [Term] id: UBERON:0000418 name: obsolete tubercle is_obsolete: true [Term] id: UBERON:0000420 name: myoepithelium def: "An epithelium consisting of myopethelial cells, which are contractile cells resembling smooth muscle cells that are present in glands, notably the mammary gland, and aid in secretion. This cell has long weaving dendritic processes containing myofilament[CL]." [CL:0000185, Wikipedia:Myoepithelial_cell] synonym: "myo-epithelium" EXACT [FMA:67805] synonym: "myoepitheliocytus" RELATED LATIN [Wikipedia:Myoepithelial_cell] xref: BTO:0002308 xref: FMA:67805 xref: Wikipedia:Myoepithelial_cell is_a: CARO:0000000 is_a: UBERON:0000488 ! atypical epithelium intersection_of: UBERON:0000488 ! atypical epithelium intersection_of: composed_primarily_of CL:0000185 relationship: composed_primarily_of CL:0000185 relationship: has_part GO:0036379 [Term] id: UBERON:0000423 name: eccrine sweat gland def: "A merocrine, unbranched, unbranched, coiled, tubular gland sweat gland. In humans, distributed over almost all of the body surface, and promote cooling by evaporation of their secretion." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Eccrine_sweat_gland] subset: organ_slim subset: pheno_slim synonym: "eccrine gland" RELATED [FMA:59154] synonym: "glandula sudorifera eccrina" EXACT LATIN [Wikipedia:Eccrine_sweat_gland] synonym: "glandula sudorifera merocrina" EXACT LATIN [Wikipedia:Eccrine_sweat_gland] synonym: "merocrine sweat gland" RELATED [] xref: BTO:0002323 xref: FMA:59154 xref: GAID:945 xref: MA:0003039 xref: MESH:D004439 xref: NCIT:C32490 xref: SCTID:361699008 xref: UMLS:C0013492 {source="ncithesaurus:Eccrine_Sweat_Gland"} xref: Wikipedia:Eccrine_sweat_gland is_a: UBERON:0001820 ! sweat gland is_a: UBERON:0010243 {source="MGI:anna"} ! merocrine gland relationship: part_of UBERON:0001003 {source="FMA"} ! skin epidermis relationship: part_of UBERON:0008837 {gci_relation="part_of", gci_filler="NCBITaxon:10088", source="PMID:15843440"} ! palmar/plantar part of autopod property_value: taxon_notes "in mice, found only on footpads; in humans, entire body including soles and palms" xsd:string [Term] id: UBERON:0000424 name: gastric pit alt_id: UBERON:0000425 def: "Gastric pits are indentations in the stomach which denote entrances to the gastric glands. They are deeper in the pylorus than they are in the other parts of the stomach. The human stomach has several million of these pits." [Wikipedia:Gastric_pits] synonym: "foveola gastrica" RELATED [BTO:0002364] synonym: "foveolae gastricae" EXACT PLURAL [FMA:76583, FMA:TA] synonym: "foveolae gastricae" RELATED LATIN [Wikipedia:Gastric_pits] synonym: "gastric foveola" EXACT [FMA:62947] xref: BTO:0002364 xref: FMA:62947 xref: NCIT:C32659 xref: SCTID:268426007 xref: UMLS:C0227203 {source="ncithesaurus:Gastric_Pit"} xref: Wikipedia:Gastric_pits is_a: CARO:0000000 is_a: UBERON:0002553 ! anatomical cavity relationship: part_of UBERON:0001199 {source="BTO"} ! mucosa of stomach property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/7/73/Illu_stomach_layers.jpg xsd:anyURI [Term] id: UBERON:0000426 name: extravillous trophoblast def: "The outermost layer of trophoblast, produced by cytotrophoblast where there is direct contact with maternal decidua rather than blood. The EVT cells travel into the decidua, reacting with NK cells and invading maternal blood vessels feeding the placenta, softening the walls and replacing the lining with fetal tissue, a process called conversion." [BTO:0002366] synonym: "intermediate trophoblast" EXACT [FMA:86561] synonym: "interstitial trophoblast" RELATED [BTO:0002366] xref: BTO:0002366 xref: FMA:86561 is_a: CARO:0000000 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000088 {source="BTO"} ! trophoblast [Term] id: UBERON:0000427 name: obsolete cytotrophoblastic cell is_obsolete: true consider: NCIT:C38575 [Term] id: UBERON:0000428 name: prostate epithelium alt_id: UBERON:0002452 def: "The prostate epithelium." [MP:0001168] subset: pheno_slim synonym: "epithelial tissue of prostate" EXACT [OBOL:automatic] synonym: "epithelial tissue of prostate gland" EXACT [OBOL:automatic] synonym: "epithelium of prostate" EXACT [OBOL:automatic] synonym: "epithelium of prostate gland" EXACT [OBOL:automatic] synonym: "epithelium of prostatic gland" EXACT [FMA:79643] synonym: "prostate epithelial tissue" EXACT [OBOL:automatic] synonym: "prostate gland epithelial tissue" EXACT [OBOL:automatic] synonym: "prostate gland epithelium" EXACT [] synonym: "prostatic epithelium" EXACT [FMA:66812] synonym: "prostatic gland epithelium" EXACT [] xref: BTO:0002397 xref: CALOHA:TS-2065 xref: EMAPA:35711 xref: FMA:66812 xref: FMA:79643 xref: MA:0001737 xref: NCIT:C13103 xref: UMLS:C1179826 {source="ncithesaurus:Prostatic_Epithelium"} is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0000485 ! simple columnar epithelium is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002367 ! prostate gland relationship: part_of UBERON:0002367 ! prostate gland property_value: editor_note "TODO - check 2 FMA IDs" xsd:string [Term] id: UBERON:0000429 name: enteric plexus alt_id: UBERON:0012372 def: "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." [BTO:0002437] synonym: "enteric nerve plexus" EXACT [FMA:77597] synonym: "intrinsic nerve plexus" EXACT [MA:0001147] synonym: "plexus entericus" EXACT [BTO:0002437] synonym: "plexus nervosus entericus" EXACT LATIN [FMA:77597, FMA:TA] synonym: "sympathetic enteric nerve plexus" EXACT [FMA:77597] xref: BTO:0002437 xref: EMAPA:35446 xref: FMA:77597 xref: MA:0001147 is_a: UBERON:0001816 ! autonomic nerve plexus is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001810 ! nerve plexus intersection_of: part_of UBERON:0002005 ! enteric nervous system relationship: part_of UBERON:0002005 ! enteric nervous system [Term] id: UBERON:0000430 name: ventral intermediate nucleus of thalamus def: "A nucleus medially located within the ventral nuclei of the thalamus." [BTO:0002469] subset: vertebrate_core synonym: "intermediate thalamic nuclei" RELATED PLURAL [ZFA:0000370] synonym: "intermediate thalamic nucleus" RELATED [TAO:0000370] synonym: "nucleus ventralis intermedius thalami" RELATED [BTO:0002469] xref: BTO:0002469 xref: EV:0100208 xref: FMA:84347 xref: TAO:0000370 xref: ZFA:0000370 is_a: UBERON:0015234 ! nucleus of ventral thalamus relationship: part_of UBERON:0001900 {source="BTO-definition", source="ZFA"} ! ventral thalamus [Term] id: UBERON:0000431 name: ventral medial complex of thalamus def: "A group of nuclei located in the medial portion of the ventral thalamic nuclei." [BTO:0002470] synonym: "nuclei ventrales mediales thalami" RELATED LATIN [BTO:0002470] synonym: "set of ventral medial nuclei of thalamus" RELATED [FMA:77795] synonym: "ventral medial complex of thalamus" EXACT [FMA:77795] synonym: "ventral medial nuclei of thalamus" EXACT [FMA:77795] xref: BTO:0002470 xref: FMA:77795 is_a: UBERON:0010009 {source="FMA"} ! aggregate regional part of brain relationship: part_of UBERON:0002776 {source="BTO-modified"} ! ventral nuclear group [Term] id: UBERON:0000432 name: endopeduncular nucleus def: "A portion of the nucleus of ansa lenticularis located medial to the posterior limb of the internal capsule, along the course of the ansa lenticularis and the inferior thalamic peduncle or as a separate nucleus within the internal capsule adjacent to the medial GLOBUS PALLIDUS (NeuroNames, http://rprcsgi.rprc. washington.edu/neuronames/ (September 28, 1998)). In non-primates, the entopeduncular nucleus is analogous to both the medial globus pallidus and the entopeduncular nucleus of human." [MESH:A08.186.211.730.385.800.240] comment: The term entopeduncular nucleus in human neuroanatomy refers to a portion of the nucleus of the ansa lenticularis described variously as located medial to the posterior limb of the internal capsule ( Riley-1943 ), along the course of the ansa lenticularis and the inferior thalamic peduncle ( Crosby-1962 ), or as a separate nucleus within the internal capsule adjacent to the medial segment of the globus pallidus ( Nomina-1983 ).[NN] synonym: "entopeduncular nucleus" RELATED [] synonym: "nucleus endopeduncularis" RELATED [BTO:0002475] synonym: "nucleus entopeduncularis" RELATED [] xref: BAMS:EN xref: BTO:0002475 xref: DHBA:13057 xref: FMA:77691 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2284 xref: MESH:A08.186.211.730.385.800.240 xref: SCTID:82705008 is_a: UBERON:0015234 ! nucleus of ventral thalamus relationship: part_of UBERON:0009641 {source="NN"} ! ansa lenticularis [Term] id: UBERON:0000433 name: posterior paraventricular nucleus of thalamus def: "The posterior of the two nuclei paraventriculares thalami." [BTO:0002456] synonym: "caecal epithelium" RELATED [BTO:0002477] synonym: "dorsal paraventricular nucleus of thalamus" EXACT [FMA:76961] synonym: "nucleus paraventricularis posterior thalami" RELATED [BTO:0002477] synonym: "nucleus paraventricularis posterior thalami" RELATED [BTO:0002456] synonym: "posterior paraventricular nuclei" RELATED [BTO:0002456] synonym: "posterior paraventricular nucleus of thalamus" RELATED [BTO:0002456] synonym: "posterior paraventricular nucleus of the thalamus" RELATED [BAMS:PARP] xref: BAMS:PARP xref: BTO:0002456 xref: FMA:76961 xref: HBA:4536 is_a: UBERON:0001920 ! paraventricular nucleus of thalamus disjoint_from: UBERON:0000434 {source="lexical"} ! anterior paraventricular nucleus of thalamus [Term] id: UBERON:0000434 name: anterior paraventricular nucleus of thalamus def: "The anterior of the two nuclei paraventriculares thalami." [BTO:0002455, Dorlands_Medical_Dictionary:MerckSource] synonym: "anterior paraventricular nuclei" RELATED [BTO:0002455] synonym: "anterior paraventricular nucleus" EXACT [BTO:0002455] synonym: "anterior paraventricular nucleus of thalamus" RELATED [BTO:0002455] synonym: "anterior paraventricular nucleus of the thalamus" RELATED [BAMS:PARA] synonym: "anterior periventricular nucleus of the hypothalamus" RELATED [BAMS:PVa] synonym: "nucleus paraventricularis anterior thalami" RELATED [BTO:0002478] synonym: "nucleus paraventricularis anterior thalami" RELATED [BTO:0002455] synonym: "periventricular hypothalamic nucleus, anterior part" RELATED [BAMS:PVa] synonym: "ventral paraventricular nucleus of thalamus" EXACT [FMA:76962] xref: BAMS:PARA xref: BAMS:PVa xref: BTO:0002455 xref: DMBA:16400 xref: FMA:76962 xref: HBA:12906 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2928 xref: MBA:30 is_a: UBERON:0001920 ! paraventricular nucleus of thalamus disjoint_from: UBERON:0002708 {source="lexical"} ! posterior periventricular nucleus [Term] id: UBERON:0000435 name: lateral tuberal nucleus def: "Nerve cell nuclei situated ventrally in the intermediate hypothalamic region, mainly in the lateral hypothalamic area." [BTO:0002481] synonym: "lateral tuberal hypothalamic nuclei" EXACT [FMA:62336] synonym: "lateral tuberal nuclear complex" EXACT [BIRNLEX:1206] synonym: "lateral tuberal nuclei" EXACT [FMA:62336] synonym: "LTu" BROAD ABBREVIATION [BIRNLEX:1206, NIFSTD:NeuroNames_abbrevSource] synonym: "nuclei tuberales laterales" RELATED [BTO:0002481] synonym: "nucleus tuberis" RELATED LATIN [NeuroNames:428] synonym: "nucleus tuberis hypothalami" RELATED LATIN [NeuroNames:428] synonym: "nucleus tuberis lateralis" RELATED LATIN [NeuroNames:428] xref: BAMS:LTu xref: BIRNLEX:1206 xref: BM:TU xref: BTO:0002481 xref: DHBA:10493 xref: DMBA:16271 xref: EV:0100240 xref: FMA:62336 xref: HBA:12915 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=428 {source="BIRNLEX:1206"} xref: MBA:614 xref: UMLS:C0086527 {source="BIRNLEX:1206"} is_a: UBERON:0006568 ! hypothalamic nucleus relationship: part_of UBERON:0002430 ! lateral hypothalamic area [Term] id: UBERON:0000437 name: arachnoid barrier layer def: "The arachnoid barrier layer is a part of the arachnoid meningeal layer. It is formed by tight junctions between the endothelial cells of cerebral capillaries in the arachnoid mater." [BTO:0002498] xref: BTO:0002498 xref: FMA:231559 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004923 {source="FMA"} ! organ component layer is_a: UBERON:0010313 ! neural crest-derived structure relationship: composed_primarily_of GO:0005923 relationship: part_of UBERON:0000201 {source="cjm"} ! endothelial blood brain barrier relationship: part_of UBERON:0002362 {source="FMA"} ! arachnoid mater [Term] id: UBERON:0000438 name: obsolete set of arachnoid trabecula synonym: "Arachnoid trabeculae set" EXACT [FMA:77761] synonym: "trabeculae arachnoideae" EXACT LATIN [FMA:77761, FMA:TA] is_obsolete: true consider: FMA:77761 [Term] id: UBERON:0000439 name: arachnoid trabecula def: "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." [Wikipedia:Arachnoid_trabeculae] synonym: "arachnoid trabeculae" RELATED PLURAL [] synonym: "trabecula arachnoideum" RELATED LATIN [] xref: BTO:0002500 xref: FMA:83979 xref: Wikipedia:Arachnoid_trabeculae is_a: UBERON:0000440 ! trabecula is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0000440 ! trabecula intersection_of: part_of UBERON:0002362 ! arachnoid mater relationship: has_part GO:0005581 relationship: part_of UBERON:0002362 ! arachnoid mater [Term] id: UBERON:0000440 name: trabecula def: "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]." [GO:0060343, Wikipedia:Trabecula] subset: grouping_class subset: pheno_slim xref: BTO:0002501 xref: FMA:85273 xref: Wikipedia:Trabecula is_a: UBERON:0000064 ! organ part relationship: has_part UBERON:0002384 ! connective tissue relationship: has_quality PATO:0001873 property_value: has_relational_adjective "trabecular" xsd:string [Term] id: UBERON:0000442 name: right testicular vein def: "A vein that drains the left pampiniform plexus and empties into the left renal vein." [Dorlands_Medical_Dictionary:MerckSource] synonym: "right spermatic vein" EXACT [MA:0002220] synonym: "vena testicularis (adrenalis) dextra" EXACT [FMA:14341] synonym: "vena testicularis dextra" RELATED [BTO:0002679] synonym: "vena testicularis sinistra" RELATED [BTO:0002680] xref: BTO:0002679 xref: EMAPA:37383 {source="MA:th"} xref: FMA:14341 xref: MA:0002220 xref: NCIT:C52697 xref: SCTID:53500001 is_a: UBERON:0001144 ! testicular vein intersection_of: UBERON:0001144 ! testicular vein intersection_of: drains UBERON:0004534 ! right testis relationship: connected_to UBERON:0001142 ! left renal vein relationship: drains UBERON:0004534 ! right testis relationship: in_left_side_of UBERON:0000468 ! multicellular organism [Term] id: UBERON:0000443 name: left testicular vein def: "A vein that drains the right pampiniform plexus and empties into the inferior vena cava." [Dorlands_Medical_Dictionary:MerckSource] synonym: "left spermatic vein" EXACT [MA:0002219] synonym: "vena testicularis dextra" RELATED [BTO:0002679] synonym: "vena testicularis sinistra" RELATED [BTO:0002680] xref: BTO:0002680 xref: EMAPA:37167 {source="MA:th"} xref: FMA:14345 xref: MA:0002219 xref: NCIT:C52696 xref: SCTID:90988008 is_a: UBERON:0001144 ! testicular vein intersection_of: UBERON:0001144 ! testicular vein intersection_of: drains UBERON:0004533 ! left testis relationship: drains UBERON:0004533 ! left testis relationship: in_left_side_of UBERON:0000468 ! multicellular organism [Term] id: UBERON:0000444 name: lymphoid follicle def: "." [https://github.com/obophenotype/uberon/issues/6, https://github.com/obophenotype/uberon/issues/7] synonym: "folliculus lymphaticus" RELATED [BTO:0002684] synonym: "lymphatic follicle" RELATED [BTO:0002684] synonym: "lymphatic nodule" RELATED [BTO:0002684] synonym: "lymphoid nodule" EXACT [FMA:55222] synonym: "nodular lymphoid tissue" EXACT [FMA:55222] synonym: "nodulus lymphaticus" RELATED [BTO:0002684] synonym: "nodulus lymphoideus" RELATED [BTO:0002684] xref: BTO:0002684 xref: FMA:55222 xref: NCIT:C33040 xref: SCTID:64626006 xref: UMLS:C0229654 {source="ncithesaurus:Lymphoid_Follicle"} is_a: UBERON:0001744 {source="FMA"} ! lymphoid tissue relationship: dc-contributor https://github.com/cmungall relationship: dc-contributor https://github.com/tmeehan property_value: editor_note "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'" xsd:string [Term] id: UBERON:0000445 name: habenular trigone def: "The habenular trigone is a small depressed triangular area situated in front of the superior colliculus and on the lateral aspect of the posterior part of the taenia thalami. It contains a group of nerve cells termed the ganglion habenulC&. Fibers enter it from the stalk of the pineal body, and others, forming what is termed the habenular commissure, pass across the middle line to the corresponding ganglion of the opposite side. Most of its fibers are, however, directed downward and form a bundle, the fasciculus retroflexus of Meynert, which passes medial to the red nucleus, and, after decussating with the corresponding fasciculus of the opposite side, ends in the interpeduncular ganglion." [Wikipedia:Habenular_trigone] comment: superclass in BTO is thalamic nucleus, not present in most ontologies synonym: "trigone of habenulae" RELATED [BTO:0002700] synonym: "trigonum habenulae" RELATED LATIN [Wikipedia:Habenular_trigone] synonym: "trigonum habenulae" RELATED [BTO:0002700] xref: BAMS:hbt xref: BTO:0002700 xref: FMA:74868 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=293 xref: Wikipedia:Habenular_trigone is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0001894 ! diencephalon relationship: part_of UBERON:0001904 ! habenula [Term] id: UBERON:0000446 name: septum of telencephalon def: "Gray matter structure located on the midline of the forebrain consisting of the septum pellucidum (in some species) and the septal nuclei (Heimer, 1996)." [BIRNLEX:963] subset: pheno_slim synonym: "area septalis" EXACT LATIN [FMA:61842, FMA:TA] synonym: "massa praecommissuralis" RELATED LATIN [NeuroNames:255] synonym: "Se" BROAD ABBREVIATION [PMID:23375746] synonym: "septal area" EXACT [FMA:61842] synonym: "septal region" RELATED [BAMS:SEP] synonym: "septum" BROAD [BIRNLEX:963] synonym: "septum (NN)" EXACT [FMA:61842] synonym: "septum pellucidum (BNA,PNA)" RELATED LATIN [NeuroNames:255] synonym: "septum telencephali" RELATED LATIN [NeuroNames:255] synonym: "telencephalon septum" EXACT [FMA:61842] xref: BAMS:SA xref: BAMS:SEP xref: BAMS:Sep xref: BAMS:Spt xref: BIRNLEX:963 xref: BM:Tel-Spt xref: BTO:0002705 xref: EMAPA:32837 xref: FMA:61842 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=255 {source="BIRNLEX:963"} xref: MA:0000924 xref: MESH:A08.186.211.577.750 xref: UMLS:C0752060 {source="BIRNLEX:963"} is_a: UBERON:0005401 ! cerebral hemisphere gray matter relationship: part_of UBERON:0001869 ! cerebral hemisphere property_value: external_definition "Subdivision of the telencephalon on the midline between the lateral ventricles which contains the septum pellucidum and the septal nuclei[FMA][FMA:61842]." xsd:string {source="FMA:61842"} [Term] id: UBERON:0000449 name: obsolete decidual cell is_obsolete: true replaced_by: CL:2000002 consider: BTO:0002770 consider: FMA:86480 consider: NCIT:C32429 consider: UMLS:C1511740 {source="ncithesaurus:Decidual_Cell"} consider: Wikipedia:Decidual_cells [Term] id: UBERON:0000450 name: corpus albicans def: "White fibrous tissue that replaces the regressing corpus luteum in the human ovary in the latter half of pregnancy, or soon after ovulation when pregnancy does not supervene." [BTO:0002784] synonym: "corpus albicans of ovary" EXACT [FMA:18620] synonym: "corpus fibrosum" RELATED [BTO:0002784] synonym: "corpus mamillare" RELATED [BTO:0002784] synonym: "mamillary body" RELATED INCONSISTENT [BTO:0002784] synonym: "mammillary body" RELATED INCONSISTENT [BTO:0002784] xref: BTO:0002784 xref: EMAPA:29888 xref: FMA:18620 xref: SCTID:258043001 is_a: UBERON:0003982 {source="BTO"} ! mature ovarian follicle [Term] id: UBERON:0000451 name: prefrontal cortex def: "The anterior part of the frontal lobes of the brain, lying in front of the motor and premotor areas.nnThis brain region has been implicated in planning complex cognitive behaviors, personality expression, decision making and moderating correct social behavior. The basic activity of this brain region is considered to be orchestration of thoughts and actions in accordance with internal goals.nnThe most typical psychological term for functions carried out by the pre-frontal cortex area is executive function. Executive function relates to abilities to differentiate among conflicting thoughts, determine good and bad, better and best, same and different, future consequences of current activities, working toward a defined goal, prediction of outcomes, expectation based on actions, and social 'control' (the ability to suppress urges that, if not suppressed, could lead to socially-unacceptable outcomes).nnMany authors have indicated an integral link between a person's personality and the functions of the prefrontal cortex. - definition adapted from Wikipedia" [NLXANAT:090801] subset: efo_slim synonym: "frontal association cortex" RELATED PENDING_REVIEW [MA:0000906] synonym: "prefrontal association complex" RELATED [BTO:0002807] synonym: "prefrontal association cortex" EXACT [FMA:224850] xref: BAMS:FrA xref: BTO:0002807 xref: DHBA:10172 xref: EFO:0001384 xref: EMAPA:35356 xref: FMA:224850 xref: GAID:676 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1072 xref: MA:0000906 xref: MESH:A08.186.211.730.885.213.270.700 xref: NLXANAT:090801 xref: Wikipedia:Prefrontal_cortex is_a: UBERON:0002616 ! regional part of brain is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0000956 ! cerebral cortex relationship: part_of UBERON:0001870 ! frontal cortex property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/5/59/Gray726-Brodman-prefrontal.svg xsd:anyURI property_value: editor_note "TODO - check MA" xsd:string [Term] id: UBERON:0000453 name: decidua basalis def: "Area of uterine endometrium found between the implanted chorionic vesicle and the myometrium." [https://sourceforge.net/p/obo/mammalian-phenotype-requests/1599, MP:0012529] subset: efo_slim subset: pheno_slim synonym: "basal decidua" RELATED [MGI:anna] synonym: "decidua serotina" RELATED [BTO:0002819] xref: BTO:0002819 xref: EFO:0001918 xref: EMAPA:35270 xref: FMA:86477 xref: MA:0002905 xref: NCIT:C32426 xref: SCTID:362841006 xref: UMLS:C0230965 {source="ncithesaurus:Decidua_Basalis"} is_a: UBERON:0000478 ! extraembryonic structure relationship: part_of UBERON:0002450 ! decidua property_value: development_notes "As the embryo enlarges, the decidua capsularis becomes stretched and smooth. Eventually the decidua capsularis merges with the decidua parietalis, obliterating the uterine cavity" xsd:string [Term] id: UBERON:0000454 name: cerebral subcortex def: "The layer located below the cerebral cortex that includes the forebrain, midbrain and hindbrain." [ncithesaurus:Cerebral_Subcortex] subset: pheno_slim synonym: "cerebral medulla" EXACT [FMA:242188] synonym: "subcortex" RELATED [BTO:0002858] xref: BTO:0002858 xref: FMA:242188 xref: NCIT:C98712 xref: UMLS:C0815008 {source="ncithesaurus:Cerebral_Subcortex"} is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000955 ! brain [Term] id: UBERON:0000456 name: secretion of exocrine gland alt_id: UBERON:0006540 def: "A portion of organism substance that is produced by exocrine glands." [http://orcid.org/0000-0002-6601-2165] synonym: "bodily secretion" EXACT [MESH:D012634] synonym: "exocrine gland fluid" RELATED [] synonym: "exocrine gland fluid or secretion" RELATED [] synonym: "exocrine gland fluid/secretion" EXACT [MA:0002504] synonym: "exocrine gland secretion" RELATED [] synonym: "external secretion" RELATED [BTO:0002977] synonym: "secreted substance" EXACT [] synonym: "secretion" BROAD [FMA:9675] xref: AEO:0001005 xref: BTO:0002977 xref: BTO:0002979 xref: EMAPA:36535 xref: FMA:9675 xref: galen:Secretion xref: MA:0002504 xref: MESH:D012634 xref: NCIT:C34062 xref: UMLS:C1516992 {source="ncithesaurus:Exocrine_Gland_Fluid_or_Secretion"} is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance intersection_of: produced_by UBERON:0002365 ! exocrine gland relationship: produced_by UBERON:0002365 ! exocrine gland property_value: external_ontology_notes "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" xsd:string {external_ontology="BTO"} [Term] id: UBERON:0000457 name: cavernous artery def: "Any of several small branches of the internal carotid artery that supply the trigeminal ganglion and the walls of the cavernous and petrosal sinuses." [BTO:0002996] synonym: "cavernous branch of cavernous part of internal carotid artery" EXACT [FMA:70527] synonym: "ramus sinus cavernosi (pars cavernosa) (arteria carotis interna)" EXACT LATIN [FMA:70527, FMA:TA] xref: BTO:0002996 xref: FMA:70527 is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0004573 ! systemic artery is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0001637 ! artery intersection_of: branching_part_of UBERON:0001532 ! internal carotid artery intersection_of: supplies UBERON:0001675 ! trigeminal ganglion relationship: branching_part_of UBERON:0001532 ! internal carotid artery relationship: part_of UBERON:0001532 ! internal carotid artery relationship: supplies UBERON:0001675 ! trigeminal ganglion [Term] id: UBERON:0000458 name: endocervix def: "The region of the opening of the uterine cervix into the uterine cavity." [BTO:0003002] xref: BTO:0003002 xref: FMA:86485 xref: NCIT:C12309 xref: SCTID:264460007 xref: UMLS:C0227837 {source="ncithesaurus:Endocervix"} is_a: CARO:0000000 is_a: UBERON:0000064 ! organ part is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000064 ! organ part intersection_of: proximalmost_part_of UBERON:0000002 ! uterine cervix relationship: has_part UBERON:0000485 ! simple columnar epithelium relationship: part_of UBERON:0000002 ! uterine cervix relationship: proximalmost_part_of UBERON:0000002 ! uterine cervix [Term] id: UBERON:0000459 name: uterine wall def: "An anatomical wall that is part of a uterus [Automatically generated definition]." [OBOL:automatic] synonym: "anatomical wall of uterus" EXACT [OBOL:automatic] synonym: "uterus anatomical wall" EXACT [OBOL:automatic] synonym: "uterus wall" EXACT [OBOL:automatic] synonym: "wall of uterus" EXACT [OBOL:automatic] xref: BTO:0003083 xref: FMA:17560 xref: SCTID:245485002 is_a: CARO:0000000 is_a: UBERON:0000060 ! anatomical wall is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000995 ! uterus relationship: part_of UBERON:0000995 ! uterus [Term] id: UBERON:0000460 name: major vestibular gland def: "the paired glands located slightly posterior and to the left and right of the opening of the vagina in the superficial perineal pouch in females; they secrete mucus to lubricate the vagina and are homologous to bulbourethral (Cowper's) glands in males" [MGI:anna, MP:0011787] subset: organ_slim subset: pheno_slim synonym: "Bartholin gland" EXACT [] synonym: "Bartholin's gland" EXACT [FMA:9598] synonym: "Duverney's gland" RELATED [FMA:9598] synonym: "glandula vestibularis major" RELATED [BTO:0003115] synonym: "greater vestibular gland" RELATED [MA:0002936] synonym: "greater vestibular glands of Bartholin" RELATED [Wikipedia:Bartholin%27s_gland] synonym: "Tiedemann's gland" EXACT [FMA:9598] synonym: "vulvovaginal gland" EXACT [FMA:9598] xref: BTO:0003115 xref: EMAPA:36429 xref: FMA:9598 xref: GAID:384 xref: MA:0002936 xref: MESH:D001472 xref: NCIT:C12675 xref: SCTID:362244005 xref: Wikipedia:Bartholin's_gland is_a: UBERON:0000414 {source="MP"} ! mucous gland is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0011826 ! vestibular gland is_a: UBERON:0015212 ! lateral structure is_a: UBERON:0019319 ! exocrine gland of integumental system disjoint_from: UBERON:0010048 ! Duvernoy's gland relationship: develops_from UBERON:0000164 {source="Wikipedia"} ! primitive urogenital sinus relationship: in_lateral_side_of UBERON:0005056 {source="FMA-abduced-lr"} ! external female genitalia relationship: part_of UBERON:0002330 ! exocrine system relationship: part_of UBERON:0002416 {source="FMA"} ! integumental system relationship: produces UBERON:0000912 ! mucus relationship: sexually_homologous_to UBERON:0002366 {source="Wikipedia"} ! bulbo-urethral gland property_value: editor_note "resolve difference in WP vs MP, superficial vs deep perineal pouch" xsd:string [Term] id: UBERON:0000461 name: minor vestibular gland def: "Small mucous glands opening upon the vestibular mucous membrane between the urethral and the vaginal orifice." [BTO:0003116] subset: organ_slim synonym: "glandula vestibular minor" EXACT [FMA:20019] synonym: "glandula vestibulares minor" RELATED [BTO:0003116] synonym: "Guerin's gland" RELATED [BTO:0003116] synonym: "Guérin's gland" RELATED [] synonym: "lesser vestibular gland" EXACT [FMA:20019] synonym: "paraurethral gland" RELATED [BTO:0003116] synonym: "periurethral gland" RELATED [BTO:0003116] synonym: "Schueller's gland" RELATED [BTO:0003116] synonym: "Skene gland" RELATED INCONSISTENT [] synonym: "Skene's gland" RELATED INCONSISTENT [BTO:0003116] synonym: "urethral gland of female urethra" RELATED [BTO:0003116] xref: BTO:0003116 xref: FMA:20019 xref: NCIT:C61122 xref: SCTID:279869001 is_a: UBERON:0010145 {source="ncithesaurus"} ! paraurethral gland is_a: UBERON:0010187 ! female urethral gland is_a: UBERON:0011826 ! vestibular gland relationship: part_of UBERON:0000474 {source="FMA"} ! female reproductive system relationship: part_of UBERON:0001334 ! female urethra property_value: editor_note "compare with Skene's gland" xsd:string property_value: structure_notes "check and part_of relationships to mammalian vulva / urethra" xsd:string [Term] id: UBERON:0000462 name: obsolete villus is_obsolete: true [Term] id: UBERON:0000463 name: organism substance def: "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." [http://orcid.org/0000-0001-9114-8737] subset: pheno_slim subset: upper_level synonym: "body fluid or substance" EXACT [MA:0002450] synonym: "body substance" EXACT [FMA:9669] synonym: "organism substance" EXACT [CARO:0000004] synonym: "portion of body substance" EXACT [FMA:9669] synonym: "portion of organism substance" EXACT [ZFA:0001487] xref: AAO:0010839 xref: AEO:0000004 xref: BILA:0000004 xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 xref: FBbt:00007019 xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 xref: MA:0002450 xref: NCIT:C13236 xref: SPD:0000008 xref: TAO:0001487 xref: TGMA:0001824 xref: VHOG:0001726 xref: XAO:0004001 xref: ZFA:0001487 is_a: UBERON:0000465 ! material anatomical entity relationship: has_quality PATO:0002198 relationship: part_of UBERON:0000468 {notes="this relationship may be too strong and may be weakened in future"} ! multicellular organism [Term] id: UBERON:0000464 name: anatomical space def: "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." [http://orcid.org/0000-0001-9114-8737] subset: upper_level synonym: "anatomical spaces" RELATED PLURAL [ZFA:0001643] synonym: "lumen" BROAD [] synonym: "lumen space" EXACT [] synonym: "space" BROAD [] xref: AAO:0010110 xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 xref: FBbt:00007017 xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 xref: TAO:0001668 xref: TGMA:0001825 xref: UMLS:C0524461 {source="ncithesaurus:Lumen_Space"} xref: VHOG:0001728 xref: XAO:0003190 xref: ZFA:0001643 is_a: UBERON:0000466 ! immaterial anatomical entity disjoint_from: UBERON:0006800 ! anatomical line relationship: surrounded_by UBERON:0000061 ! anatomical structure [Term] id: UBERON:0000465 name: material anatomical entity def: "Anatomical entity that has mass." [http://orcid.org/0000-0001-9114-8737] subset: upper_level xref: AAO:0010264 xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 xref: FBbt:00007016 xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 xref: TGMA:0001826 xref: VHOG:0001721 is_a: BFO:0000040 is_a: UBERON:0001062 ! anatomical entity [Term] id: UBERON:0000466 name: immaterial anatomical entity def: "Anatomical entity that has no mass." [http://orcid.org/0000-0001-9114-8737] subset: upper_level synonym: "immaterial physical anatomical entity" EXACT [FMA:67112] xref: AAO:0010265 xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 xref: FBbt:00007015 xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 xref: TGMA:0001827 xref: VHOG:0001727 is_a: BFO:0000141 is_a: UBERON:0001062 ! anatomical entity [Term] id: UBERON:0000467 name: anatomical system def: "Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function." [CARO:0000011] subset: pheno_slim subset: uberon_slim subset: upper_level synonym: "anatomical systems" RELATED PLURAL [ZFA:0001439] synonym: "body system" EXACT [BIRNLEX:14] synonym: "connected anatomical system" EXACT [CARO:0000011] synonym: "organ system" EXACT [] synonym: "system" BROAD [GO:0048731] xref: AAO:0000007 xref: AEO:0000011 xref: BILA:0000011 xref: BIRNLEX:14 xref: BSA:0000049 xref: CALOHA:TS-2088 xref: CARO:0000011 xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 xref: FBbt:00004856 xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 xref: MA:0000003 xref: NCIT:C12919 xref: OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ xref: SCTID:278195005 xref: TAO:0001439 xref: TGMA:0001831 xref: UMLS:C0460002 {source="ncithesaurus:Organ_System"} xref: VHOG:0001725 xref: WBbt:0005746 xref: WBbt:0005763 xref: Wikipedia:Organ_system xref: XAO:0003002 xref: ZFA:0001439 is_a: UBERON:0000061 ! anatomical structure relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage relationship: has_part UBERON:0000062 ! organ relationship: part_of UBERON:0000468 ! multicellular organism relationship: seeAlso EHDAA2:0001330 [Term] id: UBERON:0000468 name: multicellular organism def: "Anatomical structure that is an individual member of a species and consists of more than one cell." [CARO:0000012, http://orcid.org/0000-0001-9114-8737, Wikipedia:Multi-cellular_organism] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: upper_level synonym: "animal" NARROW [BTO:0000042] synonym: "body" RELATED [AEO:0000103, BIRNLEX:18, FMA:256135, NCIT:C13041] synonym: "Koerper" RELATED [BTO:0001489] synonym: "multi-cellular organism" EXACT [CARO:0000012] synonym: "organism" BROAD [FBbt:00000001, VHOG:0000671, WBbt:0007833] synonym: "whole body" RELATED [BTO:0001489] synonym: "whole organism" RELATED [FBbt:00000001] xref: AAO:0010026 xref: AEO:0000191 xref: BILA:0000012 xref: BIRNLEX:18 xref: BSA:0000038 xref: BTO:0000042 xref: CARO:0000012 xref: EFO:0002906 xref: EHDAA2:0003103 xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 xref: FBbt:00000001 xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 xref: NCIT:C13041 xref: ncithesaurus:Whole_Organism xref: SCTID:243928005 xref: TADS:0000001 xref: TAO:0001094 xref: TGMA:0001832 xref: VHOG:0000671 xref: WBbt:0007833 xref: Wikipedia:Multi-cellular_organism xref: XAO:0003004 xref: ZFA:0001094 is_a: UBERON:0010000 ! multicellular anatomical structure property_value: editor_note "TODO - split body and mc organism? body continues after death stage" xsd:string property_value: has_relational_adjective "organismal" xsd:string [Term] id: UBERON:0000470 name: obsolete cell part def: "Anatomical structure that is a direct part of the cell." [http://orcid.org/0000-0001-9114-8737] subset: upper_level synonym: "cell component" RELATED [CARO:0000014] property_value: editor_note "TODO - move metadata to GO and obsolete this class once homes have been found for existing children. Note the inconsistency between the usage of the label 'cell component' in GO and CARO" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/489 xsd:anyURI is_obsolete: true consider: AAO:0010271 consider: BILA:0000014 consider: CARO:0000014 consider: FBbt:00007012 consider: FMA:86454 consider: GO:0044464 consider: HAO:0000014 consider: NCIT:C34070 consider: NIF_Subcellular:sao-1337158144 consider: OpenCyc:Mx4rwQwkcZwpEbGdrcN5Y29ycA consider: TGMA:0001834 consider: UMLS:C1178969 {source="ncithesaurus:Cell_Part"} [Term] id: UBERON:0000471 name: compound organ component def: "Multi-tissue structure that is part of a compound organ." [CARO:0000019, http://orcid.org/0000-0001-9114-8737] subset: upper_level synonym: "compound organ components" RELATED PLURAL [ZFA:0001489] xref: AAO:0010017 xref: AEO:0000019 xref: BILA:0000019 xref: CARO:0000019 xref: EHDAA2:0003019 xref: HAO:0000019 xref: TAO:0001489 xref: TGMA:0001835 xref: XAO:0003039 xref: ZFA:0001489 is_a: UBERON:0000481 ! multi-tissue structure relationship: part_of UBERON:0003103 ! compound organ property_value: curator_notes "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" xsd:string [Term] id: UBERON:0000472 name: simple organ def: "Multi-tissue structure that is not part of a compound organ." [CARO:0000021, http://orcid.org/0000-0001-9114-8737] subset: upper_level synonym: "simple organs" RELATED PLURAL [ZFA:0001492] xref: AAO:0010051 xref: AEO:0000190 xref: BILA:0000021 xref: CARO:0000021 xref: EHDAA2:0003190 xref: HAO:0000021 xref: TAO:0001492 xref: TGMA:0001836 xref: XAO:0003038 xref: ZFA:0001492 is_a: UBERON:0000062 ! organ property_value: curator_notes "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" xsd:string [Term] id: UBERON:0000473 name: testis alt_id: UBERON:0002117 def: "A gonad of a male animal. A gonad produces and releases sperm." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "gonad of male genitalia" EXACT [OBOL:automatic] synonym: "gonad of male reproductive system" EXACT [OBOL:automatic] synonym: "male gonad" EXACT [OBOL:automatic] synonym: "orchis" RELATED [BTO:0001363] synonym: "testes" RELATED PLURAL [] synonym: "testicle" EXACT [FMA:7210] synonym: "testiculus" RELATED LATIN [BTO:0001363] xref: AAO:0000606 xref: BILA:0000124 xref: BSA:0000085 xref: BTO:0001363 xref: CALOHA:TS-1030 xref: EFO:0000984 xref: EHDAA2:0002007 xref: EHDAA:8146 xref: EMAPA:17972 xref: EV:0100102 xref: FBbt:00004928 xref: FMA:7210 xref: GAID:396 xref: galen:Testis xref: HAO:0001007 xref: MA:0000411 xref: MAT:0000132 xref: MESH:D013737 xref: MIAA:0000132 xref: NCIT:C12412 xref: OpenCyc:Mx4rvVjM25wpEbGdrcN5Y29ycA xref: SCTID:181431007 xref: TAO:0000598 xref: UMLS:C0039597 {source="ncithesaurus:Testis"} xref: VHOG:0000252 xref: WBbt:0006794 xref: Wikipedia:Testis xref: XAO:0000157 xref: ZFA:0000598 is_a: UBERON:0000991 ! gonad is_a: UBERON:0003135 ! male reproductive organ intersection_of: UBERON:0000991 ! gonad intersection_of: part_of UBERON:0000079 ! male reproductive system disjoint_from: UBERON:0000992 ! ovary disjoint_from: UBERON:0009117 ! indifferent gonad relationship: develops_from UBERON:0009117 ! indifferent gonad relationship: in_lateral_side_of UBERON:0000468 {gci_relation="part_of", gci_filler="NCBITaxon:7742", notes="vertebrates"} ! multicellular organism relationship: part_of UBERON:0000079 ! male reproductive system property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/c/c3/Gray1144.png xsd:anyURI property_value: external_definition "Male reproductive organ.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000598", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "testicular" xsd:string property_value: homology_notes "(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]" xsd:string {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/"} property_value: taxon_notes "The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally" xsd:string {source="ISBN:0123971756", taxon="NCBITaxon:40674"} [Term] id: UBERON:0000474 name: female reproductive system def: "The organs and associated structures associated with bearing offspring in a female animal." [http://orcid.org/0000-0002-6601-2165, MP:0001119, Wikipedia:Female_genitalia] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "female genital system" RELATED [] synonym: "female genital tract" RELATED [] synonym: "female genitalia" RELATED [] synonym: "female genitals" RELATED PLURAL [XAO:0000156] synonym: "female organism genitalia" EXACT [OBOL:automatic] synonym: "female organism reproductive system" EXACT [OBOL:automatic] synonym: "female reproductive tract" RELATED [MA:0000381] synonym: "genitalia of female organism" EXACT [OBOL:automatic] synonym: "gynaecological tissue" RELATED [BTO:0000083] synonym: "reproductive system of female organism" EXACT [OBOL:automatic] synonym: "systema genitale femininum" RELATED [BTO:0000083] xref: BTO:0000083 xref: CALOHA:TS-1303 xref: EFO:0000969 xref: EHDAA2:0000506 xref: EHDAA:8116 xref: EMAPA:17959 xref: EV:0100110 xref: FBbt:00004864 xref: FMA:45663 xref: GAID:364 xref: HAO:0000324 xref: MA:0000381 xref: MESH:D005836 xref: MIAA:0000028 xref: NCIT:C12402 xref: OpenCyc:Mx4rvVipTZwpEbGdrcN5Y29ycA xref: SCTID:361386004 xref: TGMA:0000635 xref: UMLS:C0700038 {source="ncithesaurus:Female_Reproductive_System"} xref: VHOG:0000726 xref: Wikipedia:Female_genitalia xref: WikipediaCategory:Female_reproductive_system xref: XAO:0000156 is_a: UBERON:0000990 ! reproductive system intersection_of: UBERON:0000990 ! reproductive system intersection_of: part_of UBERON:0003100 ! female organism relationship: part_of UBERON:0003100 ! female organism property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg xsd:anyURI property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000475 name: organism subdivision def: "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." [CARO:0000032, CARO:DOS, http://orcid.org/0000-0001-9114-8737] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: upper_level synonym: "anatomic region" EXACT [MA:0002433] synonym: "body part" RELATED [] synonym: "body region" RELATED [FMA:7153] synonym: "cardinal body part" RELATED [FMA:7153] xref: AAO:0010053 xref: AEO:0000032 xref: BILA:0000032 xref: BIRNLEX:7 xref: CALOHA:TS-2084 xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 xref: FBbt:00007009 xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 xref: MA:0002433 xref: MAT:0000293 xref: MESH:D001829 xref: MIAA:0000293 xref: NCIT:C32221 xref: OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA xref: TAO:0001308 xref: TGMA:0001840 xref: UMLS:C0229962 {source="ncithesaurus:Body_Part"} xref: VHOG:0001758 xref: Wikipedia:Body_part xref: XAO:0003013 xref: ZFA:0001308 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part UBERON:0000075 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! subdivision of skeletal system relationship: has_part UBERON:0034929 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! external soft tissue zone relationship: part_of UBERON:0000468 ! multicellular organism property_value: editor_note "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string [Term] id: UBERON:0000476 name: acellular anatomical structure def: "Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue." [http://orcid.org/0000-0001-9114-8737] subset: vertebrate_core synonym: "acellular anatomical structures" RELATED PLURAL [ZFA:0000382] xref: AAO:0010268 xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 xref: FBbt:00007013 xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 xref: TGMA:0001841 xref: XAO:0003162 xref: ZFA:0000382 is_a: UBERON:0000061 ! anatomical structure disjoint_from: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure [Term] id: UBERON:0000477 name: anatomical cluster def: "Anatomical group that has its parts adjacent to one another." [http://orcid.org/0000-0001-9114-8737] subset: upper_level xref: AAO:0010009 xref: AEO:0000041 xref: BILA:0000041 xref: CARO:0000041 xref: EHDAA2:0003041 xref: FBbt:00007277 xref: FMA:49443 xref: HAO:0000041 xref: TADS:0000605 xref: TAO:0001478 xref: TGMA:0001842 xref: VHOG:0001737 xref: XAO:0003160 xref: ZFA:0001478 is_a: UBERON:0001062 ! anatomical entity property_value: editor_note "Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3]" xsd:string [Term] id: UBERON:0000478 name: extraembryonic structure def: "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." [CARO:DOS, http://orcid.org/0000-0001-9114-8737, https://cedar.bio.indiana.edu/trac/env/ontologies/ticket/279] comment: see also conceptus extraembryonic component in EHDAA2. subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "extra-embryonic structure" EXACT [] synonym: "extraembryonic structures" RELATED PLURAL [ZFA:0000020] synonym: "extraembryonic tissue" RELATED [] xref: AAO:0010020 xref: AEO:0000042 xref: BILA:0000042 xref: CALOHA:TS-2119 xref: CARO:0000042 xref: EHDAA2:0003042 xref: EHDAA:46 xref: FBbt:00005835 xref: FMA:85537 xref: HAO:0000042 xref: NCIT:C34055 xref: SCTID:314908006 xref: TAO:0000020 xref: TGMA:0001843 xref: UMLS:C1282438 {source="ncithesaurus:Extraembryonic_Structure"} xref: VHOG:0000292 xref: XAO:0004005 xref: ZFA:0000020 is_a: CARO:0000000 is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: part_of UBERON:0016887 ! entire extraembryonic component relationship: existence_starts_and_ends_during UBERON:0000068 ! embryo stage relationship: part_of UBERON:0016887 ! entire extraembryonic component [Term] id: UBERON:0000479 name: tissue def: "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." [CARO:0000043] subset: pheno_slim subset: upper_level synonym: "portion of tissue" EXACT [CARO:0000043] synonym: "simple tissue" NARROW [AEO:0000043] synonym: "tissue portion" EXACT [] xref: AAO:0000607 xref: AAO:0010054 xref: AEO:0000043 xref: BILA:0000043 xref: BIRNLEX:19 xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 xref: FBbt:00007003 xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 xref: MA:0003002 xref: MESH:D014024 xref: NCIT:C12801 xref: TAO:0001477 xref: TGMA:0001844 xref: UMLS:C0040300 {source="ncithesaurus:Tissue"} xref: VHOG:0001757 xref: WBbt:0005729 xref: XAO:0003040 xref: ZFA:0001477 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part GO:0031012 relationship: part_of UBERON:0000468 ! multicellular organism property_value: editor_note "changed label and definition to reflect CARO2" xsd:string [Term] id: UBERON:0000480 name: anatomical group def: "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue." [CARO:0000054, http://orcid.org/0000-0001-9114-8737] subset: upper_level xref: AAO:0010008 xref: AEO:0000054 xref: BILA:0000054 xref: CARO:0000054 xref: EHDAA2:0003054 xref: FBbt:00007276 xref: HAO:0000054 xref: TAO:0001512 xref: TGMA:0001846 xref: VHOG:0001724 xref: XAO:0003001 xref: ZFA:0001512 is_a: UBERON:0000061 ! anatomical structure relationship: part_of UBERON:0000468 ! multicellular organism property_value: editor_note "Obsoleted in v2 of CARO [https://github.com/obophenotype/caro/issues/2]" xsd:string [Term] id: UBERON:0000481 name: multi-tissue structure def: "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." [CARO:0000055, http://orcid.org/0000-0001-9114-8737] subset: upper_level synonym: "multi-tissue structures" RELATED PLURAL [ZFA:0001488] xref: AAO:0010048 xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 xref: FBbt:00007010 xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 xref: VHOG:0001762 xref: XAO:0003037 xref: ZFA:0001488 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part UBERON:0000479 ! tissue relationship: part_of NCBITaxon:6072 [Term] id: UBERON:0000482 name: basal lamina of epithelium def: "Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue." [http://orcid.org/0000-0001-9114-8737] subset: uberon_slim subset: vertebrate_core synonym: "basal lamina" RELATED [CARO:0000065] synonym: "basal lamina of connective tissue" EXACT [FMA:62918] synonym: "basal laminae" RELATED PLURAL [VHOG:0001592] synonym: "lamina basalis" RELATED LATIN [Wikipedia:Basal_lamina] xref: AAO:0010269 xref: AEO:0000065 xref: BILA:0000065 xref: CARO:0000065 xref: EHDAA2:0003065 xref: FMA:62918 xref: HAO:0000065 xref: MESH:D001485 xref: NCIT:C32186 xref: NIF_Subcellular:sao1397492660 xref: TAO:0001485 xref: TGMA:0001850 xref: UMLS:C0085872 {source="ncithesaurus:Basal_Lamina"} xref: VHOG:0001592 xref: WBbt:0005756 xref: Wikipedia:Basal_lamina xref: XAO:0003163 xref: ZFA:0001485 is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: composed_primarily_of GO:0005605 relationship: part_of UBERON:0005769 {source="FMA"} ! basement membrane of epithelium property_value: curator_notes "this class represents a continuous sheet of basal lamina which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal lamina' represents a portion of substance on the scale of a single cell." xsd:string property_value: depicted_by Basal:lamina.jpg xsd:anyURI property_value: homology_notes "A basal lamina is certainly present in Bilateria and was evaluated as an autapomorphy of this taxon.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001592", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.57", source="http://bgee.unil.ch/"} [Term] id: UBERON:0000483 name: epithelium def: "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]." [http://orcid.org/0000-0001-9114-8737, Wikipedia:Epithelium] 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? subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "epithelial tissue" EXACT [] synonym: "portion of epithelium" EXACT [FMA:9639] xref: AAO:0000144 xref: AAO:0010055 xref: AEO:0000066 xref: BILA:0000066 xref: BTO:0000416 xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 xref: FBbt:00007005 xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 xref: MA:0003060 xref: MESH:D004848 xref: NCIT:C12710 xref: SCTID:31610004 xref: TAO:0001486 xref: UMLS:C0014609 {source="ncithesaurus:Epithelium"} xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: composed_primarily_of CL:0000066 union_of: UBERON:0000486 ! multilaminar epithelium union_of: UBERON:0000490 ! unilaminar epithelium relationship: composed_primarily_of CL:0000066 relationship: has_part GO:0005911 relationship: has_part UBERON:0005769 ! basement membrane of epithelium relationship: only_in_taxon NCBITaxon:6072 property_value: depicted_by Tkanka:nablonkowa.png xsd:anyURI property_value: has_relational_adjective "epithelial" xsd:string property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000484 name: simple cuboidal epithelium def: "Unilaminar epithelium that consists of a single layer of cuboidal cells." [http://orcid.org/0000-0001-9114-8737, Wikipedia:Simple_cuboidal_epithelium] subset: uberon_slim subset: vertebrate_core synonym: "epithelium simplex cuboideum" EXACT [] synonym: "simple cuboidal epithelia" RELATED PLURAL [ZFA:0001497] xref: AAO:0010064 xref: AEO:0000067 xref: BILA:0000067 xref: CARO:0000067 xref: EHDAA2:0003067 xref: FMA:45566 xref: HAO:0000067 xref: NCIT:C33553 xref: TAO:0001497 xref: UMLS:C0836134 {source="ncithesaurus:Simple_Cuboidal_Epithelium"} xref: Wikipedia:Simple_cuboidal_epithelium xref: XAO:0004009 xref: ZFA:0001497 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0010077 ! cuboidal epithelium property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/d/d0/Gray1133.png xsd:anyURI property_value: editor_note "needs to be synchronized with CL - there is no distinct cuboidal cell in CL" xsd:string [Term] id: UBERON:0000485 name: simple columnar epithelium def: "Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]" [FMA:FMA, http://orcid.org/0000-0001-9114-8737, Wikipedia:Simple_columnar_epithelium] subset: uberon_slim subset: vertebrate_core synonym: "columnar epithelium" BROAD [EHDAA2:0003068] synonym: "columnar epithlium" BROAD [AEO:0000068] synonym: "epithelium simplex columnare" EXACT [] synonym: "simple columnar epithelia" RELATED PLURAL [ZFA:0001496] synonym: "simple columnar epithelium" EXACT [] xref: AAO:0010063 xref: AEO:0000068 xref: BILA:0000068 xref: CARO:0000068 xref: EHDAA2_RETIRED:0003068 xref: FBbt:00007027 xref: FMA:45567 xref: HAO:0000068 xref: NCIT:C33552 xref: SCTID:32210007 xref: TAO:0001496 xref: UMLS:C0836135 {source="ncithesaurus:Simple_Columnar_Epithelium"} xref: Wikipedia:Simple_columnar_epithelium xref: XAO:0004008 xref: ZFA:0001496 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0012274 ! columnar epithelium property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png xsd:anyURI [Term] id: UBERON:0000486 name: multilaminar epithelium def: "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]" [FMA:FMA, http://orcid.org/0000-0001-9114-8737, Wikipedia:Stratified_epithelium] subset: uberon_slim subset: vertebrate_core synonym: "laminated epithelium" RELATED [BTO:0002074] synonym: "stratified epithelium" EXACT [] xref: AAO:0010059 xref: AEO:0000069 xref: BILA:0000069 xref: BTO:0002074 xref: CARO:0000069 xref: EHDAA2:0003069 xref: FMA:45562 xref: HAO:0000069 xref: NCIT:C33622 xref: SCTID:309044005 xref: TAO:0001494 xref: UMLS:C0682575 {source="ncithesaurus:Stratified_Epithelium"} xref: Wikipedia:Stratified_epithelium xref: XAO:0004006 xref: ZFA:0001494 is_a: UBERON:0000483 ! epithelium property_value: external_definition "Epithelium that consists of more than one layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000069", ontology="CARO", source="FMA:45562", source="http://orcid.org/0000-0001-9114-8737"} [Term] id: UBERON:0000487 name: simple squamous epithelium def: "Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]" [FMA:45565, http://orcid.org/0000-0001-9114-8737, Wikipedia:Simple_squamous_epithelium] subset: uberon_slim subset: vertebrate_core synonym: "epithelium simplex squamosum" EXACT [] synonym: "simple squamous epithelia" RELATED PLURAL [ZFA:0001498] xref: AAO:0010066 xref: AEO:0000070 xref: BILA:0000070 xref: BTO:0002073 xref: CARO:0000070 xref: EHDAA2:0003070 xref: FMA:45565 xref: HAO:0000070 xref: NCIT:C13178 xref: TAO:0001498 xref: UMLS:C0836133 {source="ncithesaurus:Simple_Squamous_Epithelium"} xref: Wikipedia:Simple_squamous_epithelium xref: XAO:0004010 xref: ZFA:0001498 is_a: UBERON:0000490 ! unilaminar epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: has_part CL:0000076 relationship: has_part CL:0000076 property_value: depicted_by Illu:epithelium.jpg xsd:anyURI property_value: external_definition "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000070", ontology="CARO", source="FMA:45565", source="http://orcid.org/0000-0001-9114-8737"} [Term] id: UBERON:0000488 name: atypical epithelium def: "Epithelium that consists of epithelial cells not arranged in one ore more layers." [http://orcid.org/0000-0001-9114-8737] subset: vertebrate_core synonym: "atypical epithelia" RELATED PLURAL [ZFA:0001493] synonym: "heterogenous epithelium" EXACT [] xref: AAO:0010057 xref: AEO:0000071 xref: BILA:0000071 xref: CARO:0000071 xref: EHDAA2:0003071 xref: FMA:61741 xref: HAO:0000071 xref: TAO:0001493 xref: XAO:0004004 xref: ZFA:0001493 is_a: UBERON:0000483 ! epithelium [Term] id: UBERON:0000489 name: cavitated compound organ def: "Compound organ that contains one or more macroscopic anatomical spaces." [http://orcid.org/0000-0001-9114-8737] subset: organ_slim subset: upper_level synonym: "cavitated compound organs" RELATED PLURAL [ZFA:0001490] synonym: "cavitated organ" EXACT [FMA:55671] xref: AAO:0010016 xref: AEO:0000072 xref: BILA:0000072 xref: CARO:0000072 xref: EHDAA2:0003072 xref: FMA:55671 xref: HAO:0000072 xref: TAO:0001490 xref: TGMA:0001857 xref: VHOG:0001730 xref: XAO:0003165 xref: ZFA:0001490 is_a: UBERON:0003103 ! compound organ intersection_of: UBERON:0003103 ! compound organ intersection_of: has_part UBERON:0002553 ! anatomical cavity relationship: has_part UBERON:0002553 ! anatomical cavity property_value: curator_notes "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" xsd:string [Term] id: UBERON:0000490 name: unilaminar epithelium def: "Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]" [FMA:45561, http://orcid.org/0000-0001-9114-8737] subset: vertebrate_core synonym: "simple epithelium" EXACT [FMA:45561] synonym: "unilaminar epithelia" RELATED PLURAL [ZFA:0001495] xref: AAO:0010062 xref: AEO:0000073 xref: BILA:0000073 xref: BTO:0002073 xref: CARO:0000073 xref: EHDAA2:0003073 xref: FMA:45561 xref: HAO:0000073 xref: NCIT:C33554 xref: SCTID:309043004 xref: TAO:0001495 xref: UMLS:C0682574 {source="ncithesaurus:Simple_Epithelium"} xref: XAO:0004007 xref: ZFA:0001495 is_a: UBERON:0000483 ! epithelium property_value: editor_note "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string property_value: external_definition "Epithelium that consists of a single layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000073", ontology="CARO", source="FMA:45561", source="http://orcid.org/0000-0001-9114-8737"} [Term] id: UBERON:0000491 name: solid compound organ def: "Compound organ that does not contain macroscopic anatomical spaces." [http://orcid.org/0000-0001-9114-8737] subset: organ_slim subset: upper_level synonym: "solid compound organs" RELATED PLURAL [ZFA:0001491] synonym: "solid organ" RELATED [FMA:55670] xref: AAO:0010019 xref: AEO:0000074 xref: BILA:0000074 xref: CARO:0000074 xref: EHDAA2:0003074 xref: FMA:55670 xref: HAO:0000074 xref: TAO:0001491 xref: TGMA:0001859 xref: XAO:0003164 xref: ZFA:0001491 is_a: UBERON:0003103 ! compound organ property_value: curator_notes "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. Note also that we place the FMA class 'solid organ' here, and the FMA includes many glands plus the liver as solid organs, which some may find confusing" xsd:string [Term] id: UBERON:0000569 name: ileocecal valve def: "The ileocecal valve is a sphincter muscle situated at the junction of the small intestine (ileum) and the large intestine. Its critical function is to limit the reflux of colonic contents into the ileum." [Wikipedia:Ileocecal_valve] synonym: "Tulp's valve" RELATED [Wikipedia:Ileocecal_valve] synonym: "valva ileocaecalis" RELATED LATIN [Wikipedia:Ileocecal_valve] synonym: "valva ileocaecalis (valva ilealis)" EXACT [FMA:15973] xref: FMA:15973 xref: galen:IleocecalValve xref: NCIT:C13066 xref: SCTID:362153007 xref: UMLS:C0020880 {source="ncithesaurus:Ileocecal_Valve"} xref: Wikipedia:Ileocecal_valve is_a: UBERON:0003978 {source="Obol"} ! valve is_a: UBERON:0004590 {source="Wikipedia"} ! sphincter muscle is_a: UBERON:0011185 ! gastrointestinal sphincter relationship: part_of UBERON:0001073 {source="FMA"} ! ileocecal junction property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/f/fc/Gray1075.png xsd:anyURI [Term] id: UBERON:0000642 name: suspensory ligament of duodenum def: "A thin muscle connecting the junction between the duodenum, jejunum, and duodenojejunal flexure to connective tissue surrounding the superior mesenteric artery and coeliac artery" [Wikipedia:Suspensory_muscle_of_duodenum] synonym: "ligament of Treitz" EXACT [FMA:20509] synonym: "muscle of Treitz" EXACT [FMA:20509] synonym: "musculus suspensorius duodeni" EXACT [FMA:20509] synonym: "musculus suspensorius duodeni" RELATED LATIN [Wikipedia:Suspensory_muscle_of_duodenum] synonym: "suspensory muscle of duodenum" EXACT [FMA:20509] xref: FMA:20509 xref: SCTID:279979000 xref: Wikipedia:Suspensory_muscle_of_duodenum is_a: CARO:0000003 is_a: UBERON:0008841 {source="Obol"} ! suspensory ligament intersection_of: UBERON:0008841 ! suspensory ligament intersection_of: attaches_to UBERON:0002114 ! duodenum relationship: attaches_to UBERON:0001103 {source="Obol"} ! diaphragm relationship: attaches_to UBERON:0002114 {source="Obol"} ! duodenum property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/ed/Gray1042.png xsd:anyURI [Term] id: UBERON:0000711 name: splenius capitis def: "A muscle that arises from the lower half of the ligamentum nuchæ, from the spinous process of the seventh cervical vertebra, and from the spinous processes of the upper three or four thoracic vertebræ and inserts the mastoid process of the temporal bone, and into the rough surface on the occipital bone just below the lateral third of the superior nuchal line[WP,modified]." [Wikipedia:Splenius_capitis_muscle] synonym: "musculus splenius capitis" RELATED LATIN [Wikipedia:Splenius_capitis_muscle] synonym: "splenius capitis muscle" EXACT [Wikipedia:Splenius_capitis_muscle] xref: FMA:22653 xref: SCTID:244850004 xref: Wikipedia:Splenius_capitis_muscle is_a: UBERON:0002252 {source="FMA"} ! splenius is_a: UBERON:0002377 ! muscle of neck relationship: has_muscle_insertion UBERON:0011220 {source="Wikipedia:Mastoid_process"} ! mastoid process of temporal bone relationship: has_muscle_origin UBERON:0000351 {notes="Ligamentum nuchae spinous process of C7-T6", source="dbpedia"} ! nuchal ligament relationship: part_of UBERON:0012477 ! dorsal part of neck property_value: action_notes "Extend, rotate, and laterally flex the head" xsd:string property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/5/51/Splenius.png xsd:anyURI [Term] id: UBERON:0000908 name: hippocampal commissure alt_id: UBERON:Commissure-MA_0002723 def: "the triangular subcallosal plate of commissural fibers resulting from the converging of the right and left fornix bundles which exchange numerous fibers and which curve back in the contralateral fornix to end in the hippocampus of the opposite side" [ISBN:0-683-40008-8, MP:0008221] subset: pheno_slim subset: uberon_slim synonym: "commissura hippocampi" EXACT LATIN [FMA:61970, FMA:TA] synonym: "commissure of fornix" RELATED [Wikipedia:Commissure_of_fornix] synonym: "commissure of fornix of forebrain" EXACT [FMA:61970] synonym: "commissure of the fornix" RELATED [BAMS:FG] synonym: "commissure of the fornix" RELATED [BAMS:FC] synonym: "delta fornicis" EXACT [MP:0008221] synonym: "dorsal hippocampal commissure" EXACT [FMA:61970] synonym: "fornical commissure" EXACT [FMA:61970] synonym: "fornix commissure" EXACT [FMA:61970] synonym: "hippocampal commissures" RELATED [BAMS:hc] synonym: "hippocampus commissure" EXACT [MP:0008221] xref: BAMS:cfx xref: BAMS:dhc xref: BAMS:FC xref: BAMS:FG xref: BAMS:hc xref: BIRNLEX:746 xref: DHBA:10560 xref: DMBA:17769 xref: EMAPA:35404 xref: FMA:61970 xref: HBA:9228 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=273 xref: MA:0002723 xref: MBA:618 xref: SCTID:369115003 xref: UMLS:C0228287 {source="BIRNLEX:746"} xref: Wikipedia:Commissure_of_fornix is_a: UBERON:0005340 {source="MP"} ! dorsal telencephalic commissure disjoint_from: UBERON:0014539 {source="NIFSTD"} ! precommissural fornix of forebrain relationship: connects UBERON:0001954 ! Ammon's horn relationship: part_of UBERON:0002437 ! cerebral hemisphere white matter property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/2/21/Gray747.png xsd:anyURI [Term] id: UBERON:0000910 name: chyme def: "A semifluid mass of partly digested food expelled by the stomach into the duodenum." [Wikipedia:Chyme] comment: Chyme has a low pH that is countered by the production of bile, helping to further digest food. Chyme is also part liquid and part solid: a thick semifluid mass of partially digested food and digestive secretions that is formed in the stomach and intestine during digestion. synonym: "chymus" EXACT [ENVO:02000026] xref: ENVO:02000026 xref: FMA:62961 xref: Wikipedia:Chyme is_a: UBERON:0006314 {source="WP"} ! bodily fluid is_a: UBERON:0012112 {editor_note="consider changing to derivation relationship", source="FMA"} ! ingested food disjoint_from: UBERON:0012113 ! bolus of food relationship: has_quality PATO:0001429 {gci_relation="part_of", gci_filler="UBERON:0000945"} relationship: located_in UBERON:0004908 ! upper digestive tract relationship: only_in_taxon NCBITaxon:7742 relationship: output_of GO:0007586 [Term] id: UBERON:0000911 name: chyle def: "Chyle is a bodily fluid consisting of a milky fluid consisting of lymph and emulsified fats; formed in the small intestine during digestion of ingested fats." [http://wordnet.princeton.edu/perl/webwn?s=chyle, Wikipedia:Chyle] xref: ENVO:02000030 xref: FMA:61403 xref: GAID:1187 xref: MESH:A12.207.630.350 xref: NCIT:C93166 xref: UMLS:C0008730 {source="ncithesaurus:Chyle"} xref: Wikipedia:Chyle is_a: CARO:0000000 is_a: UBERON:0000463 ! organism substance relationship: has_part CHEBI:18059 relationship: has_part UBERON:0002391 ! lymph relationship: output_of GO:0007586 relationship: produced_by UBERON:0002108 ! small intestine [Term] id: UBERON:0000912 name: mucus def: "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." [Wikipedia:Mucus] xref: CALOHA:TS-2144 xref: ENVO:02000040 xref: FMA:66938 xref: GAID:1164 xref: galen:Mucus xref: MESH:D009093 xref: NCIT:C13259 xref: OpenCyc:Mx4rvVjHq5wpEbGdrcN5Y29ycA xref: UMLS:C0026727 {source="ncithesaurus:Mucus"} xref: Wikipedia:Mucus is_a: UBERON:0000456 ! secretion of exocrine gland relationship: has_part CHEBI:37395 relationship: has_quality PATO:0000998 relationship: produced_by UBERON:0000344 ! mucosa property_value: has_relational_adjective "mucoid" xsd:string property_value: has_relational_adjective "mucous" xsd:string [Term] id: UBERON:0000913 name: interstitial fluid def: "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." [Wikipedia:Interstitial_fluid] subset: pheno_slim synonym: "intercellular fluid" EXACT [ENVO:02000042] synonym: "tissue fluid" EXACT [ENVO:02000042] xref: ENVO:02000042 xref: FMA:9673 xref: NCIT:C120839 xref: Wikipedia:Interstitial_fluid is_a: UBERON:0000463 ! organism substance relationship: only_in_taxon NCBITaxon:6072 relationship: part_of UBERON:0000479 ! tissue relationship: surrounds CL:0000000 [Term] id: UBERON:0000914 name: organismal segment def: "One of the repeated divisions of the whole organism." [FB:gg, Wikipedia:Segmentation_(biology)] subset: uberon_slim subset: upper_level synonym: "segment" EXACT [FBbt:00000003] synonym: "serial element" EXACT [] xref: FBbt:00000003 xref: HAO:0000929 xref: MAT:0000271 xref: MIAA:0000271 xref: Wikipedia:Segmentation_(biology) is_a: UBERON:0000475 ! organism subdivision property_value: editor_note "review this post-CARO2" xsd:string [Term] id: UBERON:0000915 name: thoracic segment of trunk def: "Subdivision of trunk that lies between the head and the abdomen." [http://orcid.org/0000-0002-6601-2165] subset: uberon_slim synonym: "anterior subdivision of trunk" RELATED [] synonym: "thorax" EXACT [MA:0000022] synonym: "upper body" RELATED [] synonym: "upper trunk" RELATED [FMA:259209] xref: EMAPA:35862 xref: FMA:259209 xref: MA:0000022 xref: SCTID:302551006 xref: Wikipedia:Thorax is_a: CARO:0000003 is_a: UBERON:0009569 {source="FMA"} ! subdivision of trunk is_a: UBERON:0011676 ! subdivision of organism along main body axis intersection_of: UBERON:0011676 ! subdivision of organism along main body axis intersection_of: has_skeleton UBERON:0014477 ! thoracic skeleton relationship: has_skeleton UBERON:0014477 ! thoracic skeleton property_value: curator_notes "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" xsd:string [Term] id: UBERON:0000916 name: abdomen def: "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." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "abdominopelvic region" EXACT [FMA:9577] synonym: "abdominopelvis" EXACT [FMA:9577] synonym: "adult abdomen" RELATED [] synonym: "belly" RELATED [] synonym: "celiac region" RELATED [] xref: BTO:0000020 xref: CALOHA:TS-0001 xref: EFO:0000968 xref: EMAPA:35102 xref: EV:0100011 xref: FMA:9577 xref: GAID:16 xref: galen:Abdomen xref: MA:0000029 xref: MAT:0000298 xref: MESH:A01.047 xref: MIAA:0000298 xref: OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA xref: SCTID:302553009 xref: Wikipedia:Abdomen is_a: UBERON:0009569 ! subdivision of trunk relationship: only_in_taxon NCBITaxon:7742 relationship: part_of UBERON:0002417 {source="MA"} ! abdominal segment of trunk property_value: editor_note "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" xsd:string property_value: has_relational_adjective "abdominal" xsd:string property_value: has_relational_adjective "celiac" xsd:string [Term] id: UBERON:0000917 name: obsolete abdominal segment synonym: "segment of abdomen" EXACT [OBOL:automatic] is_obsolete: true consider: FBbt:00000021 consider: HAO:0000016 consider: SPD:0000055 consider: UBERON:0002417 [Term] id: UBERON:0000918 name: obsolete yolk def: "The nutritive substance contained in the egg." [FB:gg] synonym: "vegetal yolk mass" BROAD [] synonym: "yolk cell" RELATED [] xref: MAT:0000335 xref: MIAA:0000335 is_obsolete: true consider: BTO:0000371 consider: FBbt:00000035 consider: GO:0060417 consider: UBERON:0007378 consider: XAO:0000281 consider: ZFA:0000084 [Term] id: UBERON:0000919 name: obsolete lipid droplet is_obsolete: true replaced_by: GO:0005811 consider: FMA:62962 consider: GO:0005811 [Term] id: UBERON:0000920 name: egg chorion def: "A protective, noncellular membrane that surrounds the eggs of various animals including insects and fish [GO]." [GO:0042600, Wikipedia:Chorion_(egg)] subset: dubious_grouping subset: uberon_slim subset: vertebrate_core synonym: "chorion" RELATED [] synonym: "chorion (egg)" EXACT [] xref: FBbt:00000038 xref: TAO:0000329 xref: TGMA:0000681 xref: Wikipedia:Chorion_(egg) xref: ZFA:0000329 is_a: CARO:0000000 is_a: UBERON:0000476 ! acellular anatomical structure disjoint_from: UBERON:0003124 ! chorion membrane relationship: only_in_taxon NCBITaxon:6072 relationship: part_of UBERON:0016887 ! entire extraembryonic component relationship: surrounds UBERON:0003125 ! vitelline membrane property_value: external_definition "The egg shell. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000329", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0000921 name: obsolete pronucleus def: "." [Wikipedia:Pronucleus] xref: Wikipedia:Pronucleus is_obsolete: true replaced_by: GO:0045120 consider: FBbt:00000048 consider: FMA:84673 consider: GO:0045120 [Term] id: UBERON:0000922 name: embryo def: "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." [BTO:0000379, FB:FBrf0039741, FB:FBrf0041814, GO:0009790, Wikipedia:Embryo] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "developing organism" RELATED [BILA:0000056] synonym: "developmental tissue" RELATED [] synonym: "embryonic organism" EXACT [BILA:0000056] xref: AAO:0011035 xref: AEO:0000169 xref: BILA:0000056 xref: BSA:0000039 xref: BTO:0000379 xref: CALOHA:TS-0229 xref: EFO:0001367 xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 xref: FBbt:00000052 xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism xref: MAT:0000226 xref: MESH:D004622 xref: MIAA:0000019 xref: NCIT:C28147 xref: OGEM:000001 xref: OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA xref: SCTID:57991002 xref: UMLS:C0013935 {source="ncithesaurus:Embryo"} xref: VHOG:0001766 xref: Wikipedia:Embryo xref: XAO:0000113 xref: ZFA:0000103 is_a: UBERON:0000468 ! multicellular organism intersection_of: UBERON:0000468 ! multicellular organism intersection_of: existence_ends_with UBERON:0000068 ! embryo stage intersection_of: existence_starts_with UBERON:0000068 ! embryo stage relationship: existence_ends_with UBERON:0000068 ! embryo stage relationship: existence_starts_with UBERON:0000068 ! embryo stage property_value: depicted_by Wrinkledfrog:embryos.jpg xsd:anyURI property_value: external_ontology_notes "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" xsd:string {external_ontology="ZFA"} property_value: has_relational_adjective "embryonic" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/503 xsd:anyURI [Term] id: UBERON:0000923 name: germ layer def: "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." [https://github.com/obophenotype/uberon/issues/203, Wikipedia:Germ_layer] 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] subset: uberon_slim subset: vertebrate_core synonym: "embryonic germ layer" RELATED [] synonym: "embryonic germ layers" RELATED [] synonym: "embryonic tissue" BROAD [FMA:69069] synonym: "germinal layer" EXACT [ncithesaurus:Germinal_Layer] synonym: "primary germ layer" NARROW [GO:0001704, ZFA:0001122] xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 xref: FBbt:00000110 xref: FMA:69069 xref: GAID:1303 xref: MESH:A16.254.425 xref: NCIT:C12950 xref: NCIT:C54105 xref: TAO:0001122 xref: UMLS:C0920502 {source="ncithesaurus:Embryonic_Tissue"} xref: UMLS:C1708239 {source="ncithesaurus:Germinal_Layer"} xref: VHOG:0001223 xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest relationship: develops_from UBERON:0002532 ! epiblast (generic) relationship: only_in_taxon NCBITaxon:6072 relationship: part_of UBERON:0000922 ! embryo property_value: homology_notes "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0000924 name: ectoderm def: "Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue." [Wikipedia:Ectoderm] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "embryonic ectoderm" EXACT [VHOG:0000153] xref: AAO:0000137 xref: BILA:0000036 xref: BTO:0000315 xref: CALOHA:TS-0216 xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 xref: FBbt:00000111 xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 xref: MAT:0000173 xref: MESH:A16.254.425.273 xref: MIAA:0000173 xref: NCIT:C12703 xref: SCTID:362851007 xref: TAO:0000016 xref: UMLS:C0013574 {source="ncithesaurus:Ectoderm"} xref: VHOG:0000153 xref: Wikipedia:Ectoderm xref: XAO:0000001 xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: develops_from UBERON:0006601 ! presumptive ectoderm relationship: has_part CL:0000221 relationship: immediate_transformation_of UBERON:0006601 {source="Bgee:AN"} ! presumptive ectoderm property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png xsd:anyURI property_value: external_definition "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000137", ontology="AAO", source="AAO:EJS"} property_value: has_relational_adjective "ectodermal" xsd:string property_value: homology_notes "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0000925 name: endoderm def: "Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut." [Wikipedia:Endoderm] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "entoderm" RELATED DEPRECATED [DOI:10.5962/bhl.title.1013] xref: AAO:0000139 xref: BILA:0000038 xref: BTO:0000800 xref: CALOHA:TS-0273 xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 xref: FBbt:00000125 xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 xref: MESH:A16.254.425.407 xref: MIAA:0000175 xref: NCIT:C12706 xref: SCTID:362855003 xref: TAO:0000017 xref: UMLS:C0014144 {source="ncithesaurus:Endoderm"} xref: VHOG:0000154 xref: Wikipedia:Endoderm xref: XAO:0000090 xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: develops_from UBERON:0006595 ! presumptive endoderm relationship: has_part CL:0000223 relationship: immediate_transformation_of UBERON:0006595 {source="Bgee:AN"} ! presumptive endoderm property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png xsd:anyURI property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png xsd:anyURI property_value: has_relational_adjective "endodermal" xsd:string property_value: homology_notes "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0000926 name: mesoderm alt_id: UBERON:0003263 def: "The middle germ layer of the embryo, between the endoderm and ectoderm." [Wikipedia:Mesoderm] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "embryonic mesoderm" RELATED [VHOG:0000152] synonym: "entire mesoderm" RELATED [https://orcid.org/0000-0002-6601-2165, SCTID:362854004] synonym: "mesodermal mantle" RELATED [] xref: AAO:0000304 xref: BILA:0000037 xref: BTO:0000839 xref: CALOHA:TS-0623 xref: EFO:0001981 xref: EHDAA2:0001128 xref: EHDAA:124 xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 xref: FBbt:00000126 xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 xref: MESH:A16.254.425.660 xref: MIAA:0000174 xref: NCIT:C12750 xref: SCTID:362854004 xref: TAO:0000041 xref: UMLS:C0025485 {source="ncithesaurus:Mesoderm"} xref: VHOG:0000152 xref: Wikipedia:Mesoderm xref: XAO:0000050 xref: ZFA:0000041 is_a: UBERON:0000923 {notes="sometimes not considered primary"} ! germ layer relationship: develops_from UBERON:0006603 ! presumptive mesoderm relationship: has_part CL:0000222 relationship: immediate_transformation_of UBERON:0006603 {source="Bgee:AN"} ! presumptive mesoderm relationship: never_in_taxon NCBITaxon:6040 relationship: only_in_taxon NCBITaxon:6072 property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png xsd:anyURI property_value: external_definition "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000304", ontology="AAO", source="AAO:EJS"} property_value: has_relational_adjective "mesodermal" xsd:string property_value: homology_notes "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {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/"} property_value: taxon_notes "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" xsd:string {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} [Term] id: UBERON:0000927 name: mesectoderm def: "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." [FB:FBrf0089570] 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] subset: efo_slim subset: uberon_slim synonym: "MesEc" RELATED [] xref: EFO:0003336 xref: FBbt:00000136 xref: MAT:0000243 xref: MIAA:0000243 is_a: UBERON:0000923 ! germ layer relationship: adjacent_to UBERON:0000924 ! ectoderm property_value: has_relational_adjective "mesectodermal" xsd:string [Term] id: UBERON:0000928 name: obsolete embryonic segment synonym: "segment - embryonic" EXACT [] is_obsolete: true consider: FBbt:00000154 consider: MAT:0000244 consider: MIAA:0000244 [Term] id: UBERON:0000929 name: pharyngeal branch of vagus nerve def: "Motor nerve of the pharynx, arises from the upper part of the ganglion nodosum, and consists principally of filaments from the cranial portion of the accessory nerve." [Wikipedia:Pharyngeal_part_of_vagus_nerve] subset: uberon_slim synonym: "pharyngeal branch" EXACT [FMA:6234] synonym: "pharyngeal branch of inferior vagal ganglion" EXACT [FMA:6234] synonym: "pharyngeal branch of vagus" EXACT [FMA:6234] synonym: "ramus pharyngealis nervi vagalis" EXACT [FMA:6234] synonym: "ramus pharyngeus" EXACT LATIN [FMA:6234, FMA:TA] synonym: "ramus pharyngeus" EXACT [FMA:TA] synonym: "ramus pharyngeus nervi vagi" RELATED LATIN [Wikipedia:Pharyngeal_part_of_vagus_nerve] synonym: "tenth cranial nerve pharyngeal branch" EXACT [FMA:6234] synonym: "vagal pharyngeal branch" EXACT [FMA:6234] synonym: "vagus nerve pharyngeal branch" EXACT [FMA:6234] xref: FMA:6234 xref: SCTID:280298006 xref: Wikipedia:Pharyngeal_part_of_vagus_nerve is_a: UBERON:0011779 ! nerve of head region relationship: branching_part_of UBERON:0001759 ! vagus nerve relationship: extends_fibers_into UBERON:0005363 ! inferior vagus X ganglion relationship: part_of UBERON:0001005 ! respiratory airway relationship: part_of UBERON:0001759 ! vagus nerve property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png xsd:anyURI [Term] id: UBERON:0000930 name: stomodeum def: "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." [http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/326, Wikipedia:Stomodeum] subset: grouping_class subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "mouth pit" RELATED [EMAPA:16263] synonym: "mouth primordium" EXACT [XAO:0000269] synonym: "oral ectoderm" RELATED [ZFA:0001290, ZFIN:ZDB-PUB-100726-23] synonym: "oral pit" RELATED [EMAPA:16263] synonym: "primitive oral cavity" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "stomatodeum" EXACT [Wikipedia:Stomodeum] synonym: "stomodaeum" EXACT [] synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 xref: FBbt:00000439 xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 xref: TGMA:0000135 xref: UMLS:C1514977 {source="ncithesaurus:Stomodeum"} xref: Wikipedia:Stomodeum xref: XAO:0000269 xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube relationship: only_in_taxon NCBITaxon:6072 relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png xsd:anyURI property_value: editor_note "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" xsd:string property_value: external_definition "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001290", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "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" xsd:string {source="MP:0012522", taxon="NCBITaxon:40674"} property_value: has_relational_adjective "stomodeal" xsd:string property_value: taxon_notes "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." xsd:string [Term] id: UBERON:0000931 name: proctodeum def: "Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract." [https://github.com/obophenotype/uberon/issues/685, https://sourceforge.net/p/fbbtdv/tickets/52, ZFA:0000066] subset: uberon_slim synonym: "amnioproctodeal invagination" NARROW [FBbt:00000123] synonym: "anal pit" RELATED [VHOG:0000139] synonym: "anus porus" RELATED [XAO:0001019] synonym: "embryonic proctodaeum" EXACT [] synonym: "proctodaeum" EXACT [] xref: AAO:0011087 xref: EHDAA2:0000121 xref: EMAPA:25038 xref: FBbt:00000123 xref: NCIT:C34278 xref: TAO:0000066 xref: UMLS:C0231054 {source="ncithesaurus:Proctodeum"} xref: VHOG:0000139 xref: Wikipedia:Proctodeum xref: XAO:0001019 xref: ZFA:0000066 is_a: UBERON:0016566 {source="EHDAA2"} ! pit relationship: dc-contributor https://github.com/ANiknejad relationship: dc-contributor https://github.com/cmungall relationship: dc-contributor https://github.com/dosumis relationship: dc-contributor https://github.com/mmc46 relationship: develops_from UBERON:0000924 ! ectoderm relationship: has_potential_to_develop_into UBERON:0001353 ! anal region relationship: located_in UBERON:0012469 {source="EHDAA2"} ! external anal region relationship: only_in_taxon NCBITaxon:6072 relationship: part_of UBERON:0007026 ! presumptive gut property_value: editor_note "removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male." xsd:string property_value: external_definition "An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000066", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011087", ontology="AAO", source="ZFA:0000066"} property_value: has_relational_adjective "proctodeal" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/685 xsd:anyURI [Term] id: UBERON:0000932 name: obsolete ventral longitudinal muscle comment: originally unified on basis of terminological similarity is_obsolete: true consider: FBbt:00000482 consider: WBbt:0005814 [Term] id: UBERON:0000933 name: pharyngeal muscle def: "A muscle that acts on the pharynx[WP, vetted]." [https://orcid.org/0000-0002-6601-2165, Wikipedia:Pharyngeal_muscles] 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] subset: efo_slim subset: pheno_slim synonym: "branchial muscle" EXACT [ZFA:0000172] synonym: "branchial muscles" RELATED PLURAL [TAO:0000172] synonym: "muscle of pharynx" EXACT [] synonym: "muscle organ of pharynx" EXACT [OBOL:automatic] synonym: "musculi pharyngis" RELATED LATIN [Wikipedia:Pharyngeal_muscles] synonym: "musculus pharyngis" RELATED [BTO:0001048] synonym: "pharynx muscle" EXACT [] synonym: "pharynx muscle organ" EXACT [OBOL:automatic] synonym: "tunica muscularis pharyngis" RELATED LATIN [Wikipedia:Pharyngeal_muscles] xref: BTO:0001048 xref: EFO:0003504 xref: EMAPA:18963 xref: FMA:46619 xref: GAID:154 xref: MA:0001797 xref: MESH:D010609 xref: NCIT:C13075 xref: SCTID:244798004 xref: TAO:0000172 xref: UMLS:C0031346 {source="ncithesaurus:Pharyngeal_Muscle"} xref: Wikipedia:Pharyngeal_muscles xref: ZFA:0000172 is_a: UBERON:0001630 ! muscle organ intersection_of: UBERON:0001630 ! muscle organ intersection_of: part_of UBERON:0004467 ! musculature of pharynx relationship: contributes_to_morphology_of UBERON:0001015 ! musculature relationship: fma_set_term FMA:67169 relationship: part_of UBERON:0004467 ! musculature of pharynx property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/35/Gray1030.png xsd:anyURI property_value: external_definition "A pharyngeal muscle is any muscle that forms part of the pharynx[GO]." xsd:string {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"} [Term] id: UBERON:0000934 name: ventral nerve cord def: "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]." [BTO:0002328, GO:0007419, WB:Paper00000938, Wikipedia:Ventral_nerve_cord] subset: efo_slim subset: uberon_slim synonym: "ventral cord" EXACT [GO:0007419] xref: BTO:0002328 xref: EFO:0000896 xref: FBbt:00001102 xref: MAT:0000339 xref: MIAA:0000339 xref: NLX:146329 xref: WBbt:0005829 xref: Wikipedia:Ventral_nerve_cord is_a: UBERON:0005053 ! primary nerve cord intersection_of: UBERON:0005053 ! primary nerve cord intersection_of: intersects_midsagittal_plane_of UBERON:0013235 ! ventrum relationship: intersects_midsagittal_plane_of UBERON:0013235 ! ventrum relationship: never_in_taxon NCBITaxon:7711 relationship: part_of UBERON:0013235 ! ventrum property_value: external_definition "A cluster of neurons that extends posteriorly from the embryonic and larval brain and is surrounded by a connective tissue sheath." xsd:string {source="FBbt:00001102"} property_value: taxon_notes "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." xsd:string [Term] id: UBERON:0000935 name: anterior commissure def: "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)." [BTO:0002169] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "AC" RELATED ABBREVIATION [NLX:144088] synonym: "anterior cerebral commissure" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "anterior commissural nucleus" RELATED [BAMS:AC] synonym: "commissura anterior" RELATED LATIN [Wikipedia:Anterior_commissure] synonym: "commissura anterior cerebri" EXACT LATIN [NeuroNames:205] synonym: "commissura rostral" RELATED [] synonym: "commissura rostralis" EXACT [] synonym: "paleocortical commissure" RELATED [NeuroNames:205] synonym: "precommisure" RELATED [Wikipedia:Anterior_commisure] synonym: "rostral commissure" RELATED [NeuroNames:205] xref: BAMS:AC xref: BAMS:Ac xref: BAMS:ac xref: BAMS:AG xref: BIRNLEX:1557 xref: BM:Tel-AC xref: BTO:0002169 xref: DHBA:10559 xref: DMBA:17751 xref: EMAPA:19038 xref: FMA:61961 xref: HBA:9221 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=205 xref: MA:0002722 xref: NCIT:C32086 xref: NLX:144088 xref: SCTID:279313001 xref: SCTID:369119009 xref: TAO:0001108 xref: UMLS:C0152335 {source="BIRNLEX:1557"} xref: UMLS:C0152335 {source="ncithesaurus:Anterior_Commissure"} xref: VHOG:0001558 xref: Wikipedia:Anterior_commissure xref: ZFA:0001108 is_a: UBERON:0002473 {source="FMA", source="MA"} ! intercerebral commissure is_a: UBERON:0005341 {source="MP"} ! ventral commissure disjoint_from: UBERON:0000936 {source="lexical"} ! posterior commissure property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/b/b4/Gray744.png xsd:anyURI property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000936 name: posterior commissure def: "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]." [Wikipedia:Posterior_commissure, ZFA:0000320] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "caudal commissure" EXACT [FMA:62072, ZFA:0000320] synonym: "commissura epithalami" RELATED LATIN [NeuroNames:484] synonym: "commissura epithalamica" RELATED LATIN [NeuroNames:484] synonym: "commissura posterior" RELATED LATIN [Wikipedia:Posterior_commissure] synonym: "epithalamic commissure" EXACT [FMA:62072] synonym: "posterior commissure (Lieutaud)" RELATED [NeuroNames:484] xref: BAMS:PC xref: BAMS:pc xref: BIRNLEX:1026 xref: BM:MB-Tec-PC xref: DHBA:10567 xref: DMBA:17787 xref: EMAPA:35695 xref: FMA:62072 xref: HBA:9229 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=484 {source="BIRNLEX:1026"} xref: MA:0002743 xref: MBA:158 xref: NCIT:C33356 xref: TAO:0000320 xref: UMLS:C0152327 {source="BIRNLEX:1026"} xref: UMLS:C0152327 {source="ncithesaurus:Posterior_Commissure"} xref: Wikipedia:Posterior_commissure xref: ZFA:0000320 is_a: UBERON:0011590 ! commissure of diencephalon intersection_of: UBERON:0001020 ! nervous system commissure intersection_of: connects UBERON:0014450 ! pretectal nucleus relationship: connects UBERON:0014450 ! pretectal nucleus relationship: only_in_taxon NCBITaxon:7742 relationship: part_of UBERON:0003931 {source="FMA"} ! diencephalic white matter property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/d/d7/Gray715.png xsd:anyURI property_value: editor_note "add connects relationships and check these outside mammalia" xsd:string property_value: external_ontology_notes "part_of brainstem in MA; midbrain tectum in NIF" xsd:string {external_ontology="MA"} [Term] id: UBERON:0000937 name: obsolete proneural cluster comment: obsoleted because inconsistencies arise due to ZFA term being both embryonic and extraembryonic synonym: "proneural clusters" RELATED [ZFA:0000068] is_obsolete: true consider: FBbt:00001135 consider: ZFA:0000068 [Term] id: UBERON:0000939 name: imaginal disc def: "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." [Wikipedia:Imaginal_disc] subset: uberon_slim synonym: "imaginal disk" RELATED [] xref: BTO:0004658 xref: FBbt:00001761 xref: MAT:0000064 xref: MIAA:0000064 xref: Wikipedia:Imaginal_disc is_a: UBERON:0007499 {source="FBbt text definition"} ! epithelial sac relationship: only_in_taxon NCBITaxon:50557 {source="Wikipedia"} relationship: part_of UBERON:0002548 ! larva [Term] id: UBERON:0000941 name: cranial nerve II def: "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]." [ISBN:0471209627, ISBN:0471888893] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "02 optic nerve" EXACT [AAO:0010345] synonym: "2n" BROAD ABBREVIATION [BIRNLEX:1640, NIFSTD:NeuroNames_abbrevSource] synonym: "CN-II" RELATED [ZFA:0000435] synonym: "cranial II" EXACT [] synonym: "nerve II" RELATED [NeuroNames:289] synonym: "nervus opticus" EXACT LATIN [] synonym: "nervus opticus [II]" EXACT LATIN [FMA:50863, FMA:TA] synonym: "optic" RELATED [TAO:0000435] synonym: "optic II" EXACT [EHDAA2:0001313] synonym: "optic II nerve" EXACT [EHDAA2:0001313] synonym: "optic nerve" BROAD SENSU [FMA:50863, ZFA:0000435] synonym: "optic nerve [II]" EXACT [] synonym: "second cranial nerve" EXACT [] xref: AAO:0010345 xref: BAMS:2n xref: BAMS:IIn xref: BAMS:nII xref: BIRNLEX:1640 xref: CALOHA:TS-0713 xref: DHBA:15544 xref: EFO:0004258 xref: EHDAA2:0001313 xref: EHDAA:6788 xref: EMAPA:17575 xref: FMA:50863 xref: GAID:831 xref: HBA:9307 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=289 {source="BIRNLEX:1640"} xref: MA:0001097 xref: MBA:848 xref: MESH:D009900 xref: NCIT:C12761 xref: OpenCyc:Mx4rvVjLm5wpEbGdrcN5Y29ycA xref: SCTID:180938001 xref: TAO:0000435 xref: UMLS:C0029130 {source="BIRNLEX:1640"} xref: UMLS:C0029130 {source="ncithesaurus:Optic_Nerve"} xref: VHOG:0000543 xref: Wikipedia:Optic_nerve xref: XAO:0000188 xref: ZFA:0000435 is_a: CARO:0001001 is_a: UBERON:0011215 ! central nervous system cell part cluster is_a: UBERON:0034713 ! cranial neuron projection bundle intersection_of: UBERON:0034713 ! cranial neuron projection bundle intersection_of: extends_fibers_into UBERON:0000959 ! optic chiasma intersection_of: innervates UBERON:0000966 ! retina relationship: develops_from UBERON:0003902 {source="EHDAA2"} ! retinal neural layer relationship: extends_fibers_into UBERON:0000959 ! optic chiasma relationship: extends_fibers_into UBERON:0003098 ! optic stalk relationship: innervates UBERON:0000966 ! retina relationship: part_of UBERON:0001017 ! central nervous system relationship: part_of UBERON:0002104 ! visual system property_value: editor_note "Do not classify under 'cranial nerve', as this is not a true nerve - should be classified as evaginated sensory afferent[ISBN:0471888893]" xsd:string property_value: external_definition "A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000435", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "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]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010345", ontology="AAO", source="AAO:EJS"} property_value: external_ontology_notes "(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" xsd:string {external_ontology="MA"} property_value: homology_notes "(...) 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]" xsd:string {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/"} [Term] id: UBERON:0000942 name: frontal nerve (branch of ophthalmic) def: "The frontal nerve is the largest branch of the ophthalmic, and may be regarded, both from its size and direction, as the continuation of the nerve. It enters the orbit through the supraorbital foramen, and runs forward between the Levator palpebræ superioris and the periosteum. Midway between the apex and base of the orbit it divides into two branches, supratrochlear nerve and supraorbital nerve. [WP,unvetted]." [Wikipedia:Frontal_nerve] subset: uberon_slim synonym: "frontal nerve" EXACT [FMA:52638] synonym: "nervus frontalis" RELATED LATIN [Wikipedia:Frontal_nerve] xref: FMA:52638 xref: NCIT:C32638 xref: SCTID:280219004 xref: UMLS:C0228712 {source="ncithesaurus:Frontal_Nerve"} xref: Wikipedia:Frontal_nerve is_a: UBERON:0011779 ! nerve of head region relationship: branching_part_of UBERON:0000348 {source="FMA"} ! ophthalmic nerve relationship: part_of UBERON:0000348 ! ophthalmic nerve property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/4/45/Gray787.png xsd:anyURI [Term] id: UBERON:0000943 name: obsolete labial sensillum is_obsolete: true consider: FBbt:00002721 consider: WBbt:0005107 [Term] id: UBERON:0000944 name: obsolete dorsal branch synonym: "dorsal vein" EXACT [] synonym: "ramus dorsalis" EXACT LATIN [FMA:76733, FMA:TA] is_obsolete: true consider: FBbt:00003051 consider: FMA:76733 [Term] id: UBERON:0000945 name: stomach def: "An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium." [https://orcid.org/0000-0002-6601-2165, ISBN:0073040584, Wikipedia:Stomach] subset: efo_slim subset: major_organ subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "anterior intestine" RELATED [] synonym: "gaster" RELATED [BTO:0001307] synonym: "mesenteron" RELATED [] synonym: "stomach chamber" NARROW [] synonym: "ventriculus" RELATED LATIN [Wikipedia:Stomach] xref: AAO:0000579 xref: ANISEED:1235297 xref: BTO:0001307 xref: CALOHA:TS-0980 xref: EFO:0000837 xref: EHDAA2:0001915 xref: EHDAA:2993 xref: EMAPA:17021 xref: EV:0100070 xref: FMA:7148 xref: GAID:293 xref: galen:Stomach xref: MA:0000353 xref: MAT:0000051 xref: MESH:A03.492.766 xref: MIAA:0000051 xref: NCIT:C12391 xref: OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA xref: SCTID:181246003 xref: TAO:0002121 xref: UMLS:C0038351 {source="ncithesaurus:Stomach"} xref: VHOG:0000408 xref: Wikipedia:Stomach xref: XAO:0000128 is_a: UBERON:0004921 {source="cjm"} ! subdivision of digestive tract is_a: UBERON:0010039 {source="cjm"} ! food storage organ relationship: capable_of GO:0001696 {evidence="ISBN:0486692132"} relationship: contributes_to_morphology_of UBERON:0001007 ! digestive system relationship: never_in_taxon NCBITaxon:7864 {source="Wikipedia"} relationship: never_in_taxon NCBITaxon:7878 {source="Wikipedia"} relationship: never_in_taxon NCBITaxon:7955 {source="ZFA"} relationship: never_in_taxon NCBITaxon:9259 {source="Wikipedia"} relationship: only_in_taxon NCBITaxon:7742 {source="Wikipedia"} relationship: only_in_taxon NCBITaxon:7776 {notes="absent in lampreys and hagfishes", source="ISBN:0073040584"} relationship: part_of UBERON:0001041 ! foregut property_value: depicted_by Stomach:diagram.svg xsd:anyURI property_value: external_definition "Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000579", ontology="AAO", source="AAO:EJS"} property_value: homology_notes "It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]" xsd:string {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/"} property_value: taxon_notes "We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa" xsd:string {source="WP:Stomach#In_other_animals"} [Term] id: UBERON:0000946 name: cardial valve def: "A membranous fold of the heart that prevents reflux of fluid" [MESH:A07.541.510, MP:0000285, PMID:7926784] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "cardiac valve" RELATED [GO:0003170] synonym: "heart valve" EXACT [] synonym: "heart valve" RELATED [XAO:0004126] synonym: "heart valves" RELATED [] synonym: "stomodaeal valve" RELATED [] synonym: "valve of heart" EXACT [] synonym: "valvule" RELATED [] xref: BTO:0000564 xref: EMAPA:17869 xref: EV:0100024 xref: FMA:7110 xref: GAID:176 xref: galen:HeartValve xref: MA:0000086 xref: MESH:D006351 xref: NCIT:C12729 xref: OpenCyc:Mx4rv8oyuJwpEbGdrcN5Y29ycA xref: SCTID:181285005 xref: TAO:0005065 xref: UMLS:C0018826 {source="ncithesaurus:Cardiac_Valve"} xref: VHOG:0000818 xref: Wikipedia:Cardiac_valve xref: XAO:0004126 xref: ZFA:0005065 is_a: UBERON:0003978 ! valve is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure disjoint_from: UBERON:0004754 ! foramen ovale of heart relationship: develops_from UBERON:0002062 {source="PMID:15797462"} ! endocardial cushion relationship: part_of UBERON:0000948 ! heart property_value: external_definition "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000818", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/heart+valve"} property_value: homology_notes "Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human.[well established][VHOG]" xsd:string {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/"} property_value: terminology_notes "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" xsd:string [Term] id: UBERON:0000947 name: aorta def: "The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation" [http://orcid.org/0000-0002-6601-2165, ISBN:0-683-40008-8, MESH:A07.231.114.056, MP:0000272, Wikipedia:Aorta] subset: efo_slim subset: grouping_class subset: pheno_slim subset: uberon_slim synonym: "arteria maxima" RELATED LATIN [Wikipedia:Aorta] synonym: "dorsal aorta" NARROW SENSU [Wikipedia:Aorta#In_other_animals, ZFA:0000014] synonym: "trunk of aortic tree" EXACT [] synonym: "trunk of systemic arterial tree" EXACT [] xref: AAO:0010213 xref: BTO:0000135 xref: CALOHA:TS-0046 xref: EFO:0000265 xref: EMAPA:18601 xref: EV:0100027 xref: FMA:3734 xref: GAID:469 xref: galen:Aorta xref: MA:0000062 xref: MAT:0000035 xref: MESH:D001011 xref: MIAA:0000035 xref: NCIT:C12669 xref: OpenCyc:Mx4rvVjvTpwpEbGdrcN5Y29ycA xref: SCTID:181298001 xref: UMLS:C0003483 {source="ncithesaurus:Aorta"} xref: VHOG:0001523 xref: Wikipedia:Aorta xref: XAO:0003010 is_a: UBERON:0003509 {source="MA"} ! arterial blood vessel is_a: UBERON:0003519 ! thoracic cavity blood vessel is_a: UBERON:0013768 ! great vessel of heart relationship: located_in UBERON:0002224 {source="MA-modified"} ! thoracic cavity relationship: part_of UBERON:0010191 {source="EHDAA2"} ! aortic system property_value: depicted_by Aorta:scheme.jpg xsd:anyURI property_value: editor_note "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." xsd:string {source="WP"} property_value: external_definition "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]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010213", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "aortic" xsd:string property_value: homology_notes "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]" xsd:string {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/"} property_value: taxon_notes "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" xsd:string [Term] id: UBERON:0000948 name: heart def: "A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Heart] 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 subset: efo_slim subset: major_organ subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "branchial heart" NARROW SENSU [] synonym: "cardium" RELATED [EMAPA:16105] synonym: "chambered heart" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "vertebrate heart" EXACT [] xref: AAO:0010210 xref: BILA:0000020 xref: BTO:0000562 xref: CALOHA:TS-0445 xref: EFO:0000815 xref: EHDAA2:0000738 xref: EHDAA:420 xref: EMAPA:16105 xref: EV:0100018 xref: FMA:7088 xref: GAID:174 xref: galen:Heart xref: MA:0000072 xref: MAT:0000036 xref: MESH:D006321 xref: MIAA:0000036 xref: NCIT:C12727 xref: OpenCyc:Mx4rvVjvDpwpEbGdrcN5Y29ycA xref: SCTID:302509004 xref: TAO:0000114 xref: UMLS:C0018787 {source="ncithesaurus:Heart"} xref: VHOG:0000276 xref: Wikipedia:Heart xref: XAO:0000064 xref: ZFA:0000114 is_a: UBERON:0007100 ! primary circulatory organ intersection_of: UBERON:0007100 ! primary circulatory organ intersection_of: has_part UBERON:0004151 ! cardiac chamber relationship: contributes_to_morphology_of UBERON:0004535 ! cardiovascular system relationship: develops_from UBERON:0004141 ! heart tube relationship: has_developmental_contribution_from UBERON:0002342 {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neural crest relationship: has_part UBERON:0004151 ! cardiac chamber relationship: never_in_taxon NCBITaxon:6239 relationship: never_in_taxon NCBITaxon:7227 relationship: only_in_taxon NCBITaxon:7742 relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium property_value: axiom_lost_from_external_ontology "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO"} property_value: external_definition "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000114", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "cardiac" xsd:string property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000949 name: endocrine system def: "Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity." [NLM:endocrine+system, Wikipedia:Endocrine_system] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "endocrine glandular system" EXACT [EHDAA2:0002224] synonym: "endocrine system" EXACT [] synonym: "systema endocrinum" EXACT [] xref: AAO:0010279 xref: CALOHA:TS-1301 xref: EFO:0002969 xref: EHDAA2:0002224 xref: EMAPA:35306 xref: EV:0100128 xref: FBbt:00005068 xref: FMA:9668 xref: GAID:439 xref: MA:0000012 xref: MESH:D004703 xref: NCIT:C12705 xref: SCTID:278876000 xref: TAO:0001158 xref: UMLS:C0014136 {source="ncithesaurus:Endocrine_System"} xref: VHOG:0000098 xref: Wikipedia:Endocrine_system xref: XAO:0000158 xref: ZFA:0001158 is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of GO:0050886 disjoint_from: UBERON:0000990 ! reproductive system disjoint_from: UBERON:0001004 ! respiratory system disjoint_from: UBERON:0001007 ! digestive system disjoint_from: UBERON:0001008 ! renal system disjoint_from: UBERON:0001009 ! circulatory system disjoint_from: UBERON:0001016 ! nervous system disjoint_from: UBERON:0001033 ! gustatory system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002294 ! biliary system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0050886 relationship: composed_primarily_of UBERON:0002368 ! endocrine gland relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: only_in_taxon NCBITaxon:6072 property_value: external_definition "Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010279", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "endocrine" xsd:string property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000950 name: gracilis def: "The most superficial muscle on the medial side of the thigh. It is thin and flattened, broad above, narrow and tapering below. It arises by a thin aponeurosis from the anterior margins of the lower half of the symphysis pubis and the upper half of the pubic arch." [Wikipedia:Gracilis_muscle] subset: uberon_slim synonym: "gracilis muscle" EXACT [BTO:0000536] synonym: "musculus gracilis" EXACT LATIN [Wikipedia:Gracilis_muscle] xref: BTO:0000536 xref: EMAPA:36231 xref: FMA:43882 xref: galen:Gracilis xref: MA:0002311 xref: NCIT:C52935 xref: OpenCyc:Mx4rv7If8pwpEbGdrcN5Y29ycA xref: SCTID:181689005 xref: UMLS:C0224439 {source="ncithesaurus:Gracilis"} xref: Wikipedia:Gracilis_muscle is_a: UBERON:0004252 ! hindlimb stylopod muscle is_a: UBERON:0011144 {source="Wikipedia"} ! adductor muscle of hip relationship: has_muscle_insertion UBERON:0000979 {notes="pes anserinus", source="dbpedia"} ! tibia relationship: has_muscle_origin UBERON:0001272 {notes="ischiopubic ramus", source="dbpedia"} ! innominate bone relationship: part_of UBERON:0000376 ! hindlimb stylopod property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/e2/Anterior_Hip_Muscles_2.PNG xsd:anyURI property_value: editor_note "AAO has minor and major gracilis, which merge together, attaching the pelvic rim to the tibiofibula - this could be grouped with the mammalian gracilis at some level; note the current insertion site is 'tibia' which would be modified for amphibian tibiafibula" xsd:string property_value: taxon_notes "A&P heads in rat, single head in humans[DOI:10.1002/ar.22919]" xsd:string [Term] id: UBERON:0000951 name: rotator muscle of the vertebral column def: "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." [http://medical-dictionary.thefreedictionary.com/rotator+muscle] synonym: "rotator muscle" BROAD [FMA:23081] xref: FMA:23081 xref: SCTID:244872002 is_a: CARO:0000003 is_a: UBERON:0001630 ! muscle organ is_a: UBERON:0005174 ! dorsal region element intersection_of: UBERON:0001630 ! muscle organ intersection_of: has_muscle_insertion UBERON:0001076 ! neural spine intersection_of: has_muscle_origin UBERON:0001077 ! transverse process of vertebra intersection_of: part_of UBERON:0001137 ! dorsum relationship: has_muscle_insertion UBERON:0001076 ! neural spine relationship: has_muscle_origin UBERON:0001077 ! transverse process of vertebra relationship: part_of UBERON:0001137 ! dorsum [Term] id: UBERON:0000952 name: obsolete adductor muscle comment: obsoleted as it conflated a generic functional grouping with a specific group of muscles in the leg/hip is_obsolete: true consider: UBERON:0011144 consider: UBERON:0011145 [Term] id: UBERON:0000953 name: obsolete visceral muscle def: "involuntary non-striated muscle." [Wikipedia:Smooth_muscle] synonym: "adult visceral muscle" RELATED [] synonym: "smooth muscle" EXACT [] xref: Wikipedia:Smooth_muscle property_value: terminology_notes "GO uses visceral and smooth interchangeably" xsd:string is_obsolete: true [Term] id: UBERON:0000954 name: obsolete intestine muscle def: "intestinal muscle cell, attach to intestine and body wall anterior to anus" [WB:Paper00000653] subset: uberon_slim synonym: "intestinal muscle" EXACT [] is_obsolete: true consider: FBbt:00003537 consider: WBbt:0005796 [Term] id: UBERON:0000955 name: brain def: "The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]." [https://github.com/obophenotype/uberon/issues/300, Wikipedia:Brain] subset: cumbo subset: efo_slim subset: major_organ subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "encephalon" RELATED [BTO:0000142] synonym: "suprasegmental levels of nervous system" RELATED [NeuroNames:21] synonym: "suprasegmental structures" RELATED [NeuroNames:21] synonym: "synganglion" RELATED [] synonym: "the brain" RELATED [NeuroNames:21] xref: AAO:0010478 xref: ABA:Brain xref: BAMS:Br xref: BAMS:Brain xref: BILA:0000135 xref: BIRNLEX:796 xref: BTO:0000142 xref: CALOHA:TS-0095 xref: DHBA:10155 xref: EFO:0000302 xref: EHDAA2:0000183 xref: EHDAA:2641 xref: EHDAA:6485 xref: EMAPA:16894 xref: EV:0100164 xref: FBbt:00005095 xref: FMA:50801 xref: GAID:571 xref: galen:Brain xref: HBA:4005 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 {source="BIRNLEX:796"} xref: MA:0000168 xref: MAT:0000098 xref: MBA:8 xref: MBA:997 xref: MESH:D001921 xref: MIAA:0000098 xref: NCIT:C12439 xref: OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA xref: PBA:3999 xref: SCTID:258335003 xref: TAO:0000008 xref: UMLS:C0006104 {source="ncithesaurus:Brain"} xref: UMLS:C0006104 {source="BIRNLEX:796"} xref: UMLS:C1269537 {source="BIRNLEX:796"} xref: VHOG:0000157 xref: Wikipedia:Brain xref: XAO:0000010 xref: ZFA:0000008 is_a: UBERON:0000062 {source="GO"} ! organ relationship: capable_of GO:0050890 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} relationship: composed_primarily_of CL:0002319 relationship: contributes_to_morphology_of UBERON:0001016 ! nervous system relationship: dc-contributor https://github.com/cmungall relationship: develops_from UBERON:0001049 {gci_relation="part_of", gci_filler="NCBITaxon:7711"} ! neural tube relationship: develops_from UBERON:0006238 ! future brain relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: immediate_transformation_of UBERON:0006238 {source="Bgee:AN"} ! future brain relationship: in_anterior_side_of UBERON:0000468 ! multicellular organism relationship: part_of UBERON:0001017 {source="FMA"} ! central nervous system property_value: editor_note "requires review for applicability to invertebrate structures, e.g. synganglion" xsd:string property_value: external_definition "Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000008", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010478", ontology="AAO", source="AAO:BJB"} property_value: external_definition "The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} property_value: homology_notes "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0000956 name: cerebral cortex def: "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." [BIRNLEX:1494] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "brain cortex" RELATED [BTO:0000233] synonym: "cortex cerebralis" RELATED LATIN [NeuroNames:39] synonym: "cortex cerebri" RELATED LATIN [Wikipedia:Cerebral_cortex] synonym: "cortex of cerebral hemisphere" EXACT [BTO:0000233, FMA:61830] synonym: "cortical plate (areas)" RELATED [NeuroNames:39] synonym: "cortical plate (CTXpl)" RELATED [NeuroNames:39] synonym: "pallium of the brain" RELATED [BTO:0000233] xref: BAMS:C xref: BAMS:Cerebral_cortex xref: BAMS:CTX xref: BAMS:Cx xref: BIRNLEX:1494 xref: BM:Tel-Cx xref: BTO:0000233 xref: CALOHA:TS-0091 xref: DHBA:10159 xref: EFO:0000328 xref: EHDAA2:0000234 xref: EHDAA:5464 xref: EMAPA:17544 xref: EV:0100166 xref: FMA:61830 xref: GAID:629 xref: HBA:4008 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=39 {source="BIRNLEX:1494"} xref: MA:0000185 xref: MAT:0000108 xref: MBA:688 xref: MESH:A08.186.211.730.885.213 xref: MIAA:0000108 xref: NCIT:C12443 xref: PBA:128011354 xref: SCTID:362880003 xref: UMLS:C0007776 {source="BIRNLEX:1494"} xref: UMLS:C0007776 {source="ncithesaurus:Cortex"} xref: VHOG:0000722 xref: Wikipedia:Cerebral_cortex is_a: UBERON:0016548 {source="FMA"} ! central nervous system gray matter layer relationship: capable_of_part_of GO:0007613 {source="Wikipedia"} relationship: contributes_to_morphology_of UBERON:0001893 ! telencephalon relationship: has_developmental_contribution_from UBERON:0004035 ! cortical subplate relationship: has_developmental_contribution_from UBERON:0005343 ! cortical plate relationship: part_of UBERON:0000203 {source="GO", source="ISBN:0471888893"} ! pallium relationship: part_of UBERON:0005401 {source="FMA", source="MA"} ! cerebral hemisphere gray matter relationship: present_in_taxon NCBITaxon:117569 property_value: curator_notes "We follow NIFSTD in defining cerebral cortex and including both neocortex and hippocampal formation (DG+hippocampus)." xsd:string property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/7/7b/Cerebral_Cortex_location.jpg xsd:anyURI property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/9/9a/Brainmaps-macaque-hippocampus.jpg xsd:anyURI property_value: external_definition "The cerebral cortex is a structure within the brain that plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It constitutes the outermost layer of the cerebrum. In preserved brains, it has a grey color, hence the name 'grey matter'. Grey matter is formed by neurons and their unmyelinated fibers, whereas the white matter below the grey matter of the cortex is formed predominantly by myelinated axons interconnecting different regions of the central nervous system. The human cerebral cortex is 2-4 mm (0.08-0.16 inches) thick. The surface of the cerebral cortex is folded in large mammals, such that more than two-thirds of the cortical surface is buried in the grooves, called 'sulci. ' The phylogenetically most recent part of the cerebral cortex, the neocortex, also called isocortex, is differentiated into six horizontal layers; the more ancient part of the cerebral cortex, the hippocampus (also called archicortex), has at most three cellular layers, and is divided into subfields. Relative variations in thickness or cell type (among other parameters) allow us to distinguish between different neocortical architectonic fields. The geometry of at least some of these fields seems to be related to the anatomy of the cortical folds, and, for example, layers in the upper part of the cortical ridges seem to be more clearly differentiated than in its deeper parts. [WP,unvetted][Wikipedia:Cerebral_cortex]." xsd:string {source="Wikipedia:Cerebral_cortex"} property_value: homology_notes "Migration of neurons from the basal or striatal portions of the anterior part of the neural tube occurs to varying degrees in different vertebrate classes, but a true cerebral cortex is generally acknowledged to have made its first appearance in reptiles. The definition can be unambiguous, since 'cortex' simply implies the existence of a surface neuronal layer with an overlying 'zonal lamina' or 'molecular' layer containing dendrites and axons, which is separated from the underlying basal 'matrix' by white matter. Although reptilian cerebral cortex does indeed fulfill these conditions in certain locations, the separation from striatal structures is often indistinct, so that it may even be argued that some primitive dipnoans possess a pallium or cortex. Nevertheless, an extensive laminated layer separated by underlying white matter is well represented only in reptiles and mammals.[well established][VHOG]" xsd:string {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/"} property_value: taxon_notes "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]" xsd:string [Term] id: UBERON:0000957 name: lamina def: "Any thin layer or plate." [Wikipedia:Lamina_of_the_vertebral_arch] subset: non_informative subset: uberon_slim subset: upper_level synonym: "laminar tissue" EXACT [] xref: Wikipedia:Lamina_of_the_vertebral_arch is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: has_quality PATO:0002124 relationship: has_quality PATO:0002124 property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png xsd:anyURI property_value: editor_note "TODO - merge with cell layer?" xsd:string property_value: has_relational_adjective "laminar" xsd:string [Term] id: UBERON:0000958 name: medulla of organ def: "Middle part of an organ, surrounded by the cortex." [http://orcid.org/0000-0002-6601-2165] subset: upper_level synonym: "medulla" EXACT [FMA:61108] xref: FMA:61108 xref: galen:Medulla is_a: UBERON:0000471 ! compound organ component relationship: only_in_taxon NCBITaxon:6072 relationship: surrounded_by UBERON:0001851 ! cortex property_value: curator_notes "this class is used in a very general sense" xsd:string property_value: has_relational_adjective "medullary" xsd:string [Term] id: UBERON:0000959 name: optic chiasma def: "A decussation of the diencephalon where the fibers of the optic nerve cross" [http://orcid.org/0000-0002-6601-2165, MGI:llw2, MP:0009770, Wikipedia:Optic_chiasm] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "chiasma" RELATED LATIN [NeuroNames:459] synonym: "chiasma nervorum opticorum" RELATED LATIN [NeuroNames:459] synonym: "chiasma opticum" EXACT LATIN [Wikipedia:Optic_chiasm] synonym: "decussation of optic nerve fibers" EXACT [FMA:62045] synonym: "optic chiasm" EXACT [Wikipedia:Optic_chiasm] synonym: "optic chiasm (Rufus of Ephesus)" RELATED [NeuroNames:459] xref: AAO:0010622 xref: BAMS:DC xref: BAMS:OC xref: BAMS:och xref: BAMS:ox xref: BIRNLEX:1416 xref: BM:Tel-OCX xref: DHBA:10644 xref: DMBA:17783 xref: EHDAA2:0001302 xref: EHDAA:10227 xref: EMAPA:17603 xref: FMA:62045 xref: GAID:832 xref: HBA:9310 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=459 {source="BIRNLEX:1416"} xref: MA:0001098 xref: MBA:117 xref: MESH:D009897 xref: NCIT:C90609 xref: SCTID:244453006 xref: TAO:0000556 xref: UMLS:C0029126 {source="BIRNLEX:1416"} xref: UMLS:C0029126 {source="ncithesaurus:Optic_Chiasm"} xref: VHOG:0000190 xref: Wikipedia:Optic_chiasm xref: XAO:0004071 xref: ZFA:0000556 is_a: UBERON:0007418 {source="cjm"} ! neural decussation is_a: UBERON:0007425 ! decussation of diencephalon intersection_of: UBERON:0007418 ! neural decussation intersection_of: extends_fibers_into UBERON:0000941 ! cranial nerve II intersection_of: extends_fibers_into UBERON:0001908 ! optic tract intersection_of: part_of UBERON:0001894 ! diencephalon relationship: extends_fibers_into UBERON:0000941 ! cranial nerve II relationship: extends_fibers_into UBERON:0001908 ! optic tract relationship: part_of UBERON:0001894 ! diencephalon property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/b/b3/1543%2CVisalius%27OpticChiasma.jpg xsd:anyURI property_value: external_definition "The point at which fibers of the optic nerves cross.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010622", ontology="AAO", source="AAO:DSM"} property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000960 name: obsolete pharyngeal nerve def: "OBSOLETE. Original definition: The pharyngeal nerve (pterygopalatine nerve) is a small branch arising from the posterior part of the pterygopalatine ganglion. It passes through the pharyngeal canal with the pharyngeal branch of the maxillary artery, and is distributed to the mucous membrane of the nasal part of the pharynx, behind the auditory tube. [WP,unvetted]." [Wikipedia:Pharyngeal_nerve] subset: uberon_slim xref: Wikipedia:Pharyngeal_nerve property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/d/d7/Gray780.png xsd:anyURI is_obsolete: true consider: FBbt:00004021 consider: FMA:77524 consider: WBbt:0005441 [Term] id: UBERON:0000961 name: thoracic ganglion def: "The thoracic ganglia are paravertebral ganglia. The thoracic portion of the sympathetic trunk typically has 12 thoracic ganglia. Emerging from the ganglia are thoracic splancic nerves (the cardiopulmonary, the greater, lesser, and least splanchic nerves) that help provide sympathetic innervation to abdominal structures. Also, the ganglia of the thoracic sympathetic trunk have both white and gray rami communicantes. The white rami carry sympathetic fibers arising in the spinal cord into the sympathetic trunk. [WP,unvetted]." [Wikipedia:Thoracic_ganglion] subset: uberon_slim synonym: "ganglion of thorax" EXACT [OBOL:automatic] synonym: "ganglion thoracicum splanchnicum" EXACT LATIN [FMA:6471, FMA:TA] synonym: "thoracic paravertebral ganglion" EXACT [MA:0001159] synonym: "thoracic splanchnic ganglion" EXACT [] synonym: "thoracic sympathetic ganglion" EXACT [] synonym: "thorax ganglion" EXACT [OBOL:automatic] xref: BTO:0001831 xref: EHDAA:4664 xref: EMAPA:17158 xref: FMA:6471 xref: MA:0001159 xref: NCIT:C52829 xref: RETIRED_EHDAA2:0002012 xref: SCTID:181102004 xref: UMLS:C0229010 {source="ncithesaurus:Thoracic_Ganglion"} xref: VHOG:0000515 xref: Wikipedia:Thoracic_ganglion is_a: UBERON:0001807 ! paravertebral ganglion is_a: UBERON:0005181 ! thoracic segment organ intersection_of: UBERON:0001807 ! paravertebral ganglion intersection_of: part_of UBERON:0004863 ! thoracic sympathetic nerve trunk relationship: extends_fibers_into UBERON:0018679 ! thoracic splanchnic nerve relationship: part_of UBERON:0004863 ! thoracic sympathetic nerve trunk property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/3e/Gray849.png xsd:anyURI [Term] id: UBERON:0000962 name: nerve of cervical vertebra def: "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]." [Wikipedia:Cervical_nerves] comment: Innervates: sternohyoid muscle, sternothyroid muscle, omohyoid muscle[WP] subset: uberon_slim synonym: "cervical nerve" EXACT [FMA:5859] synonym: "cervical nerve tree" EXACT [] synonym: "cervical spinal nerve" EXACT [] synonym: "nervus cervicalis" EXACT LATIN [FMA:5859, FMA:TA] xref: BAMS:cern xref: FMA:5859 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2351 xref: NCIT:C32299 xref: NLXANAT:20090207 xref: SCTID:360497008 xref: UMLS:C0228815 {source="ncithesaurus:Cervical_Nerve"} xref: Wikipedia:Cervical_nerves is_a: UBERON:0001780 ! spinal nerve intersection_of: UBERON:0001780 ! spinal nerve intersection_of: extends_fibers_into UBERON:0002726 ! cervical spinal cord relationship: extends_fibers_into UBERON:0002726 ! cervical spinal cord property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray795.png xsd:anyURI [Term] id: UBERON:0000963 name: head sensillum xref: FBbt:00004114 xref: MAT:0000204 xref: MIAA:0000204 is_a: UBERON:0002536 ! arthropod sensillum intersection_of: UBERON:0002536 ! arthropod sensillum intersection_of: part_of UBERON:0000033 ! head relationship: part_of UBERON:0000033 ! head property_value: editor_note "this term should be ceded to the arthropod anatomy ontology" xsd:string [Term] id: UBERON:0000964 name: cornea def: "the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure" [ISBN:0-683-40008-8, MESH:A09.371.060.217, MP:0001312] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "cornea of camera-type eye" EXACT [GO:0061303] synonym: "corneas" RELATED PLURAL [ZFA:0000640] synonym: "tunica cornea" RELATED [] xref: AAO:0010344 xref: BTO:0000286 xref: CALOHA:TS-0171 xref: EFO:0000377 xref: EHDAA2:0000316 xref: EHDAA:10199 xref: EMAPA:17161 xref: EV:0100341 xref: FMA:58238 xref: GAID:892 xref: MA:0000266 xref: MESH:D003315 xref: NCIT:C12342 xref: OpenCyc:Mx4rvViBa5wpEbGdrcN5Y29ycA xref: SCTID:181162001 xref: TAO:0000640 xref: UMLS:C0010031 {source="ncithesaurus:Cornea"} xref: VHOG:0000164 xref: Wikipedia:Cornea xref: XAO:0000180 xref: ZFA:0000640 is_a: CARO:0000003 is_a: UBERON:0003102 {source="XAO"} ! surface structure is_a: UBERON:0010000 ! multicellular anatomical structure relationship: continuous_with UBERON:0001773 ! sclera relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball relationship: developmentally_induced_by UBERON:0005426 ! lens vesicle relationship: develops_from UBERON:0004348 {evidence="definitional"} ! optic eminence relationship: develops_from UBERON:0005427 ! corneal primordium relationship: has_part UBERON:0001772 ! corneal epithelium relationship: has_part UBERON:0004370 ! anterior limiting lamina of cornea relationship: has_quality PATO:0000964 relationship: part_of UBERON:0001801 {source="MA"} ! anterior segment of eyeball relationship: part_of UBERON:0010409 {source="MA"} ! ocular surface region relationship: part_of UBERON:0012430 {source="FMA-isa"} ! tunica fibrosa of eyeball property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg xsd:anyURI property_value: has_relational_adjective "corneal" xsd:string property_value: taxon_notes "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" xsd:string [Term] id: UBERON:0000965 name: lens of camera-type eye def: "Transparent part of camera-type eye that helps to refract light to be focused on the retina." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Lens_(anatomy)] comment: The lens is avascular and nourished by diffusion from the aqueous and vitreous subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "camera-type eye lens" EXACT [GO:0002088] synonym: "crystalline lens" RELATED [BTO:0000723] synonym: "eye lens" EXACT SENSU [] synonym: "lens" EXACT SENSU [] synonym: "lens crystallina" EXACT [Wikipedia:Lens_(anatomy)] synonym: "lenses" RELATED PLURAL [ZFA:0000035] synonym: "ocular lens" RELATED [BTO:0000723] xref: AAO:0010348 xref: BTO:0000723 xref: CALOHA:TS-0545 xref: EHDAA:9057 xref: EMAPA:17838 xref: EV:0100343 xref: FMA:58241 xref: MA:0000275 xref: MAT:0000141 xref: MESH:A09.371.509 xref: MIAA:0000141 xref: NCIT:C12743 xref: OpenCyc:Mx4rvVj0fZwpEbGdrcN5Y29ycA xref: RETIRED_EHDAA2:0000975 xref: SCTID:181169005 xref: TAO:0000035 xref: UMLS:C0023317 {source="ncithesaurus:Crystalline_Lens"} xref: VHOG:0000169 xref: Wikipedia:Lens_(anatomy) xref: XAO:0000008 xref: ZFA:0000035 is_a: CARO:0000003 is_a: UBERON:0005389 ! transparent eye structure relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball relationship: developmentally_induced_by UBERON:0003902 ! retinal neural layer relationship: develops_from UBERON:0003073 ! lens placode relationship: develops_from UBERON:0005426 ! lens vesicle relationship: part_of UBERON:0001801 ! anterior segment of eyeball property_value: homology_notes "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]" xsd:string {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/"} property_value: taxon_notes "This class excludes compound eye corneal lenses." xsd:string [Term] id: UBERON:0000966 name: retina def: "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." [Wikipedia:Retina, ZFIN:curator] 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 subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "inner layer of eyeball" EXACT [] synonym: "Netzhaut" RELATED [BTO:0001175] synonym: "retina of camera-type eye" EXACT [GO:0060041] synonym: "retinas" RELATED PLURAL [ZFA:0000152] synonym: "tunica interna of eyeball" EXACT [] xref: AAO:0010352 xref: BAMS:R xref: BIRNLEX:1153 xref: BTO:0001175 xref: CALOHA:TS-0865 xref: EFO:0000832 xref: EHDAA2:0001627 xref: EHDAA:4757 xref: EMAPA:17168 xref: EV:0100348 xref: FMA:58301 xref: GAID:755 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1862 xref: MA:0000276 xref: MAT:0000142 xref: MBA:304325711 xref: MESH:D012160 xref: MIAA:0000142 xref: NCIT:C12343 xref: NIFSTD_RETIRED:birnlex_1156 xref: OpenCyc:Mx4rvViTfpwpEbGdrcN5Y29ycA xref: SCTID:181171005 xref: TAO:0000152 xref: UMLS:C0035298 {source="BIRNLEX:1153"} xref: UMLS:C0035298 {source="ncithesaurus:Retina"} xref: UMLS:C1278894 {source="BIRNLEX:1153"} xref: VHOG:0000229 xref: Wikipedia:Retina xref: XAO:0000009 xref: ZFA:0000152 is_a: UBERON:0005388 ! photoreceptor array relationship: develops_from UBERON:0003072 {source="EHDAA2"} ! optic cup relationship: has_part CL:0000573 {source="FMA"} relationship: has_part CL:0000604 {source="FMA"} relationship: has_part CL:0000740 {source="FMA"} relationship: never_in_taxon NCBITaxon:6656 relationship: part_of UBERON:0001802 ! posterior segment of eyeball relationship: part_of UBERON:0019207 ! chorioretinal region property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png xsd:anyURI property_value: external_definition "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]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000152", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "retinal" xsd:string property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000967 name: obsolete adult thoracic sensillum synonym: "arthropod sensillum of thorax" EXACT [OBOL:automatic] synonym: "sensillum of thorax" EXACT [OBOL:automatic] synonym: "thoracic sensillum" EXACT [] synonym: "thorax arthropod sensillum" EXACT [OBOL:automatic] synonym: "thorax sensillum" EXACT [OBOL:automatic] is_obsolete: true consider: FBbt:00004245 consider: MAT:0000205 consider: MIAA:0000205 [Term] id: UBERON:0000968 name: obsolete adult abdominal sensillum synonym: "abdomen arthropod sensillum" EXACT [OBOL:automatic] synonym: "abdomen sensillum" EXACT [OBOL:automatic] synonym: "abdominal sensillum" EXACT [] synonym: "arthropod sensillum of abdomen" EXACT [OBOL:automatic] synonym: "sensillum of abdomen" EXACT [OBOL:automatic] is_obsolete: true consider: FBbt:00004461 consider: MAT:0000206 consider: MIAA:0000206 [Term] id: UBERON:0000969 name: obsolete joint connecting hardened body parts is_obsolete: true [Term] id: UBERON:0000970 name: eye def: "An organ that detects light." [https://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: functional_classification subset: major_organ subset: organ_slim subset: uberon_slim synonym: "light-detecting organ" RELATED [] synonym: "visual apparatus" RELATED [EV:0100336] xref: BILA:0000017 xref: BTO:0000439 xref: CALOHA:TS-0309 xref: EFO:0000827 xref: EV:0100336 xref: FBbt:00005162 xref: GAID:69 xref: MAT:0000140 xref: MESH:D005123 xref: MIAA:0000140 xref: OpenCyc:Mx4rvViTvpwpEbGdrcN5Y29ycA xref: Wikipedia:Eye is_a: CARO:0000000 is_a: UBERON:0000020 ! sense organ relationship: capable_of GO:0009584 relationship: has_part CL:0000149 {source="PMID:21062451"} relationship: has_part CL:0000210 {source="PMID:21062451"} relationship: part_of UBERON:0002104 ! visual system property_value: curator_notes "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)" xsd:string property_value: has_relational_adjective "ocular" xsd:string property_value: has_relational_adjective "optic" xsd:string property_value: structure_notes "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," xsd:string [Term] id: UBERON:0000971 name: ommatidium def: "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." [PMID:21062451] subset: uberon_slim synonym: "omatidia" RELATED PLURAL [] synonym: "omatidium" EXACT [] xref: BTO:0001922 xref: FBbt:00004510 xref: HAO:0000666 xref: MAT:0000143 xref: MIAA:0000143 xref: Wikipedia:Ommatidium is_a: UBERON:0000970 {source="PMID:21062451"} ! eye is_a: UBERON:0002536 ! arthropod sensillum relationship: part_of UBERON:0000018 ! compound eye property_value: has_relational_adjective "ommatidial" xsd:string [Term] id: UBERON:0000972 name: antenna def: "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." [FB:gg, ISBN:3110148986, Wikipedia:Antenna_(biology)] subset: efo_slim subset: uberon_slim synonym: "feeler" RELATED [BTO:0000074] xref: AEO:0000198 xref: BTO:0000074 xref: EFO:0000874 xref: FBbt:00004511 xref: HAO:0000101 xref: MAT:0000086 xref: MIAA:0000086 xref: OpenCyc:Mx4rvVjSAZwpEbGdrcN5Y29ycA xref: TGMA:0000007 xref: Wikipedia:Antenna_(biology) is_a: UBERON:0000026 {source="FBbt"} ! appendage is_a: UBERON:0015212 ! lateral structure relationship: has_quality PATO:0000402 {gci_relation="part_of", gci_filler="NCBITaxon:6657", source="Wikipedia"} relationship: in_lateral_side_of UBERON:0000033 ! head relationship: never_in_taxon NCBITaxon:6843 relationship: only_in_taxon NCBITaxon:6656 relationship: part_of UBERON:0000033 ! head property_value: editor_note "this term should be ceded to the arthropod anatomy ontology" xsd:string property_value: has_relational_adjective "antennal" xsd:string property_value: has_relational_adjective "antenno" xsd:string [Term] id: UBERON:0000973 name: obsolete labrum is_obsolete: true [Term] id: UBERON:0000974 name: neck def: "An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "collum" RELATED LATIN [Wikipedia:Neck] synonym: "neck (volume)" RELATED [FMA:7155] xref: AEO:0000108 xref: BTO:0000420 xref: CALOHA:TS-2045 xref: EFO:0000967 xref: EHDAA2:0003108 xref: EMAPA:35587 xref: FMA:7155 xref: GAID:86 xref: galen:Neck xref: MA:0000024 xref: MAT:0000297 xref: MESH:D009333 xref: MIAA:0000297 xref: NCIT:C13063 xref: OpenCyc:Mx4rvVjLF5wpEbGdrcN5Y29ycA xref: SCTID:302550007 xref: UMLS:C0027530 {source="ncithesaurus:Neck"} xref: Wikipedia:Neck is_a: UBERON:0000475 ! organism subdivision relationship: anteriorly_connected_to UBERON:0000033 ! head relationship: dubious_for_taxon NCBITaxon:32443 {source="ISBN:9780674021839"} relationship: only_in_taxon NCBITaxon:8287 relationship: part_of UBERON:0000153 ! anterior region of body relationship: part_of UBERON:0007811 ! craniocervical region relationship: posteriorly_connected_to UBERON:0002100 ! trunk property_value: curator_notes "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." xsd:string property_value: depicted_by Female:neck.jpg xsd:anyURI property_value: has_relational_adjective "cervical" xsd:string [Term] id: UBERON:0000975 name: sternum def: "A midventral endochondral skeletal element which represents the origin site of the pectoral muscles[PHENOSCAPE:ad]." [https://github.com/obophenotype/uberon/issues/67, PHENOSCAPE:ad] subset: pheno_slim subset: uberon_slim synonym: "breastbone" RELATED [BTO:0001302] synonym: "vertebrate sternum" EXACT [] xref: AAO:0000765 xref: BTO:0001302 xref: CALOHA:TS-0972 xref: EHDAA2:0001914 xref: EHDAA:9561 xref: EMAPA:18344 xref: FMA:7485 xref: GAID:246 xref: galen:Sternum xref: MA:0001331 xref: MESH:D013249 xref: NCIT:C12793 xref: OpenCyc:Mx4rvVjO6JwpEbGdrcN5Y29ycA xref: SCTID:302522007 xref: UMLS:C0038293 {source="ncithesaurus:Sternum"} xref: VHOG:0000856 xref: Wikipedia:Sternum is_a: CARO:0000000 is_a: UBERON:0005181 ! thoracic segment organ is_a: UBERON:0010363 {source="ISBN:0073040584"} ! endochondral element relationship: connected_to UBERON:0002228 ! rib relationship: connected_to UBERON:0007831 ! pectoral girdle skeleton relationship: connected_to UBERON:0008255 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! right clavicle relationship: connected_to UBERON:0008256 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! left clavicle relationship: contributes_to_morphology_of UBERON:0003252 ! thoracic rib cage relationship: dc-contributor https://github.com/alex-dececchi relationship: dc-contributor https://github.com/cmungall relationship: never_in_taxon NCBITaxon:8570 {source="Wikipedia"} relationship: only_in_taxon NCBITaxon:32523 {source="ISBN:0073040584"} relationship: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0003252 {source="FMA"} ! thoracic rib cage property_value: axiom_lost_from_external_ontology "relationship loss: part_of postzonal element (AAO:0000938)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000765", ontology="AAO"} property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/1/12/Illu_thoracic_cage.jpg xsd:anyURI property_value: development_notes "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]." xsd:string {source="WP"} property_value: editor_note "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" xsd:string property_value: external_definition "Single element that constitutes the postzonal area of the pectoral girdle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000765", ontology="AAO", source="AAO:LAP"} property_value: has_relational_adjective "sternal" xsd:string property_value: homology_notes "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]" xsd:string {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/"} property_value: taxon_notes "in birds, either ratite (no keel or carina) or carinate (keel and carina present)" xsd:string property_value: taxon_notes "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" xsd:string [Term] id: UBERON:0000976 name: humerus def: "Paired endochondral long bone that extends between the pectoral girdle and the skeletal parts of the forelimb. [PHENOSCAPE:mah]" [AAO:0000679, https://github.com/obophenotype/uberon/issues/106, PHENOSCAPE:mah] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "humeri" EXACT PLURAL [PHENOSCAPE:ad] synonym: "humerus bone" EXACT [] synonym: "mesomere 1 of pectoral appendage" RELATED HOMOLOGY [ISBN:0226313409] synonym: "proximal metapterygial mesomere of pectoral appendage" RELATED HOMOLOGY [ISBN:0226313409] synonym: "proximal metapterygial mesomere of pectoral fin" RELATED HOMOLOGY [ISBN:0226313409] xref: AAO:0000679 xref: CALOHA:TS-2202 xref: EFO:0001398 xref: EMAPA:19106 xref: FMA:13303 xref: GAID:183 xref: galen:Humerus xref: MA:0001356 xref: MESH:A02.835.232.087.412 xref: NCIT:C12731 xref: SCTID:181923006 xref: UMLS:C0020164 {source="ncithesaurus:Humerus"} xref: VHOG:0001158 xref: Wikipedia:Humerus xref: XAO:0003210 is_a: UBERON:0002495 {source="FMA"} ! long bone is_a: UBERON:0003461 ! shoulder bone is_a: UBERON:0003607 ! forelimb long bone is_a: UBERON:0004250 ! upper arm bone is_a: UBERON:0015053 ! humerus endochondral element intersection_of: UBERON:0015053 ! humerus endochondral element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: composed_primarily_of UBERON:0002481 ! bone tissue relationship: dc-contributor https://github.com/cmungall relationship: dc-contributor https://github.com/mellybelly relationship: develops_from UBERON:0006245 {evidence="definitional"} ! humerus cartilage element relationship: part_of UBERON:0001440 {source="FMA"} ! forelimb skeleton relationship: part_of UBERON:0003822 {source="FMA"} ! forelimb stylopod relationship: proximally_connected_to UBERON:0007831 ! pectoral girdle skeleton property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/67/Illu_upper_extremity.jpg xsd:anyURI property_value: external_definition "Paired, elongate, cylindrical bones of endochondral origin that extend from the pectoral girdle to the elbows.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000679", ontology="AAO", source="AAO:LAP"} property_value: has_relational_adjective "humeral" xsd:string property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000977 name: pleura def: "The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion)." [https://github.com/obophenotype/uberon/issues/1231, ISBN:0-683-40008-8, MP:0010820, UBERON:cjm, Wikipedia:Pulmonary_pleurae] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "pleura" RELATED [] synonym: "pleural tissue" RELATED [BTO:0001791, NCIT:C12469] synonym: "wall of pleural sac" EXACT [] xref: BTO:0001791 xref: CALOHA:TS-2081 xref: EFO:0001980 xref: EMAPA:16775 xref: EV:0100044 xref: FMA:9583 xref: GAID:360 xref: MA:0000433 xref: MESH:D010994 xref: NCIT:C12469 xref: OpenCyc:Mx4rv3zwLZwpEbGdrcN5Y29ycA xref: SCTID:181609007 xref: UMLS:C0032225 {source="ncithesaurus:Pleural_Tissue"} xref: VHOG:0000394 xref: Wikipedia:Pleura is_a: UBERON:0000042 ! serous membrane is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure intersection_of: UBERON:0000042 ! serous membrane intersection_of: has_part UBERON:0002400 ! parietal pleura intersection_of: has_part UBERON:0002401 ! visceral pleura intersection_of: part_of UBERON:0009778 ! pleural sac relationship: contributes_to_morphology_of UBERON:0001004 ! respiratory system relationship: develops_from UBERON:0003081 ! lateral plate mesoderm relationship: has_part UBERON:0002400 ! parietal pleura relationship: has_part UBERON:0002401 ! visceral pleura relationship: has_quality PATO:0001748 relationship: only_in_taxon NCBITaxon:32524 relationship: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0009778 {source="https://github.com/obophenotype/uberon/issues/86"} ! pleural sac relationship: present_in_taxon NCBITaxon:8782 {source="BGEE:AN", source="ISBN:978-0030223693"} property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png xsd:anyURI property_value: external_definition "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000394", ontology="VHOG", source="ISBN:0124020607", source="http://bgee.unil.ch/"} property_value: external_ontology_notes "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" xsd:string property_value: has_relational_adjective "pleural" xsd:string [Term] id: UBERON:0000978 name: leg def: "The portion of the hindlimb that contains both the stylopod and zeugopod." [Wikipedia:Leg#Limb] 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 subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "lower extremity" RELATED [MESH:A01.378.610] synonym: "tetrapod leg" EXACT [] xref: BTO:0000721 xref: CALOHA:TS-2206 xref: EFO:0001411 xref: EHDAA2:0000972 xref: EHDAA:5151 xref: EHDAA:6176 xref: EHDAA:8289 xref: EMAPA:17489 xref: GAID:49 xref: MA:0000047 xref: MESH:D035002 xref: OpenCyc:Mx4rvViYzZwpEbGdrcN5Y29ycA xref: VHOG:0000345 xref: Wikipedia:Leg#Limb is_a: UBERON:0006058 ! multi-limb segment region is_a: UBERON:0008784 ! lower limb segment relationship: distally_connected_to UBERON:0002387 ! pes relationship: part_of UBERON:0002103 ! hindlimb relationship: proximally_connected_to UBERON:0001464 ! hip property_value: homology_notes "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]" xsd:string {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/"} property_value: terminology_notes "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" xsd:string {source="3"} [Term] id: UBERON:0000979 name: tibia def: "The major preaxial endochondral bone in the posterior zeugopod[Phenoscape]." [PHENOSCAPE:mah] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "shankbone" EXACT [Wikipedia:Tibia] synonym: "shinbone" EXACT [Wikipedia:Tibia] xref: AAO:0000890 xref: BTO:0001252 xref: CALOHA:TS-1048 xref: EFO:0003054 xref: EMAPA:19142 xref: FMA:24476 xref: GAID:204 xref: galen:Tibia xref: MA:0001361 xref: MESH:A02.835.232.500.883 xref: NCIT:C12800 xref: OpenCyc:Mx4rvtq3-ZwpEbGdrcN5Y29ycA xref: SCTID:182061009 xref: UMLS:C0040184 {source="ncithesaurus:Tibia"} xref: Wikipedia:Tibia is_a: UBERON:0002495 {source="FMA"} ! long bone is_a: UBERON:0003608 ! hindlimb long bone is_a: UBERON:0004251 ! hindlimb zeugopod bone is_a: UBERON:0015004 ! tibia endochondral element intersection_of: UBERON:0015004 ! tibia endochondral element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: composed_primarily_of UBERON:0002481 ! bone tissue relationship: develops_from UBERON:0010849 ! tibia cartilage element relationship: only_in_taxon NCBITaxon:7742 relationship: part_of UBERON:0010720 ! hindlimb zeugopod skeleton relationship: preaxialmost_part_of UBERON:0010720 ! hindlimb zeugopod skeleton property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray260.png xsd:anyURI property_value: external_definition "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]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000890", ontology="AAO", source="AAO:LAP"} [Term] id: UBERON:0000980 name: trochanter def: "A bony prominence near the extremity of the femur that normally serves as attachment points for hip and thigh muscles[MP,modified]" [MP:0004627] subset: pheno_slim subset: uberon_slim synonym: "femoral trochanter" EXACT [AAO:0000897] synonym: "trochanter of femur" EXACT [] xref: AAO:0000897 xref: FMA:82513 xref: MA:0002821 xref: NCIT:C33814 xref: SCTID:182047004 xref: UMLS:C0162370 {source="ncithesaurus:Trochanter"} xref: Wikipedia:Trochanter is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005055 ! zone of long bone is_a: UBERON:0005913 {source="FMA"} ! zone of bone organ is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: contributes_to_morphology_of UBERON:0000981 ! femur relationship: only_in_taxon NCBITaxon:7742 relationship: part_of UBERON:0000981 {source="MA"} ! femur property_value: external_definition "Process on the ventral surface of the shaft of the femur.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000897", ontology="AAO", source="AAO:LAP"} property_value: taxon_notes "there are two in human (greater and lesser trochanters) and three in many other mammalian species (greater, lesser and third)" xsd:string {source="MP"} [Term] id: UBERON:0000981 name: femur def: "Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified]." [VSAO:0000186, Wikipedia:Femur] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "femoral bone" RELATED [BTO:0001284] synonym: "mesomere 1 of pevlic appendage" RELATED HOMOLOGY [ISBN:0226313409] synonym: "os femorale" RELATED LATIN [BTO:0001284] synonym: "os femoris" RELATED LATIN [BTO:0001284] synonym: "os longissimum" RELATED LATIN [Wikipedia:Femur] synonym: "proximal metapterygial mesomere of pelvic appendage" RELATED HOMOLOGY [ISBN:0226313409] synonym: "proximal metapterygial mesomere of pelvic fin" RELATED HOMOLOGY [ISBN:0226313409] synonym: "thigh bone" EXACT [] xref: AAO:0000887 xref: AAO:0000889 xref: BTO:0001284 xref: CALOHA:TS-0322 xref: EFO:0001396 xref: EMAPA:19143 xref: FMA:9611 xref: GAID:199 xref: galen:Femur xref: MA:0001359 xref: MESH:A02.835.232.500.247 xref: NCIT:C12717 xref: OpenCyc:Mx4rvVjOJJwpEbGdrcN5Y29ycA xref: SCTID:182046008 xref: UMLS:C0015811 {source="ncithesaurus:Femur"} xref: VHOG:0001159 xref: VSAO:0000186 xref: Wikipedia:Femur xref: XAO:0003214 is_a: UBERON:0003608 ! hindlimb long bone is_a: UBERON:0003826 ! upper leg bone is_a: UBERON:0008202 {source="MA"} ! bone of hip region is_a: UBERON:0015052 ! femur endochondral element intersection_of: UBERON:0015052 ! femur endochondral element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: composed_primarily_of UBERON:0002481 ! bone tissue relationship: connected_to UBERON:0000979 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! tibia relationship: connected_to UBERON:0001272 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! innominate bone relationship: connected_to UBERON:0002446 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! patella relationship: develops_from UBERON:0010129 {evidence="definitional"} ! femur cartilage element relationship: only_in_taxon NCBITaxon:7742 relationship: part_of UBERON:0000376 {source="FMA"} ! hindlimb stylopod relationship: part_of UBERON:0001441 {source="FMA"} ! hindlimb skeleton relationship: proximally_connected_to UBERON:0007832 ! pelvic girdle skeleton property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/7/73/Gray252.png xsd:anyURI property_value: external_definition "Endochondral longbone connecting the pelvic girdle with posterior zeugopodium.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000186", ontology="VSAO", source="VSAO:NI"} property_value: external_definition "Paired, elongate, cylindrical bones of endochondral origin that form the thighs, extending from the pelvic girdles to the knees.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000889", ontology="AAO", source="AAO:LAP"} property_value: has_relational_adjective "femoral" xsd:string property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000982 name: skeletal joint def: "Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000101, Wikipedia:Joint] subset: efo_slim subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "articular joint" RELATED [BTO:0001686] synonym: "articulation" BROAD [VSAO:0000101] synonym: "joint" BROAD [FMA:7490, VSAO:0000101] synonym: "joints" RELATED PLURAL [ZFA:0001596] xref: AEO:0000182 xref: BTO:0001686 xref: CALOHA:TS-2023 xref: EFO:0000948 xref: EMAPA:35456 xref: FMA:7490 xref: GAID:102 xref: galen:Joint xref: MA:0000319 xref: MAT:0000188 xref: MESH:D007596 xref: MIAA:0000188 xref: NCIT:C13044 xref: OpenCyc:Mx4rvVjjdpwpEbGdrcN5Y29ycA xref: RETIRED_EHDAA2:0003182 xref: SCTID:302536002 xref: TAO:0000367 xref: UMLS:C0022417 {source="ncithesaurus:Joint"} xref: VHOG:0001276 xref: VSAO:0000101 xref: Wikipedia:Joint xref: XAO:0000171 xref: ZFA:0001596 is_a: UBERON:0004905 ! articulation union_of: UBERON:0002217 ! synovial joint union_of: UBERON:0011134 ! nonsynovial joint disjoint_from: UBERON:0001474 ! bone element relationship: connects UBERON:0004765 ! skeletal element relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system relationship: part_of UBERON:0004770 ! articular system property_value: external_definition "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000101", ontology="VSAO", source="PSPUB:0000170"} property_value: external_definition "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000367", ontology="TAO", source="TAO:pem"} [Term] id: UBERON:0000983 name: metatarsus region def: "A metapodium region that is part of a pes." [OBOL:automatic] subset: uberon_slim synonym: "hind metapodium" EXACT [AAO:0000221, http://en.wiktionary.org/wiki/metapodial, MA:th] synonym: "hindlimb cannon region" NARROW [http://orcid.org/0000-0002-6601-2165, NCBITaxon:9788] synonym: "hindlimb equine cannon region" NARROW [http://orcid.org/0000-0002-6601-2165, NCBITaxon:9788] synonym: "metatarsal part of foot" EXACT [FMA:24997] synonym: "metatarsal region" EXACT [FMA:24997] synonym: "metatarsus" RELATED [MA:0000049] synonym: "regio metatarsalis" EXACT LATIN [FMA:24997, FMA:TA] xref: CALOHA:TS-2221 xref: FMA:24997 xref: MA:0000049 xref: SCTID:280711000 xref: SCTID:370639003 is_a: UBERON:0008784 ! lower limb segment is_a: UBERON:0009877 ! metapodium region intersection_of: UBERON:0009877 ! metapodium region intersection_of: part_of UBERON:0002387 ! pes relationship: has_skeleton UBERON:0010545 ! metatarsus skeleton relationship: part_of UBERON:0002387 ! pes relationship: part_of UBERON:0012142 {source="PHENOSCAPE:ni"} ! pedal digitopodium region property_value: external_ontology_notes "mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton" xsd:string [Term] id: UBERON:0000984 name: imaginal disc-derived wing def: "A flight organ of the adult external thorax that is derived from a dorsal mesothoracic disc." [FB:gg] subset: uberon_slim synonym: "adult mesothoracic wing" RELATED [] synonym: "adult metathoracic wing" RELATED [] synonym: "thoracic wing" RELATED [] synonym: "thorax wing" RELATED [OBOL:automatic] synonym: "wing" BROAD SENSU [FBbt:00004729] synonym: "wing of thorax" RELATED [OBOL:automatic] xref: FBbt:00004729 xref: HAO:0001089 xref: TGMA:0000196 is_a: UBERON:0000023 ! wing intersection_of: UBERON:0000023 ! wing intersection_of: develops_from UBERON:0000939 ! imaginal disc relationship: develops_from UBERON:0000939 ! imaginal disc property_value: editor_note "TODO - review. hymenoptera thorax = fusion of thorax and mesosoma/metasoma" xsd:string [Term] id: UBERON:0000985 name: axillary vein def: "Vein that drains the axilla" [http://orcid.org/0000-0002-6601-2165] subset: uberon_slim synonym: "subcostal vein" RELATED [] synonym: "vena axillaris" EXACT LATIN [Wikipedia:Axillary_vein] xref: EMAPA:18758 xref: FMA:13329 xref: GAID:527 xref: galen:AxillaryVein xref: MA:0002084 xref: MESH:D001367 xref: NCIT:C32171 xref: OpenCyc:Mx4rwLSHK5wpEbGdrcN5Y29ycA xref: SCTID:181389002 xref: UMLS:C0004456 {source="ncithesaurus:Axillary_Vein"} xref: Wikipedia:Axillary_vein is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0009472 ! axilla relationship: drains UBERON:0009472 ! axilla relationship: part_of UBERON:0001467 ! shoulder property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray576.png xsd:anyURI property_value: taxon_notes "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" xsd:string {source="WP"} [Term] id: UBERON:0000987 name: haltere def: "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." [FB:gg, ISBN:3110148986, Wikipedia:Haltere] subset: efo_slim subset: uberon_slim synonym: "balancer organ" RELATED [] xref: EFO:0000886 xref: FBbt:00004783 xref: MAT:0000203 xref: MIAA:0000203 xref: OpenCyc:Mx4rwL1JcJwpEbGdrcN5Y29ycA xref: Wikipedia:Haltere is_a: UBERON:0000026 {source="FBbt"} ! appendage relationship: develops_from UBERON:0000939 ! imaginal disc relationship: part_of UBERON:0000914 ! organismal segment property_value: editor_note "this term should be ceded to the arthropod anatomy ontology" xsd:string [Term] id: UBERON:0000988 name: pons def: "The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum." [VHOG:0001176] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "pons cerebri" RELATED LATIN [NeuroNames:547] synonym: "pons of Varolius" EXACT [] synonym: "pons Varolii" EXACT [ncithesaurus:Pons_Varolii] xref: BAMS:PONS xref: BAMS:Pons xref: BIRNLEX:733 xref: BM:Pons xref: BTO:0001101 xref: CALOHA:TS-0813 xref: DHBA:10661 xref: EFO:0001394 xref: EHDAA2:0004394 xref: EMAPA:17563 xref: EV:0100253 xref: FMA:67943 xref: GAID:578 xref: HBA:9131 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=547 {source="BIRNLEX:733"} xref: MA:0000204 xref: MAT:0000115 xref: MBA:771 xref: MESH:D011149 xref: MIAA:0000115 xref: NCIT:C12511 xref: SCTID:279103004 xref: UMLS:C0032639 {source="BIRNLEX:733"} xref: UMLS:C0032639 {source="ncithesaurus:Pons_Varolii"} xref: UMLS:C1280999 {source="BIRNLEX:733"} xref: VHOG:0001176 xref: Wikipedia:Pons is_a: UBERON:0002616 ! regional part of brain is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: contributes_to_morphology_of UBERON:0001895 ! metencephalon relationship: contributes_to_morphology_of UBERON:0002298 ! brainstem relationship: dubious_for_taxon NCBITaxon:7955 relationship: only_in_taxon NCBITaxon:7742 relationship: part_of UBERON:0001895 {source="neuronames"} ! metencephalon relationship: part_of UBERON:0002298 ! brainstem property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/36/Gray768.png xsd:anyURI property_value: editor_note "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" xsd:string property_value: external_definition "The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001176", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/pons"} property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000989 name: penis def: "A intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination" [http://orcid.org/0000-0002-6601-2165, ISBN:0-683-40008-8, MP:0005187, Wikipedia:Penis] subset: efo_slim subset: organ_slim subset: pheno_slim subset: uberon_slim synonym: "penes" RELATED PLURAL [] synonym: "phallus" RELATED [] xref: BTO:0000405 xref: CALOHA:TS-0758 xref: EFO:0000987 xref: EHDAA2:0001433 xref: EHDAA:9380 xref: EMAPA:18682 xref: EMAPA_RETIRED:18996 xref: EV:0100107 xref: FMA:9707 xref: GAID:389 xref: galen:Penis xref: MA:0000408 xref: MAT:0000186 xref: MESH:D010413 xref: MIAA:0000186 xref: NCIT:C12409 xref: OpenCyc:Mx4rvVjkCZwpEbGdrcN5Y29ycA xref: SCTID:265793009 xref: UMLS:C0030851 {source="ncithesaurus:Penis"} xref: VHOG:0000727 xref: Wikipedia:Penis is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0008811 {source="Wikipedia"} ! intromittent organ relationship: develops_from UBERON:0004876 {source="Wikipedia"} ! urogenital fold relationship: develops_from UBERON:0005876 {source="EHDAA2"} ! undifferentiated genital tubercle property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/8/87/Labelled_flaccid_penis.jpg xsd:anyURI property_value: has_relational_adjective "penile" xsd:string property_value: has_relational_adjective "phallic" xsd:string property_value: taxon_notes "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" xsd:string {source="WP"} [Term] id: UBERON:0000990 name: reproductive system def: "Anatomical system that has as its parts the organs concerned with reproduction." [Wikipedia:Reproductive_system] subset: efo_slim subset: functional_classification subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "animal reproductive system" RELATED [BTO:0000081] synonym: "genital system" RELATED [] synonym: "genital tract" RELATED [] synonym: "genitalia" RELATED PLURAL [] synonym: "Geschlechtsorgan" RELATED [BTO:0000081] synonym: "organa genitalia" RELATED [BTO:0000081] synonym: "reproductive tissue" RELATED [BTO:0000081] synonym: "reproductive tract" RELATED [] synonym: "systemata genitalia" RELATED LATIN [Wikipedia:Reproductive_system] xref: AAO:0010258 xref: BILA:0000103 xref: BTO:0000081 xref: CALOHA:TS-1318 xref: EFO:0000809 xref: EHDAA2:0001603 xref: EHDAA:5923 xref: EMAPA:17381 xref: EV:0100100 xref: FBbt:00004857 xref: FMA:7160 xref: GAID:363 xref: HAO:0000374 xref: HAO:0000895 xref: MA:0000326 xref: MIAA:0000305 xref: NCIT:C12841 xref: OpenCyc:Mx4rvVja4ZwpEbGdrcN5Y29ycA xref: SCTID:278875001 xref: TAO:0000632 xref: UMLS:C1261210 {source="ncithesaurus:Reproductive_System"} xref: VHOG:0000182 xref: WBbt:0005747 xref: Wikipedia:Reproductive_system xref: XAO:0000142 xref: ZFA:0000632 is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of_part_of GO:0000003 disjoint_from: UBERON:0001004 ! respiratory system disjoint_from: UBERON:0001007 ! digestive system disjoint_from: UBERON:0001008 ! renal system disjoint_from: UBERON:0001009 ! circulatory system disjoint_from: UBERON:0001016 ! nervous system disjoint_from: UBERON:0001033 ! gustatory system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002294 ! biliary system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of_part_of GO:0000003 relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: fma_set_term FMA:75572 relationship: has_part UBERON:0000991 ! gonad property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg xsd:anyURI property_value: editor_note "consider splitting genitalia from reproductive system" xsd:string property_value: external_definition "Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010258", ontology="AAO", source="AAO:BJB"} property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000991 name: gonad def: "Reproductive organ that produces and releases eggs (ovary) or sperm (testis)." [ISBN:0140512888, Wikipedia:Gonad, ZFA:0000413, ZFIN:curator] subset: major_organ subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "gonada" EXACT [] synonym: "gonads" RELATED PLURAL [ZFA:0000413] xref: AAO:0000213 xref: BILA:0000123 xref: BSA:0000079 xref: BTO:0000534 xref: EMAPA:17383 xref: FBbt:00004858 xref: FMA:18250 xref: GAID:368 xref: HAO:0000379 xref: MA:0002420 xref: MESH:D006066 xref: NCIT:C12725 xref: OpenCyc:Mx4rwQvdiZwpEbGdrcN5Y29ycA xref: SCTID:304623008 xref: TAO:0000413 xref: UMLS:C0018067 {source="ncithesaurus:Gonad"} xref: VHOG:0000397 xref: WBbt:0005175 xref: Wikipedia:Gonad xref: XAO:0003146 xref: ZFA:0000413 is_a: UBERON:0003133 ! reproductive organ intersection_of: UBERON:0003133 ! reproductive organ intersection_of: has_part CL:0000586 relationship: contains_process GO:0007276 relationship: develops_from UBERON:0005564 ! gonad primordium relationship: has_part CL:0000586 relationship: part_of UBERON:0000990 ! reproductive system property_value: external_definition "Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000213", ontology="AAO", source="AAO:BJB"} property_value: external_definition "The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000413", ontology="TAO", source="ZFIN:curator"} property_value: external_ontology_notes "FMA xref is a 'general anatomical term'" xsd:string {external_ontology="FMA"} property_value: has_relational_adjective "gonadal" xsd:string property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0000992 name: ovary def: "the gonad of a female organism which contains germ cells" [ISBN:0-683-40008-8, MP:0001126, Wikipedia:Ovary] subset: efo_slim subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "animal ovary" EXACT [EFO:0000973] synonym: "female gonad" EXACT [] synonym: "female organism genitalia gonad" EXACT [OBOL:automatic] synonym: "female organism genitalia gonada" EXACT [OBOL:automatic] synonym: "female organism reproductive system gonad" EXACT [OBOL:automatic] synonym: "female organism reproductive system gonada" EXACT [OBOL:automatic] synonym: "female reproductive system gonad" EXACT [OBOL:automatic] synonym: "female reproductive system gonada" EXACT [OBOL:automatic] synonym: "genitalia of female organism gonad" EXACT [OBOL:automatic] synonym: "genitalia of female organism gonada" EXACT [OBOL:automatic] synonym: "gonad of female organism genitalia" EXACT [OBOL:automatic] synonym: "gonad of female organism reproductive system" EXACT [OBOL:automatic] synonym: "gonad of female reproductive system" EXACT [OBOL:automatic] synonym: "gonad of genitalia of female organism" EXACT [OBOL:automatic] synonym: "gonad of reproductive system of female organism" EXACT [OBOL:automatic] synonym: "gonada of female organism genitalia" EXACT [OBOL:automatic] synonym: "gonada of female organism reproductive system" EXACT [OBOL:automatic] synonym: "gonada of female reproductive system" EXACT [OBOL:automatic] synonym: "gonada of genitalia of female organism" EXACT [OBOL:automatic] synonym: "gonada of reproductive system of female organism" EXACT [OBOL:automatic] synonym: "ovaries" RELATED PLURAL [] synonym: "ovarium" RELATED LATIN [Wikipedia:Ovary] synonym: "ovum-producing ovary" EXACT SENSU [GO:0061039] synonym: "reproductive system of female organism gonad" EXACT [OBOL:automatic] synonym: "reproductive system of female organism gonada" EXACT [OBOL:automatic] xref: AAO:0000371 xref: BILA:0000125 xref: BSA:0000080 xref: BTO:0000975 xref: CALOHA:TS-0730 xref: EFO:0000973 xref: EHDAA2:0001360 xref: EHDAA:8124 xref: EMAPA:17962 xref: EV:0100111 xref: FBbt:00004865 xref: FMA:7209 xref: GAID:367 xref: MA:0000384 xref: MESH:D010053 xref: MIAA:0000125 xref: NCIT:C12404 xref: OpenCyc:Mx4rvVi9QJwpEbGdrcN5Y29ycA xref: SCTID:181464007 xref: TAO:0000403 xref: UMLS:C0029939 {source="ncithesaurus:Ovary"} xref: VHOG:0000251 xref: Wikipedia:Ovary xref: XAO:0000258 xref: ZFA:0000403 is_a: UBERON:0000991 ! gonad is_a: UBERON:0003134 ! female reproductive organ intersection_of: UBERON:0000991 ! gonad intersection_of: part_of UBERON:0000474 ! female reproductive system disjoint_from: UBERON:0009117 ! indifferent gonad relationship: develops_from UBERON:0009117 ! indifferent gonad relationship: in_lateral_side_of UBERON:0003975 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA-abduced-lr"} ! internal female genitalia relationship: only_in_taxon NCBITaxon:33208 relationship: part_of UBERON:0000474 ! female reproductive system property_value: depicted_by Female:anatomy.png xsd:anyURI property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png xsd:anyURI property_value: external_definition "Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000371", ontology="AAO", source="AAO:BJB"} property_value: external_definition "Female reproductive organ.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000403", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "ovarian" xsd:string property_value: homology_notes "(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]" xsd:string {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/"} property_value: taxon_notes "Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo" xsd:string {source="WP"} [Term] id: UBERON:0000993 name: oviduct def: "A tube or collection of tubes in an animal from the ovaries to the outside of the body." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: uberon_slim subset: vertebrate_core synonym: "female reproductive tracts" RELATED [http://orcid.org/0000-0002-6601-2165] synonym: "ovarian duct" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "ovarian tube" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "oviducts" RELATED PLURAL [ZFA:0000560] synonym: "tuba uterina" RELATED [BTO:0000980] synonym: "tuba uterinae" RELATED [BTO:0000980] synonym: "tubular parts of female reproductive system" RELATED [http://orcid.org/0000-0002-6601-2165] synonym: "uterine tube" EXACT [] xref: AAO:0010533 xref: BSA:0000083 xref: BTO:0000980 xref: EFO:0000974 xref: EMAPA:18984 xref: GAID:366 xref: MAT:0000126 xref: MESH:D010057 xref: MIAA:0000126 xref: NCIT:C77957 xref: TAO:0000560 xref: UMLS:C0029954 {source="ncithesaurus:Oviduct"} xref: VHOG:0001136 xref: Wikipedia:Oviduct xref: XAO:0003052 xref: ZFA:0000560 is_a: UBERON:0000025 ! tube is_a: UBERON:0005156 ! reproductive structure relationship: connects UBERON:0000992 ! ovary relationship: connects UBERON:0013514 ! space surrounding organism relationship: only_in_taxon NCBITaxon:6072 relationship: part_of UBERON:0000474 ! female reproductive system property_value: curator_notes "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" xsd:string property_value: external_definition "A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001136", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/oviduct"} property_value: homology_notes "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]" xsd:string {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/"} property_value: taxon_notes "in birds divided into infundibulum, magnum, isthmus, uterus, and vagina" xsd:string property_value: taxon_notes "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]" xsd:string [Term] id: UBERON:0000994 name: spermathecum def: "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." [https://github.com/obophenotype/uberon/issues/1405, Wikipedia:Spermatheca] subset: dubious_grouping subset: efo_slim subset: uberon_slim synonym: "receptaculum seminis" RELATED [BTO:0001273] synonym: "seminal receptacle" RELATED [] synonym: "spermatheca" RELATED PLURAL [] synonym: "spermathecae" RELATED PLURAL [] xref: BTO:0001273 xref: EFO:0000977 xref: FBbt:00004921 xref: HAO:0000945 xref: MAT:0000168 xref: MIAA:0000168 xref: TGMA:0000560 xref: WBbt:0005319 xref: Wikipedia:Spermatheca is_a: CARO:0000000 is_a: UBERON:0000062 ! organ is_a: UBERON:0005156 ! reproductive structure relationship: only_in_taxon NCBITaxon:33213 relationship: part_of UBERON:0000991 ! gonad property_value: taxon_notes "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" xsd:string [Term] id: UBERON:0000995 name: uterus def: "the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth" [MGI:csmith, MP:0001120] subset: efo_slim subset: organ_slim subset: pheno_slim subset: uberon_slim xref: BTO:0001424 xref: CALOHA:TS-1102 xref: EFO:0000975 xref: EMAPA:29915 xref: EV:0100113 xref: FMA:17558 xref: GAID:172 xref: galen:Uterus xref: MA:0000389 xref: MAT:0000127 xref: MESH:D014599 xref: MIAA:0000127 xref: NCIT:C12405 xref: OpenCyc:Mx4rvViojJwpEbGdrcN5Y29ycA xref: SCTID:181452004 xref: UMLS:C0042149 {source="ncithesaurus:Uterus"} xref: VHOG:0001137 xref: Wikipedia:Uterus is_a: CARO:0000000 is_a: UBERON:0013515 {source="cjm"} ! subdivision of oviduct relationship: develops_from UBERON:0005795 ! embryonic uterus relationship: immediate_transformation_of UBERON:0005795 ! embryonic uterus relationship: only_in_taxon NCBITaxon:32525 relationship: part_of UBERON:0004175 ! internal genitalia property_value: depicted_by Female:anatomy.png xsd:anyURI property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/6a/Female_reproductive_system_lateral_nolabel.png xsd:anyURI property_value: development_notes "Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus]" xsd:string property_value: external_definition "The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001137", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/uterus"} property_value: has_relational_adjective "uterine" xsd:string property_value: homology_notes "An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]" xsd:string {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/"} property_value: taxon_notes "Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream." xsd:string [Term] id: UBERON:0000996 name: vagina def: "A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Vagina] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "distal oviductal region" RELATED [] synonym: "distal portion of oviduct" RELATED [] synonym: "vaginae" RELATED PLURAL [] xref: BTO:0000243 xref: CALOHA:TS-1103 xref: EFO:0000976 xref: EMAPA:18986 xref: EV:0100117 xref: FMA:19949 xref: GAID:381 xref: galen:Vagina xref: MA:0000394 xref: MAT:0000128 xref: MESH:D014621 xref: MIAA:0000128 xref: NCIT:C12407 xref: OpenCyc:Mx4rvVj1B5wpEbGdrcN5Y29ycA xref: SCTID:181441005 xref: UMLS:C0042232 {source="ncithesaurus:Vagina"} xref: VHOG:0001138 xref: Wikipedia:Vagina is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0013515 {source="cjm"} ! subdivision of oviduct relationship: contributes_to_morphology_of UBERON:0003975 ! internal female genitalia relationship: develops_from UBERON:0000164 {source="Wikipedia"} ! primitive urogenital sinus relationship: part_of UBERON:0003975 {source="FMA"} ! internal female genitalia property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/1/1b/Illu_repdt_female.jpg xsd:anyURI property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/a4/Vaginal_opening_-_english_description.jpg xsd:anyURI property_value: development_notes "'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" xsd:string property_value: external_definition "Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA]" xsd:string {date_retrieved="2012-11-29", external_class="FMA:19949", ontology="FMA"} property_value: external_definition "The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001138", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/vagina"} property_value: has_relational_adjective "vaginal" xsd:string property_value: homology_notes "The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0000997 name: mammalian vulva def: "external genital organs of the female mammal[WP]." [Wikipedia:Vulva] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "female pudendum" EXACT [BTO:0003101, FMA:20462] synonym: "mammalian vulva" EXACT [] synonym: "puboperineal region" EXACT [FMA:20462] synonym: "pudendum" RELATED [BTO:0003101] synonym: "pudendum femininum" EXACT LATIN [FMA:20462, FMA:TA] synonym: "pudendum femininum" RELATED LATIN [Wikipedia:Vulva] synonym: "pudendum muliebre" RELATED [BTO:0003101] synonym: "skin of female pudendum" EXACT [] synonym: "skin of vulva" EXACT [] synonym: "vulva" EXACT [MA:0000395] xref: BTO:0003101 xref: CALOHA:TS-1168 xref: EFO:0000978 xref: EMAPA:36631 xref: EV:0100118 xref: FMA:20462 xref: GAID:383 xref: galen:Vulva xref: MA:0000395 xref: MAT:0000169 xref: MESH:D014844 xref: MIAA:0000169 xref: NCIT:C12408 xref: OpenCyc:Mx4rvgAWeJwpEbGdrcN5Y29ycA xref: SCTID:265796001 xref: UMLS:C0042993 {source="ncithesaurus:Vulva"} xref: VHOG:0001458 xref: Wikipedia:Vulva is_a: UBERON:0000062 ! organ is_a: UBERON:0005156 ! reproductive structure relationship: only_in_taxon NCBITaxon:40674 relationship: part_of UBERON:0005056 ! external female genitalia property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/d/da/Female_unshaved_genitalia.jpg xsd:anyURI property_value: external_definition "The external genital organs of the female, including the labia majora, labia minora, clitoris, and vestibule of the vagina. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001458", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/vulva"} property_value: has_relational_adjective "vulval" xsd:string [Term] id: UBERON:0000998 name: seminal vesicle def: "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." [BTO:0001234, Wikipedia:Seminal_vesicle] subset: efo_slim subset: organ_slim subset: pheno_slim subset: uberon_slim synonym: "glandula seminalis" RELATED [BTO:0001234] synonym: "glandula vesiculosa" RELATED [BTO:0001234] synonym: "gonecyst" RELATED [] synonym: "seminal gland" BROAD [] synonym: "vas efferens" RELATED [] synonym: "vesicula seminalis" RELATED [BTO:0001234] synonym: "vesicula seminalis" RELATED [Wikipedia:Seminal_vesicle] synonym: "vesiculae seminales" RELATED LATIN [Wikipedia:Seminal_vesicle] synonym: "vesiculae seminales" RELATED [Wikipedia:Seminal_vesicle] synonym: "vesicular gland" RELATED [Wikipedia:Seminal_vesicle] synonym: "vesicular glands" RELATED [Wikipedia:Seminal_vesicle] synonym: "vesicular seminalis" RELATED [Wikipedia:Seminal_vesicle] synonym: "vesiculæ seminales" RELATED [Wikipedia:Seminal_vesicle] xref: AAO:0010788 xref: BTO:0001234 xref: CALOHA:TS-0919 xref: EFO:0000986 xref: EMAPA:19180 xref: EV:0100106 xref: FMA:19386 xref: GAID:394 xref: MA:0000410 xref: MAT:0000171 xref: MESH:D012669 xref: MIAA:0000171 xref: NCIT:C12787 xref: OpenCyc:Mx4rwTtRpJwpEbGdrcN5Y29ycA xref: SCTID:181434004 xref: UMLS:C0036628 {source="ncithesaurus:Seminal_Vesicle"} xref: VHOG:0001379 xref: Wikipedia:Seminal_vesicle is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0006868 ! seminal fluid secreting gland relationship: contributes_to_morphology_of UBERON:0004054 ! internal male genitalia relationship: develops_from UBERON:0000080 ! mesonephros relationship: part_of UBERON:0000473 ! testis relationship: produces UBERON:0010143 ! seminal vesicle fluid property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg xsd:anyURI property_value: external_definition "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001379", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/prominence"} property_value: function_notes "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." xsd:string property_value: homology_notes "(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]" xsd:string {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/"} [Term] id: UBERON:0000999 name: ejaculatory duct def: "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]." [Wikipedia:Ejaculatory_duct] subset: efo_slim subset: uberon_slim synonym: "ductus ejaculatorii" EXACT PLURAL [BTO:0001580] synonym: "ductus ejaculatorii" RELATED LATIN [Wikipedia:Ejaculatory_duct] synonym: "ductus ejaculatorius" EXACT [BTO:0001580] xref: BTO:0001580 xref: CALOHA:TS-0211 xref: EFO:0000985 xref: EMAPA:19088 xref: FMA:19325 xref: GAID:388 xref: MA:0003247 xref: MAT:0000170 xref: MESH:D004543 xref: MIAA:0000170 xref: NCIT:C32493 xref: OpenCyc:Mx4rwOt7MJwpEbGdrcN5Y29ycA xref: SCTID:279665005 xref: UMLS:C0013747 {source="ncithesaurus:Ejaculatory_Duct"} xref: Wikipedia:Ejaculatory_duct is_a: UBERON:0000025 ! tube is_a: UBERON:0005904 ! duct of male reproductive system is_a: UBERON:0015212 ! lateral structure relationship: capable_of_part_of GO:0042713 relationship: channel_for UBERON:0001968 ! semen relationship: channel_for UBERON:0010143 ! seminal vesicle fluid relationship: channels_from UBERON:0000998 ! seminal vesicle relationship: channels_from UBERON:0001000 ! vas deferens relationship: channels_into UBERON:0000057 ! urethra relationship: in_lateral_side_of UBERON:0000079 ! male reproductive system relationship: only_in_taxon NCBITaxon:7742 relationship: part_of UBERON:0000079 ! male reproductive system property_value: depicted_by Male:anatomy.png xsd:anyURI [Term] id: UBERON:0001000 name: vas deferens def: "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" [http://orcid.org/0000-0002-6601-2165, ISBN:0-683-40008-8, MGI:pvb, MP:0002769, Wikipedia:Vas_deferens] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "deferent duct" EXACT [] synonym: "ductus deferens" EXACT [Wikipedia:Vas_deferens] synonym: "sperm duct" RELATED [] synonym: "vas deferen" EXACT [] synonym: "vasa deferentia" RELATED [] xref: BTO:0001427 xref: CALOHA:TS-1105 xref: EFO:0000981 xref: EMAPA:18681 xref: EV:0100105 xref: FMA:19234 xref: GAID:404 xref: galen:VasDeferens xref: MA:0000413 xref: MESH:D014649 xref: MIAA:0000129 xref: NCIT:C12813 xref: OpenCyc:Mx4rvjv7bpwpEbGdrcN5Y29ycA xref: SCTID:245467009 xref: UMLS:C0042360 {source="ncithesaurus:Vas_Deferens"} xref: VHOG:0001135 xref: Wikipedia:Vas_deferens is_a: UBERON:0000025 ! tube is_a: UBERON:0005904 ! duct of male reproductive system relationship: channel_for UBERON:0001968 ! semen relationship: channels_from UBERON:0001301 ! epididymis relationship: channels_into UBERON:0000999 ! ejaculatory duct relationship: contributes_to_morphology_of UBERON:0004054 ! internal male genitalia relationship: only_in_taxon NCBITaxon:32524 relationship: part_of UBERON:0005352 {source="FMA"} ! spermatic cord relationship: part_of UBERON:0006947 ! male genital duct property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg xsd:anyURI property_value: homology_notes "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]" xsd:string {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/"} property_value: taxon_notes "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." xsd:string {source="WP"} [Term] id: UBERON:0001001 name: chitin-based cuticle alt_id: UBERON:FBbt_00004970 def: "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]." [https://orcid.org/0000-0002-6601-2165, https://sourceforge.net/tracker/index.php?func=detail&aid=3348965&group_id=36855&atid=440764, Wikipedia:Arthropod_exoskeleton, Wikipedia:Cuticle#Invertebrate_zoology] subset: efo_slim subset: uberon_slim synonym: "arthropod cuticle" RELATED [] synonym: "arthropod exoskeleton" RELATED [Wikipedia:Arthropod_exoskeleton] synonym: "cuticle" NARROW [FBbt:00004970] synonym: "exoskeleton" BROAD [] synonym: "insect cuticle" RELATED [] xref: EFO:0000944 xref: FBbt:00004970 xref: HAO:0000240 xref: MAT:0000150 xref: MIAA:0000150 xref: OpenCyc:Mx4rvVkBTJwpEbGdrcN5Y29ycA xref: Wikipedia:Arthropod_exoskeleton is_a: UBERON:0001002 ! cuticle is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0007491 ! chitin-based acellular structure intersection_of: UBERON:0001002 ! cuticle intersection_of: composed_primarily_of CHEBI:17029 relationship: composed_primarily_of CHEBI:17029 relationship: develops_from UBERON:0007376 ! outer epithelium relationship: only_in_taxon NCBITaxon:6656 relationship: part_of UBERON:0002416 ! integumental system property_value: editor_note "TODO - split from exoskeleton? Also: See above sf item to see if this belongs in GO" xsd:string [Term] id: UBERON:0001002 name: cuticle def: "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]." [http://sourceforge.net/tracker/?func=detail&aid=3348965&group_id=36855&atid=440764, Wikipedia:Cuticle] subset: grouping_class subset: non_informative subset: uberon_slim synonym: "cuticula" RELATED [BTO:0001600] synonym: "cuticular exoskeleton" RELATED [] xref: BTO:0001600 xref: Wikipedia:Cuticle is_a: UBERON:0000476 ! acellular anatomical structure disjoint_from: UBERON:0004882 ! eponychium relationship: only_in_taxon NCBITaxon:6072 {source="Rieger - Evolution of the Cuticle in the Lower Eumetazoa"} property_value: 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" xsd:string property_value: has_relational_adjective "cuticular" xsd:string [Term] id: UBERON:0001003 name: skin epidermis def: "The outer epithelial layer of the skin that is superficial to the dermis." [http://orcid.org/0000-0002-6601-2165, ISBN:0073040584] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "epidermis" BROAD [] synonym: "skin" BROAD [] synonym: "vertebrate epidermis" EXACT [] xref: AAO:0000143 xref: BTO:0000404 xref: CALOHA:TS-0283 xref: EFO:0000954 xref: EMAPA:17528 xref: EV:0100153 xref: FMA:70596 xref: GAID:932 xref: MA:0000153 xref: MAT:0000154 xref: MESH:D004817 xref: MIAA:0000154 xref: NCIT:C12708 xref: SCTID:361694003 xref: TAO:0000105 xref: UMLS:C0014520 {source="ncithesaurus:Epidermis"} xref: VHOG:0000077 xref: Wikipedia:Epidermis_(skin) xref: XAO:0000028 xref: ZFA:0000105 is_a: UBERON:0007376 ! outer epithelium intersection_of: UBERON:0007376 ! outer epithelium intersection_of: part_of UBERON:0002097 ! skin of body relationship: adjacent_to UBERON:0002067 ! dermis relationship: developmentally_replaces UBERON:0003055 ! periderm relationship: part_of UBERON:0002097 ! skin of body property_value: axiom_lost_from_external_ontology "relationship loss: subclass external integument structures (AAO:0000961)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000143", ontology="AAO"} property_value: external_definition "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]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000105", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000143", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "epidermal" xsd:string property_value: homology_notes "(...) 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]" xsd:string {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/"} property_value: taxon_notes "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)." xsd:string [Term] id: UBERON:0001004 name: respiratory system def: "Functional system which consists of structures involved in respiration." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Respiratory_system] subset: efo_slim subset: functional_classification subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "apparatus respiratorius" EXACT [] synonym: "apparatus respiratorius" RELATED [BTO:0000203] synonym: "Atmungssystem" RELATED [BTO:0000203] synonym: "respiratory system" EXACT [] synonym: "systema respiratorium" RELATED LATIN [Wikipedia:Respiratory_system] xref: AAO:0000541 xref: BTO:0000203 xref: CALOHA:TS-1319 xref: EFO:0000804 xref: EHDAA2:0001604 xref: EHDAA:2203 xref: EMAPA:16727 xref: EV:0100036 xref: FMA:7158 xref: GAID:78 xref: MA:0000327 xref: MAT:0000030 xref: MESH:D012137 xref: MIAA:0000030 xref: NCIT:C12779 xref: OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA xref: SCTID:278197002 xref: TAO:0000272 xref: UMLS:C0035237 {source="ncithesaurus:Respiratory_System"} xref: VHOG:0000202 xref: Wikipedia:Respiratory_system xref: XAO:0000117 xref: ZFA:0000272 is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of GO:0007585 disjoint_from: UBERON:0001007 ! digestive system disjoint_from: UBERON:0001008 ! renal system disjoint_from: UBERON:0001009 ! circulatory system disjoint_from: UBERON:0001016 ! nervous system disjoint_from: UBERON:0001033 ! gustatory system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002294 ! biliary system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0003016 relationship: capable_of GO:0007585 relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} relationship: only_in_taxon NCBITaxon:33213 property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg xsd:anyURI property_value: external_definition "The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000541", ontology="AAO", source="AAO:BJB"} property_value: homology_notes "There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0001005 name: respiratory airway def: "An airway through which respiratory air passes in organisms." [Wikipedia:Trachea] subset: grouping_class subset: uberon_slim synonym: "airway" BROAD [http://orcid.org/0000-0002-6601-2165] synonym: "airways" BROAD PLURAL [http://orcid.org/0000-0002-6601-2165] xref: FMA:265130 xref: SCTID:361380005 xref: Wikipedia:Trachea is_a: UBERON:0003103 ! compound organ is_a: UBERON:0004111 ! anatomical conduit relationship: channel_for UBERON:0034874 ! air in respiratory system relationship: part_of UBERON:0001004 ! respiratory system property_value: curator_notes "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" xsd:string [Term] id: UBERON:0001006 name: obsolete spiracle def: "OBSOLETE: The mostly slit-like opening on the body surface through which air is taken into the respiratory system." [ISBN:3110148986, Wikipedia:Spiracle] comment: This class was obsoleted as it grouped together disparate classes. For the fish structure, see UBERON:0010019. The arthropod structure will presumably be added to the arthropod anatomy subset: efo_slim synonym: "open tracheal system spiracle" NARROW [GO:0035277] synonym: "spiracle of open tracheal system" NARROW [GO:0035277] synonym: "spiracular gland" RELATED [] xref: EFO:0000936 xref: MAT:0000208 xref: MIAA:0000208 xref: Wikipedia:Spiracle is_obsolete: true consider: FBbt:00005054 consider: HAO:0000950 consider: TGMA:0000578 consider: UBERON:0010019 [Term] id: UBERON:0001007 name: digestive system def: "Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes." [FB:gg, NLM:alimentary+system, Wikipedia:Digestive_system] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "alimentary system" RELATED [] synonym: "alimentary tract" RELATED [] synonym: "gastrointestinal system" RELATED [] synonym: "gut" RELATED [] xref: AAO:0000129 xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 xref: EV:0100056 xref: FBbt:00005055 xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem xref: MA:0002431 xref: MAT:0000018 xref: MESH:D004064 xref: MIAA:0000018 xref: ncithesaurus:Digestive_System xref: SCTID:278859004 xref: TADS:0000170 xref: TAO:0000339 xref: WBbt:0005748 xref: Wikipedia:Digestive_system xref: XAO:0000125 xref: ZFA:0000339 is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of GO:0022600 disjoint_from: UBERON:0001008 ! renal system disjoint_from: UBERON:0001009 ! circulatory system disjoint_from: UBERON:0001016 ! nervous system disjoint_from: UBERON:0001033 ! gustatory system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002294 ! biliary system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0022600 relationship: existence_ends_during UBERON:0000066 ! fully formed stage property_value: external_definition "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000129", ontology="AAO", source="AAO:BJB"} property_value: external_ontology_notes "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" xsd:string {external_ontology="MA"} property_value: has_relational_adjective "digestive" xsd:string [Term] id: UBERON:0001008 name: renal system def: "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.." [DOI:10.1371/journal.pone.0099864, GO:0072001] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "excretory system" EXACT [] synonym: "renal or urinary system" RELATED [EHDAA:5901] synonym: "renal system" EXACT [GO:0001977] synonym: "renal/urinary system" RELATED [] synonym: "systema urinaria" EXACT [FMA:7159] synonym: "systema urinarium" EXACT [BTO:0003092] synonym: "urinary system" EXACT [] synonym: "urinary tract" EXACT [] xref: AAO:0010257 xref: BILA:0000015 xref: BTO:0001244 xref: BTO:0003092 xref: CALOHA:TS-1323 xref: EFO:0000803 xref: EHDAA2:0001601 xref: EHDAA:5901 xref: EMAPA:17366 xref: EV:0100095 xref: FBbt:00005056 xref: FMA:7159 xref: GAID:391 xref: galen:UrinaryTract xref: MA:0000325 xref: MAT:0000027 xref: MESH:D014551 xref: MIAA:0000027 xref: NCIT:C12413 xref: SCTID:362204003 xref: TADS:0000162 xref: TAO:0000163 xref: UMLS:C1508753 {source="ncithesaurus:Urinary_System"} xref: VHOG:0000723 xref: WBbt:0005736 xref: Wikipedia:Excretory_system xref: XAO:0000143 xref: ZFA:0000163 is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of GO:0007588 disjoint_from: UBERON:0001009 ! circulatory system disjoint_from: UBERON:0001016 ! nervous system disjoint_from: UBERON:0001033 ! gustatory system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002294 ! biliary system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0007588 relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} relationship: only_in_taxon NCBITaxon:6072 property_value: 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" xsd:string property_value: external_definition "An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010257", ontology="AAO", source="AAO:BJB"} property_value: homology_notes "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]" xsd:string {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/"} property_value: taxon_notes "In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels" xsd:string {source="GO"} property_value: taxon_notes "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" xsd:string {source="DOI:10.1371/journal.pone.0099864"} [Term] id: UBERON:0001009 name: circulatory system def: "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]." [Wikipedia:Circulatory_system] subset: uberon_slim synonym: "systema cardiovasculare" RELATED LATIN [Wikipedia:Circulatory_system] xref: AAO:0000959 xref: CALOHA:TS-2103 xref: FBbt:00005057 xref: OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA xref: VHOG:0001248 xref: Wikipedia:Circulatory_system is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0001016 ! nervous system disjoint_from: UBERON:0001033 ! gustatory system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002294 ! biliary system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0003013 relationship: dubious_for_taxon NCBITaxon:6231 {notes="WBbt coelomocyte currently classified as circulating cell"} relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} relationship: never_in_taxon NCBITaxon:6073 relationship: never_in_taxon NCBITaxon:6157 relationship: only_in_taxon NCBITaxon:33213 property_value: curator_notes "the cardiovascular system and the lymphatic system are parts of the circulatory system" xsd:string property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg xsd:anyURI property_value: external_definition "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]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000959", ontology="AAO", source="AAO:BJB"} property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0001010 name: diaphysis of ulna def: "The body of the ulna at its upper part is prismatic in form, and curved so as to be convex behind and lateralward; its central part is straight; its lower part is rounded, smooth, and bent a little lateralward. It tapers gradually from above downward, and has three borders and three surfaces." [Wikipedia:Body_of_ulna] synonym: "body of ulna" EXACT [FMA:33760] synonym: "corpus ulnae" EXACT [FMA:33760] synonym: "shaft of ulna" EXACT [FMA:33760] synonym: "shaft of ulna" RELATED [Wikipedia:Body_of_ulna] synonym: "supinator crest" RELATED [Wikipedia:Body_of_ulna] synonym: "ulnar diaphysis" EXACT [FMA:33760] xref: FMA:33760 xref: NCIT:C120676 xref: SCTID:302520004 xref: Wikipedia:Body_of_ulna is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004769 ! diaphysis is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0004769 ! diaphysis intersection_of: part_of UBERON:0001424 ! ulna relationship: part_of UBERON:0001424 ! ulna [Term] id: UBERON:0001011 name: hemolymph def: "Blood analogue used by all arthropods and most mollusks that have an open circulatory system. In these animals there is no distinction between blood and interstitial fluid. The liquid fills all of the interior (the hemocoel) of the body and surrounds all cells." [Wikipedia:Hemolymph] subset: uberon_slim synonym: "haemolymph" RELATED [] xref: BTO:0000572 xref: FBbt:00005061 xref: GAID:1220 xref: MAT:0000054 xref: MESH:D006458 xref: MIAA:0000054 xref: TGMA:0000000 xref: Wikipedia:Hemolymph is_a: UBERON:0000463 ! organism substance relationship: never_in_taxon NCBITaxon:33511 relationship: part_of UBERON:0001009 ! circulatory system [Term] id: UBERON:0001012 name: head of radius def: "The head of the radius has a cylindrical form, and on its upper surface is a shallow cup or fovea for articulation with the capitulum (or capitellum) of the humerus. The circumference of the head is smooth; it is broad medially where it articulates with the radial notch of the ulna, narrow in the rest of its extent, which is embraced by the annular ligament. The deepest point in the fovea is not axi-symmetric with the long axis of the radius, creating a cam effect during pronation and supination[WP]." [Wikipedia:Head_of_radius] subset: pheno_slim synonym: "caput radii" RELATED LATIN [Wikipedia:Head_of_radius] synonym: "radial head" EXACT [FMA:33773] xref: FMA:33773 xref: galen:HeadOfRadius xref: SCTID:181941003 xref: Wikipedia:Head_of_radius is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005055 ! zone of long bone is_a: UBERON:0005913 {source="FMA"} ! zone of bone organ is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001490 {source="FMA"} ! elbow joint relationship: part_of UBERON:0004413 {source="FMA"} ! proximal epiphysis of radius property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/4/47/Gray214.png xsd:anyURI [Term] id: UBERON:0001013 name: adipose tissue def: "Portion of connective tissue composed of adipocytes enmeshed in areolar tissue" [http://orcid.org/0000-0002-6601-2165, MESH:A10.165.114, MGI:cwg, MP:0000003, Wikipedia:Adipose_tissue] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "adipose" RELATED [BTO:0001487] synonym: "bodyfat" RELATED [BTO:0001487] synonym: "fat" EXACT [MA:0000009] synonym: "fat tissue" EXACT [] synonym: "fatty depot" RELATED [] synonym: "fatty tissue" EXACT [] xref: AAO:0000001 xref: AEO:000020 xref: BTO:0001487 xref: CALOHA:TS-0013 xref: EFO:0000790 xref: EHDAA2:0003120 xref: EMAPA:35112 xref: EV:0100381 xref: FMA:20110 xref: GAID:920 xref: galen:FattyTissue xref: MA:0000009 xref: MAT:0000015 xref: MESH:D000273 xref: MIAA:0000015 xref: NCIT:C12472 xref: OpenCyc:Mx4rvVjc_ZwpEbGdrcN5Y29ycA xref: SCTID:55603005 xref: TAO:0002134 xref: UMLS:C0001527 {source="ncithesaurus:Adipose_Tissue"} xref: VHOG:0001284 xref: Wikipedia:Adipose_tissue xref: XAO:0003049 xref: ZFA:0005345 is_a: CARO:0000000 is_a: UBERON:0011822 {source="FMA"} ! dense irregular connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: composed_primarily_of CL:0000136 disjoint_from: UBERON:0003714 ! neural tissue relationship: composed_primarily_of CL:0000136 relationship: only_in_taxon NCBITaxon:6072 property_value: axiom_lost_from_external_ontology "relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000001", ontology="AAO"} property_value: external_definition "Connective tissue in which fat is stored.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002134", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000001", ontology="AAO", source="AAO:LAP"} property_value: external_ontology_notes "in FMA this is dense irregular connective tissue" xsd:string {external_ontology="FMA"} property_value: has_relational_adjective "adipose" xsd:string property_value: homology_notes "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]" xsd:string {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/"} property_value: taxon_notes "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." xsd:string [Term] id: UBERON:0001014 name: obsolete fat body synonym: "fat pad" EXACT [] is_obsolete: true consider: UBERON:0003917 [Term] id: UBERON:0001015 name: musculature def: "A subdivision of the muscular system corresponding to a subdisivision of an organism." [https://orcid.org/0000-0002-6601-2165, Wikipedia:Muscular_system] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "muscle group" EXACT [] synonym: "muscle system" RELATED [] synonym: "muscles" RELATED [] synonym: "muscles set" EXACT [] synonym: "musculature" EXACT [] synonym: "musculature system" RELATED [] synonym: "musculi" EXACT LATIN [FMA:32558, FMA:TA] synonym: "set of muscles" EXACT [FMA:32558] synonym: "set of skeletal muscles" EXACT [MA:0000165] xref: AAO:0011066 xref: BTO:0000887 xref: EFO:0001949 xref: EMAPA:32715 xref: EMAPA:35577 xref: FMA:32558 xref: MA:0000165 xref: NCIT:C13056 xref: OpenCyc:Mx4rvVjmr5wpEbGdrcN5Y29ycA xref: TAO:0000548 xref: UMLS:C0026845 {source="ncithesaurus:Muscle"} xref: VSAO:0005038 xref: WBbt:0005737 xref: Wikipedia:Muscular_system xref: ZFA:0000548 is_a: UBERON:0011216 ! organ system subdivision relationship: composed_primarily_of UBERON:0001630 ! muscle organ relationship: part_of UBERON:0000383 ! musculature of body property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png xsd:anyURI property_value: external_ontology_notes "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." xsd:string {external_ontology="FMA"} [Term] id: UBERON:0001016 name: nervous system def: "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]." [BIRNLEX:844, ISBN:0-14-051288-8, ISBN:3110148986, NLM:nervous+system, WB:rynl, Wikipedia:Nervous_system, ZFIN:curator] subset: cumbo subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "nerve net" NARROW [Wikipedia:Nerve_net] synonym: "neurological system" EXACT [GO:0050877] synonym: "systema nervosum" RELATED LATIN [Wikipedia:Nervous_system] xref: AAO:0000324 xref: BILA:0000079 xref: BIRNLEX:844 xref: BTO:0001484 xref: CALOHA:TS-1313 xref: EFO:0000802 xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 xref: FBbt:00005093 xref: FMA:7157 xref: GAID:466 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=3236 xref: MA:0000016 xref: MAT:0000026 xref: MESH:D009420 xref: MIAA:0000026 xref: NCIT:C12755 xref: OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA xref: SCTID:278196006 xref: TAO:0000396 xref: UMLS:C0027763 {source="ncithesaurus:Nervous_System"} xref: VHOG:0000402 xref: WBbt:0005735 xref: Wikipedia:Nervous_system xref: XAO:0000177 xref: ZFA:0000396 is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0001033 ! gustatory system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002294 ! biliary system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0050877 relationship: composed_primarily_of CL:0002319 relationship: develops_from UBERON:0016880 ! future nervous system relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part CL:0000540 relationship: immediate_transformation_of UBERON:0016880 {source="Bgee:AN"} ! future nervous system relationship: never_in_taxon NCBITaxon:6040 relationship: only_in_taxon NCBITaxon:6072 property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg xsd:anyURI property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png xsd:anyURI property_value: external_definition "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000396", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000324", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "nervous" xsd:string property_value: has_relational_adjective "neural" xsd:string property_value: homology_notes "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0001017 name: central nervous system def: "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." [GO:0021551, http://www.frontiersinzoology.com/content/7/1/29, https://sourceforge.net/p/geneontology/ontology-requests/11422/] subset: cumbo subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "cerebrospinal axis" NARROW [FMA:55675] synonym: "CNS" EXACT ABBREVIATION [] synonym: "neuraxis" RELATED [FMA:55675] synonym: "systema nervosum centrale" EXACT LATIN [FMA:55675, FMA:TA] xref: AAO:0000090 xref: BAMS:CNS xref: BILA:0000080 xref: BIRNLEX:1099 xref: BTO:0000227 xref: CALOHA:TS-0150 xref: EFO:0000908 xref: EHDAA2:0000225 xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 xref: FBbt:00005094 xref: FMA:55675 xref: GAID:570 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=854 xref: MA:0000167 xref: MAT:0000457 xref: MESH:D002490 xref: NCIT:C12438 xref: OpenCyc:Mx4rvzYt3pwpEbGdrcN5Y29ycA xref: SCTID:278199004 xref: TAO:0000012 xref: UMLS:C0927232 {source="ncithesaurus:Central_Nervous_System"} xref: UMLS:C0927232 {source="BIRNLEX:1099"} xref: VHOG:0000293 xref: Wikipedia:Central_nervous_system xref: XAO:0000215 xref: ZFA:0000012 is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision relationship: develops_from UBERON:0001049 {gci_relation="part_of", gci_filler="NCBITaxon:7742", evidence="definitional"} ! neural tube relationship: develops_from UBERON:0016879 ! future central nervous system relationship: immediate_transformation_of UBERON:0016879 {source="Bgee:AN"} ! future central nervous system relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} relationship: only_in_taxon NCBITaxon:33213 relationship: part_of UBERON:0001016 ! nervous system property_value: external_definition "Part of the nervous system which includes the brain and spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000090", ontology="AAO", source="AAO:BJB"} property_value: external_definition "The brain and spinal cord. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000012", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "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)." xsd:string {source="BIRNLEX:1099"} property_value: homology_notes "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); 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]" xsd:string {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/"} [Term] id: UBERON:0001018 name: axon tract def: "A group of axons linking two or more neuropils and having a common origin, termination[FBbt]." [http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html, https://github.com/obophenotype/uberon/issues/286] comment: WP says this is the analog of peripheral nerves in CNS. subset: cumbo subset: pheno_slim synonym: "axonal tract" EXACT [] synonym: "nerve tract" NARROW [BIRNLEX:1649] synonym: "nerve tract" RELATED [] synonym: "neuraxis tract" EXACT [FMA:83847] synonym: "tract" RELATED [] synonym: "tract of neuraxis" EXACT [FMA:83847] xref: BIRNLEX:1649 xref: EV:0100304 xref: FBbt:00005100 xref: FMA:83847 xref: NLX:147822 is_a: UBERON:0000122 ! neuron projection bundle is_a: UBERON:0011215 ! central nervous system cell part cluster relationship: part_of UBERON:0001017 ! central nervous system property_value: external_definition "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)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} [Term] id: UBERON:0001019 name: nerve fasciculus def: "A slender neuron projection bundle[FBbt]; A bundle of anatomical fibers, as of muscle or nerve (American Heritage Dictionary 4th ed)." [BIRNLEX:872, FBbt:00005101] subset: uberon_slim synonym: "fascicle" BROAD [FBbt:00005101] synonym: "fasciculus" EXACT LATIN [] synonym: "nerve bundle" EXACT [FMA:12235] synonym: "nerve fasciculus" EXACT [FMA:12235] synonym: "nerve fiber tract" RELATED [BTO:0002191] synonym: "neural fasciculus" EXACT [FMA:12235] xref: BIRNLEX:872 xref: BTO:0002191 xref: EMAPA:36605 xref: FBbt:00005101 xref: FMA:12235 xref: NCIT:C32586 xref: TGMA:0000088 xref: UMLS:C1185741 {source="ncithesaurus:Fascicle"} xref: Wikipedia:Nervous_system_fascicle is_a: UBERON:0000122 ! neuron projection bundle property_value: editor_note "note FBbt class not disjoint from tract. Consider merging with 'neuron projection bundle'" xsd:string [Term] id: UBERON:0001020 name: nervous system commissure def: "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]." [https://github.com/obophenotype/uberon/issues/300, https://github.com/obophenotype/uberon/issues/325, NLXANAT:20090513] comment: *not* the same as FMA:76741 Commissure subset: cumbo subset: uberon_slim synonym: "commissure" BROAD [] synonym: "commissure of neuraxis" EXACT [FMA:83906] synonym: "neuraxis commissure" EXACT [FMA:83906] synonym: "white matter commissure" NARROW [CUMBO:CUMBO] xref: FBbt:00005103 xref: FMA:83906 xref: NCIT:C32349 xref: NLX:110 xref: NLXANAT:20090513 xref: OpenCyc:Mx4rdBrmE6gOEdudWQACs5b6Bw xref: TADS:0000201 xref: UMLS:C1185742 {source="ncithesaurus:Commissure"} xref: Wikipedia:Commissure is_a: UBERON:0001018 ! axon tract relationship: dc-contributor https://github.com/cmungall relationship: dc-contributor https://github.com/mellybelly relationship: intersects_midsagittal_plane_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0002316 {gci_relation="part_of", gci_filler="NCBITaxon:7742", notes="myelin not present in all taxa that have a commissure"} ! white matter property_value: external_definition "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)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} property_value: has_relational_adjective "commissural" xsd:string [Term] id: UBERON:0001021 name: nerve def: "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." [FBbt:00005105, http://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "nerves" EXACT PLURAL [TAO:0007009] synonym: "neural subtree" RELATED [FMA:65132] synonym: "peripheral nerve" EXACT [http://orcid.org/0000-0002-6601-2165] xref: AAO:0011070 xref: AEO:0000137 xref: BAMS:n xref: BIRNLEX:1615 xref: BSA:0000098 xref: BTO:0000925 xref: BTO:0001027 xref: CALOHA:TS-0772 xref: EHDAA2:0003137 xref: EHDAA:2851 xref: EHDAA:3776 xref: EHDAA:4657 xref: EMAPA:32808 xref: EMAPA:32815 xref: EV:0100371 xref: FBbt:00005105 xref: FMA:65132 xref: FMA:65239 xref: GAID:747 xref: GAID:758 xref: galen:Nerve xref: MA:0000217 xref: MA:0000228 xref: MESH:D010525 xref: NCIT:C12466 xref: NCIT:C12768 xref: NLX:147826 xref: OpenCyc:Mx4rwP3lkpwpEbGdrcN5Y29ycA xref: SCTID:244457007 xref: SCTID:256864008 xref: TAO:0007009 xref: UMLS:C0027740 {source="ncithesaurus:Nerve"} xref: UMLS:C0031119 {source="ncithesaurus:Peripheral_Nerve"} xref: VHOG:0000901 xref: Wikipedia:Nervous_system xref: XAO:0000204 xref: XAO:0003047 xref: ZFA:0007009 is_a: UBERON:0000122 {source="FBbt"} ! neuron projection bundle relationship: has_developmental_contribution_from UBERON:0002342 {gci_relation="part_of", gci_filler="NCBITaxon:7742", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neural crest relationship: has_quality PATO:0002045 relationship: part_of UBERON:0000010 ! peripheral nervous system property_value: external_definition "A portion of tissue which is a fasiculated group of axons.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0007009", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "nervous" xsd:string [Term] id: UBERON:0001022 name: obsolete cell body is_obsolete: true consider: FBbt:00005107 consider: FMA:67301 consider: GO:0043025 consider: NIF_Subcellular:sao1044911821 [Term] id: UBERON:0001023 name: obsolete dendrite def: "The region of a neuron receiving inputs from other neurons, typically a slender neurite, often branched. In insect neurons, this is often not a clear designation and often presynaptic sites co-extend with postsynaptic ones." [http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html, Wikipedia:Dendrite] comment: Made obsolete as it was equivalent to GO class subset: uberon_slim xref: Wikipedia:Dendrite property_value: has_relational_adjective "dendritic" xsd:string is_obsolete: true consider: FBbt:00005110 consider: FMA:67314 consider: GAID:749 consider: GO:0030425 consider: MESH:A08.663.256 consider: NCIT:C32447 consider: NIF_Subcellular:sao1211023249 consider: OpenCyc:Mx4rviIdspwpEbGdrcN5Y29ycA consider: TGMA:0001373 consider: UMLS:C0011305 [Term] id: UBERON:0001024 name: obsolete neurite def: "One of the processes or extensions of a neuron, axon or dendrite or cell body fiber. // Cell appendage of the neuron which includes the axon and the dendrite." [http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html, Wikipedia:Neurite] comment: Made obsolete as it was equivalent to GO class subset: uberon_slim xref: Wikipedia:Neurite is_obsolete: true consider: FBbt:00005113 consider: FMA:61814 consider: GAID:751 consider: GO:0043005 consider: MESH:A08.663.256.500 consider: NIF_Subcellular:sao-867568886 [Term] id: UBERON:0001025 name: obsolete synapse def: "The structural contact that is the site of transmission between neurons, identified by a presynaptic ribbon and synaptic vesicles as the input element and one or (usually) more postsynaptic elements with various specializations (membrane densities, cisternae, etc.)." [http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html, Wikipedia:Synapse] comment: Made obsolete as it was equivalent to GO class subset: uberon_slim synonym: "synaptic junction" EXACT [] xref: Wikipedia:Synapse property_value: has_relational_adjective "synaptic" xsd:string is_obsolete: true consider: FBbt:00005114 consider: FMA:67408 consider: GAID:766 consider: GO:0045202 consider: MESH:A08.850 consider: NCIT:C13281 consider: NIF_Subcellular:sao914572699 consider: SCTID:362298009 consider: UMLS:C0039062 [Term] id: UBERON:0001026 name: obsolete motor nerve def: "A motor nerve is an efferent nerve that exclusively contains the axons of somatic and branchial motoneurons, which innervate skeletal muscles (that ensure locomotion) and branchial muscles (that motorize the face and neck)[WP]." [Wikipedia:Motor_nerve] synonym: "efferent nerve" RELATED [] synonym: "nervus motorius" EXACT [] xref: Wikipedia:Motor_nerve is_obsolete: true replaced_by: UBERON:0006798 [Term] id: UBERON:0001027 name: sensory nerve def: "A nerve that transmits from sensory receptors on the surface of the body to the central nervous system." [UBERON:cjm, Wikipedia:Sensory_nerve] subset: pheno_slim subset: uberon_slim synonym: "afferent nerve" RELATED [] synonym: "nervus sensorius" EXACT LATIN [Wikipedia:Sensory_nerve] xref: AEO:0000201 xref: EHDAA2:0003200 xref: FBbt:00005136 xref: FMA:5868 xref: OpenCyc:Mx4rv0GdXpwpEbGdrcN5Y29ycA xref: Wikipedia:Sensory_nerve is_a: UBERON:0001021 ! nerve relationship: has_part CL:0000526 {source="AEO"} [Term] id: UBERON:0001028 name: diaphysis of radius def: "A diaphysis that is part of a radius bone[Automatically generated definition]." [OBOL:automatic, Wikipedia:Body_of_radius] subset: pheno_slim synonym: "body of radius" EXACT [FMA:33782] synonym: "corpus radii" EXACT [FMA:33782] synonym: "radial diaphysis" EXACT [FMA:33782] synonym: "radial shaft" RELATED [Wikipedia:Body_of_radius] synonym: "shaft of radius" EXACT [FMA:33782] synonym: "shaft of radius" RELATED [Wikipedia:Body_of_radius] xref: FMA:33782 xref: NCIT:C120674 xref: SCTID:302518002 xref: Wikipedia:Body_of_radius is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004769 ! diaphysis is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0004769 ! diaphysis intersection_of: part_of UBERON:0001423 ! radius bone relationship: part_of UBERON:0001423 ! radius bone property_value: external_definition "The body of the radius (or shaft of radius) is prismoid in form, narrower above than below, and slightly curved, so as to be convex lateralward. It presents three borders and three surfaces[Wikipedia:Body_of_radius]." xsd:string {source="Wikipedia:Body_of_radius"} [Term] id: UBERON:0001029 name: obsolete neuromuscular junction subset: uberon_slim synonym: "junctio neuromuscularis" RELATED LATIN [Wikipedia:Neuromuscular_junction] synonym: "synapsis neuromuscularis" RELATED LATIN [Wikipedia:Neuromuscular_junction] xref: Wikipedia:Neuromuscular_junction is_obsolete: true replaced_by: GO:0031594 consider: FBbt:00005142 consider: FMA:61803 consider: GAID:809 consider: MESH:D009469 consider: NIF_Subcellular:sao1124888485 [Term] id: UBERON:0001030 name: obsolete synaptic ribbon synonym: "ribbon synapse" EXACT [] is_obsolete: true consider: FBbt:00005143 consider: FMA:67107 consider: GO:0048788 consider: NIF_Subcellular:sao1884931180 [Term] id: UBERON:0001031 name: sheath of Schwann def: "The outermost nucleated cytoplasmic layer of Schwann cells that surrounds the axon of the neuron. It forms the outermost layer of the nerve fiber in the peripheral nervous system. The neurolemma is underlain by the basal lamina (referred to as the medullary sheath in the included illustrations. In CNS, axons are myelinated by oligodendrocytes, thus lack neurolemma." [Wikipedia:Neurolemma] subset: uberon_slim synonym: "endoneural membrane" RELATED [BTO:0003048] synonym: "neurilemma" EXACT [FMA:62976] synonym: "neurolemma" EXACT [] synonym: "Schwann's membrane" RELATED [BTO:0003048] synonym: "sheath of Schwann" EXACT [] xref: BTO:0003048 xref: FMA:62976 xref: GAID:730 xref: MESH:D009441 xref: NCIT:C33544 xref: UMLS:C0027807 {source="ncithesaurus:Sheath_of_Schwann"} xref: Wikipedia:Neurilemma is_a: CARO:0000000 is_a: UBERON:0000119 ! cell layer relationship: composed_primarily_of CL:0002573 relationship: part_of UBERON:0000010 ! peripheral nervous system relationship: surrounds GO:0030424 property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/34/Gray631.png xsd:anyURI property_value: external_ontology_notes "FMA def is 'Neural tissue which consists of Schwann cells' which does not fit, but we still use 'neural tissue' here. WP def specifically states Schwann cells, which would restrict it to PNS" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0001032 name: sensory system def: "Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information." [Wikipedia:Sensory_system] subset: efo_slim subset: uberon_slim subset: vertebrate_core synonym: "organa sensuum" EXACT LATIN [FMA:75259, FMA:TA] synonym: "organa sensuum" RELATED LATIN [Wikipedia:Sensory_system] synonym: "sense organ subsystem" EXACT [] synonym: "sense organs" EXACT [FMA:75259] synonym: "sense organs set" EXACT [FMA:75259] synonym: "sensory organ system" RELATED [] synonym: "sensory subsystem" EXACT [] synonym: "sensory systems" EXACT PLURAL [TAO:0000282] synonym: "set of sense organs" RELATED [FMA:75259] xref: AAO:0000555 xref: BAMS:SEN xref: BILA:0000099 xref: EFO:0000805 xref: EHDAA2:0003094 xref: EMAPA:16192 xref: FBbt:00007692 xref: FMA:75259 xref: MA:0002442 xref: MAT:0000031 xref: MIAA:0000031 xref: NLXANAT:090816 xref: TAO:0000282 xref: VHOG:0001674 xref: Wikipedia:Sensory_system xref: XAO:0003194 xref: ZFA:0000282 is_a: UBERON:0000467 ! anatomical system relationship: capable_of_part_of GO:0007600 relationship: part_of UBERON:0004456 ! entire sense organ system property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png xsd:anyURI property_value: external_ontology_notes "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" xsd:string property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0001033 name: gustatory system def: "The sensory system for the sense of taste." [NLXANAT:090803] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "gustatory organ system" EXACT [] synonym: "taste system" EXACT [] xref: AAO:0010577 xref: BILA:0000143 xref: EFO:0000830 xref: FMA:7194 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2889 xref: MA:0002446 xref: MAT:0000275 xref: MIAA:0000275 xref: NLXANAT:090803 xref: SCTID:423940004 xref: TAO:0001101 xref: Wikipedia:Gustatory_system xref: XAO:0003197 xref: ZFA:0001101 is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of_part_of GO:0050912 disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002294 ! biliary system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of_part_of GO:0050912 relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: only_in_taxon NCBITaxon:6072 property_value: external_definition "The sensory system for the sense of taste[NLXANAT:090803]." xsd:string {source="NLXANAT:090803"} property_value: external_definition "The sensory system used for the sense of taste.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010577", ontology="AAO", source="AAO:EJS"} property_value: external_ontology_notes "in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes" xsd:string {external_ontology="ZFA"} property_value: has_relational_adjective "gustatory" xsd:string [Term] id: UBERON:0001034 name: obsolete photoreceptor def: "Can refer to a light sensitive organ, a photoreceptor cell or a photoreceptor protein. This class was made obsolete because it was ambiguous" [Wikipedia:Photoreceptor] xref: BTO:0001060 xref: Wikipedia:Photoreceptor is_obsolete: true consider: CL:0000210 consider: FBbt:00005162 consider: FMA:85613 consider: GAID:778 [Term] id: UBERON:0001035 name: dento-alveolar joint def: "A joint that binds the teeth to the alveolar ridge." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Gomphosis] synonym: "dento-alveolar syndesmosis" EXACT [FMA:7495] synonym: "gomphosis" EXACT [MA:0001499] synonym: "peg-and-socket joint" EXACT [FMA:7495] synonym: "socket" BROAD [FMA:7495] synonym: "syndesmosis dentoalveolaris" EXACT LATIN [FMA:7495, FMA:TA] xref: EMAPA:37464 {source="MA:th"} xref: FMA:7495 xref: MA:0001499 xref: OpenCyc:Mx4rveAQeZwpEbGdrcN5Y29ycA xref: SCTID:50870008 xref: Wikipedia:Gomphosis is_a: UBERON:0002209 {source="FMA"} ! fibrous joint is_a: UBERON:0010313 ! neural crest-derived structure relationship: connects UBERON:0001091 ! calcareous tooth relationship: connects UBERON:0004103 ! alveolar ridge relationship: part_of UBERON:0001708 ! jaw skeleton property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray1003.png xsd:anyURI property_value: external_ontology_notes "MA classifies this as a cartilaginous joint" xsd:string {external_ontology="MA"} property_value: structure_notes "Specifically, the connection is made between the maxillary or mandible to the cementum of the tooth. The motion of a gomphosis is very minimal, though considerable movement can be achieved over time--the basis of using braces to realign teeth. The joint can be considered a synarthrosis or an amphiarthrosis. The gomphosis is the only joint-type in which a bone does not join another bone, as teeth are not technically bone. In modern, more anatomical, joint classification, the gomphosis is simply considered a fibrous joint because the tissue linking the structures is ligamentous[WP]" xsd:string [Term] id: UBERON:0001037 name: strand of hair def: "A filament, mostly protein, that grows from follicles found in the dermis[WP]." [Wikipedia:Hair] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "coat hair" RELATED [] synonym: "coat/ hair" RELATED [] synonym: "fur" RELATED [] synonym: "hair" EXACT [] synonym: "microchaeta" RELATED [] synonym: "quill" RELATED SENSU [] synonym: "setulae" RELATED [] synonym: "vibrissa" RELATED SENSU [] synonym: "whisker" RELATED SENSU [] xref: BTO:0001501 xref: CALOHA:TS-0430 xref: EFO:0000958 xref: EMAPA:18769 xref: EV:0100157 xref: FMA:53667 xref: GAID:71 xref: MA:0000155 xref: MAT:0000160 xref: MESH:D006197 xref: MIAA:0000160 xref: NCIT:C32705 xref: OpenCyc:Mx4rvVjOX5wpEbGdrcN5Y29ycA-Mp88EdaAAACgycbRww xref: SCTID:361702001 xref: UMLS:C0018494 {source="ncithesaurus:Hair"} xref: VHOG:0001191 xref: Wikipedia:Hair is_a: UBERON:0000021 {source="FMA"} ! cutaneous appendage is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0002073 ! hair follicle relationship: has_part GO:0045095 relationship: only_in_taxon NCBITaxon:40674 relationship: part_of UBERON:0001003 {source="FMA"} ! skin epidermis relationship: part_of UBERON:0011932 {source="FMA"} ! pilosebaceous unit property_value: curator_notes "this class defines an individual hair" xsd:string property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/2/25/Gray945.png xsd:anyURI property_value: editor_note "TODO for now we treat vibrissa/whisker as a syonym, but these have different follicles. We could introduce subclasses (see also: Pangolin scales)" xsd:string [Term] id: UBERON:0001038 name: chordotonal organ def: "Chordotonal organs are arthropod sensory structures consisting of special sensilla called the scolopidia, which are mechano-transducers and respond mainly to stretch or flexion. In insects, they consist of bundles of internal sensilla, each of which has a cap cell, an enveloping cell and one or more sense cells. The distal end of the organ is usually attached to the cuticle of the body wall, marked by a pit, a thickened disc or a nodule of chitin, and the base of the organ is connected with the hypodermis, often by a special ligament." [FB:FBrf0056378, Wikipedia:Chordotonal_organ] comment: To be ceded to Arthropod anatomy ontology subset: efo_slim subset: organ_slim subset: uberon_slim synonym: "ch" RELATED [] synonym: "scolopophorous organ" RELATED [] xref: EFO:0000940 xref: FBbt:00005215 xref: MAT:0000209 xref: MIAA:0000209 xref: Wikipedia:Chordotonal_organ is_a: UBERON:0000020 ! sense organ relationship: only_in_taxon NCBITaxon:6656 [Term] id: UBERON:0001040 name: yolk sac def: "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]." [Wikipedia:Yolk_sac] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "saccus vitellinus" RELATED LATIN [Wikipedia:Yolk_sac] synonym: "vesicula umbilicalis" RELATED LATIN [Wikipedia:Yolk_sac] xref: BTO:0001471 xref: CALOHA:TS-1130 xref: EFO:0003078 xref: EHDAA2:0002212 xref: EHDAA:164 xref: EMAPA:16085 xref: FMA:87180 xref: GAID:1301 xref: MESH:A16.254.403.981 xref: NCIT:C14128 xref: SCTID:362845002 xref: UMLS:C0043425 {source="ncithesaurus:Yolk_Sac"} xref: VHOG:0000830 xref: Wikipedia:Yolk_sac is_a: UBERON:0005292 ! extraembryonic tissue is_a: UBERON:0005631 {seeAlso="https://github.com/obophenotype/uberon/issues/635"} ! extraembryonic membrane is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac relationship: has_developmental_contribution_from UBERON:0000925 {source="ISBN:0073040584"} ! endoderm relationship: has_developmental_contribution_from UBERON:0004872 {source="ISBN:0073040584"} ! splanchnic layer of lateral plate mesoderm property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/1/17/Gray22.png xsd:anyURI property_value: editor_note "consider splitting class" xsd:string property_value: external_definition "One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000830", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/yolk+sac"} property_value: external_definition "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" xsd:string {source="MP:0001718"} property_value: homology_notes "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]" xsd:string {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/"} property_value: taxon_notes "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)]" xsd:string [Term] id: UBERON:0001041 name: foregut def: "Anterior subdivision of a digestive tract." [http://orcid.org/0000-0002-6601-2165] subset: developmental_classification subset: pheno_slim subset: uberon_slim synonym: "praeenteron" RELATED LATIN [Wikipedia:Foregut] synonym: "proenteron" RELATED LATIN [Wikipedia:Foregut] xref: AAO:0011042 xref: BILA:0000085 xref: BTO:0000507 xref: EHDAA2:0000557 xref: EHDAA:520 xref: EMAPA:16548 xref: FBbt:00005379 xref: FMA:45616 xref: MA:0001526 xref: NCIT:C34180 xref: SCTID:361409009 xref: TGMA:0001014 xref: UMLS:C0231051 {source="ncithesaurus:Foregut"} xref: VHOG:0000285 xref: Wikipedia:Foregut xref: XAO:0000232 is_a: UBERON:0004921 ! subdivision of digestive tract property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png xsd:anyURI property_value: editor_note "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" xsd:string property_value: external_definition "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." xsd:string {source="MP:0000474"} property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0001042 name: chordate pharynx def: "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]." [http://www.feedexp.org] comment: Consider generalizing to deuterostome pharynx subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "pharynx" BROAD SENSU [FMA:46688] xref: AAO:0000967 xref: BTO:0001049 xref: CALOHA:TS-0785 xref: EFO:0000836 xref: EHDAA2:0001458 xref: EHDAA:2947 xref: EMAPA:16706 xref: EV:0100065 xref: FMA:46688 xref: GAID:155 xref: galen:Pharynx xref: MA:0000432 xref: MESH:A03.867 xref: NCIT:C12425 xref: OpenCyc:Mx4rvViv7ZwpEbGdrcN5Y29ycA xref: SCTID:181211006 xref: TAO:0000056 xref: UMLS:C0031354 {source="ncithesaurus:Pharynx"} xref: VHOG:0000462 xref: Wikipedia:Pharynx xref: XAO:0003227 xref: ZFA:0000056 is_a: UBERON:0006562 ! pharynx relationship: continuous_with UBERON:0001043 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! esophagus relationship: develops_from UBERON:0009145 {source="EHDAA2"} ! pharyngeal region of foregut relationship: distally_connected_to UBERON:0001043 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! esophagus relationship: has_skeleton UBERON:0008895 {gci_relation="part_of", gci_filler="NCBITaxon:89593"} ! splanchnocranium relationship: only_in_taxon NCBITaxon:7711 relationship: part_of UBERON:0001004 ! respiratory system property_value: axiom_lost_from_external_ontology "relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000967", ontology="AAO"} property_value: axiom_lost_from_external_ontology "relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000967", ontology="AAO"} property_value: external_definition "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]." xsd:string {source="MESH:A03.867"} property_value: external_definition "Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000967", ontology="AAO", source="AAO:EJS"} property_value: external_definition "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]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000056", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "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]." xsd:string {source="ZFIN:ZDB-PUB-961014-576"} property_value: external_definition "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000462", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: external_ontology_notes "MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme" xsd:string {external_ontology="MA"} property_value: homology_notes "(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0001043 name: esophagus def: "Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993)." [http://www.rivm.nl/interspeciesinfo/inter/oesophagus/, Wikipedia:Esophagus] subset: efo_slim subset: major_organ subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "gullet" EXACT [] synonym: "oesophagus" EXACT [] xref: AAO:0000145 xref: ANISEED:1235301 xref: BTO:0000959 xref: CALOHA:TS-0700 xref: EFO:0000835 xref: EHDAA2:0001285 xref: EHDAA:2937 xref: EMAPA:16833 xref: EV:0100069 xref: FMA:7131 xref: GAID:291 xref: galen:Esophagus xref: MA:0000352 xref: MAT:0000048 xref: MESH:A03.365 xref: MIAA:0000048 xref: NCIT:C12389 xref: OpenCyc:Mx4rvVj9Q5wpEbGdrcN5Y29ycA xref: SCTID:181245004 xref: TAO:0000204 xref: UMLS:C0014876 {source="ncithesaurus:Esophagus"} xref: VHOG:0000450 xref: Wikipedia:Esophagus xref: XAO:0000127 xref: ZFA:0000204 is_a: UBERON:0000062 {source="FMA", source="MA"} ! organ is_a: UBERON:0004921 ! subdivision of digestive tract is_a: UBERON:0005178 ! thoracic cavity element is_a: UBERON:0013765 ! digestive system element relationship: develops_from UBERON:0001041 ! foregut relationship: distally_connected_to UBERON:0000945 {gci_relation="part_of", gci_filler="NCBITaxon:40674", notes="only in species that have a stomach"} ! stomach relationship: located_in UBERON:0002224 ! thoracic cavity relationship: part_of UBERON:0004908 ! upper digestive tract relationship: proximally_connected_to UBERON:0001042 ! chordate pharynx property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg xsd:anyURI property_value: external_definition "Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000145", ontology="AAO", source="AAO:EJS"} property_value: external_ontology_notes "esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995)" xsd:string {external_ontology="MA"} property_value: has_relational_adjective "esophageal" xsd:string property_value: homology_notes "The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0001044 name: saliva-secreting gland def: "saliva-secreting exocrine glands of the oral cavity[GO]" [GO:0007431, Wikipedia:Salivary_gland] subset: efo_slim subset: functional_classification subset: organ_slim subset: pheno_slim subset: uberon_slim synonym: "glandulae salivariae" RELATED LATIN [Wikipedia:Salivary_gland] synonym: "salivary gland" EXACT [MA:0000346] xref: BTO:0001203 xref: CALOHA:TS-0892 xref: EFO:0000859 xref: EHDAA2:0001775 xref: EHDAA:7987 xref: EMAPA:17751 xref: EV:0100059 xref: FBbt:00005382 xref: FMA:9597 xref: GAID:937 xref: galen:SalivaryGland xref: MA:0000346 xref: MAT:0000079 xref: MESH:D012469 xref: MIAA:0000079 xref: NCIT:C12426 xref: OpenCyc:Mx4rvVjl5ZwpEbGdrcN5Y29ycA xref: SCTID:181236000 xref: UMLS:C0036098 {source="ncithesaurus:Salivary_Gland"} xref: VHOG:0000376 xref: Wikipedia:Salivary_gland is_a: UBERON:0010047 ! oral gland intersection_of: UBERON:0002530 ! gland intersection_of: produces UBERON:0001836 ! saliva relationship: capable_of GO:0046541 relationship: contributes_to_morphology_of UBERON:0001007 ! digestive system relationship: located_in UBERON:0000167 ! oral cavity relationship: only_in_taxon NCBITaxon:33213 relationship: part_of UBERON:0002330 ! exocrine system relationship: produces UBERON:0001836 ! saliva property_value: curator_notes "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." xsd:string {source="3"} property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/5/51/Illu_quiz_hn_02.jpg xsd:anyURI property_value: external_definition "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000376", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "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]" xsd:string {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/"} property_value: taxon_notes "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" xsd:string [Term] id: UBERON:0001045 name: midgut def: "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]." [GO:0007494, Wikipedia:Midgut] subset: developmental_classification subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "mesenteron" RELATED LATIN [Wikipedia:Midgut] xref: BILA:0000086 xref: BTO:0000863 xref: EFO:0001950 xref: EHDAA2:0001185 xref: EHDAA:983 xref: EMAPA:16255 xref: FBbt:00005383 xref: FMA:45617 xref: MA:0001564 xref: NCIT:C34210 xref: SCTID:361410004 xref: TGMA:0001036 xref: UMLS:C0231052 {source="ncithesaurus:Midgut"} xref: VHOG:0000290 xref: Wikipedia:Midgut xref: XAO:0000103 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: proximally_connected_to UBERON:0001041 ! foregut property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg xsd:anyURI property_value: editor_note "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" xsd:string property_value: external_ontology_notes "in FMA this represents an embryonic region." xsd:string {external_ontology="FMA"} property_value: homology_notes "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]" xsd:string {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/"} property_value: taxon_notes "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" xsd:string {source="WP"} [Term] id: UBERON:0001046 name: hindgut def: "The caudalmost subdivision of a digestive tract." [http://orcid.org/0000-0002-6601-2165] subset: developmental_classification subset: pheno_slim subset: uberon_slim synonym: "metenteron" RELATED LATIN [Wikipedia:Hindgut] xref: AAO:0011052 xref: BILA:0000087 xref: BTO:0000510 xref: EHDAA2:0000779 xref: EHDAA:975 xref: EMAPA:16715 xref: FBbt:00005384 xref: FMA:45618 xref: MA:0001527 xref: NCIT:C34188 xref: SCTID:362856002 xref: TGMA:0001020 xref: UMLS:C0231053 {source="ncithesaurus:Hindgut"} xref: VHOG:0000459 xref: Wikipedia:Hindgut xref: XAO:0000104 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: develops_from UBERON:0003104 {source="Wikipedia"} ! mesenchyme relationship: proximally_connected_to UBERON:0001045 ! midgut property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png xsd:anyURI property_value: editor_note "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" xsd:string property_value: external_definition "the caudal portion of the primitive digestive tube of the embryo" xsd:string {source="MP:0008786"} property_value: external_ontology_notes "in FMA this class has no children. In MA it has a single child hindgut epithelium" xsd:string {external_ontology="FMA"} property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0001047 name: neural glomerulus alt_id: UBERON:FBbt_00005386 def: "Large synaptic bouton found in areas like olfactory bulb, cerebellar cortex and thalamus, that contacts many post-synaptic targets[NIF]." [http://ccdb.ucsd.edu/SAO/images/glomerulus_sw_512x512.jpg, http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html] comment: isa or partof neuropil? TODO. Add to GO-CC? subset: uberon_slim synonym: "glomerulus" BROAD [FBbt:00005386, NIF_Subcellular:sao587858733] xref: FBbt:00005386 xref: NIF_Subcellular:sao587858733 is_a: UBERON:0002606 ! neuropil property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg xsd:anyURI [Term] id: UBERON:0001048 name: primordium def: "Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]." [BTO:0001886, FB:DJS, FB:FBrf0089570, http://flybase.org/reports/FBrf0178740.html] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "bud" RELATED [] synonym: "future organ" RELATED [] synonym: "placode" RELATED [FBbt:00005495] synonym: "primordia" RELATED PLURAL [XAO:0003043] synonym: "rudiment" RELATED [] xref: AEO:0000171 xref: BTO:0001886 xref: EFO:0001652 xref: EHDAA2:0003171 xref: FBbt:00005495 xref: FMA:86589 xref: MAT:0000482 xref: NCIT:C34275 xref: UMLS:C0678727 {source="ncithesaurus:Primordium"} xref: Wikipedia:Primordium xref: XAO:0003043 is_a: UBERON:0005423 {source="EHDAA2"} ! developing anatomical structure relationship: part_of UBERON:0000468 ! multicellular organism [Term] id: UBERON:0001049 name: neural tube def: "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]." [Wikipedia:Neural_tube] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "neural primordium" RELATED [] synonym: "presumptive central nervous system" RELATED [] synonym: "tubus neuralis" RELATED LATIN [Wikipedia:Neural_tube] xref: AAO:0010617 xref: BTO:0001057 xref: CALOHA:TS-2371 xref: DHBA:10154 xref: EHDAA2:0001254 xref: EHDAA:2869 xref: EHDAA:908 xref: EMAPA:16164 xref: EMAPA:16757 xref: FMA:293882 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1365 xref: MAT:0000069 xref: MIAA:0000069 xref: NCIT:C34226 xref: SCTID:362852000 xref: TAO:0001135 xref: UMLS:C0231024 {source="ncithesaurus:Neural_Tube"} xref: VHOG:0000307 xref: Wikipedia:Neural_tube xref: XAO:0003204 xref: ZFA:0001135 is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0016879 ! future central nervous system relationship: develops_from UBERON:0005068 ! neural rod property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png xsd:anyURI property_value: development_notes "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" xsd:string {source="GO:0021915"} property_value: external_definition "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010617", ontology="AAO", source="AAO:JOR"} property_value: external_definition "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/neural+tube"} property_value: homology_notes "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0001050 name: obsolete atrium comment: obsoleted because 'atrium' as a general grouping class that encompasses the cardiac atrium and atrium of alveolus atrium is of questionable value. Furthermore, the use of the term 'atrium' in the generic sense is misleading, as this is commonly used to refer specifically to the cardiac atrium is_obsolete: true consider: FMA:85574 consider: UBERON:0002081 [Term] id: UBERON:0001051 name: hypopharynx def: "Bottom part of the pharynx that connects to the esophagus." [Wikipedia:Hypopharynx] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "laryngeal pharynx" EXACT [FMA:54877] synonym: "laryngopharynx" EXACT [FMA:54877] synonym: "pars laryngea pharyngis" RELATED LATIN [Wikipedia:Hypopharynx] synonym: "pars laryngea pharyngis" RELATED [BTO:0001740] xref: BTO:0001740 xref: CALOHA:TS-2020 xref: EFO:0001388 xref: EHDAA2:0004574 xref: EV:0100068 xref: FMA:54880 xref: GAID:338 xref: MA:0001796 xref: MESH:A03.867.490 xref: NCIT:C12246 xref: OpenCyc:Mx4rvq5O0JwpEbGdrcN5Y29ycA xref: SCTID:281490009 xref: UMLS:C0020629 {source="ncithesaurus:Hypopharynx"} xref: VHOG:0000445 xref: Wikipedia:Hypopharynx is_a: CARO:0000000 is_a: UBERON:0013522 ! subdivision of tube relationship: continuous_with UBERON:0013472 ! upper esophagus relationship: contributes_to_morphology_of UBERON:0001042 ! chordate pharynx relationship: part_of UBERON:0001042 ! chordate pharynx property_value: depicted_by Illu:pharynx.jpg xsd:anyURI property_value: external_definition "The inferior portion of the pharynx, between the epiglottis and the larynx. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000445", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/hypopharynx"} property_value: has_relational_adjective "hypopharyngeal" xsd:string [Term] id: UBERON:0001052 name: rectum def: "the terminal portion of the intestinal tube, terminating with the anus" [http://orcid.org/0000-0002-6601-2165, ISBN:0-683-40008-8, MP:0000492] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "intestinum rectum" RELATED [BTO:0001158] synonym: "rectal sac" RELATED [] synonym: "terminal portion of intestine" EXACT [] synonym: "terminal portion of large intestine" RELATED [] xref: AAO:0010401 xref: BTO:0001158 xref: CALOHA:TS-1180 xref: EFO:0000848 xref: EHDAA2:0001592 xref: EHDAA:5836 xref: EMAPA:17896 xref: EV:0100081 xref: FMA:14544 xref: GAID:311 xref: galen:Rectum xref: MA:0000336 xref: MAT:0000050 xref: MESH:A03.492.411.495.767 xref: MIAA:0000050 xref: NCIT:C12390 xref: OpenCyc:Mx4rvVjaU5wpEbGdrcN5Y29ycA xref: SCTID:181261002 xref: UMLS:C0034896 {source="ncithesaurus:Rectum"} xref: VHOG:0001751 xref: Wikipedia:Rectum xref: XAO:0000238 is_a: UBERON:0004921 {order="4", source="cjm"} ! subdivision of digestive tract relationship: continuous_with UBERON:0001159 ! sigmoid colon relationship: contributes_to_morphology_of UBERON:0000059 ! large intestine relationship: distalmost_part_of UBERON:0000059 {source="ISBN:0073040584"} ! large intestine relationship: part_of UBERON:0000059 {source="MA"} ! large intestine relationship: part_of UBERON:0006866 ! terminal part of digestive tract relationship: part_of UBERON:0012361 {source="EHDAA2"} ! internal anal region property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif xsd:anyURI property_value: external_definition "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001751", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: has_relational_adjective "rectal" xsd:string property_value: taxon_notes "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" xsd:string [Term] id: UBERON:0001053 name: arthropod neurohemal organ def: "A system of neurons that has the specialized function to produce and secrete hormones, and that constitutes, in whole or in part, an endocrine organ or system." [BTO:0002106] comment: brain areas from which substances enter blood for example, the neurohypophysis from which oxytocin and vasopressin enter blood. subset: efo_slim subset: organ_slim synonym: "neurohaemal organ" RELATED [] xref: BTO:0002106 xref: EFO:0000864 xref: FBbt:00005757 xref: MAT:0000212 xref: MIAA:0000212 is_a: UBERON:0010133 ! neuroendocrine gland relationship: part_of UBERON:0001016 {source="BTO"} ! nervous system property_value: external_ontology_notes "currently intended for invert structure; alt definitions include: organs in which intimate relationships between axons and terminal blood vessels are established" xsd:string [Term] id: UBERON:0001054 name: Malpighian tubule def: "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]." [Wikipedia:Malpighian_tubule_system] subset: efo_slim subset: uberon_slim synonym: "Malphigian tube" RELATED MISSPELLING [BTO:0000810] synonym: "Malpighian tube" RELATED [UBERON:cjm] synonym: "tuba Malpighii" RELATED [BTO:0000810] xref: BTO:0000810 xref: EFO:0000243 xref: FBbt:00005786 xref: GAID:1228 xref: MAT:0000123 xref: MESH:D008317 xref: MIAA:0000123 xref: SCTID:41055008 xref: TADS:0000163 xref: TGMA:0001038 xref: Wikipedia:Malpighian_tubule is_a: UBERON:0009773 {source="GO"} ! renal tubule relationship: only_in_taxon NCBITaxon:6656 property_value: editor_note "this will be ceded to the Arthropod Anatomy Ontology" xsd:string property_value: taxon_notes "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]" xsd:string [Term] id: UBERON:0001055 name: obsolete ureter is_obsolete: true consider: UBERON:0000056 consider: UBERON:0000057 [Term] id: UBERON:0001056 name: corpus cardiacum def: "One of a pair of neurohemal organs located on the walls of the aorta just behind the brain. The corpora cardiaca release their store of PTTH only after they receive a signal from neurosecretory cells in the brain." [BTO:0000432, http://en.wikipedia.org/wiki/Corpus_cardiacum#Endocrine_system, http://www.cals.ncsu.edu/course/ent425/tutorial/endocrine.html] comment: will be ceded to arthropod anatomy ontology subset: efo_slim synonym: "corpora cardiaca" RELATED PLURAL [BTO:0000432] xref: BTO:0000432 xref: EFO:0000380 xref: FBbt:00005799 xref: MAT:0000211 xref: MIAA:0000211 is_a: UBERON:0001053 ! arthropod neurohemal organ relationship: only_in_taxon NCBITaxon:50557 relationship: part_of UBERON:0012325 {source="BTO-modified"} ! retrocerebral complex [Term] id: UBERON:0001057 name: corpus allatum def: "One of a pair of separate or fused bodies in many insects that are sometimes closely associated with the corpora cardiaca and that secrete hormones (as juvenile hormone)[BTO]." [BTO:0000291, http://en.wikipedia.org/wiki/Corpora_allata, http://www.cals.ncsu.edu/course/ent425/tutorial/endocrine.html] comment: will be ceded to arthropod anatomy ontology subset: efo_slim subset: uberon_slim synonym: "corpora allata" RELATED PLURAL [BTO:0000291] xref: BTO:0000291 xref: EFO:0000379 xref: FBbt:00005800 xref: MAT:0000210 xref: MESH:D003335 xref: MIAA:0000210 is_a: UBERON:0002368 {source="BTO"} ! endocrine gland relationship: capable_of GO:0045443 {source="Wikipedia"} relationship: part_of UBERON:0012325 {source="BTO-modified"} ! retrocerebral complex property_value: taxon_notes "In Lepidoptera species, the corpus allatum acts as a release site for prothoracicotropic hormone which is generated by the brain" xsd:string property_value: taxon_notes "In many Diptera species, the corpus allatum is fused with the corpus cardiacum, forming Weismann's ring" xsd:string [Term] id: UBERON:0001058 name: mushroom body def: "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." [http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html, MESH:A13.641, Wikipedia:Mushroom_body] subset: efo_slim subset: uberon_slim synonym: "corpora pedunculata" RELATED [FBbt:00005801, PMID:21062451] synonym: "mushroom bodies" EXACT PLURAL [] xref: BTO:0002675 xref: EFO:0000925 xref: FBbt:00005801 xref: GAID:1231 xref: MAT:0000336 xref: MESH:D024521 xref: MIAA:0000336 xref: Wikipedia:Mushroom_body is_a: BFO:0000040 is_a: CARO:0000000 is_a: UBERON:0000477 ! anatomical cluster relationship: capable_of_part_of GO:0007613 {source="Wikipedia"} relationship: capable_of_part_of GO:0008355 {source="Wikipedia"} relationship: never_in_taxon NCBITaxon:6217 relationship: only_in_taxon NCBITaxon:33317 {notes="annelids and arthropods"} relationship: part_of UBERON:0000955 ! brain relationship: present_in_taxon NCBITaxon:6340 relationship: present_in_taxon NCBITaxon:6656 property_value: taxon_notes "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'" xsd:string {source="PMID:20813265"} [Term] id: UBERON:0001059 name: pars intercerebralis def: "A neurosecretory center of the insect brain, located along the anterior midline[wiktionary]. A medial cleft or depression dividing the left and right protocerebrum and containing numerous large and small somata of neurosecretory and neuromodulatory neurons[FBbt]." [http://en.wiktionary.org/wiki/pars_intercerebralis, http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html] comment: will be ceded to arthropod anatomy ontology subset: efo_slim subset: uberon_slim xref: EFO:0000926 xref: FBbt:00005802 xref: MAT:0000337 xref: MIAA:0000337 is_a: UBERON:0011215 ! central nervous system cell part cluster relationship: only_in_taxon NCBITaxon:6656 relationship: part_of UBERON:0000955 {source="FBbt"} ! brain [Term] id: UBERON:0001062 name: anatomical entity def: "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." [FMA:62955, http://orcid.org/0000-0001-9114-8737] subset: upper_level xref: AAO:0010841 xref: AEO:0000000 xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 xref: FBbt:10000000 xref: FBbt_root:00000000 xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 xref: NCIT:C12219 xref: TAO:0100000 xref: TGMA:0001822 xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance"} xref: WBbt:0000100 xref: XAO:0000000 xref: ZFA:0100000 is_a: BFO:0000004 [Term] id: UBERON:0001063 name: flocculus alt_id: UBERON:Flocculus-MA_0000992 def: "the small lobe of the cerebellum at the posterior border of the middle cerebellar peduncle anterior to the biventer lobule that receives input from the inferior and medial vestibular nuclei and sends fibers back to the vestibular nuclei, and processes and integrates these signals to allow for the constant maintenance of balance" [http://orcid.org/0000-0002-6601-2165, ISBN:0838580343, MGI:csmith, MP:0010006, Wikipedia:Flocculus_(cerebellar)] subset: pheno_slim subset: uberon_slim synonym: "flocculus of cerebellum" EXACT [FMA:83881] synonym: "H X" RELATED [FMA:83881] synonym: "hemispheric lobule X" RELATED INCONSISTENT [NLXANAT:20081213] synonym: "lobule H X of Larsell" RELATED [FMA:83881] synonym: "lobule X" RELATED [FMA:83881] synonym: "lobule X of hemisphere of cerebellum" RELATED [FMA:83881] synonym: "neuraxis flocculus" EXACT [FMA:83881] xref: BAMS:FL xref: BAMS:Fl xref: BIRNLEX:1329 xref: DMBA:16946 xref: EMAPA:35346 xref: FMA:83881 xref: HBA:12945 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=680 xref: MA:0000992 xref: MBA:1049 xref: SCTID:279368002 xref: SCTID:30711003 xref: Wikipedia:Flocculus_(cerebellar) is_a: UBERON:0027331 ! flocculonodular lobe, hemisphere portion relationship: contributes_to_morphology_of UBERON:0002245 ! cerebellar hemisphere relationship: part_of UBERON:0002129 ! cerebellar cortex relationship: part_of UBERON:0002245 ! cerebellar hemisphere relationship: part_of UBERON:0003012 {source="FMA-abduced-lr"} ! flocculonodular lobe property_value: external_ontology_notes "flocculus is an exact label for two distinct classes in NIF." xsd:string {external_ontology="NIF"} property_value: function_notes "At its base, the flocculus receives input from the middle ears vestibular system and regulates balance. Many floccular projections descend to the spinal cord and connect to the motor nuclei involved in control of eye movement." xsd:string {source="WP"} property_value: taxon_notes "enlarged in pterosaurs" xsd:string {source="PMID:14586467"} [Term] id: UBERON:0001064 name: ventral pancreatic duct alt_id: UBERON:0005627 def: "A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla." [Wikipedia:Pancreatic_duct] subset: uberon_slim synonym: "canal of Wirsung" RELATED [BTO:0002362] synonym: "chief pancreatic duct" EXACT [FMA:16003] synonym: "duct of Wirsung" EXACT [Wikipedia:Pancreatic_duct] synonym: "ductus pancreatis ventralis" RELATED [] synonym: "hepaticopancreatic duct" RELATED [BTO:0002362] synonym: "main pancreatic duct" EXACT [MA:0000126] synonym: "pancreatic duct" BROAD [MESH:A03.734.667] xref: BTO:0002362 xref: EHDAA2:0001396 xref: EHDAA:6905 xref: EMAPA:17510 xref: FMA:16003 xref: GAID:337 xref: MA:0000126 xref: MESH:D010183 xref: NCIT:C12272 xref: RETIRED_EHDAA2:0002177 xref: SCTID:245385001 xref: UMLS:C0030288 {source="ncithesaurus:Pancreatic_Duct"} xref: VHOG:0000256 xref: Wikipedia:Pancreatic_duct is_a: UBERON:0000025 ! tube is_a: UBERON:0007329 {source="FMA"} ! pancreatic duct relationship: channel_for UBERON:0001970 ! bile relationship: channels_into UBERON:0004913 ! hepatopancreatic ampulla relationship: continuous_with UBERON:0001174 ! common bile duct relationship: develops_from UBERON:0003924 {source="EHDAA2"} ! ventral pancreatic bud relationship: part_of UBERON:0000017 ! exocrine pancreas property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png xsd:anyURI property_value: development_notes "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." xsd:string {source="WP"} property_value: editor_note "in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue" xsd:string property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0001065 name: parotid main excretory duct def: "The main excretory tubular canal that connects the parotid gland and the buccal mucosa and secretes a serous saliva into the vestibule of the oral cavity; it arises from the anterior surface of the gland, traversing the masseter muscle; the duct then pierces the buccinator muscle, moving medially, and opens out into the oral cavity near the second upper molar; saliva produced by acinar secretory cells in the glandular body flows sequentially through the intercalated ducts, striated ducts, and excretory ducts." [MP:0009530] subset: pheno_slim subset: uberon_slim synonym: "duct of parotid" BROAD [OBOL:automatic] synonym: "duct of parotid gland" BROAD [] synonym: "ductus parotideus" RELATED LATIN [Wikipedia:Parotid_duct] synonym: "ductus stenonianus" RELATED LATIN [BTO:0004554] synonym: "excretory duct of parotid gland" BROAD [] synonym: "main duct of parotid gland" EXACT [] synonym: "main excretory duct of parotid gland" EXACT [] synonym: "parotid duct" BROAD [MA:0002697] synonym: "parotid excretory duct" BROAD [] synonym: "parotid gland duct" BROAD [OBOL:automatic] synonym: "Stenon duct" EXACT [] synonym: "stenonianus" RELATED [BTO:0004554] synonym: "Stensen's duct" EXACT [] synonym: "Stensens's duct" EXACT [] xref: BTO:0004554 xref: EMAPA:36563 xref: FMA:10420 xref: MA:0002697 xref: NCIT:C33277 xref: SCTID:362175009 xref: UMLS:C0227458 {source="ncithesaurus:Parotid_Duct"} xref: Wikipedia:Parotid_duct is_a: UBERON:0035048 ! parotid gland excretory duct relationship: channels_from UBERON:0001831 ! parotid gland relationship: contributes_to_morphology_of UBERON:0001831 ! parotid gland relationship: part_of UBERON:0001831 ! parotid gland property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1023.png xsd:anyURI property_value: editor_note "we follow MP in identifying the 'parotid duct' with the main excretory duct, although in fact the parotid has many other ducts of different types" xsd:string [Term] id: UBERON:0001066 name: intervertebral disk def: "A pad of fibrocartilage between the articular surfaces of two successive vertebral centra which has nucleus pulposus at its core." [ISBN:0073040584, Wikipedia:Intervertebral_disk] comment: whose gel-like core is nucleus puloposus, by this definition only in mammals subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "discus intervertebralis" EXACT LATIN [FMA:10446, FMA:TA] synonym: "intervertebral disc" EXACT [] synonym: "intervertebral fibrocartilage" RELATED [BTO:0003625] synonym: "spinal disc" EXACT [Wikipedia:Spinal_disc] synonym: "spinal disk" RELATED [BTO:0003625] xref: BTO:0003625 xref: EFO:0001370 xref: EMAPA:32739 xref: FMA:10446 xref: GAID:105 xref: MA:0000110 xref: MESH:A02.165.410 xref: NCIT:C49571 xref: OpenCyc:Mx4rv11AcpwpEbGdrcN5Y29ycA xref: SCTID:244570000 xref: UMLS:C0021815 {source="ncithesaurus:Intervertebral_Disc"} xref: Wikipedia:Intervertebral_disk is_a: UBERON:0011135 ! intervertebral cartilage intersection_of: UBERON:0011135 ! intervertebral cartilage intersection_of: has_part UBERON:0002242 ! nucleus pulposus relationship: has_part UBERON:0002242 ! nucleus pulposus property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/9/92/Gray301.png xsd:anyURI property_value: taxon_notes "strictly speaking the term intervertebral disk [applies to intervertebral cartilage]" xsd:string [Term] id: UBERON:0001067 name: vertebral arch joint def: "A synovial joint between the prezygapophysis of one vertebra and the postzygapophysis of the vertebra directly above it. There are two facet joints in each spinal motion segment[WP]." [Wikipedia:Zygapophysial_joint] subset: pheno_slim subset: uberon_slim synonym: "articulationes zygapophysiales" RELATED LATIN [Wikipedia:Zygapophysial_joint] synonym: "facet joint" EXACT [] synonym: "joint of vertebral arch" EXACT [] synonym: "joint of vertebral articular process" EXACT [] synonym: "spinal facet joint" EXACT [HP:0008482] synonym: "zygapophyseal joint" EXACT [] synonym: "zygapophysial joint" EXACT [] xref: FMA:10447 xref: GAID:275 xref: MA:0001513 xref: MESH:D021801 xref: NCIT:C32577 xref: OpenCyc:Mx4rvorHEpwpEbGdrcN5Y29ycA xref: SCTID:89836005 xref: UMLS:C0224521 {source="ncithesaurus:Facet_Joint"} xref: Wikipedia:Zygapophysial_joint is_a: UBERON:0002217 ! synovial joint is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0002217 ! synovial joint intersection_of: connects UBERON:0001079 ! prezygapophysis intersection_of: connects UBERON:0001080 ! postzygapophysis relationship: connects UBERON:0001079 ! prezygapophysis relationship: connects UBERON:0001080 ! postzygapophysis relationship: part_of UBERON:0003861 ! neural arch property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray90.png xsd:anyURI [Term] id: UBERON:0001068 name: skin of back def: "A zone of skin that is part of a back [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "back skin" EXACT [] synonym: "back zone of skin" EXACT [OBOL:automatic] synonym: "skin, dorsal region" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "zone of skin of back" EXACT [OBOL:automatic] xref: EMAPA:36392 xref: FMA:10462 xref: FMA:22985 xref: MA:0000498 xref: SCTID:181492002 is_a: UBERON:0001085 {source="MA"} ! skin of trunk intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001137 ! dorsum relationship: part_of UBERON:0001137 ! dorsum relationship: part_of UBERON:0011270 {source="MA"} ! dorsal trunk property_value: editor_note "TODO - distinguish between entire skin of region and arbitrary zone of skin on region" xsd:string [Term] id: UBERON:0001069 name: head of pancreas def: "The head of pancreas is a portion of the pancreas that is lodged within the curve of the duodenum, and is flattened anteriorly (from before). The other parts of the pancreas are the body and the tail. Its upper border is overlapped by the superior part of the duodenum and its lower overlaps the horizontal part; its right and left borders overlap in front, and insinuate themselves behind, the descending and ascending parts of the duodenum respectively. [WP,unvetted]." [Wikipedia:Head_of_pancreas] subset: uberon_slim synonym: "caput pancreatis" RELATED LATIN [Wikipedia:Head_of_pancreas] synonym: "pancreas head" EXACT [] synonym: "pancreatic head" EXACT [] synonym: "right extremity of pancreas" EXACT [] xref: EHDAA2:0001374 xref: EMAPA:17507 xref: FMA:10468 xref: MA:0000122 xref: NCIT:C12269 xref: SCTID:362201006 xref: UMLS:C0227579 {source="ncithesaurus:Head_of_the_Pancreas"} xref: VHOG:0000448 xref: Wikipedia:Head_of_pancreas is_a: UBERON:0000064 ! organ part is_a: UBERON:0004119 ! endoderm-derived structure relationship: develops_from UBERON:0003924 {source="EHDAA2-inferred", source="WP"} ! ventral pancreatic bud relationship: part_of UBERON:0001264 ! pancreas property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/f/fe/Illu_pancreas_duodenum.jpg xsd:anyURI property_value: homology_notes "Hagfish and lampreys may have one or more endocrine buds - and later the vertebrate pancreas develop as independent ventral and dorsal buds that eventually fuse to become one organ.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000448", ontology="VHOG", source="DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. Comptes Rendus Biologies (2007)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001070 name: external carotid artery def: "A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP]" [MGI:anna] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "arteria carotis externa" RELATED LATIN [Wikipedia:External_carotid_artery] synonym: "external carotid" EXACT [AAO:0010218] xref: AAO:0010218 xref: AAO:0010416 xref: BTO:0004696 xref: EFO:0001953 xref: EHDAA2:0000461 xref: EMAPA:18611 xref: FMA:10635 xref: GAID:480 xref: MA:0001929 xref: MESH:D002342 xref: NCIT:C32551 xref: OpenCyc:Mx4rwVJkPZwpEbGdrcN5Y29ycA xref: SCTID:362044002 xref: UMLS:C0007275 {source="ncithesaurus:External_Carotid_Artery"} xref: VHOG:0000265 xref: Wikipedia:External_carotid_artery xref: XAO:0000345 is_a: UBERON:0005396 {source="MA"} ! carotid artery segment is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: branching_part_of UBERON:0001530 {source="FMA"} ! common carotid artery plus branches relationship: develops_from UBERON:0001530 {source="EHDAA2"} ! common carotid artery plus branches relationship: develops_from UBERON:0004363 ! pharyngeal arch artery relationship: part_of UBERON:0001530 {source="FMA"} ! common carotid artery plus branches property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/1/13/External_carotid_a.gif xsd:anyURI property_value: seeAlso https://sourceforge.net/tracker/?func=detail&aid=3486863&group_id=76834&atid=1127722 xsd:anyURI property_value: taxon_notes "not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO" xsd:string [Term] id: UBERON:0001071 name: superficial cervical artery def: "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." [Wikipedia:Superficial_part_of_transverse_cervical_artery] comment: The transverse cervical artery splits into two branches, a superficial one and a deep one[WP] subset: uberon_slim synonym: "superficial branch of transverse cervical artery" EXACT [Wikipedia:Superficial_part_of_transverse_cervical_artery] xref: EMAPA:37117 {source="MA:th"} xref: FMA:10665 xref: MA:0002052 xref: NCIT:C53005 xref: SCTID:161746006 xref: UMLS:C0226271 {source="ncithesaurus:Superficial_Cervical_Artery"} xref: Wikipedia:Superficial_part_of_transverse_cervical_artery is_a: UBERON:0012320 ! cervical artery intersection_of: UBERON:0012320 ! cervical artery intersection_of: part_of UBERON:0035549 ! vasculature of integument relationship: part_of UBERON:0035549 ! vasculature of integument [Term] id: UBERON:0001072 name: posterior vena cava def: "A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Inferior_vena_cava] subset: pheno_slim subset: uberon_slim synonym: "caudal vena cava" RELATED [VHOG:0001194] synonym: "inferior caval vein" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "inferior vena cava" EXACT [Wikipedia:Venae_cavae] synonym: "postcava" RELATED [] synonym: "posterior vena cava" EXACT [Wikipedia:Venae_cavae] synonym: "vena cava inferior" RELATED [BTO:0002682] synonym: "vena cava inferior" RELATED LATIN [Wikipedia:Inferior_vena_cava] xref: AAO:0011083 xref: BTO:0002682 xref: EHDAA2:0000611 xref: EMAPA:18416 xref: FMA:10951 xref: GAID:548 xref: galen:InferiorVenaCava xref: MA:0000480 xref: MESH:D014682 xref: NCIT:C12815 xref: SCTID:181369003 xref: UMLS:C0042458 {source="ncithesaurus:Inferior_Vena_Cava"} xref: VHOG:0001194 xref: Wikipedia:Inferior_vena_cava xref: XAO:0000388 is_a: UBERON:0004087 ! vena cava intersection_of: UBERON:0004087 ! vena cava intersection_of: drains UBERON:0000154 ! posterior region of body disjoint_from: UBERON:0001585 {source="lexical"} ! anterior vena cava relationship: channels_into UBERON:0002078 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! right cardiac atrium relationship: develops_from UBERON:0005487 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="Wikipedia:Vitelline_vein"} ! vitelline vein relationship: drains UBERON:0000154 ! posterior region of body property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png xsd:anyURI property_value: external_definition "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]." xsd:string {source="FMA:10951"} property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0001073 name: ileocecal junction def: "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" [http://www.medilexicon.com/medicaldictionary.php?t=46539] synonym: "ileocaecal junction" EXACT [] xref: EMAPA:37601 {source="MA:th"} xref: FMA:11338 xref: MA:0000332 xref: SCTID:264021000 is_a: UBERON:8410024 ! intestinal junction intersection_of: UBERON:0007651 ! anatomical junction intersection_of: connects UBERON:0000059 ! large intestine intersection_of: connects UBERON:0002108 ! small intestine relationship: connects UBERON:0000059 ! large intestine relationship: connects UBERON:0002108 ! small intestine relationship: only_in_taxon NCBITaxon:7742 relationship: part_of UBERON:0000160 ! intestine [Term] id: UBERON:0001074 name: pericardial cavity def: "A potential space between the visceral and parietal layers of the pericardium." [Wikipedia:Pericardium] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "cavitas pericardiaca" RELATED LATIN [Wikipedia:Pericardial_cavity] synonym: "cavity of pericardial sac" EXACT [] synonym: "pericardial space" EXACT [Wikipedia:Pericardial_cavity] xref: BSA:0000091 xref: EHDAA2:0001434 xref: EMAPA:16131 xref: EMAPA:16132 xref: FMA:11350 xref: galen:PericardialSpace xref: MA:0000053 xref: NCIT:C38662 xref: SCTID:362027001 xref: TAO:0002220 xref: UMLS:C0225972 {source="ncithesaurus:Pericardial_Cavity"} xref: VHOG:0000556 xref: Wikipedia:Pericardial_cavity xref: ZFA:0001655 is_a: UBERON:0002323 {source="MA"} ! coelemic cavity lumen intersection_of: UBERON:0002553 ! anatomical cavity intersection_of: luminal_space_of UBERON:0002406 ! pericardial sac relationship: contains UBERON:0002409 ! pericardial fluid relationship: develops_from UBERON:0003887 {source="Wikipedia"} ! intraembryonic coelom relationship: luminal_space_of UBERON:0002406 ! pericardial sac relationship: part_of UBERON:0002406 {source="FMA"} ! pericardial sac relationship: present_in_taxon NCBITaxon:7718 {source="PMID:20959416"} relationship: surrounded_by UBERON:0002357 ! serous pericardium property_value: external_definition "Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002220", ontology="TAO", source="ZFIN:curator"} property_value: external_ontology_notes "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)" xsd:string {external_ontology="ZFA"} property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0001075 name: bony vertebral centrum def: "Ossified form of a vertebral centrum, a skeletal element that functionally replaces the notochord[VSAP,modified]." [http://orcid.org/0000-0002-6601-2165, VSAO:0000183, VSAO:curator] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "arcocentrum" NARROW INCONSISTENT [PMID:11746457] synonym: "autocentrum" NARROW [PMID:11746457, ZFA:0000126] synonym: "body of vertebra" EXACT [FMA:11945] synonym: "centra" RELATED PLURAL [PHENOSCAPE:ad] synonym: "corpus vertebra" EXACT LATIN [] synonym: "corpus vertebrae" RELATED PLURAL [Wikipedia:Body_of_vertebra] synonym: "corpus vertebrae (vertebrale)" EXACT [FMA:11945] synonym: "holocentrum" NARROW [PMID:11746457] synonym: "vertebral body" EXACT [FMA:11945] synonym: "vertebral centra" RELATED PLURAL [PHENOSCAPE:ad] synonym: "vertebral centrum" RELATED [MA:0001457] xref: AAO:0000697 xref: EMAPA:36588 xref: FMA:11945 xref: MA:0001457 xref: NCIT:C12852 xref: OpenCyc:Mx4rvXU4VpwpEbGdrcN5Y29ycA xref: SCTID:361745008 xref: SCTID:362867001 xref: TAO:0000126 xref: UMLS:C0223084 {source="ncithesaurus:Vertebral_Body"} xref: Wikipedia:Body_of_vertebra xref: ZFA:0000126 is_a: UBERON:0002513 ! endochondral bone is_a: UBERON:0016491 ! vertebral centrum element intersection_of: UBERON:0016491 ! vertebral centrum element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: composed_primarily_of UBERON:0002481 ! bone tissue relationship: part_of UBERON:0002412 ! vertebra property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/63/Corpusvertebrae.png xsd:anyURI property_value: external_comment "The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification.[VSAO]" xsd:string {date_retrieved="2012-09-06", external_class="VSAO:0000183", ontology="VSAO", source="Curator"} property_value: external_definition "Centra are represented by mineralized, calcified, or ossified portions that surround the notochord. The autocentrum, present in Danio and all other living teleosts, is formed by direct ossification outside the elastica externa of the notochord (Arratia, 1999).[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000126", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Cylindrical body of bone, round or oval in cross section, which functionally replaces the notochord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000697", ontology="AAO", source="AAO:Duellman_and_Trueb_2008"} property_value: external_definition "The body is the largest part of a vertebra, and is more or less cylindrical in shape. Its upper and lower surfaces are flattened and rough, and give attachment to the intervertebral fibrocartilages, and each presents a rim around its circumference. In front, the body is convex from side to side and concave from above downward. Behind, it is flat from above downward and slightly concave from side to side. Its anterior surface presents a few small apertures, for the passage of nutrient vessels. On the posterior surface is a single large, irregular aperture, or occasionally more than one, for the exit of the basi-vertebral veins from the body of the vertebra. [WP,unvetted][Wikipedia:Body_of_vertebra]." xsd:string {source="Wikipedia:Body_of_vertebra"} property_value: external_ontology_notes "VSAO definition states it surrounds notochord but not applicable to post-natal." xsd:string {external_ontology="VSAO"} [Term] id: UBERON:0001076 name: neural spine def: "A extension of a neural arches dorsal to the neural canal[TAO,modified]." [http://orcid.org/0000-0002-6601-2165, TAO:0001336] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "neural spine" RELATED [] synonym: "neural spines" RELATED PLURAL [ZFA:0001336] synonym: "processus spinosus" EXACT [] synonym: "processus spinosus vertebrae" EXACT [] synonym: "spine of verterba" RELATED [FMA:11948] synonym: "spinous process" BROAD [] synonym: "spinous process of vertebra" EXACT HUMAN_PREFERRED [FMA:11948] synonym: "vertebra spinous process" EXACT [MA:0001455] xref: AAO:0000705 xref: EMAPA:25107 xref: FMA:11948 xref: MA:0001455 xref: NCIT:C116112 xref: SCTID:264259004 xref: TAO:0001336 xref: Wikipedia:Spinous_process xref: ZFA:0001336 is_a: UBERON:0006061 ! process of vertebra relationship: part_of UBERON:0003861 ! neural arch property_value: axiom_lost_from_external_ontology "relationship loss: part_of mid-dorsal keel (AAO:0000735)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000705", ontology="AAO"} property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/4/48/Processusspinosusvertebrae.png xsd:anyURI property_value: external_definition "Elaboration of the mid-dorsal keel into a posterior or posterolateral process.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000705", ontology="AAO", source="AAO:Pugener_and_Maglia_2008"} property_value: external_definition "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]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001336", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Small, posteriorly directed process at the posterior margin of each neural arch lamina; it is not a neural spine.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000739", ontology="AAO", source="AAO:Pugener_2002"} property_value: taxon_notes "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]" xsd:string [Term] id: UBERON:0001077 name: transverse process of vertebra def: "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]." [Wikipedia:Transverse_process] subset: pheno_slim subset: uberon_slim synonym: "diapophyses" RELATED [] synonym: "diapophysis" RELATED [] synonym: "processus transversus" EXACT [] synonym: "processus transversus vertebrae" EXACT [] synonym: "transverse process" EXACT [] synonym: "vertebra transverse process" EXACT [] xref: AAO:0000698 xref: FMA:11949 xref: MA:0001456 xref: SCTID:264238006 xref: Wikipedia:Transverse_process xref: XAO:0003102 is_a: UBERON:0006061 ! process of vertebra property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/a1/Processustransversusvertebrae.PNG xsd:anyURI property_value: external_definition "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." xsd:string {source="AAO:0000698"} [Term] id: UBERON:0001078 name: pedicle of vertebra def: "the two short, thick processes, which project backward, one on either side, from the upper part of the body to the laminae" [ISBN:0-683-40008-8, MGI:csmith, MP:0004604] subset: pheno_slim subset: uberon_slim synonym: "pedicle" BROAD [] synonym: "pedicle of vertebral arch" EXACT [FMA:11950] synonym: "pediculus arcus vertebrae" EXACT LATIN [FMA:TA] synonym: "pediculus arcus vertebrae" RELATED LATIN [Wikipedia:Pedicle_of_vertebral_arch] synonym: "radix arcus vertebrae" RELATED LATIN [Wikipedia:Pedicle_of_vertebral_arch] synonym: "vertebra pedicle" EXACT [] synonym: "vertebral pedicle" EXACT [FMA:11950] xref: FMA:11950 xref: MA:0001458 xref: NCIT:C96274 xref: OpenCyc:Mx4rvYdjdJwpEbGdrcN5Y29ycA xref: SCTID:277422007 xref: UMLS:C0223080 {source="ncithesaurus:Pedicle_of_Vertebral_Arch"} xref: Wikipedia:Pedicle_of_vertebral_arch is_a: UBERON:0006061 ! process of vertebra relationship: part_of UBERON:0003861 ! neural arch property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/d/d0/Pediculusarcusvertebrae.png xsd:anyURI [Term] id: UBERON:0001079 name: prezygapophysis def: "Paired processes at the cephalic end of the neural arch. The articular facets of the prezygapophyses face dorsomedially and articulate with the lateroventrally facing facets of the postzygapophyses of the preceding vertebra." [AAO:Pugener_and_Maglia_2008] subset: vertebrate_core synonym: "cranial articular process of vertebra" EXACT [] synonym: "neural prezygapophyses" RELATED PLURAL [TAO:0001325] synonym: "neural prezygapophysis" NARROW DUBIOUS [ZFA:0001325] synonym: "neural prezygopophyses" NARROW DUBIOUS [ZFA:0001325] synonym: "prezygapophysis" EXACT [] synonym: "processus articularis superior" EXACT [] synonym: "processus articularis superior vertebrae" EXACT LATIN [FMA:11953, FMA:TA] synonym: "superior articular process of vertebra" EXACT HUMAN_PREFERRED [FMA:11953] synonym: "vertebra cranial articular process" EXACT [] synonym: "zygapophysis superior" EXACT LATIN [FMA:11953, FMA:TA] xref: AAO:0000703 xref: EMAPA:37802 {source="MA:th"} xref: FMA:11953 xref: http://www.informatics.jax.org/cookbook/figures/figure20.shtml xref: MA:0001452 xref: SCTID:42424006 xref: TAO:0001325 xref: ZFA:0001325 is_a: UBERON:0006062 ! zygapophysis property_value: editor_note "TODO - add distinct classes for hemal vs neural?" xsd:string property_value: external_definition "Paired, anteromedially directed processes from the neural arches, ligamentously joined to the postzygapophyses of the preceding vertebra.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001325", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0001080 name: postzygapophysis alt_id: UBERON:4300122 def: "Paired processes at the caudal end of the neural arch. The articular facets of the postzygapophyses face lateroventrally and articulate with the dorsomedially facing facets of the prezygapophyses of the succeeding vertebra." [AAO:LAP] comment: Posteriorly projecting processes allowing de facto contact between consecutive vertebrae (some soft tissues are also present) via articular facets. [PHENOSCAPE:NI] subset: pheno_slim subset: vertebrate_core synonym: "caudal articular process of vertebra" EXACT [] synonym: "inferior articular process of vertebra" EXACT HUMAN_PREFERRED [FMA:11954] synonym: "neural postzygapophyses" RELATED PLURAL [TAO:0000681] synonym: "neural postzygapophysis" NARROW DUBIOUS [ZFA:0000681] synonym: "neural postzygopophyses" RELATED [TAO:0000681] synonym: "neural postzygopophysis" EXACT [ZFA:0000681] synonym: "postzygapophysis" EXACT [] synonym: "processus articularis inferior" EXACT [] synonym: "processus articularis inferior vertebrae" EXACT LATIN [FMA:11954, FMA:TA] synonym: "processus obliquus posterior" RELATED [AAO:0000702] synonym: "vertebra caudal articular process" EXACT [] synonym: "zygapophysis inferior" EXACT LATIN [FMA:11954, FMA:TA] xref: AAO:0000702 xref: EMAPA:35918 xref: FMA:11954 xref: MA:0001451 xref: SCTID:30079000 xref: TAO:0000681 xref: ZFA:0000681 is_a: UBERON:0006062 ! zygapophysis property_value: external_definition "Paired, dorsomedially directed processes on the posterior ends of the centra, ligamentously joined to the neural prezygapophyses of the immediately posterior vertebra.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000681", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0001081 name: endocardium of ventricle def: "Endocardium that is part of the cardiac ventricle." [ZFIN:curator] subset: pheno_slim subset: vertebrate_core synonym: "cardiac ventricle endocardium" EXACT [OBOL:automatic] synonym: "endocardium of cardiac ventricle" EXACT [OBOL:automatic] synonym: "endocardium of heart ventricle" EXACT [OBOL:automatic] synonym: "endocardium of lower chamber of heart" EXACT [OBOL:automatic] synonym: "endocardium of ventricle of heart" EXACT [OBOL:automatic] synonym: "heart ventricle endocardium" EXACT [OBOL:automatic] synonym: "lower chamber of heart endocardium" EXACT [OBOL:automatic] synonym: "ventricle endocardial tissue" RELATED [VHOG:0000607] synonym: "ventricle endocardium" EXACT [] synonym: "ventricle of heart endocardium" EXACT [OBOL:automatic] synonym: "ventricular endocardium" EXACT [] xref: EMAPA:32747 xref: FMA:12148 xref: MA:0000079 xref: SCTID:192172004 xref: TAO:0002247 xref: VHOG:0000607 xref: ZFA:0001615 is_a: UBERON:0000490 {source="EHDAA2-abduced"} ! unilaminar epithelium is_a: UBERON:0002165 ! endocardium intersection_of: UBERON:0002165 ! endocardium intersection_of: part_of UBERON:0002082 ! cardiac ventricle relationship: contributes_to_morphology_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0004784 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! heart ventricle wall [Term] id: UBERON:0001082 name: epicardium of ventricle def: "An epicardial layer that lines a cardiac ventricle" [http://orcid.org/0000-0002-6601-2165] subset: vertebrate_core synonym: "cardiac ventricle epicardium" EXACT [OBOL:automatic] synonym: "ventricular epicardium" EXACT [] xref: FMA:12150 xref: TAO:0005058 xref: ZFA:0005058 is_a: UBERON:0002348 ! epicardium intersection_of: UBERON:0002348 ! epicardium intersection_of: part_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0002082 ! cardiac ventricle property_value: external_definition "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]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005058", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0001083 name: myocardium of ventricle def: "Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer." [ZFIN:curator] subset: efo_slim subset: pheno_slim subset: vertebrate_core synonym: "ventricle cardiac muscle" RELATED [VHOG:0000604] synonym: "ventricle myocardium" EXACT [] synonym: "ventricular myocardium" EXACT [] xref: EFO:0003088 xref: EMAPA:32748 xref: FMA:12151 xref: MA:0000082 xref: SCTID:192084000 xref: TAO:0005061 xref: VHOG:0000604 xref: ZFA:0005061 is_a: UBERON:0002349 ! myocardium intersection_of: UBERON:0002349 ! myocardium intersection_of: part_of UBERON:0002082 ! cardiac ventricle relationship: contributes_to_morphology_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0004784 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! heart ventricle wall property_value: external_definition "Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005061", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0001084 name: skin of head def: "A zone of skin that is part of a head [Automatically generated definition]." [OBOL:automatic] synonym: "adult head zone of skin" EXACT [OBOL:automatic] synonym: "head skin" EXACT [] synonym: "head zone of skin" EXACT [OBOL:automatic] synonym: "zone of skin of adult head" EXACT [OBOL:automatic] synonym: "zone of skin of head" EXACT [OBOL:automatic] xref: FMA:12166 xref: FMA:24756 xref: MA:0000582 xref: NCIT:C52757 xref: SCTID:181484006 xref: UMLS:C0205029 {source="ncithesaurus:Head_Skin"} intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0000033 ! head relationship: part_of UBERON:0000033 ! head property_value: editor_note "TODO - distinguish between entire skin of region and arbitrary zone of skin on region" xsd:string [Term] id: UBERON:0001085 name: skin of trunk def: "A zone of skin that is part of a trunk [Automatically generated definition]." [OBOL:automatic] synonym: "torso zone of skin" EXACT [OBOL:automatic] synonym: "trunk skin" EXACT [] synonym: "trunk zone of skin" EXACT [OBOL:automatic] synonym: "zone of skin of torso" EXACT [OBOL:automatic] synonym: "zone of skin of trunk" EXACT [OBOL:automatic] xref: EMAPA:37278 {source="MA:th"} xref: FMA:12167 xref: FMA:23093 xref: MA:0000517 xref: NCIT:C12295 xref: SCTID:181489001 xref: UMLS:C0205031 {source="ncithesaurus:Skin_of_the_Trunk"} is_a: UBERON:0000014 ! zone of skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0002100 ! trunk relationship: part_of UBERON:0002100 ! trunk property_value: editor_note "TODO - distinguish between entire skin of region and arbitrary zone of skin on region" xsd:string [Term] id: UBERON:0001086 name: obsolete articular cartilage comment: obsoleted as it conflated two distinct classes is_obsolete: true consider: UBERON:0010996 consider: UBERON:0011002 [Term] id: UBERON:0001087 name: pleural fluid def: "Transudate contained in the pleural cavity." [FMA:12273] subset: uberon_slim xref: BTO:0003080 xref: FMA:12273 xref: MA:0002532 xref: MAT:0000500 xref: ncithesaurus:Pleural_Fluid xref: Wikipedia:Pleural_fluid is_a: UBERON:0036244 ! secretion of serous membrane intersection_of: UBERON:0007779 ! transudate intersection_of: located_in UBERON:0002402 ! pleural cavity relationship: located_in UBERON:0002402 ! pleural cavity [Term] id: UBERON:0001088 name: urine def: "Excretion that is the output of a kidney" [https://github.com/geneontology/go-ontology/issues/11025, Wikipedia:Urine] subset: efo_slim subset: pheno_slim subset: uberon_slim xref: BTO:0001419 xref: CALOHA:TS-1092 xref: EFO:0001939 xref: EMAPA:36554 xref: ENVO:00002047 xref: FMA:12274 xref: GAID:1189 xref: galen:Urine xref: MA:0002545 xref: MAT:0000058 xref: MESH:D014556 xref: MIAA:0000058 xref: NCIT:C13283 xref: OpenCyc:Mx4rvVjGppwpEbGdrcN5Y29ycA xref: UMLS:C0042036 {source="ncithesaurus:Urine"} xref: Wikipedia:Urine is_a: UBERON:0000174 ! excreta intersection_of: UBERON:0000174 ! excreta intersection_of: produced_by UBERON:0002113 ! kidney relationship: has_quality PATO:0001548 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} relationship: produced_by UBERON:0002113 ! kidney property_value: taxon_notes "kidney excreta from some taxa (e.g. in aves) may not be liquid" xsd:string [Term] id: UBERON:0001089 name: sweat def: "Secretion produced by a sweat gland." [FMA:12275] subset: pheno_slim subset: uberon_slim synonym: "skin exudate" RELATED [BTO:0001254] xref: BTO:0001254 xref: ENVO:02000025 xref: FMA:12275 xref: GAID:1172 xref: MA:0002539 xref: MESH:D013542 xref: NCIT:C13280 xref: OpenCyc:Mx4rvVjJtZwpEbGdrcN5Y29ycA xref: UMLS:C0038984 {source="ncithesaurus:Sweat"} xref: Wikipedia:Sweat is_a: UBERON:0000456 ! secretion of exocrine gland intersection_of: UBERON:0000456 ! secretion of exocrine gland intersection_of: produced_by UBERON:0001820 ! sweat gland relationship: has_quality PATO:0001548 relationship: produced_by UBERON:0001820 ! sweat gland [Term] id: UBERON:0001090 name: synovial fluid def: "Joint fluid is a transudate of plasma that is actively secreted by synovial cells." [https://www.ncbi.nlm.nih.gov/books/NBK274/] subset: uberon_slim subset: vertebrate_core synonym: "joint fluid" EXACT [https://www.ncbi.nlm.nih.gov/books/NBK274/] xref: BTO:0001339 xref: CALOHA:TS-0996 xref: ENVO:02000039 xref: FMA:12277 xref: GAID:265 xref: galen:SynovialFluid xref: MA:0002544 xref: MESH:D013582 xref: NCIT:C33718 xref: TAO:0005154 xref: UMLS:C0039097 {source="ncithesaurus:Synovial_Fluid"} xref: Wikipedia:Synovial_fluid xref: ZFA:0005154 is_a: UBERON:0007779 ! transudate is_a: UBERON:0007794 {source="FMA"} ! secretion of serous gland intersection_of: UBERON:0007779 ! transudate intersection_of: produced_by CL:0000214 relationship: has_part CHEBI:16336 relationship: located_in UBERON:0007617 ! synovial cavity of joint relationship: produced_by CL:0000214 property_value: external_definition "Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005154", ontology="TAO", source="ZFIN:curator"} property_value: function_notes "It provides nutrients and lubrication for articular cartilage" xsd:string property_value: structure_notes "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" xsd:string [Term] id: UBERON:0001091 name: calcareous tooth def: "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." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Tooth_(animal)] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "dental element" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "dentine containing tooth" EXACT [] synonym: "tooth" EXACT [] synonym: "vertebrate tooth" EXACT [] xref: AEO:0000220 xref: BTO:0000397 xref: CALOHA:TS-1055 xref: EFO:0000839 xref: EHDAA2:0004605 xref: EMAPA:32906 xref: EV:0100063 xref: FMA:12516 xref: GAID:1260 xref: MA:0000348 xref: MAT:0000041 xref: MESH:A14.254.860 xref: MIAA:0000041 xref: NCIT:C12506 xref: OpenCyc:Mx4rvVjUEZwpEbGdrcN5Y29ycA xref: SCTID:302214001 xref: TAO:0001625 xref: UMLS:C0040426 {source="ncithesaurus:Tooth"} xref: VHOG:0001733 xref: Wikipedia:Tooth xref: XAO:0000431 xref: ZFA:0000694 is_a: UBERON:0003913 ! tooth-like structure is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0008281 ! tooth bud relationship: has_developmental_contribution_from UBERON:0000930 {source="XAO-modified"} ! stomodeum relationship: has_developmental_contribution_from UBERON:0005176 {source="ZFA-modified"} ! tooth enamel organ relationship: has_part UBERON:0001751 ! dentine relationship: has_part UBERON:0001752 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! enamel relationship: immediate_transformation_of UBERON:0008281 {source="cjm"} ! tooth bud relationship: in_lateral_side_of UBERON:0011595 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! jaw region relationship: never_in_taxon NCBITaxon:189497 {source="Wikipedia"} relationship: never_in_taxon NCBITaxon:8782 relationship: never_in_taxon NCBITaxon:9257 {source="PMID:10210685"} relationship: never_in_taxon NCBITaxon:9761 relationship: part_of UBERON:0011595 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! jaw region property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/1/14/Teeth_by_David_Shankbone.jpg xsd:anyURI property_value: 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" xsd:string property_value: has_relational_adjective "dental" xsd:string property_value: homology_notes "The ancestor of recent vertebrate teeth was a tooth-like structure on the outer body surface of jawless fishes.[well established][VHOG]" xsd:string {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/"} property_value: taxon_notes "absent in living platypus, present in toothed Miocene platypus Obduron dicksoni" xsd:string {source="PMID:10210685"} [Term] id: UBERON:0001092 name: vertebral bone 1 def: "The first vertebral bone in the vertebral column." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "atlas" EXACT [] synonym: "atlas (CI)" EXACT [] synonym: "atlas [C I]" EXACT LATIN [FMA:12519, FMA:TA] synonym: "atlas vertebra" EXACT [] synonym: "C1" BROAD [] synonym: "C1 vertebra" EXACT [] synonym: "cervical atlas" EXACT [MP:0011576] synonym: "cervical vertebra 1" EXACT HUMAN_PREFERRED [MA:0001421] synonym: "first cervical vertebra" EXACT [] synonym: "vertebra 1" EXACT [TAO:0001167] xref: AAO:0000709 xref: EHDAA:10606 xref: EMAPA:19431 xref: FMA:12519 xref: GAID:236 xref: MA:0001421 xref: MESH:A02.835.232.834.151.213 xref: NCIT:C32239 xref: SCTID:181818007 xref: TAO:0001167 xref: UMLS:C0004170 {source="ncithesaurus:C1_Vertebra"} xref: Wikipedia:Atlas_(anatomy) xref: ZFA:0001167 is_a: UBERON:0002412 ! vertebra relationship: anterior_to UBERON:0001093 ! vertebral bone 2 relationship: anteriorly_connected_to UBERON:0001676 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! occipital bone relationship: part_of UBERON:0006072 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! cervical region of vertebral column property_value: external_definition "First postcranial vertebra, which is modified anteriorly to articulate with the skull.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000709", ontology="AAO", source="AAO:Duellman_and_Trueb_1994"} property_value: external_definition "Vertebra that is posteriorly adjacent to the neurocranium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001167", ontology="TAO", source="TAO:wd"} property_value: vertebra_number "1" xsd:nonNegativeInteger [Term] id: UBERON:0001093 name: vertebral bone 2 def: "The second vertebral bone in the vertebral column." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "axis" RELATED INCONSISTENT [MA:0001422] synonym: "axis (CII)" EXACT [] synonym: "axis [C II]" EXACT LATIN [FMA:12520, FMA:TA] synonym: "axis vertebra" EXACT [] synonym: "C2" RELATED [] synonym: "C2 vertebra" NARROW [] synonym: "cervical axis" EXACT [MP:0004608] synonym: "cervical vertebra 2" NARROW HUMAN_PREFERRED [MA:0001422] synonym: "second cervical vertebra" NARROW [] synonym: "vertebra 2" EXACT [ZFA:0001168] xref: EHDAA:10608 xref: EMAPA:19432 xref: FMA:12520 xref: GAID:237 xref: MA:0001422 xref: MESH:D001368 xref: NCIT:C32240 xref: OpenCyc:Mx4rv-zaJJwpEbGdrcN5Y29ycA xref: SCTID:181819004 xref: TAO:0001168 xref: UMLS:C0004457 {source="ncithesaurus:C2_Vertebra"} xref: Wikipedia:Axis_(anatomy) xref: ZFA:0001168 is_a: UBERON:0002412 ! vertebra relationship: anteriorly_connected_to UBERON:0001092 {source="FMA"} ! vertebral bone 1 relationship: part_of UBERON:0006072 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! cervical region of vertebral column property_value: external_definition "Vertebra that is posteriorly adjacent to vertebra 1.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001168", ontology="TAO", source="TAO:wd"} property_value: terminology_notes "not the same as ZFA term 'axis'" xsd:string property_value: vertebra_number "2" xsd:nonNegativeInteger [Term] id: UBERON:0001094 name: sacral vertebra def: "A vertebra bone that is part of the sacral region of the vertebral column." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim synonym: "sacral segment" EXACT [] synonym: "segment of sacrum" EXACT [] xref: AAO:0000552 xref: EMAPA:18336 xref: FMA:12526 xref: galen:SacralVertebra xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1706 xref: MA:0000313 xref: NCIT:C12853 xref: OpenCyc:Mx4rv-ZsXpwpEbGdrcN5Y29ycA xref: SCTID:361773005 xref: UMLS:C1261045 {source="ncithesaurus:Sacral_Vertebra"} xref: Wikipedia:Sacrum xref: XAO:0003078 is_a: UBERON:0002412 ! vertebra is_a: UBERON:0003828 ! abdominal segment bone is_a: UBERON:0004247 ! bone of dorsum is_a: UBERON:0015010 ! sacral vertebra endochondral element intersection_of: UBERON:0015010 ! sacral vertebra endochondral element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: composed_primarily_of UBERON:0002481 ! bone tissue relationship: develops_from UBERON:0010745 ! sacral vertebra cartilage element property_value: editor_note "todo - AAO placement to be confirmed by AAO curators (the AAO class may also include modified ribs)" xsd:string property_value: external_definition "Enlarged vertebra with transverse processes (diapophyses), and ocassionally ribs, that are modified and elaborated for support of the pelvic girdle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000552", ontology="AAO", source="AAO:Duellman_and_Trueb_1994"} [Term] id: UBERON:0001095 name: caudal vertebra alt_id: UBERON:0006070 def: "Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx)." [http://orcid.org/0000-0002-6601-2165] 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 subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "caudal vertebra" BROAD SENSU [FMA:12527] synonym: "caudal vertebrae" EXACT PLURAL [] synonym: "caudal vertebral bone" EXACT [] synonym: "caudal vertebral bone element" EXACT [] synonym: "coccygea" RELATED [MA:0001420] synonym: "coccygeal segment" EXACT [] synonym: "coccygeal vertebra" EXACT [FMA:12527] synonym: "fused tail vertebra" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "tail vertebra" RELATED [MA:0000310] xref: EMAPA:18374 xref: FMA:12527 xref: galen:CoccygealVertebra xref: MA:0000310 xref: MA:0001420 xref: NCIT:C32334 xref: OpenCyc:Mx4rv9IEzZwpEbGdrcN5Y29ycA xref: SCTID:361774004 xref: TAO:0000326 xref: UMLS:C0223616 {source="ncithesaurus:Coccygeal_Vertebra"} xref: Wikipedia:Caudal_vertebra xref: XAO:0003079 xref: ZFA:0000326 is_a: UBERON:0002412 ! vertebra is_a: UBERON:0004247 ! bone of dorsum is_a: UBERON:0018142 ! caudal vertebra endochondral element intersection_of: UBERON:0018142 ! caudal vertebra endochondral element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: composed_primarily_of UBERON:0002481 ! bone tissue property_value: external_definition "Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000326", ontology="TAO", source="ZFIN:curator"} property_value: external_ontology_notes "we deliberately merge the MA classes as we believe them equivalent" xsd:string {external_ontology="MA"} [Term] id: UBERON:0001096 name: wall of esophagus def: "An anatomical wall that is part of a esophagus [Automatically generated definition]." [OBOL:automatic] synonym: "anatomical wall of esophagus" EXACT [OBOL:automatic] synonym: "anatomical wall of gullet" EXACT [OBOL:automatic] synonym: "anatomical wall of oesophagus" EXACT [OBOL:automatic] synonym: "esophageal wall" EXACT [] synonym: "esophagus anatomical wall" EXACT [OBOL:automatic] synonym: "esophagus wall" EXACT [] synonym: "gullet anatomical wall" EXACT [OBOL:automatic] synonym: "gullet wall" EXACT [OBOL:automatic] synonym: "oesophagus anatomical wall" EXACT [OBOL:automatic] synonym: "oesophagus wall" EXACT [OBOL:automatic] synonym: "wall of gullet" EXACT [OBOL:automatic] synonym: "wall of oesophagus" EXACT [OBOL:automatic] xref: EMAPA:35326 xref: FMA:12611 xref: MA:0002691 is_a: UBERON:0000328 ! gut wall intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001043 ! esophagus [Term] id: UBERON:0001097 name: axillary lymph node def: "the lymph nodes located around the axillary vein that receive lymphatic drainage from the upper or forelimb, scapular region and pectoral region" [ISBN:0-683-40008-8, MP:0002340] subset: pheno_slim subset: uberon_slim synonym: "axillary node" EXACT [] synonym: "nodi lymphoidei axillares" RELATED LATIN [Wikipedia:Axillary_lymph_nodes] xref: FMA:276805 xref: MA:0000735 xref: NCIT:C12904 xref: SCTID:181759007 xref: UMLS:C0729594 {source="ncithesaurus:Axillary_Lymph_Node"} xref: Wikipedia:Axillary_lymph_nodes is_a: UBERON:0003968 {source="CL:tm"} ! peripheral lymph node relationship: part_of UBERON:0001467 ! shoulder property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/7/73/Gray607.png xsd:anyURI [Term] id: UBERON:0001098 name: incisor tooth def: "Incisors are the first kind of tooth in heterodont mammals. They are located in the premaxilla above and mandible below. [WP,unvetted]." [https://github.com/obophenotype/uberon/issues/221, Wikipedia:Incisor_tooth] comment: Humans normally have eight (8) incisors; Among other animals, some other primates, cats and horses have twelve. Rodents have four, while Foxes have nine. Rabbits and hares (lagomorphs) were once considered rodents, but are distinguished by having eight - one small pair, called 'peg teeth', is located directly behind the most anterior pair. Incisors are used to bite off tough foods, such as red meat subset: pheno_slim subset: uberon_slim synonym: "incisor" EXACT [MA:0000349] xref: BTO:0001741 xref: EHDAA:8011 xref: EHDAA:8047 xref: EMAPA:32889 xref: FMA:12823 xref: GAID:1263 xref: MA:0000349 xref: MESH:A14.254.860.425 xref: NCIT:C32769 xref: OpenCyc:Mx4rwP1ch5wpEbGdrcN5Y29ycA xref: SCTID:420856006 xref: UMLS:C0021156 {source="ncithesaurus:Incisor"} xref: Wikipedia:Incisor_tooth is_a: UBERON:0001091 ! calcareous tooth disjoint_from: UBERON:0003655 ! molar tooth disjoint_from: UBERON:0003674 ! cuspid disjoint_from: UBERON:0007120 ! premolar tooth relationship: part_of UBERON:0003672 ! dentition property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/4/4c/Gray997.png xsd:anyURI [Term] id: UBERON:0001099 name: subcostal vein def: "A vein that runs along the bottom of the lowest rib. Each subcostal vein gives off a posterior (dorsal) branch which has a similar distribution to the posterior ramus of an intercostal artery. [WP,modified]." [Wikipedia:Subcostal_vein] subset: uberon_slim synonym: "vena subcostalis" RELATED LATIN [Wikipedia:Subcostal_vein] xref: EMAPA:37189 {source="MA:th"} xref: FMA:12845 xref: MA:0002222 xref: NCIT:C53121 xref: SCTID:25248001 xref: UMLS:C0226653 {source="ncithesaurus:Subcostal_Vein"} xref: Wikipedia:Subcostal_vein is_a: UBERON:0001638 ! vein relationship: posterior_to UBERON:0014478 ! rib skeletal system [Term] id: UBERON:0001100 name: pectoralis minor def: "The Pectoralis minor is a thin, triangular muscle, situated at the upper part of the chest, beneath the Pectoralis major. [WP,unvetted]." [Wikipedia:Pectoralis_minor_muscle] subset: organ_slim subset: pheno_slim subset: uberon_slim synonym: "musculus pectoralis minor" RELATED LATIN [Wikipedia:Pectoralis_minor_muscle] synonym: "pectoralis minor muscle" EXACT [] synonym: "supracoracoideus" NARROW SENSU [] synonym: "supracoracoideus muscle" NARROW SENSU [] xref: EHDAA2:0001425 xref: EHDAA:8313 xref: EMAPA:18180 xref: FMA:13109 xref: MA:0002355 xref: NCIT:C33285 xref: SCTID:181625002 xref: UMLS:C0224347 {source="ncithesaurus:Pectoralis_Minor"} xref: VHOG:0000902 xref: Wikipedia:Pectoralis_minor_muscle is_a: CARO:0000003 is_a: UBERON:0001495 {source="FMA"} ! pectoral muscle relationship: has_muscle_insertion UBERON:0007174 {notes="medial border and superior surface of the coracoid process of the scapula", source="dbpedia"} ! medial border of scapula relationship: has_muscle_origin UBERON:0002228 {notes="third to fifth ribs near their costal cartilages", source="dbpedia"} ! rib property_value: depicted_by Pectoralis:minor.png xsd:anyURI [Term] id: UBERON:0001101 name: external jugular vein def: "The external jugular vein receives the greater part of the blood from the exterior of the cranium and the deep parts of the face, being formed by the junction of the posterior division of the posterior facial with the posterior auricular vein. [WP,unvetted]." [Wikipedia:External_jugular_vein] subset: uberon_slim synonym: "external jugular" RELATED [EHDAA2:0000468] synonym: "external jugular venous tree" EXACT [] synonym: "vena jugularis externa" RELATED LATIN [Wikipedia:External_jugular_vein] xref: AAO:0010508 xref: EHDAA2:0000468 xref: EHDAA:9887 xref: EMAPA:17875 xref: FMA:13110 xref: galen:ExternalJugularVein xref: MA:0002156 xref: NCIT:C32562 xref: OpenCyc:Mx4rvrm0c5wpEbGdrcN5Y29ycA xref: SCTID:181373000 xref: UMLS:C0226543 {source="ncithesaurus:External_Jugular_Vein"} xref: Wikipedia:External_jugular_vein xref: XAO:0000379 is_a: UBERON:0004711 ! jugular vein relationship: part_of UBERON:0001587 ! subclavian vein relationship: tributary_of UBERON:0001587 {source="FMA"} ! subclavian vein property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png xsd:anyURI property_value: external_definition "Vein which collects blood from the muscles of the head and tongue and the thyroid gland.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010508", ontology="AAO", source="AAO:BJB"} [Term] id: UBERON:0001102 name: cartilage of main bronchus def: "A cartilage that is part of a main bronchus [Automatically generated definition]." [OBOL:automatic] synonym: "bronchus principalis cartilage" EXACT [OBOL:automatic] synonym: "cartilage of bronchus principalis" EXACT [OBOL:automatic] synonym: "cartilage of primary bronchus" EXACT [OBOL:automatic] synonym: "cartilage of principal bronchus" EXACT [OBOL:automatic] synonym: "cartilaginous ring of main bronchus" EXACT [EMAPA:19092] synonym: "main bronchial cartilage" EXACT [] synonym: "main bronchus cartilage" EXACT [] synonym: "primary bronchus cartilage" EXACT [OBOL:automatic] synonym: "principal bronchus cartilage" EXACT [OBOL:automatic] xref: EMAPA:19092 xref: FMA:13117 xref: MA:0001846 is_a: UBERON:0001956 ! cartilage of bronchus intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0002182 ! main bronchus relationship: part_of UBERON:0002182 ! main bronchus [Term] id: UBERON:0001103 name: diaphragm def: "A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control" [MP:0002279] subset: efo_slim subset: organ_slim subset: pheno_slim subset: uberon_slim synonym: "diaphragm muscle" EXACT [BTO:0000341] synonym: "diaphragm of thorax" EXACT [] synonym: "midriff" RELATED [BTO:0000341] synonym: "phren" RELATED [BTO:0000341] synonym: "thoracic diaphragm" EXACT [] xref: BTO:0000341 xref: CALOHA:TS-0198 xref: EFO:0000937 xref: EHDAA2:0003495 xref: EMAPA:17701 xref: EV:0100376 xref: FMA:13295 xref: GAID:158 xref: MA:0001904 xref: MAT:0000502 xref: MESH:D003964 xref: NCIT:C12702 xref: OpenCyc:Mx4rvVivz5wpEbGdrcN5Y29ycA xref: SCTID:181614006 xref: UMLS:C0011980 {source="ncithesaurus:Diaphragm"} xref: VHOG:0000713 xref: Wikipedia:Thoracid_diaphragm is_a: CARO:0000003 is_a: UBERON:0003830 ! thoracic segment muscle is_a: UBERON:0003831 ! respiratory system muscle relationship: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue relationship: develops_from UBERON:0010084 ! future diaphragm relationship: immediate_transformation_of UBERON:0010084 {evidence="definitional"} ! future diaphragm relationship: innervated_by UBERON:0001884 ! phrenic nerve relationship: never_in_taxon NCBITaxon:8782 {source="Wikipedia:Thoracic_diaphragm#Comparative_anatomy_and_evolution"} relationship: only_in_taxon NCBITaxon:40674 {source="PMID:23586979"} relationship: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0001004 ! respiratory system property_value: development_notes "originate from the cervical somites, likely C3-C5[PMID:23586979]" xsd:string property_value: external_definition "The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO]." xsd:string {source="GO:0060539"} property_value: function_notes "barrier between thoracic and abdominal cavities; stop gastric contents from refluxing into the oesophagus" xsd:string property_value: function_notes "breathing control" xsd:string property_value: has_relational_adjective "phrenic" xsd:string property_value: homology_notes "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]" xsd:string {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/"} property_value: taxon_notes "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]" xsd:string property_value: taxon_notes "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)" xsd:string [Term] id: UBERON:0001104 name: anterior jugular vein def: "The anterior jugular vein begins near the hyoid bone by the confluence of several superficial veins from the submaxillary region. It descends between the median line and the anterior border of the Sternocleidomastoideus, and, at the lower part of the neck, passes beneath that muscle to open into the termination of the external jugular, or, in some instances, into the subclavian vein. It varies considerably in size, bearing usually an inverse proportion to the external jugular; most frequently there are two anterior jugulars, a right and left; but sometimes only one. Its tributaries are some laryngeal veins, and occasionally a small thyroid vein. Just above the sternum the two anterior jugular veins communicate by a transverse trunk, the venous jugular arch, which receive tributaries from the inferior thyroid veins; each also communicates with the internal jugular. There are no valves in this vein. [WP,unvetted]." [Wikipedia:Anterior_jugular_vein] subset: uberon_slim synonym: "anterior external jugular vein" EXACT [] synonym: "vena jugularis anterior" RELATED LATIN [Wikipedia:Anterior_jugular_vein] xref: EMAPA:37134 {source="MA:th"} xref: FMA:13318 xref: MA:0002155 xref: NCIT:C32094 xref: SCTID:65478008 xref: UMLS:C0226545 {source="ncithesaurus:Anterior_Jugular_Vein"} xref: Wikipedia:Anterior_jugular_vein is_a: UBERON:0004711 ! jugular vein disjoint_from: UBERON:0035249 {source="lexical"} ! posterior external jugular vein relationship: part_of UBERON:0001101 ! external jugular vein relationship: tributary_of UBERON:0001101 {source="Wikipedia"} ! external jugular vein relationship: tributary_of UBERON:0001587 {source="FMA", source="Wikipedia"} ! subclavian vein property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray558.png xsd:anyURI [Term] id: UBERON:0001105 name: clavicle bone def: "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]." [https://github.com/obophenotype/uberon/issues/103, PHENOSCAPE:ad] subset: pheno_slim subset: uberon_slim synonym: "clavicle" EXACT [VSAO:0005031] synonym: "clavicula" EXACT [VSAO:0005031] synonym: "collar bone" EXACT [] synonym: "collarbone" EXACT [] xref: AAO:0000761 xref: EMAPA:18721 xref: FMA:13321 xref: GAID:182 xref: galen:Clavicle xref: MA:0001329 xref: MESH:D002968 xref: MFMO:0000047 xref: NCIT:C12695 xref: OpenCyc:Mx4rvVjijZwpEbGdrcN5Y29ycA xref: SCTID:181910004 xref: UMLS:C0008913 {source="ncithesaurus:Clavicle"} xref: VHOG:0000849 xref: VSAO:0005031 xref: Wikipedia:Clavicle is_a: UBERON:0002495 {source="FMA"} ! long bone is_a: UBERON:0003461 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! shoulder bone is_a: UBERON:0007829 ! pectoral girdle bone is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0015212 ! lateral structure relationship: connected_to UBERON:0000975 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! sternum relationship: dc-contributor https://github.com/cmungall relationship: dc-contributor https://github.com/mellybelly relationship: develops_from UBERON:0010905 {editor="mah", source="ISBN:978-0-12-319060-4"} ! clavicle bone primordium relationship: has_developmental_contribution_from UBERON:0010843 {notes="from secondary cartilage of fusion", source="ISBN:978-0-12-319060-4"} ! clavicle cartilage element relationship: in_lateral_side_of UBERON:0002091 ! appendicular skeleton relationship: part_of UBERON:0007831 {source="FMA", source="VSAO"} ! pectoral girdle skeleton property_value: axiom_lost_from_external_ontology "relationship loss: part_of zonal element (AAO:0000936)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000761", ontology="AAO"} property_value: depicted_by Pectoral:girdles-en.svg xsd:anyURI property_value: development_notes "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." xsd:string {source="ISBN:978-0-12-319060-4"} property_value: external_definition "Slender, paired bones of intramembranous origin that invest the anterior margins of the procoracoids.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000761", ontology="AAO", source="AAO:LAP"} property_value: external_ontology_notes "FMA and MA differ in whether they consider this part of the shoulder" xsd:string {external_ontology="FMA"} property_value: has_relational_adjective "clavicular" xsd:string property_value: homology_notes "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]" xsd:string {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/"} property_value: taxon_notes "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]." xsd:string [Term] id: UBERON:0001106 name: cephalic vein def: "A superficial vein of the upper limb that communicates with the basilic vein via the median cubital vein at the elbow and is located in the superficial fascia along the anterolateral surface of the biceps brachii muscle. Superiorly the cephalic vein passes between the deltoid and pectoralis major muscles and through the deltopectoral triangle, where it empties into the axillary vein. It is often visible through the skin, and its location in the deltopectoral groove is fairly consistent, making this site a good candidate for cannulation. It is often referred to as the 'House-man's Friend' for this reason and is generally a good place for cannulaton when a large bore cannula needs to be sited. [WP,modified]." [Wikipedia:Cephalic_vein] subset: uberon_slim synonym: "cephalic vein of forearm" EXACT [] synonym: "vena cephalica" RELATED LATIN [Wikipedia:Cephalic_vein] synonym: "vena cephalica antebrachii" EXACT LATIN [FMA:13324, FMA:TA] xref: EMAPA:25075 xref: FMA:13324 xref: galen:CephalicVein xref: MA:0002092 xref: NCIT:C32286 xref: OpenCyc:Mx4rwTpbQZwpEbGdrcN5Y29ycA xref: SCTID:181391005 xref: UMLS:C0226802 {source="ncithesaurus:Cephalic_Vein"} xref: Wikipedia:Cephalic_vein is_a: UBERON:0003507 ! arm blood vessel is_a: UBERON:0035550 ! superficial vein relationship: part_of UBERON:0000985 ! axillary vein relationship: part_of UBERON:0001460 ! arm relationship: part_of UBERON:0001587 ! subclavian vein relationship: tributary_of UBERON:0000985 {source="FMA/obol"} ! axillary vein relationship: tributary_of UBERON:0001587 {source="FMA/obol"} ! subclavian vein property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/b/ba/Gray574.png xsd:anyURI [Term] id: UBERON:0001107 name: sternohyoid muscle def: "The sternohyoid muscle is a thin, narrow muscle attaching the hyoid bone to the sternum, one of the paired strap muscles of the infrahyoid muscles serving to depress the hyoid bone. It is innervated by the ansa cervicalis. The muscle arises from the posterior border of the medial end of the clavicle, the posterior sternoclavicular ligament, and the upper and posterior part of the manubrium sterni. Passing upward and medially, it is inserted by short tendinous fibers into the lower border of the body of the hyoid bone. [WP,unvetted]." [Wikipedia:Sternohyoid_muscle] subset: uberon_slim subset: vertebrate_core synonym: "m. sternohyoideus" EXACT [] synonym: "musculus sternohyoideus" RELATED LATIN [Wikipedia:Sternohyoid_muscle] synonym: "sternohyoid" EXACT [Wikipedia:Sternohyoid_muscle] synonym: "sternohyoidei" RELATED PLURAL [Wikipedia:Sternohyoid_muscle] synonym: "sternohyoideus" EXACT [Wikipedia:Sternohyoid_muscle] synonym: "sternohyoideus muscle" EXACT [Wikipedia:Sternohyoid_muscle] xref: EMAPA:19271 xref: FMA:13341 xref: MA:0002383 xref: NCIT:C53044 xref: SCTID:244830003 xref: UMLS:C0224162 {source="ncithesaurus:Sternohyoid"} xref: Wikipedia:Sternohyoid_muscle is_a: UBERON:0008523 {source="FMA"} ! infrahyoid muscle relationship: has_muscle_insertion UBERON:0001685 {source="dbpedia"} ! hyoid bone relationship: has_muscle_origin UBERON:0002205 {notes="manubrium of sternum", source="dbpedia"} ! manubrium of sternum relationship: innervated_by UBERON:0001780 {notes="inferred", source="dbpedia"} ! spinal nerve relationship: innervated_by UBERON:0005430 {source="dbpedia"} ! ansa cervicalis property_value: action_notes "draws hyoid posteriorly." xsd:string property_value: depicted_by Sternohyoid:muscle.PNG xsd:anyURI property_value: external_definition "The sternohyoid is a somitic muscle that participates in oral/pharyngeal behaviors and is innervated by the cervical plexus; it attaches to the hyoid appratus and the sternum.[FEED]" xsd:string {date_retrieved="2012-07-02", ontology="FEED", url="http://www.feedexp.org"} property_value: external_ontology_notes "Note that as defined here, this structure attaches to the sternum, which is a tetrapod structure. TAO has class 'sternohyoid' as part of mandibular muscle, but no sternum, so excluded here. The TAO/ZFA class has no definition, but the dictionary of icthyology states: 'a large muscle originating on the ventral spine of the postcleithrum and inserting on the sides of the urohyal. It functions in rapid opening of the jaw and expanding the buccal cavity' - a generic way of grouping these is via a hyoid - girdle connection" xsd:string {external_ontology="TAO"} [Term] id: UBERON:0001108 name: omohyoid muscle def: "The omohyoid muscle is a muscle at the front of the neck that consists of two bellies separated by an intermediate tendon. It belongs to the group of infrahyoid muscles. [WP,unvetted]." [Wikipedia:Omohyoid_muscle] comment: interior and superior belly subset: uberon_slim synonym: "musculus omohyoideus" RELATED LATIN [Wikipedia:Omohyoid_muscle] synonym: "omohyoid" EXACT [] synonym: "omohyoideus" EXACT [Wikipedia:Omohyoid_muscle] synonym: "omohyoideus muscle" EXACT [Wikipedia:Omohyoid_muscle] xref: EMAPA:37689 {source="MA:th"} xref: FMA:13342 xref: MA:0002348 xref: NCIT:C52971 xref: SCTID:244833001 xref: UMLS:C0224163 {source="ncithesaurus:Omohyoid"} xref: Wikipedia:Omohyoid_muscle is_a: UBERON:0008523 {source="FMA"} ! infrahyoid muscle relationship: has_muscle_insertion UBERON:0001685 {source="dbpedia"} ! hyoid bone relationship: innervated_by UBERON:0001780 {notes="inferred", source="dbpedia"} ! spinal nerve relationship: innervated_by UBERON:0005430 {source="dbpedia"} ! ansa cervicalis property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/b/b0/Gray1210.png xsd:anyURI property_value: external_definition "The omohyoid is a somitic muscle that participates in oral/pharyngeal behaviors and is innervated by the cervical plexus; it attaches to the hyoid appratus and the scapula.[FEED]" xsd:string {date_retrieved="2012-07-02", ontology="FEED", url="http://www.feedexp.org"} [Term] id: UBERON:0001109 name: sternothyroid muscle def: "The Sternothyreoideus (or Sternothyroid muscle) is shorter and wider than the Sternohyoideus, beneath which it is situated. It arises from the posterior surface of the manubrium sterni, below the origin of the Sternohyoideus, and from the edge of the cartilage of the first rib, and sometimes that of the second rib, it is inserted into the oblique line on the lamina of the thyroid cartilage. This muscle is in close contact with its fellow at the lower part of the neck, but diverges somewhat as it ascends; it is occasionally traversed by a transverse or oblique tendinous inscription. [WP,unvetted]." [Wikipedia:Sternothyroid_muscle] subset: uberon_slim synonym: "musculus sternothyroideus" RELATED LATIN [Wikipedia:Sternothyroid_muscle] synonym: "sterno-thyroideus" RELATED [Wikipedia:Sternothyroid_muscle] synonym: "sternothyreoidei" RELATED PLURAL [Wikipedia:Sternothyroid_muscle] synonym: "sternothyreoideus" RELATED [Wikipedia:Sternothyroid_muscle] synonym: "sternothyroid" EXACT [] synonym: "sternothyroideus" RELATED [Wikipedia:Sternothyroid_muscle] xref: EMAPA:19272 xref: FMA:13343 xref: MA:0002386 xref: NCIT:C53070 xref: SCTID:244831004 xref: UMLS:C0224166 {source="ncithesaurus:Sternothyroid"} xref: Wikipedia:Sternothyroid_muscle is_a: UBERON:0008523 {source="FMA"} ! infrahyoid muscle relationship: has_muscle_insertion UBERON:0001738 {source="dbpedia"} ! thyroid cartilage relationship: has_muscle_origin UBERON:0002205 {source="dbpedia"} ! manubrium of sternum relationship: innervated_by UBERON:0001780 {notes="inferred", source="dbpedia"} ! spinal nerve relationship: innervated_by UBERON:0005430 {source="dbpedia"} ! ansa cervicalis property_value: action_notes "draws larynx caudally" xsd:string property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/1/10/Sternothyroideus.png xsd:anyURI property_value: external_definition "The sternothyroid is a somitic muscle that participates in oral/pharyngeal behaviors and is innervated by the cervical plexus; it attaches to the thyroid cartilage and the sternum.[FEED]" xsd:string {date_retrieved="2012-07-02", ontology="FEED", url="http://www.feedexp.org"} [Term] id: UBERON:0001110 name: thyrohyoid muscle def: "The thyrohyoid muscle is a small, quadrilateral muscle appearing like an upward continuation of the Sternothyreoideus. It belongs to the infrahyoid muscles group. It arises from the oblique line on the lamina of the thyroid cartilage, and is inserted into the lower border of the greater cornu of the hyoid bone. [WP,unvetted]." [Wikipedia:Thyrohyoid_muscle] subset: uberon_slim synonym: "musculus thyrohyoideus" RELATED LATIN [Wikipedia:Thyrohyoid_muscle] synonym: "thyreohyoideus" RELATED [Wikipedia:Thyrohyoid_muscle] synonym: "thyreohyoideus muscle" RELATED [Wikipedia:Thyrohyoid_muscle] synonym: "thyrohyoid" EXACT [Wikipedia:Thyrohyoid_muscle] synonym: "thyrohyoideus" RELATED [Wikipedia:Thyrohyoid_muscle] xref: EMAPA:19273 xref: FMA:13344 xref: MA:0002393 xref: NCIT:C53178 xref: SCTID:244832006 xref: UMLS:C0224167 {source="ncithesaurus:Thyrohyoid"} xref: Wikipedia:Thyrohyoid_muscle is_a: UBERON:0008523 {source="FMA"} ! infrahyoid muscle relationship: has_muscle_insertion UBERON:0001685 {source="dbpedia"} ! hyoid bone relationship: innervated_by UBERON:0000962 {notes="first cervical nerve via hypoglossal nerve", source="dbpedia"} ! nerve of cervical vertebra relationship: innervated_by UBERON:0001650 {notes="first cervical nerve via hypoglossal nerve", source="dbpedia"} ! hypoglossal nerve property_value: depicted_by Thyrohyoid:muscle.PNG xsd:anyURI property_value: external_definition "The thyrohyoid is a somitic muscle that participates in oral/pharyngeal behaviors and is innervated by C1 and Cranial Nerve XII ; it attaches to the thyroid cartilage and the hyoid apparatus.[FEED]" xsd:string {date_retrieved="2012-07-02", ontology="FEED", url="http://www.feedexp.org"} [Term] id: UBERON:0001111 name: intercostal muscle def: "the respiratory muscles that arise from the lower border of one rib and insert into the upper border of the adjoining rib" [MESH:A02.633.567.900.500, MGI:csmith, MP:0002280] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "intercostales" RELATED [] synonym: "musculus intercostalis" EXACT LATIN [FMA:13354, FMA:TA] synonym: "respiratory muscle" RELATED [] synonym: "rib muscle" RELATED [] xref: BTO:0005281 xref: EFO:0001368 xref: EHDAA2:0000841 xref: EHDAA:5988 xref: EMAPA:18521 xref: FMA:13354 xref: GAID:159 xref: MA:0002324 xref: MA:0003165 xref: MESH:D007366 xref: NCIT:C32824 xref: OpenCyc:Mx4rwQo8QJwpEbGdrcN5Y29ycA xref: SCTID:181746004 xref: UMLS:C0021724 {source="ncithesaurus:Intercostal_Muscle"} xref: VHOG:0000903 xref: Wikipedia:Intercostal_muscle is_a: CARO:0000003 is_a: UBERON:0001630 ! muscle organ is_a: UBERON:0005175 ! chest organ intersection_of: UBERON:0001630 ! muscle organ intersection_of: has_muscle_insertion UBERON:0002228 ! rib intersection_of: has_muscle_origin UBERON:0002228 ! rib intersection_of: located_in UBERON:0012198 ! intercostal space relationship: develops_from UBERON:0010970 {source="EHDAA2"} ! intercostal pre-muscle mass relationship: has_muscle_insertion UBERON:0002228 {notes="ribs 2-12", source="dbpedia"} ! rib relationship: has_muscle_origin UBERON:0002228 {notes="ribs 1-11", source="dbpedia"} ! rib relationship: innervated_by UBERON:0003727 {source="dbpedia"} ! intercostal nerve relationship: located_in UBERON:0012198 ! intercostal space relationship: part_of UBERON:0001443 ! chest property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/f/f2/Gray411.png xsd:anyURI property_value: homology_notes "Inspiration by active expansion of the thorax evolved later, in the ancestor of reptiles, birds, and mammals. This was powered originally by the intercostal muscles (as in lizards or crocodilians) and later (in mammals only) by a muscular diaphragm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000903", ontology="VHOG", source="ISBN:978-0262112789 Kent RD, The MIT Encyclopedia of Communication Disorders (20039 p.56", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001112 name: latissimus dorsi muscle def: "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]." [Wikipedia:Latissimus_dorsi_muscle] comment: Dorsal group[Kardong] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "dorsal latissimus muscle" EXACT [] synonym: "latissimi dorsi" EXACT PLURAL [] synonym: "latissimus dorsi" EXACT [] synonym: "musculus latissimus dorsi" EXACT [] synonym: "musculus latissimus dorsi" RELATED LATIN [Wikipedia:Latissimus_dorsi_muscle] xref: EFO:0003067 xref: EHDAA2:0000932 xref: EHDAA:8307 xref: EMAPA:18178 xref: FMA:13357 xref: MA:0002331 xref: NCIT:C33150 xref: SCTID:181747008 xref: UMLS:C0224362 {source="ncithesaurus:Musculus_Latissimus_Dorsi"} xref: VHOG:0000930 xref: Wikipedia:Latissimus_dorsi_muscle is_a: UBERON:0001482 ! muscle of shoulder is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0034908 ! scapular muscle relationship: develops_from UBERON:0010982 {source="EHDAA2"} ! latissimus dorsi pre-muscle mass relationship: has_muscle_antagonist UBERON:0001476 {source="dbpedia"} ! deltoid relationship: has_muscle_antagonist UBERON:0002380 {source="dbpedia"} ! trapezius muscle relationship: has_muscle_insertion UBERON:0000976 {notes="floor of intertubercular groove of the humerus", source="dbpedia"} ! humerus relationship: has_muscle_origin UBERON:0006849 ! scapula relationship: has_muscle_origin UBERON:0007175 {notes="spinous processes of thoracic T7-T12 thoracolumbar fascia iliac crest and inferior 3 or 4 ribs inferior angle of scapula", source="dbpedia"} ! inferior angle of scapula relationship: part_of UBERON:0008713 {source="EHDAA2"} ! pectoral girdle and thoracic body wall skeletal muscle property_value: depicted_by Latissimus:dorsi.png xsd:anyURI property_value: taxon_notes "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]" xsd:string [Term] id: UBERON:0001113 name: lobe of liver def: "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." [Wikipedia:Liver#Lobes] synonym: "hepatic lobe" EXACT [] synonym: "liver lobe" EXACT [] synonym: "lobus hepatis" EXACT [] xref: EMAPA:18306 xref: FMA:13361 xref: MA:0000360 xref: NCIT:C49579 xref: SCTID:245378000 xref: UMLS:C0447541 {source="ncithesaurus:Liver_Lobe"} xref: Wikipedia:Liver#Lobes is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0009912 {source="FMA"} ! anatomical lobe relationship: part_of UBERON:0002107 ! liver property_value: editor_note "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" xsd:string [Term] id: UBERON:0001114 name: right lobe of liver def: "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]." [Wikipedia:Right_lobe_of_liver] subset: uberon_slim subset: vertebrate_core synonym: "2nd lobe" RELATED [TAO:0005173] synonym: "gall bladder lobe" RELATED SENSU [ZFA:0005173] synonym: "liver right lobe" EXACT [] synonym: "lobus hepaticus dexter" EXACT LATIN [] synonym: "lobus hepatis dexter" RELATED LATIN [Wikipedia:Right_lobe_of_liver] synonym: "right hepatic lobe" RELATED [EMAPA:18311] synonym: "right liver lobe" EXACT [ZFA:0005173] synonym: "second lobe" RELATED [TAO:0005173] xref: EHDAA2:0001008 xref: EHDAA:4001 xref: EMAPA:18311 xref: FMA:13362 xref: MA:0000363 xref: NCIT:C33481 xref: SCTID:362182008 xref: TAO:0005173 xref: UMLS:C0227481 {source="ncithesaurus:Right_Lobe_of_the_Liver"} xref: VHOG:0001424 xref: Wikipedia:Right_lobe_of_liver xref: ZFA:0005173 is_a: UBERON:0001113 ! lobe of liver property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png xsd:anyURI property_value: external_definition "Portion of the liver which develops on the fish's right side adjacent to the gall bladder.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005173", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0001115 name: left lobe of liver def: "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]." [Wikipedia:Left_lobe_of_liver] subset: uberon_slim subset: vertebrate_core synonym: "left hepatic lobe" RELATED [EMAPA:18307] synonym: "left liver lobe" EXACT [] synonym: "liver left lobe" EXACT [] synonym: "lobus hepaticus sinister" EXACT LATIN [] synonym: "lobus hepatis sinister" RELATED LATIN [Wikipedia:Left_lobe_of_liver] xref: EHDAA2:0001000 xref: EHDAA:3995 xref: EMAPA:18307 xref: FMA:13363 xref: MA:0000361 xref: NCIT:C32965 xref: SCTID:362183003 xref: TAO:0005172 xref: UMLS:C0227486 {source="ncithesaurus:Left_Lobe_of_the_Liver"} xref: VHOG:0001423 xref: Wikipedia:Left_lobe_of_liver xref: ZFA:0005172 is_a: UBERON:0001113 ! lobe of liver property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png xsd:anyURI property_value: external_definition "Portion of the liver which develops on the fish's left side.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005172", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0001116 name: quadrate lobe of liver def: "The quadrate lobe is an area of the liver situated on the under surface of the right lobe, bounded in front by the anterior margin of the liver; behind by the porta hepatis; on the right, by the fossa for the gall-bladder; and on the left, by the fossa for the umbilical vein. It is oblong in shape, its antero-posterior diameter being greater than its transverse. [WP,unvetted]." [Wikipedia:Quadrate_lobe_of_liver] subset: uberon_slim synonym: "liver quadrate lobe" EXACT [] synonym: "lobus quadratus" EXACT [] synonym: "lobus quadratus" RELATED LATIN [Wikipedia:Quadrate_lobe_of_liver] synonym: "lobus quadratus hepatis" EXACT LATIN [FMA:13364, FMA:TA] xref: EHDAA2:0001012 xref: EHDAA:8082 xref: EMAPA:18318 xref: FMA:13364 xref: MA:0000365 xref: NCIT:C33001 xref: SCTID:279929003 xref: VHOG:0000509 xref: Wikipedia:Quadrate_lobe_of_liver is_a: UBERON:0001114 ! right lobe of liver property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png xsd:anyURI property_value: external_definition "The portion of the right lobe of the liver between the gall bladder, the porta hepatis, the round ligament and the lower margin of the organ. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000509", ontology="VHOG", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001117 name: caudate lobe of liver def: "The caudate lobe (posterior hepatic segment I, Spigelian lobe) is situated upon the postero-superior surface of the liver on the right lobe of the liver, opposite the tenth and eleventh thoracic vertebrae. It is bounded on the left side by the physiological division of the liver called the ligamentum venosum. It is bounded, below, by the porta; on the right, by the fossa for the inferior vena cava; and, on the left, by the fossa for the ductus venosus. It looks backward, being nearly vertical in position; it is longer from above downward than from side to side, and is somewhat concave in the transverse direction. The caudate process is a small elevation of the hepatic substance extending obliquely and laterally, from the lower extremity of the caudate lobe to the under surface of the right lobe. It is situated behind the porta, and separates the fossa for the gall-bladder from the commencement of the fossa for the inferior vena cava. Budd-Chiari syndrome, caused by occlusion of hepatic venous outflow, can lead to hypertrophy of the caudate lobe due to its own caval anastomosis that allows for continued function of this lobe of the liver. [WP,unvetted]." [Wikipedia:Caudate_lobe_of_liver] subset: uberon_slim synonym: "couinaud hepatic segment I" EXACT [FMA:13365] synonym: "hepatovenous segment I" EXACT [] synonym: "liver caudate lobe" EXACT [] synonym: "liver caudate process" RELATED [] synonym: "lobus caudatus" EXACT LATIN [] synonym: "lobus caudatus hepatis" EXACT LATIN [FMA:13365, FMA:TA] synonym: "pars posterior hepatis" EXACT LATIN [FMA:13365, FMA:TA] synonym: "posterior hepatic segment i" EXACT [] synonym: "posterior liver" EXACT [] synonym: "posterior part of liver" EXACT [] synonym: "segment hepatis posterius I" RELATED LATIN [Wikipedia:Caudate_lobe_of_liver] synonym: "segment I of liver" EXACT [] synonym: "segmentum hepatis I" EXACT LATIN [FMA:13365, FMA:TA] synonym: "Spiegelian lobe" EXACT [] synonym: "Spigel lobe" EXACT [] xref: EHDAA2:0001005 xref: EHDAA:6990 xref: EMAPA:18313 xref: FMA:13365 xref: MA:0000364 xref: NCIT:C33000 xref: SCTID:362184009 xref: UMLS:C0227489 {source="ncithesaurus:Lobus_Caudatus"} xref: VHOG:0000508 xref: Wikipedia:Caudate_lobe_of_liver is_a: UBERON:0001114 {source="MA"} ! right lobe of liver relationship: part_of UBERON:0001115 {source="FMA"} ! left lobe of liver property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png xsd:anyURI property_value: editor_note "Check left vs right in mouse and human" xsd:string property_value: external_definition "The portion of the right lobe of the liver between the fissure of the ligamentum venosum and the bare area of the liver. It ends into the superior recess of the lesser peritoneal sac. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000508", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "The caudate lobe is the only real and constant hepatic lobe of mammals (...) .[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000508", ontology="VHOG", source="PMID:1610084 Van Minh T, Galizia G, Lieto E, Anatomy of the caudate lobe of the liver. New aspects and surgical applications. (Article in French) Annales de chirurgie (1992)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001118 name: lobe of thyroid gland def: "A lobe of tissue that is part of a thyroid gland." [http://orcid.org/0000-0002-6601-2165] 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 synonym: "lobuli glandulae thyroideae" RELATED LATIN [Wikipedia:Lobes_of_thyroid_gland] synonym: "lobus (glandula thyroidea)" EXACT [] synonym: "lobus glandulae thyroideae" EXACT LATIN [FMA:13367, FMA:TA] synonym: "thyroid gland lobe" EXACT [] synonym: "thyroid lobe" EXACT [] xref: EHDAA2:0002032 xref: EMAPA:18196 xref: FMA:13367 xref: MA:0000131 xref: NCIT:C33784 xref: SCTID:245537001 xref: UMLS:C0447647 {source="ncithesaurus:Thyroid_Gland_Lobe"} xref: VHOG:0000732 xref: Wikipedia:Lobes_of_thyroid_gland is_a: UBERON:0009912 ! anatomical lobe is_a: UBERON:0015212 ! lateral structure is_a: UBERON:0035075 ! thymus subunit intersection_of: UBERON:0009912 ! anatomical lobe intersection_of: part_of UBERON:0002046 ! thyroid gland relationship: in_lateral_side_of UBERON:0002046 {source="FMA-abduced-lr"} ! thyroid gland relationship: part_of UBERON:0002046 ! thyroid gland property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png xsd:anyURI property_value: homology_notes "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000732", ontology="VHOG", source="http://bgee.unil.ch/", source="http://www.thyroidmanager.org/Chapter1/chapter01.htm"} [Term] id: UBERON:0001119 name: right lobe of thyroid gland def: "A lobe of thyroid gland that is in the right side of a thyroid gland." [OBOL:automatic] synonym: "lobus dexter (glandula thyroidea)" EXACT [] synonym: "right thyroid lobe" EXACT [] synonym: "thyroid gland right lobe" EXACT [] xref: EHDAA2:0001759 xref: EMAPA:18198 xref: FMA:13368 xref: MA:0000729 xref: NCIT:C33491 xref: SCTID:170482008 xref: UMLS:C0229581 {source="ncithesaurus:Right_Thyroid_Gland_Lobe"} xref: VHOG:0000733 is_a: UBERON:0001118 ! lobe of thyroid gland intersection_of: UBERON:0001118 ! lobe of thyroid gland intersection_of: in_right_side_of UBERON:0002046 ! thyroid gland relationship: in_right_side_of UBERON:0002046 ! thyroid gland property_value: homology_notes "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000733", ontology="VHOG", source="http://bgee.unil.ch/", source="http://www.thyroidmanager.org/Chapter1/chapter01.htm"} property_value: implements_design_pattern https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI [Term] id: UBERON:0001120 name: left lobe of thyroid gland def: "A lobe of thyroid gland that is in the left side of a thyroid gland." [OBOL:automatic] synonym: "left thyroid lobe" EXACT [] synonym: "lobus sinister (glandula thyroidea)" EXACT [] synonym: "thyroid gland left lobe" EXACT [] xref: EHDAA2:0000965 xref: EMAPA:18197 xref: FMA:13369 xref: MA:0000728 xref: NCIT:C32973 xref: SCTID:170784008 xref: UMLS:C0229582 {source="ncithesaurus:Left_Thyroid_Gland_Lobe"} xref: VHOG:0000734 is_a: UBERON:0001118 ! lobe of thyroid gland intersection_of: UBERON:0001118 ! lobe of thyroid gland intersection_of: in_left_side_of UBERON:0002046 ! thyroid gland relationship: in_left_side_of UBERON:0002046 ! thyroid gland property_value: homology_notes "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000734", ontology="VHOG", source="http://bgee.unil.ch/", source="http://www.thyroidmanager.org/Chapter1/chapter01.htm"} property_value: implements_design_pattern https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI [Term] id: UBERON:0001121 name: longus colli muscle def: "The Longus colli muscle is a muscle of the human body. The Longus colli is situated on the anterior surface of the vertebral column, between the atlas and the third thoracic vertebra. It is broad in the middle, narrow and pointed at either end, and consists of three portions, a superior oblique, an inferior oblique, and a vertical. The superior oblique portion arises from the anterior tubercles of the transverse processes of the third, fourth, and fifth cervical vertebræ and, ascending obliquely with a medial inclination, is inserted by a narrow tendon into the tubercle on the anterior arch of the atlas. The inferior oblique portion, the smallest part of the muscle, arises from the front of the bodies of the first two or three thoracic vertebræ; and, ascending obliquely in a lateral direction, is inserted into the anterior tubercles of the transverse processes of the fifth and sixth cervical vertebræ. The vertical portion arises, below, from the front of the bodies of the upper three thoracic and lower three cervical vertebræ, and is inserted into the front of the bodies of the second, third, and fourth cervical vertebræ. [WP,unvetted]." [Wikipedia:Longus_colli_muscle] subset: organ_slim subset: uberon_slim synonym: "longi colli" RELATED [Wikipedia:Longus_colli_muscle] synonym: "longus colli" EXACT [MA:0002341] synonym: "longus colli muscle" EXACT [Wikipedia:Longus_colli_muscle] synonym: "musculus longus colli" RELATED LATIN [Wikipedia:Longus_colli_muscle] xref: EMAPA:37654 {source="MA:th"} xref: FMA:13370 xref: MA:0002341 xref: NCIT:C52959 xref: SCTID:244836009 xref: UMLS:C0224169 {source="ncithesaurus:Longus_Colli"} xref: Wikipedia:Longus_colli_muscle is_a: CARO:0000003 is_a: UBERON:0001630 ! muscle organ is_a: UBERON:0005178 ! thoracic cavity element relationship: has_muscle_insertion UBERON:0003996 {source="dbpedia"} ! cervical vertebra 1 arcus anterior relationship: has_muscle_origin UBERON:0001077 {notes="Transverse processes of C-5 to T-3", source="dbpedia"} ! transverse process of vertebra relationship: located_in UBERON:0008818 {source="FMA-modified"} ! superior mediastinum property_value: depicted_by Longus:colli.png xsd:anyURI [Term] id: UBERON:0001122 name: scalenus medius def: "The Scalenus medius, the largest and longest of the three scalene muscles, arises from the posterior tubercles of the transverse processes of the lower six cervical vertebræ. It descendes along the side of the vertebral column to insert by a broad attachment into the upper surface of the first rib, between the tubercle and the subclavian groove. The brachial plexus and the subclavian artery pass anterior to it. Because it elevates the upper ribs, the middle scalene muscle is also one of the accessory muscles of respiration. [WP,unvetted]." [Wikipedia:Scalenus_medius] subset: uberon_slim synonym: "medial scalene muscle" EXACT [] synonym: "middle scalene" EXACT [] synonym: "musculus scalenus medius" EXACT LATIN [FMA:13386, FMA:TA] synonym: "musculus scalenus medius" RELATED LATIN [Wikipedia:Scalenus_medius] synonym: "scalenus medius muscle" EXACT [] xref: EMAPA:37738 {source="MA:th"} xref: FMA:13386 xref: MA:0002370 xref: NCIT:C52986 xref: SCTID:244844009 xref: UMLS:C0224174 {source="ncithesaurus:Scalenus_Medius"} xref: Wikipedia:Scalenus_medius is_a: UBERON:0002377 ! muscle of neck is_a: UBERON:0003897 ! axial muscle is_a: UBERON:0004518 ! muscle of vertebral column relationship: has_muscle_insertion UBERON:0004601 {source="dbpedia"} ! rib 1 relationship: has_muscle_origin UBERON:0002413 {source="dbpedia"} ! cervical vertebra relationship: innervated_by UBERON:0000962 {notes="Ventral rami of the third to eighth cervical spinal nerves", source="dbpedia"} ! nerve of cervical vertebra property_value: depicted_by Scalenus:medius.png xsd:anyURI [Term] id: UBERON:0001123 name: scalenus posterior def: "The Scalenus posterior (Scalenus posticus), the smallest and most deeply seated of the three Scaleni, arises, by two or three separate tendons, from the posterior tubercles of the transverse processes of the lower two or three cervical vertebræ, and is inserted by a thin tendon into the outer surface of the second rib, behind the attachment of the serratus ventralis. It is occasionally blended with the Scalenus medius. [WP,unvetted]." [Wikipedia:Scalenus_posterior] subset: uberon_slim synonym: "musculus scalenus posterior" EXACT LATIN [FMA:13387, FMA:TA] synonym: "musculus scalenus posterior" RELATED LATIN [Wikipedia:Scalenus_posterior] synonym: "posterior scalene" EXACT [] synonym: "posterior scalene muscle" EXACT [] synonym: "scalenus dorsalis" EXACT [] synonym: "scalenus dorsalis muscle" EXACT [] xref: EMAPA:37737 {source="MA:th"} xref: FMA:13387 xref: MA:0002369 xref: NCIT:C52985 xref: UMLS:C1710019 {source="ncithesaurus:Scalenus_Dorsalis"} xref: Wikipedia:Scalenus_posterior is_a: CARO:0000003 is_a: UBERON:0002377 ! muscle of neck disjoint_from: UBERON:0008622 {source="lexical"} ! scalenus anterior relationship: has_muscle_origin UBERON:0001077 {notes="transverse processes of C4 - C6", source="dbpedia"} ! transverse process of vertebra property_value: depicted_by Scalenus:posterior.png xsd:anyURI [Term] id: UBERON:0001125 name: serratus ventralis def: "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]." [Wikipedia:Serratus_anterior_muscle] subset: pheno_slim subset: uberon_slim synonym: "Boxer's muscle" EXACT [] synonym: "musculus serratus anterior" RELATED LATIN [Wikipedia:Serratus_anterior_muscle] synonym: "serratus anterior" EXACT [VHOG:0000679] synonym: "serratus anterior muscle" EXACT [] synonym: "serratus lateralis" RELATED LATIN [Wikipedia:Serratus_anterior_muscle] synonym: "serratus ventralis muscle" EXACT [] xref: EHDAA2:0001832 xref: EHDAA:9463 xref: EMAPA:18525 xref: FMA:13397 xref: MA:0002378 xref: NCIT:C53014 xref: OpenCyc:Mx4rvWn_D5wpEbGdrcN5Y29ycA xref: SCTID:181748003 xref: UMLS:C1710059 {source="ncithesaurus:Serratus_Ventralis"} xref: VHOG:0000679 xref: Wikipedia:Serratus_anterior_muscle is_a: UBERON:0001482 ! muscle of shoulder is_a: UBERON:0034908 ! scapular muscle relationship: develops_from UBERON:0010986 {source="EHDAA2"} ! serratus ventralis pre-muscle mass relationship: has_muscle_antagonist UBERON:0002380 {source="dbpedia"} ! trapezius muscle relationship: has_muscle_insertion UBERON:0006849 {notes="costal aspect of medial margin of the scapula", source="dbpedia"} ! scapula relationship: has_muscle_origin UBERON:0002228 {notes="fleshy slips from the outer surface of upper 8 or 9 ribs", source="dbpedia"} ! rib relationship: innervated_by UBERON:0003726 {notes="long thoracic nerve", source="dbpedia"} ! thoracic nerve property_value: depicted_by Serratus:anterior.png xsd:anyURI [Term] id: UBERON:0001126 name: serratus dorsalis superior muscle def: "The serratus dorsalis superior is a thin, quadrilateral muscle, situated at the upper and back part of the thorax. It arises by a thin and broad aponeurosis from the lower part of the ligamentum nuchae, from the spinous processes of the seventh cervical and upper two or three thoracic vertebræ and from the supraspinal ligament. Inclining downward and lateralward it becomes muscular, and is inserted, by four fleshy digitations, into the upper borders of the second, third, fourth, and fifth ribs, a little beyond their angles. [WP,unvetted]." [Wikipedia:Serratus_posterior_superior_muscle] subset: uberon_slim synonym: "serratus dorsalis cranialis" EXACT [MA:0002377] synonym: "serratus dorsalis cranialis muscle" EXACT [] synonym: "serratus posterior superior" EXACT [FMA:13401] synonym: "superior serratus dorsalis" EXACT [] synonym: "superior serratus posterior" EXACT [FMA:13401] xref: EMAPA:37698 {source="MA:th"} xref: FMA:13401 xref: MA:0002377 xref: NCIT:C53012 xref: SCTID:244935007 xref: UMLS:C1710058 {source="ncithesaurus:Serratus_Dorsalis_Cranialis"} xref: Wikipedia:Serratus_posterior_superior_muscle is_a: UBERON:0003830 ! thoracic segment muscle is_a: UBERON:0011217 {source="FMA"} ! serratus dorsalis muscle relationship: has_muscle_insertion UBERON:0002228 {notes="rib 2 thru 5 in human", source="dbpedia"} ! rib relationship: has_muscle_origin UBERON:0000351 ! nuchal ligament relationship: has_muscle_origin UBERON:0001076 {notes="C7 thru T3 in human", source="dbpedia"} ! neural spine relationship: innervated_by UBERON:0003727 {notes="2 thru 5 in human", source="dbpedia"} ! intercostal nerve relationship: part_of UBERON:0000915 ! thoracic segment of trunk [Term] id: UBERON:0001127 name: serratus dorsalis inferior muscle def: "A muscle that originates from the vertebrae and inserts in the ribs." [Wikipedia:Serratus_posterior_inferior_muscle] subset: uberon_slim synonym: "inferior serratus dorsalis" EXACT [] synonym: "inferior serratus posterior" EXACT [FMA:13402] synonym: "posterior serratus" RELATED [] synonym: "serratus dorsalis caudalis" EXACT [] synonym: "serratus posterior inferior" EXACT [FMA:13402] synonym: "serratus posterior inferior" RELATED [MA:0002376] xref: EMAPA:37697 {source="MA:th"} xref: FMA:13402 xref: MA:0002376 xref: NCIT:C53007 xref: SCTID:244936008 xref: UMLS:C1711277 {source="ncithesaurus:Serratus_Dorsalis_Caudalis"} xref: Wikipedia:Serratus_posterior_inferior_muscle is_a: UBERON:0011217 {source="FMA"} ! serratus dorsalis muscle relationship: has_muscle_insertion UBERON:0002228 {notes="inferior border of 9th thru 12th in humans", source="dbpedia"} ! rib relationship: has_muscle_origin UBERON:0002412 {notes="T11 through L2 in human", source="dbpedia"} ! vertebra relationship: innervated_by UBERON:0003727 {notes="T9 through T12 in human", source="dbpedia"} ! intercostal nerve property_value: depicted_by Serratus:posterior.PNG xsd:anyURI [Term] id: UBERON:0001128 name: sternocleidomastoid def: "A paired muscle in the superficial layers of the anterior portion of the neck. It acts to flex and rotate the head. It also acts as an accessory muscle of inspiration, along with the scalene muscles of the neck. [WP,unvetted]." [Wikipedia:Sternocleidomastoid_muscle] subset: uberon_slim synonym: "musculus sternocleidomastoideus" RELATED LATIN [Wikipedia:Sternocleidomastoid_muscle] synonym: "SCM" BROAD ABBREVIATION [] synonym: "sterno-cleido-mastoid" RELATED [Wikipedia:Sternocleidomastoid_muscle] synonym: "sterno-mastoid" EXACT [] synonym: "sterno-mastoid" RELATED [Wikipedia:Sternocleidomastoid_muscle] synonym: "sternocleidomastoid" RELATED [Wikipedia:Sternocleidomastoid_muscle] synonym: "sternocleidomastoid muscle" EXACT [BTO:0005125] synonym: "sternocleidomastoid muscles" RELATED [Wikipedia:Sternocleidomastoid_muscle] synonym: "sternocleidomastoidei" RELATED [Wikipedia:Sternocleidomastoid_muscle] synonym: "sternocleidomastoideus" RELATED [Wikipedia:Sternocleidomastoid_muscle] synonym: "sternocleidomastoideus muscle" RELATED [Wikipedia:Sternocleidomastoid_muscle] synonym: "sternocleidomastoids" RELATED [Wikipedia:Sternocleidomastoid_muscle] synonym: "sternomastoid" EXACT [] synonym: "sternomastoid" RELATED [Wikipedia:Sternocleidomastoid_muscle] synonym: "sternomastoid muscle" EXACT [] synonym: "sternomastoid muscle" RELATED [Wikipedia:Sternocleidomastoid_muscle] synonym: "supraclavicularis muscle" RELATED [Wikipedia:Sternocleidomastoid_muscle] xref: BTO:0005125 xref: EMAPA:25137 xref: FMA:13407 xref: MA:0002384 xref: NCIT:C33616 xref: OpenCyc:Mx4rv2bMg5wpEbGdrcN5Y29ycA xref: SCTID:181741009 xref: UMLS:C0224153 {source="ncithesaurus:Sternocleidomastoid_Muscle"} xref: VHOG:0000853 xref: Wikipedia:Sternocleidomastoid_muscle is_a: UBERON:0002377 ! muscle of neck is_a: UBERON:0003897 ! axial muscle is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0011364 ! cleidocephalicus muscle relationship: develops_from UBERON:0010987 ! sterno-mastoid pre-muscle mass relationship: has_muscle_insertion UBERON:0011220 {source="Wikipedia:Mastoid_process"} ! mastoid process of temporal bone relationship: has_muscle_origin UBERON:0001105 {notes="manubrium sterni medial portion of the clavicle", source="dbpedia"} ! clavicle bone relationship: has_muscle_origin UBERON:0002205 {notes="manubrium sterni medial portion of the clavicle", source="dbpedia"} ! manubrium of sternum relationship: innervated_by UBERON:0003725 {notes="sensory: cervical plexus", source="dbpedia"} ! cervical nerve plexus property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/61/Gray512.png xsd:anyURI property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/f/f9/Gray512.svg xsd:anyURI property_value: editor_note "TODO: sternocleidomastoid = sternomastoid + Cleidomastoideus. Origin: from manubrium sterni (sterno) and clavicle (cleido) and it's insertion at the mastoid process of the temporal bone." xsd:string property_value: homology_notes "The sternomastoid and the three parts of the trapezius are branchiomeric muscles that have secondarily acquired an attachment to the pectoral girdle. They evolved from the fish cucullaris.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000853", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.345", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001129 name: subscapularis muscle def: "The subscapularis is a large triangular muscle which fills the subscapular fossa and inserts into the lesser tubercle of the humerus and the front of the capsule of the shoulder-joint. [WP,unvetted]." [Wikipedia:Subscapularis_muscle] comment: Dorsal group[Kardong] subset: uberon_slim synonym: "musculus subscapularis" RELATED LATIN [Wikipedia:Subscapularis_muscle] synonym: "subcoracoscapularis" RELATED SENSU [ISBN:0073040584] synonym: "subscapularis" EXACT [MA:0002388] xref: EHDAA2:0001943 xref: EHDAA:8317 xref: EMAPA:18181 xref: FMA:13413 xref: MA:0002388 xref: NCIT:C33651 xref: OpenCyc:Mx4rviCRIJwpEbGdrcN5Y29ycA xref: SCTID:277446000 xref: UMLS:C0584884 {source="ncithesaurus:Subscapularis"} xref: VHOG:0000850 xref: Wikipedia:Subscapularis_muscle is_a: UBERON:0001482 ! muscle of shoulder is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010891 ! pectoral complex muscle relationship: develops_from UBERON:0010993 ! subscapularis pre-muscle mass relationship: has_muscle_insertion UBERON:0000976 {notes="lesser tubercle of humerus", source="dbpedia"} ! humerus relationship: has_muscle_origin UBERON:4200038 ! subscapular fossa relationship: part_of UBERON:0003683 {source="Wikipedia"} ! rotator cuff relationship: part_of UBERON:0008713 {source="EHDAA2"} ! pectoral girdle and thoracic body wall skeletal muscle property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/f/f2/Gray411.png xsd:anyURI [Term] id: UBERON:0001130 name: vertebral column def: "Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO]." [https://orcid.org/0000-0002-6601-2165, https://sourceforge.net/tracker/?func=detail&aid=3530322&group_id=76834&atid=2257941, VSAO:0000185] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "backbone" NARROW [FMA:13478] synonym: "columna vertebralis" RELATED [BTO:0000818] synonym: "dorsal spine" RELATED [BTO:0000818] synonym: "spinal column" RELATED [MESH:A02.835.232.834] synonym: "spine" BROAD [FMA:13478] synonym: "vertebral column skeleton" NARROW [AAO:0000699] synonym: "vertebral region" RELATED [] xref: AAO:0000699 xref: AAO:0000734 xref: BTO:0000818 xref: EFO:0001369 xref: EHDA:10119 xref: EMAPA:35919 xref: FMA:13478 xref: GAID:106 xref: galen:SpinalColumn xref: MA:0002416 xref: MESH:D013131 xref: NCIT:C12998 xref: NCIT:C33588 xref: NIF_Subcellular:sao1145756102 xref: OpenCyc:Mx4rv2j-CpwpEbGdrcN5Y29ycA xref: OpenCyc:Mx4rv6GF55wpEbGdrcN5Y29ycA xref: OpenCyc:Mx4rvVkFEpwpEbGdrcN5Y29ycA xref: SCTID:44300000 xref: TAO:0001559 xref: UMLS:C0037949 {source="ncithesaurus:Vertebral_Column"} xref: UMLS:C1519455 {source="ncithesaurus:Spinal_Cord_Column"} xref: VHOG:0001142 xref: VSAO:0000185 xref: Wikipedia:Vertebral_column xref: XAO:0003074 xref: ZFA:0001559 is_a: CARO:0000000 is_a: UBERON:0000075 ! subdivision of skeletal system intersection_of: UBERON:0000075 ! subdivision of skeletal system intersection_of: composed_primarily_of UBERON:0010913 ! vertebral element disjoint_from: UBERON:0008260 ! spine appendage relationship: composed_primarily_of UBERON:0010913 ! vertebral element relationship: never_in_taxon NCBITaxon:7762 relationship: only_in_taxon NCBITaxon:7742 relationship: part_of UBERON:0011138 {source="cjm"} ! postcranial axial skeletal system relationship: protects UBERON:0002240 ! spinal cord property_value: editor_note "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" xsd:string property_value: external_definition "Anatomical cluster that consists of all the vertebra in the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000185", ontology="VSAO", source="VSAO:curator"} property_value: external_definition "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001142", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/vertebral+column"} property_value: homology_notes "Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...).[well established][VHOG]" xsd:string {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/"} [Term] id: UBERON:0001131 name: vertebral foramen def: "A foramen within a vertebral element through which the spinal cord runs. It is formed by the anterior segment, and the posterior part, the vertebral arch." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Vertebral_foramen] subset: uberon_slim synonym: "foramen vertebrale" RELATED LATIN [Wikipedia:Vertebral_foramen] synonym: "vertebra neural canal" EXACT [] xref: AAO:0000729 xref: EMAPA:37803 {source="MA:th"} xref: FMA:13479 xref: MA:0001454 xref: OpenCyc:Mx4rv_EvQZwpEbGdrcN5Y29ycA xref: SCTID:280734009 xref: Wikipedia:Vertebral_foramen is_a: CARO:0000000 is_a: UBERON:0004111 ! anatomical conduit intersection_of: UBERON:0004111 ! anatomical conduit intersection_of: conduit_for UBERON:0002240 ! spinal cord intersection_of: lumen_of UBERON:0010913 ! vertebral element relationship: conduit_for UBERON:0002240 ! spinal cord relationship: lumen_of UBERON:0010913 ! vertebral element relationship: part_of UBERON:0006692 ! vertebral canal relationship: part_of UBERON:0010913 ! vertebral element property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/1/10/Foramenvertebrale.png xsd:anyURI property_value: external_definition "Opening on the vertebra for a spinal nerve as it emerges from the spinal canal.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000729", ontology="AAO", source="AAO:LAP"} [Term] id: UBERON:0001132 name: parathyroid gland def: "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." [ISBN:0-683-40008-8, MP:0000678, Wikipedia:Parathyroid_gland] subset: organ_slim subset: pheno_slim subset: uberon_slim synonym: "epithelial body" RELATED [XAO:0000167] synonym: "parathyroid" EXACT [] synonym: "parathyroid secreting cell" RELATED [] xref: AAO:0010545 xref: BTO:0000997 xref: CALOHA:TS-0745 xref: EFO:0000862 xref: EMAPA:32812 xref: EV:0100134 xref: FMA:13890 xref: GAID:452 xref: MA:0000128 xref: MAT:0000082 xref: MESH:D010280 xref: MIAA:0000082 xref: NCIT:C12765 xref: SCTID:181121007 xref: UMLS:C0030518 {source="ncithesaurus:Parathyroid_Gland"} xref: VHOG:0001188 xref: Wikipedia:Parathyroid_gland xref: XAO:0000167 is_a: UBERON:0002368 ! endocrine gland relationship: capable_of GO:0035898 relationship: capable_of_part_of GO:0055074 {source="Wikipedia"} relationship: develops_from UBERON:0007124 {gci_relation="part_of", gci_filler="NCBITaxon:10090", source="PMID:16313389"} ! pharyngeal pouch 3 relationship: develops_from UBERON:0007125 {gci_relation="part_of", gci_filler="NCBITaxon:9606", notes="pouches 3 and 4 in human", source="PMID:16313389"} ! pharyngeal pouch 4 relationship: develops_from UBERON:0007125 {gci_relation="part_of", gci_filler="NCBITaxon:9030", notes="pouches 3 and 4 in chick", source="PMID:16313389"} ! pharyngeal pouch 4 relationship: has_developmental_contribution_from UBERON:0010025 {gci_relation="part_of", gci_filler="NCBITaxon:40674", notes="Mammals", source="ISBN:0073040584-table13.1"} ! dorsal part of pharyngeal pouch 3 relationship: has_developmental_contribution_from UBERON:0010026 {gci_relation="part_of", gci_filler="NCBITaxon:8782", notes="Aves", source="ISBN:0073040584-table13.1"} ! ventral part of pharyngeal pouch 3 relationship: has_developmental_contribution_from UBERON:0010026 {gci_relation="part_of", gci_filler="NCBITaxon:8342", notes="Anurans", source="ISBN:0073040584-table13.1", source="XAO"} ! ventral part of pharyngeal pouch 3 relationship: has_developmental_contribution_from UBERON:0010026 {gci_relation="part_of", gci_filler="NCBITaxon:8293", notes="Urodele", source="ISBN:0073040584-table13.1"} ! ventral part of pharyngeal pouch 3 relationship: has_developmental_contribution_from UBERON:0010027 {gci_relation="part_of", gci_filler="NCBITaxon:40674", notes="Mammals", source="ISBN:0073040584-table13.1"} ! dorsal part of pharyngeal pouch 4 relationship: has_developmental_contribution_from UBERON:0010028 {gci_relation="part_of", gci_filler="NCBITaxon:8342", notes="Anurans", source="ISBN:0073040584-table13.1"} ! ventral part of pharyngeal pouch 4 relationship: has_developmental_contribution_from UBERON:0010028 {gci_relation="part_of", gci_filler="NCBITaxon:8782", notes="Aves", source="ISBN:0073040584-table13.1"} ! ventral part of pharyngeal pouch 4 relationship: has_developmental_contribution_from UBERON:0010028 {gci_relation="part_of", gci_filler="NCBITaxon:8293", notes="Urodele", source="ISBN:0073040584-table13.1"} ! ventral part of pharyngeal pouch 4 relationship: only_in_taxon NCBITaxon:32523 {source="PMID:16313389"} relationship: part_of UBERON:0000949 ! endocrine system property_value: development_notes "In humans and chick it emerges from pouches 3 and 4, but in mice it is exclusively generated by the third pouch" xsd:string property_value: development_notes "table 13.1 of Kardong is used to create the taxon-specific developmental relationships here, although some omissions are made for simplicity." xsd:string {source="PMID:16313389"} property_value: external_definition "Any one of several small structures, usually four, attached to the dorsal surfaces of the lateral lobes of the thyroid gland. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001188", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/parathyroid+gland"} property_value: external_definition "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]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010545", ontology="AAO", source="AAO:BJB"} property_value: homology_notes "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]" xsd:string {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/"} property_value: taxon_notes "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]" xsd:string [Term] id: UBERON:0001133 name: cardiac muscle tissue alt_id: UBERON:0007096 def: "Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]." [ZFA:0005280] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "cardiac muscle" EXACT [] synonym: "cardiac muscle muscle tissue" EXACT [OBOL:automatic] synonym: "cardiac muscle textus muscularis" EXACT [OBOL:automatic] synonym: "cardiac musculature" RELATED [BILA:0000134] synonym: "heart muscle muscle tissue" EXACT [OBOL:automatic] synonym: "heart muscle textus muscularis" EXACT [OBOL:automatic] synonym: "heart myocardium muscle tissue" EXACT [OBOL:automatic] synonym: "heart myocardium textus muscularis" EXACT [OBOL:automatic] synonym: "muscle of heart muscle tissue" EXACT [OBOL:automatic] synonym: "muscle of heart textus muscularis" EXACT [OBOL:automatic] synonym: "muscle tissue of cardiac muscle" EXACT [OBOL:automatic] synonym: "muscle tissue of heart muscle" EXACT [OBOL:automatic] synonym: "muscle tissue of heart myocardium" EXACT [OBOL:automatic] synonym: "muscle tissue of muscle of heart" EXACT [OBOL:automatic] synonym: "muscle tissue of myocardium" EXACT [OBOL:automatic] synonym: "myocardium muscle tissue" EXACT [OBOL:automatic] synonym: "myocardium textus muscularis" EXACT [OBOL:automatic] synonym: "textus muscularis of cardiac muscle" EXACT [OBOL:automatic] synonym: "textus muscularis of heart muscle" EXACT [OBOL:automatic] synonym: "textus muscularis of heart myocardium" EXACT [OBOL:automatic] synonym: "textus muscularis of muscle of heart" EXACT [OBOL:automatic] synonym: "textus muscularis of myocardium" EXACT [OBOL:automatic] xref: AAO:0010245 xref: AEO:0000142 xref: BILA:0000134 xref: BTO:0000199 xref: CALOHA:TS-0440 xref: EHDAA2:0003142 xref: EMAPA:32688 xref: FMA:14068 xref: galen:CardiacMuscle xref: galen:CardiacMuscleTissue xref: ncithesaurus:Heart_Muscle xref: TAO:0005280 xref: Wikipedia:Cardiac_muscle xref: ZFA:0005280 is_a: UBERON:0002036 ! striated muscle tissue intersection_of: UBERON:0002036 ! striated muscle tissue intersection_of: has_part CL:0000746 disjoint_from: UBERON:0001134 ! skeletal muscle tissue relationship: composed_primarily_of CL:0000746 relationship: has_part CL:0000746 relationship: part_of UBERON:0000948 {source="ZFA"} ! heart property_value: editor_note "check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit" xsd:string [Term] id: UBERON:0001134 name: skeletal muscle tissue def: "Muscle tissue that consists primarily of skeletal muscle fibers." [https://github.com/obophenotype/uberon/issues/324] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "skeletal muscle" BROAD [] synonym: "skeletal muscle system" RELATED [BTO:0001103] synonym: "somatic muscle" RELATED [BTO:0001103] xref: EMAPA:32716 xref: FMA:14069 xref: MA:0002439 xref: NCIT:C13050 xref: SCTID:426215008 xref: UMLS:C0242692 {source="ncithesaurus:Skeletal_Muscle_Tissue"} xref: Wikipedia:Skeletal_striated_muscle is_a: UBERON:0002036 ! striated muscle tissue intersection_of: UBERON:0002385 ! muscle tissue intersection_of: composed_primarily_of CL:0008002 relationship: composed_primarily_of CL:0008002 relationship: dc-contributor https://github.com/cmungall relationship: dc-contributor https://github.com/dosumis relationship: dc-contributor https://github.com/mellybelly relationship: dc-contributor https://github.com/RDruzinsky relationship: develops_from UBERON:0003082 ! myotome relationship: part_of UBERON:0014892 ! skeletal muscle organ property_value: depicted_by Skeletal:muscle.jpg xsd:anyURI property_value: editor_note "TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle." xsd:string property_value: external_definition "Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005277", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]" xsd:string {external_class="FMA:14069", ontology="FMA"} property_value: homology_notes "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]" xsd:string {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/"} [Term] id: UBERON:0001135 name: smooth muscle tissue def: "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]." [GO:0006939, Wikipedia:Smooth_muscle_tissue] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "involuntary muscle" EXACT [] synonym: "non-striated muscle" EXACT [] synonym: "smooth muscle" EXACT [] synonym: "textus muscularis levis; textus muscularis nonstriatus" RELATED LATIN [Wikipedia:Smooth_muscle_tissue] synonym: "textus muscularis nonstriatus" EXACT LATIN [FMA:14070, FMA:TA] synonym: "visceral muscle" NARROW SENSU [] synonym: "visceral muscle tissue" NARROW SENSU [] xref: AAO:0010244 xref: AEO:0000141 xref: BTO:0001260 xref: CALOHA:TS-0943 xref: EFO:0000889 xref: EHDAA2:0003141 xref: EMAPA:32717 xref: EV:0100378 xref: FBbt:00003525 xref: FMA:14070 xref: GAID:167 xref: galen:SmoothMuscle xref: galen:SmoothMuscleTissue xref: MA:0000166 xref: MAT:0000303 xref: MESH:D009130 xref: MIAA:0000303 xref: NCIT:C12437 xref: OpenCyc:Mx4rvvSS3pwpEbGdrcN5Y29ycA xref: TAO:0005274 xref: UMLS:C1267092 {source="ncithesaurus:Smooth_Muscle_Tissue"} xref: VHOG:0001246 xref: WBbt:0005781 xref: Wikipedia:Smooth_muscle_tissue xref: XAO:0000175 xref: ZFA:0005274 is_a: UBERON:0002385 ! muscle tissue intersection_of: UBERON:0002385 ! muscle tissue intersection_of: has_part CL:0000192 disjoint_from: UBERON:0002036 ! striated muscle tissue relationship: composed_primarily_of CL:0000192 relationship: has_part CL:0000192 relationship: has_part GO:0071953 property_value: depicted_by Glatte:Muskelzellen.jpg xsd:anyURI property_value: external_definition "A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005274", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010244", ontology="AAO", source="AAO:CAM"} property_value: homology_notes "(...) 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]" xsd:string {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/"} property_value: terminology_notes "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." xsd:string [Term] id: UBERON:0001136 name: mesothelium def: "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)." [FMA:14074, Wikipedia:Mesothelium] subset: uberon_slim xref: AEO:0000111 xref: BTO:0002422 xref: CALOHA:TS-1183 xref: EHDAA2_RETIRED:0003111 xref: EHDAA:2331 xref: EHDAA:2349 xref: EHDAA:295 xref: EHDAA:6073 xref: EHDAA:640 xref: EHDAA:646 xref: EMAPA:32856 xref: FMA:14074 xref: MA:0000565 xref: NCIT:C33105 xref: SCTID:361918002 xref: UMLS:C0086610 {source="ncithesaurus:Mesothelium"} xref: Wikipedia:Mesothelium is_a: UBERON:0000487 ! simple squamous epithelium intersection_of: UBERON:0000487 ! simple squamous epithelium intersection_of: develops_from UBERON:0000926 ! mesoderm intersection_of: part_of UBERON:0000042 ! serous membrane relationship: composed_primarily_of CL:0000077 {source="FMA"} relationship: develops_from UBERON:0000926 ! mesoderm relationship: part_of UBERON:0000042 ! serous membrane property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg xsd:anyURI [Term] id: UBERON:0001137 name: dorsum def: "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.." [BSPO:0000063, UBERONREF:0000006, Wikipedia:Dorsum_(anatomy)] subset: efo_slim subset: uberon_slim synonym: "back" EXACT [FMA:14181] synonym: "back of body proper" EXACT [FMA:14181] synonym: "dorsal part of organism" EXACT [] xref: BTO:0001713 xref: CALOHA:TS-2223 xref: EFO:0001405 xref: FMA:14181 xref: GAID:30 xref: galen:Back xref: MESH:A01.176 xref: NCIT:C13062 xref: OpenCyc:Mx4rvVkEU5wpEbGdrcN5Y29ycA xref: SCTID:123961009 xref: UMLS:C0004600 {source="ncithesaurus:Back"} xref: Wikipedia:Dorsum_(anatomy) is_a: UBERON:0000475 ! organism subdivision relationship: only_in_taxon NCBITaxon:33213 property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG xsd:anyURI property_value: has_relational_adjective "dorsal" xsd:string property_value: taxon_notes "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" xsd:string [Term] id: UBERON:0001138 name: superior mesenteric vein def: "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]." [Wikipedia:Superior_mesenteric_vein] subset: uberon_slim synonym: "upper mesenteric vein" RELATED [BTO:0002783] synonym: "vena mesenterica superior" RELATED LATIN [Wikipedia:Superior_mesenteric_vein] xref: BTO:0002783 xref: EHDAA2:0001951 xref: EHDAA:5414 xref: EMAPA:18643 xref: FMA:14332 xref: MA:0002179 xref: NCIT:C33687 xref: OpenCyc:Mx4rwFjmM5wpEbGdrcN5Y29ycA xref: SCTID:278031001 xref: UMLS:C0226742 {source="ncithesaurus:Superior_Mesenteric_Vein"} xref: VHOG:0000552 xref: Wikipedia:Superior_mesenteric_vein is_a: UBERON:0005617 ! mesenteric vein intersection_of: UBERON:0005617 ! mesenteric vein intersection_of: drains UBERON:0002108 ! small intestine relationship: develops_from UBERON:0005487 {source="Wikipedia:Vitelline_vein"} ! vitelline vein relationship: drains UBERON:0002108 ! small intestine relationship: part_of UBERON:0005806 ! portal system property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png xsd:anyURI [Term] id: UBERON:0001139 name: common iliac vein def: "A vein that drains the pelvis and lower limbs into the inferior vena cava." [MURDOCH:403, Wikipedia:Common_iliac_vein] subset: uberon_slim synonym: "common iliac venous tree" EXACT [] synonym: "vena iliaca communis" RELATED LATIN [Wikipedia:Common_iliac_vein] xref: EMAPA:17874 xref: FMA:14333 xref: galen:CommonIliacVein xref: MA:0002143 xref: NCIT:C32359 xref: OpenCyc:Mx4rv92CGZwpEbGdrcN5Y29ycA xref: SCTID:181398004 xref: UMLS:C0226758 {source="ncithesaurus:Common_Iliac_Vein"} xref: Wikipedia:Common_iliac_vein is_a: UBERON:0005610 {source="MA"} ! iliac vein is_a: UBERON:0015212 ! lateral structure relationship: drains UBERON:0010708 ! pectoral complex relationship: in_lateral_side_of UBERON:0001072 {source="FMA-abduced-lr"} ! posterior vena cava relationship: part_of UBERON:0001072 ! posterior vena cava property_value: depicted_by Iliac:veins.gif xsd:anyURI property_value: taxon_notes "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." xsd:string {source="Wikipedia:Common_iliac_vein"} [Term] id: UBERON:0001140 name: renal vein def: "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." [ISBN:0-683-40008-8, MGI:csmith, MP:0011323] subset: pheno_slim subset: uberon_slim synonym: "kidney vein" EXACT [OBOL:automatic] synonym: "renal venous tree" EXACT [] synonym: "vein of kidney" EXACT [OBOL:automatic] synonym: "venae renales" RELATED LATIN [Wikipedia:Renal_vein] xref: BTO:0002681 xref: EHDAA2:0001602 xref: EHDAA:8722 xref: EMAPA:28376 xref: FMA:14334 xref: GAID:544 xref: galen:RenalVein xref: MA:0002210 xref: MESH:D012082 xref: NCIT:C33462 xref: OpenCyc:Mx4rvdUXKJwpEbGdrcN5Y29ycA xref: SCTID:116358006 xref: UMLS:C0035092 {source="ncithesaurus:Renal_Vein"} xref: Wikipedia:Renal_vein is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0002113 ! kidney relationship: drains UBERON:0002113 ! kidney relationship: part_of UBERON:0001072 ! posterior vena cava relationship: tributary_of UBERON:0001072 ! posterior vena cava property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png xsd:anyURI property_value: external_definition "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]." xsd:string {source="Wikipedia:Renal_vein"} property_value: external_ontology_notes "in EHDAA2, the renal vein is part of the kidney" xsd:string {external_ontology="EHDAA2"} [Term] id: UBERON:0001141 name: right renal vein def: "A renal vein that drains the right kidney" [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim xref: EMAPA:37381 {source="MA:th"} xref: FMA:14335 xref: MA:0002212 xref: NCIT:C52695 xref: OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvdUXKJwpEbGdrcN5Y29ycA xref: SCTID:116357001 xref: UMLS:C0508000 {source="ncithesaurus:Right_Renal_Vein"} is_a: UBERON:0001140 ! renal vein intersection_of: UBERON:0001140 ! renal vein intersection_of: drains UBERON:0004539 ! right kidney relationship: drains UBERON:0004539 ! right kidney property_value: external_definition "A vein that drains blood from the right kidney into the inferior vena cava[ncithesaurus]." xsd:string {source="ncithesaurus:Right_Renal_Vein"} [Term] id: UBERON:0001142 name: left renal vein def: "A renal vein that drains the left kidney" [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim xref: EMAPA:37166 {source="MA:th"} xref: FMA:14336 xref: MA:0002211 xref: NCIT:C52693 xref: OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvdUXKJwpEbGdrcN5Y29ycA xref: SCTID:116356005 xref: UMLS:C0508001 {source="ncithesaurus:Left_Renal_Vein"} is_a: UBERON:0001140 ! renal vein intersection_of: UBERON:0001140 ! renal vein intersection_of: drains UBERON:0004538 ! left kidney relationship: drains UBERON:0004538 ! left kidney property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png xsd:anyURI property_value: external_definition "A vein that drains blood from the left kidney into the inferior vena cava[ncithesaurus]." xsd:string {source="ncithesaurus:Left_Renal_Vein"} [Term] id: UBERON:0001143 name: hepatic vein def: "Vein that carries blood away from the liver[ZFA]." [https://sourceforge.net/tracker/?func=detail&aid=3565355&group_id=76834&atid=1205376, Wikipedia:Hepatic_vein, ZFA:0000670] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "hepatic veins" RELATED PLURAL [] synonym: "liver vein" EXACT [OBOL:automatic] synonym: "vein of liver" EXACT [OBOL:automatic] synonym: "vena hepatica" EXACT LATIN [] synonym: "venae hepaticae" RELATED LATIN [Wikipedia:Hepatic_vein] xref: AAO:0010216 xref: EMAPA:19221 xref: FMA:14337 xref: GAID:534 xref: galen:HepaticVein xref: MA:0003015 xref: MESH:D006503 xref: NCIT:C32736 xref: OpenCyc:Mx4rv5GivJwpEbGdrcN5Y29ycA xref: SCTID:278191001 xref: TAO:0000670 xref: UMLS:C0019155 {source="ncithesaurus:Hepatic_Vein"} xref: Wikipedia:Hepatic_vein xref: XAO:0000387 xref: ZFA:0000670 is_a: UBERON:0013126 ! vein of abdomen is_a: UBERON:0015796 ! liver blood vessel intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0002107 ! liver disjoint_from: UBERON:0001639 ! hepatic portal vein relationship: develops_from UBERON:0005487 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="Wikipedia:Vitelline_vein"} ! vitelline vein relationship: drains UBERON:0002107 ! liver relationship: part_of UBERON:0001072 ! posterior vena cava relationship: part_of UBERON:0006877 ! vasculature of liver relationship: tributary_of UBERON:0001072 {source="FMA-abduced-lr"} ! posterior vena cava property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png xsd:anyURI property_value: editor_note "todo - add developmental relationships for other taxa" xsd:string [Term] id: UBERON:0001144 name: testicular vein def: "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." [http://orcid.org/0000-0002-6601-2165, https://sourceforge.net/tracker/?func=detail&aid=3220553&group_id=76834&atid=1205376, Wikipedia:Testicular_vein] subset: uberon_slim synonym: "male gonadal vein" EXACT [Wikipedia:Testicular_vein] synonym: "spermatic vein" EXACT [Wikipedia:Testicular_vein] synonym: "testicle vein" EXACT [OBOL:automatic] synonym: "testicular venous tree" EXACT [Wikipedia:Testicular_vein] synonym: "vein of testicle" EXACT [OBOL:automatic] synonym: "vena tesicularis" RELATED [BTO:0002678] synonym: "vena testicularis dextra" RELATED LATIN [Wikipedia:Testicular_vein] synonym: "vena testicularis sinistra" RELATED LATIN [Wikipedia:Testicular_vein] synonym: "venae spermaticae" RELATED LATIN [Wikipedia:Testicular_vein] xref: BTO:0002678 xref: EMAPA:18647 xref: FMA:14344 xref: MA:0002218 xref: MA:0002234 xref: NCIT:C53050 xref: OpenCyc:Mx4rv1WIHpwpEbGdrcN5Y29ycA xref: SCTID:264496006 xref: UMLS:C0226718 {source="ncithesaurus:Spermatic_Vein"} xref: Wikipedia:Testicular_vein is_a: UBERON:0001638 ! vein is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0000473 ! testis relationship: connected_to UBERON:0001072 ! posterior vena cava relationship: connected_to UBERON:0001330 ! pampiniform plexus relationship: drains UBERON:0000473 ! testis relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism relationship: sexually_homologous_to UBERON:0001145 ! ovarian vein property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/1/1b/Gray590.png xsd:anyURI property_value: editor_note "TODO - check testicular vs spermatic vein (MA:0002218)" xsd:string property_value: taxon_notes "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" xsd:string [Term] id: UBERON:0001145 name: ovarian vein def: "A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries." [Wikipedia:Ovarian_vein] subset: uberon_slim synonym: "female reproductive system gonad vein" EXACT [OBOL:automatic] synonym: "female reproductive system gonada vein" EXACT [OBOL:automatic] synonym: "gonad of female reproductive system vein" EXACT [OBOL:automatic] synonym: "gonada of female reproductive system vein" EXACT [OBOL:automatic] synonym: "ovary vein" EXACT [OBOL:automatic] synonym: "vein of female reproductive system gonad" EXACT [OBOL:automatic] synonym: "vein of female reproductive system gonada" EXACT [OBOL:automatic] synonym: "vein of gonad of female reproductive system" EXACT [OBOL:automatic] synonym: "vein of gonada of female reproductive system" EXACT [OBOL:automatic] synonym: "vein of ovary" EXACT [OBOL:automatic] synonym: "vena ovarica dextra" RELATED LATIN [Wikipedia:Ovarian_vein] synonym: "vena ovarica sinistra" RELATED LATIN [Wikipedia:Ovarian_vein] xref: EMAPA:18644 xref: FMA:14346 xref: MA:0002186 xref: NCIT:C53058 xref: OpenCyc:Mx4rvrST5ZwpEbGdrcN5Y29ycA xref: SCTID:278193003 xref: UMLS:C0226720 {source="ncithesaurus:Ovarian_Vein"} xref: Wikipedia:Ovarian_vein is_a: UBERON:0001638 ! vein is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0000992 ! ovary relationship: drains UBERON:0000992 ! ovary relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/c/cf/Ovarschaf.jpg xsd:anyURI [Term] id: UBERON:0001146 name: suprarenal vein def: "A vein that drains the adrenal gland." [http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/mouse-anatomy-ontology/issues/110] subset: uberon_slim synonym: "adrenal vein" RELATED [MA:0002081] xref: EHDAA2:0001966 xref: EHDAA:8731 xref: FMA:14348 xref: MA:0002081 xref: MA:0002229 xref: NCIT:C53129 xref: SCTID:278194009 xref: UMLS:C0226717 {source="ncithesaurus:Suprarenal_Vein"} xref: Wikipedia:Suprarenal_vein is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0002369 ! adrenal gland relationship: drains UBERON:0002369 ! adrenal gland property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png xsd:anyURI [Term] id: UBERON:0001148 name: median nerve def: "A nerve of the arm that originates from the brachial plexus and is formed from parts of the medial and lateral cords of the brachial plexus, and continues down the arm to enter the forearm with the brachial artery. It originates from the brachial plexus with roots from C5, C6, C7, C8 & T1." [Wikipedia:Median_nerve] comment: The median nerve is the only nerve that passes through the carpal tunnel, where it may be compressed to cause carpal tunnel syndrome. [WP] subset: uberon_slim synonym: "nervus medianus" RELATED LATIN [Wikipedia:Median_nerve] xref: EHDAA2:0001086 xref: EHDAA:5648 xref: EMAPA:17277 xref: FMA:14385 xref: GAID:843 xref: MA:0001168 xref: MESH:D008475 xref: NCIT:C52815 xref: OpenCyc:Mx4rwF4HF5wpEbGdrcN5Y29ycA xref: SCTID:181010001 xref: UMLS:C0025058 {source="ncithesaurus:Median_Nerve"} xref: Wikipedia:Median_nerve is_a: UBERON:0003433 ! arm nerve relationship: branching_part_of UBERON:0001814 ! brachial nerve plexus relationship: part_of UBERON:0001460 ! arm relationship: part_of UBERON:0001814 ! brachial nerve plexus property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/a7/Nerves_of_the_left_upper_extremity.gif xsd:anyURI [Term] id: UBERON:0001149 name: bare area of liver def: "A large triangular surface of the liver devoid of peritoneal covering." [Wikipedia:Bare_area_of_the_liver] synonym: "area nuda" RELATED [Wikipedia:Bare_area_of_the_liver] synonym: "area nuda (hepar)" EXACT [] synonym: "area nuda hepatis" EXACT [] synonym: "bare area" RELATED [Wikipedia:Bare_area_of_the_liver] synonym: "hepatic bare area" RELATED [EMAPA:17945] synonym: "liver bare area" EXACT [] xref: EMAPA:17945 xref: FMA:14480 xref: MA:0000359 xref: SCTID:279965008 xref: Wikipedia:Bare_area_of_the_liver is_a: CARO:0000000 is_a: UBERON:0000466 ! immaterial anatomical entity relationship: part_of UBERON:0001114 ! right lobe of liver [Term] id: UBERON:0001150 name: body of pancreas def: "The body of the pancreas is a subsection of the pancreas organ in the human body. It is somewhat prismatic in shape, and has three surfaces: anterior, posterior, and inferior. It is at the same level as the transpyloric plane. [WP,unvetted]." [Wikipedia:Body_of_pancreas] subset: uberon_slim synonym: "corpus pancreatis" RELATED LATIN [Wikipedia:Body_of_pancreas] synonym: "pancreas body" EXACT [] synonym: "pancreas corpus" RELATED [] synonym: "pancreatic body" EXACT [] xref: EHDAA2:0001368 xref: EHDAA:9178 xref: EMAPA:17504 xref: FMA:14518 xref: MA:0000121 xref: NCIT:C12270 xref: SCTID:362202004 xref: UMLS:C0227582 {source="ncithesaurus:Body_of_the_Pancreas"} xref: VHOG:0000451 xref: Wikipedia:Body_of_pancreas is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0001264 ! pancreas property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/f/fe/Illu_pancreas_duodenum.jpg xsd:anyURI property_value: homology_notes "Hagfish and lampreys may have one or more endocrine buds - and later the vertebrate pancreas develop as independent ventral and dorsal buds that eventually fuse to become one organ.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000451", ontology="VHOG", source="DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. Comptes Rendus Biologies (2007)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001151 name: tail of pancreas def: "The tail of the pancreas, located anatomically left near the hilum of the spleen, is not simply an anatomical distinction. The tail is the only part of the pancreas which contains Pancreatic Polypeptide (PP) cells, which are responsible for secreting pancreatic polypeptide to coordinate exocrine and islet enzyme release. PP cells are found in the tail's periphery. Beta cells and delta cells are found in the central part of the tail as with the rest of the pancreas. The cells described above are located exclusively in the islet cells; their secretions reach exocrine portions of the pancreas via the capillary network surrounding the islet cell populations. [WP,unvetted]." [Wikipedia:Tail_of_pancreas] subset: uberon_slim synonym: "cauda pancreatis" RELATED LATIN [Wikipedia:Tail_of_pancreas] synonym: "left extremity of pancreas" EXACT [FMA:14519] synonym: "pancreas tail" EXACT [] synonym: "pancreatic tail" EXACT [FMA:14519] xref: EHDAA2:0001390 xref: EMAPA:17511 xref: FMA:14519 xref: MA:0000123 xref: NCIT:C12271 xref: SCTID:245382003 xref: UMLS:C0227590 {source="ncithesaurus:Tail_of_the_Pancreas"} xref: VHOG:0000452 xref: Wikipedia:Tail_of_pancreas is_a: UBERON:0000064 ! organ part is_a: UBERON:0004119 ! endoderm-derived structure relationship: develops_from UBERON:0009708 {source="EHDAA2"} ! dorsal pancreas relationship: part_of UBERON:0001264 {source="FMA"} ! pancreas property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/f/fe/Illu_pancreas_duodenum.jpg xsd:anyURI property_value: homology_notes "Hagfish and lampreys may have one or more endocrine buds - and later the vertebrate pancreas develop as independent ventral and dorsal buds that eventually fuse to become one organ.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000452", ontology="VHOG", source="DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. Comptes Rendus Biologies (2007)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001152 name: cystic duct def: "the tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct" [ISBN:0-683-40008-8, MP:0009493] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "ductus cysticus" RELATED LATIN [Wikipedia:Cystic_duct] xref: EHDAA2:0000333 xref: EHDAA:3045 xref: EMAPA:16841 xref: FMA:14539 xref: GAID:290 xref: galen:CysticDuct xref: MA:0000355 xref: MESH:A03.159.183.419 xref: NCIT:C32421 xref: OpenCyc:Mx4rveBeC5wpEbGdrcN5Y29ycA xref: SCTID:245398005 xref: TAO:0005166 xref: UMLS:C0010672 {source="ncithesaurus:Cystic_Duct"} xref: VHOG:0000213 xref: Wikipedia:Cystic_duct xref: ZFA:0005166 is_a: UBERON:0003703 {source="FMA"} ! extrahepatic bile duct intersection_of: UBERON:0000058 ! duct intersection_of: continuous_with UBERON:0001174 ! common bile duct intersection_of: continuous_with UBERON:0002110 ! gall bladder disjoint_from: UBERON:0005171 ! hepatic duct relationship: channel_for UBERON:0001970 ! bile relationship: channels_into UBERON:0001174 ! common bile duct relationship: continuous_with UBERON:0001174 ! common bile duct relationship: continuous_with UBERON:0002110 ! gall bladder relationship: develops_from UBERON:0005604 {source="EHDAA2"} ! extrahepatic part of hepatic duct relationship: part_of UBERON:0001173 {source="FMA"} ! biliary tree property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg xsd:anyURI property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png xsd:anyURI property_value: external_definition "Duct that connects the gall bladder and the common bile duct.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005166", ontology="TAO", source="ZFIN:Curator"} property_value: external_definition "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000213", ontology="VHOG", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001153 name: caecum def: "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." [Wikipedia:Cecum] comment: Taxon notes: in some herbivorous lizards, a cecum is present between small and large intestines[Kardong] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "blind intestine" RELATED [BTO:0000166] synonym: "blindgut" RELATED [BTO:0000166] synonym: "caeca" NARROW PLURAL [NCBITaxon:8782] synonym: "caecum" EXACT [VHOG:0001559] synonym: "ceca" NARROW PLURAL [NCBITaxon:8782] synonym: "cecum" EXACT [FMA:14541] synonym: "intestinum caecum" RELATED [BTO:0000166] synonym: "intestinum crassum caecum" EXACT [] synonym: "intestinum crassum cecum" RELATED [BTO:0000166] xref: BTO:0000166 xref: CALOHA:TS-0122 xref: EFO:0000850 xref: EHDAA2:0000206 xref: EHDAA:3913 xref: EMAPA:35197 xref: EV:0100397 xref: FMA:14541 xref: GAID:307 xref: galen:Cecum xref: MA:0000334 xref: MESH:A03.492.411.495.209 xref: MIAA:0000288 xref: NCIT:C12381 xref: OpenCyc:Mx4rve6u4JwpEbGdrcN5Y29ycA xref: SCTID:181256004 xref: UMLS:C0007531 {source="ncithesaurus:Cecum"} xref: VHOG:0001559 xref: Wikipedia:Cecum is_a: UBERON:0009854 ! digestive tract diverticulum relationship: continuous_with UBERON:0001156 {source="Wikipedia"} ! ascending colon relationship: contributes_to_morphology_of UBERON:0000059 ! large intestine relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut relationship: never_in_taxon NCBITaxon:32443 {source="Wikipedia"} relationship: only_in_taxon NCBITaxon:7776 relationship: part_of UBERON:0000059 {source="MA"} ! large intestine relationship: part_of UBERON:0001155 {source="EHDAA2"} ! colon property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg xsd:anyURI property_value: has_relational_adjective "caecal" xsd:string property_value: taxon_notes "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." xsd:string {source="WP"} [Term] id: UBERON:0001154 name: vermiform appendix def: "A blind-ended tube connected to the cecum, from which it develops embryologically[WP]." [https://orcid.org/0000-0002-6826-8770, Wikipedia:Vermiform_appendix] subset: efo_slim subset: organ_slim subset: uberon_slim synonym: "apex of caecum" RELATED [EMAPA:35140] synonym: "apex of cecum" RELATED [VHOG:0001306] synonym: "appendix" EXACT [] synonym: "appendix vermiformis" EXACT LATIN [FMA:14542, FMA:TA] synonym: "appendix vermiformis" RELATED LATIN [Wikipedia:Vermiform_appendix] synonym: "caecal appendix" EXACT [] synonym: "cecal appendix" EXACT [] synonym: "vermix" BROAD [] xref: BTO:0000084 xref: CALOHA:TS-1267 xref: EFO:0000849 xref: EHDAA2:0000588 xref: EMAPA:35140 xref: EV:0100076 xref: EV:0100080 xref: FMA:14542 xref: GAID:308 xref: galen:AppendixVermiformis xref: MA:0001540 xref: MAT:0000287 xref: MESH:A03.492.411.495.209.290 xref: MIAA:0000287 xref: NCIT:C12380 xref: OpenCyc:Mx4rvVjGgJwpEbGdrcN5Y29ycA xref: SCTID:181255000 xref: UMLS:C0003617 {source="ncithesaurus:Vermiform_Appendix"} xref: VHOG:0001306 xref: Wikipedia:Vermiform_appendix is_a: CARO:0000000 is_a: UBERON:0013765 ! digestive system element relationship: continuous_with UBERON:0001153 {xref="http://orcid.org/0000-0002-1572-1316"} ! caecum relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut relationship: part_of UBERON:0000059 ! large intestine property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray536.png xsd:anyURI property_value: external_definition "Organ with organ cavity which is continuous proximally with the cecum and distally terminates in the tip of the appendix. Examples: There is only one appendix[FMA:14542]." xsd:string {source="FMA:14542"} property_value: has_relational_adjective "appendiceal" xsd:string property_value: homology_notes "A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001306", ontology="VHOG", source="DOI:10.1111/j.1420-9101.2009.01809.x Smith HF, Fisher RE, Everett ML, Thomas AD, Randal Bollinger R, Parker W, Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. Journal of Evolutionary Biology (2009)", source="http://bgee.unil.ch/"} property_value: present_in_taxon "Mammalia" xsd:string [Term] id: UBERON:0001155 name: colon def: "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." [http://orcid.org/0000-0002-2825-0621, http://orcid.org/0000-0002-6601-2165, Wikipedia:Colon_(anatomy), ZFIN:curator] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "hindgut" RELATED [] synonym: "large bowel" EXACT [] synonym: "posterior intestine" NARROW [] xref: AAO:0010400 xref: BTO:0000269 xref: CALOHA:TS-0158 xref: EFO:0000361 xref: EMAPA:18939 xref: EV:0100079 xref: FMA:14543 xref: GAID:309 xref: galen:Colon xref: MA:0000335 xref: MAP:0000001 xref: MAT:0000526 xref: MESH:A03.492.411.495.356 xref: NCIT:C12382 xref: OpenCyc:Mx4rvgLEM5wpEbGdrcN5Y29ycA xref: SCTID:302508007 xref: TAO:0000706 xref: UMLS:C0009368 {source="ncithesaurus:Colon"} xref: VHOG:0000648 xref: Wikipedia:Colon_(anatomy) xref: XAO:0000243 xref: ZFA:0000706 is_a: UBERON:0004921 {order="3", source="cjm"} ! subdivision of digestive tract relationship: contributes_to_morphology_of UBERON:0000059 ! large intestine relationship: only_in_taxon NCBITaxon:7742 relationship: part_of UBERON:0000059 {source="FMA"} ! large intestine property_value: editor_note "Some references do not consider the caecum to be part of the colon." xsd:string {xref="http://orcid.org/0000-0002-1572-1316"} property_value: editor_note "TODO - abstract this such that it legitimately covers all vertebrates" xsd:string property_value: external_definition "The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010400", ontology="AAO", source="UBERON:0001155"} property_value: external_definition "The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000706", ontology="TAO", source="ZFIN:curator"} property_value: function_notes "it extracts water and salt from solid wastes before they are eliminated from the body[WP]" xsd:string property_value: has_relational_adjective "colonic" xsd:string property_value: homology_notes "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]" xsd:string {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/"} property_value: taxon_notes "In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]" xsd:string property_value: taxon_notes "In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN]" xsd:string [Term] id: UBERON:0001156 name: ascending colon def: "Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified]" [FMA:14545, Wikipedia:Ascending_colon] subset: efo_slim subset: uberon_slim synonym: "colon ascendens" EXACT LATIN [Wikipedia:Ascending_colon] synonym: "spiral colon" RELATED SENSU [Wikipedia:Spiral_colon] xref: BTO:0000270 xref: CALOHA:TS-0057 xref: EFO:0000843 xref: EMAPA:35151 xref: FMA:14545 xref: galen:AscendingColon xref: MA:0001541 xref: MAT:0000311 xref: MIAA:0000311 xref: NCIT:C12265 xref: OpenCyc:Mx4rv3H0FZwpEbGdrcN5Y29ycA xref: SCTID:362162009 xref: UMLS:C0227375 {source="ncithesaurus:Ascending_Colon"} xref: Wikipedia:Ascending_colon is_a: UBERON:0000168 {source="FMA"} ! proximal-distal subdivision of colon relationship: continuous_with UBERON:0001157 ! transverse colon relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg xsd:anyURI property_value: external_ontology_notes "in MA, this is a subclass of colon" xsd:string {external_ontology="MA"} [Term] id: UBERON:0001157 name: transverse colon def: "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]." [BTO:0000272, Wikipedia:Transverse_colon] subset: efo_slim subset: uberon_slim synonym: "colon transversum" EXACT LATIN [Wikipedia:Transverse_colon] xref: BTO:0000272 xref: CALOHA:TS-2052 xref: EFO:0000844 xref: EMAPA:35880 xref: FMA:14546 xref: galen:TransverseColon xref: MA:0001543 xref: MAT:0000312 xref: MIAA:0000312 xref: NCIT:C12385 xref: OpenCyc:Mx4rvg7qyJwpEbGdrcN5Y29ycA xref: SCTID:362163004 xref: UMLS:C0227386 {source="ncithesaurus:Transverse_Colon"} xref: Wikipedia:Transverse_colon is_a: UBERON:0000168 {source="FMA"} ! proximal-distal subdivision of colon relationship: continuous_with UBERON:0001158 ! descending colon relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg xsd:anyURI [Term] id: UBERON:0001158 name: descending colon def: "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." [BTO:0000641] subset: efo_slim subset: uberon_slim synonym: "colon descendens" EXACT LATIN [Wikipedia:Descending_colon] xref: BTO:0000641 xref: CALOHA:TS-2010 xref: EFO:0000845 xref: EMAPA:35285 xref: FMA:14547 xref: galen:DescendingColon xref: MA:0001542 xref: MAT:0000313 xref: MIAA:0000313 xref: NCIT:C12268 xref: OpenCyc:Mx4rwHsNhpwpEbGdrcN5Y29ycA xref: SCTID:362165006 xref: UMLS:C0227389 {source="ncithesaurus:Descending_Colon"} xref: Wikipedia:Descending_colon is_a: UBERON:0000168 {source="FMA"} ! proximal-distal subdivision of colon relationship: continuous_with UBERON:0001159 ! sigmoid colon relationship: develops_from UBERON:0001046 {source="Wikipedia"} ! hindgut property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/c/ca/Gray1223.png xsd:anyURI [Term] id: UBERON:0001159 name: sigmoid colon def: "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." [Wikipedia:Sigmoid_colon] subset: efo_slim subset: uberon_slim synonym: "colon sigmoideum" RELATED LATIN [Wikipedia:Sigmoid_colon] synonym: "pelvic colon" RELATED [] synonym: "sigmoid colon" RELATED [] synonym: "sigmoid flexure" RELATED [] xref: BTO:0000645 xref: CALOHA:TS-2044 xref: EFO:0000846 xref: EMAPA:36391 xref: FMA:14548 xref: galen:SigmoidColon xref: MAT:0000314 xref: MESH:A03.492.411.495.356.668 xref: MIAA:0000314 xref: NCIT:C12384 xref: NCIT:C33550 xref: OpenCyc:Mx4rwHX_-5wpEbGdrcN5Y29ycA xref: SCTID:362166007 xref: UMLS:C0227391 {source="ncithesaurus:Sigmoid_Colon"} xref: UMLS:C0682612 {source="ncithesaurus:Sigmoid_Flexure"} xref: Wikipedia:Sigmoid_colon is_a: UBERON:0000168 {source="FMA"} ! proximal-distal subdivision of colon relationship: continuous_with UBERON:0001052 ! rectum relationship: develops_from UBERON:0001046 {source="Wikipedia"} ! hindgut property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg xsd:anyURI [Term] id: UBERON:0001160 name: fundus of stomach def: "The fundus is the portion of the stomach that lies above the cardiac notch, and contains the fundic glands[GO, Kardong]." [GO:0014825, ISBN:0073040584, Wikipedia:Fundus_(stomach)] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "fundus gastricus" RELATED [BTO:0000502] synonym: "fundus gastricus (ventricularis)" EXACT [] synonym: "fundus gastricus ventricularis" RELATED [BTO:0000502] synonym: "fundus ventricularis" RELATED [BTO:0000502] synonym: "fundus ventriculi" RELATED [BTO:0000502] synonym: "gastric fundus" EXACT [] synonym: "stomach fundus" EXACT [] xref: BTO:0000502 xref: EFO:0002554 xref: EHDAA2:0001919 xref: EHDAA:4844 xref: EMAPA:17886 xref: FMA:14559 xref: GAID:320 xref: galen:GastricFundus xref: MA:0001612 xref: MESH:A03.492.766.419 xref: NCIT:C12257 xref: SCTID:362139007 xref: UMLS:C0017129 {source="ncithesaurus:Fundus_of_the_Stomach"} xref: VHOG:0000421 xref: Wikipedia:Fundus_(stomach) is_a: UBERON:0009870 ! zone of stomach relationship: contributes_to_morphology_of UBERON:0000945 ! stomach relationship: has_part UBERON:0010038 ! fundic gastric gland property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg xsd:anyURI property_value: external_definition "The greater curvature of the stomach. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000421", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000421", 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/"} [Term] id: UBERON:0001161 name: body of stomach def: "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]." [GO:0014845, Wikipedia:Body_of_stomach] subset: uberon_slim synonym: "corpus gastricum" RELATED [BTO:0000505] synonym: "corpus gastricum" RELATED LATIN [Wikipedia:Body_of_stomach] synonym: "corpus gastricum (ventriculare)" EXACT [] synonym: "corpus ventriculare" RELATED [BTO:0000505] synonym: "corpus ventriculi" RELATED [BTO:0000505] synonym: "gastric body" EXACT [] synonym: "gastric corpus" RELATED [] synonym: "stomach body" EXACT [] xref: BTO:0000505 xref: EMAPA:35810 xref: FMA:14560 xref: galen:GastricCorpus xref: MA:0002559 xref: NCIT:C12258 xref: SCTID:362140009 xref: UMLS:C0227230 {source="ncithesaurus:Body_of_Stomach"} xref: Wikipedia:Body_of_stomach is_a: UBERON:0009870 {source="FMA"} ! zone of stomach property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg xsd:anyURI property_value: editor_note "we include this as zone of stomach even though it is not distinguished by gland type" xsd:string [Term] id: UBERON:0001162 name: cardia of stomach alt_id: UBERON:0004712 def: "The part of the stomach attached to the esophagus. The cardia begins immediately distal to the z-line of the gastroeosphageal junction, where the squamous epithelium of the esophagus gives way to the columnar epithelium of the gastrointestinal tract[WP]" [BTO:0000198, Wikipedia:Cardia] subset: pheno_slim synonym: "antrum cardiacum" RELATED LATIN [Wikipedia:Cardia] synonym: "antrum cardiacum" RELATED [Wikipedia:Cardia] synonym: "cardiac antrum" RELATED [] synonym: "cardiac orifice" RELATED [Wikipedia:Cardia] synonym: "cardiac region" RELATED [Wikipedia:Cardia] synonym: "cardial orifice" RELATED [Wikipedia:Cardia] synonym: "cardial part of stomach" EXACT [] synonym: "gastric cardia" EXACT [] synonym: "pars cardiaca (gaster)" EXACT [] synonym: "pars cardiaca gastricae" EXACT LATIN [FMA:14561, FMA:TA] synonym: "stomach cardiac region" EXACT [MA:0001609] xref: BTO:0000198 xref: EMAPA:35811 xref: FMA:14561 xref: GAID:319 xref: MA:0001609 xref: MESH:A03.492.766.163 xref: NCIT:C12256 xref: SCTID:362138004 xref: UMLS:C0007144 {source="ncithesaurus:Cardia"} xref: Wikipedia:Cardia is_a: UBERON:0009870 ! zone of stomach intersection_of: UBERON:0009870 ! zone of stomach intersection_of: has_part UBERON:0008859 ! cardiac gastric gland relationship: continuous_with UBERON:0001043 ! esophagus relationship: continuous_with UBERON:0001161 ! body of stomach relationship: contributes_to_morphology_of UBERON:0000945 ! stomach relationship: has_part UBERON:0008859 ! cardiac gastric gland relationship: only_in_taxon NCBITaxon:40674 {source="ISBN:0073040584"} property_value: depicted_by Illu:stomach.jpg xsd:anyURI property_value: editor_note "There were previously conflicting statements in the academic anatomy community[10][11][12] over whether the cardia is part of the stomach, part of the esophagus or a distinct entity. Modern surgical and medical textbooks have agreed that 'The gastric cardia is now clearly considered to be part of the stomach'[13][14]. Classical anatomy textbooks, and some other resources[15], describe the cardia as the first of 4 regions of the stomach. This makes sense histologically because the mucosa of the cardia is the same as that of the stomach[WP]" xsd:string property_value: editor_note "We follow Kardong in defining stomach regions by glands." xsd:string [Term] id: UBERON:0001163 name: lesser curvature of stomach def: "The lesser curvature of the stomach, extending between the cardiac and pyloric orifices, forms the right or posterior border of the stomach. It descends as a continuation of the right margin of the esophagus in front of the fibers of the right crus of the diaphragm, and then, turning to the right, it crosses the first lumbar vertebra and ends at the pylorus. Nearer its pyloric than its cardiac end is a well-marked notch, the incisura angularis, which varies somewhat in position with the state of distension of the viscus; it serves to separate the stomach into a right and a left portion. The lesser curvature gives attachment to the two layers of the hepatogastric ligament, and between these two layers are the left gastric artery and the right gastric branch of the hepatic artery. [WP,unvetted]." [Wikipedia:Lesser_curvature_of_stomach] subset: uberon_slim synonym: "stomach lesser curvature" EXACT [] xref: EMAPA:37754 {source="MA:th"} xref: FMA:14572 xref: galen:LesserCurvatureOfStomach xref: MA:0001616 xref: NCIT:C12261 xref: SCTID:362133008 xref: UMLS:C0227221 {source="ncithesaurus:Lesser_Curvature"} xref: Wikipedia:Lesser_curvature_of_stomach is_a: UBERON:0009870 {source="FMA"} ! zone of stomach property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg xsd:anyURI [Term] id: UBERON:0001164 name: greater curvature of stomach def: "The greater curvature of the stomach is directed mainly forward, and is four or five times as long as the lesser curvature. [WP,unvetted]." [Wikipedia:Greater_curvature_of_stomach] subset: uberon_slim synonym: "stomach greater curvature" EXACT [] xref: EMAPA:37753 {source="MA:th"} xref: FMA:14574 xref: galen:GreaterCurvatureOfStomach xref: MA:0001615 xref: NCIT:C12262 xref: SCTID:362134002 xref: UMLS:C0227223 {source="ncithesaurus:Greater_Curvature"} xref: Wikipedia:Greater_curvature_of_stomach is_a: UBERON:0009870 {source="FMA"} ! zone of stomach property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg xsd:anyURI [Term] id: UBERON:0001165 name: pyloric antrum def: "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" [ISBN:0-683-40008-8, MP:0010790] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "antrum" BROAD [] synonym: "antrum of stomach" EXACT [] synonym: "antrum of Willis" RELATED [BTO:0001732] synonym: "antrum pylori" RELATED [BTO:0001732] synonym: "antrum pyloricum" RELATED LATIN [Wikipedia:Pyloric_antrum] synonym: "antrum pyloricum" RELATED [BTO:0001732] synonym: "gastric antrum" RELATED [BTO:0001732] synonym: "stomach antrum" RELATED [] synonym: "stomach pyloric antrum" EXACT [] xref: BTO:0001732 xref: EFO:0002555 xref: EMAPA:17891 xref: FMA:14579 xref: GAID:332 xref: galen:PyloricAntrum xref: MA:0001624 xref: MESH:A03.492.766.716 xref: NCIT:C12259 xref: SCTID:362142001 xref: UMLS:C0034193 {source="ncithesaurus:Antrum_Pylori"} xref: Wikipedia:Pyloric_antrum is_a: UBERON:0009870 {source="FMA"} ! zone of stomach relationship: continuous_with UBERON:0001161 ! body of stomach relationship: contributes_to_morphology_of UBERON:0001166 ! pylorus relationship: has_part CL:0000502 relationship: has_part CL:0000508 relationship: part_of UBERON:0001166 {source="Wikipedia"} ! pylorus property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg xsd:anyURI [Term] id: UBERON:0001166 name: pylorus def: "the stomach tissue region surrounding and controlling the distal outlet of the stomach, which opens into the duodenum" [MGI:csmith, MP:0010785] subset: pheno_slim subset: uberon_slim synonym: "pars pylorica" EXACT LATIN [] synonym: "pars pylorica gastricae" EXACT LATIN [FMA:14581, FMA:TA] synonym: "pyloric part of stomach" EXACT [] synonym: "pyloric region" EXACT [] synonym: "stomach pyloric region" EXACT [EHDAA2:0001580] synonym: "valvula pylori" RELATED LATIN [Wikipedia:Pylorus] xref: BTO:0001146 xref: EHDAA2:0001580 xref: EHDAA:4860 xref: EMAPA:17631 xref: FMA:14581 xref: GAID:333 xref: galen:Pylorus xref: MA:0002560 xref: MESH:A03.492.766.799 xref: NCIT:C12260 xref: SCTID:362143006 xref: UMLS:C0034196 {source="ncithesaurus:Pylorus"} xref: VHOG:0000420 xref: Wikipedia:Pylorus is_a: UBERON:0009870 ! zone of stomach intersection_of: UBERON:0009870 ! zone of stomach intersection_of: has_part UBERON:0001165 ! pyloric antrum intersection_of: has_part UBERON:0008858 ! pyloric canal intersection_of: has_part UBERON:0008861 ! pyloric gastric gland relationship: contributes_to_morphology_of UBERON:0000945 ! stomach relationship: has_part UBERON:0001165 ! pyloric antrum relationship: has_part UBERON:0008858 ! pyloric canal relationship: has_part UBERON:0008861 ! pyloric gastric gland property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg xsd:anyURI property_value: editor_note "We follow Kardong in defining stomach regions by glands" xsd:string property_value: external_definition "The orifice which allows the passage from the stomach into the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000420", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: has_relational_adjective "pyloric" xsd:string property_value: homology_notes "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000420", 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/"} [Term] id: UBERON:0001167 name: wall of stomach def: "the layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between" [MGI:csmith, MP:0010783] subset: pheno_slim synonym: "anatomical wall of stomach" EXACT [OBOL:automatic] synonym: "anatomical wall of ventriculus" EXACT [OBOL:automatic] synonym: "gastric wall" EXACT [] synonym: "stomach anatomical wall" EXACT [OBOL:automatic] synonym: "stomach wall" EXACT [] synonym: "ventriculus anatomical wall" EXACT [OBOL:automatic] synonym: "ventriculus wall" EXACT [OBOL:automatic] synonym: "wall of ventriculus" EXACT [OBOL:automatic] xref: EMAPA:35826 xref: FMA:14582 xref: galen:WallOfStomach xref: MA:0002692 xref: SCTID:279995000 is_a: UBERON:0000328 ! gut wall intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000945 ! stomach relationship: contributes_to_morphology_of UBERON:0000945 ! stomach relationship: part_of UBERON:0000945 ! stomach [Term] id: UBERON:0001168 name: wall of small intestine def: "An anatomical wall that is part of a small intestine [Automatically generated definition]." [OBOL:automatic] synonym: "anatomical wall of small bowel" EXACT [OBOL:automatic] synonym: "anatomical wall of small intestine" EXACT [OBOL:automatic] synonym: "small bowel anatomical wall" EXACT [OBOL:automatic] synonym: "small bowel wall" EXACT [OBOL:automatic] synonym: "small intestinal wall" EXACT [] synonym: "small intestine anatomical wall" EXACT [OBOL:automatic] synonym: "small intestine wall" EXACT [] synonym: "wall of small bowel" EXACT [OBOL:automatic] xref: EMAPA:35785 xref: FMA:14615 xref: MA:0002696 xref: NCIT:C33573 xref: UMLS:C1519375 {source="ncithesaurus:Small_Intestinal_Wall_Tissue"} is_a: UBERON:0001262 ! wall of intestine intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0002108 ! small intestine [Term] id: UBERON:0001169 name: wall of large intestine def: "An anatomical wall that is part of a large intestine [Automatically generated definition]." [OBOL:automatic] synonym: "anatomical wall of large intestine" EXACT [OBOL:automatic] synonym: "large intestinal wall" EXACT [] synonym: "large intestine anatomical wall" EXACT [OBOL:automatic] synonym: "large intestine wall" EXACT [] xref: EMAPA:35470 xref: FMA:14619 xref: MA:0002695 intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0000059 ! large intestine [Term] id: UBERON:0001170 name: mesentery of small intestine def: "The peritoneum responsible for connecting the jejunum and ileum (parts of the small intestine) to the back wall of the abdomen. Between the two sheets of peritoneum are blood vessels, lymph vessels, and nerves. This allows these parts of the small intestine to move relatively freely within the abdominopelvic cavity. The brain, however, cannot map sensation accurately, so sensation is usually referred to the midline, an example of referred pain[WP]." [Wikipedia:Mesentery#Mesentery_.28proper.29] synonym: "mesentery (proper)" EXACT [Wikipedia:Mesentery] synonym: "mesentery proper" EXACT [FMA:14643] synonym: "small intestinal mesentery" EXACT [FMA:14643] synonym: "small intestine mesentery" EXACT [OBOL:automatic] xref: EMAPA:37745 {source="MA:th"} xref: FMA:14643 xref: MA:0001555 xref: SCTID:245456008 xref: Wikipedia:Mesentery#Mesentery_.28proper.29 is_a: UBERON:0001206 ! serosa of small intestine is_a: UBERON:0004854 ! gastrointestinal system mesentery is_a: UBERON:0007826 {source="FMA"} ! peritoneal mesentery intersection_of: UBERON:0002095 ! mesentery intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0002108 ! small intestine [Term] id: UBERON:0001171 name: portal lobule def: "The triangular region on the periphery of the liver lobules that contain a bile duct and a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel." [MP:0008992] subset: pheno_slim xref: FMA:14653 xref: MA:0002498 xref: NCIT:C33341 xref: UMLS:C0682620 {source="ncithesaurus:Portal_Lobule"} is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0009911 {source="FMA"} ! lobule relationship: contributes_to_morphology_of UBERON:0001280 ! liver parenchyma relationship: part_of UBERON:0001280 {source="MA", source="MP"} ! liver parenchyma [Term] id: UBERON:0001172 name: hepatic acinus def: "The functional unit of the liver, consisting of a mass of hepatocytes from adjacent liver lobules aligned around the hepatic arterioles and portal venules just as they anastomose into sinusoids." [http://orcid.org/0000-0002-6601-2165, http://www.vivo.colostate.edu/hbooks/pathphys/digestion/liver/histo_acinus.html] synonym: "liver acinus" EXACT [] synonym: "portal acinus" EXACT [] xref: EMAPA:35497 xref: FMA:14654 xref: MA:0002496 xref: NCIT:C32992 xref: SCTID:272214009 xref: UMLS:C0227519 {source="ncithesaurus:Liver_Acinus"} is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0009842 {source="FMA"} ! glandular acinus is_a: UBERON:0011858 ! acinus of exocrine gland relationship: part_of UBERON:0001280 {source="cjm"} ! liver parenchyma [Term] id: UBERON:0001173 name: biliary tree def: "A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder." [DOI:10.1002/ar.20664] comment: The path in many species is as follows: Bile canaliculi -> Canals of Hering (intralobar bile duct) -> interlobular bile ducts -> intrahepatic bile ducts -> left and right hepatic ducts merge to form -> common hepatic duct *exits liver* and joins -> cystic duct (from gall bladder) forming -> common bile duct -> joins with pancreatic duct -> forming ampulla of Vater -> enters duodenum [WP] subset: organ_slim subset: pheno_slim subset: uberon_slim synonym: "biliary tract" RELATED [MA:0001273] xref: AAO:0011020 xref: EMAPA:35172 xref: FMA:14665 xref: SCTID:181267003 xref: UMLS:C0005423 {source="ncithesaurus:Biliary_Tract"} xref: Wikipedia:Biliary_tract xref: XAO:0000455 is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0000062 ! organ intersection_of: composed_primarily_of UBERON:0002394 ! bile duct intersection_of: part_of UBERON:0002294 ! biliary system relationship: composed_primarily_of UBERON:0002394 ! bile duct relationship: contributes_to_morphology_of UBERON:0002423 ! hepatobiliary system relationship: develops_from UBERON:0004912 ! biliary bud relationship: has_part UBERON:0001246 ! interlobular bile duct relationship: has_part UBERON:0001282 ! intralobular bile duct relationship: has_part UBERON:0003703 ! extrahepatic bile duct relationship: part_of UBERON:0002294 ! biliary system property_value: external_definition "Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011020", ontology="AAO", source="UBERON:0001173"} [Term] id: UBERON:0001174 name: common bile duct def: "the part of the biliary tree formed by the union of the cystic duct and the common hepatic duct" [MGI:csmith, MP:0009495] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "ductus choledochus" RELATED LATIN [Wikipedia:Common_bile_duct] synonym: "ductus choledochus (biliaris)" EXACT [] xref: EHDAA2:0000303 xref: EHDAA:3981 xref: EMAPA:17201 xref: FMA:14667 xref: GAID:282 xref: galen:CommonBileDuct xref: MA:0001631 xref: MESH:D003135 xref: NCIT:C12698 xref: SCTID:362199009 xref: TAO:0005165 xref: UMLS:C0009437 {source="ncithesaurus:Common_Bile_Duct"} xref: VHOG:0000214 xref: Wikipedia:Common_bile_duct xref: ZFA:0005165 is_a: UBERON:0003703 ! extrahepatic bile duct relationship: channel_for UBERON:0001970 ! bile relationship: channels_into UBERON:0001064 ! ventral pancreatic duct relationship: continuous_with UBERON:0001152 ! cystic duct relationship: continuous_with UBERON:0001175 ! common hepatic duct relationship: part_of UBERON:0001173 ! biliary tree property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png xsd:anyURI property_value: external_definition "Digestive system duct that collects bile from the hepatic bile duct and the cystic duct.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005165", ontology="TAO", source="ZFIN:Curator"} property_value: external_definition "The duct formed by the union of the common hepatic and cystic ducts. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000214", ontology="VHOG", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001175 name: common hepatic duct def: "Predominantly extrahepatic bile duct which is formed by the junction of the right and left hepatic ducts, which are predominantly intrahepatic, and, in turn, joins the cystic duct to form the common bile duct[GAID]. The common hepatic duct is the duct formed by the convergence of the right hepatic duct (which drains bile from the right functional lobe of the liver) and the left hepatic duct (which drains bile from the left functional lobe of the liver). The common hepatic duct then joins the cystic duct coming from the gallbladder to form the common bile duct[WP]." [Wikipedia:Common_hepatic_duct, ZFIN:curator] subset: pheno_slim subset: uberon_slim synonym: "ductus hepaticus communis" RELATED LATIN [Wikipedia:Common_hepatic_duct] synonym: "hepatic duct" RELATED [] xref: EMAPA:19101 xref: FMA:14668 xref: GAID:286 xref: MA:0002660 xref: MESH:D006500 xref: NCIT:C32356 xref: SCTID:245403006 xref: UMLS:C0019149 {source="ncithesaurus:Common_Hepatic_Duct"} xref: VHOG:0000220 xref: Wikipedia:Common_hepatic_duct is_a: UBERON:0003703 {source="FMA"} ! extrahepatic bile duct relationship: channel_for UBERON:0001970 ! bile relationship: channels_into UBERON:0001174 ! common bile duct relationship: continuous_with UBERON:0001176 {source="Wikipedia"} ! right hepatic duct relationship: continuous_with UBERON:0001177 {source="Wikipedia"} ! left hepatic duct relationship: develops_from UBERON:0010081 ! future common hepatic duct relationship: immediate_transformation_of UBERON:0010081 {evidence="definitional"} ! future common hepatic duct relationship: part_of UBERON:0005604 {source="MA"} ! extrahepatic part of hepatic duct property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg xsd:anyURI property_value: editor_note "TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same. Common is part of extra-hepatic part" xsd:string property_value: external_definition "The duct which conveys the bile from the liver and unites with the cystic duct to form the common bile duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000220", ontology="VHOG", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001176 name: right hepatic duct def: "The duct that drains bile from the right half of the liver and joins the left hepatic duct to form the common hepatic duct." [http://www.medterms.com/script/main/art.asp?articlekey=26034] synonym: "ductus hepaticus dexter" RELATED LATIN [] xref: EHDAA2:0001727 xref: EHDAA:3992 xref: EMAPA:32797 xref: FMA:14669 xref: MA:0001639 xref: NCIT:C33476 xref: SCTID:245401008 xref: UMLS:C0227557 {source="ncithesaurus:Right_Hepatic_Duct"} xref: VHOG:0000217 is_a: UBERON:0003703 ! extrahepatic bile duct intersection_of: UBERON:0003703 ! extrahepatic bile duct intersection_of: continuous_with UBERON:0001114 ! right lobe of liver relationship: continuous_with UBERON:0001114 ! right lobe of liver relationship: part_of UBERON:0005171 ! hepatic duct property_value: external_definition "The duct which drains bile from the right half of the liver and unites with the left hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000217", ontology="VHOG", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001177 name: left hepatic duct def: "The duct that drains bile from the left half of the liver and joins the right hepatic duct to form the common hepatic duct." [http://www.medterms.com/script/main/art.asp?articlekey=26035] synonym: "ductus hepaticus sinister" RELATED LATIN [] xref: EHDAA2:0000941 xref: EHDAA:3990 xref: EMAPA:32795 xref: FMA:14670 xref: MA:0001638 xref: NCIT:C32960 xref: SCTID:245400009 xref: UMLS:C0227560 {source="ncithesaurus:Left_Hepatic_Duct"} xref: VHOG:0000218 is_a: UBERON:0003703 ! extrahepatic bile duct intersection_of: UBERON:0003703 ! extrahepatic bile duct intersection_of: continuous_with UBERON:0001115 ! left lobe of liver relationship: continuous_with UBERON:0001115 ! left lobe of liver relationship: part_of UBERON:0005171 ! hepatic duct property_value: external_definition "The duct which drains bile from the left half of the liver and unites with the right hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000218", ontology="VHOG", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001178 name: visceral peritoneum def: "The inner layer of peritoneum that is wrapped around organs located inside the intraperitoneal space." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Peritoneum#Types] subset: uberon_slim subset: vertebrate_core synonym: "visceral serous membrane of peritoneum" EXACT [UBERON:cjm] xref: EMAPA:16592 xref: FMA:14703 xref: SCTID:362702003 xref: TAO:0005132 xref: VHOG:0001528 xref: Wikipedia:Visceral_peritoneum xref: ZFA:0005132 is_a: UBERON:0022350 ! visceral serous membrane intersection_of: UBERON:0022350 ! visceral serous membrane intersection_of: part_of UBERON:0002358 ! peritoneum relationship: part_of UBERON:0002358 ! peritoneum property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png xsd:anyURI [Term] id: UBERON:0001179 name: peritoneal cavity def: "Anatomical cavity bounded by visceral and parietal peritoneum" [http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/86, Wikipedia:Peritoneal_cavity] subset: pheno_slim subset: uberon_slim synonym: "cavitas peritonealis" RELATED [BTO:0001782] synonym: "cavitas peritonealis" RELATED LATIN [Wikipedia:Peritoneal_cavity] synonym: "saccus serosus peritonei" RELATED LATIN [Wikipedia:Peritoneal_cavity] xref: BTO:0001782 xref: EHDAA2:0001446 xref: EMAPA:16138 xref: FMA:14704 xref: GAID:24 xref: MA:0000054 xref: MESH:A01.047.025.600.678 xref: NCIT:C12769 xref: SCTID:181616008 xref: UMLS:C1704247 {source="ncithesaurus:Peritoneal_Cavity"} xref: VHOG:0000852 xref: Wikipedia:Peritoneal_cavity is_a: CARO:0000000 is_a: UBERON:0035809 ! serous cavity intersection_of: UBERON:0002553 ! anatomical cavity intersection_of: adjacent_to UBERON:0001178 ! visceral peritoneum intersection_of: adjacent_to UBERON:0001366 ! parietal peritoneum intersection_of: luminal_space_of UBERON:0035820 ! peritoneal sac relationship: adjacent_to UBERON:0001178 ! visceral peritoneum relationship: adjacent_to UBERON:0001366 ! parietal peritoneum relationship: develops_from UBERON:0003887 {source="Wikipedia"} ! intraembryonic coelom relationship: luminal_space_of UBERON:0035820 ! peritoneal sac relationship: part_of UBERON:0035820 ! peritoneal sac property_value: external_definition "The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000852", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/peritoneal+cavity"} property_value: homology_notes "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]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000852", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001180 name: superior recess of lesser sac alt_id: UBERON:0006299 synonym: "omental bursa superior recess" EXACT [MA:0000447] synonym: "recessus superior bursae omentalis" EXACT LATIN [FMA:TA] synonym: "recessus superior bursae omentalis" EXACT LATIN [FMA:14708, FMA:TA] synonym: "recessus superior omentalis" EXACT [FMA:14708] synonym: "superior omental bursa" EXACT [FMA:14708] synonym: "superior recess" EXACT [EHDAA2:0001958] synonym: "superior recess of omental bursa" EXACT [FMA:14708] xref: EHDAA2:0001958 xref: EHDAA:2343 xref: EMAPA:18049 xref: FMA:14708 xref: MA:0000447 xref: SCTID:263190002 is_a: CARO:0000000 is_a: UBERON:0002553 ! anatomical cavity relationship: develops_from UBERON:0005252 {source="EHDAA2"} ! lesser sac cavity relationship: part_of UBERON:0001341 {source="EMAPA"} ! lesser sac property_value: external_ontology_notes "classified as a cavity in EHDAA2, organ segment in FMA. We hedge and use a union" xsd:string {external_ontology="EHDAA2"} [Term] id: UBERON:0001181 name: inferior recess of lesser sac alt_id: UBERON:0006249 synonym: "inferior omental bursa" EXACT [FMA:14709] synonym: "inferior recess" EXACT [EHDAA2:0000825] synonym: "inferior recess of omental bursa" EXACT [FMA:14709] synonym: "omental bursa inferior recess" EXACT [MA:0000446] synonym: "recessus inferior bursae omentalis" EXACT LATIN [FMA:TA] synonym: "recessus inferior bursae omentalis" EXACT LATIN [FMA:14709, FMA:TA] synonym: "recessus inferior omentalis" EXACT [FMA:14709] xref: EHDAA2:0000825 xref: EHDAA:6083 xref: EMAPA:18048 xref: FMA:14709 xref: MA:0000446 xref: SCTID:263261002 is_a: UBERON:0002553 ! anatomical cavity relationship: part_of UBERON:0001341 ! lesser sac [Term] id: UBERON:0001182 name: superior mesenteric artery def: "Mesenteric artery that supplies the whole length of the small intestine except the superior part of the duodenum. It also supplies the cecum and the ascending part of the colon and about half the transverse part of the colon. It arises from the anterior surface of the aorta below the celiac artery at the level of the first lumbar vertebra." [MESH:A07.231.114.565.755] subset: pheno_slim subset: uberon_slim synonym: "arteria mesenterica superior" RELATED LATIN [Wikipedia:Superior_mesenteric_artery] synonym: "arteria mesenterica superior" RELATED [BTO:0002303] synonym: "superior mesenteric arterial tree" EXACT [] xref: BTO:0002303 xref: EHDAA2:0001949 xref: EHDAA:3358 xref: EHDAA:5313 xref: EMAPA:18619 xref: FMA:14749 xref: GAID:502 xref: galen:SuperiorMesentericArtery xref: MA:0002005 xref: MESH:D017538 xref: NCIT:C33685 xref: OpenCyc:Mx4rwE5KipwpEbGdrcN5Y29ycA xref: SCTID:362048004 xref: UMLS:C0162861 {source="ncithesaurus:Superior_Mesenteric_Artery"} xref: VHOG:0000754 xref: Wikipedia:Superior_mesenteric_artery is_a: UBERON:0005616 ! mesenteric artery intersection_of: UBERON:0005616 ! mesenteric artery intersection_of: supplies UBERON:0002115 ! jejunum intersection_of: supplies UBERON:0002116 ! ileum relationship: supplies UBERON:0002115 ! jejunum relationship: supplies UBERON:0002116 ! ileum property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/68/Gray1099.png xsd:anyURI property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/c/c0/Superior_mesenteric_a.gif xsd:anyURI property_value: structure_notes "Origin: abdominal aorta; branches, inferior pancreaticoduodenal, jejunal, ileal, ileocolic, right colic, and middle colic arteries; distribution: small intestine, proximal half of colon" xsd:string {source="BTO"} [Term] id: UBERON:0001183 name: inferior mesenteric artery def: "Mesenteric artery that supplies the large intestine from the left colic (or splenic) flexure to the upper part of the rectum, which includes the descending colon, the sigmoid colon, and part of the rectum. Proximally, its territory of distribution overlaps (forms a watershed) with the middle colic artery, and therefore the superior mesenteric artery. The SMA and IMA anastomose via the marginal artery (artery of Drummond). The territory of distribution of the IMA is more or less equivalent to the embryonic hindgut. [WP,unvetted]." [Wikipedia:Inferior_mesenteric_artery] subset: pheno_slim subset: uberon_slim synonym: "arteria mesenterica inferior" RELATED LATIN [Wikipedia:Inferior_mesenteric_artery] synonym: "arteria mesenterica inferior" RELATED [BTO:0002302] synonym: "IMA" BROAD ABBREVIATION [] synonym: "inferior mesenteric arterial tree" EXACT [] xref: BTO:0002302 xref: EHDAA2:0000817 xref: EHDAA:4345 xref: EMAPA:18618 xref: FMA:14750 xref: GAID:501 xref: galen:InferiorMesentericArtery xref: MA:0002004 xref: MESH:D017537 xref: NCIT:C32780 xref: OpenCyc:Mx4rv-t-S5wpEbGdrcN5Y29ycA xref: SCTID:181341006 xref: UMLS:C0162860 {source="ncithesaurus:Inferior_Mesenteric_Artery"} xref: VHOG:0001116 xref: Wikipedia:Inferior_mesenteric_artery is_a: UBERON:0005616 ! mesenteric artery is_a: UBERON:0035039 ! rectal artery intersection_of: UBERON:0005616 ! mesenteric artery intersection_of: supplies UBERON:0001052 ! rectum intersection_of: supplies UBERON:0001158 ! descending colon intersection_of: supplies UBERON:0001159 ! sigmoid colon relationship: supplies UBERON:0001052 ! rectum relationship: supplies UBERON:0001158 ! descending colon relationship: supplies UBERON:0001159 ! sigmoid colon property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/e4/Gray538.png xsd:anyURI [Term] id: UBERON:0001184 name: renal artery def: "One of two laterally paired arteries that supplies the kidneys. These are large arteries that branch from the dorsal aorta in primitive vertebrates." [ISBN:0073040584, Wikipedia:Renal_artery] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "arteria renalis" RELATED LATIN [Wikipedia:Renal_artery] synonym: "renal arterial tree" EXACT [] synonym: "renal arteries" RELATED PLURAL [] xref: AAO:0010223 xref: BTO:0001165 xref: EFO:0002552 xref: EHDAA2:0004100 xref: EHDAA:5321 xref: EHDAA:8594 xref: EMAPA:28373 xref: FMA:14751 xref: GAID:507 xref: galen:RenalArtery xref: MA:0002035 xref: MESH:D012077 xref: NCIT:C12778 xref: OpenCyc:Mx4rveOFHpwpEbGdrcN5Y29ycA xref: RETIRED_EHDAA2:0001600 xref: SCTID:181339005 xref: TAO:0000420 xref: UMLS:C0035065 {source="ncithesaurus:Renal_Artery"} xref: Wikipedia:Renal_artery xref: ZFA:0000420 is_a: UBERON:0012254 ! abdominal aorta artery intersection_of: UBERON:0001637 ! artery intersection_of: supplies UBERON:0002113 ! kidney relationship: branching_part_of UBERON:0001516 {notes="dorsal aorta in Kardong", source="Wikipedia"} ! abdominal aorta relationship: supplies UBERON:0002113 ! kidney property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png xsd:anyURI property_value: editor_note "renal arteries vary widely even in humans. Sub-structures should be checked for taxon variability." xsd:string property_value: external_definition "Artery which supplies blood via branches to the gonads, oviducts, and kidneys.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010223", ontology="AAO", source="AAO:BJB"} property_value: external_definition "The renal arteries normally arise off the side of the abdominal aorta, immediately below the superior mesenteric artery, and supply the kidneys with blood. Each is directed across the crus of the diaphragm, so as to form nearly a right angle with the aorta. The renal arteries carry a large portion of total blood flow to the kidneys. Up to a third of total cardiac output can pass through the renal arteries to be filtered by the kidneys. The arterial supply of the kidneys is variable and there may be one or more renal arteries supplying each kidney. It is located above the renal vein. It has a radius of approximately 0.25cm, 0.26 cm at the root. The measured mean diameter can differ depending on the imaging method used. For example, the diameter was found to be 5.04 ± 0.74 mm using ultrasound, but 5.68 ± 1.19 mm using angiography. [WP,unvetted].[Wikipedia]" xsd:string {ontology="Wikipedia", source="Wikipedia:Renal_artery"} [Term] id: UBERON:0001185 name: right renal artery def: "Renal artery that supplies the right kidney" [https://orcid.org/0000-0002-6601-2165] comment: The right [renal artery] passes behind the inferior vena cava, the right renal vein, the head of the pancreas, and the descending part of the duodenum[WP] subset: pheno_slim subset: uberon_slim synonym: "right renal arterial tree" EXACT [] xref: EMAPA:37380 {source="MA:th"} xref: FMA:14752 xref: MA:0002037 xref: NCIT:C52740 xref: OpenCyc:Mx4rtW8I0KgEEdudWQACs5b6Bw xref: OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rveOFHpwpEbGdrcN5Y29ycA xref: SCTID:36800007 xref: UMLS:C0226332 {source="ncithesaurus:Right_Renal_Artery"} is_a: UBERON:0001184 ! renal artery intersection_of: UBERON:0001184 ! renal artery intersection_of: supplies UBERON:0004539 ! right kidney relationship: supplies UBERON:0004539 ! right kidney property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png xsd:anyURI [Term] id: UBERON:0001186 name: left renal artery def: "Renal artery that supplies the left kidney" [https://orcid.org/0000-0002-6601-2165] comment: The left [renal artery] is somewhat higher than the right; it lies behind the left renal vein, the body of the pancreas and the splenic vein, and is crossed by the inferior mesenteric vein[WP] subset: pheno_slim synonym: "left renal arterial tree" EXACT [] xref: EMAPA:37098 {source="MA:th"} xref: FMA:14753 xref: MA:0002036 xref: NCIT:C52741 xref: OpenCyc:Mx4rtW8I0agEEdudWQACs5b6Bw xref: OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rveOFHpwpEbGdrcN5Y29ycA xref: SCTID:19215005 xref: UMLS:C0226333 {source="ncithesaurus:Left_Renal_Artery"} is_a: UBERON:0001184 ! renal artery intersection_of: UBERON:0001184 ! renal artery intersection_of: supplies UBERON:0004538 ! left kidney relationship: supplies UBERON:0004538 ! left kidney [Term] id: UBERON:0001187 name: testicular artery def: "One of a pair of arteries that is a branch of the abdominal aorta that supplies blood to a male gonad." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Testicular_artery] subset: uberon_slim synonym: "arteria testicularis" RELATED LATIN [Wikipedia:Testicular_artery] synonym: "internal spermatic" RELATED [Wikipedia:Testicular_artery] synonym: "internal spermatic arteries" RELATED [Wikipedia:Testicular_artery] synonym: "internal spermatic artery" RELATED [Wikipedia:Testicular_artery] synonym: "internal spermatic vessels" RELATED [Wikipedia:Testicular_artery] synonym: "spermatic arteries" RELATED [Wikipedia:Testicular_artery] synonym: "spermatic artery" RELATED [Wikipedia:Testicular_artery] synonym: "spermatic vessels" RELATED [Wikipedia:Testicular_artery] synonym: "testicular arterial tree" EXACT [] synonym: "testicular arteries" RELATED [Wikipedia:Testicular_artery] xref: EMAPA:18621 xref: FMA:14758 xref: MA:0002063 xref: SCTID:244281003 xref: Wikipedia:Testicular_artery is_a: UBERON:0010192 ! genital artery intersection_of: UBERON:0001637 ! artery intersection_of: supplies UBERON:0000473 ! testis relationship: branching_part_of UBERON:0001516 {source="Wikipedia"} ! abdominal aorta relationship: supplies UBERON:0000473 ! testis property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png xsd:anyURI [Term] id: UBERON:0001188 name: right testicular artery def: "A testicular artery that supplies a right testicle." [OBOL:automatic] synonym: "right spermatic artery" EXACT [] synonym: "trunk of right testicular arterial tree" EXACT [] xref: EMAPA:37382 {source="MA:th"} xref: FMA:14759 xref: MA:0002042 xref: NCIT:C52738 xref: UMLS:C0734076 {source="ncithesaurus:Right_Spermatic_Artery"} is_a: UBERON:0001187 ! testicular artery is_a: UBERON:0003468 ! ureteric segment of renal artery intersection_of: UBERON:0001187 ! testicular artery intersection_of: supplies UBERON:0004534 ! right testis relationship: supplies UBERON:0001222 ! right ureter relationship: supplies UBERON:0004534 ! right testis [Term] id: UBERON:0001189 name: left testicular artery def: "A testicular artery that supplies a left testicle." [OBOL:automatic] synonym: "left spermatic artery" EXACT [] synonym: "trunk of left testicular arterial tree" EXACT [] xref: EMAPA:37099 {source="MA:th"} xref: FMA:14760 xref: MA:0002041 xref: NCIT:C52739 xref: UMLS:C0734077 {source="ncithesaurus:Left_Spermatic_Artery"} is_a: UBERON:0001187 ! testicular artery is_a: UBERON:0003468 ! ureteric segment of renal artery intersection_of: UBERON:0001187 ! testicular artery intersection_of: supplies UBERON:0004533 ! left testis relationship: supplies UBERON:0001223 ! left ureter relationship: supplies UBERON:0004533 ! left testis [Term] id: UBERON:0001190 name: ovarian artery def: "An artery that supplies an ovary." [OBOL:automatic] subset: uberon_slim synonym: "arteria ovarica" RELATED LATIN [Wikipedia:Ovarian_artery] synonym: "ovarian arterial tree" EXACT [] xref: EMAPA:18620 xref: FMA:14761 xref: MA:0002012 xref: NCIT:C33242 xref: OpenCyc:Mx4rwOa9PZwpEbGdrcN5Y29ycA xref: SCTID:244280002 xref: UMLS:C0226411 {source="ncithesaurus:Ovarian_Artery"} xref: Wikipedia:Ovarian_artery is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery intersection_of: supplies UBERON:0000992 ! ovary relationship: supplies UBERON:0000992 ! ovary property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/ae/Gray1170.png xsd:anyURI property_value: external_definition "In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP]." xsd:string {source="Wikipedia:Ovarian_artery"} [Term] id: UBERON:0001191 name: common iliac artery def: "The common iliac arteries are two large arteries, about 4cm long in adults but more than a centimetre in diameter, that originate from the aortic bifurcation. The arteries run inferolaterally, along the medial border of the psoas muscles to the pelvic brim, where they bifurcate into the external iliac artery and internal iliac artery. The common iliac artery, and all of its branches, exist as paired structures (that is to say, there is one on the left side and one on the right). The distribution of the common iliac artery is basically the pelvis and lower limb on the corresponding side. Both common iliac arteries are accompanied along their course by common iliac veins. [WP,unvetted]." [Wikipedia:Common_iliac_artery] comment: See notes for parent class subset: uberon_slim synonym: "arteria iliaca communis" RELATED LATIN [Wikipedia:Common_iliac_artery] synonym: "common iliac arterial tree" EXACT [] xref: EHDAA2:0000311 xref: EHDAA:2553 xref: EMAPA:17310 xref: FMA:14764 xref: MA:0001972 xref: NCIT:C32357 xref: OpenCyc:Mx4rvkZ7ZpwpEbGdrcN5Y29ycA xref: SCTID:362050007 xref: UMLS:C1261084 {source="ncithesaurus:Common_Iliac_Artery"} xref: Wikipedia:Common_iliac_artery is_a: UBERON:0005609 {source="MA"} ! iliac artery is_a: UBERON:0012254 ! abdominal aorta artery relationship: branching_part_of UBERON:0001516 {source="Wikipedia"} ! abdominal aorta relationship: develops_from UBERON:0005458 {gci_relation="part_of", gci_filler="NCBITaxon:9606", notes="requires review", source="EHDAA2"} ! left umbilical artery relationship: develops_from UBERON:0005470 {gci_relation="part_of", gci_filler="NCBITaxon:9606", notes="requires review", source="EHDAA2"} ! right umbilical artery property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/6e/Iliac_artery_bifurcation_and_aorta.PNG xsd:anyURI [Term] id: UBERON:0001192 name: left gastric artery def: "An artery that arises from the celiac artery and supplies the stomach." [http://orcid.org/0000-0002-6601-2165] subset: uberon_slim synonym: "arteria gastrica sinistra" RELATED LATIN [Wikipedia:Left_gastric_artery] synonym: "gastric artery" RELATED [FMA:14768] xref: EMAPA:35374 xref: FMA:14768 xref: galen:LeftGastricArtery xref: MA:0001961 xref: NCIT:C32654 xref: OpenCyc:Mx4rwMjqKZwpEbGdrcN5Y29ycA xref: SCTID:244267000 xref: UMLS:C0226299 {source="ncithesaurus:Gastric_Artery"} xref: Wikipedia:Left_gastric_artery is_a: UBERON:0004573 ! systemic artery relationship: branching_part_of UBERON:0001640 ! celiac artery relationship: part_of UBERON:0001640 ! celiac artery relationship: supplies UBERON:0000945 ! stomach property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png xsd:anyURI [Term] id: UBERON:0001193 name: hepatic artery def: "An artery that supplies the liver." [https://orcid.org/0000-0002-6601-2165, Wikipedia:Hepatic_artery_proper] subset: uberon_slim subset: vertebrate_core synonym: "arteria hepatica" RELATED [BTO:0004307] synonym: "arteria hepatica propria" EXACT LATIN [] xref: BTO:0004307 xref: EMAPA:17859 xref: FMA:14769 xref: GAID:496 xref: galen:HepaticArtery xref: MA:0001963 xref: MESH:D006499 xref: NCIT:C32729 xref: OpenCyc:Mx4rvzKtFpwpEbGdrcN5Y29ycA xref: SCTID:76015000 xref: TAO:0005161 xref: UMLS:C0019145 {source="ncithesaurus:Hepatic_Artery"} xref: ZFA:0005161 is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery intersection_of: supplies UBERON:0002107 ! liver relationship: supplies UBERON:0002107 ! liver property_value: curator_notes "currently defined in a generic fashion." xsd:string property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/4/4c/Common_and_proper_hepatic_artery.png xsd:anyURI property_value: external_definition "Artery that supplies blood to the liver.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005161", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0001194 name: splenic artery def: "An artery that supplies the spleen." [http://orcid.org/0000-0002-6601-2165] subset: uberon_slim synonym: "arteria lienalis" RELATED LATIN [Wikipedia:Splenic_artery] synonym: "arteria splenica" EXACT LATIN [Wikipedia:Splenic_artery] synonym: "lienal artery" EXACT [MA:0001991] xref: EMAPA:19216 xref: FMA:14773 xref: GAID:510 xref: galen:SplenicArtery xref: MA:0001991 xref: MA:0003177 xref: MESH:D013157 xref: NCIT:C33597 xref: OpenCyc:Mx4rv0cb2ZwpEbGdrcN5Y29ycA xref: SCTID:244266009 xref: UMLS:C0037996 {source="ncithesaurus:Splenic_Artery"} xref: Wikipedia:Splenic_artery is_a: UBERON:0004573 ! systemic artery intersection_of: UBERON:0001637 ! artery intersection_of: supplies UBERON:0002106 ! spleen disjoint_from: UBERON:0001640 ! celiac artery relationship: branching_part_of UBERON:0001640 ! celiac artery relationship: part_of UBERON:0001640 ! celiac artery relationship: supplies UBERON:0002106 ! spleen property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/a2/Gray1188.png xsd:anyURI property_value: seeAlso https://github.com/obophenotype/uberon/issues/268 xsd:anyURI [Term] id: UBERON:0001195 name: inferior pancreaticoduodenal artery def: "The inferior pancreaticoduodenal artery is a branch of the superior mesenteric artery or from its first intestinal branch, opposite the upper border of the inferior part of the duodenum. It courses to the right between the head of the pancreas and duodenum, and then ascends to anastomose with the anterior and posterior superior pancreaticoduodenal artery. It distributes branches to the head of the pancreas and to the descending and inferior parts of the duodenum. [WP,unvetted]." [Wikipedia:Inferior_pancreaticoduodenal_artery] subset: uberon_slim synonym: "arteriae pancreaticoduodenales inferiores" RELATED LATIN [Wikipedia:Inferior_pancreaticoduodenal_artery] synonym: "inferior pancreatico-duodenal artery" EXACT [] xref: EMAPA:37086 {source="MA:th"} xref: FMA:14805 xref: MA:0002014 xref: NCIT:C32786 xref: SCTID:244273004 xref: UMLS:C0226319 {source="ncithesaurus:Inferior_Pancreatico-duodenal_artery"} xref: Wikipedia:Inferior_pancreaticoduodenal_artery is_a: UBERON:0004573 ! systemic artery is_a: UBERON:0009658 ! pancreaticoduodenal artery relationship: branching_part_of UBERON:0001182 ! superior mesenteric artery relationship: part_of UBERON:0001182 ! superior mesenteric artery property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/3b/Gray533.png xsd:anyURI [Term] id: UBERON:0001196 name: middle colic artery def: "The middle colic artery is a branch of the superior mesenteric artery that mostly supplies the transverse colon. It arises just below the pancreas, and, passing downward and forward between the layers of the transverse mesocolon, divides into two branches: right and left. The right branch anastomoses with the right colic artery The left branch anastomoses with the left colic artery, a branch of the inferior mesenteric artery. The arches thus formed are placed about two fingers' breadth from the transverse colon, to which they distribute branches. [WP,unvetted]." [Wikipedia:Middle_colic_artery] subset: uberon_slim synonym: "arteria colica media" RELATED LATIN [Wikipedia:Middle_colic_artery] xref: EMAPA:37106 {source="MA:th"} xref: FMA:14810 xref: galen:MiddleColicArtery xref: MA:0002007 xref: NCIT:C52981 xref: SCTID:244276007 xref: UMLS:C0226328 {source="ncithesaurus:Middle_Colic_Artery"} xref: Wikipedia:Middle_colic_artery is_a: UBERON:0004573 ! systemic artery intersection_of: UBERON:0001637 ! artery intersection_of: branching_part_of UBERON:0001182 ! superior mesenteric artery intersection_of: supplies UBERON:0001157 ! transverse colon relationship: branching_part_of UBERON:0001182 ! superior mesenteric artery relationship: part_of UBERON:0001182 ! superior mesenteric artery relationship: supplies UBERON:0001157 ! transverse colon property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray537.png xsd:anyURI [Term] id: UBERON:0001197 name: ileocolic artery def: "The Ileocolic Artery is the lowest branch arising from the concavity of the superior mesenteric artery. It passes downward and to the right behind the peritoneum toward the right iliac fossa, where it divides into a superior and an inferior branch; the inferior anastomoses with the end of the superior mesenteric artery, the superior with the right colic artery. Supplies the cecum, ileum, and appendix. [WP,unvetted]." [Wikipedia:Ileocolic_artery] subset: uberon_slim synonym: "arteria ileocolica" RELATED LATIN [Wikipedia:Ileocolic_artery] xref: EMAPA:37083 {source="MA:th"} xref: FMA:14815 xref: galen:IleocolicArtery xref: MA:0001970 xref: NCIT:C32760 xref: SCTID:244279000 xref: UMLS:C0226323 {source="ncithesaurus:Ileo-colic_Artery"} xref: Wikipedia:Ileocolic_artery is_a: UBERON:0004573 ! systemic artery intersection_of: UBERON:0001637 ! artery intersection_of: branching_part_of UBERON:0001182 ! superior mesenteric artery intersection_of: supplies UBERON:0001153 ! caecum intersection_of: supplies UBERON:0001154 ! vermiform appendix intersection_of: supplies UBERON:0002116 ! ileum relationship: branching_part_of UBERON:0001182 ! superior mesenteric artery relationship: part_of UBERON:0001182 ! superior mesenteric artery relationship: supplies UBERON:0001153 ! caecum relationship: supplies UBERON:0001154 ! vermiform appendix relationship: supplies UBERON:0002116 ! ileum property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray536.png xsd:anyURI [Term] id: UBERON:0001198 name: superior suprarenal artery def: "Each (left and right) superior suprarenal artery is a branch of the inferior phrenic artery on that side of the body. The left and right phrenic arteries supply the diaphragm, and come off the aorta. [WP,unvetted]." [Wikipedia:Superior_suprarenal_artery] subset: uberon_slim synonym: "arteriae suprarenales superiores" EXACT LATIN [Wikipedia:Superior_suprarenal_artery] synonym: "superior adrenal branch of inferior phrenic artery" EXACT [] synonym: "superior suprarenal branch of inferior phrenic artery" EXACT [] xref: EMAPA:37122 {source="MA:th"} xref: FMA:14863 xref: MA:0002057 xref: NCIT:C52736 xref: SCTID:303424001 xref: UMLS:C0580876 {source="ncithesaurus:Superior_Suprarenal_Artery"} xref: Wikipedia:Superior_suprarenal_artery is_a: UBERON:0004573 ! systemic artery is_a: UBERON:0005624 ! suprarenal artery intersection_of: UBERON:0005624 ! suprarenal artery intersection_of: branching_part_of UBERON:0012255 ! inferior phrenic artery relationship: branching_part_of UBERON:0012255 ! inferior phrenic artery relationship: part_of UBERON:0012255 ! inferior phrenic artery property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png xsd:anyURI [Term] id: UBERON:0001199 name: mucosa of stomach def: "The mucosal layer that lines the stomach." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim synonym: "gastric mucosa" EXACT [] synonym: "gastric mucous membrane" EXACT [] synonym: "Magenschleimhaut" RELATED [BTO:0001308] synonym: "mucosa of organ of stomach" EXACT [OBOL:automatic] synonym: "mucosa of organ of ventriculus" EXACT [OBOL:automatic] synonym: "mucosa of ventriculus" EXACT [OBOL:automatic] synonym: "mucous membrane of stomach" EXACT [] synonym: "mucous membrane of ventriculus" EXACT [OBOL:automatic] synonym: "organ mucosa of stomach" EXACT [OBOL:automatic] synonym: "organ mucosa of ventriculus" EXACT [OBOL:automatic] synonym: "stomach mucosa" EXACT [] synonym: "stomach mucosa of organ" EXACT [OBOL:automatic] synonym: "stomach mucous membrane" EXACT [OBOL:automatic] synonym: "stomach organ mucosa" EXACT [OBOL:automatic] synonym: "tunica mucosa (gaster)" EXACT [] synonym: "tunica mucosa gastricae" EXACT LATIN [FMA:14907, FMA:TA] synonym: "tunica mucosa gastris" RELATED [BTO:0001308] synonym: "tunica mucosa gastris" RELATED LATIN [Wikipedia:Gastric_mucosa] synonym: "ventriculus mucosa" EXACT [OBOL:automatic] synonym: "ventriculus mucosa of organ" EXACT [OBOL:automatic] synonym: "ventriculus mucous membrane" EXACT [OBOL:automatic] synonym: "ventriculus organ mucosa" EXACT [OBOL:automatic] xref: BTO:0001308 xref: CALOHA:TS-0404 xref: EMAPA:35817 xref: FMA:14907 xref: GAID:321 xref: galen:GastricMucosa xref: MA:0002683 xref: MESH:A03.492.766.440 xref: NCIT:C32656 xref: OpenCyc:Mx8NhB4rvcD6KJwpEbGdrcN5Y29ycB4rvmKNOpwpEbGdrcN5Y29ycB4rvVj5FpwpEbGdrcN5Y29ycB4rvVjlqpwpEbGdrcN5Y29ycA xref: SCTID:362131005 xref: UMLS:C0017136 {source="ncithesaurus:Gastric_Mucosa"} xref: Wikipedia:Gastric_mucosa is_a: UBERON:0004786 ! gastrointestinal system mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0000945 ! stomach relationship: capable_of GO:0001696 relationship: contributes_to_morphology_of UBERON:0001167 ! wall of stomach relationship: part_of UBERON:0000945 ! stomach relationship: part_of UBERON:0001167 ! wall of stomach property_value: depicted_by Wikipedia:File:Normal_gastric_mucosa_intermed_mag.jpg xsd:anyURI property_value: external_definition "The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa]." xsd:string {source="Wikipedia:Gastric_mucosa"} [Term] id: UBERON:0001200 name: submucosa of stomach def: "the fibrous connective tissue layer beneath the stomach mucosa" [MGI:csmith, MP:0010794] subset: pheno_slim synonym: "gastric submucosa" EXACT [] synonym: "stomach submucosa" EXACT [] synonym: "submucosa of ventriculus" EXACT [OBOL:automatic] synonym: "submucous layer of stomach" RELATED [BTO:0002110] synonym: "tela submucosa (gaster)" EXACT [] synonym: "tela submucosa gastricae" EXACT LATIN [FMA:14908, FMA:TA] synonym: "tela submucosa ventriculi" RELATED [BTO:0002110] synonym: "ventriculus submucosa" EXACT [OBOL:automatic] xref: BTO:0002110 xref: EMAPA:35825 xref: FMA:14908 xref: MA:0002685 xref: NCIT:C32663 xref: SCTID:52459002 xref: UMLS:C0227211 {source="ncithesaurus:Gastric_Submucosa"} is_a: UBERON:0018257 ! submucosa of digestive tract intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0000945 ! stomach relationship: contributes_to_morphology_of UBERON:0001167 ! wall of stomach relationship: part_of UBERON:0000945 ! stomach relationship: part_of UBERON:0001167 ! wall of stomach [Term] id: UBERON:0001201 name: serosa of stomach def: "the outermost layer of the stomach wall, consisting of layers of connective tissue continuous with the peritoneum" [MGI:csmith, MP:0010793] subset: pheno_slim synonym: "anatomical wall of stomach serosa" EXACT [OBOL:automatic] synonym: "anatomical wall of stomach serous membrane" EXACT [OBOL:automatic] synonym: "anatomical wall of ventriculus serosa" EXACT [OBOL:automatic] synonym: "anatomical wall of ventriculus serous membrane" EXACT [OBOL:automatic] synonym: "gastric serosa" RELATED [] synonym: "gastric wall serosa" EXACT [OBOL:automatic] synonym: "gastric wall serous membrane" EXACT [OBOL:automatic] synonym: "serosa of anatomical wall of stomach" EXACT [OBOL:automatic] synonym: "serosa of anatomical wall of ventriculus" EXACT [OBOL:automatic] synonym: "serosa of gastric wall" EXACT [OBOL:automatic] synonym: "serosa of stomach anatomical wall" EXACT [OBOL:automatic] synonym: "serosa of stomach wall" EXACT [OBOL:automatic] synonym: "serosa of ventriculus anatomical wall" EXACT [OBOL:automatic] synonym: "serosa of ventriculus wall" EXACT [OBOL:automatic] synonym: "serosa of wall of stomach" EXACT [OBOL:automatic] synonym: "serosa of wall of ventriculus" EXACT [OBOL:automatic] synonym: "serous coat of stomach" EXACT [] synonym: "serous membrane of anatomical wall of stomach" EXACT [OBOL:automatic] synonym: "serous membrane of anatomical wall of ventriculus" EXACT [OBOL:automatic] synonym: "serous membrane of gastric wall" EXACT [OBOL:automatic] synonym: "serous membrane of stomach anatomical wall" EXACT [OBOL:automatic] synonym: "serous membrane of stomach wall" EXACT [OBOL:automatic] synonym: "serous membrane of ventriculus anatomical wall" EXACT [OBOL:automatic] synonym: "serous membrane of ventriculus wall" EXACT [OBOL:automatic] synonym: "serous membrane of wall of stomach" EXACT [OBOL:automatic] synonym: "serous membrane of wall of ventriculus" EXACT [OBOL:automatic] synonym: "stomach anatomical wall serosa" EXACT [OBOL:automatic] synonym: "stomach anatomical wall serous membrane" EXACT [OBOL:automatic] synonym: "stomach serosa" EXACT [] synonym: "stomach wall serosa" EXACT [OBOL:automatic] synonym: "stomach wall serous membrane" EXACT [OBOL:automatic] synonym: "tunica serosa (gaster)" EXACT [] synonym: "tunica serosa gastricae" EXACT LATIN [FMA:14914, FMA:TA] synonym: "ventriculus anatomical wall serosa" EXACT [OBOL:automatic] synonym: "ventriculus anatomical wall serous membrane" EXACT [OBOL:automatic] synonym: "ventriculus wall serosa" EXACT [OBOL:automatic] synonym: "ventriculus wall serous membrane" EXACT [OBOL:automatic] synonym: "visceral peritoneum of stomach" EXACT [] synonym: "wall of stomach serosa" EXACT [OBOL:automatic] synonym: "wall of stomach serous membrane" EXACT [OBOL:automatic] synonym: "wall of ventriculus serosa" EXACT [OBOL:automatic] synonym: "wall of ventriculus serous membrane" EXACT [OBOL:automatic] xref: EMAPA:35822 xref: FMA:14914 xref: MA:0001626 xref: NCIT:C32662 xref: SCTID:1353004 xref: UMLS:C1517453 {source="ncithesaurus:Gastric_Serosal_Surface"} is_a: UBERON:0004782 ! gastrointestinal system serosa intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0001167 ! wall of stomach relationship: contributes_to_morphology_of UBERON:0001167 ! wall of stomach relationship: part_of UBERON:0001167 ! wall of stomach property_value: editor_note "TODO - check serosa/peritoneum" xsd:string [Term] id: UBERON:0001202 name: pyloric sphincter def: "A strong ring of smooth muscle at the end of the pyloric canal which lets food pass from the stomach to the duodenum. It receives sympathetic innervation from the celiac ganglion[WP]." [https://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim synonym: "pyloric valve" EXACT [Wikipedia:Pylorus] xref: AAO:0011093 xref: EMAPA:19251 xref: FMA:14916 xref: MA:0002952 xref: NCIT:C33433 xref: OpenCyc:Mx4rvly2ZZwpEbGdrcN5Y29ycA xref: SCTID:268073008 xref: UMLS:C0227238 {source="ncithesaurus:Pyloric_Sphincter"} xref: VHOG:0001466 xref: XAO:0000457 is_a: UBERON:0011185 ! gastrointestinal sphincter intersection_of: UBERON:0004590 ! sphincter muscle intersection_of: part_of UBERON:0001166 ! pylorus relationship: adjacent_to UBERON:0002114 ! duodenum relationship: continuous_with UBERON:0008858 ! pyloric canal relationship: contributes_to_morphology_of UBERON:0001166 ! pylorus relationship: never_in_taxon NCBITaxon:8355 relationship: part_of UBERON:0001166 ! pylorus property_value: homology_notes "(...) the adult Xenopus stomach exhibits both glandular and aglandular regions and a distinct pyloric sphincter similar to that of the amniotic vertebrates (...).[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001466", ontology="VHOG", source="DOI:10.1046/j.1525-142x.2000.00076.x", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001203 name: muscularis mucosae of stomach def: "the thin layer of smooth muscle in the mucosal layer of the stomach that functions to agitate the surface area stomach mucosa by moving the villi back and forth" [MGI:csmith, MP:0010806] subset: pheno_slim synonym: "gastric muscularis mucosa" EXACT [] synonym: "lamina muscularis mucosae (tunica mucosa)(gaster)" EXACT [] synonym: "lamina muscularis mucosae gastricae" EXACT LATIN [FMA:14924, FMA:TA] synonym: "lamina muscularis of gastric mucosa" EXACT [] synonym: "muscular coat of stomach" EXACT [] synonym: "stomach muscularis mucosa" EXACT [] synonym: "tunica muscularis gastricae" EXACT LATIN [FMA:14924, FMA:TA] xref: EMAPA:35818 xref: FMA:14924 xref: MA:0002684 xref: NCIT:C32658 xref: SCTID:64551004 xref: UMLS:C0227200 {source="ncithesaurus:Gastric_Muscularis_Mucosa"} is_a: UBERON:0004222 ! stomach smooth muscle is_a: UBERON:0006676 ! muscularis mucosa intersection_of: UBERON:0006676 ! muscularis mucosa intersection_of: part_of UBERON:0001199 ! mucosa of stomach relationship: contributes_to_morphology_of UBERON:0001199 ! mucosa of stomach relationship: part_of UBERON:0001199 ! mucosa of stomach property_value: function_notes "agitate the surface area stomach mucosa by moving the villi back and forth" xsd:string [Term] id: UBERON:0001204 name: mucosa of small intestine def: "A mucosa that is part of a small intestine [Automatically generated definition]." [OBOL:automatic] synonym: "mucosa of organ of small bowel" EXACT [OBOL:automatic] synonym: "mucosa of organ of small intestine" EXACT [OBOL:automatic] synonym: "mucosa of small bowel" EXACT [OBOL:automatic] synonym: "mucous membrane of small bowel" EXACT [OBOL:automatic] synonym: "mucous membrane of small intestine" EXACT [] synonym: "organ mucosa of small bowel" EXACT [OBOL:automatic] synonym: "organ mucosa of small intestine" EXACT [OBOL:automatic] synonym: "small bowel mucosa" EXACT [OBOL:automatic] synonym: "small bowel mucosa of organ" EXACT [OBOL:automatic] synonym: "small bowel mucous membrane" EXACT [OBOL:automatic] synonym: "small bowel organ mucosa" EXACT [OBOL:automatic] synonym: "small intestinal mucosa" EXACT [] synonym: "small intestine mucosa" EXACT [] synonym: "small intestine mucosa of organ" EXACT [OBOL:automatic] synonym: "small intestine mucous membrane" EXACT [] synonym: "small intestine organ mucosa" EXACT [OBOL:automatic] synonym: "tunica mucosa (intestinum tenue)" EXACT [] synonym: "tunica mucosa intestini tenuis" EXACT LATIN [FMA:14933, FMA:TA] xref: BTO:0001259 xref: CALOHA:TS-0941 xref: EMAPA:35780 xref: FMA:14933 xref: MA:0002686 xref: NCIT:C33568 xref: SCTID:362144000 xref: UMLS:C0227261 {source="ncithesaurus:Small_Intestinal_Mucosa"} is_a: UBERON:0001242 ! intestinal mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0001168 ! wall of small intestine relationship: part_of UBERON:0001242 ! intestinal mucosa relationship: part_of UBERON:0002108 ! small intestine [Term] id: UBERON:0001205 name: submucosa of small intestine def: "submucosal tissue in the small intestines." [Wikipedia:Small_intestinal_submucosa] subset: uberon_slim synonym: "small bowel submucosa" EXACT [OBOL:automatic] synonym: "small intestinal submucosa" EXACT [] synonym: "small intestine submucosa" EXACT [] synonym: "submucosa of small bowel" EXACT [OBOL:automatic] synonym: "tela submucosa (intestinum tenue)" EXACT [] synonym: "tela submucosa intestini tenuis" EXACT LATIN [BTO:0002112] xref: BTO:0002112 xref: EMAPA:37564 {source="MA:th"} xref: FMA:14934 xref: MA:0001562 xref: NCIT:C33572 xref: SCTID:691000 xref: UMLS:C0227268 {source="ncithesaurus:Small_Intestinal_Submucosa"} xref: Wikipedia:Small_intestinal_submucosa is_a: UBERON:0009566 ! intestinal submucosa intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0001168 ! wall of small intestine relationship: part_of UBERON:0002108 ! small intestine [Term] id: UBERON:0001206 name: serosa of small intestine def: "A serous membrane that is part of a small intestine [Automatically generated definition]." [OBOL:automatic] synonym: "serosa of small bowel" EXACT [OBOL:automatic] synonym: "serous coat of small intestine" EXACT [] synonym: "serous membrane of small bowel" EXACT [OBOL:automatic] synonym: "serous membrane of small intestine" EXACT [OBOL:automatic] synonym: "small bowel serosa" EXACT [OBOL:automatic] synonym: "small bowel serous membrane" EXACT [OBOL:automatic] synonym: "small intestinal serosa" EXACT [] synonym: "small intestine serosa" EXACT [] synonym: "small intestine serous membrane" EXACT [OBOL:automatic] synonym: "tunica serosa (intestinum tenue)" EXACT [] synonym: "tunica serosa intestini tenuis" EXACT LATIN [FMA:14938, FMA:TA] synonym: "visceral peritoneum of small intestine" EXACT [] xref: EMAPA:37561 {source="MA:th"} xref: FMA:14938 xref: MA:0001558 xref: SCTID:8266009 is_a: UBERON:0001243 ! serosa of intestine intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0001168 ! wall of small intestine relationship: part_of UBERON:0001243 ! serosa of intestine relationship: part_of UBERON:0002108 ! small intestine property_value: structure_notes "duodenum, 1st part serosa, 2nd - 4th adventitia" xsd:string [Term] id: UBERON:0001207 name: mucosa of large intestine def: "A mucosa that is part of a large intestine [Automatically generated definition]." [OBOL:automatic] synonym: "large intestinal mucosa" EXACT [] synonym: "large intestine mucosa" EXACT [] synonym: "large intestine mucosa of organ" EXACT [OBOL:automatic] synonym: "large intestine mucous membrane" EXACT [OBOL:automatic] synonym: "large intestine organ mucosa" EXACT [OBOL:automatic] synonym: "mucosa of organ of large intestine" EXACT [OBOL:automatic] synonym: "mucous membrane of large intestine" EXACT [] synonym: "organ mucosa of large intestine" EXACT [OBOL:automatic] synonym: "tunica mucosa intestini crassi" EXACT LATIN [FMA:14969, FMA:TA] xref: CALOHA:TS-2106 xref: EMAPA:35467 xref: FMA:14969 xref: MA:0002688 xref: NCIT:C32926 xref: UMLS:C0734203 {source="ncithesaurus:Large_Intestinal_Mucosa"} is_a: UBERON:0001242 ! intestinal mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0001169 ! wall of large intestine relationship: part_of UBERON:0001242 ! intestinal mucosa [Term] id: UBERON:0001208 name: submucosa of large intestine def: "A submucosa that is part of a large intestine [Automatically generated definition]." [OBOL:automatic] synonym: "large intestinal submucosa" EXACT [] synonym: "large intestine submucosa" EXACT [] synonym: "submucous layer of large intestine" RELATED [BTO:0002111] synonym: "tela submucosa intestini crassi" EXACT LATIN [FMA:14970, FMA:TA] xref: BTO:0002111 xref: EMAPA:37560 {source="MA:th"} xref: FMA:14970 xref: MA:0002690 xref: NCIT:C32930 xref: UMLS:C0734204 {source="ncithesaurus:Large_Intestinal_Submucosa"} intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0001169 ! wall of large intestine [Term] id: UBERON:0001209 name: serosa of large intestine def: "A serous membrane that is part of a large intestine [Automatically generated definition]." [OBOL:automatic] synonym: "large intestinal serosa" EXACT [] synonym: "large intestine serosa" EXACT [] synonym: "large intestine serous membrane" EXACT [OBOL:automatic] synonym: "serous coat of large intestine" EXACT [] synonym: "serous membrane of large intestine" EXACT [OBOL:automatic] synonym: "tunica serosa intestini crassi" EXACT LATIN [FMA:14975, FMA:TA] synonym: "visceral peritoneum of large intestine" EXACT [] xref: EMAPA:37557 {source="MA:th"} xref: FMA:14975 xref: MA:0001546 xref: NCIT:C32929 xref: UMLS:C1517727 {source="ncithesaurus:Large_Intestinal_Serosal_Surface"} is_a: UBERON:0001243 ! serosa of intestine intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0001169 ! wall of large intestine relationship: part_of UBERON:0001243 ! serosa of intestine property_value: editor_note "TODO - check serosa/peritoneum" xsd:string [Term] id: UBERON:0001210 name: muscularis mucosae of small intestine def: "A muscularis mucosa that is part of a small intestine." [OBOL:automatic] synonym: "lamina muscularis mucosae (tunica mucosa)(intestinum tenue)" EXACT [] synonym: "lamina muscularis mucosae intestini tenuis" EXACT LATIN [FMA:15051, FMA:TA] synonym: "lamina muscularis of small intestine mucous membrane" EXACT [] synonym: "small intestine muscularis mucosa" EXACT [] xref: EMAPA:35781 xref: FMA:15051 xref: MA:0002687 xref: NCIT:C33570 xref: SCTID:36401004 xref: UMLS:C0227262 {source="ncithesaurus:Small_Intestinal_Muscularis_Mucosa"} is_a: UBERON:0001240 ! muscularis mucosae of intestine is_a: UBERON:0004239 ! small intestine smooth muscle intersection_of: UBERON:0006676 ! muscularis mucosa intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0001204 ! mucosa of small intestine relationship: part_of UBERON:0001240 ! muscularis mucosae of intestine relationship: part_of UBERON:0002108 ! small intestine [Term] id: UBERON:0001211 name: Peyer's patch def: "the protruding lymphoid tissue located on the mucosa of the intestine that is composed of densely packed B cell follicles" [http://orcid.org/0000-0002-6601-2165, MESH:A10.549.600, MP:0000696, PMID:15841100] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "aggregated lymphoid follicle of intestine" RELATED [] synonym: "aggregated lymphoid nodule" RELATED [] synonym: "noduli lymphoidei aggregati" EXACT LATIN [] synonym: "Peyers gland" RELATED [BTO:0001784] synonym: "Peyers patch" RELATED [BTO:0001784] xref: BTO:0001784 xref: CALOHA:TS-0780 xref: EFO:0001381 xref: EMAPA:19028 xref: GAID:950 xref: MA:0000137 xref: MESH:A10.549.598 xref: NCIT:C12771 xref: UMLS:C0031272 {source="ncithesaurus:Peyer_s_Patch"} xref: Wikipedia:Peyer's_patch is_a: UBERON:0001962 {source="FMA", source="MA"} ! gut-associated lymphoid tissue relationship: never_in_taxon NCBITaxon:8459 {source="PMID:PMID:20181529"} relationship: only_in_taxon NCBITaxon:32524 {source="PMID:PMID:20181529"} relationship: part_of UBERON:0000030 {editor_note="check this"} ! lamina propria relationship: part_of UBERON:0001242 ! intestinal mucosa property_value: external_ontology_notes "FMA has [set of?] [aggregated,small] lymphoid [follice,nodule] of [colon, SI, I, etc]" xsd:string {external_ontology="FMA"} property_value: external_ontology_notes "Pp is a syn for Aggregated lymphoid follicle of small intestine; but MA uses Pp as covering both SI and LI. MA also includes follicle as a part. WP says duodenum and jejunum lack PPs" xsd:string {external_ontology="MA"} property_value: taxon_notes "Reptiles have accumulations of lymphocytes in their guts that may be primitive Peyer's patches (Zapata and Solas)." xsd:string [Term] id: UBERON:0001212 name: duodenal gland def: "A compound tubular submucosal gland found in that portion of the duodenum which is above the hepatopancreatic sphincter (Sphincter of Oddi). The main function of these glands is to produce a mucus-rich alkaline secretion (containing bicarbonate)[WP]." [Wikipedia:Brunner's_glands] subset: organ_slim subset: pheno_slim subset: uberon_slim synonym: "Brunner's gland" EXACT [FMA:15060] synonym: "gland of Brunner" EXACT [FMA:15060] synonym: "glandula duodenales" RELATED LATIN [BTO:0002376] synonym: "glandula duodenales Brunneri" RELATED LATIN [BTO:0002376] synonym: "submucosal gland of duodenum" EXACT [] xref: BTO:0002376 xref: EMAPA:36522 xref: FMA:15060 xref: GAID:314 xref: MA:0001551 xref: MESH:A03.492.411.620.270.322 xref: NCIT:C13010 xref: SCTID:41298001 xref: UMLS:C0006323 {source="ncithesaurus:Brunner_s_Gland"} xref: Wikipedia:Brunner's_glands is_a: UBERON:0000414 {source="MP"} ! mucous gland is_a: UBERON:0003408 ! gland of digestive tract is_a: UBERON:0011148 {notes="compound tubular"} ! submucosal gland intersection_of: UBERON:0011148 ! submucosal gland intersection_of: part_of UBERON:0002114 ! duodenum relationship: located_in UBERON:0003332 {source="FMA, modified"} ! submucosa of duodenum relationship: only_in_taxon NCBITaxon:40674 {notes="unclear for Aves", source="ISBN:9780521617147"} relationship: part_of UBERON:0002114 ! duodenum relationship: part_of UBERON:0002330 {source="MA-inferred"} ! exocrine system relationship: produces UBERON:0000912 ! mucus property_value: editor_note "currently defined as equivalent to any submucosal gland in the duodenum." xsd:string property_value: taxon_notes "Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds" xsd:string {source="ISBN:9780521617147"} [Term] id: UBERON:0001213 name: intestinal villus alt_id: UBERON:0007607 def: "the tiny hair-like projections that protrude from the inside of the small intestine that contain blood vessels that capture digested nutrients that are absorbed through the intestinal wall; the villi increase the absorptive surface area of the small intestine by approximately 30-fold" [MGI:csmith, MGI:rbabiuk, MP:0008108] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "enteric villi" EXACT PLURAL [HP:0011473] synonym: "enteric villous" EXACT [HP:0011473] synonym: "enteric villus" EXACT [HP:0011473] synonym: "intestinal villi" EXACT PLURAL [ZFA:0005125] synonym: "intestinal villus layer" RELATED [] synonym: "small intestine villus" RELATED [MA:0001563] synonym: "villi intestinales" EXACT PLURAL [] synonym: "villi intestinales" RELATED LATIN [Wikipedia:Intestinal_villus] synonym: "villus" EXACT [BTO:0003121] synonym: "villus intestinalis (intestinum tenue)" EXACT [FMA:15072] xref: BTO:0003121 xref: EMAPA:35784 xref: FMA:15072 xref: MA:0001563 xref: NCIT:C33874 xref: SCTID:23230007 xref: TAO:0005125 xref: UMLS:C1519988 {source="ncithesaurus:Villus"} xref: Wikipedia:Intestinal_villus xref: ZFA:0005125 is_a: CARO:0000000 is_a: UBERON:0004923 {source="FMA"} ! organ component layer relationship: has_part CL:0000066 relationship: has_part UBERON:0001981 ! blood vessel relationship: has_part UBERON:0012425 ! striated border microvillus layer relationship: part_of UBERON:0001204 {gci_relation="part_of", gci_filler="NCBITaxon:9606", notes="may be present in other parts in other species", source="FMA"} ! mucosa of small intestine relationship: part_of UBERON:0001277 {source="ZFA"} ! intestinal epithelium property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg xsd:anyURI property_value: editor_note "in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all species for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine" xsd:string property_value: external_definition "The entire digestive tract is lined by well developed villi, which are longest in the intestinal bulb and decrease progressively in size towards the caudal end of the intestine. No crypts are present, but, the regions between the villi, the intervillus pockets, have a crypt-like function. Cells are produced in the intervillus pockets and shed from the villus tips. Crosnier et al. 2005[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005125", ontology="TAO", source="ZFIN:curator"} property_value: external_ontology_notes "the BTO class refers to a generic villous" xsd:string {external_ontology="BTO"} [Term] id: UBERON:0001214 name: pancreatic tributary of splenic vein def: "The pancreatic veins consist of several small vessels which drain the body and tail of the pancreas, and open into the trunk of the great pancreatic vein. [WP,unvetted]." [Wikipedia:Pancreatic_vein] subset: uberon_slim synonym: "pancreatic vein" EXACT [] xref: EMAPA:37678 {source="MA:th"} xref: FMA:15388 xref: MA:0002189 xref: NCIT:C53059 xref: SCTID:264492008 xref: UMLS:C0226743 {source="ncithesaurus:Pancreatic_Vein"} xref: Wikipedia:Pancreatic_vein is_a: UBERON:0002017 ! portal vein relationship: part_of UBERON:0003713 ! splenic vein relationship: tributary_of UBERON:0003713 {source="FMA/obol"} ! splenic vein property_value: external_ontology_notes "see also MA:0002165 ! lieno-pancreatic vein" xsd:string {external_ontology="MA"} [Term] id: UBERON:0001215 name: inferior mesenteric vein def: "A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]." [Wikipedia:Inferior_mesenteric_vein] subset: uberon_slim synonym: "lower mesenteric vein" RELATED [BTO:0002782] synonym: "vena mesenterica inferior" RELATED LATIN [Wikipedia:Inferior_mesenteric_vein] xref: BTO:0002782 xref: EHDAA2:0000819 xref: EHDAA:8712 xref: EMAPA:18642 xref: FMA:15391 xref: MA:0002178 xref: NCIT:C32782 xref: OpenCyc:Mx4rvcV53ZwpEbGdrcN5Y29ycA xref: SCTID:281055007 xref: UMLS:C0226754 {source="ncithesaurus:Inferior_Mesenteric_Vein"} xref: VHOG:0001118 xref: Wikipedia:Inferior_mesenteric_vein is_a: UBERON:0005617 ! mesenteric vein intersection_of: UBERON:0005617 ! mesenteric vein intersection_of: drains UBERON:0000059 ! large intestine relationship: drains UBERON:0000059 ! large intestine relationship: part_of UBERON:0003713 ! splenic vein relationship: tributary_of UBERON:0003713 {source="FMA/obol"} ! splenic vein property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png xsd:anyURI [Term] id: UBERON:0001216 name: jejunal vein def: "A tributary of the superior mesenteric vein that drains the jejunum." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Jejunal_veins] synonym: "venae jejunales" RELATED LATIN [Wikipedia:Jejunal_veins] xref: EMAPA:37160 {source="MA:th"} xref: FMA:15402 xref: MA:0002153 xref: Wikipedia:Jejunal_veins is_a: UBERON:0002017 {source="FMA"} ! portal vein intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0002115 ! jejunum relationship: drains UBERON:0002115 ! jejunum relationship: part_of UBERON:0001138 ! superior mesenteric vein relationship: tributary_of UBERON:0001138 {source="FMA/obol"} ! superior mesenteric vein property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png xsd:anyURI [Term] id: UBERON:0001217 name: ileal vein def: "The veins that drain blood from the ileum into the superior mesenteric vein." [ncithesaurus:Ileal_Vein] xref: EMAPA:37149 {source="MA:th"} xref: FMA:15405 xref: MA:0002140 xref: NCIT:C53046 xref: UMLS:C1301431 {source="ncithesaurus:Ileal_Vein"} xref: Wikipedia:Ileal_veins is_a: UBERON:0002017 ! portal vein intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0002116 ! ileum relationship: drains UBERON:0002116 ! ileum relationship: part_of UBERON:0001138 ! superior mesenteric vein relationship: tributary_of UBERON:0001138 {source="FMA", source="Wikipedia"} ! superior mesenteric vein [Term] id: UBERON:0001218 name: middle colic vein def: "The middle colic vein drains the transverse colon. It is a tributary of the superior mesenteric vein, and follows the path of its corresponding artery, the middle colic artery. [WP,unvetted]." [Wikipedia:Middle_colic_vein] subset: uberon_slim synonym: "vena colica media" RELATED LATIN [Wikipedia:Middle_colic_vein] synonym: "vena colica media (intermedia)" EXACT [] xref: EMAPA:37174 {source="MA:th"} xref: FMA:15406 xref: MA:0002181 xref: OpenCyc:Mx4rvywYIpwpEbGdrcN5Y29ycA xref: SCTID:9018004 xref: Wikipedia:Middle_colic_vein is_a: UBERON:0002017 ! portal vein intersection_of: UBERON:0002017 ! portal vein intersection_of: drains UBERON:0001157 ! transverse colon intersection_of: tributary_of UBERON:0001138 ! superior mesenteric vein relationship: drains UBERON:0001157 ! transverse colon relationship: part_of UBERON:0001138 ! superior mesenteric vein relationship: tributary_of UBERON:0001138 ! superior mesenteric vein property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png xsd:anyURI [Term] id: UBERON:0001219 name: ileocolic vein def: "The ileocolic vein is a vein which drains the ileum, colon, and cecum. [WP,unvetted]." [Wikipedia:Ileocolic_vein] subset: uberon_slim synonym: "vena ileocolica" RELATED LATIN [Wikipedia:Ileocolic_vein] xref: EMAPA:37150 {source="MA:th"} xref: FMA:15408 xref: MA:0002141 xref: NCIT:C53047 xref: SCTID:36208008 xref: UMLS:C0226744 {source="ncithesaurus:Ileocolic_Vein"} xref: Wikipedia:Ileocolic_vein is_a: UBERON:0001217 ! ileal vein intersection_of: UBERON:0002017 ! portal vein intersection_of: drains UBERON:0001153 ! caecum intersection_of: drains UBERON:0001155 ! colon intersection_of: drains UBERON:0002116 ! ileum intersection_of: tributary_of UBERON:0001138 ! superior mesenteric vein relationship: drains UBERON:0001153 ! caecum relationship: drains UBERON:0001155 ! colon relationship: drains UBERON:0002116 ! ileum relationship: tributary_of UBERON:0001138 ! superior mesenteric vein property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png xsd:anyURI [Term] id: UBERON:0001220 name: quadratus lumborum def: "An abdominal muscle that inserts on the last rib and transverse processes of lumbar vertebrae. It is irregular and quadrilateral in shape, and broader below than above." [Wikipedia:Quadratus_lumborum_muscle] subset: organ_slim subset: uberon_slim synonym: "muscle of posterior abdominal wall" EXACT [] xref: EMAPA:18524 xref: FMA:15569 xref: MA:0002362 xref: NCIT:C33440 xref: OpenCyc:Mx4rvj1wcpwpEbGdrcN5Y29ycA xref: UMLS:C0224380 {source="ncithesaurus:Quadratus_Lumborum"} xref: Wikipedia:Quadratus_lumborum_muscle is_a: UBERON:0002378 ! muscle of abdomen is_a: UBERON:0003897 ! axial muscle is_a: UBERON:0004518 ! muscle of vertebral column relationship: has_muscle_insertion UBERON:0001077 {notes="Last rib and transverse processes of lumbar vertebrae", source="dbpedia"} ! transverse process of vertebra relationship: has_muscle_insertion UBERON:0002228 {notes="Last rib and transverse processes of lumbar vertebrae", source="dbpedia"} ! rib relationship: has_muscle_insertion UBERON:0002414 {notes="Last rib and transverse processes of lumbar vertebrae", source="dbpedia"} ! lumbar vertebra property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/d/de/Gray1124.png xsd:anyURI [Term] id: UBERON:0001221 name: transversus abdominis muscle def: "The lateral abdominal wall muscle that is deep to the internal oblique." [ISBN:9781435464339, UBERON:cjm] subset: organ_slim subset: uberon_slim synonym: "musculus transversus abdominis" EXACT LATIN [FMA:TA] synonym: "musculus transversus abdominis" EXACT LATIN [FMA:15570, FMA:TA] synonym: "transversalis" RELATED [Wikipedia:Transversus_abdominis_muscle] synonym: "transversalis muscle" RELATED [Wikipedia:Transversus_abdominis_muscle] synonym: "transverse abdominal" EXACT [FMA:15570] synonym: "transverse abdominal" RELATED [Wikipedia:Transversus_abdominis_muscle] synonym: "transverse abdominal muscle" RELATED [Wikipedia:Transversus_abdominis_muscle] synonym: "transverse abdominis" RELATED [Wikipedia:Transversus_abdominis_muscle] synonym: "transverse abdominus" RELATED [Wikipedia:Transversus_abdominis_muscle] synonym: "transversis abdominus" EXACT LATIN [Wikipedia:Transversus_abdominis_muscle] synonym: "transversus" RELATED [Wikipedia:Transversus_abdominis_muscle] synonym: "transversus abdominis" EXACT LATIN [] synonym: "transversus abdominis" RELATED [Wikipedia:Transversus_abdominis_muscle] synonym: "transversus abdominus" RELATED [Wikipedia:Transversus_abdominis_muscle] synonym: "transversus abdominus muscle" RELATED [Wikipedia:Transversus_abdominis_muscle] xref: EHDAA2:0002078 xref: EHDAA:8254 xref: EMAPA:18165 xref: FMA:15570 xref: MA:0002396 xref: NCIT:C53179 xref: SCTID:244949003 xref: UMLS:C0224378 {source="ncithesaurus:Transversus_Abdominis"} xref: VHOG:0000845 xref: Wikipedia:Transversus_abdominis_muscle is_a: CARO:0000003 is_a: UBERON:0002461 {is_inferred="true"} ! anterior abdominal wall muscle intersection_of: UBERON:0014892 ! skeletal muscle organ intersection_of: immediately_deep_to UBERON:0005454 ! abdominal internal oblique muscle intersection_of: part_of UBERON:0006635 ! anterior abdominal wall relationship: immediately_deep_to UBERON:0005454 ! abdominal internal oblique muscle relationship: innervated_by UBERON:0003727 {source="dbpedia"} ! intercostal nerve relationship: part_of UBERON:0006635 ! anterior abdominal wall property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/32/Illu_trunk_muscles.jpg xsd:anyURI property_value: external_definition "One of a pair of transverse abdominal muscles that is the anterolateral muscle of the abdomen, lying immediately under the internal abdominal oblique. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000845", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/transversus+abdominis"} property_value: homology_notes "Behind the thorax, the lateral group (of muscles in reptiles and mammals) remains essentially as for amphibians. (It breaks into three sheet-like layers: external oblique muscle, the internal oblique, and the transversus). More anteriorly, however, the ribs, now enlarged, penetrate and alter this group of muscles. The transversus is excluded from the thorax and the external and internal obliques become, respectively, the external and internal intercostal muscles, which contribute to the new function of ventilation of the lungs.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000845", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.193", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001222 name: right ureter def: "An ureter that is part of a right side of organism [Automatically generated definition]." [OBOL:automatic] xref: EMAPA:37373 {source="MA:th"} xref: FMA:15571 xref: MA:0001685 xref: NCIT:C49327 xref: SCTID:276251000 xref: UMLS:C0227682 {source="ncithesaurus:Right_Ureter"} is_a: UBERON:0000056 ! ureter intersection_of: UBERON:0000056 ! ureter intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism relationship: in_right_side_of UBERON:0000468 ! multicellular organism property_value: implements_design_pattern https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI [Term] id: UBERON:0001223 name: left ureter def: "An ureter that is part of a left side of organism [Automatically generated definition]." [OBOL:automatic] xref: EMAPA:37372 {source="MA:th"} xref: FMA:15572 xref: MA:0001684 xref: NCIT:C49324 xref: SCTID:276340002 xref: UMLS:C0227683 {source="ncithesaurus:Left_Ureter"} is_a: UBERON:0000056 ! ureter intersection_of: UBERON:0000056 ! ureter intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism relationship: in_left_side_of UBERON:0000468 ! multicellular organism property_value: implements_design_pattern https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI [Term] id: UBERON:0001224 name: renal pelvis def: "A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP]." [MP:0004194] comment: In this ontology, the renal pelvis is represented as the area of part-overlap between the kidney and the ureter subset: pheno_slim subset: uberon_slim synonym: "kidney pelvis" EXACT [] synonym: "p. renallis" RELATED LATIN [Wikipedia:Renal_pelvis] synonym: "pelvis of ureter" EXACT [] synonym: "pyelum" RELATED [MP:0004194] xref: CALOHA:TS-2230 xref: EMAPA:17948 xref: FMA:15575 xref: GAID:426 xref: galen:RenalPelvis xref: MA:0000374 xref: MESH:D007682 xref: NCIT:C12887 xref: SCTID:362221007 xref: UMLS:C0227666 {source="ncithesaurus:Renal_Pelvis"} xref: Wikipedia:Renal_pelvis is_a: UBERON:0000064 ! organ part disjoint_from: UBERON:0002355 ! pelvic region of trunk relationship: channel_for UBERON:0001088 ! urine relationship: channels_from UBERON:0002113 ! kidney relationship: channels_into UBERON:0000056 ! ureter relationship: continuous_with UBERON:0000056 {source="FMA"} ! ureter relationship: contributes_to_morphology_of UBERON:0000056 ! ureter relationship: part_of UBERON:0002113 {source="MA"} ! kidney relationship: part_of UBERON:0036295 ! renal pelvis/ureter property_value: depicted_by Illu:kidney2.jpg xsd:anyURI [Term] id: UBERON:0001225 name: cortex of kidney def: "Outer cortical portion of the kidney, between the renal capsule and the renal medulla." [Wikipedia:Renal_cortex] subset: pheno_slim subset: uberon_slim synonym: "cortex renalis" EXACT LATIN [FMA:15581, FMA:TA] synonym: "kidney cortex" EXACT [] synonym: "renal cortex" EXACT [] xref: BTO:0001166 xref: CALOHA:TS-0503 xref: EMAPA:17952 xref: FMA:15581 xref: GAID:424 xref: galen:CortexOfKidney xref: MA:0000372 xref: MESH:D007672 xref: NCIT:C12739 xref: SCTID:362211004 xref: UMLS:C0022655 {source="ncithesaurus:Renal_Cortex"} xref: Wikipedia:Renal_cortex is_a: CARO:0000000 is_a: UBERON:0001851 ! cortex intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0002113 ! kidney relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0008987 {source="FMA"} ! renal parenchyma property_value: depicted_by Illu:kidney.jpg xsd:anyURI property_value: structure_notes "In the adult metanephros, it forms a continuous smooth outer zone with a number of projections that extend down between the pyramids. It contains the renal corpuscles and the renal tubules except for parts of the loop of Henle which descend into the renal medulla. It also contains blood vessels and cortical collecting ducts. The renal cortex is the part of the kidney where ultrafiltration occurs.[WP]" xsd:string [Term] id: UBERON:0001226 name: major calyx def: "portion of the urinary collecting system within the kidney that drains several minor calyces" [http://anatomy.uams.edu/anatomyhtml/kidney.html] comment: major calyx collects urine from several renal papillae; all major calyces unite to form the renal pelvis subset: uberon_slim synonym: "calices renales majores" EXACT LATIN [Wikipedia:Major_calyx] synonym: "calices renales majores" RELATED LATIN [Wikipedia:Major_calyx] synonym: "major calix" EXACT [] xref: EMAPA:18677 xref: FMA:15613 xref: MA:0001644 xref: SCTID:1106008 xref: Wikipedia:Major_calyx is_a: UBERON:0006517 ! kidney calyx is_a: UBERON:0013126 ! vein of abdomen is_a: UBERON:0014401 ! renal venous blood vessel relationship: drains UBERON:0001227 ! minor calyx property_value: depicted_by Kidney:PioM.png xsd:anyURI [Term] id: UBERON:0001227 name: minor calyx def: "portion of the urinary collecting system within the kidney that drains one renal papilla" [http://anatomy.uams.edu/anatomyhtml/kidney.html] comment: one renal papilla projects into the lumen of one minor calyx; several minor calyces unite to form a major calyx subset: uberon_slim synonym: "calices renales minores" EXACT LATIN [Wikipedia:Minor_calyx] synonym: "calices renales minores" RELATED LATIN [Wikipedia:Minor_calyx] synonym: "minor calix" EXACT [] xref: EMAPA:18678 xref: FMA:15614 xref: MA:0001645 xref: SCTID:26293004 xref: Wikipedia:Minor_calyx is_a: UBERON:0006517 ! kidney calyx is_a: UBERON:0013126 ! vein of abdomen is_a: UBERON:0014401 ! renal venous blood vessel relationship: drains UBERON:0001228 ! renal papilla property_value: depicted_by Kidney:PioM.png xsd:anyURI [Term] id: UBERON:0001228 name: renal papilla def: "Tip of renal pyramid projecting into a minor calyx." [http://anatomy.uams.edu/anatomyhtml/kidney.html] subset: pheno_slim subset: uberon_slim synonym: "kidney papilla" EXACT [MP:0011303] xref: BTO:0003925 xref: EMAPA:35727 xref: FMA:15622 xref: galen:RenalPapilla xref: MA:0002730 xref: MESH:D007679 xref: NCIT:C33460 xref: SCTID:362214007 xref: UMLS:C0022666 {source="ncithesaurus:Renal_Papilla"} xref: Wikipedia:Renal_papilla is_a: CARO:0000000 is_a: UBERON:0000064 ! organ part relationship: contributes_to_morphology_of UBERON:0001224 ! renal pelvis relationship: part_of UBERON:0001224 ! renal pelvis relationship: part_of UBERON:0001294 ! inner medulla of kidney property_value: depicted_by Kidney:PioM.png xsd:anyURI [Term] id: UBERON:0001229 name: renal corpuscle def: "the structure containing the glomerular capsule and the glomerulus that serves as the initial blood-filtering component of a nephron" [ISBN:0-683-40008-8, MP:0002827] comment: Together, the Bowmans capsule and the glomerulus comprise the definitive renal corpuscle. http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "corpusculum renale" EXACT LATIN [] synonym: "corpusculum renis" RELATED LATIN [Wikipedia:Renal_corpuscle] synonym: "cortical renal corpuscle" RELATED [MA:0000376] synonym: "kidney corpuscle" RELATED [Wikipedia:Renal_corpuscle] synonym: "Malphigian corpuscle" EXACT MISSPELLING [MA:0000376] synonym: "Malpighian corpuscle" EXACT [ZFA:0005281] xref: BTO:0000333 xref: CALOHA:TS-1317 xref: EMAPA:28236 xref: EMAPA:35726 xref: EV:0100385 xref: FMA:15625 xref: MA:0000376 xref: NCIT:C33456 xref: SCTID:361329009 xref: TAO:0005281 xref: UMLS:C0227635 {source="ncithesaurus:Renal_Corpuscle"} xref: VHOG:0001262 xref: Wikipedia:Renal_corpuscle xref: ZFA:0005281 is_a: CARO:0000000 is_a: UBERON:0000063 ! organ subunit relationship: contributes_to_morphology_of UBERON:0001225 ! cortex of kidney relationship: contributes_to_morphology_of UBERON:0001285 ! nephron relationship: part_of UBERON:0001225 ! cortex of kidney relationship: part_of UBERON:0001285 {source="MA", source="ZFA"} ! nephron relationship: part_of UBERON:0007684 {source="FMA"} ! uriniferous tubule property_value: depicted_by Renal:corpuscle.svg xsd:anyURI property_value: external_definition "A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO]" xsd:string {date_retrieved="2012-11-28", external_class="BTO:0000333", ontology="BTO", source="BTO:curator"} property_value: external_definition "A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO]" xsd:string {date_retrieved="2012-11-28", external_class="XAO:0000146", ontology="XAO", source="XAO:curator"} property_value: external_definition "The part of the nephron that filters blood.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005281", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0001230 name: glomerular capsule def: "A cup-like sac at the expanded beginning of a tubular component of a nephron that contains the glomerulus" [MGI:pvb, MP:0002828, Wikipedia:Bowman%27s_capsule] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "Bowman's capsule" EXACT [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron] synonym: "Bowman's capsule" RELATED [TAO:0005254] synonym: "Bowmans capsule" EXACT [KUPO:0001001] synonym: "capsula glomerularis" EXACT LATIN [] synonym: "capsula glomeruli" RELATED LATIN [] synonym: "Malphigian capsule" RELATED MISSPELLING [BTO:0002297] synonym: "Malpighian capsule" RELATED [UBERO:cjm] synonym: "Mueller capsule" RELATED [BTO:0002297] synonym: "Muellerian capsule" RELATED [BTO:0002297] synonym: "pronephric glomerular capsule" RELATED [TAO:0005310] synonym: "renal glomerular capsule" EXACT [TAO:0005254] xref: AAO:0010526 xref: BTO:0002297 xref: EMAPA:27973 xref: EMAPA:28257 xref: FMA:15626 xref: KUPO:0001001 xref: MA:0001660 xref: NCIT:C32225 xref: SCTID:361331000 xref: TAO:0005254 xref: TAO:0005310 xref: UMLS:C0524448 {source="ncithesaurus:Bowman_s_Capsule"} xref: Wikipedia:Bowman%27s_capsule xref: ZFA:0005254 xref: ZFA:0005310 is_a: CARO:0000000 is_a: UBERON:0000064 ! organ part disjoint_from: UBERON:0002015 ! kidney capsule relationship: capable_of_part_of GO:0003094 {source="Wikipedia"} relationship: contributes_to_morphology_of UBERON:0001229 ! renal corpuscle relationship: develops_from UBERON:0004199 ! S-shaped body relationship: part_of UBERON:0001229 ! renal corpuscle property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg xsd:anyURI property_value: development_notes "One fold of the S-shaped body gives rise to Bowman's capsule[GUDMAP]" xsd:string property_value: external_definition "Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010526", ontology="AAO", source="AAO:BJB"} property_value: function_notes "Fluids from blood in the glomerulus are collected in the Bowman's capsule and further processed along the nephron to form urine. This process is known as ultrafiltration[WP]." xsd:string [Term] id: UBERON:0001231 name: nephron tubule alt_id: UBERON:0004210 def: "An epithelial tube that is part of the nephron, the functional part of the kidney." [GO:0072078, Wikipedia:Renal_tubule] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "kidney tubule" EXACT [GAID:433] synonym: "renal tubule" BROAD [] synonym: "tubulus renalis" EXACT [] synonym: "uriniferous tubule" RELATED [MA:0000377] xref: BTO:0000343 xref: CALOHA:TS-1262 xref: EFO:0003666 xref: EMAPA:27782 xref: EV:0100387 xref: FMA:15627 xref: GAID:433 xref: MA:0000377 xref: MESH:D007684 xref: NCIT:C49274 xref: SCTID:361332007 xref: TAO:0001287 xref: UMLS:C0022674 {source="ncithesaurus:Renal_Tubule"} xref: Wikipedia:Renal_tubule xref: ZFA:0001287 is_a: UBERON:0004211 ! nephron epithelium is_a: UBERON:0009773 {source="GO"} ! renal tubule intersection_of: UBERON:0003914 {source="GO", source="MA", source="ZFA"} ! epithelial tube intersection_of: part_of UBERON:0001285 {source="GO", source="MA", source="ZFA"} ! nephron relationship: contributes_to_morphology_of UBERON:0001285 ! nephron relationship: develops_from UBERON:0003918 {notes="checkme"} ! kidney mesenchyme relationship: has_part CL:0005009 {source="ZFA"} relationship: part_of UBERON:0001285 ! nephron property_value: external_ontology_notes "note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA" xsd:string {external_ontology="MA"} [Term] id: UBERON:0001232 name: collecting duct of renal tubule def: "The collecting duct is a portion of the nephron through which water flows, moving passively down its concentration gradient" [GO:0072044, Wikipedia:Collecting_tubule] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "arcuate renal tubule" RELATED [Wikipedia:Connecting_tubule] synonym: "collecting duct" EXACT [GO:0072044] synonym: "collecting duct system" RELATED [BTO:0000761] synonym: "collecting tubule" RELATED [] synonym: "junctional tube" RELATED [Wikipedia:Connecting_tubule] synonym: "kidney collecting duct" EXACT [] synonym: "kidney collecting tubule" RELATED [] synonym: "renal collecting tubule" EXACT [FMA:15628] synonym: "tubulus renalis arcuatus" EXACT LATIN [Wikipedia:Connecting_tubule] synonym: "tubulus renalis colligens" EXACT [] synonym: "ureteric tree" RELATED [EMAPA:28407] xref: BTO:0000761 xref: CALOHA:TS-0860 xref: EMAPA:28407 xref: EV:0100391 xref: FMA:15628 xref: GAID:434 xref: MA:0000371 xref: MESH:D007685 xref: SCTID:28202009 xref: TAO:0005294 xref: Wikipedia:Collecting_tubule xref: ZFA:0005294 is_a: CARO:0000000 is_a: UBERON:0006555 ! excretory tube relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: part_of UBERON:0001285 {notes="checkme", source="GO"} ! nephron relationship: part_of UBERON:0007684 {source="FMA"} ! uriniferous tubule property_value: external_definition "Renal duct that collects the output from renal tubules.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005294", ontology="TAO", source="ZFIN:curator"} property_value: external_ontology_notes "in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0001233 name: right adrenal gland def: "An adrenal gland that is in the right side of the abdomen" [OBOL:automatic] synonym: "glandula suprarenalis dexter" EXACT LATIN [] synonym: "right suprarenal gland" EXACT [] xref: EMAPA:37357 {source="MA:th"} xref: FMA:15629 xref: MA:0000719 xref: NCIT:C49325 xref: SCTID:281625001 xref: UMLS:C0229559 {source="ncithesaurus:Right_Adrenal_Gland"} is_a: UBERON:0002369 ! adrenal gland intersection_of: UBERON:0002369 ! adrenal gland intersection_of: in_right_side_of UBERON:0000916 ! abdomen relationship: in_right_side_of UBERON:0000916 ! abdomen property_value: implements_design_pattern https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI property_value: taxon_notes "In humans, the right adrenal gland is triangular shaped" xsd:string {source="WP"} [Term] id: UBERON:0001234 name: left adrenal gland def: "An adrenal gland that is in the left side of the abdomen" [OBOL:automatic] synonym: "glandula suprarenalis sinister" EXACT LATIN [] synonym: "left suprarenal gland" EXACT [] xref: EMAPA:37356 {source="MA:th"} xref: FMA:15630 xref: MA:0000718 xref: NCIT:C49322 xref: SCTID:281626000 xref: UMLS:C0229560 {source="ncithesaurus:Left_Adrenal_Gland"} is_a: UBERON:0002369 ! adrenal gland intersection_of: UBERON:0002369 ! adrenal gland intersection_of: in_left_side_of UBERON:0000916 ! abdomen relationship: in_left_side_of UBERON:0000916 ! abdomen property_value: implements_design_pattern https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI property_value: taxon_notes "In humans, the left adrenal gland is semilunar shaped" xsd:string {source="WP"} [Term] id: UBERON:0001235 name: adrenal cortex def: "the thick outer layer of the adrenal gland that produces and secretes steroid hormones such as corticosterone, estrone and aldosterone" [ISBN:0-683-40008-8, MGI:llw2, MP:0008288] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "adrenal gland cortex" EXACT [] synonym: "cortex (glandula suprarenalis)" EXACT [] synonym: "cortex glandulae suprarenalis" RELATED LATIN [Wikipedia:Adrenal_cortex] synonym: "cortex glandulae suprarenalis" RELATED [BTO:0000045] synonym: "cortex of adrenal gland" EXACT [] synonym: "cortex of suprarenal gland" EXACT [] synonym: "suprarenal" RELATED [] synonym: "suprarenal cortex" EXACT [] xref: AAO:0011009 xref: BTO:0000045 xref: CALOHA:TS-0015 xref: EFO:0000237 xref: EMAPA:18427 xref: EV:0100136 xref: FMA:15632 xref: GAID:447 xref: MA:0000118 xref: MAT:0000494 xref: MESH:D000302 xref: NCIT:C12396 xref: SCTID:362584002 xref: UMLS:C0001613 {source="ncithesaurus:Adrenal_Cortex"} xref: VHOG:0001481 xref: Wikipedia:Adrenal_cortex xref: XAO:0000165 is_a: UBERON:0001851 ! cortex is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0002369 ! adrenal gland relationship: capable_of GO:0006704 relationship: capable_of GO:0006705 relationship: capable_of GO:0035932 relationship: contributes_to_morphology_of UBERON:0002369 ! adrenal gland relationship: develops_from UBERON:0000926 {source="Wikipedia"} ! mesoderm relationship: part_of UBERON:0002369 ! adrenal gland property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png xsd:anyURI property_value: homology_notes "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001481", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9", source="http://bgee.unil.ch/"} property_value: taxon_notes "Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO" xsd:string [Term] id: UBERON:0001236 name: adrenal medulla def: "the inner portion of the adrenal gland that consists mainly of chromaffin cells which produce, store and secrete neurotransmitters such as epinephrine and norepinephrine" [MESH:A06.407.071.265, MGI:llw2, MP:0008289] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "adrenal central medulla" RELATED [] synonym: "adrenal gland medulla" EXACT [] synonym: "chromaffin cells" RELATED [] synonym: "medulla (glandula suprarenalis)" EXACT [] synonym: "medulla glandulae suprarenalis" EXACT LATIN [FMA:15633, FMA:TA] synonym: "medulla of adrenal gland" EXACT [OBOL:automatic] synonym: "medulla of glandula suprarenalis" RELATED [BTO:0000049] synonym: "medulla of suprarenal gland" EXACT [] synonym: "suprarenal medulla" EXACT [] xref: AAO:0011010 xref: BTO:0000049 xref: CALOHA:TS-0018 xref: EFO:0000852 xref: EMAPA:18428 xref: EV:0100137 xref: FMA:15633 xref: GAID:451 xref: MA:0000119 xref: MAT:0000495 xref: MESH:D019439 xref: NCIT:C12397 xref: SCTID:362585001 xref: UMLS:C0001629 {source="ncithesaurus:Adrenal_Medulla"} xref: VHOG:0001378 xref: Wikipedia:Adrenal_medulla xref: XAO:0000166 is_a: UBERON:0000958 ! medulla of organ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0000958 ! medulla of organ intersection_of: part_of UBERON:0002369 ! adrenal gland relationship: contributes_to_morphology_of UBERON:0002369 ! adrenal gland relationship: develops_from UBERON:0002342 {source="ISBN:0073040584", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neural crest relationship: has_part CL:0002082 {source="FMA"} relationship: has_part CL:0002083 {source="FMA"} relationship: has_part CL:1000426 relationship: part_of UBERON:0002369 ! adrenal gland relationship: surrounded_by UBERON:0001235 {source="Wikipedia"} ! adrenal cortex property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png xsd:anyURI property_value: homology_notes "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001378", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001237 name: paraaortic body def: "A chromaffin paraganglion located at the bifurcation of the aorta or at the origin of the inferior mesenteric artery." [Wikipedia:Organ_of_Zuckerkandl] comment: The largest chromaffin paraganglia, and the largest source of circulating catecholamines in the fetus and young infants, and gradually atrophies to microscopic loci[WP] subset: organ_slim subset: uberon_slim synonym: "organ of Zuckerkandl" EXACT [] synonym: "para-aortic body" RELATED [] synonym: "paraganglia of Zuckerkandl" RELATED PLURAL [] synonym: "paraganglion of Zuckerkandl" EXACT [EMAPA:18223] xref: EMAPA:18223 xref: FMA:15647 xref: GAID:444 xref: MA:0001137 xref: MESH:D010220 xref: NCIT:C25316 xref: SCTID:276159005 xref: UMLS:C0442134 {source="ncithesaurus:Paraaortic"} xref: Wikipedia:Organ_of_Zuckerkandl is_a: UBERON:0012279 ! chromaffin paraganglion property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png xsd:anyURI [Term] id: UBERON:0001238 name: lamina propria of small intestine def: "Lamina propria that is part_of the small intestine." [GOC:Obol] synonym: "lamina propria mucosa of small bowel" EXACT [OBOL:automatic] synonym: "lamina propria mucosa of small intestine" EXACT [OBOL:automatic] synonym: "lamina propria mucosae of small bowel" EXACT [OBOL:automatic] synonym: "lamina propria mucosae of small intestine" EXACT [] synonym: "lamina propria of mucosa of small intestine" EXACT [] synonym: "lamina propria of small bowel" EXACT [OBOL:automatic] synonym: "small bowel lamina propria" EXACT [OBOL:automatic] synonym: "small bowel lamina propria mucosa" EXACT [OBOL:automatic] synonym: "small bowel lamina propria mucosae" EXACT [OBOL:automatic] synonym: "small intestine lamina propria" EXACT [] synonym: "small intestine lamina propria mucosa" EXACT [OBOL:automatic] synonym: "small intestine lamina propria mucosae" EXACT [OBOL:automatic] xref: EMAPA:35779 xref: FMA:15651 xref: MA:0001554 xref: NCIT:C49297 xref: SCTID:63588008 xref: UMLS:C1711325 {source="ncithesaurus:Small_Intestinal_Lamina_Propria"} is_a: UBERON:0004780 ! gastrointestinal system lamina propria intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0001168 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! wall of small intestine relationship: part_of UBERON:0001204 ! mucosa of small intestine relationship: part_of UBERON:0002108 ! small intestine [Term] id: UBERON:0001239 name: muscularis mucosae of large intestine def: "A muscularis mucosa that is part of a large intestine." [OBOL:automatic] synonym: "lamina muscularis mucosae intestini crassi" EXACT LATIN [FMA:15655, FMA:TA] synonym: "lamina muscularis of large intestine mucosa" EXACT [] synonym: "lamina muscularis of large intestine mucous membrane" EXACT [] synonym: "large intestine muscularis mucosa" EXACT [] xref: EMAPA:37556 {source="MA:th"} xref: FMA:15655 xref: MA:0002689 xref: NCIT:C32928 xref: UMLS:C0734776 {source="ncithesaurus:Large_Intestinal_Muscularis_Mucosa"} is_a: UBERON:0001240 ! muscularis mucosae of intestine is_a: UBERON:0004220 ! large intestine smooth muscle intersection_of: UBERON:0006676 ! muscularis mucosa intersection_of: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0001207 ! mucosa of large intestine relationship: part_of UBERON:0001240 ! muscularis mucosae of intestine [Term] id: UBERON:0001240 name: muscularis mucosae of intestine def: "A muscularis mucosa that is part of a intestine." [OBOL:automatic] synonym: "intestinal muscularis mucosa" RELATED [EMAPA:35442] synonym: "intestine muscularis mucosa" EXACT [MA:0002694] xref: EMAPA:35442 xref: FMA:15691 xref: MA:0002694 is_a: UBERON:0004221 ! intestine smooth muscle is_a: UBERON:0006676 ! muscularis mucosa intersection_of: UBERON:0006676 ! muscularis mucosa intersection_of: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0001242 ! intestinal mucosa [Term] id: UBERON:0001241 name: crypt of Lieberkuhn of small intestine def: "the tubular intestinal glands found in the mucosal membranes of the small intestine" [ISBN:0-683-40008-8, MP:0004841] subset: pheno_slim synonym: "crypt of Lieberkuhn of small bowel" EXACT [OBOL:automatic] synonym: "crypt of Lieberkuhn of small intestine" EXACT [OBOL:automatic] synonym: "intestinal gland of small bowel" EXACT [OBOL:automatic] synonym: "intestinal gland of small intestine" EXACT [OBOL:automatic] synonym: "lieberkuhn crypt of small bowel" EXACT [OBOL:automatic] synonym: "lieberkuhn crypt of small intestine" EXACT [OBOL:automatic] synonym: "small bowel crypt of Lieberkuhn" EXACT [OBOL:automatic] synonym: "small bowel intestinal gland" EXACT [OBOL:automatic] synonym: "small bowel lieberkuhn crypt" EXACT [OBOL:automatic] synonym: "small intestinal crypt of Lieberkuhn" EXACT [] synonym: "small intestine crypt of Lieberkuhn" EXACT [OBOL:automatic] synonym: "small intestine intestinal gland" EXACT [OBOL:automatic] synonym: "small intestine lieberkuhn crypt" EXACT [OBOL:automatic] xref: EMAPA:35777 xref: FMA:15693 xref: MA:0001552 xref: NCIT:C33565 xref: SCTID:52688008 xref: UMLS:C0227267 {source="ncithesaurus:Small_Intestinal_Crypt_of_Lieberkuhn"} is_a: UBERON:0001983 ! crypt of Lieberkuhn intersection_of: UBERON:0001983 ! crypt of Lieberkuhn intersection_of: part_of UBERON:0002108 ! small intestine relationship: contributes_to_morphology_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0002108 ! small intestine [Term] id: UBERON:0001242 name: intestinal mucosa def: "Mucosal layer that lines the intestine." [UBERON:cjm] subset: pheno_slim subset: uberon_slim synonym: "bowel mucosa" EXACT [OBOL:automatic] synonym: "bowel mucosa of organ" EXACT [OBOL:automatic] synonym: "bowel mucous membrane" EXACT [OBOL:automatic] synonym: "bowel organ mucosa" EXACT [OBOL:automatic] synonym: "intestine mucosa" EXACT [] synonym: "intestine mucosa of organ" EXACT [OBOL:automatic] synonym: "intestine mucous membrane" EXACT [OBOL:automatic] synonym: "intestine organ mucosa" EXACT [OBOL:automatic] synonym: "mucosa of bowel" EXACT [OBOL:automatic] synonym: "mucosa of intestine" EXACT [] synonym: "mucosa of organ of bowel" EXACT [OBOL:automatic] synonym: "mucosa of organ of intestine" EXACT [OBOL:automatic] synonym: "mucous membrane of bowel" EXACT [OBOL:automatic] synonym: "mucous membrane of intestine" EXACT [OBOL:automatic] synonym: "organ mucosa of bowel" EXACT [OBOL:automatic] synonym: "organ mucosa of intestine" EXACT [OBOL:automatic] synonym: "tunica mucosa intestini" EXACT [] xref: BTO:0000642 xref: EMAPA:35440 xref: FMA:15695 xref: GAID:296 xref: MA:0001537 xref: MESH:A03.492.411.369 xref: NCIT:C49241 xref: SCTID:362080002 xref: UMLS:C0021839 {source="ncithesaurus:Intestinal_Mucosa"} intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0001262 ! wall of intestine [Term] id: UBERON:0001243 name: serosa of intestine def: "A serous membrane that is part of a wall of intestine [Automatically generated definition]." [OBOL:automatic] synonym: "anatomical wall of bowel serosa" EXACT [OBOL:automatic] synonym: "anatomical wall of bowel serous membrane" EXACT [OBOL:automatic] synonym: "anatomical wall of intestine serosa" EXACT [OBOL:automatic] synonym: "anatomical wall of intestine serous membrane" EXACT [OBOL:automatic] synonym: "bowel anatomical wall serosa" EXACT [OBOL:automatic] synonym: "bowel anatomical wall serous membrane" EXACT [OBOL:automatic] synonym: "bowel wall serosa" EXACT [OBOL:automatic] synonym: "bowel wall serous membrane" EXACT [OBOL:automatic] synonym: "intestinal serosa" EXACT [] synonym: "intestinal wall serosa" EXACT [OBOL:automatic] synonym: "intestinal wall serous membrane" EXACT [OBOL:automatic] synonym: "intestine anatomical wall serosa" EXACT [OBOL:automatic] synonym: "intestine anatomical wall serous membrane" EXACT [OBOL:automatic] synonym: "intestine serosa" EXACT [] synonym: "intestine wall serosa" EXACT [OBOL:automatic] synonym: "intestine wall serous membrane" EXACT [OBOL:automatic] synonym: "serosa of anatomical wall of bowel" EXACT [OBOL:automatic] synonym: "serosa of anatomical wall of intestine" EXACT [OBOL:automatic] synonym: "serosa of bowel anatomical wall" EXACT [OBOL:automatic] synonym: "serosa of bowel wall" EXACT [OBOL:automatic] synonym: "serosa of intestinal wall" EXACT [OBOL:automatic] synonym: "serosa of intestine anatomical wall" EXACT [OBOL:automatic] synonym: "serosa of intestine wall" EXACT [OBOL:automatic] synonym: "serosa of wall of bowel" EXACT [OBOL:automatic] synonym: "serosa of wall of intestine" EXACT [OBOL:automatic] synonym: "serous membrane of anatomical wall of bowel" EXACT [OBOL:automatic] synonym: "serous membrane of anatomical wall of intestine" EXACT [OBOL:automatic] synonym: "serous membrane of bowel anatomical wall" EXACT [OBOL:automatic] synonym: "serous membrane of bowel wall" EXACT [OBOL:automatic] synonym: "serous membrane of intestinal wall" EXACT [OBOL:automatic] synonym: "serous membrane of intestine anatomical wall" EXACT [OBOL:automatic] synonym: "serous membrane of intestine wall" EXACT [OBOL:automatic] synonym: "serous membrane of wall of bowel" EXACT [OBOL:automatic] synonym: "serous membrane of wall of intestine" EXACT [OBOL:automatic] synonym: "visceral peritoneum of intestine" EXACT [] synonym: "wall of bowel serosa" EXACT [OBOL:automatic] synonym: "wall of bowel serous membrane" EXACT [OBOL:automatic] synonym: "wall of intestine serosa" EXACT [OBOL:automatic] synonym: "wall of intestine serous membrane" EXACT [OBOL:automatic] xref: EMAPA:37619 {source="MA:th"} xref: FMA:15701 xref: MA:0001538 intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0001262 ! wall of intestine property_value: editor_note "TODO - check serosa/peritoneum" xsd:string [Term] id: UBERON:0001244 name: internal anal sphincter def: "the smooth muscle ring, formed by an increase of the circular muscle fibers of the rectum, situated at the upper end of the anal canal, internal to the outer voluntary external anal sphincter" [MGI:anna, MP:0009055] subset: pheno_slim subset: uberon_slim synonym: "circular layer of anal muscularis externa" EXACT [] synonym: "circular layer of muscularis externa of anal canal" EXACT [] synonym: "circular layer of muscularis propria of anal canal" EXACT [] synonym: "circular muscle layer of anal canal" EXACT [] xref: EMAPA:18266 xref: FMA:15710 xref: MA:0001534 xref: NCIT:C32833 xref: UMLS:C0224394 {source="ncithesaurus:Internal_Anal_Sphincter"} xref: Wikipedia:Internal_anal_sphincter is_a: UBERON:0004231 {source="MA"} ! anal region smooth muscle is_a: UBERON:0004916 ! anal sphincter is_a: UBERON:0007521 ! smooth muscle sphincter is_a: UBERON:0012368 ! circular muscle layer of muscular coat relationship: part_of UBERON:0001353 ! anal region relationship: surrounds UBERON:0000159 ! anal canal property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray1079.png xsd:anyURI [Term] id: UBERON:0001245 name: anus def: "Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts." [Wikipedia:Anus, ZFIN:curator] subset: pheno_slim subset: uberon_slim synonym: "anal opening" EXACT [] synonym: "anal orifice" EXACT [] synonym: "opening of terminal part of digestive tract" EXACT [] synonym: "proctodeum" RELATED [] xref: BTO:0001680 xref: CALOHA:TS-2005 xref: EV:0100082 xref: FBbt:00003148 xref: FMA:15711 xref: GAID:312 xref: galen:Anus xref: MA:0000331 xref: MESH:A03.492.411.495.767.288 xref: NCIT:C43362 xref: OpenCyc:Mx4rvVjaEZwpEbGdrcN5Y29ycA xref: SCTID:181262009 xref: TADS:0000066 xref: TGMA:0001279 xref: UMLS:C0003461 {source="ncithesaurus:Anus"} xref: WBbt:0005364 xref: Wikipedia:Anus is_a: UBERON:0000161 ! orifice intersection_of: UBERON:0000161 ! orifice intersection_of: distalmost_part_of UBERON:0001555 ! digestive tract relationship: develops_from UBERON:0000931 ! proctodeum relationship: distalmost_part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg xsd:anyURI property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif xsd:anyURI property_value: has_relational_adjective "anal" xsd:string property_value: taxon_notes "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" xsd:string [Term] id: UBERON:0001246 name: interlobular bile duct def: "The canals that carry bile in the liver between the intralobular ducts and the biliary ductules; interlobular bile ducts are part of the interlobular portal triad." [MP:0009500] subset: pheno_slim synonym: "interlobular ductule" EXACT [MP:0009500] xref: FMA:15767 xref: MA:0002668 xref: NCIT:C32827 xref: SCTID:83488001 xref: UMLS:C0227515 {source="ncithesaurus:Interlobular_Bile_Duct"} xref: Wikipedia:Interlobular_bile_ducts is_a: UBERON:0003704 {source="FMA", source="MA-part-of"} ! intrahepatic bile duct relationship: connects UBERON:0004058 ! biliary ductule relationship: connects UBERON:0014719 ! intralobular duct relationship: contributes_to_morphology_of UBERON:0001279 ! portal triad relationship: part_of UBERON:0001279 {source="FMA", source="MA", source="MP"} ! portal triad [Term] id: UBERON:0001247 name: falciform ligament def: "A ligament that attaches the liver to the anterior body wall. It is a broad and thin antero-posterior peritoneal fold, falciform in shape, its base being directed downward and backward and its apex upward and backward. It is a remnant of the ventral mesentery of the fetus. It is situated in an antero-posterior plane but lies obliquely, so that one surface faces forward and is in contact with the peritoneum behind the right rectus and the diaphragm, while the other is directed backward and is in contact with the left lobe of the liver. It is attached by its left margin to the under surface of the diaphragm and the posterior surface of the sheath of the right Rectus as low down as the umbilicus; by its right margin it extends from the notch on the anterior margin of the liver, as far back as the posterior surface. It is composed of two layers of peritoneum closely united together. Its base or free edge contains between its layers the round ligament and the paraumbilical veins[WP]." [Wikipedia:Falciform_ligament] subset: uberon_slim synonym: "falciform ligament of liver" EXACT [] synonym: "ligamentum falciforme (hepatis)" EXACT [] synonym: "ligamentum falciforme hepatis" EXACT LATIN [FMA:15823, FMA:TA] xref: EHDAA2:0000499 xref: EHDAA:4856 xref: EMAPA:18288 xref: FMA:15823 xref: MA:0001622 xref: NCIT:C32582 xref: SCTID:362705001 xref: UMLS:C0230240 {source="ncithesaurus:Falciform_Ligament"} xref: VHOG:0000355 xref: Wikipedia:Falciform_ligament is_a: CARO:0000003 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0013139 ! ligament of liver intersection_of: UBERON:0008845 ! nonskeletal ligament intersection_of: attaches_to UBERON:0000309 ! body wall intersection_of: attaches_to UBERON:0002107 ! liver relationship: attaches_to UBERON:0000309 ! body wall relationship: attaches_to UBERON:0002107 ! liver relationship: part_of UBERON:0002095 {source="FMA-modified"} ! mesentery relationship: part_of UBERON:0005626 {source="MA"} ! ventral mesogastrium property_value: external_ontology_notes "in FMA this is a subclass of mesentery. In MA it is a subclass of ligament, we infer and assert this is a nonskeletal ligament" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0001248 name: hilum of spleen def: "The splenic hilum is a location on the surface of the spleen. It is the point of attachment for the gastrosplenic ligament, and the point of insertion for the splenic artery and splenic vein. [WP,unvetted]." [Wikipedia:Splenic_hilum] subset: uberon_slim synonym: "hilum" BROAD [EMAPA:19303] synonym: "hilum lienale" EXACT LATIN [FMA:15841, FMA:TA] synonym: "hilum splenicum" EXACT LATIN [FMA:15841, FMA:TA] synonym: "hilum splenicum" RELATED LATIN [Wikipedia:Splenic_hilum] synonym: "spleen hilum" EXACT [] synonym: "splenic hilum" EXACT [] xref: EMAPA:19303 xref: FMA:15841 xref: MA:0002670 xref: NCIT:C33601 xref: SCTID:245377005 xref: UMLS:C0229685 {source="ncithesaurus:Splenic_Hilum"} xref: Wikipedia:Splenic_hilum is_a: CARO:0000000 is_a: UBERON:0004885 ! hilum intersection_of: UBERON:0004885 ! hilum intersection_of: part_of UBERON:0002106 ! spleen relationship: part_of UBERON:0002106 ! spleen property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/a/a2/Gray1188.png xsd:anyURI [Term] id: UBERON:0001249 name: spleen lymphoid follicle alt_id: UBERON:0003969 def: "The area of the white pulp where the affinity maturation of B cells and the generation of memory B cells and plasma cells occur" [CL:tm, https://github.com/obophenotype/uberon/issues/6, MP:0008470] subset: pheno_slim synonym: "lymphatic follicle of spleen" EXACT [FMA:15843] synonym: "lymphoid follicle of spleen" EXACT [FMA:15843] synonym: "lymphoid nodule of spleen" EXACT [FMA:15843] synonym: "Malpighian body" EXACT [FMA:15843] synonym: "spleen B cell follicle" EXACT [CL:tm] synonym: "spleen lymphoid follicle" EXACT [MA:0002672] synonym: "spleen lymphoid nodule" RELATED [MA:0002672] synonym: "splenic B cell follicle" EXACT [CL:tm] synonym: "splenic lymphatic follicle" EXACT [FMA:15843] synonym: "splenic lymphoid follicle" EXACT [] xref: EMAPA:35804 xref: MA:0002672 xref: NCIT:C33602 xref: SCTID:35845000 xref: UMLS:C1519475 {source="ncithesaurus:Splenic_Lymphoid_Follicle"} is_a: UBERON:0000444 ! lymphoid follicle is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000444 ! lymphoid follicle intersection_of: part_of UBERON:0002106 ! spleen relationship: contains_process GO:0002319 relationship: contributes_to_morphology_of UBERON:0001959 ! white pulp of spleen relationship: dc-contributor https://github.com/cmungall relationship: dc-contributor https://github.com/tmeehan relationship: part_of UBERON:0001959 {source="CL:tm", source="MA"} ! white pulp of spleen relationship: part_of UBERON:0002106 ! spleen relationship: part_of UBERON:0006561 {source="FMA"} ! non-lymphatic part of lymphoid system relationship: part_of UBERON:1000024 {source="FMA"} ! parenchyma of spleen [Term] id: UBERON:0001250 name: red pulp of spleen def: "the parenchymatous tissue network of the spleen that consists of loose plates or cords (sinuses) infiltrated with red blood cells where most of the blood filtration occurs and degenerate erythrocytes are removed from the circulation" [MGI:csmith, MP:0002356] subset: pheno_slim subset: uberon_slim synonym: "pulpa rubra" EXACT LATIN [FMA:15844, FMA:TA] synonym: "pulpa splenica" RELATED LATIN [Wikipedia:Red_pulp] synonym: "red pulp" EXACT [] synonym: "spleen red pulp" EXACT [] synonym: "splenic red pulp" EXACT [] xref: CALOHA:TS-1263 xref: EMAPA:35806 xref: FMA:15844 xref: MA:0000756 xref: NCIT:C12992 xref: SCTID:27579002 xref: UMLS:C0229687 {source="ncithesaurus:Splenic_Red_Pulp"} xref: Wikipedia:Red_pulp is_a: UBERON:1000023 ! spleen pulp relationship: composed_primarily_of CL:0000542 relationship: contributes_to_morphology_of UBERON:0002106 ! spleen relationship: present_in_taxon NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png xsd:anyURI [Term] id: UBERON:0001251 name: marginal zone of spleen def: "the zone between the red and white pulp of the spleen containing numerous macrophages and lymphocytes, and a rich plexus of sinusoids supplied by white pulp arterioles carrying blood-borne antigens" [ISBN:0-683-40008-8, MP:0002362] subset: pheno_slim synonym: "junctional zone of spleen" EXACT [] synonym: "marginal zone" BROAD [Wikipedia:Marginal_zone] synonym: "spleen marginal zone" EXACT [MA:0000755] xref: CALOHA:TS-2395 xref: EMAPA:36650 xref: FMA:15852 xref: MA:0000755 xref: NCIT:C49767 xref: UMLS:C1711368 {source="ncithesaurus:Marginal_Zone"} xref: Wikipedia:Marginal_zone is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:0004879 ! marginal zone of embryo relationship: adjacent_to UBERON:0001250 ! red pulp of spleen relationship: adjacent_to UBERON:0001959 ! white pulp of spleen relationship: part_of UBERON:0002106 ! spleen property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png xsd:anyURI property_value: external_ontology_notes "WP says - (Some sources consider it to be the part of red pulp which borders on the white pulp, while other sources consider it to be neither red pulp nor white pulp.) - we use the adjacency relation here so it overlaps neither. FMA considers this an anatomical line." xsd:string {external_ontology="FMA"} [Term] id: UBERON:0001252 name: adventitia of ureter def: "An adventitia that is part of a ureter." [OBOL:automatic] synonym: "external adventitia of ureter" EXACT [] synonym: "tunica adventitia (ureter)" EXACT LATIN [FMA:15892, FMA:TA] synonym: "tunica adventitia ureteris" EXACT LATIN [FMA:15892, FMA:TA] synonym: "ureter adventitia" EXACT [] synonym: "ureteral adventitia" EXACT [] xref: EMAPA:28114 xref: FMA:15892 xref: MA:0002652 xref: SCTID:392273001 xref: SCTID:47879001 is_a: UBERON:0005742 ! adventitia intersection_of: UBERON:0005742 ! adventitia intersection_of: part_of UBERON:0000056 ! ureter relationship: part_of UBERON:0000056 ! ureter relationship: part_of UBERON:0009916 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! wall of ureter [Term] id: UBERON:0001253 name: lamina propria of ureter def: "A lamina propria that is part of a ureter [Automatically generated definition]." [OBOL:automatic] synonym: "lamina propria mucosa of ureter" EXACT [OBOL:automatic] synonym: "lamina propria mucosae of ureter" EXACT [OBOL:automatic] synonym: "ureter lamina propria" EXACT [] synonym: "ureter lamina propria mucosa" EXACT [OBOL:automatic] synonym: "ureter lamina propria mucosae" EXACT [OBOL:automatic] xref: EMAPA:28841 xref: FMA:15896 xref: MA:0002653 xref: SCTID:2771005 is_a: UBERON:0000030 ! lamina propria intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0000056 ! ureter relationship: part_of UBERON:0000056 ! ureter relationship: part_of UBERON:0001008 ! renal system relationship: part_of UBERON:0004980 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! mucosa of ureter relationship: part_of UBERON:0009916 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! wall of ureter [Term] id: UBERON:0001254 name: urothelium of ureter def: "The luminal epithelium of the tube that conducts the urine from the renal pelvis to the bladder[MP]" [MP:0000535] subset: pheno_slim synonym: "transitional epithelium of ureter" EXACT [] synonym: "ureter luminal urothelium" RELATED INCONSISTENT [MP:0000535] synonym: "ureter transitional epithelium" EXACT [] synonym: "ureter urothelium" EXACT [] xref: EMAPA:28089 xref: FMA:15897 xref: MA:0002655 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0000365 ! urothelium is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000365 ! urothelium intersection_of: part_of UBERON:0000056 ! ureter relationship: contributes_to_morphology_of UBERON:0000056 ! ureter relationship: part_of UBERON:0000056 ! ureter property_value: external_ontology_notes "MP treats ureter urothelium and ureter luminal urothelium as exact synonyms, yes MA treats these as distinct; see also: transitional epithelium vs urothelium" xsd:string {external_ontology="MP"} [Term] id: UBERON:0001255 name: urinary bladder def: "distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]." [MGI:anna, Wikipedia:Urinary_bladder] subset: efo_slim subset: major_organ subset: organ_slim subset: pheno_slim subset: uberon_slim synonym: "bladder" BROAD [EHDAA2:0000174] synonym: "urocyst" RELATED [Wikipedia:Urinary_bladder] synonym: "vesica" RELATED [BTO:0001418] synonym: "vesica urinaria" EXACT LATIN [Wikipedia:Urinary_bladder] xref: AAO:0000623 xref: BTO:0001418 xref: CALOHA:TS-1090 xref: EFO:0000290 xref: EHDAA2:0000174 xref: EHDAA:9328 xref: EMAPA:18321 xref: EV:0100098 xref: FMA:15900 xref: GAID:0000004 xref: galen:UrinaryBladder xref: MA:0000380 xref: MAT:0000122 xref: MESH:A05.810.161 xref: MIAA:0000122 xref: NCIT:C12414 xref: OpenCyc:Mx4rvVjMmZwpEbGdrcN5Y29ycA xref: SCTID:302512001 xref: UMLS:C0005682 {source="ncithesaurus:Bladder"} xref: VHOG:0000740 xref: Wikipedia:Urinary_bladder xref: XAO:0000154 is_a: UBERON:0018707 {source="BTO"} ! bladder organ relationship: develops_from UBERON:0000164 {notes="upper part of UG sinus"} ! primitive urogenital sinus relationship: located_in UBERON:0002323 ! coelemic cavity lumen relationship: never_in_taxon NCBITaxon:8782 {editor="BGEE:Ann", id="GOTAX:0010073", source="https://github.com/obophenotype/uberon/issues/454"} relationship: part_of UBERON:0001556 {source="FMA"} ! lower urinary tract property_value: depicted_by Urinary:system.svg xsd:anyURI property_value: external_definition "A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000740", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: external_definition "Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000623", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "vesical" xsd:string property_value: homology_notes "In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000740", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.577-78", source="http://bgee.unil.ch/"} property_value: taxon_notes "The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454]" xsd:string [Term] id: UBERON:0001256 name: wall of urinary bladder def: "An anatomical wall that lines the insider of a urinary bladder." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "anatomical wall of bladder" EXACT [OBOL:automatic] synonym: "anatomical wall of urinary bladder" EXACT [OBOL:automatic] synonym: "bladder anatomical wall" EXACT [OBOL:automatic] synonym: "bladder wall" EXACT [OBOL:automatic] synonym: "urinary bladder anatomical wall" EXACT [OBOL:automatic] synonym: "urinary bladder wall" EXACT [] synonym: "wall of bladder" EXACT [OBOL:automatic] xref: BTO:0001462 xref: EMAPA:35175 xref: FMA:15902 xref: MA:0002493 xref: NCIT:C48941 xref: SCTID:362225003 xref: UMLS:C0458421 {source="ncithesaurus:Bladder_Wall"} is_a: UBERON:0000060 ! anatomical wall intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001255 ! urinary bladder [Term] id: UBERON:0001257 name: trigone of urinary bladder def: "the smooth triangular region of the wall of the urinary bladder formed by the two ureteral orifices and the internal urethral orifice; it is an area in which the muscle fibers are closely adherent to the mucosa" [MGI:anna, MP:0011768] subset: pheno_slim subset: uberon_slim synonym: "bladder trigone" EXACT [] synonym: "deep trigone" EXACT [] synonym: "dorsal bladder neck" RELATED [EMAPA:35174] synonym: "Lieutaud's trigone" EXACT [] synonym: "musculus trigoni vesicae profundus" EXACT LATIN [FMA:15910, FMA:TA] synonym: "trigone of bladder" EXACT [] synonym: "trigonum vesicae" EXACT LATIN [FMA:15910, FMA:TA] synonym: "trigonum vesicae urinariae" RELATED LATIN [Wikipedia:Trigone_of_urinary_bladder] synonym: "urinary bladder trigone" EXACT [] synonym: "vesical trigone" EXACT [] xref: EMAPA:35174 xref: FMA:15910 xref: galen:TrigoneOfUrinaryBladder xref: MA:0002492 xref: NCIT:C12331 xref: SCTID:272663002 xref: UMLS:C0447586 {source="ncithesaurus:Bladder_Trigone"} xref: Wikipedia:Trigone_of_urinary_bladder is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure relationship: contributes_to_morphology_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0006082 ! fundus of urinary bladder property_value: depicted_by Illu:bladder.jpg xsd:anyURI property_value: development_notes "Embryologically, the trigone of the bladder is derived from the caudal end of mesonephric ducts, which is of mesodermal origin (the rest of the bladder is endodermal). In the female the mesonephric ducts regresses, causing the trigone to be less prominent, but still present" xsd:string {source="WP"} property_value: function_notes "The area is very sensitive to expansion and once stretched to a certain degree, the urinary bladder signals the brain of its need to empty. The signals become stronger as the bladder continues to fill." xsd:string [Term] id: UBERON:0001258 name: neck of urinary bladder def: "The constricted portion of the urinary bladder, formed by the meeting of its inferolateral surfaces proximal to the opening of the urethra[MP]." [MP:anna, Wikipedia:Neck_of_urinary_bladder] subset: pheno_slim subset: uberon_slim synonym: "bladder neck" EXACT [] synonym: "cervix vesicae" EXACT LATIN [FMA:15912, FMA:TA] synonym: "cervix vesicae urinariae" RELATED LATIN [Wikipedia:Neck_of_urinary_bladder] synonym: "collum vesicae" EXACT LATIN [FMA:15912, FMA:TA] synonym: "neck of bladder" EXACT [] synonym: "urinary bladder neck" EXACT [] synonym: "vesical neck" EXACT [] xref: EMAPA:36078 xref: FMA:15912 xref: galen:UrinaryBladderNeck xref: MA:0002491 xref: NCIT:C12336 xref: SCTID:362227006 xref: UMLS:C0227716 {source="ncithesaurus:Bladder_Neck"} xref: Wikipedia:Neck_of_urinary_bladder is_a: UBERON:0001560 ! neck of organ is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001560 ! neck of organ intersection_of: part_of UBERON:0001255 ! urinary bladder relationship: contributes_to_morphology_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001255 ! urinary bladder property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/6/63/Gray1156.png xsd:anyURI [Term] id: UBERON:0001259 name: mucosa of urinary bladder def: "the mucous membrane lining the urinary bladder" [MGI:anna, MP:0011766] subset: efo_slim subset: pheno_slim synonym: "bladder mucosa" EXACT [] synonym: "bladder mucous membrane" EXACT [OBOL:automatic] synonym: "bladder organ mucosa" EXACT [OBOL:automatic] synonym: "mucosa of bladder" EXACT [OBOL:automatic] synonym: "mucous membrane of bladder" EXACT [] synonym: "mucous membrane of urinary bladder" EXACT [] synonym: "tunica mucosa (vesica urinaria)" EXACT LATIN [FMA:15928, FMA:TA] synonym: "tunica mucosa vesicae" EXACT LATIN [FMA:15928, FMA:TA] synonym: "tunica mucosa vesicae urinariae" EXACT [MP:MP] synonym: "urinary bladder mucosa" EXACT [] synonym: "urinary bladder mucous membrane" EXACT [OBOL:automatic] xref: EFO:0000293 xref: EMAPA:35897 xref: FMA:15928 xref: galen:MucousMembraneOfUrinaryBladder xref: MA:0001692 xref: NCIT:C32205 xref: SCTID:362224004 xref: UMLS:C0227691 {source="ncithesaurus:Bladder_Mucosa"} is_a: UBERON:0000344 ! mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001255 ! urinary bladder relationship: contributes_to_morphology_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001256 ! wall of urinary bladder [Term] id: UBERON:0001260 name: serosa of urinary bladder def: "A serous membrane that is part of a urinary bladder [Automatically generated definition]." [OBOL:automatic] synonym: "bladder serosa" EXACT [] synonym: "bladder serous membrane" EXACT [OBOL:automatic] synonym: "serosa of bladder" EXACT [] synonym: "serous coat of bladder" EXACT [] synonym: "serous coat of urinary bladder" EXACT [] synonym: "serous membrane of bladder" EXACT [OBOL:automatic] synonym: "serous membrane of urinary bladder" EXACT [OBOL:automatic] synonym: "tunica serosa (vesica urinaria)" EXACT LATIN [FMA:15932, FMA:TA] synonym: "tunica serosa vesicae" EXACT LATIN [FMA:15932, FMA:TA] synonym: "urinary bladder serosa" EXACT [] synonym: "urinary bladder serous membrane" EXACT [OBOL:automatic] synonym: "visceral peritoneum of urinary bladder" EXACT [] xref: EMAPA:28661 xref: FMA:15932 xref: MA:0001696 xref: SCTID:5868002 is_a: UBERON:0000042 ! serous membrane intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001256 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! wall of urinary bladder property_value: editor_note "TODO - check serosa/peritoneum" xsd:string [Term] id: UBERON:0001261 name: lamina propria of urinary bladder def: "A lamina propria that is part of a urinary bladder [Automatically generated definition]." [OBOL:automatic] synonym: "bladder lamina propria" EXACT [OBOL:automatic] synonym: "bladder lamina propria mucosa" EXACT [OBOL:automatic] synonym: "bladder lamina propria mucosae" EXACT [OBOL:automatic] synonym: "lamina propria mucosa of bladder" EXACT [OBOL:automatic] synonym: "lamina propria mucosa of urinary bladder" EXACT [OBOL:automatic] synonym: "lamina propria mucosae of bladder" EXACT [OBOL:automatic] synonym: "lamina propria mucosae of urinary bladder" EXACT [OBOL:automatic] synonym: "lamina propria of bladder" EXACT [OBOL:automatic] synonym: "urinary bladder lamina propria" EXACT [] synonym: "urinary bladder lamina propria mucosa" EXACT [OBOL:automatic] synonym: "urinary bladder lamina propria mucosae" EXACT [OBOL:automatic] xref: EMAPA:30088 xref: FMA:15935 xref: MA:0001695 xref: NCIT:C48940 xref: UMLS:C1706967 {source="ncithesaurus:Bladder_Lamina_Propria"} is_a: UBERON:0000030 ! lamina propria intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001256 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! wall of urinary bladder relationship: part_of UBERON:0001259 ! mucosa of urinary bladder property_value: structure_notes "Contains loose to dense connective tissue, variably sized blood vessels that may be close to epithelium, lymphatics, variable adipose tissue" xsd:string [Term] id: UBERON:0001262 name: wall of intestine def: "An anatomical wall that is part of a intestine [Automatically generated definition]." [OBOL:automatic] synonym: "anatomical wall of bowel" EXACT [OBOL:automatic] synonym: "anatomical wall of intestine" EXACT [OBOL:automatic] synonym: "bowel anatomical wall" EXACT [OBOL:automatic] synonym: "bowel wall" EXACT [OBOL:automatic] synonym: "bowel wall" RELATED [MA:0001525] synonym: "intestinal wall" EXACT [] synonym: "intestine anatomical wall" EXACT [OBOL:automatic] synonym: "intestine wall" EXACT [] synonym: "wall of bowel" EXACT [OBOL:automatic] xref: BTO:0000647 xref: EMAPA:35444 xref: FMA:15949 xref: MA:0001525 xref: MA:0002693 xref: NCIT:C49478 xref: UMLS:C1708548 {source="ncithesaurus:Intestinal_Wall_Tissue"} intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0000160 ! intestine property_value: editor_note "we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different" xsd:string [Term] id: UBERON:0001263 name: pancreatic acinus def: "The secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct." [MP:0009145] subset: pheno_slim synonym: "acinus pancreaticus" EXACT LATIN [FMA:16011] synonym: "pancreas acinus" EXACT [] synonym: "pancreatic acinar" RELATED [TEMP:MP] synonym: "pancreatic acini" RELATED PLURAL [] xref: EMAPA:35651 xref: FMA:16011 xref: MA:0002417 xref: NCIT:C49268 xref: SCTID:247604006 xref: UMLS:C0227578 {source="ncithesaurus:Pancreatic_Acinus"} is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0013232 ! serous acinus intersection_of: UBERON:0009842 ! glandular acinus intersection_of: part_of UBERON:0000017 ! exocrine pancreas relationship: composed_primarily_of CL:0002064 relationship: contributes_to_morphology_of UBERON:0000017 ! exocrine pancreas relationship: part_of UBERON:0000017 ! exocrine pancreas relationship: part_of UBERON:0007324 {source="FMA"} ! pancreatic lobule [Term] id: UBERON:0001264 name: pancreas def: "An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]." [GO:0031016] subset: efo_slim subset: major_organ subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core xref: AAO:0010112 xref: BTO:0000988 xref: CALOHA:TS-0736 xref: EFO:0000855 xref: EHDAA2:0001367 xref: EHDAA:6893 xref: EMAPA:17503 xref: EV:0100092 xref: FMA:7198 xref: GAID:334 xref: galen:Pancreas xref: MA:0000120 xref: MAT:0000075 xref: MESH:D010179 xref: MIAA:0000075 xref: NCIT:C12393 xref: OpenCyc:Mx4rvVimZZwpEbGdrcN5Y29ycA xref: SCTID:181277001 xref: TAO:0000140 xref: UMLS:C0030274 {source="ncithesaurus:Pancreas"} xref: VHOG:0000050 xref: Wikipedia:Pancreas xref: XAO:0000136 xref: ZFA:0000140 is_a: CARO:0000000 is_a: UBERON:0002075 ! viscus disjoint_from: UBERON:0010264 ! hepatopancreas relationship: has_developmental_contribution_from UBERON:0003922 ! pancreatic epithelial bud relationship: has_developmental_contribution_from UBERON:0003923 {source="Wikipedia"} ! dorsal pancreatic bud relationship: has_developmental_contribution_from UBERON:0003924 {source="Wikipedia"} ! ventral pancreatic bud relationship: has_part UBERON:0000016 ! endocrine pancreas relationship: has_part UBERON:0000017 {gci_relation="part_of", gci_filler="NCBITaxon:89593"} ! exocrine pancreas relationship: located_in UBERON:0002323 ! coelemic cavity lumen relationship: only_in_taxon NCBITaxon:7742 {source="PMID:16417468"} property_value: depicted_by https://upload.wikimedia.org/wikipedia/commons/7/7e/Blausen_0699_PancreasAnatomy2.png xsd:anyURI property_value: external_definition "Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010112", ontology="AAO", source="AAO:BJB"} property_value: function_notes "The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans" xsd:string {source="PMID:16417468"} property_value: has_relational_adjective "pancreatic" xsd:string property_value: homology_notes "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000050", 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/"} property_value: taxon_notes "As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52)" xsd:string {source="PMID:20959416"} property_value: taxon_notes "The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm" xsd:string [Term] id: UBERON:0001265 name: trabecula of spleen def: "A trabecula that is part of a spleen." [OBOL:automatic] synonym: "spleen trabeculum" EXACT [] synonym: "splenic trabecula" EXACT [] xref: EMAPA:35808 xref: FMA:16027 xref: MA:0000758 xref: NCIT:C33607 xref: SCTID:61987002 xref: UMLS:C0229688 {source="ncithesaurus:Splenic_Trabecula"} xref: Wikipedia:Trabeculae_of_spleen is_a: UBERON:0000440 ! trabecula is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000440 ! trabecula intersection_of: part_of UBERON:0002106 ! spleen relationship: part_of UBERON:0002106 ! spleen relationship: part_of UBERON:1000024 {source="FMA"} ! parenchyma of spleen [Term] id: UBERON:0001266 name: splenic cord def: "A structure found in the red pulp of the spleen between the sinusoids, consisting of fibrils and connective tissue cells with a large population of monocytes and macrophages. These cords contain half of the human body's monocytes as a reserve so that after tissue injury these monocytes can move in and aid locally sourced monocytes in wound healing. Erythrocytes pass through the cords of Billroth before entering the sinusoids. The passage into the sinusoids may be seen as a bottleneck, where erythrocytes need to be flexible in order to pass through. In disorders of erythrocyte shape and/or flexibility, such as hereditary spherocytosis, erythrocytes fail to pass through and get phagocytosed, causing extravascular hemolysis." [Wikipedia:Cords_of_Billroth] synonym: "cord of Billroth" EXACT [Wikipedia:Cords_of_Billroth] synonym: "cord of Bilroth" EXACT [FMA:16031] xref: EMAPA:37752 {source="MA:th"} xref: FMA:16031 xref: MA:0002671 xref: NCIT:C33599 xref: UMLS:C0735011 {source="ncithesaurus:Splenic_Cord"} xref: Wikipedia:Cords_of_Billroth is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0001250 {source="MA"} ! red pulp of spleen [Term] id: UBERON:0001267 name: femoral nerve def: "The femoral nerve, the largest branch of the lumbar plexus, arises from the ventral divisions of the second, third, and fourth lumbar nerves. It descends through the fibers of the Psoas major, emerging from the muscle at the lower part of its lateral border, and passes down between it and the Iliacus, behind the iliac fascia; it then runs beneath the inguinal ligament, into the thigh, and splits into an anterior and a posterior division. Under the inguinal ligament, it is separated from the femoral artery by a portion of the Psoas major. [WP,unvetted]." [Wikipedia:Femoral_nerve] subset: uberon_slim synonym: "anterior crural nerve" EXACT [] synonym: "nervus femoralis" RELATED LATIN [Wikipedia:Femoral_nerve] xref: EHDAA2:0000507 xref: EHDAA:5655 xref: EMAPA:35343 xref: FMA:16486 xref: GAID:850 xref: MA:0001167 xref: MESH:D005267 xref: NCIT:C52816 xref: OpenCyc:Mx4rwGC03JwpEbGdrcN5Y29ycA xref: SCTID:181051004 xref: UMLS:C0015808 {source="ncithesaurus:Femoral_Nerve"} xref: VHOG:0001411 xref: Wikipedia:Femoral_nerve is_a: CARO:0001001 is_a: UBERON:0003431 ! leg nerve relationship: innervates UBERON:0004482 ! musculature of lower limb relationship: part_of UBERON:0000978 ! leg property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/7/7c/Gray823.png xsd:anyURI [Term] id: UBERON:0001268 name: peritoneal fluid def: "Transudate contained in the peritoneal cavity." [FMA:16515] subset: pheno_slim subset: uberon_slim xref: BTO:0001031 xref: EMAPA:35683 xref: FMA:16515 xref: MA:0002531 xref: ncithesaurus:Peritoneal_Fluid xref: Wikipedia:Peritoneal_fluid is_a: UBERON:0007779 ! transudate is_a: UBERON:0007794 {source="FMA"} ! secretion of serous gland is_a: UBERON:0036217 ! coelomic fluid intersection_of: UBERON:0007779 ! transudate intersection_of: located_in UBERON:0001179 ! peritoneal cavity relationship: located_in UBERON:0001179 ! peritoneal cavity [Term] id: UBERON:0001269 name: acetabular part of hip bone def: "The acetabulum is a concave surface of the pelvis. The head of the femur meets with the pelvis at the acetabulum, forming the hip joint. There are three bones of the os coxae (hip bone) that come together to form the acetabulum. Contributing a little more than two-fifths of the structure is the ischium, which provides lower and side boundaries to the acetabulum. The ilium forms the upper boundary, providing a little less than two-fifths of the structure of the acetabulum. The rest is formed by the pubis, near the midline. It is bounded by a prominent uneven rim, which is thick and strong above, and serves for the attachment of the acetabular labrum, which reduces its opening, and deepens the surface for formation of the hip joint. At the lower part of the acetabulum is the acetabular notch, which is continuous with a circular depression, the acetabular fossa, at the bottom of the cavity of the acetabulum. The rest of the acetabulum is formed by a curved, crescent-moon shaped surface, the lunate surface, where the joint is made with the head of the femur. Its counterpart in the pectoral girdle is the glenoid fossa.[WP,unvetted]." [Wikipedia:Acetabulum] subset: pheno_slim subset: uberon_slim synonym: "acetabular region" EXACT [VHOG:0000974] synonym: "acetabulum" EXACT [MA:0001335] xref: AAO:0000770 xref: EHDAA:10661 xref: EMAPA:18346 xref: FMA:16579 xref: GAID:206 xref: MA:0001335 xref: MESH:A02.835.232.611.108 xref: NCIT:C32042 xref: OpenCyc:Mx4rwJlP9ZwpEbGdrcN5Y29ycA xref: RETIRED_EHDAA2:0001427 xref: SCTID:182027007 xref: UMLS:C0000962 {source="ncithesaurus:Acetabulum"} xref: VHOG:0000974 xref: Wikipedia:Acetabulum is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005913 {source="FMA"} ! zone of bone organ is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001273 {source="Phenoscape"} ! ilium relationship: part_of UBERON:0001486 {source="FMA"} ! hip joint property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/2/29/Illu_pelvic_girdle.jpg xsd:anyURI property_value: external_definition "Cavity for the articulation of the proximal bone of the hind limb.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000770", ontology="AAO", source="AAO:LAP"} property_value: external_ontology_notes "whilst WP defines this as a surface, MA treats it as a bone. There are other FMA classes that may be better suited to representing the surface." xsd:string {external_ontology="MA"} property_value: homology_notes "During the transformation from the osteolepiform fins to tetrapod limbs, the appendages and girdles underwent a number of radical changes. The pelvic girdle became a weight-bearing structure by evolution of an ischium, a full mesio-ventral contact between the two sides of the girdle, an ilium, and a contact between the vertebral column and the girdle through a sacral rib. Fore- and hindlimbs shifted laterally by reorientation of the glenoid and the acetabulum.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000974", ontology="VHOG", source="DOI:10.1038/nature04119 Boisvert CA, The pelvic fin and girdle of Panderichthys and the origin of tetrapod locomotion. Nature (2005)", source="http://bgee.unil.ch/"} property_value: taxon_notes "In reptiles and in birds, the acetabula are deep sockets." xsd:string {source="WP"} [Term] id: UBERON:0001270 name: bony pelvis def: "A ring of bone formed by the sacrum and the first few coccygeal vertebrae as the roof, the pubis and ischia as the floor and the ilia and the acetabular part of the ischia as the walls." [http://medical-dictionary.thefreedictionary.com/bony+pelvis] synonym: "pelvis ossea" EXACT [] synonym: "skeletal system of pelvis" EXACT [FMA:16580] xref: FMA:16580 xref: SCTID:46633002 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system is_a: UBERON:0010314 ! structure with developmental contribution from neural crest disjoint_from: UBERON:0002355 ! pelvic region of trunk relationship: has_part UBERON:0001274 ! ischium relationship: has_part UBERON:0001275 ! pubis relationship: has_part UBERON:0003690 ! fused sacrum property_value: editor_note "TODO add taxon-specific part of relations connecting sub-structures to this." xsd:string property_value: external_ontology_notes "in FMA, this is part of the axial skeletal system" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0001271 name: pelvic girdle region def: "The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions." [DOI:10.1002/dvdy.22617, FMA:16581, FMA:23217, https://groups.google.com/d/topic/obo-anatomy/h4R4xKmINrw/discussion, https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] subset: uberon_slim subset: vertebrate_core synonym: "girdle - pelvic" RELATED [] synonym: "pelvic girdle" RELATED INCONSISTENT [] xref: EMAPA:37862 {source="MA:th"} xref: FMA:16581 xref: NCIT:C33291 xref: SCTID:360010001 xref: UMLS:C0684083 {source="ncithesaurus:Pelvic_Girdle"} xref: VSAO:0000304 is_a: UBERON:0007823 ! appendage girdle region intersection_of: UBERON:0007823 ! appendage girdle region intersection_of: part_of UBERON:0010709 ! pelvic complex disjoint_from: UBERON:0007832 ! pelvic girdle skeleton relationship: has_skeleton UBERON:0007832 ! pelvic girdle skeleton relationship: in_lateral_side_of UBERON:0002355 ! pelvic region of trunk relationship: part_of UBERON:0002355 ! pelvic region of trunk relationship: part_of UBERON:0010709 ! pelvic complex property_value: curator_notes "this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented" xsd:string property_value: external_definition "Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000304", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} [Term] id: UBERON:0001272 name: innominate bone def: "A fused bone consisting of the ilium, ischium and and pubis. Together with the sacrum and coccyx, it comprises the pelvis. [WP,modified]." [https://github.com/obophenotype/uberon/issues/290, https://orcid.org/0000-0002-6601-2165, Wikipedia:Hip_bone] subset: uberon_slim synonym: "basipterygium" RELATED [] synonym: "bone of pelvic girdle" BROAD [FMA:16585] synonym: "coxal bone" EXACT [FMA:16585] synonym: "hip bone" EXACT [FMA:16585] synonym: "innominate" BROAD [] synonym: "innominate bone" EXACT [FMA:16585] synonym: "os coxa" EXACT LATIN [] synonym: "os coxae" EXACT LATIN [FMA:16585, FMA:TA] synonym: "os innominatum" RELATED LATIN [Wikipedia:Hip_bone] synonym: "pelvic bone" EXACT [FMA:16585] xref: FMA:16585 xref: GAID:205 xref: MESH:A02.835.232.611 xref: SCTID:361776002 xref: Wikipedia:Hip_bone is_a: UBERON:0007830 ! pelvic girdle bone/zone is_a: UBERON:0010428 {source="FMA"} ! flat bone is_a: UBERON:0015212 ! lateral structure relationship: in_lateral_side_of UBERON:0007832 ! pelvic girdle skeleton relationship: part_of UBERON:0001464 {source="FMA"} ! hip relationship: part_of UBERON:0007832 ! pelvic girdle skeleton property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray341.png xsd:anyURI property_value: editor_note "currently this class is restricted to exclude the teleost bone as the definition mentions ilium, ischium and pubis. In future we may add a grouping class for girdle bones that supports the appendage" xsd:string property_value: external_ontology_notes "in FMA this is a paired structure. NCITA has 'pelvic bone' but this is the *superclass* of ilium/ischium/pubis. The MA class 'pelvis bone' is actually a superclass of 'pelvic girdle bone' and caudal/sacral vertebra." xsd:string {external_ontology="FMA"} property_value: taxon_notes "The hip/pelvic bone/basipterygium first appears in fishes, where it consists of a simple, usually triangular bone, to which the pelvic fin articulates. The hip bones on each side usually connect with each other at the forward end, and are even solidly fused in lungfishes and sharks, but they never attach to the vertebral column" xsd:string {source="WP"} [Term] id: UBERON:0001273 name: ilium def: "Paired endochondral bone that is the dorsal-most of the pelvic bones, offering attachment areas for gluteal muscles on its main surface [PHENOSCAPE:ad]." [https://github.com/obophenotype/uberon/issues/105, https://github.com/obophenotype/uberon/issues/60, PHENOSCAPE:ad] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "iliac bone" EXACT [EMAPA:18726] synonym: "ilium bone" EXACT [] synonym: "illium" RELATED [] synonym: "os iliacum" EXACT [] synonym: "os ilii" EXACT [] synonym: "os ilium" EXACT LATIN [FMA:16589, FMA:TA] xref: AAO:0000772 xref: CALOHA:TS-2200 xref: EFO:0003049 xref: EMAPA:18726 xref: FMA:16589 xref: GAID:207 xref: galen:Ilium xref: MA:0001336 xref: MESH:A02.835.232.611.434 xref: NCIT:C32765 xref: OpenCyc:Mx4rvhwFJ5wpEbGdrcN5Y29ycA xref: SCTID:182029005 xref: UMLS:C0020889 {source="ncithesaurus:Ilium"} xref: Wikipedia:Ilium_(bone) is_a: UBERON:0002513 ! endochondral bone is_a: UBERON:0007830 ! pelvic girdle bone/zone is_a: UBERON:0015054 ! iliac endochondral element is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0015054 ! iliac endochondral element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: composed_primarily_of UBERON:0002481 ! bone tissue relationship: contributes_to_morphology_of UBERON:0007830 ! pelvic girdle bone/zone relationship: dc-contributor https://github.com/cmungall relationship: dc-contributor https://github.com/mellybelly relationship: develops_from UBERON:0010714 {source="cjm"} ! iliac cartilage element relationship: dubious_for_taxon NCBITaxon:8570 {source="Wikipedia"} relationship: in_lateral_side_of UBERON:0007832 ! pelvic girdle skeleton relationship: never_in_taxon NCBITaxon:32443 {source="Wikipedia"} relationship: part_of UBERON:0001272 {source="FMA"} ! innominate bone relationship: part_of UBERON:0007832 {source="VSAO"} ! pelvic girdle skeleton property_value: external_definition "Paired, rodlike endochondral bones that constitute the anterior pelvic girdle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000772", ontology="AAO", source="AAO:LAP"} property_value: external_ontology_notes "this is_a hip bone in MA." xsd:string {external_ontology="MA"} property_value: has_relational_adjective "iliac" xsd:string property_value: taxon_notes "All reptiles have an ilium except snakes, although some snake species have a ti