diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 961ec842c..9f9438efe 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -290,7 +290,7 @@ intersection_of: UBERON:0000161 ! orifice intersection_of: connects UBERON:0001707 ! nasal cavity intersection_of: part_of UBERON:0005725 ! olfactory system 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 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000033 {source="ZFA"} ! head 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"} @@ -338,7 +338,7 @@ 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 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata 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 @@ -456,7 +456,7 @@ relationship: has_part CL:0000642 {source="ZFA"} ! folliculostellate cell relationship: has_part UBERON:0002196 ! adenohypophysis relationship: has_part UBERON:0002198 ! neurohypophysis relationship: immediate_transformation_of UBERON:0034875 {source="https://orcid.org/0000-0003-3308-6245"} ! future pituitary gland -relationship: only_in_taxon NCBITaxon:7742 {source="PMID:19084529"} ! Vertebrata +relationship: in_taxon NCBITaxon:7742 {source="PMID:19084529"} ! Vertebrata relationship: part_of UBERON:0001894 {source="MA", source="ZFA"} ! diencephalon property_value: depiction "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"} @@ -487,7 +487,7 @@ 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 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI property_value: depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI property_value: has_relational_adjective "submucosal" xsd:string @@ -792,7 +792,7 @@ xref: TGMA:0000024 xref: Wikipedia:Compound_eye intersection_of: UBERON:0000970 ! eye intersection_of: composed_primarily_of UBERON:0000971 ! ommatidium -relationship: only_in_taxon NCBITaxon:6656 {source="PMID:21062451"} ! Arthropoda +relationship: in_taxon NCBITaxon:6656 {source="PMID:21062451"} ! Arthropoda 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"} @@ -906,8 +906,8 @@ xref: Wikipedia:Feather is_a: UBERON:0000021 ! cutaneous appendage relationship: develops_from UBERON:0001003 ! skin epidermis relationship: has_part GO:0045095 ! keratin filament +relationship: in_taxon NCBITaxon:436491 ! Theropoda relationship: never_in_taxon NCBITaxon:314146 ! Euarchontoglires -relationship: only_in_taxon NCBITaxon:436491 ! Theropoda property_value: depiction "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 @@ -931,6 +931,7 @@ xref: Wikipedia:Wing intersection_of: UBERON:0000026 ! appendage intersection_of: has_quality PATO:0002236 ! aliform relationship: capable_of_part_of GO:0060361 ! flight +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: never_in_taxon NCBITaxon:118072 {source="bgee"} ! Coelacanthimorpha relationship: never_in_taxon NCBITaxon:186634 {source="bgee", seeAlso="Wikipedia:Flying_fish"} ! Otomorpha relationship: never_in_taxon NCBITaxon:314147 {source="bgee"} ! Glires @@ -942,7 +943,6 @@ relationship: never_in_taxon NCBITaxon:9254 {source="bgee"} ! Prototheria relationship: never_in_taxon NCBITaxon:9263 {source="bgee"} ! Metatheria relationship: never_in_taxon NCBITaxon:9443 {source="bgee"} ! Primates relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria property_value: has_relational_adjective "alar" xsd:string property_value: taxon_notes "This class is not monophyletic. See also: GO:0007629" xsd:string @@ -996,7 +996,7 @@ xref: VSAO:0000075 xref: Wikipedia:Appendage xref: XAO:0000218 is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa 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 @@ -1138,8 +1138,8 @@ 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: in_taxon NCBITaxon:33213 ! Bilateria relationship: mutually_spatially_disjoint_with UBERON:0000948 ! heart -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria 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"} @@ -1280,9 +1280,9 @@ subset: uberon_slim xref: Wikipedia:Leydig's_organ is_a: UBERON:0004177 ! hemopoietic organ relationship: composed_primarily_of CL:0000738 {source="Honma1983"} ! leukocyte +relationship: in_taxon NCBITaxon:7778 {source="Wikipedia"} ! Elasmobranchii relationship: located_in UBERON:0001096 ! wall of esophagus relationship: never_in_taxon NCBITaxon:7863 {source="Wikipedia"} ! Holocephali -relationship: only_in_taxon NCBITaxon:7778 {source="Wikipedia"} ! Elasmobranchii 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 @@ -1367,7 +1367,7 @@ relationship: connects UBERON:0001474 ! bone element relationship: connects UBERON:0001630 ! muscle organ relationship: has_part CL:0000057 {source="AEO"} ! fibroblast relationship: has_part CL:0000327 {source="AEO"} ! extracellular matrix secreting cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002204 {source="OG"} ! musculoskeletal system property_value: depiction "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"} @@ -1512,7 +1512,7 @@ subset: grouping_class subset: uberon_slim xref: Wikipedia:Pinhole_eye is_a: UBERON:0000047 ! simple eye -relationship: only_in_taxon NCBITaxon:32577 ! Nautiloidea +relationship: in_taxon NCBITaxon:32577 ! Nautiloidea [Term] id: UBERON:0000049 @@ -1794,7 +1794,7 @@ xref: XAO:0000131 is_a: UBERON:0000062 ! organ is_a: UBERON:0004921 {source="cjm"} ! subdivision of digestive tract relationship: contributes_to_morphology_of UBERON:0000160 ! intestine -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata 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/"} @@ -2058,7 +2058,7 @@ xref: FBdv:00005349 xref: Wikipedia:Pupa is_a: UBERON:0000105 ! life cycle stage relationship: immediately_preceded_by UBERON:0000069 ! larval stage -relationship: only_in_taxon NCBITaxon:33392 ! Endopterygota +relationship: in_taxon NCBITaxon:33392 ! Endopterygota 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"} ! pupal development property_value: seeAlso "https://github.com/obophenotype/uberon/issues/562" xsd:anyURI @@ -2165,7 +2165,7 @@ 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 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0001434 ! skeletal system [Term] @@ -2893,7 +2893,7 @@ xref: WBls:0000010 xref: XAO:1000005 xref: ZFS:0000047 is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage relationship: simultaneous_with GO:0007369 ! gastrulation @@ -2909,7 +2909,7 @@ xref: MmusDv:0000017 xref: XAO:1000006 is_a: UBERON:0000105 ! life cycle stage relationship: dubious_for_taxon NCBITaxon:7955 ! Danio rerio -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage relationship: simultaneous_with GO:0001841 ! neural tube formation @@ -2930,7 +2930,7 @@ xref: OGES:000005 xref: OGES:000032 xref: Wikipedia:Organogenesis is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000110 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! neurula stage relationship: simultaneous_with GO:0048513 ! animal organ development @@ -3025,7 +3025,7 @@ 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 -relationship: has_part CL:0000322 ! pneumocyte +relationship: has_part CL:0000322 ! pulmonary alveolar epithelial cell relationship: part_of UBERON:0002299 {source="GO"} ! alveolus of lung [Term] @@ -3191,7 +3191,7 @@ 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"} ! Chordata +relationship: in_taxon NCBITaxon:7711 {notes="we limit this structure by definition to chordate and vertebrate nervous systems"} ! Chordata 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 @@ -3338,13 +3338,13 @@ 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 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria [Term] id: UBERON:0000154 name: posterior region of body is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria [Term] id: UBERON:0000155 @@ -3541,7 +3541,7 @@ xref: Wikipedia:Cloaca xref: XAO:0000244 xref: ZFA:0005781 is_a: UBERON:0013522 ! subdivision of tube -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata 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."} ! Tenrecidae @@ -3591,7 +3591,7 @@ xref: Wikipedia:Definitive_urogenital_sinus is_a: UBERON:0005423 ! developing anatomical structure relationship: contributes_to_morphology_of UBERON:0000163 ! embryonic cloaca relationship: develops_from UBERON:0003064 ! intermediate mesoderm -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000163 {source="MP-def"} ! embryonic cloaca relationship: part_of UBERON:0001008 {source="EHDAA2"} ! renal system property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI @@ -3654,7 +3654,7 @@ is_a: UBERON:0004921 {notes="the mouth contains structures such as jaw skeleton 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 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa property_value: depiction "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"} @@ -3800,8 +3800,8 @@ xref: UMLS:C0002638 {source="ncithesaurus:Amniotic_Fluid"} xref: VHOG:0001267 is_a: UBERON:0000463 ! organism substance relationship: functionally_related_to GO:0001701 ! in utero embryonic development +relationship: in_taxon NCBITaxon:32524 ! Amniota relationship: located_in UBERON:0000305 ! amnion -relationship: only_in_taxon NCBITaxon:32524 ! Amniota relationship: surrounds UBERON:0000922 ! embryo [Term] @@ -3841,7 +3841,7 @@ def: "A bodily fluid secreted from the body via the mouth or nose." [ENVO:020000 synonym: "oronasal discharge" NARROW [] xref: ENVO:02000035 is_a: UBERON:0000463 ! organism substance -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: produced_by UBERON:0001826 ! nasal cavity mucosa [Term] @@ -3854,7 +3854,7 @@ xref: galen:Pus xref: ncithesaurus:Pus xref: Wikipedia:Pus is_a: UBERON:0000463 ! organism substance -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: output_of GO:0006954 ! inflammatory response property_value: depiction "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"} @@ -3915,7 +3915,7 @@ is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa creation_date: 2009-04-08T04:38:19Z [Term] @@ -3977,7 +3977,7 @@ xref: Wikipedia:Gyrus is_a: UBERON:0034768 ! morphological feature relationship: dubious_for_taxon NCBITaxon:10088 ! Mus relationship: fma_set_term FMA:72015 -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0000956 ! cerebral cortex relationship: part_of UBERON:0001869 ! cerebral hemisphere relationship: surrounded_by UBERON:0013118 ! sulcus of brain @@ -4063,7 +4063,7 @@ synonym: "papulli" EXACT OMO:0003004 [] xref: Wikipedia:Papula is_a: UBERON:0002535 ! gill relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall -relationship: only_in_taxon NCBITaxon:7586 ! Echinodermata +relationship: in_taxon NCBITaxon:7586 ! Echinodermata creation_date: 2009-04-18T01:13:57Z [Term] @@ -4188,7 +4188,7 @@ xref: XAO:0004031 xref: ZFA:0001675 is_a: UBERON:0000062 ! organ relationship: has_part UBERON:0002384 ! connective tissue -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/9/9a/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"} @@ -4352,7 +4352,7 @@ relationship: has_developmental_contribution_from UBERON:0000924 {source="ISBN:0 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"} ! Amniota +relationship: in_taxon NCBITaxon:32524 {source="Hymans"} ! Amniota relationship: surrounds UBERON:0000922 ! embryo property_value: depiction "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/"} @@ -4824,8 +4824,8 @@ 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: in_taxon NCBITaxon:7711 ! Chordata relationship: mutually_spatially_disjoint_with UBERON:0000009 ! submucosa -relationship: only_in_taxon NCBITaxon:7711 ! Chordata property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI property_value: depiction "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"} @@ -4844,7 +4844,7 @@ is_a: UBERON:0000061 ! anatomical structure relationship: has_part CHEBI:36498 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! galactosylceramide relationship: has_part CHEBI:64583 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! sphingomyelin relationship: has_part PR:000010228 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! myelin basic protein -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001016 ! nervous system relationship: present_in_taxon NCBITaxon:6340 {source="http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html"} ! Annelida relationship: present_in_taxon NCBITaxon:6681 {source="http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html"} ! Malacostraca @@ -5003,7 +5003,7 @@ xref: Wikipedia:Parenchyma is_a: UBERON:0000064 ! organ part disjoint_from: UBERON:0003891 ! stroma relationship: capable_of GO:0032501 ! multicellular organismal process -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa 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 @@ -5056,7 +5056,7 @@ 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 ! Theria +relationship: in_taxon NCBITaxon:32525 ! Theria relationship: part_of UBERON:0000307 ! blastula property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/72/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 @@ -5080,8 +5080,8 @@ xref: UMLS:C1947929 {source="ncithesaurus:Prepucial_Gland_MMHCC"} xref: Wikipedia:Preputial_gland is_a: UBERON:0015251 {source="ISBN:0123813611", source="MA"} ! modified sebaceous gland relationship: fma_set_term FMA:71652 +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: never_in_taxon NCBITaxon:9606 {source="ISBN:0123813611", source="MP:0013329"} ! Homo sapiens -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia 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"} @@ -5167,7 +5167,7 @@ xref: UMLS:C0035287 {source="ncithesaurus:Reticuloendothelial_System"} xref: Wikipedia:Reticuloendothelial_system is_a: UBERON:0000061 ! anatomical structure relationship: composed_primarily_of CL:0000234 ! phagocyte -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002405 ! immune system relationship: part_of UBERON:0006804 ! reticular tissue @@ -5637,8 +5637,8 @@ xref: XAO:0004042 intersection_of: UBERON:0011216 ! organ system subdivision intersection_of: composed_primarily_of UBERON:0001015 ! musculature relationship: capable_of GO:0003012 ! muscle system process +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: never_in_taxon NCBITaxon:6040 ! Porifera -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa 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"} @@ -7008,8 +7008,8 @@ consider: FBbt:00007012 consider: FMA:86454 consider: GO:0044464 consider: HAO:0000014 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao-1337158144 consider: NCIT:C34070 -consider: NIF_Subcellular:sao-1337158144 consider: OpenCyc:Mx4rwQwkcZwpEbGdrcN5Y29ycA consider: TGMA:0001834 consider: UMLS:C1178969 {source="ncithesaurus:Cell_Part"} @@ -7437,7 +7437,7 @@ union_of: UBERON:0000486 ! multilaminar epithelium union_of: UBERON:0000490 ! unilaminar epithelium relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: only_in_taxon NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! Metazoa +relationship: in_taxon NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! Metazoa property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" 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/"} @@ -7747,8 +7747,8 @@ is_a: UBERON:0006314 {source="WP"} ! bodily fluid is_a: UBERON:0012112 {source="FMA", comment="consider changing to derivation relationship"} ! ingested food disjoint_from: UBERON:0012113 ! bolus of food relationship: has_quality PATO:0001429 {gci_relation="part_of", gci_filler="UBERON:0000945"} ! acidic +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: located_in UBERON:0004908 ! upper digestive tract -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: output_of GO:0007586 ! digestion [Term] @@ -7800,8 +7800,8 @@ xref: FMA:9673 xref: NCIT:C120839 xref: Wikipedia:Interstitial_fluid is_a: UBERON:0000463 ! organism substance +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: mutually_spatially_disjoint_with UBERON:0001969 ! blood plasma -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000479 ! tissue relationship: surrounds CL:0000000 ! cell @@ -7869,7 +7869,7 @@ xref: MIAA:0000298 xref: SCTID:302553009 xref: Wikipedia:Abdomen is_a: UBERON:0009569 ! subdivision of trunk -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata 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 @@ -7924,7 +7924,7 @@ xref: Wikipedia:Chorion_(egg) xref: ZFA:0000329 is_a: UBERON:0000476 ! acellular anatomical structure disjoint_from: UBERON:0003124 ! chorion membrane -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa 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"} @@ -8014,7 +8014,7 @@ 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 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa 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/"} @@ -8134,8 +8134,8 @@ xref: ZFA:0000041 is_a: UBERON:0000923 {notes="sometimes not considered primary"} ! germ layer relationship: has_part CL:0000222 ! mesodermal cell relationship: immediate_transformation_of UBERON:0006603 {source="Bgee:AN"} ! presumptive mesoderm +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: never_in_taxon NCBITaxon:6040 ! Porifera -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa property_value: depiction "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 @@ -8217,7 +8217,7 @@ xref: Wikipedia:Stomodeum xref: XAO:0000269 xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI @@ -8250,8 +8250,8 @@ xref: ZFA:0000066 is_a: UBERON:0016566 {source="EHDAA2"} ! pit relationship: develops_from UBERON:0000924 ! ectoderm relationship: has_potential_to_develop_into UBERON:0001353 ! anal region +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: located_in UBERON:0012469 {source="EHDAA2"} ! external anal region -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa 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"} @@ -8401,7 +8401,7 @@ xref: Wikipedia:Posterior_commissure xref: ZFA:0000320 intersection_of: UBERON:0001020 ! nervous system commissure intersection_of: connects UBERON:0014450 ! pretectal nucleus -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0003931 {source="FMA"} ! diencephalic white matter property_value: depiction "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 @@ -8429,7 +8429,7 @@ xref: MESH:D060227 xref: MIAA:0000064 xref: Wikipedia:Imaginal_disc is_a: UBERON:0000481 {source="FBbt text definition"} ! multi-tissue structure -relationship: only_in_taxon NCBITaxon:50557 {source="Wikipedia"} ! Insecta +relationship: in_taxon NCBITaxon:50557 {source="Wikipedia"} ! Insecta relationship: part_of UBERON:0002548 ! larva [Term] @@ -8566,12 +8566,12 @@ 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"} ! gastric acid secretion relationship: contributes_to_morphology_of UBERON:0001007 ! digestive system +relationship: in_taxon NCBITaxon:7742 {source="Wikipedia"} ! Vertebrata +relationship: in_taxon NCBITaxon:7776 {notes="absent in lampreys and hagfishes", source="ISBN:0073040584"} ! Gnathostomata relationship: never_in_taxon NCBITaxon:7864 {source="Wikipedia"} ! Chimaeriformes relationship: never_in_taxon NCBITaxon:7878 {source="Wikipedia"} ! Dipnomorpha relationship: never_in_taxon NCBITaxon:7955 {source="ZFA"} ! Danio rerio relationship: never_in_taxon NCBITaxon:9259 {source="Wikipedia"} ! Tachyglossidae -relationship: only_in_taxon NCBITaxon:7742 {source="Wikipedia"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7776 {notes="absent in lampreys and hagfishes", source="ISBN:0073040584"} ! Gnathostomata relationship: part_of UBERON:0001041 ! foregut property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/e/e0/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"} @@ -8701,9 +8701,9 @@ 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: in_taxon NCBITaxon:7742 ! Vertebrata relationship: never_in_taxon NCBITaxon:6239 ! Caenorhabditis elegans relationship: never_in_taxon NCBITaxon:7227 ! Drosophila melanogaster -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata 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"} @@ -8759,7 +8759,7 @@ disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: composed_primarily_of UBERON:0002368 ! endocrine gland relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa 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/"} @@ -8976,7 +8976,7 @@ synonym: "medulla" EXACT [FMA:61108] xref: FMA:61108 xref: galen:Medulla is_a: UBERON:0000471 ! compound organ component -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa 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 @@ -9344,8 +9344,8 @@ xref: Wikipedia:Antenna_(biology) is_a: UBERON:0000026 {source="FBbt"} ! appendage relationship: has_quality PATO:0000402 {gci_relation="part_of", gci_filler="NCBITaxon:6657", source="Wikipedia"} ! branched relationship: in_lateral_side_of UBERON:0000033 ! head +relationship: in_taxon NCBITaxon:6656 ! Arthropoda relationship: never_in_taxon NCBITaxon:6843 ! Chelicerata -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda 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 @@ -9421,8 +9421,8 @@ 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: in_taxon NCBITaxon:32523 {source="ISBN:0073040584"} ! Tetrapoda relationship: never_in_taxon NCBITaxon:8570 {source="Wikipedia"} ! Serpentes -relationship: only_in_taxon NCBITaxon:32523 {source="ISBN:0073040584"} ! Tetrapoda 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"} @@ -9505,7 +9505,7 @@ 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_quality PATO:0001748 ! invaginated -relationship: only_in_taxon NCBITaxon:32524 ! Amniota +relationship: in_taxon NCBITaxon:32524 ! Amniota 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="ISBN:978-0030223693", source="https://orcid.org/0000-0003-3308-6245"} ! Aves @@ -9571,7 +9571,7 @@ is_a: UBERON:0002495 {source="FMA"} ! long bone intersection_of: UBERON:0015004 ! tibia endochondral element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: develops_from UBERON:0010849 ! tibia cartilage element -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0010720 ! hindlimb zeugopod skeleton relationship: preaxialmost_part_of UBERON:0010720 ! hindlimb zeugopod skeleton property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray260.png" xsd:anyURI @@ -9594,7 +9594,7 @@ xref: UMLS:C0162370 {source="ncithesaurus:Trochanter"} xref: Wikipedia:Trochanter is_a: UBERON:0005913 {source="FMA"} ! zone of bone organ relationship: contributes_to_morphology_of UBERON:0000981 ! femur -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata 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"} @@ -9640,7 +9640,7 @@ relationship: connected_to UBERON:0000979 {gci_relation="part_of", gci_filler="N 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 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata 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 @@ -9815,7 +9815,7 @@ is_a: UBERON:0002616 ! regional part of brain relationship: contributes_to_morphology_of UBERON:0001895 ! metencephalon relationship: contributes_to_morphology_of UBERON:0002298 ! brainstem relationship: dubious_for_taxon NCBITaxon:7955 ! Danio rerio -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001895 {source="neuronames"} ! metencephalon relationship: part_of UBERON:0002298 ! brainstem property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/36/Gray768.png" xsd:anyURI @@ -10034,7 +10034,7 @@ 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 ! Metazoa +relationship: in_taxon NCBITaxon:33208 ! Metazoa property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png" xsd:anyURI property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.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"} @@ -10077,7 +10077,7 @@ xref: ZFA:0000560 is_a: UBERON:0000025 ! tube relationship: connects UBERON:0000992 ! ovary relationship: connects UBERON:0013514 ! space surrounding organism -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa 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"} @@ -10105,8 +10105,8 @@ xref: TGMA:0000560 xref: WBbt:0005319 xref: Wikipedia:Spermatheca is_a: UBERON:0000062 ! organ +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: never_in_taxon NCBITaxon:314146 ! Euarchontoglires -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria 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 @@ -10137,7 +10137,7 @@ xref: VHOG:0001137 xref: Wikipedia:Uterus is_a: UBERON:0013515 {source="cjm"} ! subdivision of oviduct relationship: immediate_transformation_of UBERON:0005795 ! embryonic uterus -relationship: only_in_taxon NCBITaxon:32525 ! Theria +relationship: in_taxon NCBITaxon:32525 ! Theria relationship: part_of UBERON:0004175 ! internal genitalia property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6a/Female_reproductive_system_lateral_nolabel.png" xsd:anyURI property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI @@ -10219,7 +10219,7 @@ xref: UMLS:C0042993 {source="ncithesaurus:Vulva"} xref: VHOG:0001458 xref: Wikipedia:Vulva is_a: UBERON:0000062 ! organ -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0005056 ! external female genitalia property_value: depiction "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"} @@ -10302,7 +10302,7 @@ 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 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000079 ! male reproductive system property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png" xsd:anyURI @@ -10340,7 +10340,7 @@ 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 ! Amniota +relationship: in_taxon NCBITaxon:32524 ! Amniota relationship: part_of UBERON:0005352 {source="FMA"} ! spermatic cord relationship: part_of UBERON:0006947 ! male genital duct property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg" xsd:anyURI @@ -10367,7 +10367,7 @@ xref: Wikipedia:Arthropod_exoskeleton intersection_of: UBERON:0001002 ! cuticle intersection_of: composed_primarily_of CHEBI:17029 ! chitin relationship: develops_from UBERON:0007376 ! outer epithelium -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0002416 ! integumental system [Term] @@ -10384,7 +10384,7 @@ 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"} ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 {source="Rieger - Evolution of the Cuticle in the Lower Eumetazoa"} ! Eumetazoa property_value: has_relational_adjective "cuticular" xsd:string [Term] @@ -10483,8 +10483,8 @@ disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0003016 ! respiratory system process relationship: existence_ends_during UBERON:0000066 ! fully formed stage +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} ! Acoelomorpha -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria property_value: depiction "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/"} @@ -10621,9 +10621,9 @@ xref: ZFA:0000163 intersection_of: UBERON:8450002 ! excretory system intersection_of: capable_of GO:0097254 ! renal tubular secretion relationship: existence_ends_during UBERON:0000066 ! fully formed stage +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} ! Xenoturbella relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} ! Acoelomorpha -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa 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"} @@ -10655,10 +10655,10 @@ disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0003013 ! circulatory system process relationship: dubious_for_taxon NCBITaxon:6231 {notes="WBbt coelomocyte currently classified as circulating cell"} ! Nematoda relationship: existence_ends_during UBERON:0000066 ! fully formed stage +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} ! Acoelomorpha relationship: never_in_taxon NCBITaxon:6073 ! Cnidaria relationship: never_in_taxon NCBITaxon:6157 ! Platyhelminthes -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria property_value: curator_notes "the cardiovascular system and the lymphatic system are parts of the circulatory system" xsd:string property_value: depiction "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"} @@ -10755,7 +10755,7 @@ is_a: UBERON:0011822 {source="FMA"} ! dense irregular connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: composed_primarily_of CL:0000136 ! adipocyte disjoint_from: UBERON:0003714 ! neural tissue -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa 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"} @@ -10862,8 +10862,8 @@ relationship: composed_primarily_of CL:0002319 ! neural cell relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part CL:0000540 ! neuron relationship: immediate_transformation_of UBERON:0016880 {source="Bgee:AN"} ! future nervous system +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: never_in_taxon NCBITaxon:6040 ! Porifera -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI property_value: depiction "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"} @@ -10914,8 +10914,8 @@ 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: immediate_transformation_of UBERON:0016879 {source="Bgee:AN"} ! future central nervous system +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} ! Acoelomorpha -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria 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"} @@ -11049,7 +11049,7 @@ is_obsolete: true consider: FBbt:00005107 consider: FMA:67301 consider: GO:0043025 -consider: NIF_Subcellular:sao1044911821 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1044911821 [Term] id: UBERON:0001023 @@ -11064,9 +11064,9 @@ consider: FBbt:00005110 consider: FMA:67314 consider: GAID:749 consider: GO:0030425 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1211023249 consider: MESH:A08.663.256 consider: NCIT:C32447 -consider: NIF_Subcellular:sao1211023249 consider: OpenCyc:Mx4rviIdspwpEbGdrcN5Y29ycA consider: TGMA:0001373 consider: UMLS:C0011305 @@ -11083,8 +11083,8 @@ consider: FBbt:00005113 consider: FMA:61814 consider: GAID:751 consider: GO:0043005 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao-867568886 consider: MESH:A08.663.256.500 -consider: NIF_Subcellular:sao-867568886 [Term] id: UBERON:0001025 @@ -11100,9 +11100,9 @@ consider: FBbt:00005114 consider: FMA:67408 consider: GAID:766 consider: GO:0045202 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao914572699 consider: MESH:A08.850 consider: NCIT:C13281 -consider: NIF_Subcellular:sao914572699 consider: SCTID:362298009 consider: UMLS:C0039062 @@ -11162,8 +11162,8 @@ replaced_by: GO:0031594 consider: FBbt:00005142 consider: FMA:61803 consider: GAID:809 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1124888485 consider: MESH:D009469 -consider: NIF_Subcellular:sao1124888485 [Term] id: UBERON:0001030 @@ -11173,7 +11173,7 @@ is_obsolete: true consider: FBbt:00005143 consider: FMA:67107 consider: GO:0048788 -consider: NIF_Subcellular:sao1884931180 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1884931180 [Term] id: UBERON:0001031 @@ -11276,7 +11276,7 @@ disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa 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"} @@ -11351,7 +11351,7 @@ xref: Wikipedia:Hair is_a: UBERON:0000021 {source="FMA"} ! cutaneous appendage relationship: develops_from UBERON:0002073 ! hair follicle relationship: has_part GO:0045095 ! keratin filament -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia 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 @@ -11373,7 +11373,7 @@ xref: MAT:0000209 xref: MIAA:0000209 xref: Wikipedia:Chordotonal_organ is_a: UBERON:0000020 ! sense organ -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda [Term] id: UBERON:0001040 @@ -11475,7 +11475,7 @@ relationship: continuous_with UBERON:0001043 {gci_relation="part_of", gci_filler 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 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata 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"} @@ -11571,8 +11571,8 @@ intersection_of: UBERON:0002530 ! gland intersection_of: produces UBERON:0001836 ! saliva relationship: capable_of GO:0046541 ! saliva secretion relationship: contributes_to_morphology_of UBERON:0001007 ! digestive system +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: located_in UBERON:0000167 ! oral cavity -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0002330 ! exocrine system 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: depiction "http://upload.wikimedia.org/wikipedia/commons/5/51/Illu_quiz_hn_02.jpg" xsd:anyURI @@ -11841,7 +11841,7 @@ xref: TADS:0000163 xref: TGMA:0001038 xref: Wikipedia:Malpighian_tubule is_a: UBERON:0009773 {source="GO"} ! renal tubule -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda 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] @@ -11863,7 +11863,7 @@ xref: EFO:0000380 xref: MAT:0000211 xref: MIAA:0000211 is_a: UBERON:0001053 ! arthropod neurohemal organ -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0012325 {source="BTO-modified"} ! retrocerebral complex [Term] @@ -11903,8 +11903,8 @@ xref: Wikipedia:Mushroom_body is_a: UBERON:0000477 ! anatomical cluster relationship: capable_of_part_of GO:0007613 {source="Wikipedia"} ! memory relationship: capable_of_part_of GO:0008355 {source="Wikipedia"} ! olfactory learning +relationship: in_taxon NCBITaxon:33317 {notes="annelids and arthropods"} ! Protostomia relationship: never_in_taxon NCBITaxon:6217 ! Nemertea -relationship: only_in_taxon NCBITaxon:33317 {notes="annelids and arthropods"} ! Protostomia relationship: part_of UBERON:0000955 ! brain relationship: present_in_taxon NCBITaxon:6340 ! Annelida relationship: present_in_taxon NCBITaxon:6656 ! Arthropoda @@ -11921,7 +11921,7 @@ xref: EFO:0000926 xref: MAT:0000337 xref: MIAA:0000337 is_a: UBERON:0005162 ! multi cell part structure -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0000955 {source="FBbt"} ! brain [Term] @@ -12265,7 +12265,7 @@ xref: SCTID:264021000 intersection_of: UBERON:0007651 ! anatomical junction intersection_of: connects UBERON:0000059 ! large intestine intersection_of: connects UBERON:0002108 ! small intestine -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000160 ! intestine [Term] @@ -13061,9 +13061,9 @@ xref: Wikipedia:Thoracid_diaphragm is_a: UBERON:0014892 ! skeletal muscle organ, vertebrate relationship: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue relationship: immediate_transformation_of UBERON:0010084 {evidence="definitional"} ! future diaphragm +relationship: in_taxon NCBITaxon:40674 {source="PMID:23586979"} ! Mammalia relationship: innervated_by UBERON:0001884 ! phrenic nerve relationship: never_in_taxon NCBITaxon:8782 {source="Wikipedia:Thoracic_diaphragm#Comparative_anatomy_and_evolution"} ! Aves -relationship: only_in_taxon NCBITaxon:40674 {source="PMID:23586979"} ! Mammalia 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 @@ -13791,8 +13791,8 @@ xref: ZFA:0001559 intersection_of: UBERON:0000075 ! subdivision of skeletal system intersection_of: composed_primarily_of UBERON:0010913 ! vertebral element disjoint_from: UBERON:0008260 ! spine appendage +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: never_in_taxon NCBITaxon:7762 ! Myxinidae -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata 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 @@ -13863,7 +13863,7 @@ relationship: has_developmental_contribution_from UBERON:0010027 {gci_relation=" 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"} ! Tetrapoda +relationship: in_taxon NCBITaxon:32523 {source="PMID:16313389"} ! Tetrapoda 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"} @@ -14050,7 +14050,7 @@ 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 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria property_value: depiction "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 @@ -14445,8 +14445,8 @@ 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: in_taxon NCBITaxon:7776 ! Gnathostomata relationship: never_in_taxon NCBITaxon:32443 {source="Wikipedia"} ! Teleostei -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: part_of UBERON:0000059 {source="MA"} ! large intestine relationship: part_of UBERON:0001155 {source="EHDAA2"} ! colon property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg" xsd:anyURI @@ -14531,7 +14531,7 @@ 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 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata 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 @@ -14745,7 +14745,7 @@ 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: only_in_taxon NCBITaxon:40674 {source="ISBN:0073040584"} ! Mammalia +relationship: in_taxon NCBITaxon:40674 {source="ISBN:0073040584"} ! Mammalia property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/33/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 @@ -15931,8 +15931,8 @@ 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: in_taxon NCBITaxon:32524 {source="PMID:PMID:20181529"} ! Amniota relationship: never_in_taxon NCBITaxon:8459 {source="PMID:PMID:20181529"} ! Testudines -relationship: only_in_taxon NCBITaxon:32524 {source="PMID:PMID:20181529"} ! Amniota relationship: part_of UBERON:0000030 {comment="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"} @@ -15965,8 +15965,8 @@ is_a: UBERON:0000414 {source="MP"} ! mucous gland is_a: UBERON:0011148 {notes="compound tubular"} ! submucosal gland intersection_of: UBERON:0011148 ! submucosal gland intersection_of: part_of UBERON:0002114 ! duodenum +relationship: in_taxon NCBITaxon:40674 {notes="unclear for Aves", source="ISBN:9780521617147"} ! Mammalia relationship: located_in UBERON:0003332 {source="FMA, modified"} ! submucosa of duodenum -relationship: only_in_taxon NCBITaxon:40674 {notes="unclear for Aves", source="ISBN:9780521617147"} ! Mammalia 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 @@ -17353,8 +17353,8 @@ relationship: has_developmental_contribution_from UBERON:0003923 {source="Wikipe 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: in_taxon NCBITaxon:7742 {source="PMID:16417468"} ! Vertebrata relationship: located_in UBERON:0002323 ! coelemic cavity lumen -relationship: only_in_taxon NCBITaxon:7742 {source="PMID:16417468"} ! Vertebrata property_value: depiction "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"} @@ -18184,7 +18184,7 @@ xref: FMA:17734 xref: MA:0001652 is_a: UBERON:0000064 ! organ part relationship: contributes_to_morphology_of UBERON:0000362 ! renal medulla -relationship: only_in_taxon NCBITaxon:40674 {source="GO:0072053"} ! Mammalia +relationship: in_taxon NCBITaxon:40674 {source="GO:0072053"} ! Mammalia relationship: part_of UBERON:0000362 ! renal medulla relationship: part_of UBERON:0002113 ! kidney property_value: taxon_notes "unique to mammals" xsd:string {source="GO:0072053"} @@ -18220,7 +18220,7 @@ xref: Wikipedia:Endometrium intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0000995 ! uterus relationship: contributes_to_morphology_of UBERON:0000995 ! uterus -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0000459 {source="FMA"} ! uterine wall property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI property_value: external_definition "The mucous membrane lining the uterus. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001285", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/Endometrium"} @@ -18361,7 +18361,7 @@ xref: UMLS:C0036471 {source="ncithesaurus:Scrotum"} xref: Wikipedia:Scrotum is_a: UBERON:0034929 ! external soft tissue zone relationship: develops_from UBERON:0011756 {source="Wikipedia"} ! male genital swelling -relationship: only_in_taxon NCBITaxon:32525 ! Theria +relationship: in_taxon NCBITaxon:32525 ! Theria relationship: part_of UBERON:0004053 ! external male genitalia property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a6/Scrotum_warm_and_cold.jpg" xsd:anyURI property_value: depiction "http://upload.wikimedia.org/wikipedia/en/thumb/3/3e/HairedHumanScrotum.png/200px-HairedHumanScrotum.png" xsd:anyURI @@ -18403,7 +18403,7 @@ relationship: channels_from UBERON:0006946 ! efferent duct relationship: channels_into UBERON:0001000 ! vas deferens relationship: contributes_to_morphology_of UBERON:0004054 ! internal male genitalia relationship: develops_from UBERON:0003074 {source="Wikipedia"} ! mesonephric duct -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0006947 {source="FMA"} ! male genital duct property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_testis_surface.jpg" xsd:anyURI property_value: editor_note "Kardong has epididymis in elasmobranch" xsd:string @@ -19201,7 +19201,7 @@ is_a: UBERON:0000414 {source="MP"} ! mucous gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000057 ! urethra relationship: contributes_to_morphology_of UBERON:0000057 ! urethra -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0002330 ! exocrine system property_value: external_ontology_notes "NCIT:C12339 paraurethral gland belongs here" xsd:string {external_ontology="NCIT"} @@ -20042,8 +20042,8 @@ xref: Wikipedia:Sartorius_muscle is_a: UBERON:0001630 ! muscle organ relationship: has_muscle_insertion UBERON:0008977 {notes="anteromedial surface of the upper tibia in the pes anserinus", source="dbpedia"} ! pes anserinus of tibia relationship: has_muscle_origin UBERON:0001273 ! ilium +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: innervated_by UBERON:0001267 {notes="femoral nerve", source="dbpedia"} ! femoral nerve -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/af/Sartorius.png" xsd:anyURI property_value: editor_note "We do NOT group this AAO class here at this stage until further evidence of shared attachments" xsd:string property_value: homology_notes "The ambiens of reptiles and the iliotibialis of amphibians are likely homologues of the sartorius.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001192", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.391", source="http://bgee.unil.ch/"} @@ -22525,7 +22525,7 @@ xref: VHOG:0000342 xref: Wikipedia:Shoulder is_a: UBERON:0000475 ! organism subdivision relationship: has_part UBERON:0016884 ! shoulder joint -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda +relationship: in_taxon NCBITaxon:32523 ! Tetrapoda relationship: overlaps UBERON:0001421 {source="FMA-modified"} ! pectoral girdle region relationship: part_of UBERON:0010708 ! pectoral complex property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/90/Shoulderjoint.PNG" xsd:anyURI @@ -22728,10 +22728,10 @@ disjoint_from: UBERON:0001630 ! muscle organ disjoint_from: UBERON:0005090 ! muscle structure disjoint_from: UBERON:0010538 ! paired limb/fin segment relationship: composed_primarily_of UBERON:0002481 {source="VSAO-modified"} ! bone tissue +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: mutually_spatially_disjoint_with UBERON:0001015 ! musculature relationship: mutually_spatially_disjoint_with UBERON:0001630 ! muscle organ relationship: mutually_spatially_disjoint_with UBERON:0002385 ! muscle tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001434 ! skeletal 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:0000047", ontology="AAO"} property_value: external_definition "Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000047", ontology="AAO", source="AAO:LAP"} @@ -24590,9 +24590,9 @@ xref: ZFA:0000112 is_a: UBERON:0000025 ! tube relationship: connects UBERON:0000165 ! mouth relationship: immediate_transformation_of UBERON:0007026 {source="NCBIBook:NBK10107"} ! presumptive gut +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} ! Acoelomorpha relationship: never_in_taxon NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} ! Siboglinidae -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001007 ! digestive system property_value: external_definition "The alimentary or digestive tract, and associated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000112", ontology="TAO", source="ZFIN:curator"} property_value: external_ontology_notes "FMA also has a term 'gastrointestinal tract', but this includes the liver." xsd:string {external_ontology="FMA"} @@ -24671,7 +24671,7 @@ subset: non_informative synonym: "organ neck" EXACT [] xref: FMA:45733 is_a: UBERON:0034944 {source="FMA"} ! zone of organ -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa [Term] id: UBERON:0001561 @@ -26994,8 +26994,8 @@ intersection_of: UBERON:0001785 ! cranial nerve intersection_of: extends_fibers_into UBERON:0002682 ! abducens nucleus intersection_of: innervates UBERON:0001601 ! extra-ocular muscle relationship: develops_from UBERON:0005239 {source="Wikipedia"} ! basal plate metencephalon +relationship: in_taxon NCBITaxon:7776 {notes="found in all vertebrates except lampreys and hagfishes", source="Wikipedia"} ! Gnathostomata relationship: innervates UBERON:0001603 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! lateral rectus extra-ocular muscle -relationship: only_in_taxon NCBITaxon:7776 {notes="found in all vertebrates except lampreys and hagfishes", source="Wikipedia"} ! Gnathostomata property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/29/Abducens_nerve1.png" xsd:anyURI property_value: external_definition "Somatic motor nerve which bifurcates innervating m. rectus lateralis and m. retractor bulbi (eye muscles).[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010471", ontology="AAO", source="AAO:EJS"} property_value: homology_notes "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000697", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625", source="http://bgee.unil.ch/"} @@ -27220,10 +27220,10 @@ intersection_of: UBERON:0001785 ! cranial nerve intersection_of: extends_fibers_into UBERON:0002871 ! hypoglossal nucleus intersection_of: innervates UBERON:0000378 ! tongue muscle relationship: dubious_for_taxon NCBITaxon:8292 ! Amphibia +relationship: in_taxon NCBITaxon:32523 ! Tetrapoda relationship: innervates UBERON:0001571 ! genioglossus muscle relationship: innervates UBERON:0001572 ! hyoglossus muscle relationship: innervates UBERON:3010654 {gci_relation="part_of", gci_filler="NCBITaxon:8292", source="ISBN:080184780X"} ! rectus cervicis -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ef/Gray794.png" xsd:anyURI property_value: external_definition "Cranial nerve that innervates muscles in the tongue. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-14, 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:0000693", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: external_definition "In amphibians, represents the hypoglossal nerve in amniotes. Innverates mm. geniohyoideus, genioglossus, hyoglossus, rectus cervicis" xsd:string {source="ISBN:080184780X"} @@ -27747,7 +27747,7 @@ is_a: UBERON:0010428 {source="FMA"} ! flat bone relationship: connected_to UBERON:0001092 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! vertebral bone 1 relationship: connected_to UBERON:0001677 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! sphenoid bone relationship: develops_from UBERON:0003089 {source="PMID:11523816"} ! sclerotome -relationship: only_in_taxon NCBITaxon:117570 {source="WP"} ! Teleostomi +relationship: in_taxon NCBITaxon:117570 {source="WP"} ! Teleostomi relationship: overlaps UBERON:0002241 {notes="basi paired exo and supra occipital bones", source="MA-modified"} ! chondrocranium relationship: overlaps UBERON:0003113 {notes="interparietal (postparietal)"} ! dermatocranium relationship: part_of UBERON:0001703 {source="FMA"} ! neurocranium @@ -28158,7 +28158,7 @@ intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue disjoint_from: UBERON:0008283 ! columnella relationship: develops_from UBERON:0004368 {contradicted_by="DOI:10.1111/j.1469-7580.2006.00524.x", source="classical definition"} ! Reichert's cartilage relationship: develops_from UBERON:0010055 {source="definitional"} ! stapes cartilage element -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia +relationship: in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c1/Gray918.png" xsd:anyURI property_value: development_notes "As the stapes first develops embryologically from the 6th to 8th week of life, it surrounds the stapedial artery, which supplies the majority of the vasculature of the embryonic head. After that period, the external carotid artery is generated and takes over for the stapedial artery, which subsequently involutes, leaving the stapes with a windowframe-like structure[WP] The stapes develops at the cranial end of the second branchial arch through an independent anlage of the cartilage of this arch. Between the stapedial anlage and the cranial end of the Reichert's cartilage there is a formation called the interhyale, the internal segment of which gives rise to the tendon of the stapedial muscle. The stapedial anlage is a unique formation with two distinct parts: the superior part that will comprise the base and the inferior part that will be crossed by the stapedial artery during embryonic development and will constitute the limbs and the head of the stapes. According to the results, the otic capsule is not involved in formation of the base of the stapes." xsd:string {source="DOI:10.1111/j.1469-7580.2005.00441.x"} property_value: homology_notes "This structure (the hyomandibular), on ontogenic grounds alone, can be considered homologous with the amphibian and reptilian columella and the mammalian stapes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000688", ontology="VHOG", source="DOI:10.1017/S0022215100009087 Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948)", source="http://bgee.unil.ch/"} @@ -28185,7 +28185,7 @@ xref: Wikipedia:Incus intersection_of: UBERON:0015017 ! incus endochondral element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: develops_from UBERON:0007374 {source="EMAPA-implied"} ! incus cartilage element -relationship: only_in_taxon NCBITaxon:32525 ! Theria +relationship: in_taxon NCBITaxon:32525 ! Theria property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray917.png" xsd:anyURI property_value: homology_notes "According to this theory (Reichert-Gaupp theory), the mammalian stapes is derived from the reptilian columella, the incus from the quadrate and the malleus from the articular (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000689", ontology="VHOG", source="DOI:10.1017/S0022215100009087 Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948", source="http://bgee.unil.ch/"} @@ -28211,7 +28211,7 @@ intersection_of: UBERON:0015018 ! malleus endochondral element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: develops_from UBERON:0003107 {is_redundant="true", source="Wikipedia"} ! Meckel's cartilage relationship: develops_from UBERON:0010054 {source="cjm"} ! malleus cartilage element -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia +relationship: in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray916.png" xsd:anyURI property_value: homology_notes "According to this theory (Reichert-Gaupp theory), the mammalian stapes is derived from the reptilian columella, the incus from the quadrate and the malleus from the articular (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000690", ontology="VHOG", source="DOI:10.1017/S0022215100009087 Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948", source="http://bgee.unil.ch/"} @@ -28296,8 +28296,8 @@ disjoint_from: UBERON:0006618 ! atrium auricular region relationship: contributes_to_morphology_of UBERON:0000033 ! head relationship: contributes_to_morphology_of UBERON:0001690 ! ear relationship: in_lateral_side_of UBERON:0000033 ! head +relationship: in_taxon NCBITaxon:32523 ! Tetrapoda relationship: never_in_taxon NCBITaxon:9709 {source="Wikipedia"} ! Phocidae -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda relationship: part_of UBERON:0001690 ! ear property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Gray907.png" xsd:anyURI property_value: external_definition "The external part of the organ, which consists of an outer portion (external auditory meatus) which leads to the tympanum. [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:0000311", ontology="VHOG", source="http://bgee.unil.ch/"} @@ -28825,7 +28825,7 @@ intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: skeleton_of UBERON:0011595 ! jaw region relationship: capable_of NBO:0000073 ! chewing relationship: has_developmental_contribution_from UBERON:0002342 {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neural crest -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata +relationship: in_taxon NCBITaxon:7776 ! Gnathostomata relationship: overlaps UBERON:0008895 ! splanchnocranium relationship: part_of UBERON:0011156 {source="cjm"} ! facial skeleton relationship: part_of UBERON:0011595 ! jaw region @@ -29113,7 +29113,7 @@ is_a: UBERON:0007375 ! roof of mouth relationship: adjacent_to UBERON:0000167 ! oral cavity relationship: adjacent_to UBERON:0001707 ! nasal cavity relationship: develops_from UBERON:0005619 {notes="fusion", source="http://www.indiana.edu/~anat550/hnanim/face/face.html"} ! secondary palatal shelf -relationship: only_in_taxon NCBITaxon:32524 ! Amniota +relationship: in_taxon NCBITaxon:32524 ! Amniota relationship: part_of UBERON:0000165 {source="FMA"} ! mouth relationship: part_of UBERON:0001709 {source="EMAPA"} ! upper jaw region property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Pig_snout_sagittal_cut.jpg" xsd:anyURI @@ -29199,7 +29199,7 @@ xref: Wikipedia:Mesencephalic_nucleus_of_trigeminal_nerve xref: ZFA:0000312 is_a: UBERON:0004132 ! trigeminal sensory nucleus relationship: capable_of_part_of GO:0019230 {source="Wikipedia"} ! proprioception -relationship: only_in_taxon NCBITaxon:7776 {source="ISBN:978-0-387-09845-6"} ! Gnathostomata +relationship: in_taxon NCBITaxon:7776 {source="ISBN:978-0-387-09845-6"} ! Gnathostomata relationship: part_of UBERON:0001943 {source="NIF"} ! midbrain tegmentum property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png" xsd:anyURI property_value: development_notes "develops from NC in some species[https://github.com/obophenotype/uberon/wiki/The-neural-crest] Not of NC origin[DOI:10.1002/dvdy.1197]." xsd:string {source="PMID:11747082"} @@ -29686,7 +29686,7 @@ xref: Wikipedia:Palatine_uvula is_a: UBERON:0004529 ! anatomical projection disjoint_from: UBERON:0004078 ! cerebellum vermis lobule IX relationship: capable_of_part_of GO:0071625 ! vocalization behavior -relationship: only_in_taxon NCBITaxon:9443 {source="PMID:1408233"} ! Primates +relationship: in_taxon NCBITaxon:9443 {source="PMID:1408233"} ! Primates relationship: part_of UBERON:0001733 ! soft palate property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/81/Tonsils_diagram.jpg" xsd:anyURI property_value: taxon_notes "In a study of eight mammals a small underdeveloped uvula was found only in baboons" xsd:string {source="PMID:1408233"} @@ -29745,7 +29745,7 @@ is_a: UBERON:0001829 ! major salivary gland relationship: develops_from UBERON:0006298 ! submandibular gland primordium relationship: in_lateral_side_of UBERON:0000165 ! mouth relationship: in_lateral_side_of UBERON:0001710 {source="FMA-abduced-lr"} ! lower jaw region -relationship: only_in_taxon NCBITaxon:32524 {source="https://orcid.org/0000-0003-3308-6245"} ! Amniota +relationship: in_taxon NCBITaxon:32524 {source="https://orcid.org/0000-0003-3308-6245"} ! Amniota relationship: part_of UBERON:0035775 {gci_relation="part_of", gci_filler="NCBITaxon:9605", source="http://www.avdc.org/Nomenclature.pdf"} ! submandibular region property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/51/Illu_quiz_hn_02.jpg" xsd:anyURI property_value: development_notes "The submandibular is the first major salivary gland to develop in the embryo, followed by the neighbouring sublingual and then the parotid.[PMID:17336109]" xsd:string @@ -29955,7 +29955,7 @@ xref: Wikipedia:Lymphoid_tissue is_a: UBERON:0034769 {source="FMA"} ! lymphomyeloid tissue relationship: dubious_for_taxon NCBITaxon:7776 {notes="lampreys lack organized lymphoid tissue", source="NCBIBook:NBK27108"} ! Gnathostomata relationship: has_part CL:0000542 ! lymphocyte -relationship: only_in_taxon NCBITaxon:7742 {source="NCBIBook:NBK27108"} ! Vertebrata +relationship: in_taxon NCBITaxon:7742 {source="NCBIBook:NBK27108"} ! Vertebrata relationship: part_of UBERON:0002193 ! hemolymphoid system relationship: part_of UBERON:0002465 ! lymphoid system @@ -30068,7 +30068,7 @@ xref: Wikipedia:Lacrimal_apparatus is_a: UBERON:0000467 ! anatomical system relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye relationship: develops_from UBERON:0000076 {source="ISBN:0781772214"} ! external ectoderm -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda +relationship: in_taxon NCBITaxon:32523 ! Tetrapoda relationship: part_of UBERON:0000019 {source="FMA", source="MA"} ! camera-type eye relationship: part_of UBERON:0010409 {source="MA"} ! ocular surface region relationship: part_of UBERON:0035639 {source="HPO:pr"} ! ocular adnexa @@ -30104,7 +30104,7 @@ xref: XAO:0004051 xref: ZFA:0005143 is_a: UBERON:0010365 {source="VSAO"} ! odontoid tissue relationship: has_quality PATO:0002444 ! mineralized -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: transformation_of UBERON:0011587 {source="VSAO"} ! pre-dentine property_value: external_definition "Mineralized collagen containing substance that forms the tooth structure.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005143", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "dentinal" xsd:string @@ -30138,9 +30138,9 @@ is_a: UBERON:0010365 {source="VSAO"} ! odontoid tissue relationship: composed_primarily_of CHEBI:52255 {proportion="85", source="Wikipedia:ENAM"} ! hydroxylapatite relationship: develops_from UBERON:0011588 {source="VSAO"} ! pre-enamel relationship: has_quality PATO:0002444 ! mineralized +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: never_in_taxon NCBITaxon:9359 {source="PMID:19730686"} ! Dasypodidae relationship: never_in_taxon NCBITaxon:9816 {source="PMID:19730686"} ! Orycteropodidae -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Enamelorgan11-17-05.jpg" xsd:anyURI property_value: editor_note "current classification under substance of tooth may be turned into taxon GCI (e.g. sharks have enamel in dermal denticles)" xsd:string property_value: external_definition "Skeletal tissue that consists of an avascular, noncollagenous, hypermineralized matrix that is deposited by ameloblasts that are excluded from the matrix. Enamel develops from organic pre-enamel tissue that is replaced by a largely inorganic matrix.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000065", ontology="VSAO", source="PSPUB:0000170"} @@ -30283,7 +30283,7 @@ is_a: UBERON:0001444 ! subdivision of head relationship: continuous_with UBERON:0001352 ! external acoustic meatus relationship: develops_from UBERON:0006208 ! auditory hillocks relationship: has_quality PATO:0001297 ! reflectivity -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0001691 ! external ear property_value: external_definition "The external expanded part of the ear characterized by a funnel-shaped structure through which the sound vibrations are received. [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:0000460", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: function_notes "The purpose of the pinna is to collect sound. It does so by acting as a funnel, amplifying the sound and directing it to the ear canal. While reflecting from the pinna, sound also goes through a filtering process which adds directional information to the sound (see sound localization, head-related transfer function, pinna notch)." xsd:string @@ -30431,8 +30431,8 @@ is_a: UBERON:0005913 ! zone of bone organ intersection_of: UBERON:0035612 ! nasal turbinal intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue disjoint_from: UBERON:0006203 ! conchal part of pinna +relationship: in_taxon NCBITaxon:32524 ! Amniota relationship: never_in_taxon NCBITaxon:436486 {notes="disputed", source="http://palaeos.com/vertebrates/bones/braincase/ethmoid.html"} ! Dinosauria -relationship: only_in_taxon NCBITaxon:32524 ! Amniota relationship: transformation_of UBERON:0035007 ! nasal concha cartilage property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray153.png" xsd:anyURI property_value: external_ontology_notes "FMA considers nasal concha and nasal concha of ethmoid bone to be synonymous. We disambiguate these here" xsd:string {external_ontology="FMA"} @@ -31178,7 +31178,7 @@ intersection_of: anterior_to UBERON:0001780 ! spinal nerve intersection_of: extends_fibers_into UBERON:0000955 ! brain relationship: has_developmental_contribution_from UBERON:0003099 ! cranial neural crest relationship: in_lateral_side_of UBERON:0000033 ! head -relationship: only_in_taxon NCBITaxon:89593 ! Craniata +relationship: in_taxon NCBITaxon:89593 ! Craniata property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/18/Brain_human_normal_inferior_view_with_labels_en-2.svg" xsd:anyURI property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/84/Brain_human_normal_inferior_view_with_labels_en.svg" xsd:anyURI property_value: editor_note "classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN." xsd:string @@ -31214,7 +31214,7 @@ is_a: UBERON:0000064 ! organ part relationship: has_part CHEBI:27547 ! zeaxanthin relationship: has_part CHEBI:28838 ! lutein relationship: has_part CL:0000573 ! retinal cone cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000053 ! macula lutea property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI property_value: external_definition "A small pit in the center of the macula lutea, the area of clearest vision, where the retinal layers are spread aside, and light falls directly on the cones. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001572", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/fovea"} @@ -32219,7 +32219,7 @@ intersection_of: UBERON:0002530 ! gland intersection_of: produces UBERON:0001089 ! sweat relationship: develops_from UBERON:0005089 {evidence="definitional"} ! sweat gland placode relationship: has_quality PATO:0002299 {notes="coiled tubular", source="Wikipedia:Tubular_gland"} ! tubular -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0001003 {source="FMA"} ! skin epidermis property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg" xsd:anyURI property_value: editor_note "TODO - check if all sweat glands are epidermal - see EMAPA:29743" xsd:string @@ -32252,7 +32252,7 @@ xref: VHOG:0001468 xref: Wikipedia:Sebaceous_gland is_a: UBERON:0012344 {source="Wikipedia"} ! holocrine gland relationship: develops_from UBERON:0005088 {evidence="definitional"} ! sebaceous gland placode -relationship: only_in_taxon NCBITaxon:40674 {source="VHOG"} ! Mammalia +relationship: in_taxon NCBITaxon:40674 {source="VHOG"} ! Mammalia relationship: part_of UBERON:0001003 {inconsistent_with="BTO", source="FMA"} ! skin epidermis relationship: part_of UBERON:0002330 ! exocrine system relationship: part_of UBERON:0011932 ! pilosebaceous unit @@ -32544,7 +32544,7 @@ xref: Wikipedia:Sublingual_gland is_a: UBERON:0001829 {source="FMA"} ! major salivary gland disjoint_from: UBERON:0009964 ! crustacean maxillary gland relationship: develops_from UBERON:0006297 ! sublingual gland primordium -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata +relationship: in_taxon NCBITaxon:7776 ! Gnathostomata property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray1024.png" xsd:anyURI property_value: external_definition "One of a pair of small salivary glands situated under the mucous membrane of the floor of the mouth, beneath the tongue. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000363", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/sublingual+gland"} property_value: homology_notes "Most mammals have well-developed parotid, mandibular, and sublingual glands.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000363", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.553", source="http://bgee.unil.ch/"} @@ -33067,8 +33067,8 @@ is_a: UBERON:0000062 {source="FMA"} ! organ relationship: channel_for UBERON:0001827 ! secretion of lacrimal gland relationship: connects UBERON:0001707 ! nasal cavity relationship: connects UBERON:0010284 ! lacrimal punctum +relationship: in_taxon NCBITaxon:32523 {source="ISBN:9780674021839"} ! Tetrapoda relationship: never_in_taxon NCBITaxon:8459 {source="PMID:7559104"} ! Testudines -relationship: only_in_taxon NCBITaxon:32523 {source="ISBN:9780674021839"} ! Tetrapoda relationship: part_of UBERON:0001750 {source="FMA"} ! lacrimal apparatus property_value: taxon_notes "chelonians lack a lacrimal duct, and lacrimal/harderian secretions remain in or spill from the conjunctival sac[PMID:7559104]" xsd:string @@ -35266,7 +35266,7 @@ is_a: UBERON:0002365 {source="MA"} ! exocrine gland intersection_of: UBERON:0002530 ! gland intersection_of: capable_of GO:0007595 ! lactation relationship: develops_from UBERON:0005333 ! mammary bud -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0002416 ! integumental system relationship: produces UBERON:0001913 ! milk property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg" xsd:anyURI @@ -35843,9 +35843,9 @@ xref: Wikipedia:Supraoptic_nucleus is_a: UBERON:0002308 ! nucleus of brain relationship: capable_of GO:0030103 {source="Wikipedia"} ! vasopressin secretion relationship: contributes_to_morphology_of UBERON:0001898 ! hypothalamus +relationship: in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: mutually_spatially_disjoint_with UBERON:0001930 {source="ABA"} ! paraventricular nucleus of hypothalamus relationship: mutually_spatially_disjoint_with UBERON:0001932 {source="ABA"} ! arcuate nucleus of hypothalamus -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: part_of UBERON:0002271 {source="ABA", source="MA"} ! periventricular zone of hypothalamus relationship: part_of UBERON:0002550 {source="FMA"} ! anterior hypothalamic region property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/SONss.jpg" xsd:anyURI @@ -36558,6 +36558,7 @@ xref: Wikipedia:Red_nucleus xref: ZFA:0000552 is_a: UBERON:0002308 ! nucleus of brain relationship: capable_of_part_of NBO:0000339 ! motor coordination +relationship: in_taxon NCBITaxon:7776 {source="ISBN:0471888893"} ! Gnathostomata relationship: mutually_spatially_disjoint_with UBERON:0001715 {source="ABA"} ! oculomotor nuclear complex relationship: mutually_spatially_disjoint_with UBERON:0001944 {source="ABA"} ! pretectal region relationship: mutually_spatially_disjoint_with UBERON:0001966 {source="ABA"} ! substantia nigra pars reticulata @@ -36568,7 +36569,6 @@ relationship: mutually_spatially_disjoint_with UBERON:0002696 {source="ABA"} ! c relationship: mutually_spatially_disjoint_with UBERON:0002722 {source="ABA"} ! trochlear nucleus relationship: mutually_spatially_disjoint_with UBERON:0002995 {source="ABA"} ! substantia nigra pars lateralis relationship: mutually_spatially_disjoint_with UBERON:0003040 {source="ABA"} ! central gray substance of midbrain -relationship: only_in_taxon NCBITaxon:7776 {source="ISBN:0471888893"} ! Gnathostomata relationship: part_of UBERON:0001943 {source="FMA"} ! midbrain tegmentum property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Cn3nucleus.png" xsd:anyURI property_value: function_notes "in animals without a significant corticospinal tract, gait is mainly controlled by the red nucleus." xsd:string @@ -36641,8 +36641,8 @@ xref: UMLS:C0175173 {source="BIRNLEX:2547"} xref: Wikipedia:Neocortex is_a: UBERON:0002616 ! regional part of brain relationship: contributes_to_morphology_of UBERON:0000956 ! cerebral cortex +relationship: in_taxon NCBITaxon:7742 {source="Wikipedia"} ! Vertebrata relationship: mutually_spatially_disjoint_with UBERON:0002264 {source="ABA"} ! olfactory bulb -relationship: only_in_taxon NCBITaxon:7742 {source="Wikipedia"} ! Vertebrata relationship: part_of UBERON:0000956 ! cerebral cortex property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Neocortex.jpg" xsd:anyURI property_value: homology_notes "The 6-layer neocortex is well conserved in all extant mammals, but not present in birds or reptils" xsd:string {source="PMID:23027930"} @@ -36776,9 +36776,9 @@ xref: VHOG:0001177 xref: Wikipedia:Hippocampus is_a: UBERON:0002616 ! regional part of brain relationship: capable_of_part_of GO:0007613 {source="Wikipedia"} ! memory +relationship: in_taxon NCBITaxon:40674 {source="Wikipedia:Hippocampus"} ! Mammalia relationship: mutually_spatially_disjoint_with UBERON:0001885 {source="ABA"} ! dentate gyrus of hippocampal formation relationship: mutually_spatially_disjoint_with UBERON:0002601 {source="ABA"} ! fasciolar gyrus -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia:Hippocampus"} ! Mammalia relationship: part_of UBERON:0000349 {source="FMA"} ! limbic system relationship: part_of UBERON:0002421 {source="ABA"} ! hippocampal formation relationship: part_of UBERON:0002600 {source="FMA"} ! limbic lobe @@ -37558,7 +37558,7 @@ xref: Wikipedia:Intestinal_crypt is_a: UBERON:0002530 ! gland relationship: contributes_to_morphology_of UBERON:0001242 ! intestinal mucosa relationship: has_quality PATO:0002299 {source="Wikipedia:Tubular_gland"} ! tubular -relationship: only_in_taxon NCBITaxon:32523 {notes="further investigation required", source="ISBN:9780521617147"} ! Tetrapoda +relationship: in_taxon NCBITaxon:32523 {notes="further investigation required", source="ISBN:9780521617147"} ! Tetrapoda relationship: part_of UBERON:0001242 ! intestinal mucosa relationship: seeAlso UBERON:2005256 ! intervillus pockets property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg" xsd:anyURI @@ -37638,7 +37638,7 @@ is_a: UBERON:0000487 {source="FMA-text-def", source="https://github.com/obopheno intersection_of: UBERON:0000483 ! epithelium intersection_of: composed_primarily_of CL:0000115 ! endothelial cell relationship: develops_from UBERON:0000926 {possible_exception="UBERON:0001985", source="FMA-inferred"} ! mesoderm -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata property_value: has_relational_adjective "endothelial" xsd:string [Term] @@ -37672,7 +37672,7 @@ is_a: UBERON:0000062 ! organ relationship: develops_from UBERON:0000995 {source="ISBN:0073040584"} ! uterus relationship: develops_from UBERON:0003124 {source="Wikipedia"} ! chorion membrane relationship: develops_from UBERON:0004340 {source="ISBN:0073040584"} ! allantois -relationship: only_in_taxon NCBITaxon:32525 {source="https://github.com/obophenotype/uberon/issues/1376"} ! Theria +relationship: in_taxon NCBITaxon:32525 {source="https://github.com/obophenotype/uberon/issues/1376"} ! Theria relationship: part_of UBERON:0000474 ! female reproductive system relationship: part_of UBERON:0016887 ! entire extraembryonic component property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Placenta.jpg" xsd:anyURI @@ -38560,9 +38560,9 @@ xref: XAO:0004214 intersection_of: UBERON:0001021 ! nerve intersection_of: extends_fibers_into UBERON:0020358 ! accessory XI nerve nucleus relationship: dubious_for_taxon NCBITaxon:8292 {source="VHOG", source="Wikipedia", seeAlso="http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7"} ! Amphibia +relationship: in_taxon NCBITaxon:32523 ! Tetrapoda relationship: innervates UBERON:0001737 ! larynx relationship: innervates UBERON:3010692 {gci_relation="part_of", gci_filler="NCBITaxon:8292", source="ISBN:080184780X"} ! m. cucullaris -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png" xsd:anyURI property_value: external_definition "A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris." xsd:string {source="ISBN:080184780X", source="XAO:0004214"} property_value: external_definition "Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, 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:0000699", ontology="VHOG", source="http://bgee.unil.ch/"} @@ -38890,9 +38890,9 @@ xref: ZFA:0000029 is_a: UBERON:0002616 ! regional part of brain relationship: contributes_to_morphology_of UBERON:0000955 ! brain relationship: immediate_transformation_of UBERON:0007277 {source="Bgee:AN"} ! presumptive hindbrain +relationship: in_taxon NCBITaxon:89593 ! Craniata relationship: mutually_spatially_disjoint_with UBERON:0001891 {exceptions="ZFA", source="ABA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} ! midbrain relationship: mutually_spatially_disjoint_with UBERON:0001894 {source="ABA"} ! diencephalon -relationship: only_in_taxon NCBITaxon:89593 ! Craniata relationship: overlaps UBERON:0002298 {notes="modified-source-relation", source="ABA"} ! brainstem relationship: part_of UBERON:0000955 {source="ZFA"} ! brain relationship: present_in_taxon NCBITaxon:7762 {source="PMID:8932866"} ! Myxinidae @@ -38958,7 +38958,7 @@ xref: UMLS:C0028109 {source="ncithesaurus:Nipple"} xref: Wikipedia:Nipple is_a: UBERON:0000475 ! organism subdivision relationship: develops_from UBERON:0008425 {source="Stedmans"} ! mammary ridge -relationship: only_in_taxon NCBITaxon:32525 ! Theria +relationship: in_taxon NCBITaxon:32525 ! Theria relationship: part_of UBERON:0000310 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! breast relationship: part_of UBERON:0001911 ! mammary gland property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/59/Female_nipple_profile.jpg" xsd:anyURI @@ -39205,10 +39205,10 @@ relationship: capable_of NBO:0000347 ! gross motor coordination relationship: contributes_to_morphology_of UBERON:0001895 ! metencephalon relationship: develops_from UBERON:0006215 {evidence="definitional"} ! rhombic lip relationship: dubious_for_taxon NCBITaxon:117569 {source="http://icb.oxfordjournals.org/content/42/4/743.full"} ! Hyperoartia +relationship: in_taxon NCBITaxon:7742 {source="ISBN:0471888893"} ! Vertebrata relationship: mutually_spatially_disjoint_with UBERON:0001893 {source="ABA"} ! telencephalon relationship: mutually_spatially_disjoint_with UBERON:0002298 {exceptions="ZFA", source="ABA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} ! brainstem relationship: never_in_taxon NCBITaxon:117565 {source="ISBN:0471888893"} ! Myxini -relationship: only_in_taxon NCBITaxon:7742 {source="ISBN:0471888893"} ! Vertebrata relationship: part_of UBERON:0001895 {source="FMA", source="MA"} ! metencephalon relationship: part_of UBERON:0002028 {source="NIF", source="ZFA"} ! hindbrain relationship: present_in_taxon NCBITaxon:117569 {source="ISBN:0471888893"} ! Hyperoartia @@ -39496,7 +39496,7 @@ relationship: capable_of GO:0036161 {source="Wikipedia"} ! calcitonin secretion relationship: capable_of_part_of GO:0055074 {source="Wikipedia"} ! calcium ion homeostasis relationship: contains_process GO:0006590 ! thyroid hormone generation relationship: has_developmental_contribution_from UBERON:0002342 {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neural crest -relationship: only_in_taxon NCBITaxon:7711 {source="Wikipedia:Endostyle"} ! Chordata +relationship: in_taxon NCBITaxon:7711 {source="Wikipedia:Endostyle"} ! Chordata relationship: part_of UBERON:0000949 ! endocrine system relationship: transformation_of UBERON:0007689 ! thyroid diverticulum property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a3/Illu_thyroid_parathyroid.jpg" xsd:anyURI @@ -39577,10 +39577,10 @@ is_a: UBERON:0000171 ! respiration organ relationship: contributes_to_morphology_of UBERON:0001004 ! respiratory system relationship: develops_from UBERON:0000118 ! lung bud relationship: in_lateral_side_of UBERON:0000170 ! pair of lungs +relationship: in_taxon NCBITaxon:7776 ! Gnathostomata relationship: located_in UBERON:0002224 ! thoracic cavity relationship: never_in_taxon NCBITaxon:32443 {editor="https://orcid.org/0000-0002-9415-5104", source="https://github.com/obophenotype/uberon/issues/701"} ! Teleostei relationship: never_in_taxon NCBITaxon:7777 {editor="https://orcid.org/0000-0002-9415-5104", source="https://github.com/obophenotype/uberon/issues/701"} ! Chondrichthyes -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: part_of UBERON:0000170 {note="some species only have a single lung"} ! pair of lungs relationship: surrounded_by UBERON:0009778 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! pleural sac property_value: external_definition "Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010567", ontology="AAO", source="AAO:SBH"} @@ -40774,7 +40774,7 @@ xref: Wikipedia:Appendicular_skeleton xref: XAO:0003166 is_a: UBERON:0010912 ! subdivision of skeleton relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata +relationship: in_taxon NCBITaxon:7776 ! Gnathostomata relationship: overlaps UBERON:0000026 ! appendage relationship: part_of UBERON:0011249 ! appendicular skeletal system property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg" xsd:anyURI @@ -40887,7 +40887,7 @@ xref: SCTID:362707009 xref: UMLS:C0025474 {source="ncithesaurus:Mesentery"} xref: Wikipedia:Mesentery#Mesentery_.28general.29 is_a: UBERON:0000042 ! serous membrane -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray1038.png" xsd:anyURI property_value: external_ontology_notes "in Uberon, this term is used in the generic sense, not necessarily restricted to the peritoneum, consistent with FMA. WP: 'In anatomy, the mesentery is the double layer of peritoneum that suspends the jejunum and ileum from the posterior wall of the abdomen. Its meaning, however, is frequently extended to include double layers of peritoneum connecting various components of the abdominal cavity.'. TODO - check. Consider FMA:259286 - Region of mesentery." xsd:string {external_ontology="FMA"} property_value: has_relational_adjective "mesenteric" xsd:string @@ -41060,7 +41060,7 @@ intersection_of: has_skeleton UBERON:0004381 ! skeleton of limb relationship: confers_advantage_in ENVO:00000446 relationship: develops_from UBERON:0004347 ! limb bud relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: only_in_taxon NCBITaxon:32523 {note="extends to stem tetrapods such as Eusthenopteron"} ! Tetrapoda +relationship: in_taxon NCBITaxon:32523 {note="extends to stem tetrapods such as Eusthenopteron"} ! Tetrapoda property_value: external_definition "Organism subdivision that has as its parts the jointed appendages used for locomotion and manipulation.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010336", ontology="AAO", source="AAO:BJB"} 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:0000336", ontology="VHOG", source="ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268", source="http://bgee.unil.ch/"} @@ -41258,8 +41258,8 @@ xref: ZFA:0000436 is_a: UBERON:0002075 ! viscus disjoint_from: UBERON:0015708 ! splenium of the corpus callosum relationship: develops_from UBERON:0006293 ! spleen primordium +relationship: in_taxon NCBITaxon:7776 {source="multiple sources - true spleen appear in jawed vertebrates"} ! Gnathostomata relationship: located_in UBERON:0002323 ! coelemic cavity lumen -relationship: only_in_taxon NCBITaxon:7776 {source="multiple sources - true spleen appear in jawed vertebrates"} ! Gnathostomata relationship: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0002390 {source="FMA", source="MA"} ! hematopoietic system relationship: part_of UBERON:0002405 ! immune system @@ -41314,7 +41314,7 @@ relationship: develops_from UBERON:0003894 {evidence="definitional"} ! liver pri relationship: develops_from UBERON:0004161 {source="EHDAA2"} ! septum transversum relationship: develops_from UBERON:0008836 {source="http://www.stembook.org/node/512"} ! liver bud relationship: has_part UBERON:0004647 ! liver lobule -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: overlaps UBERON:0002405 {source="ZFA-weakened"} ! immune system relationship: part_of UBERON:0000916 {source="FMA"} ! abdomen relationship: part_of UBERON:0000949 {source="EHDAA2"} ! endocrine system @@ -41374,7 +41374,7 @@ xref: ZFA:0001323 is_a: UBERON:0000062 ! organ is_a: UBERON:0004921 {order="2", source="cjm"} ! subdivision of digestive tract relationship: contributes_to_morphology_of UBERON:0000160 ! intestine -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000160 ! intestine property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg" xsd:anyURI property_value: external_definition "The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001323", ontology="TAO", source="ZFIN:curator"} @@ -41541,8 +41541,8 @@ relationship: develops_from UBERON:0003918 {evidence="definitional"} ! kidney me relationship: develops_from UBERON:0005095 ! kidney rudiment relationship: fma_set_term FMA:264815 relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: mutually_spatially_disjoint_with UBERON:0000160 ! intestine -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0011143 {source="FMA"} ! upper urinary tract property_value: external_definition "One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000250", ontology="AAO", source="AAO:BJB"} @@ -43950,7 +43950,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria [Term] id: UBERON:0002194 @@ -44049,7 +44049,7 @@ relationship: has_part CL:0000438 ! luteinizing hormone secreting cell relationship: has_part CL:0000439 {source="ZFA"} ! prolactin secreting cell relationship: has_part CL:0000467 {source="ZFA"} ! adrenocorticotropic hormone secreting cell relationship: has_part CL:0002312 ! somatotroph -relationship: only_in_taxon NCBITaxon:7742 {source="PMID:19084529"} ! Vertebrata +relationship: in_taxon NCBITaxon:7742 {source="PMID:19084529"} ! Vertebrata relationship: part_of UBERON:0000007 ! pituitary gland property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray1181.png" xsd:anyURI property_value: external_definition "Region of the pituitary gland derived from the buccal protrusion consisting of three regions.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010540", ontology="AAO", source="AAO:BJB"} @@ -44097,7 +44097,7 @@ xref: UMLS:C0025056 {source="BIRNLEX:925"} xref: VHOG:0001179 xref: Wikipedia:Median_eminence is_a: UBERON:0005408 ! circumventricular organ -relationship: only_in_taxon NCBITaxon:8287 {source="ISBN:0471888893"} ! Sarcopterygii +relationship: in_taxon NCBITaxon:8287 {source="ISBN:0471888893"} ! Sarcopterygii relationship: part_of UBERON:0002198 ! neurohypophysis property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/HypothalamicNuclei.PNG" xsd:anyURI property_value: external_definition "Region of the neurohypophysis.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010539", ontology="AAO", source="AAO:BJB"} @@ -44159,7 +44159,7 @@ is_a: UBERON:0010134 {source="MA"} ! secretory circumventricular organ relationship: capable_of GO:0001992 {source="Wikipedia"} ! regulation of systemic arterial blood pressure by vasopressin relationship: capable_of GO:0030103 {source="Wikipedia"} ! vasopressin secretion relationship: develops_from UBERON:0002346 ! neurectoderm -relationship: only_in_taxon NCBITaxon:7742 {source="PMID:19084529"} ! Vertebrata +relationship: in_taxon NCBITaxon:7742 {source="PMID:19084529"} ! Vertebrata relationship: part_of UBERON:0000007 {source="ZFA"} ! pituitary gland relationship: present_in_taxon NCBITaxon:117569 {source="Ariens, p. 1192"} ! Hyperoartia property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b9/Pituitary_gland_representation.PNG" xsd:anyURI @@ -44198,7 +44198,7 @@ is_a: UBERON:0011216 {source="FMA"} ! organ system subdivision relationship: bounding_layer_of UBERON:0000468 ! multicellular organism relationship: has_part UBERON:0002072 ! hypodermis relationship: has_part UBERON:0002097 ! skin of body -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0002416 {source="FMA"} ! integumental system property_value: curator_notes "in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition." xsd:string property_value: external_definition "Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000239", ontology="AAO", source="AAO:EJS"} @@ -44664,7 +44664,7 @@ xref: ZFA:0005153 intersection_of: UBERON:0000982 ! skeletal joint intersection_of: surrounded_by UBERON:0001484 ! articular capsule disjoint_from: UBERON:0011134 ! nonsynovial joint -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata property_value: external_definition "Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005153", ontology="TAO", source="ZFIN:Curator"} [Term] @@ -44908,8 +44908,8 @@ relationship: capable_of GO:0050910 ! detection of mechanical stimulus involved relationship: dubious_for_taxon NCBITaxon:8292 ! Amphibia relationship: dubious_for_taxon NCBITaxon:8457 ! Sauropsida relationship: has_part CL:0000202 ! auditory hair cell +relationship: in_taxon NCBITaxon:32523 {notes="https://github.com/obophenotype/uberon/issues/387"} ! Tetrapoda relationship: located_in UBERON:0002295 {source="Wikipedia:Scala_media"} ! scala media -relationship: only_in_taxon NCBITaxon:32523 {notes="https://github.com/obophenotype/uberon/issues/387"} ! Tetrapoda relationship: part_of UBERON:0001855 {source="MA"} ! cochlear duct of membranous labyrinth relationship: present_in_taxon NCBITaxon:40674 ! Mammalia property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png" xsd:anyURI @@ -44978,7 +44978,7 @@ is_a: UBERON:0001474 ! bone element relationship: anterior_to UBERON:0001676 ! occipital bone relationship: contributes_to_morphology_of UBERON:0004339 ! vault of skull relationship: develops_from UBERON:0006251 {evidence="definitional"} ! interparietal bone primordium -relationship: only_in_taxon NCBITaxon:40674 {source="MP:0000077"} ! Mammalia +relationship: in_taxon NCBITaxon:40674 {source="MP:0000077"} ! Mammalia relationship: part_of UBERON:0001703 ! neurocranium relationship: part_of UBERON:0003113 {notes="vault series", source="ISBN:0073040584"} ! dermatocranium relationship: part_of UBERON:0004339 {source="PMID:11523816"} ! vault of skull @@ -45594,7 +45594,7 @@ relationship: capable_of GO:0043695 {source="Wikipedia"} ! detection of pheromon relationship: develops_from UBERON:0003050 {source="Wikipedia"} ! olfactory placode relationship: has_developmental_contribution_from UBERON:0009714 {source="EHDAA2-abduced"} ! intermaxillary process relationship: has_quality PATO:0000588 {gci_relation="part_of", gci_filler="NCBITaxon:314295"} ! vestigial -relationship: only_in_taxon NCBITaxon:8287 ! Sarcopterygii +relationship: in_taxon NCBITaxon:8287 ! Sarcopterygii relationship: part_of UBERON:0000004 ! nose relationship: part_of UBERON:0009954 ! vomeronasal system property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/84/Gray51.png" xsd:anyURI @@ -46301,7 +46301,7 @@ xref: ZFA:0001617 is_a: UBERON:0000476 ! acellular anatomical structure relationship: capable_of_part_of GO:0009590 ! detection of gravity relationship: composed_primarily_of CHEBI:3311 ! calcium carbonate -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002519 {source="MP", source="Wikipedia"} ! otolithic part of statoconial membrane property_value: axiom_lost_from_external_ontology "relationship loss: develops_from immature otolith (TAO:0000139)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001621", ontology="TAO"} property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg" xsd:anyURI @@ -46932,7 +46932,7 @@ intersection_of: UBERON:0003215 ! alveolus intersection_of: part_of UBERON:0002048 ! lung relationship: contains_process GO:0007585 ! respiratory gaseous exchange by respiratory system relationship: contributes_to_morphology_of UBERON:0008874 ! pulmonary acinus -relationship: only_in_taxon NCBITaxon:40674 {source="PMID:12625309", source="PMID:12869615"} ! Mammalia +relationship: in_taxon NCBITaxon:40674 {source="PMID:12625309", source="PMID:12869615"} ! Mammalia relationship: part_of UBERON:0006524 {source="MA"} ! alveolar system relationship: part_of UBERON:0008874 ! pulmonary acinus property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/4/46/Alveolus_diagram.svg" xsd:anyURI @@ -47584,7 +47584,7 @@ relationship: develops_from UBERON:0004880 {source="ZFA"} ! chordamesoderm relationship: develops_from UBERON:0006267 {source="EHDAA2"} ! notochordal plate relationship: dorsal_to UBERON:0001555 ! digestive tract relationship: existence_starts_during UBERON:0000068 ! embryo stage -relationship: only_in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata +relationship: in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata relationship: part_of UBERON:0000922 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! embryo relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein @@ -47635,8 +47635,8 @@ xref: ZFA:0000155 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle relationship: develops_from UBERON:0003059 {source="ZFA"} ! presomitic mesoderm +relationship: in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata relationship: never_in_taxon NCBITaxon:7712 {source="PMID:17237766"} ! Tunicata -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata property_value: axiom_lost_from_external_ontology "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} property_value: axiom_lost_from_external_ontology "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} property_value: axiom_lost_from_external_ontology "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO"} @@ -47672,7 +47672,7 @@ disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: composed_primarily_of UBERON:0002365 ! exocrine gland relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa [Term] id: UBERON:0002331 @@ -47818,8 +47818,8 @@ xref: Wikipedia:Corpus_callosum is_a: UBERON:0002473 {source="FMA-part_of", source="MA"} ! intercerebral commissure is_a: UBERON:0005340 {source="MP"} ! dorsal telencephalic commissure relationship: contributes_to_morphology_of UBERON:0001893 ! telencephalon +relationship: in_taxon NCBITaxon:9347 {source="Wikipedia"} ! Eutheria relationship: never_in_taxon NCBITaxon:9255 {source="Wikipedia"} ! Monotremata -relationship: only_in_taxon NCBITaxon:9347 {source="Wikipedia"} ! Eutheria property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/aa/Gray733.png" xsd:anyURI property_value: external_definition "The largest commissure of the brain connecting the cerebral hemispheres. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001608", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/corpus+callosum"} property_value: homology_notes "In addition to the anterior commissure, placental mammals have a phylogenetically new forebrain commissure, the corpus callosum, which primarily interconnects the neocortex of the cerebral hemispheres.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001608", ontology="VHOG", source="DOI:10.1111/j.1749-6632.1969.tb20447.x Ebner FF, A comparison of primitive forebrain organization in metatherian and eutherian mammals. Annals of the New York Academy of Sciences (1969)", source="http://bgee.unil.ch/"} @@ -47991,7 +47991,7 @@ relationship: develops_from UBERON:0003075 {source="BTO"} ! neural plate relationship: develops_from UBERON:0005062 {source="PMID:11523831"} ! neural fold relationship: dubious_for_taxon NCBITaxon:117565 {source="ISBN:0073040584", source="PMID:17377535"} ! Myxini relationship: existence_starts_during UBERON:0000110 {source="PMID:11523831"} ! neurula stage -relationship: only_in_taxon NCBITaxon:89593 {notes="Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells", source="ISBN:0073040584"} ! Craniata +relationship: in_taxon NCBITaxon:89593 {notes="Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells", source="ISBN:0073040584"} ! Craniata relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm property_value: curator_notes "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." xsd:string property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI @@ -48578,7 +48578,7 @@ xref: UMLS:C0031869 {source="ncithesaurus:Pia_Mater"} xref: Wikipedia:Pia_mater is_a: UBERON:0000391 ! leptomeninx relationship: composed_primarily_of UBERON:0011825 ! loose connective tissue -relationship: only_in_taxon NCBITaxon:40674 {notes="check-aves", source="ISBN:0073040584"} ! Mammalia +relationship: in_taxon NCBITaxon:40674 {notes="check-aves", source="ISBN:0073040584"} ! Mammalia property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray770-en.svg" xsd:anyURI property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Gray770.png" xsd:anyURI property_value: editor_note "consider adding adjacency relationship to neuraxis (brain+spinal cord); however note that at this time the meninges may be considered part of the nervous system" xsd:string @@ -48610,8 +48610,8 @@ xref: UMLS:C1510935 {source="ncithesaurus:Arachnoid_Membrane"} xref: Wikipedia:Arachnoid_mater is_a: UBERON:0000391 ! leptomeninx relationship: composed_primarily_of GO:0071953 ! elastic fiber +relationship: in_taxon NCBITaxon:40674 {source="ISBN:0073040584"} ! Mammalia relationship: mutually_spatially_disjoint_with UBERON:0002049 {source="ISBN:0471888893"} ! vasculature -relationship: only_in_taxon NCBITaxon:40674 {source="ISBN:0073040584"} ! Mammalia property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a0/Gray767.png" xsd:anyURI [Term] @@ -48785,7 +48785,7 @@ xref: VHOG:0001261 xref: Wikipedia:Prostate is_a: UBERON:0010147 ! male accessory sex gland relationship: develops_from UBERON:0003820 ! prostate bud -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia +relationship: in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Prostatelead.jpg" xsd:anyURI property_value: editor_note "TODO - FMA treats the gland as part of the prostate - see also FMA:74119." xsd:string property_value: has_relational_adjective "prostatic" xsd:string @@ -48908,7 +48908,7 @@ relationship: contains_process GO:0030217 ! T cell differentiation relationship: develops_from UBERON:0005562 {source="ZFA"} ! thymus primordium relationship: has_part UBERON:0003483 ! thymus lymphoid tissue relationship: has_part UBERON:0003846 ! thymus epithelium -relationship: only_in_taxon NCBITaxon:7776 {source="multiple sources - true thymus appears in jawed vertebrates"} ! Gnathostomata +relationship: in_taxon NCBITaxon:7776 {source="multiple sources - true thymus appears in jawed vertebrates"} ! Gnathostomata relationship: part_of UBERON:0000153 ! anterior region of body relationship: part_of UBERON:0000949 {source="XAO"} ! endocrine system relationship: part_of UBERON:0002390 {source="FMA", source="MA"} ! hematopoietic system @@ -49331,7 +49331,7 @@ xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue relationship: has_part GO:0031012 ! extracellular matrix -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa property_value: external_definition "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000098", ontology="AAO", source="AAO:LAP"} property_value: external_definition "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001641", ontology="TAO", source="TAO:wd"} property_value: external_definition "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000017", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} @@ -49365,8 +49365,8 @@ intersection_of: composed_primarily_of CL:0000187 ! muscle cell disjoint_from: UBERON:0003714 ! neural tissue relationship: capable_of GO:0006936 ! muscle contraction relationship: develops_from UBERON:0000926 ! mesoderm +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: mutually_spatially_disjoint_with UBERON:0003714 ! neural tissue -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001015 ! musculature property_value: external_definition "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000306", ontology="AAO", source="AAO:LAP"} @@ -49554,7 +49554,7 @@ disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: develops_from UBERON:0003061 {evidence="definitional"} ! blood island -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system property_value: external_definition "Anatomical system that consists of the blood and blood forming tissues.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011002", ontology="AAO", source="AAO:EJS"} property_value: has_relational_adjective "hematopoietic" xsd:string @@ -50180,7 +50180,7 @@ xref: Wikipedia:Autonomic_nervous_system xref: ZFA:0001574 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: contributes_to_morphology_of UBERON:0001016 ! nervous system -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000010 {source="EMAPA", source="MA", source="NIFSTD", source="ZFA-modified-from-isa"} ! peripheral nervous system property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI property_value: external_definition "Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [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:0000396", ontology="VHOG", source="http://bgee.unil.ch/"} @@ -50212,7 +50212,7 @@ xref: Wikipedia:Clitoris is_a: UBERON:0000062 {source="Wikipedia"} ! organ relationship: contributes_to_morphology_of UBERON:0005056 ! external female genitalia relationship: develops_from UBERON:0005876 {source="EHDAA2", source="Wikipedia"} ! undifferentiated genital tubercle -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia +relationship: in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: part_of UBERON:0000997 {source="MA"} ! mammalian vulva property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Clitoris_anatomy_labeled-en.svg" xsd:anyURI property_value: has_relational_adjective "clitoral" xsd:string @@ -50322,8 +50322,8 @@ xref: MIAA:0000094 xref: WBbt:0005741 xref: Wikipedia:Tail is_a: UBERON:0011676 ! subdivision of organism along main body axis +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0000154 ! posterior region of body property_value: editor_note "Note we also have a subclass post-anal tail, for the chordate specific structure. currently defined very generally, inclusive of caudal fin" xsd:string @@ -50436,7 +50436,7 @@ disjoint_from: UBERON:0002481 {source="https://github.com/obophenotype/uberon/is relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system relationship: has_part CHEBI:18085 ! glycosaminoglycan relationship: has_part CL:0000138 ! chondrocyte -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0002204 ! musculoskeletal 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:0000060", ontology="AAO"} property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg" xsd:anyURI @@ -50516,8 +50516,8 @@ xref: SCTID:422867004 xref: UMLS:C0175202 {source="BIRNLEX:715"} xref: Wikipedia:Hippocampal_formation is_a: UBERON:0002616 ! regional part of brain +relationship: in_taxon NCBITaxon:40674 {source="Wikipedia:Hippocampus"} ! Mammalia relationship: mutually_spatially_disjoint_with UBERON:0002264 {source="ABA"} ! olfactory bulb -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia:Hippocampus"} ! Mammalia relationship: part_of UBERON:0000203 {source="GO", source="ISBN:0471888893"} ! pallium relationship: part_of UBERON:0000956 {source="MBA-indirect", source="NIFSTD"} ! cerebral cortex property_value: curator_notes "The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum" xsd:string {source="NIF"} @@ -50614,7 +50614,7 @@ relationship: capable_of GO:0061007 ! hepaticobiliary system process relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0002107 ! liver relationship: has_part UBERON:0002294 ! biliary system -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001007 ! digestive system property_value: external_definition "System responsible for the production and movement of bile[ZFIN:curator]." xsd:string {source="ZFIN:curator"} property_value: function_notes "The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. The parts are: liver, bile duct, gall bladder and hepatic duct [GO:0061008]" xsd:string @@ -51338,7 +51338,7 @@ xref: UMLS:C0930557 {source="ncithesaurus:Palatine_Salivary_Gland"} xref: Wikipedia:Palatine_glands is_a: UBERON:0000414 {source="MP"} ! mucous gland is_a: UBERON:0001830 ! minor salivary gland -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0007375 ! roof of mouth [Term] @@ -51734,7 +51734,7 @@ xref: Wikipedia:Lymphoid_system xref: XAO:0003199 xref: ZFA:0000385 is_a: UBERON:0000467 ! anatomical system -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system relationship: part_of UBERON:0002405 ! immune system property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/TE-Lymphatic_system_diagram.svg" xsd:anyURI @@ -52263,7 +52263,7 @@ xref: XAO:0004040 xref: ZFA:0005621 is_a: UBERON:0004755 {source="VSAO"} ! skeletal tissue disjoint_from: UBERON:0005090 ! muscle structure -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001474 ! bone element property_value: editor_note "see https://github.com/obophenotype/uberon/issues/27" xsd:string property_value: external_definition "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000047", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} @@ -52948,7 +52948,7 @@ is_a: UBERON:0002368 {source="PMID:20959416"} ! endocrine gland relationship: capable_of GO:0042701 ! progesterone secretion relationship: develops_from UBERON:0001305 ! ovarian follicle relationship: has_part CL:0000175 ! luteal cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000949 {source="MA"} ! endocrine system relationship: part_of UBERON:0000992 {source="MA"} ! ovary relationship: present_in_taxon NCBITaxon:7762 {source="PMID:20959416"} ! Myxinidae @@ -53357,8 +53357,8 @@ xref: WikipediaCategory:Glands is_a: UBERON:0000062 ! organ disjoint_from: UBERON:0013398 ! choroidal gland relationship: capable_of GO:0046903 ! secretion +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: mutually_spatially_disjoint_with UBERON:0001434 ! skeletal system -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: produces UBERON:0000463 ! organism substance property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" xsd:anyURI property_value: has_relational_adjective "glandular" xsd:string @@ -53431,7 +53431,7 @@ xref: VHOG:0000201 xref: XAO:0000107 xref: ZFA:0000077 is_a: UBERON:0005423 ! developing anatomical structure -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000922 ! embryo property_value: editor_note "See notes from https://github.com/obophenotype/uberon/wiki/The-neural-crest" xsd:string property_value: external_definition "Rapidly proliferating mass of cells at the caudal extremity of the embryo. Its formation is reflected in a caudal carving of the posterior portion of the archenteric canal at NF stage 22. With its further outgrowth, the postanal gut primordium becomes stretched. Its lumen is in broad communication with the hindgut at NF stage 25.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011104", ontology="AAO", source="ISBN:0815318960", source="OMD:tail+bud"} @@ -53463,8 +53463,8 @@ xref: MESH:D005880 xref: Wikipedia:Gill is_a: UBERON:0000062 ! organ relationship: confers_advantage_in ENVO:00002030 +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: never_in_taxon NCBITaxon:32524 ! Amniota -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001004 ! respiratory system [Term] @@ -53482,7 +53482,7 @@ xref: MIAA:0000163 xref: TGMA:0000540 xref: Wikipedia:Sensillum is_a: UBERON:0000020 ! sense organ -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0001016 ! nervous system property_value: editor_note "this term should be ceded to the arthropod anatomy ontology" xsd:string @@ -53524,7 +53524,7 @@ xref: VHOG:0000078 xref: XAO:0000034 xref: ZFA:0000026 is_a: UBERON:0002530 {source="GO"} ! gland -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000924 ! ectoderm property_value: external_definition "A transversely oriented set of cells located deep to the EVL on the pericardial membrane, especially prominent during pharyngula period because of the brightly refractile cytoplasmic granules (containing hatching enzymes) of the principal cells of the gland. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000026", ontology="TAO", source="ZFIN:curator"} @@ -53563,7 +53563,7 @@ is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0010188 {source="EHDAA2"} ! protuberance relationship: developmentally_induced_by UBERON:0007690 {source="PMID:16313389"} ! early pharyngeal endoderm relationship: has_developmental_contribution_from UBERON:0002342 {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neural crest -relationship: only_in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata +relationship: in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata relationship: part_of UBERON:0008814 ! pharyngeal arch system relationship: part_of UBERON:0008816 {source="PMID:16313389"} ! embryonic head property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png" xsd:anyURI @@ -53594,8 +53594,8 @@ xref: XAO:0000095 xref: ZFA:0000034 is_a: UBERON:0001032 ! sensory system relationship: has_part UBERON:0010202 ! lateral line +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: never_in_taxon NCBITaxon:32524 {source="http://tolweb.org/Amniota"} ! Amniota -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: overlaps UBERON:0000010 ! peripheral nervous system property_value: axiom_lost_from_external_ontology "relationship loss: is_formed_by lateral line receptor organ (AAO:0001001)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000975", ontology="AAO"} property_value: editor_note "we model this as being potentially inclusive of lateral line scales, and thus overlapping with the skeletal system. This is to accomodate TAO" xsd:string @@ -53617,7 +53617,7 @@ xref: TAO:0000111 xref: ZFA:0000111 is_a: UBERON:0002050 ! embryonic structure relationship: dubious_for_taxon NCBITaxon:40674 ! Mammalia -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0004734 ! gastrula property_value: editor_note "TODO - check timing of appearance and disappearance - check relationship with primitive streak. he blastopore lips in amphibians appear to have the equivalent function of the germ ring in zebrafish (ES)" xsd:string property_value: external_definition "Embryonic structure that forms as a thickened annulus at the blastoderm rim. The germ ring is thickened because it is the involuting margin of the blastoderm[ZFIN:ZDB-PUB-961014-576]." xsd:string {source="ZFIN:ZDB-PUB-961014-576"} @@ -53638,6 +53638,7 @@ xref: MAT:0000257 xref: MIAA:0000257 xref: Wikipedia:Scale_(zoology) is_a: UBERON:0003102 ! surface structure +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: never_in_taxon NCBITaxon:311790 ! Afrotheria relationship: never_in_taxon NCBITaxon:314146 ! Euarchontoglires relationship: never_in_taxon NCBITaxon:33554 ! Carnivora @@ -53647,7 +53648,6 @@ relationship: never_in_taxon NCBITaxon:9348 ! Xenarthra relationship: never_in_taxon NCBITaxon:9362 ! Eulipotyphla relationship: never_in_taxon NCBITaxon:9397 ! Chiroptera relationship: never_in_taxon NCBITaxon:9787 ! Perissodactyla -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0002416 ! integumental system relationship: present_in_taxon NCBITaxon:9972 ! Manidae property_value: curator_notes "currently defined in a very inclusive fashion - may be obsoleted and replaced by more specific classes in future versions. The TAO, VSAO amd ZFA classes by this name are classified as 'dermal scales'. Can also be classified by composition - e.g. pangolin keratin scales." xsd:string @@ -53695,8 +53695,8 @@ disjoint_from: UBERON:0005880 ! prepollex disjoint_from: UBERON:0012136 ! prehallux relationship: contributes_to_morphology_of UBERON:0002470 ! autopod region relationship: has_part UBERON:0015023 ! phalanx endochondral element +relationship: in_taxon NCBITaxon:32523 ! Tetrapoda relationship: mutually_spatially_disjoint_with UBERON:0009877 ! metapodium region -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda relationship: part_of UBERON:0012140 {source="PHENOSCAPE:ni"} ! digitopodium region relationship: part_of UBERON:5002544 ! digit plus metapodial segment property_value: curator_notes "this class represents the entire organism subdivision encompassing soft tissue as well as the underlying skeletal framework. The class represents the phalangeal part only - historically the term 'digit' has also been used to represent the unit consisting of a series of phalanges together with a metapodial bone. We may in future relabel this class to avoid confusion with this concept, but the class will continue to represent the phalangeal portion" xsd:string @@ -53728,7 +53728,7 @@ xref: MAT:0000369 xref: MIAA:0000369 xref: XAO:0000305 is_a: UBERON:0005085 {source="cjm"} ! ectodermal placode -relationship: only_in_taxon NCBITaxon:7711 {source="PMID:11523831", source="PMID:22512454"} ! Chordata +relationship: in_taxon NCBITaxon:7711 {source="PMID:11523831", source="PMID:22512454"} ! Chordata relationship: part_of UBERON:0000033 ! head property_value: editor_note "Do not merge with neurogenic placode" xsd:string property_value: taxon_notes "Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons" xsd:string {source="PMID:11523831"} @@ -54160,10 +54160,10 @@ xref: UMLS:C0175359 {source="BIRNLEX:1037"} xref: Wikipedia:Olivary_pretectal_nucleus is_a: UBERON:0011214 {source="FMA"} ! nucleus of midbrain tectum relationship: contributes_to_morphology_of UBERON:0001944 ! pretectal region +relationship: in_taxon NCBITaxon:32523 ! Tetrapoda relationship: mutually_spatially_disjoint_with UBERON:0002711 {source="ABA"} ! nucleus of posterior commissure relationship: mutually_spatially_disjoint_with UBERON:0002996 {source="ABA"} ! nucleus of optic tract relationship: mutually_spatially_disjoint_with UBERON:0006848 {source="ABA"} ! posterior pretectal nucleus -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda relationship: part_of UBERON:0001944 ! pretectal region relationship: present_in_taxon NCBITaxon:8293 {source="ISBN:0471888893"} ! Caudata relationship: present_in_taxon NCBITaxon:9347 {source="ISBN:0471888893"} ! Eutheria @@ -58164,7 +58164,7 @@ xref: neuronames:50 {source="BIRNLEX:1493"} xref: SCTID:369215009 xref: UMLS:C0228263 {source="BIRNLEX:1493"} is_a: UBERON:0000200 ! gyrus -relationship: only_in_taxon NCBITaxon:9443 ! Primates +relationship: in_taxon NCBITaxon:9443 ! Primates relationship: part_of UBERON:0002022 ! insula [Term] @@ -58186,7 +58186,7 @@ xref: UMLS:C0581619 {source="BIRNLEX:1499", source="ncithesaurus:Cervical_Spinal xref: UMLS:C1278837 {source="BIRNLEX:1499"} intersection_of: UBERON:0005844 ! spinal cord segment intersection_of: adjacent_to UBERON:0005434 ! cervical region -relationship: only_in_taxon NCBITaxon:8287 ! Sarcopterygii +relationship: in_taxon NCBITaxon:8287 ! Sarcopterygii [Term] id: UBERON:0002727 @@ -59588,7 +59588,7 @@ xref: neuronames:572 {source="BIRNLEX:1682"} xref: UMLS:C0175430 {source="BIRNLEX:1682"} xref: Wikipedia:Superior_olivary_complex is_a: UBERON:0000125 ! neural nucleus -relationship: only_in_taxon NCBITaxon:40674 {source="NIFSTD"} ! Mammalia +relationship: in_taxon NCBITaxon:40674 {source="NIFSTD"} ! Mammalia relationship: part_of UBERON:0022434 {source="NIFSTD"} ! primary superior olive property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/46/Gray713.png" xsd:anyURI @@ -63904,8 +63904,8 @@ is_obsolete: true replaced_by: GO:0005883 consider: BIRNLEX:846 consider: FMA:63859 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1316272517 consider: NCIT:C13263 -consider: NIF_Subcellular:sao1316272517 consider: UMLS:C0027834 [Term] @@ -64114,10 +64114,10 @@ xref: MBA:628 xref: neuronames:470 {source="BIRNLEX:868"} xref: UMLS:C0175356 {source="BIRNLEX:868"} is_a: UBERON:0011214 {source="FMA"} ! nucleus of midbrain tectum +relationship: in_taxon NCBITaxon:9347 {source="ISBN:0471888893"} ! Eutheria relationship: mutually_spatially_disjoint_with UBERON:0002565 {source="ABA"} ! olivary pretectal nucleus relationship: mutually_spatially_disjoint_with UBERON:0002711 {source="ABA"} ! nucleus of posterior commissure relationship: mutually_spatially_disjoint_with UBERON:0006848 {source="ABA"} ! posterior pretectal nucleus -relationship: only_in_taxon NCBITaxon:9347 {source="ISBN:0471888893"} ! Eutheria relationship: part_of UBERON:0001944 ! pretectal region [Term] @@ -64189,9 +64189,9 @@ replaced_by: GO:0005882 consider: BIRNLEX:879 consider: FMA:63851 consider: GAID:1079 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao952483289 consider: MESH:A11.284.195.190.750.410 consider: NCIT:C13248 -consider: NIF_Subcellular:sao952483289 consider: UMLS:C0021770 [Term] @@ -64243,9 +64243,9 @@ is_obsolete: true consider: FMA:63850 consider: GAID:1080 consider: GO:0005884 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao2006047981 consider: MESH:A11.284.195.190.750.510 consider: NCIT:C13255 -consider: NIF_Subcellular:sao2006047981 consider: UMLS:C0025979 {source="ncithesaurus:Actin_Filament"} [Term] @@ -65320,7 +65320,7 @@ xref: WBbt:0005755 is_a: UBERON:0001002 ! cuticle relationship: has_part GO:0098643 ! banded collagen fibril relationship: has_quality PATO:0002462 ! collagenous -relationship: only_in_taxon NCBITaxon:6231 ! Nematoda +relationship: in_taxon NCBITaxon:6231 ! Nematoda property_value: taxon_notes "currently restricted to nematodes, but this may be too strict" xsd:string [Term] @@ -65563,7 +65563,7 @@ xref: XAO:0000056 xref: ZFA:0000031 is_a: UBERON:0000479 ! tissue relationship: immediate_transformation_of UBERON:0006599 {source="Bgee:AN"} ! presumptive hypochord -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata property_value: external_definition "A transient rod-like structure which is endodermally derived and located immediately ventral to the notochord. The hypochord is thought to play a role in positioning the dorsal aorta. Eriksson and Lofberg, 2000.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000031", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Unsegmented ventral structure in the caudal region of anuran larvae; near metamorphosis the hypochord fuses to the coccyx, thereby forming the urostyle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000733", ontology="AAO", source="AAO:Pugener_2002"} property_value: homology_notes "In other words, we identified variations in gene expression patterns that may contribute to a molecular basis of evolutionary variation of axial structures between Teleostei and Mammalia in the determination of body axis. As already mentioned, one such difference is illustrated by the hypochord present in lower vertebrates but absent in higher animals. Perhaps, Tbx-b and Tbx-c are involved in the mechanisms underlying the formation of this organ that were lost during later evolution leading to the disappearance of the hypochord itself, similarly to other organs, such as the lateral line.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000081", ontology="VHOG", source="PMID:11548409 Korzh VP, T-box genes and developmental decisions that cells make. Russian Journal of Developmental Biology (2001)", source="http://bgee.unil.ch/"} @@ -65702,7 +65702,7 @@ is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0010188 {source="EHDAA2"} ! protuberance relationship: contributes_to_morphology_of UBERON:0004341 ! primitive streak relationship: immediate_transformation_of UBERON:0007283 {source="Bgee:AN"} ! presumptive shield -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002541 {source="ZFA"} ! germ ring relationship: part_of UBERON:0004341 {source="EHDAA"} ! primitive streak property_value: editor_note "This class groups together possibly disparate structures, following homology class in vHOG; early development terms need review" xsd:string @@ -65865,7 +65865,7 @@ xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000926 ! mesoderm property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -66085,7 +66085,7 @@ is_a: UBERON:0016879 ! future central nervous system disjoint_from: UBERON:0011669 ! neural plate of carapace relationship: developmentally_induced_by UBERON:0002328 {source="Wikipedia"} ! notochord relationship: immediate_transformation_of UBERON:0007284 {source="Bgee:AN"} ! presumptive neural plate -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata +relationship: in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI property_value: external_definition "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000132", ontology="TAO", source="ZFIN:curator"} 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:0000068", 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/"} @@ -66236,7 +66236,7 @@ xref: ZFA:0000121 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: develops_from UBERON:0000926 {source="EHDAA2", source="XAO"} ! mesoderm -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm relationship: surrounds UBERON:0003887 ! intraembryonic coelom property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -66446,7 +66446,7 @@ xref: ZFA:0001080 is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population relationship: develops_from UBERON:0002329 {source="ZFA"} ! somite -relationship: only_in_taxon NCBITaxon:7742 {source="VHOG:0000680"} ! Vertebrata +relationship: in_taxon NCBITaxon:7742 {source="VHOG:0000680"} ! Vertebrata property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI property_value: external_definition "Skeletogenic portion of somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010571", ontology="AAO", source="AAO:EJS"} property_value: external_ontology_notes "part_of somite in XAO" xsd:string {external_ontology="XAO"} @@ -66800,7 +66800,7 @@ intersection_of: UBERON:0000479 ! tissue intersection_of: composed_primarily_of CL:0008019 ! mesenchymal cell relationship: functionally_related_to GO:0032502 ! developmental process relationship: has_developmental_contribution_from UBERON:0000926 {gci_relation="part_of", gci_filler="NCBITaxon:7711"} ! mesoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI property_value: editor_note "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string property_value: external_definition "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000393", ontology="TAO", source="ZFIN:curator"} @@ -66989,8 +66989,8 @@ xref: Wikipedia:Skull_roof xref: XAO:0003169 xref: ZFA:0000863 is_a: UBERON:0011159 ! primary subdivision of cranial skeletal system +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: never_in_taxon NCBITaxon:7777 {source="ISBN:0073040584"} ! Chondrichthyes -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0010323 {source="ZFA"} ! cranial skeletal system relationship: part_of UBERON:0010364 ! dermal skeleton property_value: editor_note "wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007" xsd:string @@ -67336,7 +67336,7 @@ relationship: adjacent_to UBERON:0000922 ! embryo relationship: develops_from UBERON:0005971 {source="ISBN:0073040584"} ! amniotic fold relationship: has_part UBERON:0003265 ! chorionic mesenchyme relationship: has_part UBERON:0003374 ! chorionic ectoderm -relationship: only_in_taxon NCBITaxon:32524 {source="Hymans"} ! Amniota +relationship: in_taxon NCBITaxon:32524 {source="Hymans"} ! Amniota property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/51/Gray24.png" xsd:anyURI property_value: development_notes "Extra-embryonic ectoderm" xsd:string {source="PMID:19829370"} property_value: external_definition "The outer membrane enclosing the embryo in reptiles, birds, and mammals. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000200", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/chorion"} @@ -67362,7 +67362,7 @@ xref: Wikipedia:Vitelline_membrane xref: XAO:0000030 is_a: UBERON:0005764 ! acellular membrane relationship: bounding_layer_of CL:0000025 ! egg cell -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria property_value: axiom_lost_from_external_ontology "relationship loss: part_of zygote (AAO:0010324)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010332", ontology="AAO"} property_value: editor_note "TODO - consider GO CC request. GO:0030704-vitelline membrane formation considered a subclass of CC organization" xsd:string property_value: external_definition "Thin membrane enclosing and immediately adjacent to the ovum. Produced in the ovary.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010332", ontology="AAO", source="AAO:EJS"} @@ -67403,8 +67403,8 @@ xref: XAO:0000118 is_a: UBERON:0000117 ! respiratory tube relationship: contributes_to_morphology_of UBERON:0001004 ! respiratory system relationship: develops_from UBERON:0008947 {source="EHDAA2"} ! respiratory primordium +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: located_in UBERON:0002224 ! thoracic cavity -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0007196 ! tracheobronchial tree property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg" xsd:anyURI property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg" xsd:anyURI @@ -67427,7 +67427,7 @@ xref: TADS:0000315 xref: Wikipedia:Invertebrate_trachea is_a: UBERON:0001005 ! respiratory airway relationship: has_part UBERON:0003914 ! epithelial tube -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0005155 ! open tracheal system [Term] @@ -67487,7 +67487,7 @@ xref: WikipediaCategory:Skull is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system relationship: has_part UBERON:0003128 ! cranium relationship: has_part UBERON:0003278 ! skeleton of lower jaw -relationship: only_in_taxon NCBITaxon:89593 ! Craniata +relationship: in_taxon NCBITaxon:89593 ! Craniata relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0010323 ! cranial skeletal system property_value: external_ontology_notes "in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible." xsd:string {external_ontology="FMA"} @@ -67502,7 +67502,7 @@ synonym: "sternum" BROAD [] xref: HAO:0000956 xref: Wikipedia:Sternum_(arthropod) is_a: UBERON:0010000 ! multicellular anatomical structure -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda property_value: editor_note "this term should be ceded to the arthropod anatomy ontology" xsd:string [Term] @@ -67513,7 +67513,7 @@ xref: HAO:0001017 xref: TADS:0000281 xref: Wikipedia:Arthropod_leg is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda property_value: editor_note "this term should be ceded to the arthropod anatomy ontology." xsd:string {source="3"} property_value: taxon_notes "homology of leg segments between groups are difficult to prove and are the source of much argument. Some authors posit up to eleven segments per leg for the most recent common ancestor of extant arthropods, but modern arthropods have eight or fewer." xsd:string @@ -67654,7 +67654,7 @@ xref: BTO:0001110 xref: HAO:0000812 is_a: UBERON:0000468 ! multicellular organism relationship: immediate_transformation_of UBERON:0002548 ! larva -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:0003143 @@ -67674,7 +67674,7 @@ intersection_of: UBERON:0000468 ! multicellular organism intersection_of: existence_starts_and_ends_during UBERON:0000070 ! pupal stage relationship: has_quality PATO:0001187 ! pupal relationship: immediate_transformation_of UBERON:0003142 {gci_relation="part_of", gci_filler="NCBITaxon:7227"} ! prepupa -relationship: only_in_taxon NCBITaxon:33392 ! Endopterygota +relationship: in_taxon NCBITaxon:33392 ! Endopterygota property_value: has_relational_adjective "pupal" xsd:string [Term] @@ -67765,7 +67765,7 @@ xref: BTO:0004711 xref: EFO:0001927 xref: HAO:0000398 is_a: UBERON:6007284 ! insect region of integument -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0000033 ! head [Term] @@ -67786,7 +67786,7 @@ xref: HAO:0000658 xref: TGMA:0000041 is_a: UBERON:0006056 ! posterior surface of head disjoint_from: UBERON:0006054 ! surface of occiput -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda [Term] id: UBERON:0003156 @@ -67839,7 +67839,7 @@ xref: BTO:0001758 xref: HAO:0000661 xref: Wikipedia:Ocellus#Ocelli is_a: UBERON:0000963 ! head sensillum -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda [Term] id: UBERON:0003162 @@ -67849,7 +67849,7 @@ xref: HAO:0000481 xref: Wikipedia:Ocellus#Ocelli is_a: UBERON:0003161 ! dorsal ocellus disjoint_from: UBERON:0003211 {source="lexical"} ! median eye -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda [Term] id: UBERON:0003163 @@ -68151,7 +68151,7 @@ synonym: "germarium derived egg chamber" EXACT [FBbt:00004894] xref: NCIT:C61362 xref: UMLS:C1571705 {source="ncithesaurus:Follicle"} is_a: UBERON:8450001 ! egg follicle -relationship: only_in_taxon NCBITaxon:50557 {source="https://github.com/obophenotype/uberon/issues/476"} ! Insecta +relationship: in_taxon NCBITaxon:50557 {source="https://github.com/obophenotype/uberon/issues/476"} ! Insecta [Term] id: UBERON:0003200 @@ -68167,7 +68167,7 @@ def: "The outer layer of the procuticle of certain crustaceans and arthropods, w xref: BTO:0001602 xref: HAO:0000311 is_a: UBERON:0000476 ! acellular anatomical structure -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda [Term] id: UBERON:0003202 @@ -68176,7 +68176,7 @@ def: "The inner layer of the procuticle in certain crustaceans and arthropods, w xref: BTO:0001603 xref: HAO:0000290 is_a: UBERON:0000476 ! acellular anatomical structure -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda [Term] id: UBERON:0003203 @@ -68230,7 +68230,7 @@ xref: Wikipedia:Blood-nerve_barrier is_a: UBERON:0000119 ! cell layer relationship: adjacent_to UBERON:0000179 ! haemolymphatic fluid relationship: adjacent_to UBERON:0001021 ! nerve -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0001016 ! nervous system [Term] @@ -68242,7 +68242,7 @@ synonym: "blood-CSF barrier" EXACT [MP:0006088] is_a: UBERON:0000119 ! cell layer relationship: adjacent_to UBERON:0000178 ! blood relationship: adjacent_to UBERON:0001359 ! cerebrospinal fluid -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001886 ! choroid plexus @@ -68256,7 +68256,7 @@ synonym: "median ocellus" EXACT [HAO:0000526] xref: HAO:0000526 xref: Wikipedia:Ocellus#Ocelli is_a: UBERON:0000970 ! eye -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda [Term] id: UBERON:0003212 @@ -68910,7 +68910,7 @@ synonym: "temporal region of head" RELATED [FMA:63867] xref: FMA:63867 xref: SCTID:362620003 is_a: UBERON:0001444 {source="FMA"} ! subdivision of head -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata property_value: editor_note "see UBERONREF:0000007 'temporal region'" xsd:string [Term] @@ -75839,8 +75839,8 @@ xref: NCIT:C33574 xref: UMLS:C0037359 {source="ncithesaurus:Smegma"} xref: Wikipedia:Smegma is_a: UBERON:0000456 ! secretion of exocrine gland +relationship: in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: located_in UBERON:0035144 ! preputial space -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia [Term] id: UBERON:0003671 @@ -75929,8 +75929,8 @@ intersection_of: UBERON:0001091 ! calcareous tooth intersection_of: has_quality PATO:0005021 ! unicuspidate disjoint_from: UBERON:0007120 ! premolar tooth relationship: has_part UBERON:0006844 {count="1", comment="EDITOR_NOTE cardinality not allowed with transitivity in OWL"} ! cusp of tooth +relationship: in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: never_in_taxon NCBITaxon:337687 {notes="Although there are a few exceptions, the dental formula for the great majority of cricetids is 1.0.0.3", source="Wikipedia:Cricetidae"} ! Muroidea -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/5/57/Azawakh_K9.jpg" xsd:anyURI property_value: taxon_notes "Most species that develop them normally have four per individual, two in the upper jaw and two in the lower, separated within each jaw by its incisors; humans and dogs are examples. In most animals, canines are the anterior-most teeth in the maxillary bone. The four canines in humans are the two maxillary canines and the two mandibular canines." xsd:string @@ -76578,7 +76578,7 @@ xref: SCTID:243966008 xref: UMLS:C0021445 {source="ncithesaurus:Inguinal_Canal"} xref: Wikipedia:Inguinal_canal is_a: UBERON:0004111 {source="FMA"} ! anatomical conduit -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0003697 {source="Wikipedia"} ! abdominal wall property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b4/Gray1227.png" xsd:anyURI property_value: taxon_notes "In most mammals the canal remains open, and the testis can pass from the scrotum to the abdominal cavity. In humans the canal closes after testicular descent[DOI:10.1046/j.1469-7580.2002.00087.x]" xsd:string @@ -76886,8 +76886,8 @@ xref: Wikipedia:Recurrent_laryngeal_nerve is_a: UBERON:0001021 ! nerve relationship: branching_part_of UBERON:0001759 ! vagus nerve relationship: develops_from UBERON:0003117 {source="Wikipedia"} ! pharyngeal arch 6 +relationship: in_taxon NCBITaxon:32523 ! Tetrapoda relationship: innervates UBERON:0001737 ! larynx -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda property_value: external_definition "Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754]." xsd:string {source="AAO:0010754"} [Term] @@ -78461,7 +78461,7 @@ relationship: connects UBERON:0000995 ! uterus relationship: connects UBERON:0003984 ! uterine tube infundibulum relationship: develops_from UBERON:0003890 ! Mullerian duct relationship: in_lateral_side_of UBERON:0003975 {source="FMA-abduced-lr"} ! internal female genitalia -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0002355 ! pelvic region of trunk property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg" xsd:anyURI property_value: taxon_notes "Homologous to appendix testis" xsd:string {source="Wikipedia:Talk:Fallopian_tube#Homology"} @@ -78510,7 +78510,7 @@ xref: NCIT:C67387 xref: UMLS:C0927195 {source="ncithesaurus:Stroma_Connective_Tissue"} is_a: UBERON:0000064 ! organ part relationship: composed_primarily_of UBERON:0002384 ! connective tissue -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa property_value: has_relational_adjective "stromal" xsd:string [Term] @@ -78644,7 +78644,7 @@ is_a: UBERON:0003037 ! septum relationship: adjacent_to UBERON:0003895 ! hypaxial myotome region relationship: adjacent_to UBERON:0003900 ! epaxial myotome region relationship: composed_primarily_of UBERON:0002384 ! connective tissue -relationship: only_in_taxon NCBITaxon:7776 {source="ISBN:0073040584"} ! Gnathostomata +relationship: in_taxon NCBITaxon:7776 {source="ISBN:0073040584"} ! Gnathostomata relationship: part_of UBERON:0000383 ! musculature of body property_value: axiom_lost_from_external_ontology "relationship loss: subclass myoseptum (TAO:0001089)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000671", ontology="TAO"} property_value: external_definition "A connective tissue partition developing at the apex of the chevron-shaped myotome and separating dorsal (epaxial) and ventral (hypaxial) body wall muscle masses. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000671", ontology="TAO", source="ZFIN:curator"} @@ -78698,7 +78698,7 @@ is_a: UBERON:0004177 ! hemopoietic organ is_a: UBERON:0011510 ! cloacal bursa relationship: contains_process GO:0030097 {source="Wikipedia"} ! hemopoiesis relationship: contains_process GO:0030183 ! B cell differentiation -relationship: only_in_taxon NCBITaxon:8457 ! Sauropsida +relationship: in_taxon NCBITaxon:8457 ! Sauropsida [Term] id: UBERON:0003904 @@ -78813,10 +78813,10 @@ xref: Wikipedia:Red_pulp#Sinusoids is_a: UBERON:0003909 ! sinusoid intersection_of: UBERON:0003909 ! sinusoid intersection_of: part_of UBERON:0001250 ! red pulp of spleen +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: never_in_taxon NCBITaxon:10088 {source="http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml"} ! Mus relationship: never_in_taxon NCBITaxon:9681 {source="http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml"} ! Felidae relationship: never_in_taxon NCBITaxon:9822 {source="http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml"} ! Sus -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0001250 ! red pulp of spleen relationship: present_in_taxon NCBITaxon:10114 {source="http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml"} ! Rattus property_value: taxon_notes "Whereas man and the rat are in the 'sinusal' group, the mouse belongs in the 'nonsinusal' group. The red pulp of spleens of rat, dog, man, and many other mammals contains an elaborate plexus of sinuses; that of mouse, cat, pig and others has no true sinuses and relatively few veins leading from the meshes into collecting veins - http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml" xsd:string @@ -78855,7 +78855,7 @@ synonym: "tooth-like organ" EXACT [http://orcid.org/0000-0002-6601-2165] xref: HAO:0001019 is_a: UBERON:0004765 ! skeletal element relationship: capable_of_part_of GO:0071626 ! mastication -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria [Term] id: UBERON:0003914 @@ -78888,7 +78888,7 @@ xref: EMAPA:35340 xref: FMA:58616 xref: MA:0002481 is_a: UBERON:0001013 ! adipose tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata property_value: external_definition "An accumulation of adipose tissue (fat cells) enclosed in fibrous tissue[BTO]." xsd:string {ontology="BTO"} property_value: external_ontology_notes "FMA says isa fascia organ. Note that XAO and AAO have structures called fat pad/body, but these are gonad-associated, so we place them with the gonad-specific subclass" xsd:string {external_ontology="FMA"} @@ -78907,7 +78907,7 @@ xref: MIAA:0000096 xref: TADS:0000321 xref: TGMA:0001856 is_a: UBERON:0000062 ! organ -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda property_value: editor_note "this term should be ceded to the arthropod anatomy ontology" xsd:string property_value: external_definition "A fatty tissue especially of nearly mature insect larvae that serves as a food reserve[BTO]." xsd:string {ontology="BTO"} @@ -79768,7 +79768,7 @@ xref: FMA:57456 intersection_of: UBERON:0001762 ! turbinate bone intersection_of: part_of UBERON:0001679 ! ethmoid bone relationship: develops_from UBERON:0006332 {source="ISBN:0073040584"} ! nasal capsule -relationship: only_in_taxon NCBITaxon:32523 {source="MP:0008971"} ! Tetrapoda +relationship: in_taxon NCBITaxon:32523 {source="MP:0008971"} ! Tetrapoda property_value: external_ontology_notes "FMA considers nasal concha and nasal concha of ethmoid bone to be synonymous. We disambiguate these here" xsd:string {external_ontology="FMA"} [Term] @@ -79950,7 +79950,7 @@ xref: FMA:18307 xref: SCTID:362262001 xref: Wikipedia:Infundibulum_of_uterine_tube is_a: UBERON:0013515 {source="FMA"} ! subdivision of oviduct -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0003889 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! fallopian tube relationship: present_in_taxon NCBITaxon:8782 ! Aves property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI @@ -80538,8 +80538,8 @@ xref: MESH:D011311 xref: Wikipedia:Baroreceptor is_a: UBERON:0018389 {source="FMA"} ! interoceptor relationship: capable_of GO:0003073 ! regulation of systemic arterial blood pressure +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: located_in UBERON:0001981 ! blood vessel -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0007798 ! vascular system property_value: seeAlso "https://github.com/obophenotype/uberon/issues/510" xsd:anyURI @@ -80562,7 +80562,7 @@ xref: EMAPA:31876 is_a: UBERON:0000119 ! cell layer relationship: composed_primarily_of CL:0002499 ! spongiotrophoblast cell relationship: develops_from UBERON:0004364 {source="PMID:19829370"} ! ectoplacental cone -relationship: only_in_taxon NCBITaxon:9989 {source="MP:0004255", source="PMID:11433360"} ! Rodentia +relationship: in_taxon NCBITaxon:9989 {source="MP:0004255", source="PMID:11433360"} ! Rodentia relationship: part_of UBERON:0001987 ! placenta property_value: development_notes "In the absence of direct lineage analysis, it has been assumed, from histological studies and from the continuity of marker gene expression, that the spongiotrophoblast largely derives from the cells of the ectoplacental cone" xsd:string {source="PMID:19829370"} property_value: structure_notes "Forms a compact layer of non-syncytial cells between the labyrinth and the outer giant cells" xsd:string @@ -80801,7 +80801,7 @@ xref: EMAPA:17545 xref: EMAPA:32712 is_a: UBERON:0014950 ! layer of developing cerebral cortex relationship: develops_from UBERON:0004061 ! neural tube mantle layer -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia +relationship: in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia [Term] id: UBERON:0004041 @@ -81309,8 +81309,8 @@ xref: neuronames:1243 xref: NLXANAT:20081242 xref: Wikipedia:Interposed_nucleus is_a: UBERON:0000125 ! neural nucleus +relationship: in_taxon NCBITaxon:32524 {source="ISBN:0471888893"} ! Amniota relationship: never_in_taxon NCBITaxon:8570 {source="ISBN:0471888893"} ! Serpentes -relationship: only_in_taxon NCBITaxon:32524 {source="ISBN:0471888893"} ! Amniota relationship: part_of UBERON:0002130 {source="NIFSTD"} ! cerebellar nuclear complex property_value: external_definition "The interposed nucleus is a deep nucleus of the cerebellum and is composed of the globose nuclei and the emboliform nuclei. It is located in in the roof (dorsal aspect) of the fourth ventricle, lateral to the fastigial nucleus. It receives its afferent supply from the anterior lobe of the cerebellum and sends output via the superior cerebellar peduncle to the red nucleus." xsd:string {source="Wikipedia:Interposed_nucleus"} property_value: function_notes "modulates muscle stretch reflexes of proximal limb muscles[WP]" xsd:string @@ -81605,7 +81605,7 @@ xref: UMLS:C0227759 {source="ncithesaurus:Labium"} is_a: UBERON:0000014 ! zone of skin relationship: contributes_to_morphology_of UBERON:0005056 ! external female genitalia relationship: in_lateral_side_of UBERON:0005056 {source="FMA-abduced-lr"} ! external female genitalia -relationship: only_in_taxon NCBITaxon:9347 ! Eutheria +relationship: in_taxon NCBITaxon:9347 ! Eutheria relationship: part_of UBERON:0000997 {source="MA"} ! mammalian vulva property_value: has_relational_adjective "labial" xsd:string @@ -81710,7 +81710,7 @@ xref: FMA:285406 xref: MA:0001910 is_a: UBERON:0001444 ! subdivision of head relationship: contributes_to_morphology_of UBERON:0001456 ! face -relationship: only_in_taxon NCBITaxon:89593 ! Craniata +relationship: in_taxon NCBITaxon:89593 ! Craniata relationship: part_of UBERON:0001456 ! face property_value: editor_note "this class is currently a union of the snout (e.g. in mouse), the midface and the lower face. Note that in MA, snout includes the whole jaw and should thus be more alike the lower face than the midface, so its placement here is not strictly accurate. In future we might introduce specific classes for each of these, and include the full parthood relationships. if this is done, then care should be taken to preserve inferences such as an abnormality of the lower face being an abnormality of the midface." xsd:string property_value: has_relational_adjective "midfacial" xsd:string @@ -81738,7 +81738,7 @@ name: hypothalamus-pituitary axis def: "Missing definition for term UBERON:0004092. Please replace it using linked reference." [HP:0000864] subset: pheno_slim is_a: UBERON:0000467 ! anatomical system -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000949 ! endocrine system [Term] @@ -81853,7 +81853,7 @@ xref: FMA:285412 intersection_of: UBERON:0006800 ! anatomical line intersection_of: connects UBERON:0000403 ! scalp intersection_of: connects UBERON:0008200 ! forehead -relationship: only_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: in_taxon NCBITaxon:9606 ! Homo sapiens relationship: part_of UBERON:0000033 ! head [Term] @@ -82078,7 +82078,7 @@ xref: ZFA:0001106 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0007690 {source="EHDAA2", source="ZFA"} ! early pharyngeal endoderm -relationship: only_in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata +relationship: in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata relationship: overlaps UBERON:0002539 ! pharyngeal arch relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0008814 ! pharyngeal arch system @@ -82296,7 +82296,7 @@ name: growth plate cartilage def: "Cartilage that will provide a scaffold for mineralization of endochondral bones as they elongate or grow." [GO:0003417] synonym: "growth plate" RELATED [] is_a: UBERON:0002418 ! cartilage tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0010363 ! endochondral element relationship: site_of GO:0030282 ! bone mineralization relationship: surrounds UBERON:0004763 ! endochondral bone tissue @@ -82500,7 +82500,7 @@ synonym: "HPS" EXACT OMO:0003000 [] synonym: "VCS" EXACT [] synonym: "ventricular conduction system" EXACT [] is_a: UBERON:0010131 {source="cjm"} ! conducting tissue of heart -relationship: only_in_taxon NCBITaxon:32523 {source="PMID:12626327", source="PMID:21234997", source="github:michaelerice"} ! Tetrapoda +relationship: in_taxon NCBITaxon:32523 {source="PMID:12626327", source="PMID:21234997", source="github:michaelerice"} ! Tetrapoda relationship: part_of UBERON:0002082 {source="GO-def"} ! cardiac ventricle relationship: part_of UBERON:0002350 {source="GO"} ! conducting system of heart property_value: external_definition "the intraventricular conduction system from the bundle of His to the distal Purkinje fibers, which carries the impulse to the ventricles." xsd:string {source="http://medical-dictionary.thefreedictionary.com/His-Purkinje+system"} @@ -82706,8 +82706,8 @@ xref: XAO:0004325 is_a: UBERON:0001630 ! muscle organ relationship: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue relationship: develops_from UBERON:0010360 {source="PMID:21610022"} ! pharyngeal arch mesenchyme from head mesenchyme +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: innervated_by UBERON:0001785 {source="ISBN:0073040584"} ! cranial nerve -relationship: only_in_taxon NCBITaxon:7711 ! Chordata property_value: external_definition "The branchiomeric muscle is derived from cranial mesoderm and controls facial expression, pharyngeal and laryngeal function, operating the jaw. Branchiomeric muscles of mammals correspond to the musculature of fish[GO][GO:0014707]." xsd:string {source="GO:0014707"} property_value: taxon_notes "It has been hypothesized that Haikouella must have been powered by branchiomeric muscles, as in living craniates, rather than by water moving through the pharynx via ciliary currents, as in lancelets[http://icb.oxfordjournals.org/content/42/4/743.full]" xsd:string @@ -83038,11 +83038,11 @@ xref: Wikipedia:Harderian_gland intersection_of: UBERON:0015153 ! medial gland of ocular region intersection_of: produces UBERON:0022282 ! secretion of Harderian gland relationship: connected_to UBERON:0010207 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! nictitating membrane +relationship: in_taxon NCBITaxon:32523 {source="PMID:7559104"} ! Tetrapoda relationship: innervated_by UBERON:0015161 ! inferior branch of oculomotor nerve relationship: never_in_taxon NCBITaxon:9443 {source="PMID:7559104"} ! Primates relationship: never_in_taxon NCBITaxon:9606 {notes="may be transient in embryos", source="PMID:7559104"} ! Homo sapiens relationship: never_in_taxon NCBITaxon:9787 {source="PMID:7559104"} ! Perissodactyla -relationship: only_in_taxon NCBITaxon:32523 {source="PMID:7559104"} ! Tetrapoda relationship: part_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0002330 {notes="some evidence suggests also endocrine", source="PMID:7559104"} ! exocrine system relationship: present_in_taxon NCBITaxon:10047 {source="ISBN:1118473523"} ! Meriones unguiculatus @@ -84695,7 +84695,7 @@ xref: BTO:0001506 xref: Wikipedia:Radula is_a: UBERON:0000062 ! organ relationship: composed_primarily_of CHEBI:17029 ! chitin -relationship: only_in_taxon NCBITaxon:6447 ! Mollusca +relationship: in_taxon NCBITaxon:6447 ! Mollusca [Term] id: UBERON:0004290 @@ -85647,7 +85647,7 @@ is_a: UBERON:0005631 ! extraembryonic membrane relationship: develops_from UBERON:0000162 {source="Hymans"} ! cloaca relationship: has_developmental_contribution_from UBERON:0000925 {notes="hindgut diverticulum endoderm", source="ISBN:0073040584"} ! endoderm relationship: has_developmental_contribution_from UBERON:0004872 {source="ISBN:0073040584"} ! splanchnic layer of lateral plate mesoderm -relationship: only_in_taxon NCBITaxon:32524 {source="Hymans"} ! Amniota +relationship: in_taxon NCBITaxon:32524 {source="Hymans"} ! Amniota relationship: overlaps UBERON:0001008 {source="EHDAA2-modified"} ! renal system property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a5/Gray25.png" xsd:anyURI property_value: development_notes "a diverticulum of the hindgut endoderm [ISBN:0073040584 (Vertebrates, Kardong)]" xsd:string @@ -85774,7 +85774,7 @@ is_a: UBERON:0004357 ! paired limb/fin bud relationship: developmentally_induced_by UBERON:0003081 {source="ISBN:9780878932504"} ! lateral plate mesoderm relationship: has_developmental_contribution_from UBERON:0005733 ! limb field relationship: has_potential_to_develop_into UBERON:0002101 ! limb -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda +relationship: in_taxon NCBITaxon:32523 ! Tetrapoda property_value: external_definition "Early outgrowth of presumptive limb.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010375", ontology="AAO", source="AAO:EJS"} [Term] @@ -87275,7 +87275,7 @@ intersection_of: part_of UBERON:0002387 ! pes disjoint_from: UBERON:0004772 ! eyelid tarsus relationship: distally_connected_to UBERON:0000983 ! metatarsus region relationship: has_skeleton UBERON:0009879 ! tarsal skeleton -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: proximally_connected_to UBERON:0003823 ! hindlimb zeugopod property_value: curator_notes "this term refers to the limb segment. See also: tarsal bones and tarsal skeleton" xsd:string property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg" xsd:anyURI @@ -88880,7 +88880,7 @@ xref: SCTID:181823007 xref: UMLS:C0459939 {source="ncithesaurus:C3_Vertebra"} is_a: UBERON:0002413 ! cervical vertebra relationship: anteriorly_connected_to UBERON:0001093 {source="FMA"} ! vertebral bone 2 -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia property_value: curator_notes "elements are to be defined spatially/topologically. all mammals have 7 cervical vertebrae" xsd:string property_value: editor_note "under discussion: whether to generalize this beyond mammals, making it purely order-defined" xsd:string property_value: vertebra_number "3" xsd:nonNegativeInteger @@ -88902,7 +88902,7 @@ xref: SCTID:181824001 xref: UMLS:C0459941 {source="ncithesaurus:C4_Vertebra"} is_a: UBERON:0002413 ! cervical vertebra relationship: anteriorly_connected_to UBERON:0004612 {source="FMA"} ! mammalian cervical vertebra 3 -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia property_value: curator_notes "elements are to be defined spatially/topologically. all mammals have 7 cervical vertebrae" xsd:string property_value: vertebra_number "4" xsd:nonNegativeInteger @@ -88923,7 +88923,7 @@ xref: SCTID:181825000 xref: UMLS:C0459943 {source="ncithesaurus:C5_Vertebra"} is_a: UBERON:0002413 ! cervical vertebra relationship: anteriorly_connected_to UBERON:0004613 {source="FMA"} ! mammalian cervical vertebra 4 -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia property_value: curator_notes "elements are to be defined spatially/topologically. all mammals have 7 cervical vertebrae" xsd:string property_value: vertebra_number "5" xsd:nonNegativeInteger @@ -88944,7 +88944,7 @@ xref: SCTID:181826004 xref: UMLS:C0459944 {source="ncithesaurus:C6_Vertebra"} is_a: UBERON:0002413 ! cervical vertebra relationship: anteriorly_connected_to UBERON:0004614 {source="FMA"} ! mammalian cervical vertebra 5 -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia property_value: curator_notes "elements are to be defined spatially/topologically. all mammals have 7 cervical vertebrae" xsd:string property_value: vertebra_number "6" xsd:nonNegativeInteger @@ -88968,7 +88968,7 @@ xref: UMLS:C0223176 {source="ncithesaurus:C7_Vertebra"} xref: Wikipedia:Vertebra_prominens is_a: UBERON:0002413 ! cervical vertebra relationship: anteriorly_connected_to UBERON:0004615 {source="FMA"} ! mammalian cervical vertebra 6 -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia property_value: curator_notes "elements are to be defined spatially/topologically. all mammals have 7 cervical vertebrae" xsd:string property_value: vertebra_number "7" xsd:nonNegativeInteger @@ -88987,7 +88987,7 @@ xref: SCTID:181841004 xref: UMLS:C0223492 {source="ncithesaurus:L1_Vertebra"} is_a: UBERON:0002414 ! lumbar vertebra relationship: anteriorly_connected_to UBERON:0004636 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! thoracic vertebra 12 -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia property_value: curator_notes "elements are to be defined spatially/topologically" xsd:string [Term] @@ -89006,7 +89006,7 @@ xref: SCTID:181842006 xref: UMLS:C0223507 {source="ncithesaurus:L2_Vertebra"} is_a: UBERON:0002414 ! lumbar vertebra relationship: anteriorly_connected_to UBERON:0004617 {source="FMA"} ! lumbar vertebra 1 -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia property_value: curator_notes "elements are to be defined spatially/topologically" xsd:string [Term] @@ -89025,7 +89025,7 @@ xref: SCTID:181843001 xref: UMLS:C0223522 {source="ncithesaurus:L3_Vertebra"} is_a: UBERON:0002414 ! lumbar vertebra relationship: anteriorly_connected_to UBERON:0004618 {source="FMA"} ! lumbar vertebra 2 -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia property_value: curator_notes "elements are to be defined spatially/topologically" xsd:string [Term] @@ -90651,7 +90651,7 @@ xref: OGES:000006 xref: Wikipedia:Pharyngula xref: ZFS:0000050 is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000111 ! organogenesis stage relationship: preceded_by UBERON:0000110 ! neurula stage property_value: taxon_notes "Corresponds to E7-E11 in Mouse (Galis et al, TREE, 2001)" xsd:string @@ -90679,7 +90679,7 @@ relationship: has_part UBERON:0000014 ! zone of skin relationship: has_part UBERON:0001015 ! musculature relationship: has_part UBERON:0002049 ! vasculature relationship: has_skeleton UBERON:0011582 ! paired limb/fin skeleton -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0010707 {source="VSAO"} ! appendage girdle complex property_value: curator_notes "this class is the union of the classes limb, pectoral fin and pelvic fin." xsd:string @@ -91071,7 +91071,7 @@ xref: UMLS:C0228280 {source="BIRNLEX:1097"} xref: Wikipedia:Piriform_cortex is_a: UBERON:0002616 ! regional part of brain relationship: contributes_to_morphology_of UBERON:0002894 ! olfactory cortex -relationship: only_in_taxon NCBITaxon:32523 {source="Wikipedia"} ! Tetrapoda +relationship: in_taxon NCBITaxon:32523 {source="Wikipedia"} ! Tetrapoda relationship: part_of UBERON:0002894 ! olfactory cortex property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b1/Human_brainstem_anterior_view_2_description.JPG" xsd:anyURI property_value: taxon_notes "Piriform cortical regions are present in the brains of amphibians, reptiles and mammals. The piriform cortex is among three areas that emerge in the telencephalon of amphibians, situated caudally to a dorsal area, which is caudal to a hippocampal area. Farther along the phylogenic timeline, the telencephalic bulb of reptiles as viewed in a cross section of the transverse plane extends with the archipallial hippocampus folding toward the midline and down as the dorsal area begins to form a recognizable cortex. As mammalian cerebrums developed, volume of the dorsal cortex increased in slightly greater proportion, as compared proportionally with increased overall brain volume, until it enveloped the hippocampal regions. Recognized as neopallium or neocortex, enlarged dorsal areas envelop the paleopallial piriform cortex in humans and Old World monkeys. Among taxonomic groupings of mammals, the piriform cortex and the olfactory bulb become proportionally smaller in the brains of phylogenically younger species. The piriform cortex occupies a greater proportion of the overall brain and of the telencephalic brains of insectivores than in primates. The piriform cortex continues to occupy a consistent albeit small and declining proportion of the increasingly large telencephalon in the most recent primate species while the volume of the olfactory bulb becomes less in proportion" xsd:string {source="WP"} @@ -91148,7 +91148,7 @@ synonym: "tadpole" NARROW SENSU [Wikipedia:Larva] synonym: "tadpole stage" NARROW SENSU [Wikipedia:Larva] xref: XtroDO:0000056 is_a: UBERON:0000069 ! larval stage -relationship: only_in_taxon NCBITaxon:8292 ! Amphibia +relationship: in_taxon NCBITaxon:8292 ! Amphibia relationship: present_in_taxon NCBITaxon:8355 ! Xenopus laevis relationship: simultaneous_with GO:0002117 ! amphibian larval development property_value: external_ontology_notes "the XAO class denotes a stage" xsd:string {external_ontology="XAO"} @@ -91160,7 +91160,7 @@ name: nematode larval stage def: "Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew." [GO:0002119] xref: WBls:0000023 is_a: UBERON:0000069 ! larval stage -relationship: only_in_taxon NCBITaxon:6231 ! Nematoda +relationship: in_taxon NCBITaxon:6231 ! Nematoda relationship: simultaneous_with GO:0002119 ! nematode larval development property_value: seeAlso "https://github.com/obophenotype/uberon/issues/567" xsd:anyURI @@ -91170,7 +91170,7 @@ name: instar larval stage def: "This begins with the newly hatched first-instar larva, through its maturation to the end of the last larval stage. An example of this process is found in Drosophila melanogaster." [GO:0002168] xref: FBdv:00005336 is_a: UBERON:0000069 ! larval stage -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: present_in_taxon NCBITaxon:7227 ! Drosophila melanogaster relationship: simultaneous_with GO:0002168 ! instar larval development property_value: seeAlso "https://github.com/obophenotype/uberon/issues/526" xsd:anyURI @@ -91682,7 +91682,7 @@ xref: XAO:0004038 xref: ZFA:0005619 is_a: UBERON:0002384 {source="VSAO"} ! connective tissue relationship: develops_from CL:0007001 {date_retrieved="2012-08-14", external_class="VSAO:0000015", source="VSAO"} ! skeletogenic cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0004765 ! skeletal element property_value: external_definition "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000015", notes="taken from version of VSAO used in TAO and used directly in Uberon", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} @@ -91709,8 +91709,8 @@ intersection_of: UBERON:0002530 ! gland intersection_of: capable_of GO:0055078 ! sodium ion homeostasis intersection_of: part_of UBERON:0001052 ! rectum relationship: confers_advantage_in ENVO:01000048 +relationship: in_taxon NCBITaxon:7776 ! Gnathostomata relationship: never_in_taxon NCBITaxon:32523 ! Tetrapoda -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: present_in_taxon NCBITaxon:118072 ! Coelacanthimorpha relationship: present_in_taxon NCBITaxon:119203 ! Selachii property_value: function_notes "shark liver produces copious amounts of urea, making the shark hyperosmotic to seawater, & thus a shark acts like a fresh water fish, constantly gaining water. Excess salts are concentrated by the rectal gland and secreted" xsd:string @@ -91728,8 +91728,8 @@ xref: Wikipedia:Salt_gland intersection_of: UBERON:0002530 ! gland intersection_of: capable_of GO:0055078 ! sodium ion homeostasis relationship: confers_advantage_in ENVO:00000447 +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: never_in_taxon NCBITaxon:40674 ! Mammalia -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata property_value: taxon_notes "In sharks, salt glands are found in the rectum, but in birds and reptiles, they are found in or on the skull, in the area of the eyes, nostrils or mouth. In crocodiles, the salt is excreted through the tongue. Such glands work by active transport via sodium-potassium pump that moves salt from the blood into the gland, where it can be excreted as a concentrated solution. Salt glands function to keep salt balance, and allow marine vertebrates to drink seawater" xsd:string [Term] @@ -91783,7 +91783,7 @@ xref: XAO:0003059 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system relationship: develops_from UBERON:0009617 {source="PMC1571569"} ! head paraxial mesoderm relationship: has_part UBERON:0002418 ! cartilage tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata property_value: external_ontology_notes "in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain)" xsd:string {external_ontology="FMA"} [Term] @@ -91901,7 +91901,7 @@ intersection_of: UBERON:0034925 ! anatomical collection intersection_of: has_member UBERON:0000982 ! skeletal joint relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: functionally_related_to GO:0040011 ! locomotion -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system [Term] @@ -92861,7 +92861,7 @@ intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002299 ! alveolus of lung relationship: contributes_to_morphology_of UBERON:0000115 ! lung epithelium relationship: contributes_to_morphology_of UBERON:0002299 ! alveolus of lung -relationship: has_part CL:0002062 {source="FMA"} ! type I pneumocyte +relationship: has_part CL:0002062 {source="FMA"} ! pulmonary alveolar type 1 cell relationship: part_of UBERON:0004894 {source="FMA"} ! alveolar wall [Term] @@ -93532,7 +93532,7 @@ xref: EFO:0003426 xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0005423 ! developing anatomical structure -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0003068 ! axial mesoderm property_value: external_definition "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." xsd:string {source="ZFIN:ZDB-PUB-961014-576"} @@ -94157,7 +94157,7 @@ def: "A part of a wall of an organ that forms a layer." [http://orcid.org/0000-0 subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000060 ! anatomical wall [Term] @@ -96279,7 +96279,7 @@ xref: UMLS:C1510668 {source="ncithesaurus:Gizzard"} xref: Wikipedia:Gizzard is_a: UBERON:0000945 {source="cjm"} ! stomach relationship: has_part UBERON:0008861 {source="Wikipedia"} ! pyloric gastric gland -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0001555 ! digestive tract property_value: external_ontology_notes "BTO also includes: A thickened part of the alimentary canal in some animals (as an insect or an earthworm) that is similar in function to the crop of a bird. However, we are refering to the Aves structure here." xsd:string {external_ontology="BTO"} property_value: taxon_notes "currently restricted to Aves, but may be found outside - e.g. Pangolins" xsd:string @@ -96294,7 +96294,7 @@ xref: BILA:0000136 xref: BTO:0001656 is_a: UBERON:0010000 ! multicellular anatomical structure relationship: develops_from UBERON:0000924 ! ectoderm -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001016 ! nervous system property_value: curator_notes "some species have multiple longitudinal nerve cords; this class refers to the most prominent one, which is dorsal in chordates and ventral in others." xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/issues/691" xsd:anyURI @@ -96310,7 +96310,7 @@ xref: Wikipedia:Dorsal_nerve_cord intersection_of: UBERON:0005053 ! primary nerve cord intersection_of: intersects_midsagittal_plane_of UBERON:0001137 ! dorsum disjoint_from: UBERON:0035607 ! accessory nerve cord of dorsal region -relationship: only_in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata +relationship: in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata [Term] id: UBERON:0005055 @@ -96454,7 +96454,7 @@ subset: organ_slim synonym: "amphid sensillum" EXACT [] xref: WBbt:0005391 is_a: UBERON:0000020 ! sense organ -relationship: only_in_taxon NCBITaxon:6231 ! Nematoda +relationship: in_taxon NCBITaxon:6231 ! Nematoda [Term] id: UBERON:0005068 @@ -96707,7 +96707,7 @@ synonym: "musculus" EXACT [FMA:30316] xref: FMA:30316 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa property_value: curator_notes "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" xsd:string [Term] @@ -96744,7 +96744,7 @@ synonym: "cement gland" BROAD [XAO:0000033] xref: AAO:0010373 xref: XAO:0000033 is_a: UBERON:0002530 ! gland -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000922 ! embryo property_value: external_definition "A simple mucus-secreting structure that is positioned at the front of the embryo, attaches the newly hatched embryo to a support before the hatchling can swim well or feed, and marks the anterior-most dorsal ectoderm.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010373", ontology="AAO", source="AAO:BJB"} @@ -96758,7 +96758,7 @@ synonym: "rostrum" RELATED [] xref: MESH:D001502 xref: Wikipedia:Beak is_a: UBERON:0003102 ! surface structure -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0000033 ! head property_value: editor_note "TODO - add superclass" xsd:string property_value: terminology_notes "The term beak is also used to refer to a similar mouthpart in some Ornithischian dinosaurs, monotremes, cephalopods, cetaceans, pufferfishes, turtles, Anuran tadpoles and sirens" xsd:string {source="WP"} @@ -97241,7 +97241,7 @@ xref: SPD:0000427 xref: TADS:0000043 is_a: UBERON:0001004 ! respiratory system relationship: capable_of GO:0007585 ! respiratory gaseous exchange by respiratory system -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda [Term] id: UBERON:0005156 @@ -97309,7 +97309,7 @@ synonym: "cloacal spur" RELATED [] xref: Wikipedia:Pelvic_spur is_a: UBERON:0000026 ! appendage is_a: UBERON:0005160 ! vestigial structure -relationship: only_in_taxon NCBITaxon:8570 {source="Wikipedia"} ! Serpentes +relationship: in_taxon NCBITaxon:8570 {source="Wikipedia"} ! Serpentes property_value: curator_notes "this class refers to the external portion and its corneal covering rather than the combined pelvis plus femur." xsd:string [Term] @@ -99027,7 +99027,7 @@ xref: SCTID:181061006 xref: UMLS:C1711378 {source="ncithesaurus:Hypogastric_Nerve_Plexus"} xref: Wikipedia:Hypogastric_nerve is_a: UBERON:0001816 ! autonomic nerve plexus -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray847.png" xsd:anyURI property_value: editor_note "check plexus vs nerve. WP indicates it is a 'transition'" xsd:string @@ -99372,7 +99372,7 @@ relationship: capable_of GO:0007585 {source="Hymans"} ! respiratory gaseous exch relationship: develops_from UBERON:0003124 ! chorion membrane relationship: develops_from UBERON:0004340 ! allantois relationship: dubious_for_taxon NCBITaxon:32525 ! Theria -relationship: only_in_taxon NCBITaxon:32524 ! Amniota +relationship: in_taxon NCBITaxon:32524 ! Amniota property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/f/f8/Smallpox_CAM.png" xsd:anyURI [Term] @@ -99560,13 +99560,13 @@ xref: EMAPA:37400 {source="MA:th"} xref: MBA:1033 xref: neuronames:1894 is_a: UBERON:0004003 ! cerebellum hemisphere lobule +relationship: in_taxon NCBITaxon:9989 ! Rodentia relationship: mutually_spatially_disjoint_with UBERON:0001063 {source="ABA"} ! flocculus relationship: mutually_spatially_disjoint_with UBERON:0005348 {source="ABA"} ! ansiform lobule relationship: mutually_spatially_disjoint_with UBERON:0005349 {source="ABA"} ! paramedian lobule relationship: mutually_spatially_disjoint_with UBERON:0005350 {source="ABA"} ! lobule simplex relationship: mutually_spatially_disjoint_with UBERON:0005351 {source="ABA"} ! paraflocculus relationship: never_in_taxon NCBITaxon:9606 {source="MP"} ! Homo sapiens -relationship: only_in_taxon NCBITaxon:9989 ! Rodentia property_value: taxon_notes "This is a structure present in rodents and is not present in humans. The cerebellum hemisphere structure and lobulation is dramatically different between these species." xsd:string [Term] @@ -100782,7 +100782,7 @@ is_a: UBERON:0006846 {source="EHDAA2"} ! surface groove relationship: contributes_to_morphology_of UBERON:0001834 ! upper lip relationship: develops_from UBERON:0004068 {source="Wikipedia"} ! medial nasal prominence relationship: has_quality PATO:0000588 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! vestigial -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0001834 {source="EMAPA"} ! upper lip property_value: seeAlso "https://github.com/obophenotype/uberon/pull/2691" xsd:string property_value: taxon_notes "vestigial in humans. In humans, the philtrum is formed where the nasomedial and maxillary processes meet during embryonic development (colloquially known as Hulse lines). When these processes fail to fuse fully in humans, a cleft lip (sometimes called a 'hare lip') can result. A flattened or smooth philtrum can be a symptom of fetal alcohol syndrome or Prader-Willi syndrome" xsd:string @@ -100846,7 +100846,7 @@ xref: FMA:74280 xref: MA:0002974 xref: Wikipedia:Paranephric_body is_a: UBERON:0001013 ! adipose tissue -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c1/Gray1125.png" xsd:anyURI property_value: editor_note "TODO - split paranephric / pararenal" xsd:string @@ -100870,7 +100870,7 @@ xref: MA:0002975 xref: SCTID:246901006 xref: Wikipedia:Adipose_capsule_of_kidney is_a: UBERON:0001013 ! adipose tissue -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI property_value: editor_note "TODO - split perinephric / perirenal" xsd:string @@ -101454,7 +101454,7 @@ synonym: "subdivision of neck" EXACT [FMA:24219] xref: FMA:24219 xref: SCTID:123958008 is_a: UBERON:0011676 ! subdivision of organism along main body axis -relationship: only_in_taxon NCBITaxon:8287 ! Sarcopterygii +relationship: in_taxon NCBITaxon:8287 ! Sarcopterygii relationship: part_of UBERON:0000974 ! neck [Term] @@ -105051,7 +105051,7 @@ xref: SCTID:30180000 xref: Wikipedia:Adventitia is_a: UBERON:0004923 ! organ component layer relationship: composed_primarily_of UBERON:0002384 ! connective tissue -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg" xsd:anyURI [Term] @@ -105243,7 +105243,7 @@ xref: UMLS:C1519838 {source="ncithesaurus:Urorectal_Septum"} xref: VHOG:0000018 xref: Wikipedia:Urorectal_septum is_a: UBERON:0003037 ! septum -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001008 {source="MA"} ! renal system relationship: part_of UBERON:0012361 {source="EHDAA2"} ! internal anal region property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray992.png" xsd:anyURI @@ -105281,7 +105281,7 @@ is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: composed_primarily_of GO:0005604 ! basement membrane relationship: has_part GO:0005587 ! collagen type IV trimer -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of UBERON:0000483 ! epithelium relationship: present_in_taxon NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! Homoscleromorpha property_value: curator_notes "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." xsd:string @@ -106202,7 +106202,7 @@ xref: Wikipedia:Genital_tubercle is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0004874 ! somatopleure relationship: has_potential_to_develop_into UBERON:0011757 ! differentiated genital tubercle -relationship: only_in_taxon NCBITaxon:32524 {source="https://github.com/obophenotype/uberon/issues/1230"} ! Amniota +relationship: in_taxon NCBITaxon:32524 {source="https://github.com/obophenotype/uberon/issues/1230"} ! Amniota relationship: part_of UBERON:0009196 {source="EHDAA2"} ! indifferent external genitalia property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d6/Gray1119.png" xsd:anyURI property_value: external_definition "embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin; GT development is indistinguishable in male and female mouse embryos until ~E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP]" xsd:string {ontology="MP"} @@ -106534,8 +106534,8 @@ xref: HAO:0000456 xref: TADS:0000039 xref: Wikipedia:Labrum_(arthropod_mouthpart) is_a: UBERON:0000064 ! organ part +relationship: in_taxon NCBITaxon:6656 ! Arthropoda relationship: never_in_taxon NCBITaxon:57294 -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0000165 ! mouth property_value: editor_note "this term should be ceded to the arthropod anatomy ontology" xsd:string @@ -107034,7 +107034,7 @@ synonym: "amnionic fold" EXACT [http://placentation.ucsd.edu/glossfs.html] xref: EMAPA:16076 is_a: UBERON:0000478 ! extraembryonic structure relationship: develops_from UBERON:0004874 {source="ISBN:0073040584"} ! somatopleure -relationship: only_in_taxon NCBITaxon:32524 ! Amniota +relationship: in_taxon NCBITaxon:32524 ! Amniota [Term] id: UBERON:0005972 @@ -107592,7 +107592,7 @@ xref: Wikipedia:Pre-botzinger_complex is_a: UBERON:0034922 ! cell cluster relationship: composed_primarily_of CL:0000099 ! interneuron relationship: continuous_with UBERON:0000011 ! parasympathetic nervous system -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia +relationship: in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: part_of UBERON:0001896 ! medulla oblongata [Term] @@ -107952,7 +107952,7 @@ xref: FMA:46479 xref: galen:Occiput xref: Wikipedia:Occiput is_a: UBERON:0006056 ! posterior surface of head -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/e/eb/Double_cowlick.jpg" xsd:anyURI [Term] @@ -109135,9 +109135,9 @@ xref: UMLS:C0027750 {source="ncithesaurus:Myelinated_Nerve_Fiber"} intersection_of: UBERON:0006134 ! nerve fiber intersection_of: has_part GO:0043209 ! myelin sheath disjoint_from: UBERON:0006136 ! unmyelinated nerve fiber +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: never_in_taxon NCBITaxon:117569 ! Hyperoartia relationship: never_in_taxon NCBITaxon:7762 ! Myxinidae -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: present_in_taxon NCBITaxon:7776 ! Gnathostomata property_value: editor_note "consider adding link to UBERON:0002316 ! white matter of neuraxis" xsd:string property_value: taxon_notes "http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html, http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=6134604, Wikipedia:Myelin#Invertebrate_myelin" xsd:string @@ -110507,7 +110507,7 @@ xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0000924 {source="EHDAA2"} ! ectoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata [Term] id: UBERON:0006270 @@ -110601,8 +110601,8 @@ xref: SCTID:361428002 xref: UMLS:C1283967 {source="ncithesaurus:Pericardioperitoneal_Canal"} xref: VHOG:0001498 is_a: UBERON:0002050 ! embryonic structure +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: located_in UBERON:0002323 ! coelemic cavity lumen -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0003887 {source="EMAPA"} ! intraembryonic coelom [Term] @@ -110627,7 +110627,7 @@ xref: EHDAA:4122 xref: EMAPA:17704 xref: VHOG:0001497 is_a: UBERON:0005423 ! developing anatomical structure -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000922 ! embryo [Term] @@ -110646,8 +110646,8 @@ xref: VHOG:0001499 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0006210 {source="EHDAA2"} ! body-wall mesenchyme relationship: in_lateral_side_of UBERON:0000922 ! embryo +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: located_in UBERON:0002323 {source="EHDAA2"} ! coelemic cavity lumen -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000922 ! embryo property_value: development_notes "As the folds grow towards the midline, carrying the phrenic nerve, the root of the folds migrate ventrally" xsd:string {source="http://www.indiana.edu/~anat550/cvanim/pericard/pericard.html"} 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:0001499", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206", source="http://bgee.unil.ch/"} @@ -110667,7 +110667,7 @@ is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube intersection_of: UBERON:0003914 ! epithelial tube intersection_of: connects UBERON:0001179 ! peritoneal cavity intersection_of: connects UBERON:0002402 ! pleural cavity -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0011997 {source="EHDAA2"} ! coelom property_value: external_definition "Each of the canal that links the peritoneal cavity and the caudal part of a pleural cavity. [ISBN:0124020607][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001505", ontology="VHOG", source="http://bgee.unil.ch/"} @@ -111005,7 +111005,7 @@ subset: emapa_ehdaa2 xref: EMAPA:16740 xref: RETIRED_EHDAA2:0002072 is_a: UBERON:0005423 ! developing anatomical structure -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000922 ! embryo [Term] @@ -111379,7 +111379,7 @@ xref: UMLS:C0930558 {source="ncithesaurus:Lingual_Salivary_Gland"} xref: Wikipedia:Anterior_lingual_glands is_a: UBERON:0000414 {source="MP"} ! mucous gland is_a: UBERON:0001830 ! minor salivary gland -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata +relationship: in_taxon NCBITaxon:7776 ! Gnathostomata relationship: part_of UBERON:0001723 ! tongue [Term] @@ -111762,8 +111762,8 @@ intersection_of: UBERON:0001037 ! strand of hair intersection_of: part_of UBERON:0011933 ! vibrissa unit disjoint_from: UBERON:0011931 ! nasal hair relationship: capable_of_part_of GO:0050975 ! sensory perception of touch +relationship: in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: never_in_taxon NCBITaxon:9606 {source="Skinbase"} ! Homo sapiens -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia property_value: taxon_notes "In harbor seals, the structure of the vibrissal shaft is undulated (wavy) and flattened. This specialization is also found in most true seals. In contrast, the whiskers of the California sea lion are circular or elliptical in cross-section and are smooth." xsd:string {source="Wikipedia:Hydrodynamic_reception#Species_differences_in_vibrissae"} [Term] @@ -111833,8 +111833,8 @@ xref: Wikipedia:Baculum is_a: UBERON:0007719 ! bone of reproductive organ intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0000989 ! penis +relationship: in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia property_value: taxon_notes "found in most mammals, with the exception of humans" xsd:string [Term] @@ -111874,8 +111874,8 @@ intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0002411 ! clitoris relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system relationship: contributes_to_morphology_of UBERON:0002411 ! clitoris +relationship: in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: sexually_homologous_to UBERON:0006435 ! os penis [Term] @@ -113237,7 +113237,7 @@ xref: MAT:0000049 xref: MESH:D010614 xref: MIAA:0000049 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria property_value: curator_notes "currently this is an extremely generic class, encompassing both protostomes and deuterostomes." xsd:string property_value: has_relational_adjective "branchial" xsd:string property_value: has_relational_adjective "pharyngeal" xsd:string @@ -113391,7 +113391,7 @@ synonym: "mantle tissue" RELATED [BTO:0000825] synonym: "pallium" RELATED [Wikipedia:Mantle_(mollusc)] xref: BTO:0000825 is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:6447 ! Mollusca +relationship: in_taxon NCBITaxon:6447 ! Mollusca [Term] id: UBERON:0006580 @@ -113501,7 +113501,7 @@ is_a: UBERON:0006592 ! transformed vein is_a: UBERON:0013139 ! ligament of liver disjoint_from: UBERON:0006589 ! round ligament of uterus relationship: develops_from UBERON:0002066 ! umbilical vein -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia +relationship: in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia [Term] id: UBERON:0006589 @@ -113582,7 +113582,7 @@ xref: ZFA:0000416 intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa [Term] id: UBERON:0006596 @@ -113682,7 +113682,7 @@ xref: ZFA:0001376 intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa [Term] id: UBERON:0006603 @@ -113697,7 +113697,7 @@ is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0000926 ! mesoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa [Term] id: UBERON:0006604 @@ -113797,7 +113797,7 @@ xref: BTO:0005454 xref: FMA:321004 xref: Wikipedia:Corpus_cavernosum is_a: UBERON:0008324 ! erectile tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata [Term] id: UBERON:0006610 @@ -113809,7 +113809,7 @@ xref: FMA:19631 xref: Wikipedia:Tunica_albuginea is_a: UBERON:0000158 ! membranous layer relationship: composed_primarily_of UBERON:0011824 ! fibrous connective tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0003133 ! reproductive organ [Term] @@ -113835,8 +113835,8 @@ subset: grouping_class xref: ncithesaurus:Shell xref: Wikipedia:Seashell is_a: UBERON:0000477 ! anatomical cluster +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: never_in_taxon NCBITaxon:32525 ! Theria -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0002416 ! integumental system property_value: editor_note "may be obsoleted after integumental system overhaul" xsd:string @@ -114009,7 +114009,7 @@ xref: FMA:13455 xref: SCTID:181912007 xref: Wikipedia:Coracoid_process is_a: UBERON:0005913 {source="FMA"} ! zone of bone organ -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0006849 {source="EMAPA", source="FMA"} ! scapula property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a6/Gray205_left_scapula_lateral_view.png" xsd:anyURI property_value: external_definition "The coracoid process is a small hook-like structure on the lateral edge of the superior anterior portion of the scapula. Pointing laterally forward, it, together with the acromion, serves to stabilize the shoulder joint. It is palpable in the deltopectoral groove between the deltoid and pectoralis major muscles. It is the site of attachment for several structures: * The pectoralis minor muscle - to 3rd to 5th ribs. * The short head of biceps brachii muscle - to Radial tuberosity. * The coracobrachialis muscle - to medial humerus. * The coracoclavicular ligament - to the clavicle. (The ligament is formed by the conoid ligament and trapezoid ligament.) * The coracoacromial ligament - to the acromion[WP][Wikipedia:Coracoid_process]." xsd:string {source="Wikipedia:Coracoid_process"} @@ -114498,9 +114498,9 @@ xref: Wikipedia:Muscular_layer is_a: UBERON:0004923 {source="FMA"} ! organ component layer relationship: adjacent_to UBERON:0000009 ! submucosa relationship: composed_primarily_of UBERON:0002385 ! muscle tissue +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: mutually_spatially_disjoint_with UBERON:0000009 ! submucosa relationship: mutually_spatially_disjoint_with UBERON:0006676 ! muscularis mucosa -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata property_value: editor_note "currently this class conflates a generic layer of muscle and a specific layer found lining the digestive tract (the muscularis externa), typically composed of circular and longitudinal layers (although this varies)" xsd:string property_value: external_definition "An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO]." xsd:string {source="BTO:0004838"} property_value: taxon_notes "typically smooth muscle, but there may be exceptions - in the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle." xsd:string @@ -114860,7 +114860,7 @@ xref: SCTID:139380001 xref: Wikipedia:Hypoglossal_canal intersection_of: UBERON:0004111 ! anatomical conduit intersection_of: conduit_for UBERON:0001650 ! hypoglossal nerve -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata +relationship: in_taxon NCBITaxon:7776 ! Gnathostomata relationship: part_of UBERON:0001676 ! occipital bone [Term] @@ -115859,7 +115859,7 @@ synonym: "quadrigeminal plate" EXACT [FMA:77488] xref: FMA:77488 xref: neuronames:1374 is_a: UBERON:0005423 ! developing anatomical structure -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0009616 ! presumptive midbrain [Term] @@ -116134,7 +116134,7 @@ name: arthropod optic lobe def: "A region of the adult brain that processes the visual information from the compound eyes." [FBC:gg, ISBN:978-3-11-014898-5] synonym: "optic lobe" RELATED SENSU [FBbt:00003701] is_a: UBERON:0006794 ! visual processing part of nervous system -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0000955 ! brain property_value: editor_note "this term should be ceded to the arthropod anatomy ontology" xsd:string @@ -116263,7 +116263,7 @@ xref: SCTID:57987007 xref: Wikipedia:Reticular_connective_tissue is_a: UBERON:0011825 {source="FMA"} ! loose connective tissue relationship: has_part GO:0005586 ! collagen type III trimer -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata 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:0000542", ontology="AAO"} property_value: external_definition "Network of reticular fibres (fine collagen) that form a soft skeleton to support the lymphoid organs (lymph nodes, bone marrow, and spleen).[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000542", ontology="AAO", source="AAO:LAP"} property_value: external_ontology_notes "in FMA this is asserted as part of smooth muscle tissue" xsd:string {external_ontology="FMA"} @@ -116530,7 +116530,7 @@ xref: TADS:0000421 xref: WBbt:0006760 intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: site_of GO:0009790 ! embryo development -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of UBERON:0000474 ! female reproductive system [Term] @@ -116765,10 +116765,10 @@ xref: MBA:1061 xref: neuronames:1865 is_a: UBERON:0006569 ! diencephalic nucleus disjoint_from: UBERON:0034918 {source="lexical"} ! anterior pretectal nucleus +relationship: in_taxon NCBITaxon:9347 {source="ISBN:0471888893"} ! Eutheria relationship: mutually_spatially_disjoint_with UBERON:0002565 {source="ABA"} ! olivary pretectal nucleus relationship: mutually_spatially_disjoint_with UBERON:0002711 {source="ABA"} ! nucleus of posterior commissure relationship: mutually_spatially_disjoint_with UBERON:0002996 {source="ABA"} ! nucleus of optic tract -relationship: only_in_taxon NCBITaxon:9347 {source="ISBN:0471888893"} ! Eutheria [Term] id: UBERON:0006849 @@ -116971,9 +116971,9 @@ is_a: UBERON:0018707 {source="BTO"} ! bladder organ relationship: capable_of_part_of GO:0031413 ! regulation of buoyancy relationship: confers_advantage_in ENVO:00002030 relationship: develops_from UBERON:0006859 ! swim bladder bud +relationship: in_taxon NCBITaxon:7898 {source="Wikipedia"} ! Actinopterygii relationship: located_in UBERON:0002323 ! coelemic cavity lumen relationship: location_of UBERON:0034873 ! bodily gas -relationship: only_in_taxon NCBITaxon:7898 {source="Wikipedia"} ! Actinopterygii property_value: external_definition "Cavitated compound organ that is double-chambered, located in the coelom and used to maintain buoyancy and may function as an acoustic resonator.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000076", ontology="TAO", source="ZFIN:curator"} property_value: function_notes "May function as one or more of: hydrostatic organ, sound producing organ, sound receptor, respiratory organ" xsd:string property_value: homology_notes "Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000310", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011)", source="http://bgee.unil.ch/"} @@ -117099,7 +117099,7 @@ xref: MESH:D004557 xref: TAO:0002037 xref: Wikipedia:Electric_organ is_a: UBERON:0000062 ! organ -relationship: only_in_taxon NCBITaxon:7898 ! Actinopterygii +relationship: in_taxon NCBITaxon:7898 ! Actinopterygii property_value: editor_note "TODO - request go term for function assignment; todo - add CL term for electrocyte" xsd:string property_value: external_definition "Organ that is used to produce an electric field, i.e. an electric organ discharge (EOD).[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002037", ontology="TAO", source="TAO:wd"} @@ -117117,8 +117117,8 @@ is_a: UBERON:0003102 ! surface structure relationship: capable_of GO:0006590 ! thyroid hormone generation relationship: has_potential_to_develop_into UBERON:0002046 {gci_relation="part_of", gci_filler="NCBITaxon:117569"} ! thyroid gland relationship: has_quality PATO:0002255 ! grooved +relationship: in_taxon NCBITaxon:7711 {source="Wikipedia:Endostyle"} ! Chordata relationship: never_in_taxon NCBITaxon:7776 ! Gnathostomata -relationship: only_in_taxon NCBITaxon:7711 {source="Wikipedia:Endostyle"} ! Chordata relationship: part_of UBERON:0000949 {source="http://webs.lander.edu/rsfox/invertebrates/ammocoetes.html"} ! endocrine system relationship: part_of UBERON:0006562 ! pharynx relationship: present_in_taxon NCBITaxon:7712 ! Tunicata @@ -117633,7 +117633,7 @@ is_a: UBERON:0000058 ! duct relationship: channel_for CL:0000019 ! sperm relationship: channels_from UBERON:0003959 ! rete testis relationship: channels_into UBERON:0001301 ! epididymis -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000079 ! male reproductive system relationship: part_of UBERON:0006947 {source="FMA"} ! male genital duct property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg" xsd:anyURI @@ -117933,8 +117933,8 @@ xref: SCTID:69221006 xref: Wikipedia:Horn_(anatomy) is_a: UBERON:0006969 ! cranial appendage disjoint_from: UBERON:0014448 ! feathered ear tuft +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: never_in_taxon NCBITaxon:9606 {source="ISBN:9780716717553"} ! Homo sapiens -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: surrounds UBERON:0001474 ! bone element [Term] @@ -117968,7 +117968,7 @@ xref: MESH:D000999 xref: SCTID:410034008 xref: Wikipedia:Antler is_a: UBERON:0006969 ! cranial appendage -relationship: only_in_taxon NCBITaxon:9850 ! Cervidae +relationship: in_taxon NCBITaxon:9850 ! Cervidae [Term] id: UBERON:0006972 @@ -118179,7 +118179,7 @@ xref: VHOG:0001382 xref: XAO:0000108 xref: ZFA:0001082 is_a: UBERON:0000479 ! tissue -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0002533 ! post-anal tail bud property_value: external_definition "Portion of tissue is a posterior to the developing notochord during tailbud extension.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001082", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "Although there is mounting evidence showing the comparability of events and formation of different nascent tissue types during gastrulation and tail development, recent work also suggests the presence of an ongoing stem cell population capable of contributing to multiple tissue types in the tail of several different vertebrates, situated in the chordoneural hinge region of the tail bud. It would seem likely that secondary signaling centers regulate the fate to be adopted by such pluripotent progenitors.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001382", ontology="VHOG", source="DOI:10.1002/dvdy.20017 Liu C, Knezevic V, Mackem S, Ventral tail bud mesenchyme is a signaling for tail paraxial mesoderm induction. Developmental Dynamics (2004)", source="http://bgee.unil.ch/"} @@ -118240,7 +118240,7 @@ xref: SCTID:280701007 xref: Wikipedia:Vitelline_duct is_a: UBERON:0000025 ! tube relationship: develops_from UBERON:0001045 ! midgut -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray30.png" xsd:anyURI property_value: development_notes "In humans, it appears at the end of the fourth week, when the yolk-sac presents the appearance of a small pear-shaped vesicle (the umbilical vesicle). The vesicle can be seen in the afterbirth as a small, somewhat oval-shaped body whose diameter varies from 1 mm to 5 mm. It is situated between the amnion and the chorion and may lie on or at a varying distance from the placenta. Generally, the duct fully obliterates (narrows and disappears) during the seventh week, but a failure of the duct to close is termed a vitelline fistula. This results in discharge of meconium from the umbilicus. About two per cent of fetuses exhibit a type of vitelline fistula characterized by persistence of the proximal part of the vitelline duct as a diverticulum protruding from the small intestine, Meckel's diverticulum, which is situated about two feet above the ileocecal junction, and may be attached by a fibrous cord to the abdominal wall at the umbilicus. Sometimes a narrowing of the lumen of the ileum is seen opposite the site of attachment of the duct" xsd:string @@ -118288,7 +118288,7 @@ xref: Wikipedia:Vernix_caseosa is_a: UBERON:0000456 ! secretion of exocrine gland relationship: develops_from UBERON:0003055 {source="MP"} ! periderm relationship: has_part UBERON:0001866 ! sebum -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000323 ! late embryo relationship: surrounds UBERON:0002097 ! skin of body @@ -118300,7 +118300,7 @@ xref: BTO:0000838 xref: MESH:D008470 xref: ncithesaurus:Meconium is_a: UBERON:0001988 ! feces -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000323 ! late embryo [Term] @@ -119431,7 +119431,7 @@ xref: EMAPA:19180 xref: MA:0000405 xref: ncithesaurus:Vesicular_Gland is_a: UBERON:0010147 ! male accessory sex gland -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata property_value: editor_note "TODO - check this against seminal vesicle" xsd:string property_value: taxon_notes "bipartite seminal vesicles, with a seminal gland and vesicular gland sharing a common duct are found in lagomorphs" xsd:string {source="Lombardi"} @@ -120211,7 +120211,7 @@ xref: VSAO:0005000 intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: skeleton_of UBERON:0004710 ! pectoral appendage relationship: has_no_connections_with UBERON:0007273 ! pelvic appendage skeleton -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0004710 {source="VSAO"} ! pectoral appendage [Term] @@ -120220,7 +120220,7 @@ name: pelvic appendage skeleton def: "The collection of all skeletal elements in a pelvic appendage region." [https://orcid.org/0000-0002-6601-2165] intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: skeleton_of UBERON:0004709 ! pelvic appendage -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0004709 {source="VSAO"} ! pelvic appendage [Term] @@ -120871,7 +120871,7 @@ synonym: "nested pallium" RELATED [BTO:0003389] xref: BTO:0003389 xref: Wikipedia:Nidopallium is_a: UBERON:0002616 ! regional part of brain -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0000203 ! pallium property_value: terminology_notes "The region was renamed from neostriatum to nidopallium in 2002 during the Avian Brain Nomenclature Consortium because the prior name suggested that the region was used for more primitive functions" xsd:string @@ -120883,7 +120883,7 @@ synonym: "hyperstriatum" RELATED [BTO:0003400, Wikipedia:Hyperpallium] xref: BTO:0003400 xref: Wikipedia:Hyperpallium is_a: UBERON:0002616 ! regional part of brain -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0000203 ! pallium [Term] @@ -120906,7 +120906,7 @@ xref: BM:ARCO xref: BTO:0003408 xref: Wikipedia:Arcopallium is_a: UBERON:0002616 ! regional part of brain -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0000203 ! pallium property_value: taxon_notes "The arcopallium refers to regions of the avian brain which partially overlap regions homologous to the amygdala of mammals. These regions have formerly been referred to as archistriatum, and before this epistriatum or amygdaloid complex, and a recent change of nomenclature has divided the region into the arcopallium and posterior pallial amygdala. The new nomenclature, adopted in 2004, reflects a modern understanding that the avian brain is broadly similar to the mammalian brain, containing large regions homologous to the mammalian neocortex, claustrum, and pallial amygdala. The outdated nomenclature it replaced perceived the avian brain as consisting almost entirely of enlarged basal ganglia, to which more complex outer layers had been added during a progress toward mammalian intelligence. [Wikipedia:Arcopallium]" xsd:string @@ -120916,7 +120916,7 @@ name: nucleus isthmo-opticus synonym: "nucleus isthmoopticus" RELATED [BTO:0003411] xref: BTO:0003411 is_a: UBERON:0000125 ! neural nucleus -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0000203 ! pallium [Term] @@ -120974,7 +120974,7 @@ xref: NCIT:C111162 xref: SCTID:68028003 xref: Wikipedia:Crop_(anatomy)#Birds is_a: UBERON:0000062 ! organ -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0001043 ! esophagus property_value: editor_note "we follow WP and place as part of the esophagus" xsd:string property_value: taxon_notes "Aves specific structure - consider adding functional grouping class. Kardong: some cetaceans have a crop-like structure" xsd:string @@ -120995,7 +120995,7 @@ relationship: capable_of GO:0001696 ! gastric acid secretion relationship: continuous_with UBERON:0005052 ! gizzard relationship: continuous_with UBERON:0007356 ! crop relationship: has_part UBERON:0010038 {source="Wikipedia"} ! fundic gastric gland -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves property_value: taxon_notes "consider extending to crocodilians. EMAPA has proventricular region" xsd:string [Term] @@ -121102,7 +121102,7 @@ synonym: "plurilocular stomach" RELATED [] xref: GAID:1240 xref: MESH:D013279 is_a: UBERON:0000945 ! stomach -relationship: only_in_taxon NCBITaxon:9845 ! Ruminantia +relationship: in_taxon NCBITaxon:9845 ! Ruminantia property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/2b/Abomasum_(PSF).png" xsd:anyURI property_value: editor_note "Consider classifying each subdivision as 'stomach chamber'" xsd:string @@ -121184,7 +121184,7 @@ is_a: UBERON:0003102 ! surface structure intersection_of: UBERON:0000483 ! epithelium intersection_of: bounding_layer_of UBERON:0000468 ! multicellular organism intersection_of: develops_from UBERON:0007383 ! enveloping layer of ectoderm -relationship: only_in_taxon NCBITaxon:6072 {source="Wikipedia:Epidermis_(zoology)"} ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 {source="Wikipedia:Epidermis_(zoology)"} ! Eumetazoa property_value: editor_note "this grouping class exists primarily to align with GO - see GO:0008544." xsd:string [Term] @@ -121320,7 +121320,7 @@ xref: TAO:0000257 xref: ZFA:0000257 intersection_of: UBERON:0002418 ! cartilage tissue intersection_of: part_of UBERON:0004710 ! pectoral appendage -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0007272 ! pectoral appendage skeleton property_value: external_definition "Cartilage which is part of the pectoral fin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000257", ontology="TAO", source="ZFIN:curator"} @@ -121333,7 +121333,7 @@ xref: TAO:0001459 xref: ZFA:0001459 intersection_of: UBERON:0002418 ! cartilage tissue intersection_of: part_of UBERON:0004709 ! pelvic appendage -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0007273 ! pelvic appendage skeleton property_value: external_definition "Cartilage which is part of the pelvic fin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001459", ontology="TAO", source="ZFIN:curator"} @@ -121878,7 +121878,7 @@ xref: Wikipedia:Pecten_oculi is_a: UBERON:0002049 ! vasculature relationship: capable_of_part_of GO:0006885 ! regulation of pH relationship: develops_from UBERON:0016855 {source="cjm"} ! ventral part of optic cup -relationship: only_in_taxon NCBITaxon:8457 ! Sauropsida +relationship: in_taxon NCBITaxon:8457 ! Sauropsida relationship: part_of UBERON:0001776 ! optic choroid property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/thumb/b/b7/Birdeye.jpg/700px-Birdeye.jpg" xsd:anyURI @@ -121893,7 +121893,7 @@ xref: MESH:D003129 xref: SCTID:37118002 xref: Wikipedia:Wattle_(anatomy) is_a: UBERON:0000021 ! cutaneous appendage -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves [Term] id: UBERON:0007625 @@ -123219,7 +123219,7 @@ subset: organ_slim xref: BTO:0004995 xref: Wikipedia:Osphradium is_a: UBERON:0002268 {source="BTO"} ! olfactory organ -relationship: only_in_taxon NCBITaxon:6447 ! Mollusca +relationship: in_taxon NCBITaxon:6447 ! Mollusca [Term] id: UBERON:0007771 @@ -123331,7 +123331,7 @@ intersection_of: filtered_through UBERON:0001982 ! capillary intersection_of: has_quality PATO:0001548 ! quality of a liquid intersection_of: transformation_of UBERON:0001969 ! blood plasma disjoint_from: UBERON:0007780 ! exudate -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata property_value: has_relational_adjective "transudative" xsd:string property_value: structure_notes "characteristically low in protein and cellular content (unless there has been secondary concentration)" xsd:string @@ -123344,7 +123344,7 @@ xref: MESH:D005122 xref: ncithesaurus:Exudate is_a: UBERON:0000463 ! organism substance relationship: filtered_through UBERON:0001981 ! blood vessel -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: output_of GO:0006954 ! inflammatory response [Term] @@ -123416,7 +123416,7 @@ xref: http://people.eku.edu/ritchisong/birdskeleton.gif xref: SCTID:416894001 xref: Wikipedia:Pygostyle is_a: UBERON:0001474 ! bone element -relationship: only_in_taxon NCBITaxon:8782 {source="Wikipedia"} ! Aves +relationship: in_taxon NCBITaxon:8782 {source="Wikipedia"} ! Aves relationship: part_of UBERON:0001130 ! vertebral column [Term] @@ -123436,7 +123436,7 @@ intersection_of: UBERON:0002365 ! exocrine gland intersection_of: produces UBERON:0007803 ! preen oil relationship: capable_of_part_of GO:0007625 ! grooming behavior relationship: capable_of_part_of NBO:0000451 ! personal grooming -relationship: only_in_taxon NCBITaxon:8782 {source="Wikipedia"} ! Aves +relationship: in_taxon NCBITaxon:8782 {source="Wikipedia"} ! Aves relationship: part_of UBERON:0002415 {source="BTO"} ! tail [Term] @@ -123583,8 +123583,8 @@ xref: ZFA:0001117 intersection_of: UBERON:0002415 ! tail intersection_of: part_of UBERON:0006071 ! caudal region relationship: capable_of_part_of GO:0007626 ! locomotory behavior +relationship: in_taxon NCBITaxon:7711 {notes="possible exception in hemichordates", source="cjm"} ! Chordata relationship: never_in_taxon NCBITaxon:314295 ! Hominoidea -relationship: only_in_taxon NCBITaxon:7711 {notes="possible exception in hemichordates", source="cjm"} ! Chordata relationship: transformation_of UBERON:0007144 ! embryonic post-anal tail property_value: external_definition "Anatomical structure that is the terminal, flexible posterior appendage of the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010338", ontology="AAO", source="AAO:EJS"} property_value: external_definition "Organism subdivision which is the part of the body posterior to the vent which includes the anal and caudal fins.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001117", ontology="TAO", source="ZFIN:curator"} @@ -123666,7 +123666,7 @@ xref: FMA:24874 xref: VSAO:0000303 intersection_of: UBERON:0000475 ! organism subdivision intersection_of: has_skeleton UBERON:0010719 ! girdle skeleton -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0010707 ! appendage girdle complex property_value: curator_notes "this encompasses non-skeletal tissue" xsd:string property_value: external_definition "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000303", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} @@ -123723,7 +123723,7 @@ xref: EMAPA:35379 xref: MA:0000291 intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0007823 ! appendage girdle region -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0010719 ! girdle skeleton [Term] @@ -123917,7 +123917,7 @@ is_a: UBERON:0008907 ! dermal bone relationship: has_fused_element UBERON:0008255 ! right clavicle relationship: has_fused_element UBERON:0008256 ! left clavicle relationship: has_fused_element UBERON:0011655 ! interclavicle -relationship: only_in_taxon NCBITaxon:8492 {source="http://people.eku.edu/ritchisong/342notes5.htm"} ! Archosauria +relationship: in_taxon NCBITaxon:8492 {source="http://people.eku.edu/ritchisong/342notes5.htm"} ! Archosauria relationship: part_of UBERON:0007831 ! pectoral girdle skeleton relationship: present_in_taxon NCBITaxon:436495 ! Tyrannosaurus rex relationship: present_in_taxon NCBITaxon:8782 ! Aves @@ -124165,7 +124165,7 @@ is_a: UBERON:0000982 {source="MA"} ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: part_of UBERON:0007823 ! appendage girdle region relationship: connects UBERON:0007828 ! girdle bone/zone -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata [Term] id: UBERON:0008115 @@ -124247,7 +124247,7 @@ intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: develops_from UBERON:0010902 ! tibiotarsus cartilage element relationship: has_fused_element UBERON:0000979 ! tibia relationship: has_fused_element UBERON:0001447 ! tarsal bone -relationship: only_in_taxon NCBITaxon:8492 ! Archosauria +relationship: in_taxon NCBITaxon:8492 ! Archosauria relationship: part_of UBERON:0001441 ! hindlimb skeleton [Term] @@ -124261,7 +124261,7 @@ intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: develops_from UBERON:0010900 ! tarsometatarsus cartilage element relationship: has_fused_element UBERON:0001448 ! metatarsal bone relationship: has_fused_element UBERON:0009879 ! tarsal skeleton -relationship: only_in_taxon NCBITaxon:8492 ! Archosauria +relationship: in_taxon NCBITaxon:8492 ! Archosauria relationship: part_of UBERON:0001445 ! skeleton of pes property_value: taxon_notes "found in birds" xsd:string {source="VSAO"} @@ -124339,7 +124339,7 @@ xref: SCTID:362614004 xref: UMLS:C0016540 {source="ncithesaurus:Forehead"} xref: Wikipedia:Forehead is_a: UBERON:0001444 ! subdivision of head -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001456 {source="FMA"} ! face property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/83/Forhead_01_ies.jpg" xsd:anyURI @@ -124484,7 +124484,7 @@ xref: BTO:0002121 xref: SCTID:280119005 xref: Wikipedia:Starfish is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: only_in_taxon NCBITaxon:7586 ! Echinodermata +relationship: in_taxon NCBITaxon:7586 ! Echinodermata relationship: part_of UBERON:0001007 ! digestive system [Term] @@ -124495,7 +124495,7 @@ synonym: "tube feet" RELATED OMO:0003004 [Wikipedia:Tube_feet] xref: BTO:0001919 xref: Wikipedia:Tube_feet is_a: UBERON:0000026 {source="cjm"} ! appendage -relationship: only_in_taxon NCBITaxon:7586 ! Echinodermata +relationship: in_taxon NCBITaxon:7586 ! Echinodermata [Term] id: UBERON:0008248 @@ -124505,7 +124505,7 @@ synonym: "pyloric caecum" BROAD [BTO:0002120] synonym: "pyloric cecum" BROAD [BTO:0002120] xref: BTO:0002120 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: only_in_taxon NCBITaxon:7586 ! Echinodermata +relationship: in_taxon NCBITaxon:7586 ! Echinodermata relationship: part_of UBERON:0001007 ! digestive system [Term] @@ -124515,7 +124515,7 @@ def: "In starfishes the cardiac stomach is connected to a pyloric stomach which subset: organ_slim xref: BTO:0002122 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: only_in_taxon NCBITaxon:7586 ! Echinodermata +relationship: in_taxon NCBITaxon:7586 ! Echinodermata [Term] id: UBERON:0008251 @@ -124526,7 +124526,7 @@ xref: Wikipedia:Water_vascular_system is_a: UBERON:0000467 ! anatomical system relationship: capable_of GO:0040011 ! locomotion relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: only_in_taxon NCBITaxon:7586 ! Echinodermata +relationship: in_taxon NCBITaxon:7586 ! Echinodermata [Term] id: UBERON:0008252 @@ -124536,9 +124536,9 @@ synonym: "ampulla" BROAD [BTO:0002124] xref: BTO:0002124 is_a: UBERON:0000062 ! organ disjoint_from: UBERON:0009474 ! ascidian ampulla +relationship: in_taxon NCBITaxon:7586 ! Echinodermata relationship: never_in_taxon NCBITaxon:35069 {source="Wikipedia"} relationship: never_in_taxon NCBITaxon:7618 {source="Wikipedia"} -relationship: only_in_taxon NCBITaxon:7586 ! Echinodermata relationship: part_of UBERON:0008247 ! tube foot relationship: part_of UBERON:0008251 {source="BTO"} ! water vascular system property_value: function_notes "The constant contraction of ampulla (to extend and retract the tube feet) helps to move a starfish" xsd:string @@ -124554,7 +124554,7 @@ xref: http://content60.eol.org/content/2012/06/14/21/52446_580_360.jpg xref: http://eol.org/data_objects/19677434 xref: Wikipedia:Aristotle's_lantern is_a: UBERON:0000481 ! multi-tissue structure -relationship: only_in_taxon NCBITaxon:7625 ! Echinoidea +relationship: in_taxon NCBITaxon:7625 ! Echinoidea relationship: part_of UBERON:0000165 {source="BTO"} ! mouth [Term] @@ -124608,8 +124608,8 @@ synonym: "oral side of organism" RELATED [] synonym: "oral subdivision" RELATED [] is_a: UBERON:0000475 ! organism subdivision relationship: has_part UBERON:0000166 ! oral opening +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: present_in_taxon NCBITaxon:6073 ! Cnidaria relationship: present_in_taxon NCBITaxon:7588 ! Asteroidea @@ -124625,9 +124625,9 @@ synonym: "aboral side of organism" RELATED [] synonym: "aboral subdivision" RELATED [] is_a: UBERON:0000475 ! organism subdivision relationship: aboral_to UBERON:0008258 ! oral subdivision of organism +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: mutually_spatially_disjoint_with UBERON:0008258 ! oral subdivision of organism relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: present_in_taxon NCBITaxon:6073 ! Cnidaria relationship: present_in_taxon NCBITaxon:7588 ! Asteroidea @@ -124641,8 +124641,8 @@ synonym: "spiny appendage" RELATED [] xref: Wikipedia:Spine_(zoology) is_a: UBERON:0000026 {status="unstable"} ! appendage relationship: has_quality PATO:0001954 ! subulate +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria property_value: editor_note "May be reclassified depending on CARO treatment of appendage" xsd:string [Term] @@ -124652,19 +124652,19 @@ def: "A small wrench or claw-shaped structure commonly found on Echinoderms, par synonym: "pedicellariae" EXACT OMO:0003004 [Wikipedia:Pedicellaria] xref: Wikipedia:Pedicellaria is_a: UBERON:0000026 {source="cjm"} ! appendage -relationship: only_in_taxon NCBITaxon:7586 ! Echinodermata +relationship: in_taxon NCBITaxon:7586 ! Echinodermata [Term] id: UBERON:0008262 name: ambulacral area is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:7586 ! Echinodermata +relationship: in_taxon NCBITaxon:7586 ! Echinodermata [Term] id: UBERON:0008263 name: inter-ambulacral area is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:7586 ! Echinodermata +relationship: in_taxon NCBITaxon:7586 ! Echinodermata [Term] id: UBERON:0008264 @@ -124672,7 +124672,7 @@ name: echinopluteus larval stage def: "Larval stage in echinoderms characterized by a planktonic and feeding larval form that possesses limb-like outgrowths bearing ciliated bands." [http://www.encyclopedia.com/doc/1O8-echinopluteuslarva.html] synonym: "pluteus larval stage" EXACT [] is_a: UBERON:0000069 ! larval stage -relationship: only_in_taxon NCBITaxon:7586 ! Echinodermata +relationship: in_taxon NCBITaxon:7586 ! Echinodermata [Term] id: UBERON:0008265 @@ -124751,7 +124751,7 @@ xref: MESH:D060734 xref: Wikipedia:Nacre is_a: UBERON:0000463 ! organism substance is_a: UBERON:0004755 ! skeletal tissue -relationship: only_in_taxon NCBITaxon:6447 ! Mollusca +relationship: in_taxon NCBITaxon:6447 ! Mollusca [Term] id: UBERON:0008270 @@ -124759,7 +124759,7 @@ name: mollusc shell def: "A calcareous exoskeleton which encloses, supports and protects the soft parts of an animal in the phylum Mollusca, which includes snails, clams, tusk shells, and several other classes. Not all shelled molluscs live in the sea, many live on the land and in freshwater." [Wikipedia:Mollusc_shell] xref: Wikipedia:Mollusc_shell is_a: UBERON:0006612 ! shell -relationship: only_in_taxon NCBITaxon:6447 ! Mollusca +relationship: in_taxon NCBITaxon:6447 ! Mollusca [Term] id: UBERON:0008271 @@ -124769,7 +124769,7 @@ synonym: "armor" RELATED [] xref: Wikipedia:Turtle_shell#Shell is_a: UBERON:0000075 ! subdivision of skeletal system is_a: UBERON:0006612 ! shell -relationship: only_in_taxon NCBITaxon:8459 ! Testudines +relationship: in_taxon NCBITaxon:8459 ! Testudines [Term] id: UBERON:0008274 @@ -124782,7 +124782,7 @@ synonym: "octopus venom" RELATED [MESH:D24.185.926.580.590] synonym: "snail venom" RELATED [MESH:D24.185.926.580.590] xref: MESH:D008978 is_a: UBERON:0007113 {source="MESH"} ! venom -relationship: only_in_taxon NCBITaxon:6447 ! Mollusca +relationship: in_taxon NCBITaxon:6447 ! Mollusca [Term] id: UBERON:0008275 @@ -124851,7 +124851,7 @@ synonym: "portuguese man-of-war venom" RELATED [MESH:D24.185.926.580.230] synonym: "sea anemone venom" RELATED [MESH:D24.185.926.580.230] xref: MESH:D003064 is_a: UBERON:0007113 {source="MESH"} ! venom -relationship: only_in_taxon NCBITaxon:6073 ! Cnidaria +relationship: in_taxon NCBITaxon:6073 ! Cnidaria [Term] id: UBERON:0008281 @@ -124877,7 +124877,7 @@ def: "A central anatomical feature of a coiled snail shell or gastropod shell. I xref: Wikipedia:Columella_(gastropod) is_a: UBERON:0000475 ! organism subdivision disjoint_from: UBERON:0008341 ! columella nasi -relationship: only_in_taxon NCBITaxon:6447 ! Mollusca +relationship: in_taxon NCBITaxon:6447 ! Mollusca relationship: part_of UBERON:0008270 ! mollusc shell [Term] @@ -124889,7 +124889,7 @@ xref: BTO:0000277 xref: Wikipedia:Columella_(gastropod)#Columellar_muscles intersection_of: UBERON:0001630 ! muscle organ intersection_of: attaches_to UBERON:0008283 ! columnella -relationship: only_in_taxon NCBITaxon:6447 ! Mollusca +relationship: in_taxon NCBITaxon:6447 ! Mollusca [Term] id: UBERON:0008285 @@ -125016,7 +125016,7 @@ def: "The perichondrium consists of two separate layers: an outer fibrous layer xref: BTO:0005090 xref: Wikipedia:The_Free_Encyclopedia is_a: UBERON:0002384 ! connective tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002222 {source="BTO"} ! perichondrium [Term] @@ -125133,7 +125133,7 @@ def: "With numerous vascular spaces that may become engorged with blood." [Wikip comment: Examples: corpus cavernosum or penis or clitoris xref: Wikipedia:Erectile_tissue is_a: UBERON:0000479 ! tissue -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria [Term] id: UBERON:0008330 @@ -125664,7 +125664,7 @@ is_a: UBERON:0014892 ! skeletal muscle organ, vertebrate relationship: has_muscle_antagonist UBERON:0003234 {source="dbpedia"} ! extensor pollicis longus muscle relationship: has_muscle_insertion UBERON:0004444 {notes="The base of the distal phalanx of the thumb", source="dbpedia"} ! proximal epiphysis of distal phalanx of manual digit 1 relationship: has_muscle_origin UBERON:0001423 {notes="The middle 2/4 of the volar surface of the radius and the adjacent interosseus membrane.", source="dbpedia"} ! radius bone -relationship: only_in_taxon NCBITaxon:9606 {source="Wikipedia"} ! Homo sapiens +relationship: in_taxon NCBITaxon:9606 {source="Wikipedia"} ! Homo sapiens relationship: part_of UBERON:0002386 ! forelimb zeugopod property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/72/FPL.png" xsd:anyURI property_value: taxon_notes "Modern humans are unique among hominids in having a flexor pollicis longus (FPL) muscle belly that is separate from that of the flexor digitorum profundus (FDP). While the FPL is not a separate muscle belly in extant great apes, a distinct tendon from the FDP belly might be present. In some individuals this tendon tend to act more like a ligament which restricts extension of the interphalangeal joint of the thumb. In orangutans there is a tendon similar in insertion and function to the FPL in humans, but which has an intrinsic origin on the oblique head of the adductor pollicis" xsd:string {source="WP"} @@ -126507,8 +126507,8 @@ intersection_of: dorsal_to UBERON:0005467 ! platysma intersection_of: ventral_to UBERON:0008593 ! zygomaticus major muscle relationship: has_muscle_insertion UBERON:0011386 ! facial modiolus relationship: has_muscle_origin UBERON:0001831 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="dbpedia"} ! parotid gland +relationship: in_taxon NCBITaxon:207598 ! Homininae relationship: innervated_by UBERON:0001647 {notes="buccal branch", source="dbpedia"} ! facial nerve -relationship: only_in_taxon NCBITaxon:207598 ! Homininae property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/af/Musculusrisorius.png" xsd:anyURI [Term] @@ -126963,7 +126963,7 @@ def: "A knob-like feature on the medial side of the femur that serves as a muscl comment: The fourth trochanter first appeared in the Erythrosuchidae, large basal archosaurian predators of the early Triassic period. This seemingly insignificant detail may have made the evolution of dinosaurs possible (all early dinosaurs and many later ones were bipeds), and may also be connected with the ability of the archosaurs or their immediate ancestors to survive the catastrophic Permian-Triassic extinction event[WP]. xref: Wikipedia:Fourth_trochanter is_a: UBERON:0000980 {source="Wikipedia"} ! trochanter -relationship: only_in_taxon NCBITaxon:8492 ! Archosauria +relationship: in_taxon NCBITaxon:8492 ! Archosauria [Term] id: UBERON:0008788 @@ -127093,7 +127093,7 @@ xref: NCIT:C111156 xref: SCTID:31293007 xref: Wikipedia:Cheek_pouch is_a: UBERON:0000014 ! zone of skin -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0000165 ! mouth relationship: part_of UBERON:0001567 {source="BTO"} ! cheek @@ -127144,7 +127144,7 @@ xref: Wikipedia:Gingival_sulcus intersection_of: UBERON:0000093 ! sulcus intersection_of: adjacent_to UBERON:0001091 ! calcareous tooth intersection_of: adjacent_to UBERON:0001828 ! gingiva -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000165 ! mouth property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/5/5e/Gingival_sulcus.PNG" xsd:anyURI @@ -127154,7 +127154,7 @@ name: buccal funnel synonym: "suctorial disc" EXACT [] synonym: "suctorial disk" EXACT [] is_a: UBERON:0000166 ! oral opening -relationship: only_in_taxon NCBITaxon:117569 ! Hyperoartia +relationship: in_taxon NCBITaxon:117569 ! Hyperoartia [Term] id: UBERON:0008807 @@ -127229,7 +127229,7 @@ xref: TGMA:0000585 xref: Wikipedia:Intromittent_organ is_a: UBERON:0003133 ! reproductive organ relationship: capable_of_part_of GO:0007620 ! copulation -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000079 ! male reproductive system relationship: part_of UBERON:0000990 ! reproductive system property_value: curator_notes "this is a broad grouping class connecting a number of different analagous organs by their function. We place the insect aedeagus here rather than penis, although this is somewhat arbitrary given the broadness of the current definition" xsd:string @@ -127244,7 +127244,7 @@ synonym: "hemipenes" RELATED OMO:0003004 [Wikipedia:Hemipenis] xref: SCTID:27265006 xref: Wikipedia:Hemipenis is_a: UBERON:0008811 {source="Wikipedia"} ! intromittent organ -relationship: only_in_taxon NCBITaxon:8509 ! Squamata +relationship: in_taxon NCBITaxon:8509 ! Squamata [Term] id: UBERON:0008813 @@ -127278,7 +127278,7 @@ xref: FMA:293041 xref: NCIT:C34248 xref: UMLS:C1519038 {source="ncithesaurus:Pharyngeal_Apparatus"} is_a: UBERON:0034921 ! multi organ part structure -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0009145 ! pharyngeal region of foregut property_value: editor_note "Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing" xsd:string @@ -127294,8 +127294,8 @@ xref: Wikipedia:Pharyngeal_slit is_a: UBERON:0000062 ! organ relationship: capable_of_part_of GO:0007631 ! feeding behavior relationship: develops_from UBERON:0007690 {source="cjm"} ! early pharyngeal endoderm +relationship: in_taxon NCBITaxon:33511 {source="PMID:11961109"} ! Deuterostomia relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: only_in_taxon NCBITaxon:33511 {source="PMID:11961109"} ! Deuterostomia relationship: part_of UBERON:0001042 ! chordate pharynx property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/thumb/2/22/Gill_slits.png/280px-Gill_slits.png" xsd:anyURI property_value: editor_note "requires review. Kardong uses the term pharyngeal slit for Chondrichthyans. 'branchial slit' may also be used for amniote structures." xsd:string @@ -127440,7 +127440,7 @@ xref: NCIT:C13273 xref: UMLS:C0034085 {source="ncithesaurus:Lung_Surfactant"} xref: Wikipedia:Pulmonary_surfactant intersection_of: UBERON:0006538 ! respiratory system fluid/secretion -intersection_of: produced_by CL:0002063 ! type II pneumocyte +intersection_of: produced_by CL:0002063 ! pulmonary alveolar type 2 cell relationship: has_part CHEBI:6495 ! lipoprotein property_value: function_notes "surfactant" xsd:string @@ -127566,7 +127566,7 @@ synonym: "acron" RELATED [BTO:0004198, Wikipedia:Prostomium] xref: BTO:0004198 xref: Wikipedia:Prostomium is_a: UBERON:0000914 ! organismal segment -relationship: only_in_taxon NCBITaxon:6340 {source="Wikipedia"} ! Annelida +relationship: in_taxon NCBITaxon:6340 {source="Wikipedia"} ! Annelida property_value: function_notes "Often functions like a kind of overlip when the animal is feeding." xsd:string property_value: structure_notes "sometimes bears antennae and eyes" xsd:string @@ -128020,8 +128020,8 @@ intersection_of: UBERON:0000353 ! parenchyma intersection_of: part_of UBERON:0002299 ! alveolus of lung relationship: contributes_to_morphology_of UBERON:0006524 ! alveolar system relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 ! Aleix Puig-Barbé -relationship: has_part CL:0002062 ! type I pneumocyte -relationship: has_part CL:0002063 ! type II pneumocyte +relationship: has_part CL:0002062 ! pulmonary alveolar type 1 cell +relationship: has_part CL:0002063 ! pulmonary alveolar type 2 cell relationship: has_part CL:0009089 ! lung pericyte [Term] @@ -128129,7 +128129,7 @@ synonym: "periproct" BROAD [Wikipedia:Periproct] synonym: "pygidium" RELATED [Wikipedia:Annelid#Segmentation] xref: Wikipedia:Periproct is_a: UBERON:0000914 ! organismal segment -relationship: only_in_taxon NCBITaxon:6340 {source="Wikipedia"} ! Annelida +relationship: in_taxon NCBITaxon:6340 {source="Wikipedia"} ! Annelida [Term] id: UBERON:0008881 @@ -128733,7 +128733,7 @@ name: gastropod albumen gland def: "The posterior oviduct opens into the large white albumen gland which adds a layer of albumen to the zygote before it reaches the egg capsule gland." [BTO:0000054] xref: BTO:0000054 is_a: UBERON:0005398 {source="BTO"} ! female reproductive gland -relationship: only_in_taxon NCBITaxon:6448 ! Gastropoda +relationship: in_taxon NCBITaxon:6448 ! Gastropoda [Term] id: UBERON:0008936 @@ -128743,7 +128743,7 @@ synonym: "genital orifice" RELATED [BTO:0004684] synonym: "genital pore" EXACT [BTO:0004684] xref: BTO:0004684 is_a: UBERON:0000161 ! orifice -relationship: only_in_taxon NCBITaxon:6448 ! Gastropoda +relationship: in_taxon NCBITaxon:6448 ! Gastropoda relationship: part_of UBERON:0000990 {source="BTO"} ! reproductive system [Term] @@ -128753,7 +128753,7 @@ def: "Mollusks have three distinct divisions of their body. The head contains th synonym: "visceral sac" RELATED [BTO:0001448] xref: BTO:0001448 is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:6447 ! Mollusca +relationship: in_taxon NCBITaxon:6447 ! Mollusca [Term] id: UBERON:0008939 @@ -128761,7 +128761,7 @@ name: pedal ganglion def: "The pedal ganglia mainly are necessary for coordination of locomotion of a snail." [BTO:0001012] xref: BTO:0001012 is_a: UBERON:0000045 {source="BTO"} ! ganglion -relationship: only_in_taxon NCBITaxon:6447 ! Mollusca +relationship: in_taxon NCBITaxon:6447 ! Mollusca relationship: part_of UBERON:0008937 {source="BTO"} ! visceral hump [Term] @@ -128770,7 +128770,7 @@ name: parietal ganglion def: "A lateral ganglion that innervates pallial cavity, gills and skin of a snail[BTO,modified]." [BTO:0001841] xref: BTO:0001841 is_a: UBERON:0000045 {source="BTO"} ! ganglion -relationship: only_in_taxon NCBITaxon:6447 ! Mollusca +relationship: in_taxon NCBITaxon:6447 ! Mollusca relationship: part_of UBERON:0008937 {source="BTO"} ! visceral hump [Term] @@ -128779,7 +128779,7 @@ name: pleural ganglion def: "A knot of nerves in The pallial cavity that innervates the mantle of a snail[BTO,modified]." [BTO:0001842] xref: BTO:0001842 is_a: UBERON:0000045 {source="BTO"} ! ganglion -relationship: only_in_taxon NCBITaxon:6447 ! Mollusca +relationship: in_taxon NCBITaxon:6447 ! Mollusca relationship: part_of UBERON:0008937 {source="BTO"} ! visceral hump property_value: editor_note "to be ceded to MOLO" xsd:string @@ -128798,7 +128798,7 @@ name: headfoot def: "The head-foot is the part you see most easily in slugs and snails. It is mostly a muscular organ covered in cilia and rich in mucous cells, which the mollusc uses to move around, it normally tapers to a tail at one end and has a head incorporated in the front. The head includes a mouth, eyes and tentacles, the last two may be much reduced or even absent. In those species with shells the head-foot can be drawn into the shell." [BTO:0003509] xref: BTO:0003509 is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:6447 ! Mollusca +relationship: in_taxon NCBITaxon:6447 ! Mollusca [Term] id: UBERON:0008944 @@ -129006,7 +129006,7 @@ name: cetacean involucrum synonym: "whale involucrum" RELATED [] is_a: UBERON:0000064 ! organ part relationship: capable_of GO:0050910 ! detection of mechanical stimulus involved in sensory perception of sound -relationship: only_in_taxon NCBITaxon:9721 ! Cetacea +relationship: in_taxon NCBITaxon:9721 ! Cetacea relationship: part_of UBERON:0001474 {source="Wikipedia:Evolution_of_cetaceans"} ! bone element [Term] @@ -129022,7 +129022,7 @@ xref: EMAPA:37433 {source="MA:th"} xref: NCIT:C112425 xref: Wikipedia:Auditory_bulla is_a: UBERON:0004530 ! bony projection -relationship: only_in_taxon NCBITaxon:32525 {source="Wikipedia"} ! Theria +relationship: in_taxon NCBITaxon:32525 {source="Wikipedia"} ! Theria relationship: part_of UBERON:0001690 ! ear relationship: part_of UBERON:0003113 {source="ISBN:0073040584"} ! dermatocranium relationship: surrounds UBERON:0004114 {source="Rose"} ! tympanic cavity @@ -129039,7 +129039,7 @@ xref: Wikipedia:Melon_(whale) is_a: UBERON:0000062 ! organ relationship: capable_of_part_of GO:0050959 ! echolocation relationship: has_part UBERON:0013182 ! core of melon organ -relationship: only_in_taxon NCBITaxon:9721 ! Cetacea +relationship: in_taxon NCBITaxon:9721 ! Cetacea relationship: part_of UBERON:0000033 ! head [Term] @@ -129052,7 +129052,7 @@ synonym: "parabronchi" RELATED OMO:0003004 [] is_a: UBERON:0002184 {notes="tertiary", source="ISBN:0073040584"} ! segmental bronchus relationship: connected_to UBERON:0009072 ! ventrobronchus relationship: connected_to UBERON:0009073 ! dorsobronchus -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0002048 ! lung [Term] @@ -129079,7 +129079,7 @@ xref: BTO:0003994 xref: SCTID:410026002 xref: Wikipedia:Hoof is_a: UBERON:0009564 ! distal limb integumentary appendage -relationship: only_in_taxon NCBITaxon:314145 ! Laurasiatheria +relationship: in_taxon NCBITaxon:314145 ! Laurasiatheria [Term] id: UBERON:0008964 @@ -129090,7 +129090,7 @@ synonym: "visceral ganglion" RELATED [BTO:0000022] xref: BTO:0000022 is_a: UBERON:0000045 {source="BTO"} ! ganglion disjoint_from: UBERON:0009758 ! abdominal ganglion -relationship: only_in_taxon NCBITaxon:6447 ! Mollusca +relationship: in_taxon NCBITaxon:6447 ! Mollusca relationship: part_of UBERON:0008937 {source="BTO"} ! visceral hump [Term] @@ -129204,7 +129204,7 @@ synonym: "venom gland" BROAD [BTO:0001440] xref: BTO:0001440 xref: SCTID:23993002 is_a: UBERON:0002365 {source="BTO"} ! exocrine gland -relationship: only_in_taxon NCBITaxon:8570 {source="ISBN:0073040584"} ! Serpentes +relationship: in_taxon NCBITaxon:8570 {source="ISBN:0073040584"} ! Serpentes relationship: produces UBERON:0013076 ! snake venom property_value: has_relational_adjective "venenosalivary" xsd:string @@ -129237,7 +129237,7 @@ xref: MESH:D000695 xref: SCTID:362169000 is_a: UBERON:0000062 ! organ is_a: UBERON:0009856 ! sac -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia [Term] id: UBERON:0008979 @@ -129591,7 +129591,7 @@ xref: MA:0001888 xref: SCTID:24306004 is_a: UBERON:0009753 {source="MA"} ! adrenal gland cortex zone relationship: contributes_to_morphology_of UBERON:0001235 ! adrenal cortex -relationship: only_in_taxon NCBITaxon:10088 ! Mus +relationship: in_taxon NCBITaxon:10088 ! Mus relationship: part_of UBERON:0001235 {source="MA"} ! adrenal cortex [Term] @@ -129930,7 +129930,7 @@ xref: NCIT:C120926 xref: SCTID:49081009 xref: Wikipedia:Bird_anatomy#Respiratory_system is_a: UBERON:0010000 ! multicellular anatomical structure -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0001004 ! respiratory system property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f2/BirdRespiration.svg" xsd:anyURI @@ -129997,7 +129997,7 @@ subset: organ_slim synonym: "mesobronchi" RELATED OMO:0003004 [] is_a: UBERON:0002182 {source="ISBN:0073040584"} ! main bronchus relationship: connected_to UBERON:0009060 ! air sac -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0002048 ! lung [Term] @@ -130007,7 +130007,7 @@ subset: organ_slim synonym: "ventrobronchi" RELATED OMO:0003004 [] is_a: UBERON:0002185 ! bronchus relationship: connected_to UBERON:0008961 ! parabronchus -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0002048 ! lung [Term] @@ -130015,7 +130015,7 @@ id: UBERON:0009073 name: dorsobronchus synonym: "dorsobronchi" RELATED OMO:0003004 [] is_a: UBERON:0002183 {notes="secondary"} ! lobar bronchus -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0002048 ! lung [Term] @@ -130029,7 +130029,7 @@ xref: NCIT:C111323 xref: Wikipedia:Syrinx_(bird_anatomy) is_a: UBERON:0000062 ! organ relationship: capable_of_part_of GO:0071625 ! vocalization behavior -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0003126 ! trachea property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/87/Syrinx.jpg" xsd:anyURI @@ -130130,7 +130130,7 @@ synonym: "pregnant stage" RELATED [BTO:0004733] xref: BTO:0004733 intersection_of: UBERON:0007023 ! adult organism intersection_of: has_part UBERON:0000922 ! embryo -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: participates_in GO:0007565 ! female pregnancy [Term] @@ -130172,7 +130172,7 @@ id: UBERON:0009101 name: ammocoete def: "Lamprey at larval stage." [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:0002548 ! larva -relationship: only_in_taxon NCBITaxon:7745 ! Petromyzontiformes +relationship: in_taxon NCBITaxon:7745 ! Petromyzontiformes [Term] id: UBERON:0009102 @@ -130182,7 +130182,7 @@ subset: organ_slim synonym: "dorsal fat body" EXACT [PMCID:PMC2093943] synonym: "pro-vertebral arch" EXACT [PMCID:PMC2093943] is_a: UBERON:0000062 ! organ -relationship: only_in_taxon NCBITaxon:7745 ! Petromyzontiformes +relationship: in_taxon NCBITaxon:7745 ! Petromyzontiformes relationship: part_of UBERON:0002390 ! hematopoietic system relationship: part_of UBERON:0002405 ! immune system property_value: taxon_notes "The supraneural body from hematopoietically stimulated lampreys appears to be histologically-similar to 'bone marrow' in higher vertebrates and contains all blood cell lineages and their precursors, including lymphocytes at all stages of maturity" xsd:string @@ -130246,7 +130246,7 @@ synonym: "marsupial pouch" EXACT [] synonym: "pouch" BROAD [] xref: Wikipedia:Pouch_(marsupial) is_a: UBERON:0034929 ! external soft tissue zone -relationship: only_in_taxon NCBITaxon:9263 ! Metatheria +relationship: in_taxon NCBITaxon:9263 ! Metatheria relationship: part_of UBERON:0003100 ! female organism relationship: site_of GO:0009790 {notes="we consider the fetus a type of or stage of the embryo"} ! embryo development @@ -130389,8 +130389,8 @@ xref: XAO:0000440 is_a: UBERON:0003067 {source="ISBN:0471888893"} ! dorsolateral placode intersection_of: UBERON:0005085 ! ectodermal placode intersection_of: has_potential_to_develop_into UBERON:0002540 ! lateral line system +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: never_in_taxon NCBITaxon:32524 {source="http://tolweb.org/Amniota"} ! Amniota -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata property_value: editor_note "TODO - compare with protoneuromast" xsd:string property_value: external_definition "Specialized series of dorsolateral ectodermal placodes.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010718", ontology="AAO", source="AAO:SIQ"} @@ -130949,7 +130949,7 @@ synonym: "paradpodia" RELATED OMO:0003004 [] synonym: "polychaete paradpodium" EXACT [] xref: Wikipedia:Parapodium is_a: UBERON:0000026 {source="cjm"} ! appendage -relationship: only_in_taxon NCBITaxon:6340 {source="Wikipedia"} ! Annelida +relationship: in_taxon NCBITaxon:6340 {source="Wikipedia"} ! Annelida relationship: part_of UBERON:0000914 ! organismal segment [Term] @@ -130958,7 +130958,7 @@ name: ascidian ampulla synonym: "ampulla" BROAD [] xref: NCIT:C93230 is_a: UBERON:0000026 ! appendage -relationship: only_in_taxon NCBITaxon:7712 ! Tunicata +relationship: in_taxon NCBITaxon:7712 ! Tunicata [Term] id: UBERON:0009475 @@ -131582,7 +131582,7 @@ id: UBERON:0009571 name: ventral midline def: "In protostomes (such as insects, snails and worms) as well as deuterostomes (vertebrates), the midline is an embryonic region that functions in patterning of the adjacent nervous tissue. The ventral midline in insects is a cell population extending along the ventral surface of the embryo and is the region from which cells detach to form the ventrally located nerve cords. In vertebrates, the midline is originally located dorsally. During development, it folds inwards and becomes the ventral part of the dorsally located neural tube and is then called the ventral midline, or floor plate." [GOC:bf, GOC:go_curators, PMID:12075342] is_a: UBERON:0002050 {source="FMA"} ! embryonic structure -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001016 ! nervous system [Term] @@ -132300,8 +132300,8 @@ xref: MA:0000400 xref: NCIT:C77955 xref: UMLS:C2698103 {source="ncithesaurus:Ampullary_Gland"} is_a: UBERON:0005399 {source="MA"} ! male reproductive gland +relationship: in_taxon NCBITaxon:9347 ! Eutheria relationship: never_in_taxon NCBITaxon:9606 {source="MP"} ! Homo sapiens -relationship: only_in_taxon NCBITaxon:9347 ! Eutheria relationship: part_of UBERON:0001000 ! vas deferens property_value: structure_notes "usually encapsulated by connective tissue and containing smooth muscle" xsd:string property_value: taxon_notes "Ampullary glands are situated in an ampulla-like enlargement of the seminal duct, or embedded in the latter; they are present, eg in the Shrew, Ruminants, and certain Carnivores and Rodents. (Wiedersheim et al., 1907)" xsd:string {source="MorphoBank"} @@ -132890,7 +132890,7 @@ id: UBERON:0009716 name: cupular organ def: "Epithelial sense organ containing the cupula housing a gelatinous material elongated from the basement of the organ toward the atrial cavity. The basement of the cupular organ consists of two cell types: sensory cells and support cell." [DOI:10.2108/zsj.27.842] is_a: UBERON:0000020 ! sense organ -relationship: only_in_taxon NCBITaxon:7712 ! Tunicata +relationship: in_taxon NCBITaxon:7712 ! Tunicata property_value: taxon_notes "possible homologues of neuromasts in the inner ear (Bone & Ryan, 1978; Wada et al 1998). In the tunicate cupular organ, the sensory cell is a primary neuron sending an axon to the CNS. The sensory cilium is within a deep indentation of the cell and is surrounded by a collar of short microvilli." xsd:string [Term] @@ -132900,7 +132900,7 @@ def: "Mechanoreceptor organ found in oral siphon of botryllid ascidians, made of subset: organ_slim xref: BSA:0000122 is_a: UBERON:0000020 ! sense organ -relationship: only_in_taxon NCBITaxon:7712 ! Tunicata +relationship: in_taxon NCBITaxon:7712 ! Tunicata relationship: part_of UBERON:0009720 ! oral siphon [Term] @@ -132909,7 +132909,7 @@ name: neurohypophyseal duct def: "Embryonic duct that is the rudiment of cerebral ganglion and and neural gland of adult in the ascidians." [DOI:10.1002/jez.b.21013] comment: Homology: candidate homolog for both neural crest and for the combined olfactory and adenohypophyseal placodes (Burighel et al., 2003; Manni et al., 2004a). Development: During formation of the adult ascidian, the ectodermal neurohypophyseal duct fuses with an evagination of the pharynx to form the neural gland rudiment is_a: UBERON:0000058 ! duct -relationship: only_in_taxon NCBITaxon:7712 ! Tunicata +relationship: in_taxon NCBITaxon:7712 ! Tunicata [Term] id: UBERON:0009719 @@ -132930,7 +132930,7 @@ synonym: "pharyngeal siphon" RELATED [] xref: BSA:0000106 is_a: UBERON:0009719 ! tunicate siphon relationship: develops_from UBERON:0009896 ! oral siphon primordia -relationship: only_in_taxon NCBITaxon:7712 ! Tunicata +relationship: in_taxon NCBITaxon:7712 ! Tunicata [Term] id: UBERON:0009721 @@ -132938,7 +132938,7 @@ name: atrial siphon xref: BSA:0000051 is_a: UBERON:0009719 ! tunicate siphon relationship: develops_from UBERON:0009895 ! atrial siphon primordia -relationship: only_in_taxon NCBITaxon:7712 ! Tunicata +relationship: in_taxon NCBITaxon:7712 ! Tunicata [Term] id: UBERON:0009722 @@ -133064,7 +133064,7 @@ def: "The cavity of the developing embryo that is formed within the epiblast tis subset: pheno_slim xref: EMAPA:36038 is_a: UBERON:0002553 ! anatomical cavity -relationship: only_in_taxon NCBITaxon:32524 ! Amniota +relationship: in_taxon NCBITaxon:32524 ! Amniota relationship: part_of UBERON:0000922 ! embryo [Term] @@ -133111,7 +133111,7 @@ synonym: "head fold" EXACT [] xref: FMA:295585 xref: SCTID:361453004 is_a: UBERON:0005291 ! embryonic tissue -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0004749 ! blastodisc [Term] @@ -133123,7 +133123,7 @@ synonym: "tail fold" EXACT [] xref: FMA:295589 xref: SCTID:361439004 is_a: UBERON:0005291 ! embryonic tissue -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0004749 ! blastodisc [Term] @@ -133187,7 +133187,7 @@ def: "A thick layer of vascularized adipose tissue found under the skin of all c xref: SCTID:83953006 xref: Wikipedia:Blubber is_a: UBERON:0002190 {source="Wikipedia"} ! subcutaneous adipose tissue -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia property_value: location_notes "Lipid-rich, collagen fiber-laced blubber comprises the hypodermis and covers the whole body, except for parts of the appendages, strongly attached to the musculature and skeleton by highly organized, fan-shaped networks of tendons and ligaments. It can comprise up to 50% of the body mass of some marine mammals during some points in their lives, and can range from two inches (5 cm) thick in dolphins and smaller whales, to more than 12 inches (30 cm)thick in some bigger whales, such as right and bowhead whales" xsd:string [Term] @@ -133197,7 +133197,7 @@ def: "Wax present in the head cavities of the sperm whale." [Wikipedia:Spermacet xref: MESH:C009301 xref: Wikipedia:Spermaceti is_a: UBERON:0000463 ! organism substance -relationship: only_in_taxon NCBITaxon:9753 ! Physeter +relationship: in_taxon NCBITaxon:9753 ! Physeter relationship: part_of UBERON:0000033 ! head [Term] @@ -133218,7 +133218,7 @@ def: "A biliary secretion of the intestines of the sperm whale." [Wikipedia:Ambe xref: MESH:D018648 xref: Wikipedia:Ambergris is_a: UBERON:0000463 ! organism substance -relationship: only_in_taxon NCBITaxon:9753 ! Physeter +relationship: in_taxon NCBITaxon:9753 ! Physeter [Term] id: UBERON:0009758 @@ -133299,7 +133299,7 @@ subset: pheno_slim synonym: "renal tubule (generic)" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "tubule of excretory system" EXACT [https://orcid.org/0000-0002-6601-2165, OBOL:automatic] is_a: UBERON:0003914 ! epithelial tube -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001008 ! renal system property_value: curator_notes "this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules" xsd:string @@ -133634,7 +133634,7 @@ name: echinoderm gastric caecum def: "Non-contractile pouch that is connected to the anterior stomach through a slit-like opening. This pouch is also well-connected to the haemal system through numerous haemal ducts within its connective tissue layer." [PMID:20955602] comment: The digestive tract of many metazoan invertebrates is characterized by the presence of caeca or diverticula that serve secretory and/or absorptive functions. With the development of various feeding habits, distinctive digestive organs may be present in certain taxa. This also holds true for sea urchins (Echinodermata: Echinoidea), in which a highly specialized gastric caecum can be found in members of a derived subgroup, the Irregularia (cake urchins, sea biscuits, sand dollars, heart urchins, and related forms)... Homologous with the more or less pronounced dilation of the anterior stomach that is observed in most "regular" sea urchin taxa[PMID:20955602] is_a: UBERON:0009854 ! digestive tract diverticulum -relationship: only_in_taxon NCBITaxon:7586 ! Echinodermata +relationship: in_taxon NCBITaxon:7586 ! Echinodermata [Term] id: UBERON:0009856 @@ -133707,14 +133707,14 @@ id: UBERON:0009860 name: ascidian digestive gland xref: ANISEED:1239655 is_a: UBERON:0006925 ! digestive system gland -relationship: only_in_taxon NCBITaxon:7712 ! Tunicata +relationship: in_taxon NCBITaxon:7712 ! Tunicata [Term] id: UBERON:0009861 name: ascidian neural complex def: "Missing definition for term UBERON:0009861. Please replace it using linked reference." [PMID:21558186] is_a: UBERON:0002530 ! gland -relationship: only_in_taxon NCBITaxon:7712 ! Tunicata +relationship: in_taxon NCBITaxon:7712 ! Tunicata [Term] id: UBERON:0009862 @@ -133738,7 +133738,7 @@ def: "Missing definition for term UBERON:0009864. Please replace it using linked comment: assumed to be a pituitary homolog. Current data from the Ciona genome suggests that the ascidian NC, including the CF, is unlikely to be a pituitary-like endocrine gland, while it is necessary to examine other ascidians before drawing a final conclusion [PMID:21558186] is_a: UBERON:0000064 ! organ part relationship: develops_from UBERON:0009718 ! neurohypophyseal duct -relationship: only_in_taxon NCBITaxon:7713 ! Ascidiacea +relationship: in_taxon NCBITaxon:7713 ! Ascidiacea relationship: part_of UBERON:0009861 ! ascidian neural complex [Term] @@ -133751,7 +133751,7 @@ relationship: capable_of GO:0070254 ! mucus secretion relationship: develops_from UBERON:0009868 ! Hatschek's left diverticulum relationship: develops_from UBERON:0009957 ! ciliated pit relationship: has_quality PATO:0002255 ! grooved -relationship: only_in_taxon NCBITaxon:7737 {source="Wikipedia"} ! Branchiostoma +relationship: in_taxon NCBITaxon:7737 {source="Wikipedia"} ! Branchiostoma [Term] id: UBERON:0009866 @@ -133759,14 +133759,14 @@ name: Hatschek's nephridium def: "An unpaired kidney whose duct opens into the anterior pharynx. It can be seen as a deep ciliated fossa on the dorsal midline of the buccal cavity (mouth). Among other things, it secrets mucus which entraps food particles from the water[WP]." [http://orcid.org/0000-0002-6601-2165] subset: organ_slim is_a: UBERON:0000062 ! organ -relationship: only_in_taxon NCBITaxon:7737 {source="Wikipedia"} ! Branchiostoma +relationship: in_taxon NCBITaxon:7737 {source="Wikipedia"} ! Branchiostoma relationship: part_of UBERON:0001008 ! renal system [Term] id: UBERON:0009867 name: Hatschek's diverticulum is_a: UBERON:0001048 ! primordium -relationship: only_in_taxon NCBITaxon:7737 {source="Wikipedia"} ! Branchiostoma +relationship: in_taxon NCBITaxon:7737 {source="Wikipedia"} ! Branchiostoma relationship: part_of UBERON:0001042 ! chordate pharynx [Term] @@ -134027,7 +134027,7 @@ subset: early_development synonym: "Kohler's sickle" EXACT [] xref: Wikipedia:Koller's_sickle is_a: UBERON:0002050 ! embryonic structure -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata [Term] id: UBERON:0009889 @@ -134041,7 +134041,7 @@ xref: XAO:0004186 is_a: UBERON:0007688 ! anlage relationship: anterior_to UBERON:0004140 {source="PMID:17276708"} ! primary heart field relationship: dorsal_to UBERON:0004140 {source="PMID:17276708"} ! primary heart field -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0003081 {source="GO:0003129"} ! lateral plate mesoderm property_value: development_notes "in mouse has left ventricular identity[PMID:22855565]" xsd:string property_value: external_definition "extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708]." xsd:string {source="PMID:17276708"} @@ -134055,7 +134055,7 @@ synonym: "fovea cardiaca" EXACT [http://www.drugs.com/dict/fovea-cardiaca.html] is_a: UBERON:0004111 ! anatomical conduit relationship: adjacent_to UBERON:0001041 ! foregut relationship: adjacent_to UBERON:0001046 ! hindgut -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0006235 ! foregut-midgut junction [Term] @@ -134074,7 +134074,7 @@ id: UBERON:0009892 name: ascidian anterior sensory vesicle xref: ANISEED:777309 is_a: UBERON:0000020 ! sense organ -relationship: only_in_taxon NCBITaxon:7712 ! Tunicata +relationship: in_taxon NCBITaxon:7712 ! Tunicata [Term] id: UBERON:0009893 @@ -134088,21 +134088,21 @@ id: UBERON:0009894 name: siphon primordium xref: ANISEED:1210451 is_a: UBERON:0005423 ! developing anatomical structure -relationship: only_in_taxon NCBITaxon:7712 ! Tunicata +relationship: in_taxon NCBITaxon:7712 ! Tunicata [Term] id: UBERON:0009895 name: atrial siphon primordia xref: ANISEED:1210456 is_a: UBERON:0009894 ! siphon primordium -relationship: only_in_taxon NCBITaxon:7712 ! Tunicata +relationship: in_taxon NCBITaxon:7712 ! Tunicata [Term] id: UBERON:0009896 name: oral siphon primordia xref: ANISEED:1225922 is_a: UBERON:0009894 ! siphon primordium -relationship: only_in_taxon NCBITaxon:7712 ! Tunicata +relationship: in_taxon NCBITaxon:7712 ! Tunicata [Term] id: UBERON:0009897 @@ -134315,7 +134315,7 @@ relationship: part_of UBERON:0007213 {source="EHDAA2"} ! mesenchyme derived from id: UBERON:0009921 name: hypophyseal tube is_a: UBERON:0000025 ! tube -relationship: only_in_taxon NCBITaxon:7745 ! Petromyzontiformes +relationship: in_taxon NCBITaxon:7745 ! Petromyzontiformes [Term] id: UBERON:0009948 @@ -134389,7 +134389,7 @@ name: vomeronasal system def: "A vertebrate nasal chemosensory system that is responsible for detecting intraspecific pheromonal cues as well as environmental odorants." [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:0001032 ! sensory system relationship: capable_of GO:0043695 {source="Wikipedia"} ! detection of pheromone -relationship: only_in_taxon NCBITaxon:8287 ! Sarcopterygii +relationship: in_taxon NCBITaxon:8287 ! Sarcopterygii relationship: part_of UBERON:0005725 ! olfactory system property_value: editor_note "check relationship to olfactory system. Evolution: The morphological components of the VNS are found only in tetrapods, but the genetic components of the system have been found in teleost fish, in addition to tetrapods. In tetrapods, the VNS was thought to be the olfactory system for detecting pheromones, while the main olfactory system detected general odorants (Scalia and Winans 1975). However, experimental evidence suggests that there is not such a clear functional distinction (Restrepo et al. 2004; Baxi, Dorries, and Eisthen 2006; Spehr et al. 2006; Kelliher 2007). Sea lampreys produce unique bile acids which act as pheromones both in migration and mate finding (Li, Sorensen, and Gallaher 1995; Li et al. 2002; Siefkes and Li 2004). However, bile acids in teleost fish are known to require components of the main olfactory signal transduction pathway (Hansen et al. 2003), and interruption of the VNS signal transduction pathway had no effect on bile acid olfactory response (Hansen et al. 2003)[Grus - EVOLUTION OF THE VOMERONASAL SYSTEM VIEWED THROUGH SYSTEM-SPECIFIC GENES]" xsd:string @@ -134421,7 +134421,7 @@ name: corpuscle of de Quatrefage def: "A specialised sensory organ located in the subepidermal connective tissue at the rostral end of late larval and adult amphioxus. They consist of between 1 and 4 nerve cells with axons, each with 2 cilia, surrounded by up to 7 sheath cells. The cilia extend into a protrusion of the basal lamina which surrounds each corpuscle. The axonal process contributes to the rostral nerve." [PMID:11523831] synonym: "organ of de Quatrefage" EXACT [] is_a: UBERON:0000020 ! sense organ -relationship: only_in_taxon NCBITaxon:7737 {source="PMID:11523831"} ! Branchiostoma +relationship: in_taxon NCBITaxon:7737 {source="PMID:11523831"} ! Branchiostoma [Term] id: UBERON:0009957 @@ -134429,7 +134429,7 @@ name: ciliated pit comment: Development: joins with Hatschek's diverticulum to form Hatschek's pit in the adult. Location: anterior to the mouth. synonym: "pre-oral pit" RELATED [] is_a: UBERON:0006846 ! surface groove -relationship: only_in_taxon NCBITaxon:7737 {source="Wikipedia"} ! Branchiostoma +relationship: in_taxon NCBITaxon:7737 {source="Wikipedia"} ! Branchiostoma [Term] id: UBERON:0009958 @@ -134506,7 +134506,7 @@ def: "Excretory gland situated in the basal article of the antennal peduncle. It synonym: "green gland" EXACT [] xref: BTO:0000075 is_a: UBERON:0009962 {source="BTO"} ! excretory gland -relationship: only_in_taxon NCBITaxon:6657 ! Crustacea +relationship: in_taxon NCBITaxon:6657 ! Crustacea property_value: editor_note "cede this term to Arthropod AO" xsd:string property_value: editor_note "consider also classifying this as a renal tubule - or separate terms for coiled/nephridial canal" xsd:string @@ -134515,7 +134515,7 @@ id: UBERON:0009964 name: crustacean maxillary gland def: "Excretory organ in maxillary segment with duct opening on maxilla." [http://crustacea.nhm.org/glossary/define.html] is_a: UBERON:0009962 {source="BTO"} ! excretory gland -relationship: only_in_taxon NCBITaxon:6657 ! Crustacea +relationship: in_taxon NCBITaxon:6657 ! Crustacea property_value: editor_note "cede this term to Arthropod AO" xsd:string property_value: taxon_notes "consider generalizing to include millipedes, centipedes. Function: Two different excretory organs are found among crustaceans: the antennal gland and the maxillary gland. Both have the same basic structure: an end sac and a convoluted duct that may expand into a bladder before opening to the outside. In most adult crustaceans only one or the other gland functions. The functional gland may change during the life cycle. Terminology note: http://crustacea.nhm.org/glossary/define.html?termID=327 suggests green gland as the generic term and antennal as the decapoda term" xsd:string @@ -134527,7 +134527,7 @@ xref: SPD:0000116 xref: TADS:0000080 xref: Wikipedia:Coxal_gland is_a: UBERON:0009962 {source="BTO"} ! excretory gland -relationship: only_in_taxon NCBITaxon:6843 ! Chelicerata +relationship: in_taxon NCBITaxon:6843 ! Chelicerata property_value: editor_note "cede this term to Arthropod AO" xsd:string property_value: taxon_notes "They are found in all arachnids (with the exception of some Acari), and in other chelicerates, such as horseshoe crabs. Homology: The coxal gland is thought to be homologous with the antennal gland of crustaceans" xsd:string @@ -135125,8 +135125,8 @@ is_a: UBERON:0004177 ! hemopoietic organ relationship: composed_primarily_of CL:0000738 {source="Honma1983"} ! leukocyte relationship: contains_process GO:0030097 ! hemopoiesis relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism +relationship: in_taxon NCBITaxon:7778 {source="Wikipedia"} ! Elasmobranchii relationship: never_in_taxon NCBITaxon:7863 {source="Wikipedia"} ! Holocephali -relationship: only_in_taxon NCBITaxon:7778 {source="Wikipedia"} ! Elasmobranchii relationship: part_of UBERON:0002390 ! hematopoietic system relationship: part_of UBERON:0002405 ! immune system relationship: surrounds UBERON:0000991 ! gonad @@ -135149,9 +135149,9 @@ xref: Wikipedia:Spiral_valve is_a: UBERON:0003978 {source="cjm"} ! valve disjoint_from: UBERON:0010017 ! spiral valve of cystic duct disjoint_from: UBERON:0010018 ! spiral valve of conus arteriosus +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: located_in UBERON:0006909 ! lumen of digestive tract relationship: never_in_taxon NCBITaxon:32523 {source="Wikipedia"} ! Tetrapoda -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002108 ! small intestine [Term] @@ -135177,8 +135177,8 @@ def: "The spiral valve alternately blocks & unblocks the entrances to the left a xref: AAO:0010251 xref: http://cwx.prenhall.com/bookbind/pubbooks/martini10/chapter21/medialib/Kardong_fig_12_29.html is_a: UBERON:0003978 {source="cjm"} ! valve +relationship: in_taxon NCBITaxon:8287 {evidence="NAS"} ! Sarcopterygii relationship: never_in_taxon NCBITaxon:32524 ! Amniota -relationship: only_in_taxon NCBITaxon:8287 {evidence="NAS"} ! Sarcopterygii relationship: part_of UBERON:0003983 {source="AAO"} ! conus arteriosus property_value: taxon_notes "found in dipnoans and amphibians" xsd:string property_value: taxon_notes "The spiral valve is considered to have evolved from the right member of the four embryonic endocardial ridges (Goodrich, 1930 - via Morris 1974)" xsd:string @@ -135192,8 +135192,8 @@ synonym: "vertebrate spiracle" EXACT [] xref: Wikipedia:Spiracle#Vertebrates is_a: UBERON:0003102 {source="cjm"} ! surface structure relationship: develops_from UBERON:0004362 ! pharyngeal arch 1 +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: never_in_taxon NCBITaxon:32523 ! Tetrapoda -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001004 ! respiratory system relationship: present_in_taxon NCBITaxon:119203 ! Selachii property_value: external_ontology_notes "GO term spiracle morphogenesis, open tracheal system - does not refer to this structure" xsd:string {isAbout="GO:0035277"} @@ -135436,7 +135436,7 @@ xref: MA:0001055 xref: MBA:231 xref: neuronames:1115 is_a: UBERON:0006331 {source="MA"} ! brainstem nucleus -relationship: only_in_taxon NCBITaxon:9989 {source="NN"} ! Rodentia +relationship: in_taxon NCBITaxon:9989 {source="NN"} ! Rodentia relationship: part_of UBERON:0001891 {source="ABA", source="MA"} ! midbrain [Term] @@ -135559,7 +135559,7 @@ def: "A gland situated on the upper lip posterior to the eye, found in non-venom comment: positioned posterior to the eye, encased in a thin cover of connective tissue, and consists mostly of serous cells. A single, short duct extends anteromedially from the lumen of the gland to the base of the posterior fangs.[WP] xref: Wikipedia:Duvernoy's_gland is_a: UBERON:0010047 ! oral gland -relationship: only_in_taxon NCBITaxon:8578 {source="Wikipedia"} ! Colubridae +relationship: in_taxon NCBITaxon:8578 {source="Wikipedia"} ! Colubridae [Term] id: UBERON:0010049 @@ -135567,8 +135567,8 @@ name: supralabial gland def: "Oral gland in reptiles situated immediately above the lip." [ISBN:0073040584] xref: Wikipedia:Duvernoy's_gland is_a: UBERON:0010047 ! oral gland +relationship: in_taxon NCBITaxon:32524 ! Amniota relationship: never_in_taxon NCBITaxon:40674 ! Mammalia -relationship: only_in_taxon NCBITaxon:32524 ! Amniota [Term] id: UBERON:0010050 @@ -135576,8 +135576,8 @@ name: infralabial gland def: "Oral gland in reptiles situated immediately below the lip." [ISBN:0073040584] xref: Wikipedia:Duvernoy's_gland is_a: UBERON:0010047 ! oral gland +relationship: in_taxon NCBITaxon:32524 ! Amniota relationship: never_in_taxon NCBITaxon:40674 ! Mammalia -relationship: only_in_taxon NCBITaxon:32524 ! Amniota [Term] id: UBERON:0010051 @@ -136210,7 +136210,7 @@ xref: SPD:0000547 xref: Wikipedia:Mating_plug is_a: UBERON:0035784 ! seminal clot relationship: capable_of_part_of GO:0046692 ! sperm competition -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: present_in_taxon NCBITaxon:10088 ! Mus relationship: present_in_taxon NCBITaxon:6656 ! Arthropoda relationship: present_in_taxon NCBITaxon:9397 ! Chiroptera @@ -136687,7 +136687,7 @@ id: UBERON:0010191 name: aortic system xref: EHDAA2:0004512 is_a: UBERON:0011216 ! organ system subdivision -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0004571 {source="Wikipedia"} ! systemic arterial system [Term] @@ -136856,7 +136856,7 @@ xref: FMA:59045 xref: SCTID:280686009 xref: Wikipedia:Plica_semilunaris_of_conjunctiva is_a: UBERON:0005160 {source="Wikipedia"} ! vestigial structure -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia +relationship: in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: part_of UBERON:0001811 {source="FMA"} ! conjunctiva property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Gray1205.png" xsd:anyURI property_value: taxon_notes "It is the vestigial remnant of the nictitating membrane" xsd:string @@ -136891,7 +136891,7 @@ is_a: UBERON:0002384 {source="BTO"} ! connective tissue relationship: has_developmental_contribution_from UBERON:0010210 ! blood clot relationship: has_part CL:0000057 ! fibroblast relationship: has_part CL:0000738 ! leukocyte -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: participates_in GO:0042060 ! wound healing [Term] @@ -137142,8 +137142,8 @@ def: "A fleshy protuberance at the pylorus of some species such as ruminants and synonym: "torus pyloricus" EXACT [] xref: SCTID:14214007 is_a: UBERON:0000064 ! organ part +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: never_in_taxon NCBITaxon:314146 ! Euarchontoglires -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0001166 ! pylorus [Term] @@ -137157,7 +137157,7 @@ xref: Wikipedia:Spiral_colon is_a: UBERON:0000168 ! proximal-distal subdivision of colon relationship: continuous_with UBERON:0001157 ! transverse colon relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut -relationship: only_in_taxon NCBITaxon:91561 ! Artiodactyla +relationship: in_taxon NCBITaxon:91561 ! Artiodactyla relationship: present_in_taxon NCBITaxon:35497 ! Suina relationship: present_in_taxon NCBITaxon:9845 ! Ruminantia property_value: editor_note "Consider merging with ascending colon" xsd:string @@ -137173,7 +137173,7 @@ synonym: "upper molar gland" RELATED [] xref: NCIT:C77624 xref: UMLS:C2700338 {source="ncithesaurus:Zygomatic_Gland"} is_a: UBERON:0012102 ! buccal salivary gland -relationship: only_in_taxon NCBITaxon:33554 ! Carnivora +relationship: in_taxon NCBITaxon:33554 ! Carnivora relationship: part_of UBERON:0001567 ! cheek [Term] @@ -137245,7 +137245,7 @@ name: choroidal guanine tapetum def: "A choroid tapetum lucidum that is made of a palisade of cells containing stacks of flat hexagonal crystals of guanine." [https://orcid.org/0000-0002-6601-2165, PMID:14738502, Wikipedia:Tapetum_lucidum#Classification] xref: Wikipedia:Tapetum_lucidum#Classification is_a: UBERON:0010244 ! choroid tapetum lucidum -relationship: only_in_taxon NCBITaxon:7777 {source="doi:10.1017/S0025315400024760"} ! Chondrichthyes +relationship: in_taxon NCBITaxon:7777 {source="doi:10.1017/S0025315400024760"} ! Chondrichthyes relationship: present_in_taxon NCBITaxon:7778 ! Elasmobranchii relationship: present_in_taxon NCBITaxon:7864 ! Chimaeriformes property_value: taxon_notes "A choroidal tapetum of reflecting cells lying immediately outside the choriocapillaris is formed in a few primitive teleosts." xsd:string {source="PMID:14738502", taxon="NCBITaxon:32443"} @@ -137260,7 +137260,7 @@ comment: The choroidal stroma adjacent to the tapetum lucidum contains numerous synonym: "choroid tapetum cellulosum" EXACT [] xref: Wikipedia:Tapetum_lucidum#Classification is_a: UBERON:0010244 ! choroid tapetum lucidum -relationship: only_in_taxon NCBITaxon:9347 ! Eutheria +relationship: in_taxon NCBITaxon:9347 ! Eutheria relationship: present_in_taxon NCBITaxon:33554 {editor="cjm", notes="most carnivores", source="PMID:14738502"} ! Carnivora relationship: present_in_taxon NCBITaxon:9721 {editor="cjm", source="PMID:14738502"} ! Cetacea relationship: present_in_taxon NCBITaxon:9989 {editor="cjm", source="PMID:14738502", taxon="spotted cavy"} ! Rodentia @@ -137272,7 +137272,7 @@ def: "A choroid tapetum lucidum that is an array of extracellular fibers." [http synonym: "fibrous tapetum" RELATED [NCBITaxon:9845, PMID:14738502] xref: Wikipedia:Tapetum_lucidum#Classification is_a: UBERON:0010244 ! choroid tapetum lucidum -relationship: only_in_taxon NCBITaxon:9347 ! Eutheria +relationship: in_taxon NCBITaxon:9347 ! Eutheria relationship: present_in_taxon NCBITaxon:9788 {editor="cjm", source="PMID:14738502"} ! Equidae relationship: present_in_taxon NCBITaxon:9845 {editor="cjm", source="PMID:14738502"} ! Ruminantia property_value: taxon_notes "cows, sheep, goats and horses" xsd:string {source="WP"} @@ -137495,7 +137495,7 @@ xref: BTO:0000597 xref: MESH:D043143 xref: Wikipedia:Hepatopancreas is_a: UBERON:0006925 {source="BTO"} ! digestive system gland -relationship: only_in_taxon NCBITaxon:33317 ! Protostomia +relationship: in_taxon NCBITaxon:33317 ! Protostomia relationship: part_of UBERON:0001045 {source="BTO"} ! midgut relationship: present_in_taxon NCBITaxon:6447 ! Mollusca relationship: present_in_taxon NCBITaxon:6657 ! Crustacea @@ -137505,7 +137505,7 @@ id: UBERON:0010265 name: mollusc hepatopancreas xref: Wikipedia:Digestive_system_of_gastropods#Hepatopancreas is_a: UBERON:0010264 ! hepatopancreas -relationship: only_in_taxon NCBITaxon:6447 ! Mollusca +relationship: in_taxon NCBITaxon:6447 ! Mollusca [Term] id: UBERON:0010266 @@ -137515,7 +137515,7 @@ synonym: "crustacean digestive gland" RELATED [] synonym: "midgut gland" RELATED [BTO:0000597] is_a: UBERON:0010264 ! hepatopancreas relationship: has_part CL:0000387 {source="PMID:18025161"} ! hemocyte (sensu Arthropoda) -relationship: only_in_taxon NCBITaxon:6657 ! Crustacea +relationship: in_taxon NCBITaxon:6657 ! Crustacea relationship: part_of UBERON:0002405 {source="PMID:18025161"} ! immune system property_value: editor_note "this term should be ceded to the arthropod anatomy ontology" xsd:string @@ -137813,8 +137813,8 @@ intersection_of: part_of UBERON:0001773 ! sclera id: UBERON:0010296 name: scleral skeletal element is_a: UBERON:0004765 ! skeletal element +relationship: in_taxon NCBITaxon:7776 {source="PMID:17051547"} ! Gnathostomata relationship: never_in_taxon NCBITaxon:40674 {source="PMID:17051547"} ! Mammalia -relationship: only_in_taxon NCBITaxon:7776 {source="PMID:17051547"} ! Gnathostomata relationship: part_of UBERON:0000019 ! camera-type eye property_value: curator_notes "An eye adnexal structure, but not necessarily part of the eyeball" xsd:string @@ -137870,7 +137870,7 @@ synonym: "amnion-serosa" RELATED [BTO:0004800] xref: BTO:0004800 xref: EFO:0000250 is_a: UBERON:0010303 {source="DOI:10.1073/pnas.0709145105"} ! extraembryonic epithelium -relationship: only_in_taxon NCBITaxon:6656 {notes="Cyclorrhapha", source="DOI:10.1073/pnas.0709145105"} ! Arthropoda +relationship: in_taxon NCBITaxon:6656 {notes="Cyclorrhapha", source="DOI:10.1073/pnas.0709145105"} ! Arthropoda property_value: editor_note "May be obsoleted once added to insect ontology. Coordinate with cell type in CL" xsd:string [Term] @@ -137955,7 +137955,7 @@ synonym: "palpebral" BROAD [] xref: Wikipedia:Palpebral_(bone) intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0001712 ! upper eyelid -relationship: only_in_taxon NCBITaxon:8457 ! Sauropsida +relationship: in_taxon NCBITaxon:8457 ! Sauropsida property_value: editor_note "PMID:16496288 says 'invests' the eyelid, is this consistent across taxa?" xsd:string property_value: taxon_notes "The most extreme development of the palpebral is found in the armored dino- saur Euoplocephalus tutus, where the bone forms a quarter-sphere and adducts to completely occlude the or- bit (Coombs, 1972; Vickaryous and Russell, 2003). Notwithstanding the superficially similar position, palpe- brals and tarsal plates differ both anatomically and developmentally and are not considered homologous (Gauthier et al., 1988)" xsd:string @@ -137980,7 +137980,7 @@ synonym: "scleral sesamoid element" EXACT [] synonym: "sesamoideum esclerae" EXACT [PMID:16496288] is_a: UBERON:0001479 ! sesamoid bone is_a: UBERON:0010290 ! scleral ossicle -relationship: only_in_taxon NCBITaxon:30458 ! Strigiformes +relationship: in_taxon NCBITaxon:30458 ! Strigiformes property_value: structure_notes "During contraction, the scleral sesamoid bone acts to anchor the pyramidal nictitating muscle to the sclera and divert the tendon from pro- jecting over the cornea. It remains to be determined whether this is indeed a true sesamoid (sensu; Vickaryous and Olson, 2006), as the scleral sesa- moid is actually invested within the synovial tendon sheath and not the tendon per se" xsd:string [Term] @@ -138055,7 +138055,7 @@ xref: VSAO:0000049 xref: XAO:0003075 xref: ZFA:0000737 is_a: UBERON:0000075 ! subdivision of skeletal system -relationship: only_in_taxon NCBITaxon:89593 ! Craniata +relationship: in_taxon NCBITaxon:89593 ! Craniata relationship: part_of UBERON:0011137 ! axial skeletal system property_value: curator_notes "that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium" xsd:string property_value: editor_note "we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints)" xsd:string @@ -138084,7 +138084,7 @@ name: optic pedicel def: "Permanent cartilage structure projecting from the site of origin of the recti muscles. Supports eyeball and aids rotation." [ISBN:071676959X, PMID:16496288] synonym: "eye stalk" RELATED [] is_a: UBERON:0003932 ! cartilage element of chondrocranium -relationship: only_in_taxon NCBITaxon:7777 {source="PMID:16496288"} ! Chondrichthyes +relationship: in_taxon NCBITaxon:7777 {source="PMID:16496288"} ! Chondrichthyes relationship: part_of UBERON:0004088 ! orbital region [Term] @@ -138412,7 +138412,7 @@ xref: Wikipedia:Endoskeleton xref: XAO:0004026 is_a: UBERON:0010912 {source="VSAO"} ! subdivision of skeleton relationship: composed_primarily_of UBERON:0010522 ! replacement element -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata property_value: external_definition "An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t" xsd:string {source="Wikipedia:Endoskeleton"} [Term] @@ -138438,7 +138438,7 @@ synonym: "exoskeleton" BROAD INCONSISTENT [VSAO:curator] xref: VSAO:0000035 xref: XAO:0004025 is_a: UBERON:0010912 {source="VSAO"} ! subdivision of skeleton -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata [Term] id: UBERON:0010365 @@ -138770,7 +138770,7 @@ id: UBERON:0010394 name: lymphocyte domain intersection_of: UBERON:0010001 ! cell cluster organ intersection_of: composed_primarily_of CL:0000542 ! lymphocyte -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0002465 ! lymphoid system property_value: editor_note "TODO - check" xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/issues/513" xsd:anyURI @@ -139040,7 +139040,7 @@ xref: NLX:81 is_a: UBERON:0035014 {source="cjm"} ! functional part of brain relationship: capable_of_part_of GO:0050975 ! sensory perception of touch relationship: contributes_to_morphology_of UBERON:0008933 ! primary somatosensory cortex -relationship: only_in_taxon NCBITaxon:9989 ! Rodentia +relationship: in_taxon NCBITaxon:9989 ! Rodentia relationship: part_of UBERON:0008933 {source="MBA"} ! primary somatosensory cortex property_value: external_definition "The term primary somatosensory area, barrel field refers to one of 6 subdivisions of the primary somesthetic area of the cerebral cortex in the mouse (Dong-2004) and the rat (Swanson-2004). It is defined as dark-staining regions in Nissl and other types of stains of layer four of the somatosensory cortex of rodents where somatosensory inputs from the contralateral side of the body come in from the thalamus, in particular input from the whiskers. Each barrel ranges in size from 100-400 um in diameter. (modified from BrainInfo and Wikipedia)" xsd:string {source="NLX:81"} @@ -139196,7 +139196,7 @@ intersection_of: UBERON:0000003 ! naris intersection_of: connects UBERON:0001707 ! nasal cavity intersection_of: connects UBERON:0006562 ! pharynx relationship: fma_set_term FMA:76585 -relationship: only_in_taxon NCBITaxon:8287 ! Sarcopterygii +relationship: in_taxon NCBITaxon:8287 ! Sarcopterygii property_value: has_relational_adjective "choanal" xsd:string property_value: taxon_notes "In humans the only internal naris is the posterior nasal aperture, which connects to the nasopharynx" xsd:string @@ -139465,7 +139465,7 @@ xref: Wikipedia:Brille is_a: UBERON:0000014 ! zone of skin relationship: has_fused_element UBERON:0001712 ! upper eyelid relationship: has_fused_element UBERON:0001713 ! lower eyelid -relationship: only_in_taxon NCBITaxon:32561 ! Sauria +relationship: in_taxon NCBITaxon:32561 ! Sauria relationship: part_of UBERON:0000019 ! camera-type eye property_value: taxon_notes "In snakes, there is no eyelid and the brille is clear and cannot be distinguished except when the animal is becoming ready for ecdysis. At that time, it becomes cloudy and is visible as a cover over the eye. When the snake moults, the brille is also shed as part of its skin. The Brilles protect their eyes from dust and dirt and gives them a 'glassy-eyed' blank appearance Snakes, flap-footed lizards, night lizards, and some skinks have brilles. All geckos except those in the subfamily Eublepharinae (eyelid geckos) possess brilles. Fish also have transparent eyelids called adipose eyelids." xsd:string @@ -139475,7 +139475,7 @@ name: clasper def: "A male anatomical structure found some groups of animals, used in mating. Male cartilaginous fish have claspers formed from the posterior portion of their pelvic fin which serve as intromittent organs used to channel semen into the female's cloaca during mating. The act of mating in some fish including sharks usually includes one of the claspers raised to allow water into the siphon through a specific orifice. The clasper is then inserted into the vagina, where it opens like an umbrella to anchor its position. The siphon then begins to contract expelling water and sperm. Male chimaeras have cephalic claspers on their heads, which are thought to aid in holding the female during mating." [Wikipedia:clasper] xref: Wikipedia:clasper is_a: UBERON:0008811 {source="Wikipedia"} ! intromittent organ -relationship: only_in_taxon NCBITaxon:7777 ! Chondrichthyes +relationship: in_taxon NCBITaxon:7777 ! Chondrichthyes property_value: taxon_notes "the term is also used for insect claspers, but we reserve it for the elasmobranchii structure" xsd:string [Term] @@ -139488,8 +139488,8 @@ synonym: "tenaculum" RELATED [] xref: Wikipedia:Chimaera#Description_and_tastes intersection_of: UBERON:0010516 ! clasper intersection_of: part_of UBERON:0000033 ! head +relationship: in_taxon NCBITaxon:7864 ! Chimaeriformes relationship: intersects_midsagittal_plane_of UBERON:0000033 ! head -relationship: only_in_taxon NCBITaxon:7864 ! Chimaeriformes [Term] id: UBERON:0010518 @@ -139700,7 +139700,7 @@ synonym: "limb/fin segment" EXACT [] intersection_of: UBERON:0010758 ! subdivision of organism along appendicular axis intersection_of: part_of UBERON:0004708 ! paired limb/fin disjoint_from: UBERON:0010912 ! subdivision of skeleton -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata [Term] id: UBERON:0010540 @@ -140656,7 +140656,7 @@ is_a: UBERON:0000475 ! organism subdivision relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 ! Melissa Haendel relationship: functionally_related_to GO:0040011 ! locomotion relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata property_value: editor_note "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string property_value: external_comment "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string {date_retrieved="2012-09-06", external_class="VSAO:0000214", ontology="VSAO", source="Curator"} property_value: external_definition "Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000214", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} @@ -141173,9 +141173,9 @@ xref: Wikipedia:Prefrontal_bone is_a: UBERON:0008907 {source="ISBN:0073040584"} ! dermal bone relationship: adjacent_to UBERON:0000209 ! tetrapod frontal bone relationship: adjacent_to UBERON:0001680 ! lacrimal bone +relationship: in_taxon NCBITaxon:8287 {source="Wikipedia"} ! Sarcopterygii relationship: never_in_taxon NCBITaxon:40674 ! Mammalia relationship: never_in_taxon NCBITaxon:8782 ! Aves -relationship: only_in_taxon NCBITaxon:8287 {source="Wikipedia"} ! Sarcopterygii relationship: overlaps UBERON:0001697 {source="ISBN:0073040584"} ! orbit of skull relationship: part_of UBERON:0003113 {notes="orbital series", source="ISBN:0073040584"} ! dermatocranium relationship: part_of UBERON:0011156 ! facial skeleton @@ -141309,7 +141309,7 @@ synonym: "navicular bone" RELATED INCONSISTENT [Wikipedia:Equine_forelimb_anatom xref: SCTID:370654009 xref: Wikipedia:Navicular_bone#Horse_anatomy is_a: UBERON:0001479 ! sesamoid bone -relationship: only_in_taxon NCBITaxon:9788 ! Equidae +relationship: in_taxon NCBITaxon:9788 ! Equidae relationship: part_of UBERON:0002470 ! autopod region [Term] @@ -141502,7 +141502,7 @@ synonym: "flight membrane" RELATED [] synonym: "patagia" RELATED OMO:0003004 [] xref: Wikipedia:Patagium is_a: UBERON:0000094 ! membrane organ -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000023 ! wing [Term] @@ -141804,7 +141804,7 @@ subset: cyclostome_subset synonym: "horny denticle" EXACT [http://tolweb.org/Hyperoartia] intersection_of: UBERON:0003913 ! tooth-like structure intersection_of: composed_primarily_of GO:0045095 ! keratin filament -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: present_in_taxon NCBITaxon:117569 ! Hyperoartia relationship: present_in_taxon NCBITaxon:7762 ! Myxinidae @@ -141830,7 +141830,7 @@ synonym: "lingual cartilage" EXACT [] synonym: "piston" RELATED [] is_a: UBERON:0007844 ! cartilage element relationship: develops_from UBERON:0034939 ! future piston -relationship: only_in_taxon NCBITaxon:117569 ! Hyperoartia +relationship: in_taxon NCBITaxon:117569 ! Hyperoartia relationship: part_of UBERON:0000033 ! head property_value: structure_notes "composed of lamprin, an elastin-like protein, unique to lampreys" xsd:string @@ -141844,9 +141844,9 @@ synonym: "gastralia" EXACT OMO:0003004 [VSAO:0000127] xref: VSAO:0000127 xref: Wikipedia:Gastralium is_a: UBERON:0008907 {source="VSAO"} ! dermal bone +relationship: in_taxon NCBITaxon:32524 {source="Wikipedia"} ! Amniota relationship: never_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: never_in_taxon NCBITaxon:8782 ! Aves -relationship: only_in_taxon NCBITaxon:32524 {source="Wikipedia"} ! Amniota relationship: part_of UBERON:0006635 {source="ISBN:0073040584"} ! anterior abdominal wall relationship: part_of UBERON:0014478 ! rib skeletal system relationship: present_in_taxon NCBITaxon:8508 {source="Wikipedia"} ! Sphenodon punctatus @@ -141920,7 +141920,7 @@ id: UBERON:0010907 name: parafibula def: "Third bone of the lower leg, normally restricted to the area of the knee, in multuberculates, monotremes and some therians." [http://palaeos.com/vertebrates/glossary/glossaryP.html#P] is_a: UBERON:0005893 ! leg bone -relationship: only_in_taxon NCBITaxon:40674 {source="Palaeos"} ! Mammalia +relationship: in_taxon NCBITaxon:40674 {source="Palaeos"} ! Mammalia relationship: part_of UBERON:0003823 ! hindlimb zeugopod relationship: present_in_taxon NCBITaxon:9255 ! Monotremata @@ -141930,8 +141930,8 @@ name: paraglossale def: "An arrowhead-shaped bone in the avian hyoid apparatus which forms the base of the tongue." [http://palaeos.com/vertebrates/glossary/glossaryP.html#P] synonym: "paraglossale bone" EXACT [] is_a: UBERON:0001474 ! bone element +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: located_in UBERON:0010033 ! posterior part of tongue -relationship: only_in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0010272 ! hyoid apparatus [Term] @@ -141994,7 +141994,7 @@ xref: NCIT:C33779 xref: SCTID:279551000 xref: UMLS:C0225534 {source="ncithesaurus:Thyrohyoid_Ligament"} is_a: UBERON:0008845 {source="FMA"} ! nonskeletal ligament -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata [Term] id: UBERON:0010925 @@ -142103,7 +142103,7 @@ xref: AAO:0010647 xref: TAO:0000369 xref: ZFA:0000369 is_a: UBERON:0001630 ! muscle organ -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata property_value: axiom_lost_from_external_ontology "relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010647", ontology="AAO"} property_value: external_definition "One of the principal muscles used in swallowing.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010647", ontology="AAO", source="AAO:BMZ"} @@ -143540,7 +143540,7 @@ def: "Subdivision of the skeletal system which consists of the axial skeleton pl xref: FMA:7483 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system relationship: has_part UBERON:0000982 ! skeletal joint -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: in_taxon NCBITaxon:7711 ! Chordata property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI [Term] @@ -143658,14 +143658,14 @@ xref: BTO:0001250 is_a: UBERON:0002365 {source="BTO"} ! exocrine gland intersection_of: UBERON:0002530 ! gland intersection_of: produces UBERON:0012245 ! silk -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda [Term] id: UBERON:0011147 name: Verson's gland def: "A gland found in the larvae of lepidoptera. Each gland is made of three cells: the secretory cell, the reservoir cell and the canal cell." [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:0002365 ! exocrine gland -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0007376 ! outer epithelium [Term] @@ -143686,7 +143686,7 @@ def: "A paired hollow organ in the genito-urinary apparatus of Raja (and probabl synonym: "alkaline gland" RELATED [BTO:0001661] xref: BTO:0001661 is_a: UBERON:0002365 ! exocrine gland -relationship: only_in_taxon NCBITaxon:117893 ! Batoidea +relationship: in_taxon NCBITaxon:117893 ! Batoidea relationship: part_of UBERON:0001008 {source="BTO"} ! renal system relationship: present_in_taxon NCBITaxon:7858 ! Rajiformes @@ -144466,7 +144466,7 @@ xref: Wikipedia:Carpometacarpus is_a: UBERON:0002513 ! endochondral bone relationship: has_fused_element UBERON:0001435 ! carpal bone relationship: has_fused_element UBERON:0002374 ! metacarpal bone -relationship: only_in_taxon NCBITaxon:8492 ! Archosauria +relationship: in_taxon NCBITaxon:8492 ! Archosauria relationship: part_of UBERON:0001442 ! skeleton of manus [Term] @@ -144900,7 +144900,7 @@ xref: Wikipedia:Eimer's_organ is_a: UBERON:0000020 {source="Wikipedia"} ! sense organ relationship: has_part CL:0000242 ! Merkel cell relationship: has_part UBERON:0003719 ! Pacinian corpuscle -relationship: only_in_taxon NCBITaxon:9373 ! Talpidae +relationship: in_taxon NCBITaxon:9373 ! Talpidae relationship: part_of UBERON:0000412 ! dermal papilla property_value: taxon_notes "present in many moles, and are particularly common in the star-nosed mole, which bears 30,000 of them on its unique tentacled snout" xsd:string @@ -144910,9 +144910,9 @@ name: rhinarium def: "Moist, hairless, crenelated area around nostrils of some mammals." [Wikipedia:Rhinarium] xref: Wikipedia:Rhinarium is_a: UBERON:0003102 ! surface structure +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: never_in_taxon NCBITaxon:9475 ! Tarsiidae relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0007827 ! external nose relationship: surrounds UBERON:0005928 ! external naris property_value: taxon_notes "Absent in Tarsiers" xsd:string @@ -144922,7 +144922,7 @@ id: UBERON:0011263 name: femoral gland def: "A gland arranged along a row on the underside of the hindlimb in some lizards[Kardong]." [ISBN:0073040584] is_a: UBERON:0002530 ! gland -relationship: only_in_taxon NCBITaxon:8509 ! Squamata +relationship: in_taxon NCBITaxon:8509 ! Squamata relationship: part_of UBERON:0000376 {source="ISBN:0073040584"} ! hindlimb stylopod relationship: part_of UBERON:0002199 {source="ISBN:0073040584"} ! integument relationship: part_of UBERON:0002330 {source="ISBN:0073040584"} ! exocrine system @@ -144992,8 +144992,8 @@ synonym: "second tongue" RELATED [Wikipedia:Sublingua] synonym: "under-tongue" RELATED [Wikipedia:Sublingua] xref: Wikipedia:Sublingua is_a: UBERON:0000062 ! organ +relationship: in_taxon NCBITaxon:9347 {source="Wikipedia"} ! Eutheria relationship: never_in_taxon NCBITaxon:9606 {source="Wikipedia"} ! Homo sapiens -relationship: only_in_taxon NCBITaxon:9347 {source="Wikipedia"} ! Eutheria relationship: part_of UBERON:0000165 ! mouth [Term] @@ -145230,8 +145230,8 @@ def: "A putative electroreceptor organ located in the medial rostral cavity in t comment: classification as electric organ is putative xref: Wikipedia:Rostral_organ is_a: UBERON:0010521 ! electroreceptor organ +relationship: in_taxon NCBITaxon:118072 ! Coelacanthimorpha relationship: innervated_by UBERON:0000348 ! ophthalmic nerve -relationship: only_in_taxon NCBITaxon:118072 ! Coelacanthimorpha relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0011241 ! ethmoid region relationship: surrounded_by UBERON:0001013 ! adipose tissue @@ -145245,7 +145245,7 @@ xref: Wikipedia:Stomochord is_a: UBERON:0000481 ! multi-tissue structure relationship: develops_from UBERON:0007026 ! presumptive gut relationship: existence_starts_during UBERON:0000068 ! embryo stage -relationship: only_in_taxon NCBITaxon:10219 ! Hemichordata +relationship: in_taxon NCBITaxon:10219 ! Hemichordata property_value: structure_notes "Their walls are composed primarily of epithelial cells, but ciliated and glandular cells are also present." xsd:string [Term] @@ -145323,8 +145323,8 @@ xref: BSA:0000042 xref: Wikipedia:Ascidiacea#Anatomy is_a: UBERON:0003102 ! surface structure relationship: bounding_layer_of UBERON:0000468 ! multicellular organism -relationship: composed_primarily_of CHEBI:18246 -relationship: only_in_taxon NCBITaxon:7712 ! Tunicata +relationship: composed_primarily_of CHEBI:18246 ! (1->4)-beta-D-glucan +relationship: in_taxon NCBITaxon:7712 ! Tunicata relationship: part_of UBERON:0002416 ! integumental system relationship: part_of UBERON:0007023 ! adult organism property_value: taxon_notes "In some species tunicin occurs in small amounts. Some species calcium salts are deposited as spicules. In ascidians, the tunic is supplied with blood vessels." xsd:string @@ -145334,7 +145334,7 @@ id: UBERON:0011303 name: lamprey sucker xref: http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:117569 ! Hyperoartia +relationship: in_taxon NCBITaxon:117569 ! Hyperoartia relationship: part_of UBERON:0000165 ! mouth property_value: function_notes "attachment" xsd:string @@ -145343,7 +145343,7 @@ id: UBERON:0011304 name: tunicate postabdomen def: "Basalmost subdivision of a tunicate containing the heart and reproductive organs." [ISBN:0030229073] is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:7712 ! Tunicata +relationship: in_taxon NCBITaxon:7712 ! Tunicata property_value: taxon_notes "Most ascidians lack a postabdomen" xsd:string [Term] @@ -145718,7 +145718,7 @@ xref: FMA:55618 xref: SCTID:142713007 xref: Wikipedia:Pterygomandibular_raphe is_a: UBERON:0002384 ! connective tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000165 ! mouth property_value: external_ontology_notes "isa anatomical line in FMA" xsd:string {external_ontology="FMA"} @@ -145727,7 +145727,7 @@ id: UBERON:0011350 name: mylohyoid raphe synonym: "raphe of the mylohyoid" RELATED [] is_a: UBERON:0002384 ! connective tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata [Term] id: UBERON:0011357 @@ -146468,7 +146468,7 @@ name: platypus crural gland def: "A kidney-shaped alveolar glands located in the upper thigh connected by a thin-walled duct to a calcaneus spur, or calcar, on each hind limb." [Wikipedia:Platypus_venom#Spur_and_crural_gland] xref: Wikipedia:Platypus_venom#Spur_and_crural_gland is_a: UBERON:0002365 ! exocrine gland -relationship: only_in_taxon NCBITaxon:9257 ! Ornithorhynchus +relationship: in_taxon NCBITaxon:9257 ! Ornithorhynchus relationship: part_of UBERON:0011581 ! platypus calcaneus spur relationship: produces UBERON:0007113 ! venom @@ -146664,7 +146664,7 @@ xref: EMAPA:32905 xref: NCIT:C114916 intersection_of: UBERON:0000475 ! organism subdivision intersection_of: has_skeleton UBERON:0001708 ! jaw skeleton -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata +relationship: in_taxon NCBITaxon:7776 ! Gnathostomata relationship: part_of UBERON:0000165 {source="EMAPA", source="FMA-abduced", source="ZFA-abduced"} ! mouth property_value: seeAlso "http://eol.org/collections/11578" xsd:anyURI @@ -146775,7 +146775,7 @@ synonym: "keel" BROAD [] xref: Wikipedia:Keel_(bird) is_a: UBERON:0000064 ! organ part relationship: capable_of_part_of GO:0060361 ! flight -relationship: only_in_taxon NCBITaxon:8782 {source="Wikipedia"} ! Aves +relationship: in_taxon NCBITaxon:8782 {source="Wikipedia"} ! Aves relationship: part_of UBERON:0000975 ! sternum property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/69/Br%C3%A9chet.png" xsd:anyURI @@ -147298,8 +147298,8 @@ name: epihyoidean comment: Muscle in sharks that is homologous to levator operculi and depressor mandibulae / stapedius is_a: UBERON:0005493 ! hyoid muscle relationship: develops_from UBERON:0003066 {source="ISBN:0073040584"} ! pharyngeal arch 2 +relationship: in_taxon NCBITaxon:119203 ! Selachii relationship: innervated_by UBERON:0001647 {source="ISBN:0073040584"} ! facial nerve -relationship: only_in_taxon NCBITaxon:119203 ! Selachii property_value: homology_notes "The depressor mandibulae of tetrapods, which opens the jaws, is the homologue of the levator operculi and epihyoidean. In mammals, the depressor mandibulae evolves into the stapedius (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000813", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.398", source="http://bgee.unil.ch/"} [Term] @@ -147691,7 +147691,7 @@ xref: NCIT:C34211 xref: UMLS:C1513298 {source="ncithesaurus:Midgut_Loop"} xref: VHOG:0000673 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001045 {source="VHOG"} ! midgut [Term] @@ -149757,7 +149757,7 @@ name: infraorbital sinus def: "An air-filled recess in the head of birds which lies lateral to the nasal cavity into which it opens." [http://medical-dictionary.thefreedictionary.com/infraorbital+sinus] synonym: "sinus infraorbitalis" EXACT OMO:0003011 [] is_a: UBERON:0001825 ! paranasal sinus -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves [Term] id: UBERON:0011986 @@ -149787,8 +149787,8 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} ! Acoelomorpha -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria property_value: editor_note "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string property_value: has_relational_adjective "coelomic" xsd:string @@ -150015,7 +150015,7 @@ name: metapterygial axis def: "Proximodistal trajectory through a metapterygium[Wagner]." [http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/128] comment: persisted in sacropterygians, precursor to limb axis is_a: UBERON:0006800 ! anatomical line -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000026 ! appendage [Term] @@ -150104,7 +150104,7 @@ synonym: "air vesicle" EXACT [] is_a: UBERON:0010000 ! multicellular anatomical structure relationship: connected_to UBERON:0008961 ! parabronchus relationship: contains_process GO:0007585 ! respiratory gaseous exchange by respiratory system -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0001004 ! respiratory system [Term] @@ -150112,7 +150112,7 @@ id: UBERON:0012088 name: lateroobronchus is_a: UBERON:0002185 ! bronchus relationship: connected_to UBERON:0009066 ! posterior thoracic air sac -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves [Term] id: UBERON:0012100 @@ -150120,7 +150120,7 @@ name: appendicocostalis muscle def: "One of of three muscles associated with the uncinate processes." [PMID:15755883] synonym: "appendicocostalis" EXACT [PMID:15755883] is_a: UBERON:0003831 ! respiratory system muscle -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves [Term] id: UBERON:0012101 @@ -150168,7 +150168,7 @@ synonym: "os peroneum" EXACT [PMCID:PMC1261702] intersection_of: UBERON:0001479 ! sesamoid bone intersection_of: located_in UBERON:0001387 ! fibularis longus relationship: connected_to UBERON:0001455 ! cuboid bone -relationship: only_in_taxon NCBITaxon:9443 ! Primates +relationship: in_taxon NCBITaxon:9443 ! Primates relationship: part_of UBERON:0003823 ! hindlimb zeugopod [Term] @@ -150190,7 +150190,7 @@ synonym: "fringe of baleen plate" EXACT [] xref: Wikipedia:baleen is_a: UBERON:0000061 ! anatomical structure relationship: has_part GO:0045095 ! keratin filament -relationship: only_in_taxon NCBITaxon:9761 ! Mysticeti +relationship: in_taxon NCBITaxon:9761 ! Mysticeti relationship: part_of UBERON:0012105 ! baleen plate [Term] @@ -150202,7 +150202,7 @@ xref: Wikipedia:Postorbital_Bar is_a: UBERON:0005913 ! zone of bone organ relationship: has_fused_element UBERON:0012109 ! zygomatic process of frontal bone relationship: has_fused_element UBERON:0012110 ! frontal process of zygomatic bone -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0003113 {notes="orbital series"} ! dermatocranium [Term] @@ -150257,8 +150257,8 @@ name: ingested food def: "A substance that is consumed by the organism for food." [http://orcid.org/0000-0002-6601-2165] xref: FMA:62964 is_a: UBERON:0000463 {source="FMA"} ! organism substance +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: located_in UBERON:0004908 ! upper digestive tract -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa property_value: external_ontology_notes "FMA def restricts this to 'oral cavity, pharynx or esophagus', but child terms includes chyme - which is in the stomach" xsd:string {external_ontology="FMA"} [Term] @@ -150285,7 +150285,7 @@ xref: Wikipedia:Cud intersection_of: UBERON:0036017 ! regurgitated substance intersection_of: has_part UBERON:0012113 ! bolus of food intersection_of: output_of GO:0036147 ! rumination -relationship: only_in_taxon NCBITaxon:9845 ! Ruminantia +relationship: in_taxon NCBITaxon:9845 ! Ruminantia [Term] id: UBERON:0012115 @@ -150359,8 +150359,8 @@ def: "A respiratory pump found in basal craniates." [Wikipedia:http\://palaeos.c synonym: "velum" BROAD [] is_a: UBERON:0000171 ! respiration organ disjoint_from: UBERON:0035960 ! velum feeding organ +relationship: in_taxon NCBITaxon:89593 ! Craniata relationship: never_in_taxon NCBITaxon:7776 ! Gnathostomata -relationship: only_in_taxon NCBITaxon:89593 ! Craniata relationship: present_in_taxon NCBITaxon:7762 ! Myxinidae property_value: function_notes "Muscular scroll-like flap that moves water through median nostril and over gills" xsd:string property_value: location_notes "trifid and posteriorly directed lamina arising from roof of pharynx, behind posterior end of naso-pharyngeal duct;" xsd:string @@ -150758,7 +150758,7 @@ name: comb def: "A vascular, red cutaneous structure attached in a sagittal plane to the dorsum of the skull of domestic fowl. It consists of a base attached to the skull, a central mass called the body, a backward projecting blade and upward projecting points." [http://medical-dictionary.thefreedictionary.com/pea+comb] xref: SCTID:3643003 is_a: UBERON:0000021 ! cutaneous appendage -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves [Term] id: UBERON:0012177 @@ -151054,7 +151054,7 @@ xref: AAO:0010177 xref: Wikipedia:Nuptial_pad is_a: UBERON:0003102 ! surface structure relationship: capable_of_part_of GO:0007620 ! copulation -relationship: only_in_taxon NCBITaxon:8292 ! Amphibia +relationship: in_taxon NCBITaxon:8292 ! Amphibia relationship: part_of UBERON:0001003 {source="ISBN:0073040584"} ! skin epidermis relationship: part_of UBERON:0002102 ! forelimb @@ -151073,7 +151073,7 @@ xref: MESH:D047011 xref: SPD:0000318 xref: Wikipedia:Silk is_a: UBERON:0000463 {source="SPD"} ! organism substance -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda [Term] id: UBERON:0012246 @@ -151235,7 +151235,7 @@ intersection_of: UBERON:0002389 ! manual digit intersection_of: part_of UBERON:5012260 ! alular digit plus metapodial segment relationship: has_developmental_contribution_from UBERON:0005692 {source="PMID:10220427"} ! manual digit 2 mesenchyme relationship: has_developmental_contribution_from UBERON:0010564 {source="PMID:10220427"} ! manual digit 1 mesenchyme -relationship: only_in_taxon NCBITaxon:8782 {source="PhenotypeRCN:Oct2012"} ! Aves +relationship: in_taxon NCBITaxon:8782 {source="PhenotypeRCN:Oct2012"} ! Aves relationship: preaxialmost_part_of UBERON:0002398 ! manus [Term] @@ -151252,7 +151252,7 @@ synonym: "wing digit II" RELATED [] intersection_of: UBERON:0002389 ! manual digit intersection_of: part_of UBERON:5012261 ! manual major digit (Aves) plus metapodial segment relationship: has_developmental_contribution_from UBERON:0005693 {source="PMID:10220427"} ! manual digit 3 mesenchyme -relationship: only_in_taxon NCBITaxon:8782 {source="PhenotypeRCN:Oct2012"} ! Aves +relationship: in_taxon NCBITaxon:8782 {source="PhenotypeRCN:Oct2012"} ! Aves [Term] id: UBERON:0012262 @@ -151268,7 +151268,7 @@ synonym: "wing digit III" RELATED [] intersection_of: UBERON:0002389 ! manual digit intersection_of: part_of UBERON:5012262 ! manual minor digit (Aves) plus metapodial segment relationship: has_developmental_contribution_from UBERON:0005694 {source="PMID:10220427"} ! manual digit 4 mesenchyme -relationship: only_in_taxon NCBITaxon:8782 {source="PhenotypeRCN:Oct2012"} ! Aves +relationship: in_taxon NCBITaxon:8782 {source="PhenotypeRCN:Oct2012"} ! Aves relationship: postaxialmost_part_of UBERON:0002398 ! manus [Term] @@ -151297,7 +151297,7 @@ synonym: "metapodial bone 2 or 4" BROAD [] synonym: "splint bone" EXACT [NCBITaxon:9788] is_a: UBERON:0003821 ! metapodium bone relationship: adjacent_to UBERON:0013583 ! metapodium bone 3 -relationship: only_in_taxon NCBITaxon:9788 ! Equidae +relationship: in_taxon NCBITaxon:9788 ! Equidae property_value: editor_note "in future this class may be replaced by a more taxon-neutral class grouping metapodial bones 2 or 4" xsd:string [Term] @@ -151872,7 +151872,7 @@ synonym: "primordium of face" RELATED [] xref: FMA:293103 xref: SCTID:89066004 is_a: UBERON:0005423 ! developing anatomical structure -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0000922 ! embryo @@ -152020,7 +152020,7 @@ def: "Corpora allata with Corpora cardiaca form the retrocerebral complex, a neu comment: will be ceded to arthropod anatomy ontology xref: BTO:0001803 is_a: UBERON:0002368 {source="BTO"} ! endocrine gland -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda [Term] id: UBERON:0012326 @@ -152128,7 +152128,7 @@ def: "A fluid-filled sac that lies between the navicular bone and the deep digit synonym: "bursa podotrochlearis" EXACT [] xref: SCTID:370660009 is_a: UBERON:0003668 ! synovial bursa -relationship: only_in_taxon NCBITaxon:9788 ! Equidae +relationship: in_taxon NCBITaxon:9788 ! Equidae relationship: part_of UBERON:0002470 ! autopod region [Term] @@ -152468,7 +152468,7 @@ xref: Wikipedia:Subserosa intersection_of: UBERON:0004923 ! organ component layer intersection_of: adjacent_to UBERON:0000042 ! serous membrane intersection_of: composed_primarily_of UBERON:0006815 ! areolar connective tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata [Term] id: UBERON:0012376 @@ -152633,7 +152633,7 @@ synonym: "urodaeum" EXACT [] synonym: "urodeal portion of cloaca" EXACT [] xref: SCTID:81191004 is_a: UBERON:0000064 ! organ part -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0000162 ! cloaca property_value: has_relational_adjective "urodeal" xsd:string property_value: taxon_notes "This is where the urates collect. In the hen the oviduct opens into this compartment." xsd:string {source="http://caiquesite.com/glossary.htm"} @@ -152762,7 +152762,7 @@ def: "An anatomical line that adjacent_to a epithelium and adjacent_to a mesench intersection_of: UBERON:0006800 ! anatomical line intersection_of: adjacent_to UBERON:0000483 ! epithelium intersection_of: adjacent_to UBERON:0003104 ! mesenchyme -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa [Term] id: UBERON:0012438 @@ -152847,7 +152847,7 @@ synonym: "corpuscles of Herbst" RELATED [Wikipedia:Corpuscles_of_Herbst] synonym: "Herbst corpuscle" RELATED [Wikipedia:Corpuscles_of_Herbst] xref: Wikipedia:Corpuscles_of_Herbst is_a: UBERON:0012449 {source="Wikipedia"} ! mechanoreceptor -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves [Term] id: UBERON:0012449 @@ -153047,7 +153047,7 @@ synonym: "cloacal tooth" RELATED [] synonym: "perianal tooth" RELATED [] intersection_of: UBERON:0003913 ! tooth-like structure intersection_of: part_of UBERON:0001353 ! anal region -relationship: only_in_taxon NCBITaxon:7586 ! Echinodermata +relationship: in_taxon NCBITaxon:7586 ! Echinodermata [Term] id: UBERON:0012469 @@ -153061,7 +153061,7 @@ id: UBERON:0012470 name: wheel papilla comment: the terminal papillae superficially resemble the 'anal teeth' of non-apodid holothurians. is_a: UBERON:0000061 ! anatomical structure -relationship: only_in_taxon NCBITaxon:7586 ! Echinodermata +relationship: in_taxon NCBITaxon:7586 ! Echinodermata [Term] id: UBERON:0012471 @@ -153112,8 +153112,8 @@ synonym: "oral tentacle" EXACT [] xref: BTO:0001357 is_a: UBERON:0000062 ! organ relationship: adjacent_to UBERON:0000165 ! mouth +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: never_in_taxon NCBITaxon:7776 ! Gnathostomata -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: present_in_taxon NCBITaxon:7568 ! Brachiopoda relationship: present_in_taxon NCBITaxon:7737 ! Branchiostoma property_value: curator_notes "this class groups a chordate (branchiostome) and lophotrochozoan (brachiopod) structure; these should probably be split" xsd:string @@ -153125,7 +153125,7 @@ def: "A ventral evagination extending anteriorly in the mid-portion of the intes synonym: "hepatic caecum" EXACT [BTO:0002855] xref: BTO:0002855 is_a: UBERON:0009854 ! digestive tract diverticulum -relationship: only_in_taxon NCBITaxon:7735 ! Cephalochordata +relationship: in_taxon NCBITaxon:7735 ! Cephalochordata relationship: part_of UBERON:0000160 {source="BTO"} ! intestine relationship: present_in_taxon NCBITaxon:7737 ! Branchiostoma property_value: taxon_notes "may be analagous to liver, Romer says not homologous" xsd:string @@ -153445,7 +153445,7 @@ name: body of tubeworm comment: to be ceded to polychaete ontology xref: http://www.pbs.org/wgbh/nova/abyss/life/images/tubeworm.gif is_a: UBERON:0000468 ! multicellular organism -relationship: only_in_taxon NCBITaxon:6425 ! Riftia +relationship: in_taxon NCBITaxon:6425 ! Riftia relationship: produces UBERON:0012646 ! tubeworm tube [Term] @@ -153612,7 +153612,7 @@ synonym: "snake rattle" EXACT [] xref: SCTID:10734004 xref: Wikipedia:Rattlesnake#Rattle is_a: UBERON:0004529 ! anatomical projection -relationship: only_in_taxon NCBITaxon:8570 ! Serpentes +relationship: in_taxon NCBITaxon:8570 ! Serpentes relationship: part_of UBERON:0007812 ! post-anal tail [Term] @@ -153646,7 +153646,7 @@ xref: MESH:D012910 xref: Wikipedia:Snake_venom intersection_of: UBERON:0007113 ! venom intersection_of: produced_by UBERON:0008976 ! snake venom gland -relationship: only_in_taxon NCBITaxon:8570 ! Serpentes +relationship: in_taxon NCBITaxon:8570 ! Serpentes [Term] id: UBERON:0013078 @@ -153736,7 +153736,7 @@ xref: Wikipedia:Sulcus_(neuroanatomy) intersection_of: UBERON:0000093 ! sulcus intersection_of: part_of UBERON:0000955 ! brain relationship: dubious_for_taxon NCBITaxon:10088 ! Mus -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: surrounds UBERON:0000200 ! gyrus property_value: editor_note "sulci are considered absent from lissencephalic mammals such as mice, but they may possess fissures. For example, the Allen mouse brain Atlas includes hippocampal, rhinal and choroid fissure. For this reason we do not place a taxon constraint on this class" xsd:string property_value: external_definition "Indentation on the surface of the brain or spinal cord that forms a recognizable landmark, e.g., central sulcus, sulcus limitans (CUMBO)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} @@ -154402,7 +154402,7 @@ def: "A wavy crest externally on the tympanic bone of cetaceans." [http://palaeo synonym: "sigmoid process" EXACT [] synonym: "sigmoid process of auditory bulla" EXACT [] is_a: UBERON:0004530 ! bony projection -relationship: only_in_taxon NCBITaxon:9721 ! Cetacea +relationship: in_taxon NCBITaxon:9721 ! Cetacea relationship: part_of UBERON:0008959 ! auditory bulla [Term] @@ -154412,8 +154412,8 @@ def: "An air sac opening into the passage of the blowhole that is hypothesized t synonym: "blowhole air sac" EXACT [] is_a: UBERON:0004111 ! anatomical conduit relationship: capable_of_part_of GO:0050959 ! echolocation +relationship: in_taxon NCBITaxon:9721 ! Cetacea relationship: located_in UBERON:0001707 ! nasal cavity -relationship: only_in_taxon NCBITaxon:9721 ! Cetacea relationship: part_of UBERON:0000033 ! head property_value: location_notes "May be positioned distally or frontally" xsd:string @@ -154424,8 +154424,8 @@ synonym: "monkey lips" RELATED [http://palaeos.com/vertebrates/cetartiodactyla/c synonym: "phonic lips" RELATED OMO:0003004 [] is_a: UBERON:0000481 ! multi-tissue structure relationship: capable_of_part_of GO:0050959 ! echolocation +relationship: in_taxon NCBITaxon:9721 {notes="absent in baleen whales"} ! Cetacea relationship: located_in UBERON:0013177 ! dorsal bursa -relationship: only_in_taxon NCBITaxon:9721 {notes="absent in baleen whales"} ! Cetacea relationship: part_of UBERON:0013188 {notes="check for sperm whales"} ! monkey lips dorsal bursa complex property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a5/Delphinschaedel.svg" xsd:anyURI property_value: editor_note "requires review w.r.t location in physeter vs other odontocetes" xsd:string @@ -154439,7 +154439,7 @@ synonym: "dorsal bursae" RELATED OMO:0003004 [] synonym: "fatty dorsal bursa" RELATED [] is_a: UBERON:0001013 ! adipose tissue relationship: in_lateral_side_of UBERON:0000033 ! head -relationship: only_in_taxon NCBITaxon:9721 ! Cetacea +relationship: in_taxon NCBITaxon:9721 ! Cetacea relationship: part_of UBERON:0013188 {notes="check for sperm whales"} ! monkey lips dorsal bursa complex property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a5/Delphinschaedel.svg" xsd:anyURI @@ -154488,8 +154488,8 @@ synonym: "MLDB complex" EXACT [] is_a: UBERON:0000481 ! multi-tissue structure relationship: capable_of_part_of GO:0050959 {source="ISBN:0120885522"} ! echolocation relationship: in_lateral_side_of UBERON:0000033 ! head +relationship: in_taxon NCBITaxon:9721 ! Cetacea relationship: located_in UBERON:0001707 ! nasal cavity -relationship: only_in_taxon NCBITaxon:9721 ! Cetacea property_value: taxon_notes "all odontocetes except sperm whales posses two bilaterally placed MLDB complexes, placed just below the floor of the vestibular sac" xsd:string [Term] @@ -154500,7 +154500,7 @@ synonym: "junk bodies" RELATED OMO:0003004 [] synonym: "junk body" RELATED [] synonym: "junk organ" RELATED [] is_a: UBERON:0000062 ! organ -relationship: only_in_taxon NCBITaxon:9753 ! Physeter +relationship: in_taxon NCBITaxon:9753 ! Physeter relationship: part_of UBERON:0000033 ! head property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Sperm_whale_head_anatomy.svg" xsd:anyURI property_value: taxon_notes "May be homologous to melon organ" xsd:string @@ -154576,8 +154576,8 @@ synonym: "wool" RELATED [MESH:A13.970] xref: MESH:D014935 xref: SCTID:90080004 is_a: UBERON:0010509 ! strand of pelage hair +relationship: in_taxon NCBITaxon:9963 {source="cjm"} ! Caprinae relationship: never_in_taxon NCBITaxon:9606 {source="https://github.com/obophenotype/uberon/issues/703"} ! Homo sapiens -relationship: only_in_taxon NCBITaxon:9963 {source="cjm"} ! Caprinae [Term] id: UBERON:0013198 @@ -154587,8 +154587,8 @@ comment: analagous to a puparium in other insects is_a: UBERON:0000476 ! acellular anatomical structure disjoint_from: UBERON:0016927 ! mucus cocoon relationship: composed_primarily_of UBERON:0012245 ! silk +relationship: in_taxon NCBITaxon:33392 ! Endopterygota relationship: never_in_taxon NCBITaxon:37572 ! Papilionoidea -relationship: only_in_taxon NCBITaxon:33392 ! Endopterygota relationship: surrounds UBERON:0003143 ! pupa [Term] @@ -154651,8 +154651,8 @@ synonym: "marsupial bone" NARROW [] xref: Wikipedia:Epipubic_bone is_a: UBERON:0007830 {source="cjm"} ! pelvic girdle bone/zone relationship: in_lateral_side_of UBERON:0001271 ! pelvic girdle region +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: never_in_taxon NCBITaxon:314146 ! Euarchontoglires -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4c/Macropus_major_hind_legs.png" xsd:anyURI property_value: external_definition "Epipubic bones are a pair of bones projecting forward from the pelvic bones of modern marsupials and of some fossil mammals: multituberculates, monotremes, and even basal eutherians (the ancestors of placental mammals). In modern marsupials the epipubic bones are often called 'marsupial bones' because they support the mother's pouch ('marsupium' is Latin for 'pouch'), but their presence on other groups of mammals indicates that this was not their original function, which some researchers think was to assist locomotion by supporting some of the muscles that flex the thigh. The epipubic bones were first described in 1698 but their functions have remained unresolved. It has been suggested that they form part of a kinetic linkage stretching from the femur on one side to the ribs on the opposite side. This linkage is formed by a series of muscles: each epipubic bone is connected to the femur by the pectineus muscle, and to the ribs and vertebrae by the pyramidalis, rectus abdominis, and external and internal obliques. According to this hypothesis, the epipubic bones act as levers to stiffen the trunk during locomotion[Wikipedia:Epipubic_bone]." xsd:string {source="Wikipedia:Epipubic_bone"} property_value: has_relational_adjective "epipubic" xsd:string @@ -154665,7 +154665,7 @@ synonym: "nasal ray" RELATED [] xref: Wikipedia:Star-nosed_mole is_a: UBERON:0000021 ! cutaneous appendage relationship: has_part UBERON:0011255 ! Eimer's organ -relationship: only_in_taxon NCBITaxon:9373 ! Talpidae +relationship: in_taxon NCBITaxon:9373 ! Talpidae relationship: part_of UBERON:0001003 ! skin epidermis [Term] @@ -154676,13 +154676,13 @@ xref: Wikipedia:Entepicondylar_foramen is_a: UBERON:0004111 ! anatomical conduit relationship: conduit_for UBERON:0001148 ! median nerve relationship: conduit_for UBERON:0001398 ! brachial artery +relationship: in_taxon NCBITaxon:32524 ! Amniota relationship: never_in_taxon NCBITaxon:91561 ! Artiodactyla relationship: never_in_taxon NCBITaxon:9365 ! Erinaceus europaeus relationship: never_in_taxon NCBITaxon:9397 ! Chiroptera relationship: never_in_taxon NCBITaxon:9604 ! Hominidae relationship: never_in_taxon NCBITaxon:9721 ! Cetacea relationship: never_in_taxon NCBITaxon:9975 ! Lagomorpha -relationship: only_in_taxon NCBITaxon:32524 ! Amniota relationship: part_of UBERON:0004404 ! distal epiphysis of humerus relationship: present_in_taxon NCBITaxon:376911 ! Strepsirrhini relationship: present_in_taxon NCBITaxon:37887 ! Notoryctes @@ -154714,7 +154714,7 @@ is_a: UBERON:0000045 ! ganglion is_a: UBERON:0015245 {source="MA", source="NCBIBook:NBK55971"} ! septal olfactory organ relationship: capable_of_part_of GO:0016048 ! detection of temperature stimulus relationship: capable_of_part_of GO:0043695 ! detection of pheromone -relationship: only_in_taxon NCBITaxon:9989 ! Rodentia +relationship: in_taxon NCBITaxon:9989 ! Rodentia [Term] id: UBERON:0013211 @@ -154759,7 +154759,7 @@ name: ossicone def: "Ossicones are horn-like protuberances on the heads of giraffes, male okapis, and their extinct relatives, such as Sivatherium, and the climacoceratids, such as Climacoceras. Only giraffids have true ossicones (as opposed to horns or antlers). The base that a deer's antlers grow from is very similar to ossicones. Ossicones are similar to the horns of antelopes and cattle, save that they are derived from ossified cartilage, and that the ossicones remain covered in skin and fur, rather than horn. Antlers (such as on deer) are derived from bone tissue: when mature, the skin and fur covering of the antlers, termed 'velvet,' is sloughed and scraped off to expose the bone of the antlers." [Wikipedia:Ossicone] xref: Wikipedia:Ossicone is_a: UBERON:0006969 ! cranial appendage -relationship: only_in_taxon NCBITaxon:9892 ! Giraffidae +relationship: in_taxon NCBITaxon:9892 ! Giraffidae [Term] id: UBERON:0013216 @@ -154806,7 +154806,7 @@ def: "The parotoid gland (alternatively, paratoid gland) is an external skin gla synonym: "paratoid gland" RELATED [] xref: Wikipedia:Parotoid_gland is_a: UBERON:0002530 ! gland -relationship: only_in_taxon NCBITaxon:8292 {source="Wikipedia"} ! Amphibia +relationship: in_taxon NCBITaxon:8292 {source="Wikipedia"} ! Amphibia [Term] id: UBERON:0013220 @@ -154816,7 +154816,7 @@ xref: Wikipedia:Foramen_of_Panizza is_a: UBERON:0000464 ! anatomical space relationship: connects UBERON:0000947 ! aorta relationship: connects UBERON:0000947 {cardinality="2"} ! aorta -relationship: only_in_taxon NCBITaxon:8493 {source="Wikipedia"} ! Crocodylidae +relationship: in_taxon NCBITaxon:8493 {source="Wikipedia"} ! Crocodylidae relationship: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0004535 {source="Wikipedia"} ! cardiovascular system property_value: taxon_notes "Crocodilians have a completely separated ventricle with deoxygenated blood from the body, or systemic circulation, in the right ventricle and oxygenated blood from the lungs, or pulmonary circulation, in the left ventricle, as in birds and mammals. Two vessels, the left aorta and the pulmonary artery, exit the right ventricle. Blood from the right ventricle goes to the lungs through the pulmonary artery, as in mammals and birds. However, when a unique active valve leading to the pulmonary artery contracts, pressure in the right ventricle can increase and blood can leave the right ventricle, enter the left aortic arch, and therefore bypass the pulmonary circulation. The foramen of panizza connects the left and right aorta. Deoxygenated blood from the right ventricle, sitting in the left aorta, can flow into the right aorta through the foramen of panizza. When the heart is relaxed, some oxygenated blood from the left ventricle, sitting in the right aorta, can flow into the left aorta across the foramen of panizza. However, some species of Crocodilians have regulatory sphincters that prevent unwanted flow of blood through the foramen of panizza during non-diving" xsd:string @@ -154846,8 +154846,8 @@ name: otic notch def: "Otic notches are invagination in the posterior margin of the skull roof, one behind each orbit. Such notches are found in labyrinthodonts and some of their immediate ancestors, but not their reptilian descendants. The presence or absence of the otic notches is one of the traits used to separate the amniotes from the amphibian grade tetrapods." [Wikipedia:Otic_notch] xref: Wikipedia:Otic_notch is_a: UBERON:0005913 ! zone of bone organ +relationship: in_taxon NCBITaxon:32523 ! Tetrapoda relationship: never_in_taxon NCBITaxon:32524 ! Amniota -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda relationship: part_of UBERON:0003113 ! dermatocranium property_value: function_notes "The notches have been interpreted as part of an auditory structure, and are often shown holding a tympanum similar to those seen in modern anurans. Analysis of the columella (the stapes in amphibians and reptiles) of labyrinthodonts however indicate it did not function in transmitting low energy vibrations, thus rendering them effectively deaf to airborne sound. The otic notch instead functioned as a spiracle, at least in the early forms" xsd:string @@ -154967,7 +154967,7 @@ def: "A lateral nasal gland that removes sodium chloride from the bloodstream." xref: Wikipedia:Supraorbital_gland is_a: UBERON:0012278 ! gland of nasal mucosa relationship: capable_of GO:0055078 ! sodium ion homeostasis -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves property_value: function_notes "The gland's function is similar to that of the kidneys, though it is much more efficient at removing salt, allowing Penguins to survive without access to fresh water. Contrary to popular belief, the gland does not directly convert saltwater to freshwater. The term supraorbital refers to the area just above the eye socket (which is known as the orbit of the eye. ) Living in saltwater environments would naturally pose a large problem for penguins because the ingestion of saltwater would be detrimental to a penguin's health. Although penguins do not directly drink water, it is taken in when they engulf prey. As a result, saltwater enters their system and must be effectively excreted. The supraorbital gland has thus enabled the penguins' survival in such environments due to its water-filtering capability. The gland is located just above the eyes and surrounds a capillary in the head. This capillary constantly strains out the salt in the saltwater that a penguin takes in. Since the byproduct of the gland has roughly five times as much salt as would normally be found in the animal's fluids, the supraorbital gland is highly efficient. The penguin excretes the salt byproduct as a brine through its bill. Often, the fluid drips out, and this gives the appearance of a runny nose. However, the fluid may also be sneezed out. In the absence of saltwater, caused by captivity, the supraorbital gland will lie dormant as it has no other purpose. Having a dormant supraorbital gland does not negatively affect the health of a penguin" xsd:string [Term] @@ -154977,7 +154977,7 @@ def: "The violet gland or supracaudal gland is an important gland located on the synonym: "supracaudal gland" RELATED [] xref: Wikipedia:Violet_gland is_a: UBERON:0011252 ! scent gland -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0007812 ! post-anal tail [Term] @@ -154991,7 +154991,7 @@ synonym: "ventral region" BROAD [] synonym: "ventral region of organism" EXACT [] xref: FMA:259204 is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria property_value: has_relational_adjective "ventral" xsd:string [Term] @@ -155453,8 +155453,8 @@ name: simian shelf def: "A bony buttress on the inner surface of the foremost part of the ape mandible, functioning to reinforce the mandible." [http://web.archive.org/web/20060830160800/www.anth.ucsb.edu/glossary/glossary.html] xref: Wikipedia:Simian_shelf is_a: UBERON:0005913 ! zone of bone organ +relationship: in_taxon NCBITaxon:314295 ! Hominoidea relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: only_in_taxon NCBITaxon:314295 ! Hominoidea relationship: part_of UBERON:0001684 ! mandible [Term] @@ -155632,7 +155632,7 @@ def: "A hole at the top of a cetacean's head through which the animal breathes a synonym: "blowhole slit" NARROW [] xref: Wikipedia:Blowhole_(anatomy) is_a: UBERON:0005928 ! external naris -relationship: only_in_taxon NCBITaxon:9721 ! Cetacea +relationship: in_taxon NCBITaxon:9721 ! Cetacea property_value: taxon_notes "Baleen whales have two blowholes positioned in a V-shape while toothed whales have only one blowhole. The blowhole of a sperm whale, a toothed whale, is located left of centre in the frontal area of the snout, and is actually its left nostril, while the right nostril lacks an opening to the surface despite the fact that its nasal passage is otherwise well developed." xsd:string [Term] @@ -155644,7 +155644,7 @@ synonym: "cecal GALT" RELATED [] xref: SCTID:14239003 intersection_of: UBERON:0001961 ! mucosa-associated lymphoid tissue intersection_of: part_of UBERON:0001153 ! caecum -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0000314 ! cecum mucosa property_value: taxon_notes "In avians the polycryptic cecal tissue is similar to the mammalian palatine tonsil" xsd:string @@ -155853,7 +155853,7 @@ def: "A fringe of muscle running along the periphery of the panniculus." [https: synonym: "orbicularis" RELATED [] synonym: "orbicularis muscle" EXACT [] is_a: UBERON:0002036 ! striated muscle tissue -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0002416 ! integumental system relationship: present_in_taxon NCBITaxon:9363 ! Erinaceidae property_value: function_notes "Hedgehogs roll into a ball via contraction of this muscle" xsd:string @@ -155999,8 +155999,8 @@ synonym: "ambiens" RELATED [] is_a: UBERON:0014892 ! skeletal muscle organ, vertebrate relationship: has_muscle_insertion UBERON:0000979 ! tibia relationship: has_muscle_origin UBERON:0001273 ! ilium +relationship: in_taxon NCBITaxon:32524 ! Amniota relationship: never_in_taxon NCBITaxon:40674 ! Mammalia -relationship: only_in_taxon NCBITaxon:32524 ! Amniota relationship: part_of UBERON:0002103 ! hindlimb property_value: external_definition "The tendon of the ambiens muscle passes obliquely over the knee joint. It assists in the control of the bird's toes. This muscle is present in some reptiles but not mammals. It is present in caiques and some other South American genera, but missing in most parrot genera. This was first noted by Garrod (1874) who proposed using this and other anatomical differences to classify parrots. For oproperty_value external_definitionanatomical differences among parrots see carotid arteries, furcula, and uropygial gland" xsd:string {source="http://caiquesite.com/glossary.htm"} @@ -156055,7 +156055,7 @@ synonym: "magnum" BROAD [] synonym: "magnum of oviduct" EXACT [] synonym: "magnum of uterine tube" EXACT [] is_a: UBERON:0013515 {source="cjm"} ! subdivision of oviduct -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves [Term] id: UBERON:0013519 @@ -156065,7 +156065,7 @@ synonym: "isthmus of oviduct" EXACT [] synonym: "isthmus of uterine tube" EXACT [] xref: Wikipedia:Isthmus_of_uterine_tube is_a: UBERON:0013515 {source="cjm"} ! subdivision of oviduct -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves [Term] id: UBERON:0013522 @@ -156086,7 +156086,7 @@ intersection_of: UBERON:0000996 ! vagina intersection_of: connected_to UBERON:0013524 ! median vaginal canal intersection_of: in_lateral_side_of UBERON:0003975 ! internal female genitalia relationship: channel_for UBERON:0001968 {notes="the lateral vaginae serve as transport for the sperm"} ! semen -relationship: only_in_taxon NCBITaxon:9263 {editor="cjm"} ! Metatheria +relationship: in_taxon NCBITaxon:9263 {editor="cjm"} ! Metatheria property_value: implements_design_pattern "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI [Term] @@ -156102,7 +156102,7 @@ intersection_of: UBERON:0000996 ! vagina intersection_of: connected_to UBERON:0013523 ! lateral vaginal canal intersection_of: intersects_midsagittal_plane_of UBERON:0003975 ! internal female genitalia relationship: channel_for UBERON:0000922 ! embryo -relationship: only_in_taxon NCBITaxon:9263 {editor="cjm"} ! Metatheria +relationship: in_taxon NCBITaxon:9263 {editor="cjm"} ! Metatheria [Term] id: UBERON:0013525 @@ -157128,7 +157128,7 @@ synonym: "sesamoid" EXACT [VSAO:0000137] xref: VSAO:0000137 is_a: UBERON:0010911 {source="VSAO"} ! ossicle relationship: develops_in UBERON:0007846 {source="VSAO"} ! dense regular connective tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata [Term] id: UBERON:0013632 @@ -157239,7 +157239,7 @@ name: lophophore def: "A ring of ciliated tentacles surrounding the mouth." [Wikipedia:Lophophore] xref: Wikipedia:Lophophore is_a: UBERON:0013642 ! ring of oral cilia -relationship: only_in_taxon NCBITaxon:1206795 ! Lophotrochozoa +relationship: in_taxon NCBITaxon:1206795 ! Lophotrochozoa relationship: present_in_taxon NCBITaxon:10205 ! Bryozoa relationship: present_in_taxon NCBITaxon:120557 relationship: present_in_taxon NCBITaxon:43120 ! Entoprocta @@ -157337,8 +157337,8 @@ def: "Subdivision of skeleton that is part of the velum and consists of a comple synonym: "skeleton of velum" EXACT [http://orcid.org/0000-0002-6601-2165] intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: skeleton_of UBERON:0012121 ! respiratory velum +relationship: in_taxon NCBITaxon:89593 ! Craniata relationship: never_in_taxon NCBITaxon:7776 ! Gnathostomata -relationship: only_in_taxon NCBITaxon:89593 ! Craniata relationship: part_of UBERON:0008895 {notes="in hagfishes it is difficult to separate neurocranium from visceral skeleton"} ! splanchnocranium relationship: present_in_taxon NCBITaxon:7762 ! Myxinidae @@ -157362,8 +157362,8 @@ synonym: "dulaa" EXACT [] synonym: "dulah" EXACT [] xref: Wikipedia:Dulla_(organ) is_a: UBERON:0000481 ! multi-tissue structure +relationship: in_taxon NCBITaxon:9836 ! Camelus relationship: located_in UBERON:0000167 ! oral cavity -relationship: only_in_taxon NCBITaxon:9836 ! Camelus relationship: part_of UBERON:0000165 ! mouth [Term] @@ -157374,7 +157374,7 @@ synonym: "camel hump" EXACT [] synonym: "CamelHump" EXACT [] is_a: UBERON:0000481 ! multi-tissue structure relationship: has_part UBERON:0001013 ! adipose tissue -relationship: only_in_taxon NCBITaxon:9836 ! Camelus +relationship: in_taxon NCBITaxon:9836 ! Camelus relationship: part_of UBERON:0001137 ! dorsum [Term] @@ -157386,7 +157386,7 @@ synonym: "palatal organ" BROAD [] synonym: "palatal reital organ" EXACT [] is_a: UBERON:0003103 ! compound organ relationship: capable_of_part_of GO:0001659 {source="PMID:23450839"} ! temperature homeostasis -relationship: only_in_taxon NCBITaxon:9761 {source="PMID:23450839"} ! Mysticeti +relationship: in_taxon NCBITaxon:9761 {source="PMID:23450839"} ! Mysticeti relationship: part_of UBERON:0007375 ! roof of mouth [Term] @@ -157418,7 +157418,7 @@ comment: Contains ducts from kidney, gonads, terminal parts of intestine[ISBN:04 synonym: "priapia" RELATED OMO:0003004 [] is_a: UBERON:0008811 ! intromittent organ relationship: has_part UBERON:0001245 ! anus -relationship: only_in_taxon NCBITaxon:8075 ! Atheriniformes +relationship: in_taxon NCBITaxon:8075 ! Atheriniformes relationship: part_of UBERON:0000033 ! head relationship: present_in_taxon NCBITaxon:270656 @@ -157735,7 +157735,7 @@ name: main body axis def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa [Term] id: UBERON:0013702 @@ -157878,7 +157878,7 @@ relationship: has_developmental_contribution_from UBERON:0008844 {source="PMC157 relationship: has_muscle_insertion UBERON:0002030 ! nipple relationship: has_muscle_insertion UBERON:0009118 ! marsupium relationship: has_muscle_origin UBERON:0013712 ! anterior iliac spine -relationship: only_in_taxon NCBITaxon:9263 ! Metatheria +relationship: in_taxon NCBITaxon:9263 ! Metatheria property_value: function_notes "Associated with lumbar musculature. originally postulated to be involved in milk ejection, or for mammary support and for retraction of the teats." xsd:string property_value: function_notes "In pouched marsupials, the ilio-marsupialis is less well developed, but may help in gland contraction to express milk during suckling (Griffiths & Slater, 1988) and it carries the genitofemoral nerve that innervates the mammary gland (Renfree, 1979) [DOI:10.1046/j.1469-7580.2002.00087.x]" xsd:string property_value: function_notes "in pouchless marsupials provides mechanical support for the attached young [DOI:10.1046/j.1469-7580.2002.00087.x]" xsd:string @@ -158454,7 +158454,7 @@ synonym: "intermammary cleavage" RELATED [] synonym: "intermammary sulcus" RELATED [] xref: FMA:55264 is_a: UBERON:0006800 {source="FMA"} ! anatomical line -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0002100 ! trunk [Term] @@ -159053,8 +159053,8 @@ synonym: "nymph" RELATED [BTO:0000954] xref: BTO:0000954 xref: Wikipedia:Nymph_(biology) is_a: UBERON:0000069 ! larval stage +relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria property_value: external_definition "Any of various immature insects; especially: a larva of an insect (as a grasshopper, true bug, or mayfly) with incomplete metamorphosis that differs from the imago especially in size and in its incompletely developed wings and genitalia[BTO:0000954]." xsd:string {source="BTO:0000954"} [Term] @@ -159265,7 +159265,7 @@ def: "A collection of feathers found on the heads of some owls." [http://orcid.o synonym: "ear horn" RELATED [] synonym: "ear tuft" EXACT [] is_a: UBERON:0011810 ! collection of feathers -relationship: only_in_taxon NCBITaxon:30458 ! Strigiformes +relationship: in_taxon NCBITaxon:30458 ! Strigiformes relationship: part_of UBERON:0000033 ! head [Term] @@ -159401,9 +159401,9 @@ def: "One of two bilaterally symmetrical holes (fenestrae) in the temporal bone. synonym: "temporal fenestrae" RELATED OMO:0003004 [] intersection_of: UBERON:0004705 ! fenestra intersection_of: part_of UBERON:0001678 ! temporal bone +relationship: in_taxon NCBITaxon:32524 {notes="not present in earliest amniotes", source="Wikipedia"} ! Amniota relationship: never_in_taxon NCBITaxon:32525 {notes="in extant mammals the synapsis temporal fenestra is closed by the sphenoid", source="Wikipedia"} ! Theria relationship: never_in_taxon NCBITaxon:8459 {source="Wikipedia"} ! Testudines -relationship: only_in_taxon NCBITaxon:32524 {notes="not present in earliest amniotes", source="Wikipedia"} ! Amniota [Term] id: UBERON:0014460 @@ -159604,7 +159604,7 @@ relationship: capable_of_part_of GO:0042048 {source="Wikipedia"} ! olfactory beh relationship: capable_of_part_of GO:0071625 {source="Wikipedia"} ! vocalization behavior relationship: has_fused_element UBERON:0001834 ! upper lip relationship: has_fused_element UBERON:0007827 ! external nose -relationship: only_in_taxon NCBITaxon:9779 ! Proboscidea +relationship: in_taxon NCBITaxon:9779 ! Proboscidea relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0001004 ! respiratory system @@ -161381,7 +161381,7 @@ name: nucleus H of ventral tegmentum def: "A nucleus present in the ventral tegmentum of squalomorph sharks." [ISBN:0471888893] synonym: "nucleus H" BROAD [] is_a: UBERON:0000125 ! neural nucleus -relationship: only_in_taxon NCBITaxon:118040 ! Squalomorphii +relationship: in_taxon NCBITaxon:118040 ! Squalomorphii relationship: part_of UBERON:0002691 ! ventral tegmental area [Term] @@ -161390,7 +161390,7 @@ name: nucleus K of ventral tegmentum def: "A nucleus present in the ventral tegmentum of skates." [ISBN:0471888893] synonym: "nucleus K" BROAD [] is_a: UBERON:0000125 ! neural nucleus -relationship: only_in_taxon NCBITaxon:117893 ! Batoidea +relationship: in_taxon NCBITaxon:117893 ! Batoidea relationship: part_of UBERON:0002691 ! ventral tegmental area [Term] @@ -162029,8 +162029,8 @@ def: "A large expansion of the lateral wall of the telencephalon, located in the synonym: "dorsal ventricular ridge" EXACT [] synonym: "DVR" RELATED OMO:0003000 [PMID:23027930] is_a: UBERON:0002616 ! regional part of brain +relationship: in_taxon NCBITaxon:32524 ! Amniota relationship: never_in_taxon NCBITaxon:40674 ! Mammalia -relationship: only_in_taxon NCBITaxon:32524 ! Amniota relationship: part_of UBERON:0000203 ! pallium relationship: present_in_taxon NCBITaxon:8782 ! Aves property_value: taxon_notes "Because of the phyletic continuity of the DVR in living reptiles and birds, and its numerous similarities in topography, histology, and connections in these two groups, there is little question that the DVR of reptiles and birds is homologous as a telencephalic neural center. In contrast, the telencephalon in living mammals does not appear to have a DVR. It has been suggested, however, that their predecessors did have such a ridge, and that its cells migrated to the surface of the telencephalon during development to form part of the cerebral cortices which characterize all living mammals (Karten, 1969, 1991)[http://icb.oxfordjournals.org/content/42/4/743.full]" xsd:string @@ -162143,7 +162143,7 @@ id: UBERON:0014742 name: central nucleus of pallium def: "A nucleus located in the dorsal pallium that is present in sharks, skates and rays and extends at some levels to the midline.." [ISBN:0471888893] is_a: UBERON:0000125 ! neural nucleus -relationship: only_in_taxon NCBITaxon:7778 ! Elasmobranchii +relationship: in_taxon NCBITaxon:7778 ! Elasmobranchii relationship: part_of UBERON:0014740 ! dorsal pallium [Term] @@ -162151,7 +162151,7 @@ id: UBERON:0014751 name: P1 area of pallium (Myxiniformes) def: "Most superficial of the areas of the pallium in the enlarged evaginated telencephalon of hagfishes." [ISBN:0471888893] is_a: UBERON:0002616 ! regional part of brain -relationship: only_in_taxon NCBITaxon:7762 ! Myxinidae +relationship: in_taxon NCBITaxon:7762 ! Myxinidae relationship: part_of UBERON:0000203 ! pallium [Term] @@ -162160,7 +162160,7 @@ name: P2 area of pallium (Myxiniformes) def: "Area directly deep to the P1 area of pallium in hagfishes." [ISBN:0471888893] is_a: UBERON:0002616 ! regional part of brain relationship: immediately_deep_to UBERON:0014751 ! P1 area of pallium (Myxiniformes) -relationship: only_in_taxon NCBITaxon:7762 ! Myxinidae +relationship: in_taxon NCBITaxon:7762 ! Myxinidae relationship: part_of UBERON:0000203 ! pallium [Term] @@ -162169,7 +162169,7 @@ name: P3 area of pallium (Myxiniformes) def: "Area directly deep to the P2 area of pallium in hagfishes." [ISBN:0471888893] is_a: UBERON:0002616 ! regional part of brain relationship: immediately_deep_to UBERON:0014752 ! P2 area of pallium (Myxiniformes) -relationship: only_in_taxon NCBITaxon:7762 ! Myxinidae +relationship: in_taxon NCBITaxon:7762 ! Myxinidae relationship: part_of UBERON:0000203 ! pallium [Term] @@ -162178,7 +162178,7 @@ name: P4 area of pallium (Myxiniformes) def: "Area directly deep to the P3 area of pallium in hagfishes." [ISBN:0471888893] is_a: UBERON:0002616 ! regional part of brain relationship: immediately_deep_to UBERON:0014753 ! P3 area of pallium (Myxiniformes) -relationship: only_in_taxon NCBITaxon:7762 ! Myxinidae +relationship: in_taxon NCBITaxon:7762 ! Myxinidae relationship: part_of UBERON:0000203 ! pallium [Term] @@ -162187,7 +162187,7 @@ name: P5 area of pallium (Myxiniformes) def: "Most deep of the areas of the pallium in the enlarged evaginated telencephalon of hagfishes." [ISBN:0471888893] is_a: UBERON:0002616 ! regional part of brain relationship: immediately_deep_to UBERON:0014754 ! P4 area of pallium (Myxiniformes) -relationship: only_in_taxon NCBITaxon:7762 ! Myxinidae +relationship: in_taxon NCBITaxon:7762 ! Myxinidae relationship: part_of UBERON:0000203 ! pallium [Term] @@ -162204,7 +162204,7 @@ def: "Missing definition for term UBERON:0014757. Please replace it using linked synonym: "HA" RELATED OMO:0003000 [PMID:23027930] xref: BTO:0003402 is_a: UBERON:0002616 ! regional part of brain -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0000203 ! pallium [Term] @@ -162213,7 +162213,7 @@ name: interstitial part of hyperpallium apicale def: "Missing definition for term UBERON:0014758. Please replace it using linked reference." [PMID:23027930] synonym: "IHA" RELATED OMO:0003000 [PMID:23027930] is_a: UBERON:0002616 ! regional part of brain -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0014757 ! hyperpallium apicale [Term] @@ -162223,7 +162223,7 @@ def: "The major telecephalic thalamorecipient zone of the tectofugal visual syst synonym: "core region of ectostriatum" RELATED [PMID:14681937] synonym: "E" RELATED OMO:0003000 [PMID:16041718] is_a: UBERON:0002616 ! regional part of brain -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0000203 ! pallium [Term] @@ -162667,7 +162667,7 @@ synonym: "tendon of Zinn" RELATED [Wikipedia:Annulus_of_Zinn] xref: FMA:49071 xref: Wikipedia:Annulus_of_Zinn is_a: UBERON:0000481 ! multi-tissue structure -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0004088 ! orbital region relationship: surrounds UBERON:0000941 ! cranial nerve II @@ -162762,7 +162762,7 @@ xref: EMAPA:35769 xref: MA:0003025 xref: Wikipedia:Serratus is_a: UBERON:0001630 {source="MA"} ! muscle organ -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata [Term] id: UBERON:0014836 @@ -162927,7 +162927,7 @@ def: "The larval form of any of the Taenia tapeworms." [BTO:0003168, http://www. synonym: "cysticercus" EXACT [BTO:0003168] xref: BTO:0003168 is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6157 ! Platyhelminthes +relationship: in_taxon NCBITaxon:6157 ! Platyhelminthes relationship: part_of UBERON:0000069 ! larval stage [Term] @@ -162936,7 +162936,7 @@ name: zoea stage def: "A crustacean larval stage characterised by the use of the thoracic appendages for swimming." [Wikipedia:Crustacean_larvae#Zoea] synonym: "zoea" RELATED [] is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6657 ! Crustacea +relationship: in_taxon NCBITaxon:6657 ! Crustacea relationship: part_of UBERON:0018378 ! crustacean larval stage relationship: preceded_by UBERON:0014406 ! nauplius stage @@ -162968,7 +162968,7 @@ name: copepodite stage def: "A development stage of copepods which follows the nauplius stage. It is segmented with more than 3 pairs of appendages." [http://www.encyclo.co.uk/define/Copepodite] synonym: "copepodite" RELATED [] is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6830 ! Copepoda +relationship: in_taxon NCBITaxon:6830 ! Copepoda relationship: part_of UBERON:0018378 ! crustacean larval stage relationship: preceded_by UBERON:0014406 ! nauplius stage @@ -162978,7 +162978,7 @@ name: glaucothoe stage def: "A developmental stage in a hermit crab that has completed the swimming larval stages." [http://www.encyclo.co.uk/define/Copepodite] synonym: "glaucothoe" RELATED [] is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6657 ! Crustacea +relationship: in_taxon NCBITaxon:6657 ! Crustacea relationship: part_of UBERON:0018378 ! crustacean larval stage [Term] @@ -162989,7 +162989,7 @@ synonym: "trochophore" RELATED [] synonym: "trocophore" RELATED [] xref: Wikipedia:Trochophore is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:33317 ! Protostomia +relationship: in_taxon NCBITaxon:33317 ! Protostomia relationship: part_of UBERON:0000069 ! larval stage [Term] @@ -162999,7 +162999,7 @@ def: "The characteristic larval stage of the gastropod, bivalve and scaphopod ta synonym: "veliger" RELATED [] xref: Wikipedia:Veliger is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6447 ! Mollusca +relationship: in_taxon NCBITaxon:6447 ! Mollusca relationship: part_of UBERON:0000069 ! larval stage [Term] @@ -163009,7 +163009,7 @@ def: "The larval stage of members of the order Lepidoptera." [Wikipedia:Caterpil synonym: "caterpillar" RELATED [] xref: Wikipedia:Caterpillar is_a: UBERON:0000069 ! larval stage -relationship: only_in_taxon NCBITaxon:7088 ! Lepidoptera +relationship: in_taxon NCBITaxon:7088 ! Lepidoptera [Term] id: UBERON:0014870 @@ -163219,7 +163219,7 @@ synonym: "m. iliotibilias" EXACT [] is_a: UBERON:0014892 ! skeletal muscle organ, vertebrate relationship: has_muscle_insertion UBERON:0000979 ! tibia relationship: has_muscle_origin UBERON:0001273 ! ilium -relationship: only_in_taxon NCBITaxon:8292 ! Amphibia +relationship: in_taxon NCBITaxon:8292 ! Amphibia relationship: part_of UBERON:0002103 ! hindlimb [Term] @@ -163287,7 +163287,7 @@ intersection_of: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue intersection_of: develops_from UBERON:0003082 ! myotome intersection_of: surrounded_by UBERON:0011899 ! epimysium intersection_of: synapsed_by CL:0000100 ! motor neuron -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0018254 ! skeletal musculature [Term] @@ -163432,7 +163432,7 @@ xref: Wikipedia:Blood-testis_barrier is_a: UBERON:0000119 ! cell layer relationship: adjacent_to UBERON:0000179 ! haemolymphatic fluid relationship: adjacent_to UBERON:0000473 ! testis -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000079 ! male reproductive system [Term] @@ -164767,7 +164767,7 @@ synonym: "tapeworm head" RELATED [] xref: BTO:0002305 is_a: UBERON:0000062 ! organ relationship: in_anterior_side_of UBERON:0000468 ! multicellular organism -relationship: only_in_taxon NCBITaxon:6199 ! Cestoda +relationship: in_taxon NCBITaxon:6199 ! Cestoda [Term] id: UBERON:0015120 @@ -165202,7 +165202,7 @@ synonym: "four-partite eye" NARROW [PMID:21062451] synonym: "three-partite eye" NARROW [PMID:21062451] is_a: UBERON:0000970 ! eye relationship: has_part UBERON:0003211 ! median eye -relationship: only_in_taxon NCBITaxon:6657 ! Crustacea +relationship: in_taxon NCBITaxon:6657 ! Crustacea [Term] id: UBERON:0015171 @@ -165353,8 +165353,8 @@ def: "A circulatory organ that is reponsible for pumping lymph throughout the bo xref: Wikipedia:Lymph_heart is_a: UBERON:0015229 ! accessory circulatory organ relationship: capable_of GO:0003017 ! lymph circulation +relationship: in_taxon NCBITaxon:8287 ! Sarcopterygii relationship: never_in_taxon NCBITaxon:40674 ! Mammalia -relationship: only_in_taxon NCBITaxon:8287 ! Sarcopterygii relationship: present_in_taxon NCBITaxon:8342 ! Anura relationship: present_in_taxon NCBITaxon:8493 ! Crocodylidae relationship: present_in_taxon NCBITaxon:8570 ! Serpentes @@ -165384,7 +165384,7 @@ subset: grouping_class subset: non_informative intersection_of: UBERON:0000061 ! anatomical structure intersection_of: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: in_taxon NCBITaxon:33213 ! Bilateria property_value: curator_notes "This class is primarily to implement taxon constraints. It may be removed in the future." xsd:string [Term] @@ -165395,7 +165395,7 @@ synonym: "cement gland" BROAD [BTO:0002738] synonym: "cementary gland" RELATED [BTO:0002738] xref: BTO:0002738 is_a: UBERON:0002365 {source="BTO"} ! exocrine gland -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda [Term] id: UBERON:0015214 @@ -165542,7 +165542,7 @@ def: "A tube that runs longitudinally through the thorax and abdomen, along the synonym: "dorsal vessel" RELATED SENSU [FBbt:00058291, NCBITaxon:50557] is_a: UBERON:0000055 ! vessel relationship: develops_from UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0001009 ! circulatory system property_value: depiction "https://genent.cals.ncsu.edu/wp-content/themes/salient/img/intanat/hemo2a.gif" xsd:anyURI @@ -165554,7 +165554,7 @@ synonym: "esophagus" RELATED [WBbt:0003681] xref: WBbt:0003681 is_a: UBERON:0000062 ! organ is_a: UBERON:0006562 {notes="parent may be obsoleted"} ! pharynx -relationship: only_in_taxon NCBITaxon:6231 ! Nematoda +relationship: in_taxon NCBITaxon:6231 ! Nematoda relationship: part_of UBERON:0001555 {source="WBbt"} ! digestive tract [Term] @@ -165654,7 +165654,7 @@ xref: MA:0002890 is_a: UBERON:0015245 {source="MA"} ! septal olfactory organ relationship: has_part CL:0000848 ! microvillous olfactory receptor neuron relationship: has_part UBERON:0002232 ! olfactory gland -relationship: only_in_taxon NCBITaxon:9989 ! Rodentia +relationship: in_taxon NCBITaxon:9989 ! Rodentia relationship: part_of UBERON:0001997 ! olfactory epithelium property_value: taxon_notes "This olfactory apparatus has been observed in many mammals, including rat, mouse, hamster, deer mouse, rabbit, opossum, guinea pig, bandicoot, and koala (Rodolfo-Masera 1943; Adams and McFarland 1971; Bojsen-Moller 1975; Katz and Merzel 1977; Breipohl et al. 1983, 1989; Kratzing 1984a, 1984b; Taniguchi et al. 1993), but not in cat (Breipohl et al. 1983) or ferret (Weiler and Farbman 2003)" xsd:string {source="NCBIBook:NBK55971"} @@ -166644,7 +166644,7 @@ intersection_of: has_quality PATO:0001154 ! elongated intersection_of: has_quality PATO:0001598 ! protruding intersection_of: has_quality PATO:0002255 ! grooved intersection_of: intersects_midsagittal_plane_of UBERON:0003672 ! dentition -relationship: only_in_taxon NCBITaxon:40151 ! Monodon monoceros +relationship: in_taxon NCBITaxon:40151 ! Monodon monoceros [Term] id: UBERON:0015853 @@ -168587,7 +168587,7 @@ id: UBERON:0016618 name: baleen feeding system xref: Wikipedia:Aquatic_predation#Lunge_feeding is_a: UBERON:0011216 ! organ system subdivision -relationship: only_in_taxon NCBITaxon:9761 ! Mysticeti +relationship: in_taxon NCBITaxon:9761 ! Mysticeti relationship: part_of UBERON:0001007 ! digestive system property_value: seeAlso "https://github.com/obophenotype/uberon/issues/479" xsd:anyURI @@ -168614,7 +168614,7 @@ name: lunge feeding organ def: "A fibrous capsule located between the jaws of rorqual whales that contains a gelatinous substance and papillae bearing mechanorecaptors." [PMID:22622577] is_a: UBERON:0000020 ! sense organ relationship: has_part UBERON:0016630 ! neurovascular bundle -relationship: only_in_taxon NCBITaxon:9765 ! Balaenopteridae +relationship: in_taxon NCBITaxon:9765 ! Balaenopteridae relationship: part_of UBERON:0006606 ! mandibular symphysis relationship: part_of UBERON:0016618 ! baleen feeding system @@ -169566,7 +169566,7 @@ id: UBERON:0017164 name: dorsal cloacal gland def: "Cloacal gland in female salamanders that secrete into the dorsal walls of the cloaca, anterior and / or posterior to the spermathecae or near the spermathecal common tube." [http://www.jstor.org/stable/1466953, PHENOSCAPE:wd] is_a: UBERON:0012478 ! cloacal gland -relationship: only_in_taxon NCBITaxon:8293 ! Caudata +relationship: in_taxon NCBITaxon:8293 ! Caudata relationship: part_of UBERON:0003100 ! female organism [Term] @@ -169605,7 +169605,7 @@ synonym: "placentomes" RELATED OMO:0003004 [] is_a: UBERON:0034921 ! multi organ part structure relationship: has_part UBERON:0010008 ! placental cotyledon relationship: has_part UBERON:0017259 ! placental caruncle -relationship: only_in_taxon NCBITaxon:9845 ! Ruminantia +relationship: in_taxon NCBITaxon:9845 ! Ruminantia relationship: part_of UBERON:0001987 ! placenta [Term] @@ -169813,7 +169813,7 @@ name: cephalic spine def: "One of the spines, probably denticle derivatives, occurring singly or in pairs just behind the orbit on the cheek area in some fossil sharks. May have occurred only in males and may have served to hold the female during copulation, e.g. in the Jurassic genera Hybodus, Asteracanthus and Acrodus." [http://www.briancoad.com/dictionary/complete%20dictionary.htm] synonym: "cephalic spines" RELATED OMO:0003004 [] is_a: UBERON:0008260 ! spine appendage -relationship: only_in_taxon NCBITaxon:7777 ! Chondrichthyes +relationship: in_taxon NCBITaxon:7777 ! Chondrichthyes relationship: part_of UBERON:0000033 ! head relationship: present_in_taxon NCBITaxon:119203 ! Selachii @@ -169824,14 +169824,14 @@ def: "A supplemental clasper in Holocephali, in front of the pelvic fin." [http: synonym: "pre-pelvic tenaculum" EXACT [] synonym: "prepelvic tenaculum" EXACT [http://www.briancoad.com/dictionary/complete%20dictionary.htm] is_a: UBERON:0010516 ! clasper -relationship: only_in_taxon NCBITaxon:7863 ! Holocephali +relationship: in_taxon NCBITaxon:7863 ! Holocephali [Term] id: UBERON:0017624 name: pseudoclasper def: "One or more pairs of stiff ossified lobes or prongs found in the tip of the intromittent organ of Bythitoidei." [http://www.briancoad.com/dictionary/complete%20dictionary.htm] is_a: UBERON:0004529 ! anatomical projection -relationship: only_in_taxon NCBITaxon:181400 ! Bythitoidei +relationship: in_taxon NCBITaxon:181400 ! Bythitoidei relationship: part_of UBERON:0008811 ! intromittent organ [Term] @@ -169840,7 +169840,7 @@ name: pterygopodial gland def: "A gland of uncertain function at the base of the clasper in skates and rays, occupying the position of the siphon of other Elasmobranchii." [http://www.briancoad.com/dictionary/complete%20dictionary.htm] is_a: UBERON:0002530 ! gland relationship: adjacent_to UBERON:0010516 ! clasper -relationship: only_in_taxon NCBITaxon:117893 ! Batoidea +relationship: in_taxon NCBITaxon:117893 ! Batoidea [Term] id: UBERON:0017626 @@ -169885,7 +169885,7 @@ def: "An innervated group of cells in a round capsule at the end of a jelly-fill synonym: "mormyromast" EXACT [http://www.briancoad.com/dictionary/complete%20dictionary.htm] synonym: "snout organ" RELATED [http://www.briancoad.com/dictionary/complete%20dictionary.htm] is_a: UBERON:0010521 ! electroreceptor organ -relationship: only_in_taxon NCBITaxon:41712 ! Osteoglossiformes +relationship: in_taxon NCBITaxon:41712 ! Osteoglossiformes relationship: part_of UBERON:0000033 ! head [Term] @@ -169919,7 +169919,7 @@ def: "A supplementary intervertebral articulation found in xenarthrans character synonym: "xenarthrous articulation" EXACT [] synonym: "xenarthrous joint" EXACT [] is_a: UBERON:0001468 ! intervertebral joint -relationship: only_in_taxon NCBITaxon:9348 ! Xenarthra +relationship: in_taxon NCBITaxon:9348 ! Xenarthra [Term] id: UBERON:0017635 @@ -170064,7 +170064,7 @@ name: intermaxillary gland (sensu Osteolepiformes) def: "A gland lodged in a fossa formed mainly of dermal bones, situated wholly in front of the nasal capsules of Osteolepiformes." [http://www.briancoad.com/dictionary/complete%20dictionary.htm] synonym: "intermaxillary gland" BROAD [] is_a: UBERON:0002530 ! gland -relationship: only_in_taxon NCBITaxon:8287 ! Sarcopterygii +relationship: in_taxon NCBITaxon:8287 ! Sarcopterygii [Term] id: UBERON:0017653 @@ -170072,7 +170072,7 @@ name: intermaxillary salivary gland def: "A gland located at the pre-nasal area being divided anteriorly by the ascendent processes of the intermaxillary bone." [DOI:10.1590/S0101-81751988000400003] synonym: "intermaxillary gland" BROAD [] is_a: UBERON:0001044 ! saliva-secreting gland -relationship: only_in_taxon NCBITaxon:8292 ! Amphibia +relationship: in_taxon NCBITaxon:8292 ! Amphibia relationship: part_of UBERON:0007375 ! roof of mouth relationship: present_in_taxon NCBITaxon:377294 property_value: function_notes "Although usually described in the literature as mucous, the secretory cells of the intermaxillary gland have serous characteristics." xsd:string @@ -170475,7 +170475,7 @@ synonym: "platypus beak" RELATED [] synonym: "platypus bill" NARROW [] is_a: UBERON:0006333 ! snout relationship: capable_of GO:0050964 {gci_filler="NCBITaxon:9257", gci_relation="part_of"} ! detection of electrical stimulus involved in electroception -relationship: only_in_taxon NCBITaxon:9255 ! Monotremata +relationship: in_taxon NCBITaxon:9255 ! Monotremata [Term] id: UBERON:0018134 @@ -170907,7 +170907,7 @@ xref: DMBA:17759 xref: Wikipedia:Posterior_column-medial_lemniscus_pathway is_a: UBERON:0000122 ! neuron projection bundle relationship: capable_of_part_of GO:0019230 {source="Wikipedia"} ! proprioception -relationship: only_in_taxon NCBITaxon:32523 {source="ISBN:978-1-4615-0037-7"} ! Tetrapoda +relationship: in_taxon NCBITaxon:32523 {source="ISBN:978-1-4615-0037-7"} ! Tetrapoda [Term] id: UBERON:0018238 @@ -170944,9 +170944,9 @@ xref: Wikipedia:Panniculus_carnosus is_a: UBERON:0008876 ! hypodermis skeletal muscle layer relationship: attaches_to UBERON:0000976 {gci_filler="NCBITaxon:9265", gci_relation="part_of", notes="in the opossum the panniculus carnosis attaches to the humerus", source="DOI:10.2307/1373999", source="FEED:rd"} ! humerus relationship: deep_to UBERON:0013488 ! panniculus adiposus +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: innervated_by UBERON:0001780 {source="FFED:cw"} ! spinal nerve relationship: never_in_taxon NCBITaxon:9606 {notes="vestigial or barely detectable"} ! Homo sapiens -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: present_in_taxon NCBITaxon:9261 {notes="by contraction of various parts of the panniculus carnosus, the short-beaked echidna can change shape, the most characteristic shape change being achieved by rolling itself into a ball when threatened, so protecting its belly and presenting a defensive array of sharp spines"} ! Tachyglossus aculeatus property_value: function_notes "They act to raise hair, quills, feathers, etc. It is also used in 'twitch' reflexes to shake off insects, etc.[Palaeos]" xsd:string property_value: has_relational_adjective "pannicular" xsd:string @@ -171356,7 +171356,7 @@ id: UBERON:0018288 name: paracone def: "The anterior cusp along the labial margin seen in the molar or premolar teeth of mammals. (modified from http://animaldiversity.ummz.umich.edu/collections/mammal_anatomy/cheek_teeth_structure/)." [PHENOSCAPE:alex] is_a: UBERON:0006844 ! cusp of tooth -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0013164 ! molariform tooth [Term] @@ -171364,7 +171364,7 @@ id: UBERON:0018289 name: paracristid def: "A crest running along the labial margin of molarifomr teeth of mammals. (modified from http://animaldiversity.ummz.umich.edu/collections/mammal_anatomy/cheek_teeth_structure/)." [PHENOSCAPE:alex] is_a: UBERON:0016930 ! ridge of tooth -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0013164 ! molariform tooth [Term] @@ -171372,7 +171372,7 @@ id: UBERON:0018290 name: postcingulum def: "A shelf like ridge on the posterior (distal) outside edge of the upper molariform teeth. (modified from http://animaldiversity.ummz.umich.edu/collections/mammal_anatomy/cheek_teeth_structure/)." [PHENOSCAPE:alex] is_a: UBERON:0016930 ! ridge of tooth -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0013164 ! molariform tooth [Term] @@ -171380,7 +171380,7 @@ id: UBERON:0018291 name: posteroloph def: "A shelf like ridge on the outside of the upper molariform teeth. (modified from http://animaldiversity.ummz.umich.edu/collections/mammal_anatomy/cheek_teeth_structure/)." [PHENOSCAPE:alex] is_a: UBERON:0016930 ! ridge of tooth -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0013164 ! molariform tooth [Term] @@ -171395,7 +171395,7 @@ id: UBERON:0018293 name: precingulum def: "A shelf like ridge on the proximal (mesial) outside edge of the upper molariform teeth. (modified from http://animaldiversity.ummz.umich.edu/collections/mammal_anatomy/cheek_teeth_structure/)." [PHENOSCAPE:alex] is_a: UBERON:0016930 ! ridge of tooth -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0013164 ! molariform tooth [Term] @@ -171411,7 +171411,7 @@ id: UBERON:0018295 name: preprotocrista def: "An enamel ridge joining the protocone and the paracone on the occlusal surface of a maxillary molar." [http://www.oxfordreference.com/view/10.1093/oi/authority.20110803100343456, PHENOSCAPE:curators] is_a: UBERON:0016930 ! ridge of tooth -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0013164 ! molariform tooth [Term] @@ -171708,7 +171708,7 @@ id: UBERON:0018333 name: labial cartilage def: "Distinct cartilage around the jaws of elasmobranchs." [PHENOSCAPE:Nizar] is_a: UBERON:0007844 ! cartilage element -relationship: only_in_taxon NCBITaxon:7778 ! Elasmobranchii +relationship: in_taxon NCBITaxon:7778 ! Elasmobranchii relationship: part_of UBERON:0003278 ! skeleton of lower jaw [Term] @@ -171844,7 +171844,7 @@ name: prismatic cartilage def: "Cartilage arranged into tesserae, blocks of calcified cartilage that fit together as tiles on a floor form a mosaic. Found only in chondrichthyans. Reference: A. Peter Klimley. 2013. The Biology of Sharks and Rays. University of Chicago Press." [PHENOSCAPE:Wasila] synonym: "prismatic calcified tissue" EXACT [PHENOSCAPE:Wasila] is_a: UBERON:0002418 ! cartilage tissue -relationship: only_in_taxon NCBITaxon:7777 ! Chondrichthyes +relationship: in_taxon NCBITaxon:7777 ! Chondrichthyes [Term] id: UBERON:0018353 @@ -171911,7 +171911,7 @@ name: suborbital shelf def: "On the neurocranium, a horizontal plate arising on the ventral junction of the orbital wall and basal plate on each side which extends from the nasal capsule to the otic capsule; it forms the floor of the orbit." [PHENOSCAPE:Wasila] comment: Definition from: LJV Compagno. 2002. Sharks of the World Volume 2; FAO Species Catalogue for Fishery Purposes No. 1 is_a: UBERON:0004529 ! anatomical projection -relationship: only_in_taxon NCBITaxon:119203 ! Selachii +relationship: in_taxon NCBITaxon:119203 ! Selachii relationship: part_of UBERON:0001703 ! neurocranium property_value: taxon_notes "A well-developed suborbital shelf is apparently primitive for shark-like fishes but is variably telescoped, reduced or lost in many squalomorph sharks and a few galeomorphs." xsd:string @@ -172015,7 +172015,7 @@ id: UBERON:0018374 name: sallet def: "A unit of the tectoral membrane that is shaped like string of flat, pearls. Modified from Manley, Fey and Popper 2008 ." [ISBN:9780387714691, PHENOSCAPE:Alex] is_a: UBERON:0000063 ! organ subunit -relationship: only_in_taxon NCBITaxon:8504 {source="ISBN:9780387714691"} ! Lepidosauria +relationship: in_taxon NCBITaxon:8504 {source="ISBN:9780387714691"} ! Lepidosauria relationship: part_of UBERON:0002233 ! tectorial membrane of cochlea relationship: present_in_taxon NCBITaxon:35033 {source="ISBN:9780387714691"} ! Scinciformata relationship: present_in_taxon NCBITaxon:8561 {source="ISBN:9780387714691"} ! Gekkonidae @@ -172060,7 +172060,7 @@ id: UBERON:0018378 name: crustacean larval stage def: "The larval stage of a crustacean, the stages of which are separated my moults. Typically this goes through a nauplius - zoea - post-larval cycle." [Wikipedia:Crustacean_larvae] is_a: UBERON:0000069 ! larval stage -relationship: only_in_taxon NCBITaxon:6657 ! Crustacea +relationship: in_taxon NCBITaxon:6657 ! Crustacea [Term] id: UBERON:0018379 @@ -172068,7 +172068,7 @@ name: metacestode def: "The larval (metacestode) stage of the tapeworm Echinococcus multilocularis." [BTO:0000859] xref: BTO:0000859 is_a: UBERON:0002548 {source="BTO"} ! larva -relationship: only_in_taxon NCBITaxon:6211 ! Echinococcus multilocularis +relationship: in_taxon NCBITaxon:6211 ! Echinococcus multilocularis [Term] id: UBERON:0018382 @@ -172076,7 +172076,7 @@ name: second instar larva def: "Instar: a stage in the life of an arthropod (as an insect) between two successive molts." [BTO:0001224] xref: BTO:0001224 is_a: UBERON:0002548 {source="BTO"} ! larva -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda [Term] id: UBERON:0018385 @@ -172084,7 +172084,7 @@ name: metacercaria def: "A tailless encysted late larva of a trematode parasite that is usually the form which is infective for the definitive host." [BTO:0003927] xref: BTO:0003927 is_a: UBERON:0002548 {source="BTO"} ! larva -relationship: only_in_taxon NCBITaxon:6178 ! Trematoda +relationship: in_taxon NCBITaxon:6178 ! Trematoda [Term] id: UBERON:0018387 @@ -172102,7 +172102,7 @@ def: "A usually tadpole-shaped larval trematode worm that develops in a mollusca xref: BTO:0005513 xref: MESH:D058487 is_a: UBERON:0002548 {source="BTO"} ! larva -relationship: only_in_taxon NCBITaxon:6178 ! Trematoda +relationship: in_taxon NCBITaxon:6178 ! Trematoda [Term] id: UBERON:0018389 @@ -173153,7 +173153,7 @@ def: "The peristomium is the second body segment in an annelid worm's body in th synonym: "peristomium" BROAD [Wikipedia:Peristomium] xref: Wikipedia:Peristomium is_a: UBERON:0000914 ! organismal segment -relationship: only_in_taxon NCBITaxon:6340 {source="Wikipedia"} ! Annelida +relationship: in_taxon NCBITaxon:6340 {source="Wikipedia"} ! Annelida [Term] id: UBERON:0018651 @@ -173171,7 +173171,7 @@ name: maxillary recess def: "A hollow space in the skull of carnivores, which do not exhibit a maxillary sinus." [http://orcid.org/0000-0002-6601-2165] synonym: "recessus maxillaris" EXACT OMO:0003011 [] is_a: UBERON:0000464 ! anatomical space -relationship: only_in_taxon NCBITaxon:33554 ! Carnivora +relationship: in_taxon NCBITaxon:33554 ! Carnivora relationship: part_of UBERON:0003129 ! skull property_value: editor_note "consider adding grouping with maxillary sinus" xsd:string property_value: location_notes "Bounded medially by the Lamina orbitalis of the Os ethmoidale and laterally by the Maxilla and Os palatinum and in the dog also by the Os lacrimale[NOMINA ANATOMICA VETERINARIA (2005)]" xsd:string @@ -173357,7 +173357,7 @@ def: "A mammalian developmental stage that covers the period from birth until we synonym: "suckling stage" EXACT [] is_a: UBERON:0000105 ! life cycle stage relationship: has_part UBERON:0007221 ! neonate stage -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0000092 ! post-embryonic stage [Term] @@ -177339,7 +177339,7 @@ alt_id: UBERON:0025487 synonym: "regional part of gustatory epithelium" EXACT HUMAN_PREFERRED [BIRNLEX:4100] is_obsolete: true consider: BIRNLEX:4100 -consider: http://uri.neuinfo.org/nif/nifstd/nifext_13 +consider: nifext:13 [Term] id: UBERON:0025236 @@ -179732,7 +179732,7 @@ synonym: "neuron projection bundle from brain" RELATED [http://orcid.org/0000-00 is_a: UBERON:0000122 ! neuron projection bundle relationship: extends_fibers_into UBERON:0000955 ! brain relationship: in_lateral_side_of UBERON:0000033 ! head -relationship: only_in_taxon NCBITaxon:89593 ! Craniata +relationship: in_taxon NCBITaxon:89593 ! Craniata [Term] id: UBERON:0034714 @@ -180951,7 +180951,7 @@ xref: DHBA:12184 xref: DMBA:16585 xref: neuronames:1176 is_a: UBERON:0011214 ! nucleus of midbrain tectum -relationship: only_in_taxon NCBITaxon:9347 {source="ISBN:0471888893"} ! Eutheria +relationship: in_taxon NCBITaxon:9347 {source="ISBN:0471888893"} ! Eutheria relationship: part_of UBERON:0001944 ! pretectal region [Term] @@ -180964,7 +180964,7 @@ xref: EMAPA:37920 {source="MA:th"} xref: neuronames:1116 xref: NLX:144456 is_a: UBERON:0011214 ! nucleus of midbrain tectum -relationship: only_in_taxon NCBITaxon:9347 {source="ISBN:0471888893"} ! Eutheria +relationship: in_taxon NCBITaxon:9347 {source="ISBN:0471888893"} ! Eutheria relationship: part_of UBERON:0001944 ! pretectal region property_value: editor_note "consider merging with olivary; however, Butler and Hodos treat as distinct within Eutherians" xsd:string @@ -180983,7 +180983,7 @@ name: infant stage def: "Nursing stage that follows the neonate stage in mammals and ends at weaning." [Bgee:AN, https://github.com/obophenotype/uberon/issues/644] is_a: UBERON:0000105 ! life cycle stage relationship: immediately_preceded_by UBERON:0007221 ! neonate stage -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0018685 ! nursing stage [Term] @@ -181182,8 +181182,8 @@ name: pharyngeal bar synonym: "branchial bar" RELATED [] synonym: "gill bar" RELATED [] is_a: UBERON:0004765 ! skeletal element +relationship: in_taxon NCBITaxon:33511 ! Deuterostomia relationship: never_in_taxon NCBITaxon:7776 ! Gnathostomata -relationship: only_in_taxon NCBITaxon:33511 ! Deuterostomia relationship: part_of UBERON:0001042 ! chordate pharynx relationship: present_in_taxon NCBITaxon:117569 ! Hyperoartia relationship: present_in_taxon NCBITaxon:7737 ! Branchiostoma @@ -181208,7 +181208,7 @@ synonym: "future piston" RELATED [UBERON:0010896] synonym: "piston mucocartilage" RELATED [] is_a: UBERON:0004765 ! skeletal element relationship: composed_primarily_of UBERON:0034938 ! mucocartilage tissue -relationship: only_in_taxon NCBITaxon:117569 ! Hyperoartia +relationship: in_taxon NCBITaxon:117569 ! Hyperoartia relationship: part_of UBERON:0000033 ! head property_value: development_notes "the mucocartilage dedifferentiaes to mesenchyme creating a blastema which differentiates to chondroblasts secreting proteoglycans resulting in the piston cartilage" xsd:string @@ -181255,8 +181255,8 @@ name: saccus vasculosus def: "A circumventricular organ of the hypothalamus of many jawed fishes, protruding from the caudal infundibular wall. It is a vascularized neuroepithelium that consists of coronet cells, cerebrospinal fluid-contacting neurons and supporting cells." [GOC:mr, https://github.com/obophenotype/uberon/issues/662, PMID:23820554, PMID:4115676] is_a: UBERON:0005408 {source="GOC:mr"} ! circumventricular organ relationship: has_part CL:0010015 ! coronet cell +relationship: in_taxon NCBITaxon:7776 ! Gnathostomata relationship: never_in_taxon NCBITaxon:32523 ! Tetrapoda -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: part_of UBERON:0001898 ! hypothalamus relationship: present_in_taxon NCBITaxon:8022 {source="PMID:4115676"} ! Oncorhynchus mykiss property_value: function_notes "Although its function remains hypothetical, it may contain sensory receptors for depth chemical detection. Other probable functions are osmoregulation ionic transport skeletal growth and tooth regeneration, although other homeostatic functions are not excluded" xsd:string @@ -181324,7 +181324,7 @@ id: UBERON:0034950 name: lymph sac of lymph heart def: "An extensive dorsal subcutaneous sac that opens into a lymph heart." [https://github.com/obophenotype/uberon/issues/1383, https://www.merriam-webster.com/dictionary/lymph%20sac] is_a: UBERON:0001473 ! lymphatic vessel -relationship: only_in_taxon NCBITaxon:8342 ! Anura +relationship: in_taxon NCBITaxon:8342 ! Anura relationship: part_of UBERON:0015202 ! lymph heart property_value: taxon_notes "The anuran lymphatic system consists of extensive subcutaneous and intrapleuroperitoneal sacs separated by connective tissue walls and interconnected by one-way valves [DOI:10.1152/japplphysiol.00201.2013]" xsd:string @@ -182099,7 +182099,7 @@ synonym: "Steno gland" EXACT [MP:0013582] synonym: "Steno's gland" EXACT [MP:0013582] xref: EMAPA:37894 {source="MA:th"} is_a: UBERON:0012278 ! gland of nasal mucosa -relationship: only_in_taxon NCBITaxon:9989 ! Rodentia +relationship: in_taxon NCBITaxon:9989 ! Rodentia relationship: site_of GO:0002377 ! immunoglobulin production [Term] @@ -182697,8 +182697,8 @@ id: UBERON:0035147 name: axochord def: "A medial muscle found in the ventral midline of annelid embryos." [https://github.com/obophenotype/uberon/issues/574, https://orcid.org/0000-0003-3308-6245, PMID:25214631] is_a: UBERON:0001630 ! muscle organ +relationship: in_taxon NCBITaxon:6340 ! Annelida relationship: intersects_midsagittal_plane_of UBERON:0000922 ! embryo -relationship: only_in_taxon NCBITaxon:6340 ! Annelida relationship: part_of UBERON:0000922 ! embryo relationship: transformation_of UBERON:0035148 ! presumptive axochord @@ -182710,8 +182710,8 @@ synonym: "axochord pre-muscle mass" EXACT [http://orcid.org/0000-0002-6601-2165] intersection_of: UBERON:0005865 ! pre-muscle condensation intersection_of: has_potential_to_develop_into UBERON:0035147 ! axochord relationship: develops_from UBERON:0000926 ! mesoderm +relationship: in_taxon NCBITaxon:6340 ! Annelida relationship: intersects_midsagittal_plane_of UBERON:0000922 ! embryo -relationship: only_in_taxon NCBITaxon:6340 ! Annelida relationship: part_of UBERON:0000922 ! embryo [Term] @@ -184356,7 +184356,7 @@ def: "An unjointed, rod-like bony or cartilaginous structures that extend from d is_a: UBERON:0010363 ! endochondral element relationship: capable_of_part_of GO:0060361 {source="DOI:10.1038/nature14423"} ! flight relationship: connected_to UBERON:0009880 ! carpal skeleton -relationship: only_in_taxon NCBITaxon:32524 ! Amniota +relationship: in_taxon NCBITaxon:32524 ! Amniota relationship: part_of UBERON:0001440 ! forelimb skeleton property_value: taxon_notes "in some mammals this is found in a cartilaginous state, and articulates with the lateral border of the carpus." xsd:string @@ -184376,9 +184376,9 @@ synonym: "PSm" RELATED OMO:0003000 [ISBN:0471888893] xref: TAO:0000235 xref: ZFA:0000235 is_a: UBERON:0006569 {source="ZFA"} ! diencephalic nucleus +relationship: in_taxon NCBITaxon:32443 ! Teleostei relationship: never_in_taxon NCBITaxon:27686 {source="ISBN:0471888893"} relationship: never_in_taxon NCBITaxon:7900 {source="ISBN:0471888893"} ! Acipenseridae -relationship: only_in_taxon NCBITaxon:32443 ! Teleostei relationship: part_of UBERON:2000687 {source="ZFA"} ! superficial pretectum property_value: external_definition "Diencephalic nucleus that is part of the superficial pretectum and is caudally contiguous with the caudal pretectal nucleus. Cells of the magnocellular superficial pretectal nucleus are slightly larger and more orderly around a central neuropil than those of the caudal pretectal nucleus. From Neuroanatomy of the Zebrafish Brain." xsd:string {source="ZFA:0000235"} @@ -184392,7 +184392,7 @@ synonym: "superficial pretectal nucleus" BROAD SENSU [ISBN:0471888893, NCBITaxon xref: TAO:0000406 xref: ZFA:0000406 is_a: UBERON:0006569 {source="ZFA"} ! diencephalic nucleus -relationship: only_in_taxon NCBITaxon:32443 ! Teleostei +relationship: in_taxon NCBITaxon:32443 ! Teleostei relationship: part_of UBERON:2000687 {source="ZFA"} ! superficial pretectum property_value: taxon_notes "in reedfishes and sturgeons this is the only nucleus in the superficial pretectal zone[ISBN:0471888893]" xsd:string @@ -184406,7 +184406,7 @@ synonym: "posterior pretectal nucleus" RELATED INCONSISTENT [ZFA:0000631] xref: TAO:0000631 xref: ZFA:0000631 is_a: UBERON:0006569 {source="ZFA"} ! diencephalic nucleus -relationship: only_in_taxon NCBITaxon:32443 ! Teleostei +relationship: in_taxon NCBITaxon:32443 ! Teleostei relationship: part_of UBERON:2000687 {source="ZFA"} ! superficial pretectum relationship: present_in_taxon NCBITaxon:32455 @@ -184434,7 +184434,7 @@ synonym: "nucleus praetectalis accessorius" EXACT OMO:0003011 [ZFA:0000714] xref: TAO:0000714 xref: ZFA:0000714 is_a: UBERON:0006569 {source="ZFA"} ! diencephalic nucleus -relationship: only_in_taxon NCBITaxon:32443 ! Teleostei +relationship: in_taxon NCBITaxon:32443 ! Teleostei relationship: part_of UBERON:2000183 {source="ZFA"} ! central pretectum [Term] @@ -184519,7 +184519,7 @@ name: nucleus geniculatus of pretectum comment: Receives retinal input synonym: "nucleus geniculatus pretectalis" EXACT OMO:0003011 [ISBN:0471888893] is_a: UBERON:0014450 ! pretectal nucleus -relationship: only_in_taxon NCBITaxon:8457 {source="ISBN:0471888893"} ! Sauropsida +relationship: in_taxon NCBITaxon:8457 {source="ISBN:0471888893"} ! Sauropsida relationship: present_in_taxon NCBITaxon:8459 {source="ISBN:0471888893"} ! Testudines relationship: present_in_taxon NCBITaxon:8504 {source="ISBN:0471888893"} ! Lepidosauria @@ -184529,7 +184529,7 @@ name: nucleus lentiformis of pretectum comment: Receives retinal input synonym: "nucleus lentiformis mesencephali" EXACT OMO:0003011 [ISBN:0471888893] is_a: UBERON:0014450 ! pretectal nucleus -relationship: only_in_taxon NCBITaxon:8457 {source="ISBN:0471888893"} ! Sauropsida +relationship: in_taxon NCBITaxon:8457 {source="ISBN:0471888893"} ! Sauropsida relationship: present_in_taxon NCBITaxon:8459 {source="ISBN:0471888893"} ! Testudines relationship: present_in_taxon NCBITaxon:8504 {source="ISBN:0471888893"} ! Lepidosauria @@ -184539,7 +184539,7 @@ name: nucleus posteriodorsalis of pretectum comment: Receives retinal input synonym: "nucleus posteriodorsalis" EXACT OMO:0003011 [ISBN:0471888893] is_a: UBERON:0014450 ! pretectal nucleus -relationship: only_in_taxon NCBITaxon:8457 {source="ISBN:0471888893"} ! Sauropsida +relationship: in_taxon NCBITaxon:8457 {source="ISBN:0471888893"} ! Sauropsida relationship: present_in_taxon NCBITaxon:8459 {source="ISBN:0471888893"} ! Testudines relationship: present_in_taxon NCBITaxon:8504 {source="ISBN:0471888893"} ! Lepidosauria @@ -184548,7 +184548,7 @@ id: UBERON:0035583 name: nucleus lentiformis thalamus synonym: "nucleus lentiformis thalami" RELATED OMO:0003011 [ISBN:0471888893] is_a: UBERON:0014450 ! pretectal nucleus -relationship: only_in_taxon NCBITaxon:8457 {source="ISBN:0471888893"} ! Sauropsida +relationship: in_taxon NCBITaxon:8457 {source="ISBN:0471888893"} ! Sauropsida relationship: present_in_taxon NCBITaxon:8504 {source="ISBN:0471888893"} ! Lepidosauria [Term] @@ -184556,7 +184556,7 @@ id: UBERON:0035584 name: ventral pretectal nucleus (sauropsida) synonym: "ventral pretectal nucleus" RELATED [ISBN:0471888893] is_a: UBERON:0014450 ! pretectal nucleus -relationship: only_in_taxon NCBITaxon:8457 {source="ISBN:0471888893"} ! Sauropsida +relationship: in_taxon NCBITaxon:8457 {source="ISBN:0471888893"} ! Sauropsida relationship: present_in_taxon NCBITaxon:8504 {source="ISBN:0471888893"} ! Lepidosauria [Term] @@ -184566,27 +184566,27 @@ synonym: "griseum tectalis" EXACT OMO:0003011 [ISBN:0471888893] synonym: "tectal gray" RELATED [ISBN:0471888893] synonym: "tectal grey" RELATED [] is_a: UBERON:0014450 ! pretectal nucleus -relationship: only_in_taxon NCBITaxon:8459 {source="ISBN:0471888893"} ! Testudines +relationship: in_taxon NCBITaxon:8459 {source="ISBN:0471888893"} ! Testudines [Term] id: UBERON:0035586 name: nucleus lentiformis mesencephali (Aves) def: "A pretectal nucleus in Aves that receives heavy retinal input and is hypothesized to be homologous to the nucleus of the optic tract of Mammals." [ISBN:0471888893] is_a: UBERON:0014450 ! pretectal nucleus -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves [Term] id: UBERON:0035587 name: nucleus pretectalis diffusus is_a: UBERON:0014450 ! pretectal nucleus -relationship: only_in_taxon NCBITaxon:8782 {source="ISBN:0471888893"} ! Aves +relationship: in_taxon NCBITaxon:8782 {source="ISBN:0471888893"} ! Aves [Term] id: UBERON:0035588 name: subpretectal complex of Aves def: "A nuclear complex in the ventral pretectal region." [ISBN:0471888893] is_a: UBERON:0007245 ! nuclear complex of neuraxis -relationship: only_in_taxon NCBITaxon:8782 {source="ISBN:0471888893"} ! Aves +relationship: in_taxon NCBITaxon:8782 {source="ISBN:0471888893"} ! Aves relationship: part_of UBERON:0001944 ! pretectal region [Term] @@ -184606,20 +184606,20 @@ id: UBERON:0035591 name: lateral spiriform nucleus is_a: UBERON:0014450 ! pretectal nucleus disjoint_from: UBERON:0035592 {source="lexical"} ! medial spiriform nucleus -relationship: only_in_taxon NCBITaxon:8782 {source="ISBN:0471888893"} ! Aves +relationship: in_taxon NCBITaxon:8782 {source="ISBN:0471888893"} ! Aves [Term] id: UBERON:0035592 name: medial spiriform nucleus is_a: UBERON:0014450 ! pretectal nucleus -relationship: only_in_taxon NCBITaxon:8782 {source="ISBN:0471888893"} ! Aves +relationship: in_taxon NCBITaxon:8782 {source="ISBN:0471888893"} ! Aves [Term] id: UBERON:0035593 name: nucleus circularis of pretectum synonym: "nucleus circularis" BROAD [ISBN:0471888893] is_a: UBERON:0014450 ! pretectal nucleus -relationship: only_in_taxon NCBITaxon:8782 {source="ISBN:0471888893"} ! Aves +relationship: in_taxon NCBITaxon:8782 {source="ISBN:0471888893"} ! Aves [Term] id: UBERON:0035594 @@ -184699,7 +184699,7 @@ id: UBERON:0035602 name: collar nerve cord def: "A nerve tract found in marine worms that is located in the collar body region (three body regions in marine worms: proboscis, collar (extending into tentacle-fringed arms) and trunk)." [Bgee:AN, PMID:25903626] is_a: UBERON:0005053 ! primary nerve cord -relationship: only_in_taxon NCBITaxon:10220 ! Enteropneusta +relationship: in_taxon NCBITaxon:10220 ! Enteropneusta relationship: part_of UBERON:0035604 ! enteropneust collar [Term] @@ -184707,21 +184707,21 @@ id: UBERON:0035603 name: enteropneust proboscis def: "Anteriormost of the three body regions of an enteropneust." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Acorn_worm] is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:10220 ! Enteropneusta +relationship: in_taxon NCBITaxon:10220 ! Enteropneusta [Term] id: UBERON:0035604 name: enteropneust collar def: "Middle of the three body regions of an enteropneust." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Acorn_worm] is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:10220 ! Enteropneusta +relationship: in_taxon NCBITaxon:10220 ! Enteropneusta [Term] id: UBERON:0035605 name: enteropneust trunk def: "Posteriormost of the three body regions of an enteropneust." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Acorn_worm] is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:10220 ! Enteropneusta +relationship: in_taxon NCBITaxon:10220 ! Enteropneusta [Term] id: UBERON:0035606 @@ -184798,8 +184798,8 @@ synonym: "nasal turbinate" EXACT [] synonym: "turbinal" EXACT [http://palaeos.com/vertebrates/bones/braincase/ethmoid.html] synonym: "turbinate" EXACT [] is_a: UBERON:0010363 ! endochondral element +relationship: in_taxon NCBITaxon:32523 ! Tetrapoda relationship: located_in UBERON:0001707 ! nasal cavity -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda relationship: part_of UBERON:0011241 {source="ISBN:0073040584"} ! ethmoid region property_value: editor_note "consult http://www.ncbi.nlm.nih.gov/pubmed/25312359 to add missing structures, e.g. ectoturbinals" xsd:string property_value: taxon_notes "unossified in dinosaurs[http://palaeos.com/vertebrates/bones/braincase/ethmoid.html]" xsd:string @@ -185324,7 +185324,7 @@ synonym: "telencephalic song nucleus HVC" EXACT [BTO:0003390] xref: BTO:0003390 is_a: UBERON:0000125 ! neural nucleus relationship: capable_of_part_of GO:0098583 ! learned vocalization behavior -relationship: only_in_taxon NCBITaxon:9126 {source="GOC:mr"} ! Passeriformes +relationship: in_taxon NCBITaxon:9126 {source="GOC:mr"} ! Passeriformes relationship: part_of UBERON:0007334 {source="Wikipedia"} ! nidopallium [Term] @@ -185422,7 +185422,7 @@ name: area X of basal ganglion def: "A nucleus in the basal ganglion of songbirds." [GOC:mr, https://github.com/geneontology/go-ontology/issues/12142, PMID15116398, PMID:18398825] synonym: "area X" BROAD [] is_a: UBERON:0000125 ! neural nucleus -relationship: only_in_taxon NCBITaxon:9126 {source="GOC:mr"} ! Passeriformes +relationship: in_taxon NCBITaxon:9126 {source="GOC:mr"} ! Passeriformes relationship: part_of UBERON:0002420 ! basal ganglion [Term] @@ -185434,7 +185434,7 @@ synonym: "robust nucleus of the arcopallium" RELATED DEPRECATED [BTO:0003366, Wi synonym: "telencephalic song nucleus RA" RELATED [BTO:0003366] xref: BTO:0003366 is_a: UBERON:0000125 {source="cjm"} ! neural nucleus -relationship: only_in_taxon NCBITaxon:9126 {source="GOC:cjm"} ! Passeriformes +relationship: in_taxon NCBITaxon:9126 {source="GOC:cjm"} ! Passeriformes relationship: part_of UBERON:0007350 {source="BTO"} ! arcopallium [Term] @@ -185600,8 +185600,8 @@ synonym: "vena cava sphincter" EXACT [] is_a: UBERON:0004590 ! sphincter muscle relationship: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue relationship: continuous_with UBERON:0014765 ! crus of diaphragm +relationship: in_taxon NCBITaxon:379584 {notes="Pinnipedia", notes="may also be in whales"} ! Caniformia relationship: innervated_by UBERON:0001884 {laterality="left"} ! phrenic nerve -relationship: only_in_taxon NCBITaxon:379584 {notes="Pinnipedia", notes="may also be in whales"} ! Caniformia relationship: present_in_taxon NCBITaxon:9709 ! Phocidae relationship: surrounds UBERON:0004087 ! vena cava property_value: function_notes "upon stimulation of right phrenic nerve, may cause complete closure of the caval passage to the right heart" xsd:string @@ -186459,7 +186459,7 @@ def: "The locomotory and feeding organ, found in the larval veliger stage of biv synonym: "velum" EXACT [BTO:0005405] xref: BTO:0005405 is_a: UBERON:0000062 ! organ -relationship: only_in_taxon NCBITaxon:6544 ! Bivalvia +relationship: in_taxon NCBITaxon:6544 ! Bivalvia relationship: part_of UBERON:0002548 ! larva [Term] @@ -186875,7 +186875,7 @@ comment: Uses to construct scent mounds is_a: UBERON:0000456 {source="cjm"} ! secretion of exocrine gland relationship: has_part UBERON:0001088 ! urine relationship: has_part UBERON:0013212 ! anal sac gland secretion -relationship: only_in_taxon NCBITaxon:29132 ! Castoridae +relationship: in_taxon NCBITaxon:29132 ! Castoridae [Term] id: UBERON:0036016 @@ -186885,7 +186885,7 @@ xref: BTO:0000605 xref: MESH:D006722 xref: Wikipedia:Honey is_a: UBERON:0036017 ! regurgitated substance -relationship: only_in_taxon NCBITaxon:7434 ! Aculeata +relationship: in_taxon NCBITaxon:7434 ! Aculeata [Term] id: UBERON:0036017 @@ -186893,7 +186893,7 @@ name: regurgitated substance def: "A bodily fluid consisting of the contents of the digestive tract expulsed through the anterior portion of the digestive tract." [UBERON:cjm] synonym: "regurgitate" RELATED [] is_a: UBERON:0000463 ! organism substance -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: in_taxon NCBITaxon:6072 ! Eumetazoa relationship: output_of GO:0022600 ! digestive system process [Term] @@ -186904,14 +186904,14 @@ comment: The contents of a bird's pellet depend on its diet, but can include the synonym: "casting" RELATED [] synonym: "pellet" RELATED [] is_a: UBERON:0036017 ! regurgitated substance -relationship: only_in_taxon NCBITaxon:8782 ! Aves +relationship: in_taxon NCBITaxon:8782 ! Aves [Term] id: UBERON:0036019 name: castor sac def: "A non-glandular region of the anal wall in which castoreum is produced." [PMID:24415179] is_a: UBERON:0008978 ! anal sac -relationship: only_in_taxon NCBITaxon:29132 ! Castoridae +relationship: in_taxon NCBITaxon:29132 ! Castoridae [Term] id: UBERON:0036043 @@ -187010,7 +187010,7 @@ name: diaphragmaticus muscle def: "A skeletal muscle found in crocodilians that is analogous to the diaphragm of mammals." [https://github.com/obophenotype/uberon/issues/1229, PMID:22323207] synonym: "diaphragmaticus" RELATED [] is_a: UBERON:0014892 ! skeletal muscle organ, vertebrate -relationship: only_in_taxon NCBITaxon:1294634 ! Crocodylia +relationship: in_taxon NCBITaxon:1294634 ! Crocodylia relationship: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0001004 ! respiratory system @@ -187099,8 +187099,8 @@ id: UBERON:0036148 name: orovelar muscle is_a: UBERON:0001630 ! muscle organ relationship: attaches_to UBERON:0013653 {comment="to be checked"} ! velar skeleton +relationship: in_taxon NCBITaxon:89593 ! Craniata relationship: never_in_taxon NCBITaxon:7776 ! Gnathostomata -relationship: only_in_taxon NCBITaxon:89593 ! Craniata property_value: seeAlso "https://github.com/obophenotype/uberon/issues/1264" xsd:anyURI [Term] @@ -187558,7 +187558,7 @@ name: cardial lymph propulsor def: "A lymphatic propulsor that lies tightly against the truncus arteriosus, the major outflow tract of the amphibian heart." [http://jap.physiology.org/content/115/3/297, PMCID:PMC1233883] is_a: UBERON:0015229 ! accessory circulatory organ relationship: capable_of GO:0003017 ! lymph circulation -relationship: only_in_taxon NCBITaxon:8293 ! Caudata +relationship: in_taxon NCBITaxon:8293 ! Caudata [Term] id: UBERON:0036260 @@ -187573,7 +187573,7 @@ id: UBERON:0036261 name: accessory lymph sac def: "An extracoelomic lateral abdominal space that accumulates body fluid." [PMID:3958676] is_a: UBERON:0007499 ! epithelial sac -relationship: only_in_taxon NCBITaxon:8457 ! Sauropsida +relationship: in_taxon NCBITaxon:8457 ! Sauropsida relationship: part_of UBERON:0000916 ! abdomen relationship: present_in_taxon NCBITaxon:65997 @@ -187661,14 +187661,14 @@ name: epihyoideum def: "An elastic ligament lying between the lateral pharyngeal muscles and the thyroglossus muscle." [PMCID:PMC1570911] is_a: UBERON:0000211 ! ligament relationship: connected_to UBERON:0000933 ! chordate pharyngeal muscle -relationship: only_in_taxon NCBITaxon:338153 ! Pantherinae +relationship: in_taxon NCBITaxon:338153 ! Pantherinae [Term] id: UBERON:0036271 name: omphalopleure def: "A fetal membrane, part of the yolk sac, that appears during some placentation processes." [https://github.com/obophenotype/uberon/issues/1426, https://orcid.org/0000-0003-3308-6245, PMID:10761048, PMID:29416852] is_a: UBERON:0000158 ! membranous layer -relationship: only_in_taxon NCBITaxon:9347 ! Eutheria +relationship: in_taxon NCBITaxon:9347 ! Eutheria relationship: part_of UBERON:0001040 ! yolk sac [Term] @@ -189732,7 +189732,7 @@ name: parallel fiber, bifurcated def: "A parallel fiber that results from the bifurcation of a cerebellar granule cell axon in the molecular layer into two diametrically opposed branches, that are oriented parallel to the long axis of the folium." [GO:1990032] is_a: UBERON:0700019 ! parallel fiber disjoint_from: UBERON:2002218 ! parallel fiber, teleost -relationship: never_in_taxon NCBITaxon:70862 +relationship: never_in_taxon NCBITaxon:70862 ! teleost fish property_value: dcterms-date "2023-07-10T11:53:19Z" xsd:dateTime [Term] @@ -189824,7 +189824,7 @@ name: midline crest def: "A ridge or peak located along the middle part of the head, located approximately equidistant from the left and the right sides of the head." [https://github.com/obophenotype/uberon/issues/34, UBERON:EJS] subset: phenotype_rcn is_a: UBERON:0001444 ! subdivision of head -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata [Term] id: UBERON:1000010 @@ -189973,7 +189973,7 @@ xref: NCIT:C77954 xref: SCTID:105587007 xref: UMLS:C0687056 {source="ncithesaurus:Zymbal_Gland"} is_a: UBERON:0015251 {source="ISBN:0123813611", source="MA"} ! modified sebaceous gland -relationship: only_in_taxon NCBITaxon:9989 ! Rodentia +relationship: in_taxon NCBITaxon:9989 ! Rodentia relationship: part_of UBERON:0001691 {source="cjm"} ! external ear property_value: location_notes "located anterior and ventral to the exterior ear canal in rodents[MP:0013384]" xsd:string property_value: structure_notes "Zymbal's glands are located beneath squamous epithelium at the anterior and posterior aspect of the ear canal, and as a single external gland that is located anterior and ventral to the base of the external ear canal. The bilateral Zymbal's glands are adjacent to the auditory canal and are made up of several lobules of modified sebaceous glands - http://ratguide.com/health/neoplasia/zymbals_gland_tumor.php." xsd:string @@ -192493,7 +192493,7 @@ xref: TAO:0000551 xref: ZFA:0000551 is_a: UBERON:0000125 ! neural nucleus is_a: UBERON:0009662 ! hindbrain nucleus -relationship: only_in_taxon NCBITaxon:32443 {contributor="michaelerice", source="PMID:2040726"} ! Teleostei +relationship: in_taxon NCBITaxon:32443 {contributor="michaelerice", source="PMID:2040726"} ! Teleostei relationship: part_of UBERON:0001896 {source="ZFA"} ! medulla oblongata property_value: provenance_notes "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} @@ -192731,7 +192731,7 @@ synonym: "valvula cerebellum" EXACT OMO:0003004 [TAO:0000603, ZFA:0000603] xref: TAO:0000603 xref: ZFA:0000603 is_a: UBERON:0002616 ! regional part of brain -relationship: only_in_taxon NCBITaxon:32443 {contributor="michaelerice", source="PMID:2040726"} ! Teleostei +relationship: in_taxon NCBITaxon:32443 {contributor="michaelerice", source="PMID:2040726"} ! Teleostei relationship: part_of UBERON:0002037 {source="ZFA"} ! cerebellum property_value: provenance_notes "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} @@ -196410,7 +196410,7 @@ xref: ZFA:0001200 is_a: UBERON:0000479 ! tissue is_a: UBERON:0002368 ! endocrine gland relationship: capable_of_part_of GO:0055074 ! calcium ion homeostasis -relationship: only_in_taxon NCBITaxon:7898 {xref="http://jeb.biologists.org/content/177/1/243.short"} ! Actinopterygii +relationship: in_taxon NCBITaxon:7898 {xref="http://jeb.biologists.org/content/177/1/243.short"} ! Actinopterygii relationship: part_of UBERON:0000080 ! mesonephros property_value: provenance_notes "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} @@ -203093,7 +203093,7 @@ synonym: "parallel fibers" EXACT OMO:0003004 [TAO:0002218] xref: ZFA:0001713 is_a: UBERON:0000479 ! tissue is_a: UBERON:0700019 ! parallel fiber -relationship: only_in_taxon NCBITaxon:32443 ! Teleostei +relationship: in_taxon NCBITaxon:32443 ! Teleostei relationship: part_of UBERON:2000394 ! molecular layer corpus cerebelli relationship: part_of UBERON:2000913 ! molecular layer valvula cerebelli property_value: provenance_notes "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} @@ -210152,7 +210152,7 @@ synonym: "annuli" BROAD OMO:0003004 [AAO:0010058] synonym: "annulus" BROAD [] synonym: "caecilian annulus" EXACT [] is_a: UBERON:3000977 ! body external integument structure -relationship: only_in_taxon NCBITaxon:43453 ! Caecilia +relationship: in_taxon NCBITaxon:43453 ! Caecilia [Term] id: UBERON:3010060 @@ -214055,7 +214055,7 @@ def: "The distinctive arrangement of four to ten spikes on the tails of stegosau comment: The arrangement of spikes originally had no distinct name; the term Thagomizer was coined in 1982 by cartoonist Gary Larson in his comic 'The Far Side', and thereafter became gradually adopted as an informal term within scientific circles, research, and education. {xref="https://en.wikipedia.org/wiki/Thagomizer"} synonym: "tail spikes" BROAD [] is_a: UBERON:0034768 ! morphological feature -relationship: only_in_taxon NCBITaxon:436486 ! Dinosauria +relationship: in_taxon NCBITaxon:436486 ! Dinosauria relationship: part_of UBERON:0007812 ! post-anal tail [Term] @@ -216556,7 +216556,7 @@ synonym: "pyloric caecum" EXACT [] xref: TAO:0002253 is_a: UBERON:0009854 ! digestive tract diverticulum relationship: dc-contributor https://orcid.org/0000-0003-3162-7490 ! Wasila M Dahdul -relationship: only_in_taxon NCBITaxon:7898 ! Actinopterygii +relationship: in_taxon NCBITaxon:7898 ! Actinopterygii property_value: editor_note "See https://github.com/obophenotype/uberon/issues/368" xsd:string [Term] @@ -218254,8 +218254,8 @@ name: arthropod tagma def: "One of the main divisions of the whole organism of arthropods formed from groups of segments." [doi:10.1016/B978-0-12-385026-3.00024-3] comment: Strictly speaking the term "tagma" cam be used for any metameric organism, however we follow the common usage which is to restrict the term to arthropods. is_a: UBERON:0011676 ! subdivision of organism along main body axis +relationship: in_taxon NCBITaxon:6656 ! Arthropoda relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0000468 ! multicellular organism [Term] @@ -218270,8 +218270,8 @@ name: insect ocular segment def: "Head segment derived from the second embryonic segment (between the labral and antennal segments). In the larva, this segment includes Bolwig's organ." [FlyBase:FBrf0055841, FlyBase:FBrf0075072] synonym: "acron" RELATED [] is_a: UBERON:6000007 ! procephalic segment +relationship: in_taxon NCBITaxon:50557 {source="cjm"} ! Insecta relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: only_in_taxon NCBITaxon:50557 {source="cjm"} ! Insecta [Term] id: UBERON:6000006 @@ -218325,7 +218325,7 @@ id: UBERON:6000015 name: insect thorax def: "The main middle section of the insect body comprising three thoracic rings: the pro-, the meso- and the metathoraces which are more or less well fused and cask-like sometimes having on the upper lateral part one of two pairs of wings, while on the ventrolateral part each thoracic ring bears a pair of legs." [FlyBase:FBrf0166419] is_a: UBERON:6000002 ! arthropod tagma -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:6000016 @@ -218371,7 +218371,7 @@ id: UBERON:6000020 name: insect abdomen def: "The most posterior of the three tagma (UBERON:6000002)." [FlyBase:FBrf0166419] is_a: UBERON:6000002 ! arthropod tagma -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:6000021 @@ -218427,8 +218427,8 @@ name: insect mesoderm anlage synonym: "ventral plate" RELATED [] is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0007688 ! anlage +relationship: in_taxon NCBITaxon:50557 {source="cjm"} ! Insecta relationship: in_taxon NCBITaxon:6656 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Arthropoda -relationship: only_in_taxon NCBITaxon:50557 {source="cjm"} ! Insecta relationship: part_of UBERON:0000922 ! embryo [Term] @@ -218445,7 +218445,7 @@ id: UBERON:6000119 name: insect anterior ectoderm def: "The region of the ectoderm anterior to the cephalic furrow." [FBC:DOS] is_a: UBERON:0010000 ! multicellular anatomical structure -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0000924 ! ectoderm [Term] @@ -218494,7 +218494,7 @@ id: UBERON:6000154 name: insect embryonic segment def: "Any insect segment that is part of some embryo." [UBERON:cjm] intersection_of: UBERON:0000914 ! organismal segment -intersection_of: only_in_taxon NCBITaxon:50557 ! Insecta +intersection_of: in_taxon NCBITaxon:50557 ! Insecta intersection_of: part_of UBERON:0000922 ! embryo relationship: in_taxon NCBITaxon:6656 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Arthropoda @@ -218503,7 +218503,7 @@ id: UBERON:6000157 name: insect embryonic head segment def: "Any segment that is part of some insect embryonic head." [UBERON:cjm] intersection_of: UBERON:0000914 ! organismal segment -intersection_of: only_in_taxon NCBITaxon:50557 ! Insecta +intersection_of: in_taxon NCBITaxon:50557 ! Insecta intersection_of: part_of UBERON:0008816 ! embryonic head [Term] @@ -218513,7 +218513,7 @@ def: "Any procephalic segment (UBERON:6000007) that is part of some embryonic he is_a: UBERON:6000007 ! procephalic segment is_a: UBERON:6000157 ! insect embryonic head segment intersection_of: UBERON:6000007 ! procephalic segment -intersection_of: only_in_taxon NCBITaxon:50557 ! Insecta +intersection_of: in_taxon NCBITaxon:50557 ! Insecta intersection_of: part_of UBERON:0008816 ! embryonic head relationship: part_of UBERON:0008816 ! embryonic head @@ -218524,7 +218524,7 @@ def: "Any antennal segment (UBERON:6000009) that is part of some embryonic head is_a: UBERON:6000009 ! antennal segment is_a: UBERON:6000158 ! insect embryonic procephalic segment intersection_of: UBERON:6000009 ! antennal segment -intersection_of: only_in_taxon NCBITaxon:50557 ! Insecta +intersection_of: in_taxon NCBITaxon:50557 ! Insecta intersection_of: part_of UBERON:0008816 ! embryonic head relationship: part_of UBERON:0008816 ! embryonic head @@ -218658,7 +218658,7 @@ synonym: "optic lobe primordium" RELATED [] is_a: UBERON:0001048 ! primordium relationship: dc-contributor https://orcid.org/0000-0001-9676-7393 relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 ! David Osumi-Sutherland -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:60005380 @@ -218687,7 +218687,7 @@ relationship: part_of UBERON:6001055 ! insect presumptive embryonic/larval nervo id: UBERON:6001057 name: insect neurogenic region is_a: UBERON:0005423 ! developing anatomical structure -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0000924 ! ectoderm [Term] @@ -218712,7 +218712,7 @@ id: UBERON:6001135 name: insect proneural cluster def: "An equivalence group of the neurectoderm where all cells can, although only one will, become a neural progenitor cell." [FlyBase:FBrf0074477, FlyBase:FBrf0089570] is_a: UBERON:0007688 ! anlage -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:6001648 @@ -218825,7 +218825,7 @@ name: insect embryonic/larval circulatory system def: "Tubular system of the embryo/larva through which hemolymph flows." [FlyBase:FBrf0031012] synonym: "larval circulatory system" EXACT [] is_a: UBERON:0001009 ! circulatory system -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0000323 ! late embryo relationship: part_of UBERON:0002548 ! larva @@ -218846,8 +218846,8 @@ name: insect ring gland def: "A closely associated cluster of three neuroendocrine glands located anterior to the aorta and dorsal to the esophagus. At embryonic stage 17 and in larva it is found anterior to the brain and is formed by the corpus cardiacum ventrally, the prothoracic gland laterally and the corpus allatum dorsally. The adult ring gland is located anterior to the proventriculus and is formed by the corpus cardiacum ventrally, the corpus allatum dorsally and the hypocerebral ganglion posterior to the corpus cardiacum. It is innervated by neurons of the nervus corporis cardiaci (NccI-III)." [FlyBase:FBrf0064803, FlyBase:FBrf0089570, FlyBase:FBrf0179777, PMID:12966498] is_a: UBERON:0000477 ! anatomical cluster relationship: capable_of GO:0046879 ! hormone secretion +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: in_taxon NCBITaxon:6656 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Arthropoda -relationship: only_in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:6001728 @@ -218863,7 +218863,7 @@ id: UBERON:6001729 name: insect larval segment def: "Any segment that is part of some larva." [FBC:auto_generated_definition] intersection_of: UBERON:0000914 ! organismal segment -intersection_of: only_in_taxon NCBITaxon:50557 ! Insecta +intersection_of: in_taxon NCBITaxon:50557 ! Insecta intersection_of: part_of UBERON:0002548 ! larva relationship: develops_from UBERON:6000154 ! insect embryonic segment @@ -218872,7 +218872,7 @@ id: UBERON:6001730 name: insect larval head def: "Any head that is part of some larva." [FBC:auto_generated_definition] intersection_of: UBERON:0000033 ! head -intersection_of: only_in_taxon NCBITaxon:50557 ! Insecta +intersection_of: in_taxon NCBITaxon:50557 ! Insecta intersection_of: part_of UBERON:0002548 ! larva [Term] @@ -219202,7 +219202,7 @@ name: insect embryonic/larval digestive system def: "Digestive system of the insect embryo or larva." [ISBN:9780879698287, ISBN:9780879698997] synonym: "larval digestive system" EXACT [] is_a: UBERON:0001007 ! digestive system -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0002548 ! larva [Term] @@ -219231,7 +219231,7 @@ name: insect embryonic/larval nervous system def: "Nervous system of the embryo/larva." [FlyBase:FBrf0045359, FlyBase:FBrf0075072, FlyBase:FBrf0105282] synonym: "larval nervous system" EXACT [] is_a: UBERON:0001016 ! nervous system -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0000323 ! late embryo relationship: part_of UBERON:0002548 ! larva @@ -219270,7 +219270,7 @@ name: insect larval sense organ def: "Any sense organ that is part of some larva." [FBC:auto_generated_definition] synonym: "larval sense organ" EXACT [] intersection_of: UBERON:0000020 ! sense organ -intersection_of: only_in_taxon NCBITaxon:50557 ! Insecta +intersection_of: in_taxon NCBITaxon:50557 ! Insecta intersection_of: part_of UBERON:0002548 ! larva [Term] @@ -219296,7 +219296,7 @@ relationship: part_of UBERON:0007023 ! adult organism id: UBERON:6003006 name: insect adult segment intersection_of: UBERON:0000914 ! organismal segment -intersection_of: only_in_taxon NCBITaxon:50557 ! Insecta +intersection_of: in_taxon NCBITaxon:50557 ! Insecta intersection_of: part_of UBERON:0007023 ! adult organism relationship: in_taxon NCBITaxon:6656 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Arthropoda @@ -219428,7 +219428,7 @@ id: UBERON:6003218 name: insect adult muscle system def: "Muscle system of the adult." [FlyBase:FBrf0007735] is_a: UBERON:0000383 ! musculature of body -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0007023 ! adult organism [Term] @@ -219445,7 +219445,7 @@ id: UBERON:6003559 name: insect adult nervous system def: "Nervous system of the adult insect." [ISBN:978-087969828-7] is_a: UBERON:0001016 ! nervous system -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0007023 ! adult organism [Term] @@ -219734,7 +219734,7 @@ id: UBERON:6005023 name: insect imaginal precursor def: "Structure that proliferates to produce a larval imaginal disc and which gives rise to adult tissues (Bate and Martinez Arias, 1991)." [FlyBase:FBrf0053815, FlyBase:FBrf0064789] is_a: UBERON:0005423 ! developing anatomical structure -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:6005036 @@ -219765,7 +219765,7 @@ name: insect trachea def: "Cuticle-lined epithelial tube that forms part of the insect tracheal system." [FBbt:00005043] synonym: "trachea" BROAD SENSU [NCBITaxon:50557] is_a: UBERON:0003127 ! open tracheal system trachea -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:6005054 @@ -219789,7 +219789,7 @@ def: "A group of small, interconnected ganglia situated posterior to and between synonym: "stomodaeal nervous system" RELATED [FlyBase:FBrf0111704] synonym: "stomodeal nervous system" RELATED [FlyBase:FBrf0111704] is_a: UBERON:0011216 ! organ system subdivision -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0001017 ! central nervous system [Term] @@ -219797,8 +219797,8 @@ id: UBERON:6005168 name: insect external sensory organ synonym: "sensillum" NARROW [] is_a: UBERON:0000020 ! sense organ +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: in_taxon NCBITaxon:6656 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Arthropoda -relationship: only_in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:6005177 @@ -219828,7 +219828,7 @@ id: UBERON:6005393 name: insect embryonic/larval integumentary system synonym: "larval integumentary system" RELATED [] is_a: UBERON:0002416 ! integumental system -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0002548 ! larva [Term] @@ -219837,7 +219837,7 @@ name: insect adult integumentary system synonym: "adult external" RELATED [] synonym: "adult integument" EXACT [] is_a: UBERON:0002416 ! integumental system -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0007023 ! adult organism [Term] @@ -219858,7 +219858,7 @@ is_obsolete: true id: UBERON:6005427 name: insect ectoderm anlage is_a: UBERON:0007688 ! anlage -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:6005428 @@ -219897,7 +219897,7 @@ id: UBERON:6005461 name: insect circulatory system primordium synonym: "embryonic/larval circulatory system specific anlage" RELATED [] is_a: UBERON:0001048 ! primordium -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:6005467 @@ -220027,7 +220027,7 @@ name: insect pharate adult def: "The developing adult after pupal-adult apolysis, i.e. from stage P8 (when yellow eye color first becomes visible through the pupal case), to eclosion." [FlyBase:FBrf0049147] is_a: UBERON:0000468 ! multicellular organism relationship: develops_from UBERON:0003143 ! pupa -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:6006032 @@ -220048,7 +220048,7 @@ id: UBERON:6007045 name: insect trunk ectoderm def: "The region of the ectoderm posterior to the cephalic furrow." [FBC:DOS] is_a: UBERON:0005423 ! developing anatomical structure -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0000924 ! ectoderm [Term] @@ -220101,7 +220101,7 @@ def: "Any appendage segment that is part of some leg." [FBC:auto_generated_defin is_a: UBERON:0010758 ! subdivision of organism along appendicular axis intersection_of: UBERON:0010758 ! subdivision of organism along appendicular axis intersection_of: part_of UBERON:0005895 ! insect leg -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0005895 ! insect leg [Term] @@ -220152,7 +220152,7 @@ relationship: part_of UBERON:6001730 ! insect larval head id: UBERON:6007245 name: insect cuticular specialization is_a: UBERON:0000476 ! acellular anatomical structure -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0001001 ! chitin-based cuticle [Term] @@ -220160,7 +220160,7 @@ id: UBERON:6007248 name: insect chorionic specialization def: "Specialized structure of the chorion of the egg." [FBC:MMC] is_a: UBERON:0000476 ! acellular anatomical structure -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0000920 ! egg chorion [Term] @@ -220178,7 +220178,7 @@ id: UBERON:6007284 name: insect region of integument def: "A region of cuticle and its underlying epidermis." [FBC:DOS] is_a: UBERON:0011216 ! organ system subdivision -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0002416 ! integumental system [Term] @@ -220202,21 +220202,21 @@ id: UBERON:6007331 name: insect segmental subdivision of organ system def: "The part of some organism that is part of some specified segment." [FBC:DOS] is_a: UBERON:0011216 ! organ system subdivision -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:6007373 name: insect internal sense organ def: "Sense organ that is internal to the animal - i.e. having no part that is part of the cuticle." [FBC:DOS] is_a: UBERON:0000020 ! sense organ -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:6007424 name: insect epithelial furrow def: "A region of an epithelium that folds inwards from the epithelial plane to form a furrow." [FBC:DOS] is_a: UBERON:0000483 ! epithelium -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:6007435 @@ -220286,14 +220286,14 @@ name: insect non-connected developing system def: "The sum of all the anlagen and primordia that will develop into a single system." [FBC:DOS] is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0034923 ! disconnected anatomical group -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:6040005 name: insect synaptic neuropil def: "The part of the neuropil consisting largely of synapsing neuron projections." [FlyBase:FBrf0224194] is_a: UBERON:0000465 ! material anatomical entity -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0002606 ! neuropil [Term] @@ -220326,7 +220326,7 @@ name: insect sensilla row def: "A row of sensilla." [FBC:DOS] is_a: UBERON:0034926 ! anatomical row relationship: composed_primarily_of UBERON:0002536 ! arthropod sensillum -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:6110636 @@ -221206,7 +221206,7 @@ name: copepodite stage 1 def: "A development stage of copepods which immediately follows the nauplius stage. It is characterized by the presence of 2 swimming legs." [http://orcid.org/0000-0002-2908-3327] is_a: UBERON:0000105 ! life cycle stage relationship: dc-contributor https://orcid.org/0000-0002-2908-3327 ! Anne Thessen -relationship: only_in_taxon NCBITaxon:6830 ! Copepoda +relationship: in_taxon NCBITaxon:6830 ! Copepoda relationship: part_of UBERON:0014860 ! copepodite stage relationship: part_of UBERON:0018378 ! crustacean larval stage relationship: preceded_by UBERON:0014406 ! nauplius stage @@ -221218,7 +221218,7 @@ name: copepodite stage 2 def: "A development stage of copepods which immediately follows copepodite stage 1. It is characterized by the presence of 3 swimming legs." [http://orcid.org/0000-0002-2908-3327] is_a: UBERON:0000105 ! life cycle stage relationship: dc-contributor https://orcid.org/0000-0002-2908-3327 ! Anne Thessen -relationship: only_in_taxon NCBITaxon:6830 ! Copepoda +relationship: in_taxon NCBITaxon:6830 ! Copepoda relationship: part_of UBERON:0014860 ! copepodite stage relationship: part_of UBERON:0018378 ! crustacean larval stage relationship: preceded_by UBERON:8200002 ! copepodite stage 1 @@ -221230,7 +221230,7 @@ name: copepodite stage 3 def: "A development stage of copepods which immediately follows copepodite stage 2. It is characterized by the presence of 4 swimming legs." [http://orcid.org/0000-0002-2908-3327] is_a: UBERON:0000105 ! life cycle stage relationship: dc-contributor https://orcid.org/0000-0002-2908-3327 ! Anne Thessen -relationship: only_in_taxon NCBITaxon:6830 ! Copepoda +relationship: in_taxon NCBITaxon:6830 ! Copepoda relationship: part_of UBERON:0014860 ! copepodite stage relationship: part_of UBERON:0018378 ! crustacean larval stage relationship: preceded_by UBERON:8200003 ! copepodite stage 2 @@ -221242,7 +221242,7 @@ name: copepodite stage 4 def: "A development stage of copepods which immediately follows copepodite stage 3. It is characterized by the presence of 5 swimming legs." [http://orcid.org/0000-0002-2908-3327] is_a: UBERON:0000105 ! life cycle stage relationship: dc-contributor https://orcid.org/0000-0002-2908-3327 ! Anne Thessen -relationship: only_in_taxon NCBITaxon:6830 ! Copepoda +relationship: in_taxon NCBITaxon:6830 ! Copepoda relationship: part_of UBERON:0014860 ! copepodite stage relationship: part_of UBERON:0018378 ! crustacean larval stage relationship: preceded_by UBERON:8200004 ! copepodite stage 3 @@ -221254,7 +221254,7 @@ name: copepodite stage 5 def: "A pre-adult stage of copepods which immediately follows copepodite stage 4. It is characterized by enlargement of the urosome and development of sexual organs." [http://orcid.org/0000-0002-2908-3327] is_a: UBERON:0000105 ! life cycle stage relationship: dc-contributor https://orcid.org/0000-0002-2908-3327 ! Anne Thessen -relationship: only_in_taxon NCBITaxon:6830 ! Copepoda +relationship: in_taxon NCBITaxon:6830 ! Copepoda relationship: part_of UBERON:0000113 ! post-juvenile adult stage relationship: preceded_by UBERON:8200005 ! copepodite stage 4 property_value: dcterms-date "2021-07-26T15:46:40Z" xsd:dateTime @@ -221265,7 +221265,7 @@ name: copepodite stage 6 def: "A fully formed stage of copepods which immediately follows copepodite stage 5. It is characterized by the complete development of the fifth swimming leg." [http://orcid.org/0000-0002-2908-3327] is_a: UBERON:0000105 ! life cycle stage relationship: dc-contributor https://orcid.org/0000-0002-2908-3327 ! Anne Thessen -relationship: only_in_taxon NCBITaxon:6830 ! Copepoda +relationship: in_taxon NCBITaxon:6830 ! Copepoda relationship: part_of UBERON:0000066 ! fully formed stage relationship: preceded_by UBERON:8200006 ! copepodite stage 5 property_value: dcterms-date "2021-07-26T15:48:54Z" xsd:dateTime @@ -223772,7 +223772,7 @@ def: "The region of the body adjacent to the vertebral column." [NCIT:C166000] synonym: "paraspinal" EXACT [NCIT:C129461] is_a: UBERON:0000154 ! posterior region of body relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 ! Paula Duek Roggli -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: in_taxon NCBITaxon:7742 ! Vertebrata property_value: dcterms-date "2023-05-16T06:37:51Z" xsd:dateTime [Term] @@ -225351,11 +225351,6 @@ expand_assertion_to: "Class: EquivalentT is_metadata_tag: true is_class_level: true -[Typedef] -id: only_in_taxon -name: only in taxon -xref: RO:0002160 - [Typedef] id: output_of name: output of