diff --git a/redundancy-removal.log b/redundancy-removal.log new file mode 100644 index 000000000..4a9f586ec --- /dev/null +++ b/redundancy-removal.log @@ -0,0 +1,377 @@ +REMOVING: UBERON:0001256 is_a: UBERON:0000060 (line 17102) - duplicates intersection_of: UBERON:0000060 +REMOVING: UBERON:0001256 relationship: part_of UBERON:0001255 (line 17105) - duplicates intersection_of: part_of UBERON:0001255 +REMOVING: UBERON:2001861 is_a: UBERON:0000982 (line 200443) - duplicates intersection_of: UBERON:0000982 +REMOVING: UBERON:2000694 is_a: UBERON:0001091 (line 193247) - duplicates intersection_of: UBERON:0001091 +REMOVING: UBERON:0005287 is_a: UBERON:0005283 (line 98685) - duplicates intersection_of: UBERON:0005283 +REMOVING: UBERON:0005287 relationship: part_of UBERON:0002422 (line 98688) - duplicates intersection_of: part_of UBERON:0002422 +REMOVING: UBERON:0004122 is_a: UBERON:0000467 (line 82130) - duplicates intersection_of: UBERON:0000467 +REMOVING: UBERON:0001487 relationship: part_of UBERON:0002387 (line 23018) - 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duplicates intersection_of: UBERON:0001638 +REMOVING: UBERON:0002212 relationship: part_of UBERON:0001854 (line 44522) - duplicates intersection_of: part_of UBERON:0001854 +REMOVING: UBERON:0000035 is_a: UBERON:0001305 (line 1161) - duplicates intersection_of: UBERON:0001305 +REMOVING: UBERON:6000167 relationship: part_of UBERON:6000166 (line 218550) - duplicates intersection_of: part_of UBERON:6000166 +REMOVING: UBERON:0004782 relationship: part_of UBERON:0005409 (line 92096) - duplicates intersection_of: part_of UBERON:0005409 +REMOVING: UBERON:0014870 is_a: UBERON:0006271 (line 162990) - duplicates intersection_of: UBERON:0006271 +REMOVING: UBERON:4200128 is_a: UBERON:0006077 (line 214999) - duplicates intersection_of: UBERON:0006077 +REMOVING: UBERON:6001728 is_a: UBERON:6000002 (line 218837) - duplicates intersection_of: UBERON:6000002 +REMOVING: UBERON:6001728 relationship: part_of UBERON:0002548 (line 218840) - duplicates intersection_of: part_of UBERON:0002548 +REMOVING: UBERON:2001844 is_a: UBERON:0000982 (line 200298) - duplicates intersection_of: UBERON:0000982 +REMOVING: UBERON:0000031 relationship: part_of UBERON:0001005 (line 1088) - duplicates intersection_of: part_of UBERON:0001005 +REMOVING: UBERON:6000162 is_a: UBERON:6000011 (line 218516) - duplicates intersection_of: UBERON:6000011 +REMOVING: UBERON:6000162 relationship: part_of UBERON:0008816 (line 218520) - duplicates intersection_of: part_of UBERON:0008816 +REMOVING: UBERON:0001518 relationship: part_of UBERON:0004452 (line 23765) - duplicates intersection_of: part_of UBERON:0004452 +REMOVING: UBERON:6007240 is_a: UBERON:0002536 (line 220113) - duplicates intersection_of: UBERON:0002536 +REMOVING: UBERON:6007240 relationship: part_of UBERON:0002548 (line 220117) - duplicates intersection_of: part_of UBERON:0002548 +REMOVING: UBERON:2001391 is_a: UBERON:2000120 (line 197274) - duplicates intersection_of: UBERON:2000120 +REMOVING: UBERON:2001711 is_a: UBERON:0000982 (line 199192) - duplicates intersection_of: UBERON:0000982 +REMOVING: UBERON:0001167 is_a: UBERON:0000060 (line 14853) - duplicates intersection_of: UBERON:0000060 +REMOVING: UBERON:0001167 relationship: part_of UBERON:0000945 (line 14857) - duplicates intersection_of: part_of UBERON:0000945 +REMOVING: UBERON:2000052 is_a: UBERON:2000089 (line 190200) - duplicates intersection_of: UBERON:2000089 +REMOVING: UBERON:2000052 relationship: part_of UBERON:2000102 (line 190203) - duplicates intersection_of: part_of UBERON:2000102 +REMOVING: UBERON:0001824 relationship: part_of UBERON:0001737 (line 32305) - duplicates intersection_of: part_of UBERON:0001737 +REMOVING: UBERON:0016442 is_a: UBERON:0035127 (line 167420) - duplicates intersection_of: UBERON:0035127 +REMOVING: UBERON:6001737 is_a: UBERON:6000011 (line 218911) - duplicates intersection_of: UBERON:6000011 +REMOVING: UBERON:6001737 relationship: part_of UBERON:6001730 (line 218915) - duplicates intersection_of: part_of UBERON:6001730 +REMOVING: UBERON:0002093 is_a: UBERON:0002363 (line 40800) - duplicates intersection_of: UBERON:0002363 +REMOVING: UBERON:2001876 is_a: UBERON:2001917 (line 200572) - duplicates intersection_of: UBERON:2001917 + +SUMMARY: Removed 375 redundant SubClassOf axioms diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 6330a214c..0d35dd03f 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -1086,7 +1086,6 @@ xref: UMLS:C1710457 {source="ncithesaurus:Trachea_Lamina_Propria"} intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0001005 ! respiratory airway relationship: part_of UBERON:0000379 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! tracheal mucosa -relationship: part_of UBERON:0001005 ! respiratory airway [Term] id: UBERON:0000032 @@ -1159,7 +1158,6 @@ xref: EMAPA:35631 xref: FMA:18634 xref: MA:0002907 xref: SCTID:258665002 -is_a: UBERON:0001305 ! ovarian follicle intersection_of: UBERON:0001305 ! ovarian follicle intersection_of: has_component UBERON:0005170 {cardinality="1"} ! granulosa cell layer relationship: develops_from UBERON:0003981 ! primordial ovarian follicle @@ -1181,7 +1179,6 @@ synonym: "secondary follicle of ovary" EXACT [] xref: EMAPA:35632 xref: FMA:18637 xref: MA:0002908 -is_a: UBERON:0001305 ! ovarian follicle intersection_of: UBERON:0001305 ! ovarian follicle intersection_of: has_component UBERON:0005170 {minCardinality="2"} ! granulosa cell layer intersection_of: has_potential_to_develop_into UBERON:0000037 ! tertiary ovarian follicle @@ -1212,7 +1209,6 @@ xref: MA:0002909 xref: NCIT:C32692 xref: SCTID:362261008 xref: UMLS:C0600225 {source="ncithesaurus:Graafian_Follicle"} -is_a: UBERON:0001305 ! ovarian follicle intersection_of: UBERON:0001305 ! ovarian follicle intersection_of: has_component UBERON:0005170 {minCardinality="2"} ! granulosa cell layer intersection_of: has_part UBERON:0000039 ! follicular antrum @@ -2258,7 +2254,6 @@ xref: XAO:0000155 intersection_of: UBERON:0000990 ! reproductive system intersection_of: part_of UBERON:0003101 ! male organism disjoint_from: UBERON:0000474 ! female reproductive system -relationship: part_of UBERON:0003101 ! male organism property_value: homology_notes "By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000725", ontology="VHOG", source="ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43", source="http://bgee.unil.ch/"} [Term] @@ -4765,10 +4760,8 @@ synonym: "organ mucosa of intestine gland" EXACT [OBOL:automatic] xref: BTO:0000640 xref: FMA:15052 xref: SCTID:266297002 -is_a: UBERON:0002530 ! gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0001242 ! intestinal mucosa -relationship: part_of UBERON:0001242 ! intestinal mucosa property_value: external_ontology_notes "Note that some sources treat 'intestinal gland' as synonymous with crypts" xsd:string [Term] @@ -5429,7 +5422,6 @@ xref: SCTID:302544002 xref: UMLS:C0039866 {source="ncithesaurus:Thigh"} xref: VHOG:0000349 xref: Wikipedia:Thigh -is_a: UBERON:0002472 ! stylopod intersection_of: UBERON:0002472 ! stylopod intersection_of: part_of UBERON:0002103 ! hindlimb relationship: contributes_to_morphology_of UBERON:0002103 ! hindlimb @@ -5848,7 +5840,6 @@ xref: MA:0003195 xref: SCTID:42978003 xref: TAO:0005128 xref: ZFA:0005128 -is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001155 ! colon property_value: external_definition "Intestinal epithelium which lines the lumen of the posterior intestine.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005128", ontology="TAO", source="ZFIN:curator"} @@ -6128,7 +6119,6 @@ intersection_of: UBERON:0002365 ! exocrine gland intersection_of: has_part CL:0000319 ! mucus secreting cell disjoint_from: UBERON:3010602 ! granular gland relationship: capable_of GO:0070254 ! mucus secretion -relationship: has_part CL:0000319 ! mucus secreting cell relationship: produces UBERON:0000912 ! mucus property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png" xsd:anyURI property_value: taxon_notes "In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong]" xsd:string {scope="NCBITaxon:8292", source="ISBN:0073040584"} @@ -6711,7 +6701,6 @@ xref: FMA:17560 xref: SCTID:245485002 intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000995 ! uterus -relationship: part_of UBERON:0000995 ! uterus [Term] id: UBERON:0000460 @@ -7095,7 +7084,6 @@ xref: WBbt:0006794 xref: Wikipedia:Testis xref: XAO:0000157 xref: ZFA:0000598 -is_a: UBERON:0000991 ! gonad intersection_of: UBERON:0000991 ! gonad intersection_of: part_of UBERON:0000079 ! male reproductive system disjoint_from: UBERON:0000992 ! ovary @@ -7147,10 +7135,8 @@ xref: VHOG:0000726 xref: Wikipedia:Female_genitalia xref: WikipediaCategory:Female_reproductive_system xref: XAO:0000156 -is_a: UBERON:0000990 ! reproductive system intersection_of: UBERON:0000990 ! reproductive system intersection_of: part_of UBERON:0003100 ! female organism -relationship: part_of UBERON:0003100 ! female organism property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg" xsd:anyURI property_value: homology_notes "By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000726", ontology="VHOG", source="ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43", source="http://bgee.unil.ch/"} @@ -9738,7 +9724,6 @@ synonym: "wing" BROAD SENSU [FBbt:00004729] synonym: "wing of thorax" RELATED [OBOL:automatic] xref: HAO:0001089 xref: TGMA:0000196 -is_a: UBERON:0000023 ! wing intersection_of: UBERON:0000023 ! wing intersection_of: develops_from UBERON:0000939 ! imaginal disc property_value: editor_note "TODO - review. hymenoptera thorax = fusion of thorax and mesosoma/metasoma" xsd:string @@ -9910,7 +9895,6 @@ xref: WBbt:0005747 xref: Wikipedia:Reproductive_system xref: XAO:0000142 xref: ZFA:0000632 -is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of_part_of GO:0022414 ! reproductive process disjoint_from: UBERON:0001004 ! respiratory system @@ -9967,7 +9951,6 @@ xref: WBbt:0005175 xref: Wikipedia:Gonad xref: XAO:0003146 xref: ZFA:0000413 -is_a: UBERON:0003133 ! reproductive organ intersection_of: UBERON:0003133 ! reproductive organ intersection_of: has_part CL:0000586 ! germ cell relationship: contains_process GO:0007276 ! gamete generation @@ -12523,10 +12506,8 @@ synonym: "ventricular epicardium" EXACT [] xref: FMA:12150 xref: TAO:0005058 xref: ZFA:0005058 -is_a: UBERON:0002348 ! epicardium intersection_of: UBERON:0002348 ! epicardium intersection_of: part_of UBERON:0002082 ! cardiac ventricle -relationship: part_of UBERON:0002082 ! cardiac ventricle property_value: external_definition "The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005058", ontology="TAO", source="ZFIN:curator"} [Term] @@ -12550,7 +12531,6 @@ xref: ZFA:0005061 intersection_of: UBERON:0002349 ! myocardium intersection_of: part_of UBERON:0002082 ! cardiac ventricle relationship: contributes_to_morphology_of UBERON:0002082 ! cardiac ventricle -relationship: part_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0004784 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! heart ventricle wall property_value: external_definition "Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005061", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000604", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481", source="http://bgee.unil.ch/"} @@ -12571,7 +12551,6 @@ xref: MA:0000582 xref: NCIT:C52757 xref: SCTID:181484006 xref: UMLS:C0205029 {source="ncithesaurus:Head_Skin"} -is_a: UBERON:0000014 ! zone of skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0000033 ! head @@ -12592,7 +12571,6 @@ xref: MA:0000517 xref: NCIT:C12295 xref: SCTID:181489001 xref: UMLS:C0205031 {source="ncithesaurus:Skin_of_the_Trunk"} -is_a: UBERON:0000014 ! zone of skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0002100 ! trunk @@ -12898,10 +12876,8 @@ synonym: "wall of oesophagus" EXACT [OBOL:automatic] xref: EMAPA:35326 xref: FMA:12611 xref: MA:0002691 -is_a: UBERON:0000060 ! anatomical wall intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001043 ! esophagus -relationship: part_of UBERON:0001043 ! esophagus [Term] id: UBERON:0001097 @@ -13034,7 +13010,6 @@ xref: MA:0001846 is_a: UBERON:0001956 ! cartilage of bronchus intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0002182 ! main bronchus -relationship: part_of UBERON:0002182 ! main bronchus [Term] id: UBERON:0001103 @@ -14136,7 +14111,6 @@ xref: NCIT:C33462 xref: SCTID:116358006 xref: UMLS:C0035092 {source="ncithesaurus:Renal_Vein"} xref: Wikipedia:Renal_vein -is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: vessel_drains_blood_from UBERON:0002113 ! kidney relationship: tributary_of UBERON:0001072 ! inferior vena cava @@ -14201,7 +14175,6 @@ xref: UMLS:C0019155 {source="ncithesaurus:Hepatic_Vein"} xref: Wikipedia:Hepatic_vein xref: XAO:0000387 xref: ZFA:0000670 -is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: vessel_drains_blood_from UBERON:0002107 ! liver disjoint_from: UBERON:0001639 ! hepatic portal vein @@ -14234,7 +14207,6 @@ xref: NCIT:C53050 xref: SCTID:264496006 xref: UMLS:C0226718 {source="ncithesaurus:Spermatic_Vein"} xref: Wikipedia:Testicular_vein -is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: vessel_drains_blood_from UBERON:0000473 ! testis relationship: connected_to UBERON:0001072 ! inferior vena cava @@ -14887,11 +14859,9 @@ xref: FMA:14582 xref: galen:WallOfStomach xref: MA:0002692 xref: SCTID:279995000 -is_a: UBERON:0000060 ! anatomical wall intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000945 ! stomach relationship: contributes_to_morphology_of UBERON:0000945 ! stomach -relationship: part_of UBERON:0000945 ! stomach [Term] id: UBERON:0001168 @@ -15635,7 +15605,6 @@ xref: MA:0002685 xref: NCIT:C32663 xref: SCTID:52459002 xref: UMLS:C0227211 {source="ncithesaurus:Gastric_Submucosa"} -is_a: UBERON:0000009 ! submucosa intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0000945 ! stomach relationship: contributes_to_morphology_of UBERON:0001167 ! wall of stomach @@ -15694,11 +15663,9 @@ xref: MA:0001626 xref: NCIT:C32662 xref: SCTID:1353004 xref: UMLS:C1517453 {source="ncithesaurus:Gastric_Serosal_Surface"} -is_a: UBERON:0000042 ! serous membrane intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0001167 ! wall of stomach relationship: contributes_to_morphology_of UBERON:0001167 ! wall of stomach -relationship: part_of UBERON:0001167 ! wall of stomach property_value: editor_note "TODO - check serosa/peritoneum" xsd:string [Term] @@ -15803,7 +15770,6 @@ xref: NCIT:C33572 xref: SCTID:691000 xref: UMLS:C0227268 {source="ncithesaurus:Small_Intestinal_Submucosa"} xref: Wikipedia:Small_intestinal_submucosa -is_a: UBERON:0000009 ! submucosa intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0001168 ! wall of small intestine @@ -15874,7 +15840,6 @@ xref: FMA:14970 xref: MA:0002690 xref: NCIT:C32930 xref: UMLS:C0734204 {source="ncithesaurus:Large_Intestinal_Submucosa"} -is_a: UBERON:0000009 ! submucosa intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0001169 ! wall of large intestine @@ -16272,7 +16237,6 @@ xref: NCIT:C12739 xref: SCTID:362211004 xref: UMLS:C0022655 {source="ncithesaurus:Renal_Cortex"} xref: Wikipedia:Renal_cortex -is_a: UBERON:0001851 ! cortex intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0002113 ! kidney relationship: contributes_to_morphology_of UBERON:0002113 ! kidney @@ -16559,7 +16523,6 @@ xref: UMLS:C0001613 {source="ncithesaurus:Adrenal_Cortex"} xref: VHOG:0001481 xref: Wikipedia:Adrenal_cortex xref: XAO:0000165 -is_a: UBERON:0001851 ! cortex intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0002369 ! adrenal gland relationship: capable_of GO:0006704 ! glucocorticoid biosynthetic process @@ -16567,7 +16530,6 @@ relationship: capable_of GO:0006705 ! mineralocorticoid biosynthetic process relationship: capable_of GO:0035932 ! aldosterone secretion relationship: contributes_to_morphology_of UBERON:0002369 ! adrenal gland relationship: develops_from UBERON:0000926 {source="Wikipedia"} ! mesoderm -relationship: part_of UBERON:0002369 ! adrenal gland property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png" xsd:anyURI property_value: homology_notes "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001481", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9", source="http://bgee.unil.ch/"} property_value: taxon_notes "Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO" xsd:string @@ -16605,7 +16567,6 @@ xref: UMLS:C0001629 {source="ncithesaurus:Adrenal_Medulla"} xref: VHOG:0001378 xref: Wikipedia:Adrenal_medulla xref: XAO:0000166 -is_a: UBERON:0000958 ! medulla of organ intersection_of: UBERON:0000958 ! medulla of organ intersection_of: part_of UBERON:0002369 ! adrenal gland relationship: contributes_to_morphology_of UBERON:0002369 ! adrenal gland @@ -16662,7 +16623,6 @@ xref: MA:0001554 xref: NCIT:C49297 xref: SCTID:63588008 xref: UMLS:C1711325 {source="ncithesaurus:Small_Intestinal_Lamina_Propria"} -is_a: UBERON:0000030 ! lamina propria intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0001168 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! wall of small intestine @@ -16723,11 +16683,9 @@ xref: MA:0001552 xref: NCIT:C33565 xref: SCTID:52688008 xref: UMLS:C0227267 {source="ncithesaurus:Small_Intestinal_Crypt_of_Lieberkuhn"} -is_a: UBERON:0001983 ! crypt of Lieberkuhn intersection_of: UBERON:0001983 ! crypt of Lieberkuhn intersection_of: part_of UBERON:0002108 ! small intestine relationship: contributes_to_morphology_of UBERON:0002108 ! small intestine -relationship: part_of UBERON:0002108 ! small intestine [Term] id: UBERON:0001242 @@ -16811,7 +16769,6 @@ synonym: "wall of intestine serous membrane" EXACT [OBOL:automatic] xref: EMAPA:37619 {source="MA:th"} xref: FMA:15701 xref: MA:0001538 -is_a: UBERON:0000042 ! serous membrane intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0001262 ! wall of intestine @@ -17049,7 +17006,6 @@ xref: EMAPA:28841 xref: FMA:15896 xref: MA:0002653 xref: SCTID:2771005 -is_a: UBERON:0000030 ! lamina propria intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0000056 ! ureter relationship: part_of UBERON:0001008 ! renal system @@ -17138,10 +17094,8 @@ xref: MA:0002493 xref: NCIT:C48941 xref: SCTID:362225003 xref: UMLS:C0458421 {source="ncithesaurus:Bladder_Wall"} -is_a: UBERON:0000060 ! anatomical wall intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001255 ! urinary bladder -relationship: part_of UBERON:0001255 ! urinary bladder [Term] id: UBERON:0001257 @@ -17250,7 +17204,6 @@ xref: EMAPA:28661 xref: FMA:15932 xref: MA:0001696 xref: SCTID:5868002 -is_a: UBERON:0000042 ! serous membrane intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001256 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! wall of urinary bladder @@ -17276,7 +17229,6 @@ xref: FMA:15935 xref: MA:0001695 xref: NCIT:C48940 xref: UMLS:C1706967 {source="ncithesaurus:Bladder_Lamina_Propria"} -is_a: UBERON:0000030 ! lamina propria intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001256 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! wall of urinary bladder @@ -17815,7 +17767,6 @@ xref: UMLS:C0227523 {source="ncithesaurus:Hepatic_Sinusoid"} xref: VHOG:0000708 xref: Wikipedia:Hepatic_sinusoid xref: ZFA:0005091 -is_a: UBERON:0003909 ! sinusoid intersection_of: UBERON:0003909 ! sinusoid intersection_of: part_of UBERON:0002107 ! liver relationship: contributes_to_morphology_of UBERON:0004647 ! liver lobule @@ -18562,7 +18513,6 @@ xref: MA:0001706 xref: NCIT:C49265 xref: SCTID:258491008 xref: UMLS:C0227877 {source="ncithesaurus:Ovarian_Capsule"} -is_a: UBERON:0003893 ! capsule intersection_of: UBERON:0003893 ! capsule intersection_of: bounding_layer_of UBERON:0000992 ! ovary @@ -18800,7 +18750,6 @@ xref: EMAPA:37796 {source="MA:th"} xref: FMA:18899 xref: MA:0002251 xref: SCTID:424336009 -is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: part_of UBERON:0000996 ! vagina relationship: tributary_of UBERON:0001317 {source="FMA/obol"} ! internal iliac vein @@ -19389,7 +19338,6 @@ is_a: UBERON:0000486 ! multilaminar epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000996 ! vagina relationship: contributes_to_morphology_of UBERON:0000996 ! vagina -relationship: part_of UBERON:0000996 ! vagina property_value: external_ontology_notes "FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous)" xsd:string {external_ontology="FMA"} [Term] @@ -22222,7 +22170,6 @@ xref: NCIT:C32414 xref: SCTID:182101009 xref: UMLS:C0376381 {source="ncithesaurus:Cuboid_Bone"} xref: Wikipedia:Cuboid_bone -is_a: UBERON:0010721 ! distal tarsal bone intersection_of: UBERON:0010721 ! distal tarsal bone intersection_of: has_fused_element UBERON:0010737 ! distal tarsal bone 4 intersection_of: has_fused_element UBERON:0010738 ! distal tarsal bone 5 @@ -22294,7 +22241,6 @@ xref: MA:0001579 xref: NCIT:C12291 xref: SCTID:244092005 xref: UMLS:C0222101 {source="ncithesaurus:Skin_of_the_Lip"} -is_a: UBERON:0000014 ! zone of skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001833 ! lip @@ -22319,7 +22265,6 @@ xref: MA:0001233 xref: NCIT:C49481 xref: SCTID:244073008 xref: UMLS:C0222110 {source="ncithesaurus:Ear_Skin"} -is_a: UBERON:0000014 ! zone of skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001691 ! external ear relationship: part_of UBERON:0001757 ! pinna @@ -22660,7 +22605,6 @@ xref: FMA:27648 xref: MA:0001744 xref: SCTID:39059001 xref: VHOG:0001342 -is_a: UBERON:0000014 ! zone of skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001332 ! prepuce of penis relationship: contributes_to_morphology_of UBERON:0000989 ! penis @@ -22756,7 +22700,6 @@ xref: VSAO:0000057 xref: Wikipedia:Bone xref: XAO:0000169 xref: ZFA:0001514 -is_a: UBERON:0004765 ! skeletal element intersection_of: UBERON:0004765 ! skeletal element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue disjoint_from: UBERON:0001630 ! muscle organ @@ -23074,7 +23017,6 @@ is_a: UBERON:0002217 ! synovial joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: part_of UBERON:0002387 ! pes relationship: fma_set_term FMA:71349 -relationship: part_of UBERON:0002387 ! pes property_value: editor_note "TODO check FMA - use the set class for now" xsd:string [Term] @@ -23131,7 +23073,6 @@ is_a: UBERON:0002217 ! synovial joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: part_of UBERON:0002398 ! manus relationship: fma_set_term FMA:71345 -relationship: part_of UBERON:0002398 ! manus property_value: editor_note "TODO check FMA - use the set class for now" xsd:string [Term] @@ -23361,7 +23302,6 @@ xref: MA:0000652 xref: SCTID:67240005 intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0002387 ! pes -relationship: part_of UBERON:0002387 ! pes relationship: part_of UBERON:0004488 {source="prolog"} ! musculature of pes [Term] @@ -23400,7 +23340,6 @@ xref: MA:0000628 xref: SCTID:110540008 intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0002398 ! manus -relationship: part_of UBERON:0002398 ! manus relationship: part_of UBERON:0004489 {source="prolog"} ! musculature of manus [Term] @@ -23639,7 +23578,6 @@ xref: UMLS:C0222275 {source="ncithesaurus:Knee_Skin"} is_a: UBERON:0001419 ! skin of limb intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001465 ! knee -relationship: part_of UBERON:0001465 ! knee [Term] id: UBERON:0001511 @@ -23674,7 +23612,6 @@ xref: UMLS:C0222286 {source="ncithesaurus:Ankle_Skin"} is_a: UBERON:0001419 ! skin of limb intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0004454 ! tarsal region -relationship: part_of UBERON:0004454 ! tarsal region [Term] id: UBERON:0001513 @@ -23693,7 +23630,6 @@ xref: UMLS:C0222289 {source="ncithesaurus:Foot_Skin"} is_a: UBERON:0003532 {source="MA"} ! hindlimb skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0002387 ! pes -relationship: part_of UBERON:0002387 ! pes [Term] id: UBERON:0001514 @@ -23801,7 +23737,6 @@ is_a: UBERON:0002427 ! arm skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001461 ! elbow relationship: part_of UBERON:0001460 ! arm -relationship: part_of UBERON:0001461 ! elbow [Term] id: UBERON:0001518 @@ -23821,7 +23756,6 @@ xref: UMLS:C0222223 {source="ncithesaurus:Wrist_Skin"} is_a: UBERON:0001419 ! skin of limb intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0004452 ! carpal region -relationship: part_of UBERON:0004452 ! carpal region [Term] id: UBERON:0001519 @@ -24589,7 +24523,6 @@ xref: MA:0000658 xref: SCTID:181518004 intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001464 ! hip -relationship: part_of UBERON:0001464 ! hip property_value: external_ontology_notes "in MA this isa hindlimb skin" xsd:string {external_ontology="MA"} [Term] @@ -24911,7 +24844,6 @@ intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0001737 ! larynx relationship: contributes_to_morphology_of UBERON:0001015 ! musculature relationship: contributes_to_morphology_of UBERON:0001737 ! larynx -relationship: part_of UBERON:0001737 ! larynx relationship: part_of UBERON:0004478 {source="prolog"} ! musculature of larynx [Term] @@ -27609,7 +27541,6 @@ xref: NCIT:C53032 xref: SCTID:40693009 xref: UMLS:C0226601 {source="ncithesaurus:Cerebellar_Vein"} xref: Wikipedia:Cerebellar_veins -is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: vessel_drains_blood_from UBERON:0002037 ! cerebellum @@ -30061,7 +29992,6 @@ intersection_of: UBERON:0000353 ! parenchyma intersection_of: part_of UBERON:0002046 ! thyroid gland relationship: has_part CL:0000570 {source="FMA"} ! parafollicular cell relationship: has_part CL:0002258 {source="FMA"} ! thyroid follicular cell -relationship: part_of UBERON:0002046 ! thyroid gland [Term] id: UBERON:0001748 @@ -30093,7 +30023,6 @@ intersection_of: UBERON:0000353 ! parenchyma intersection_of: part_of UBERON:0001132 ! parathyroid gland relationship: has_part CL:0000446 {source="FMA"} ! chief cell of parathyroid gland relationship: has_part CL:0002199 {source="FMA"} ! oxyphil cell of parathyroid gland -relationship: part_of UBERON:0001132 ! parathyroid gland [Term] id: UBERON:0001750 @@ -31821,7 +31750,6 @@ is_a: UBERON:0000484 ! simple cuboidal epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000965 ! lens of camera-type eye relationship: contributes_to_morphology_of UBERON:0000965 ! lens of camera-type eye -relationship: part_of UBERON:0000965 ! lens of camera-type eye property_value: curator_notes "this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former" xsd:string [Term] @@ -31875,7 +31803,6 @@ xref: MESH:D005725 xref: NCIT:C12720 xref: UMLS:C0017068 {source="ncithesaurus:Autonomic_Ganglion"} xref: Wikipedia:Autonomic_ganglion -is_a: UBERON:0000045 ! ganglion intersection_of: UBERON:0000045 ! ganglion intersection_of: part_of UBERON:0002410 ! autonomic nervous system relationship: extends_fibers_into UBERON:0034728 ! autonomic nerve @@ -32375,7 +32302,6 @@ xref: SCTID:361940006 xref: UMLS:C0023053 {source="ncithesaurus:Laryngeal_Mucosa"} intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001737 ! larynx -relationship: part_of UBERON:0001737 ! larynx [Term] id: UBERON:0001825 @@ -33522,7 +33448,6 @@ xref: SCTID:181496004 is_a: UBERON:0001418 ! skin of thorax intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001443 ! chest -relationship: part_of UBERON:0001443 ! chest property_value: editor_note "check FMA:61415" xsd:string [Term] @@ -35419,10 +35344,8 @@ xref: FMA:62114 xref: MA:0000711 xref: NCIT:C49215 xref: UMLS:C0006904 {source="ncithesaurus:Capillary_Endothelium"} -is_a: UBERON:0001986 ! endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001982 ! capillary -relationship: part_of UBERON:0001982 ! capillary [Term] id: UBERON:0001916 @@ -35434,10 +35357,8 @@ xref: FMA:62115 xref: MA:0000705 xref: NCIT:C49192 xref: UMLS:C1179024 {source="ncithesaurus:Arteriole_Endothelium"} -is_a: UBERON:0001986 ! endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001980 ! arteriole -relationship: part_of UBERON:0001980 ! arteriole [Term] id: UBERON:0001917 @@ -35470,10 +35391,8 @@ xref: FMA:62117 xref: MA:0000716 xref: NCIT:C49319 xref: UMLS:C1179026 {source="ncithesaurus:Venule_Endothelium"} -is_a: UBERON:0001986 ! endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001979 ! venule -relationship: part_of UBERON:0001979 ! venule [Term] id: UBERON:0001919 @@ -35491,7 +35410,6 @@ xref: NCIT:C49317 xref: UMLS:C1179027 {source="ncithesaurus:Vein_Endothelium"} xref: VHOG:0001216 xref: XAO:0000358 -is_a: UBERON:0001986 ! endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001638 ! vein property_value: homology_notes "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001216", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207", source="http://bgee.unil.ch/"} @@ -36856,7 +36774,6 @@ is_a: UBERON:0002051 ! epithelium of bronchiole intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002188 ! respiratory bronchiole relationship: has_part CL:0000158 {source="FMA"} ! club cell -relationship: part_of UBERON:0002188 ! respiratory bronchiole [Term] id: UBERON:0001956 @@ -36903,10 +36820,8 @@ xref: MA:0001837 xref: NCIT:C49214 xref: SCTID:85546005 xref: UMLS:C0225601 {source="ncithesaurus:Bronchus_Submucosa"} -is_a: UBERON:0000009 ! submucosa intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0002185 ! bronchus -relationship: part_of UBERON:0002185 ! bronchus [Term] id: UBERON:0001958 @@ -37294,7 +37209,6 @@ xref: EMAPA:35325 xref: FMA:62997 xref: MA:0002724 xref: SCTID:362128009 -is_a: UBERON:0000009 ! submucosa intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001096 ! wall of esophagus @@ -37326,7 +37240,6 @@ xref: FMA:63050 xref: MA:0001568 xref: NCIT:C49223 xref: UMLS:C1707949 {source="ncithesaurus:Esophageal_Lamina_Propria"} -is_a: UBERON:0000030 ! lamina propria intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0002469 {source="FMA"} ! esophagus mucosa @@ -37352,7 +37265,6 @@ synonym: "tunica serosa oesophageae" EXACT OMO:0003011 [FMA:63057, FMA:TA] xref: EMAPA:35322 xref: FMA:63057 xref: MA:0001571 -is_a: UBERON:0000042 ! serous membrane intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001096 ! wall of esophagus @@ -37631,7 +37543,6 @@ xref: FMA:63622 xref: MA:0001544 xref: NCIT:C32924 xref: UMLS:C1179777 {source="ncithesaurus:Large_Intestinal_Crypt_of_the_Lieberkuhn"} -is_a: UBERON:0001983 ! crypt of Lieberkuhn intersection_of: UBERON:0001983 ! crypt of Lieberkuhn intersection_of: part_of UBERON:0000059 ! large intestine relationship: contributes_to_morphology_of UBERON:0000059 ! large intestine @@ -37659,7 +37570,6 @@ xref: TAO:0002186 xref: UMLS:C0014259 {source="ncithesaurus:Corneal_Endothelium"} xref: Wikipedia:Corneal_endothelium xref: ZFA:0001687 -is_a: UBERON:0001986 ! endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0000964 ! cornea relationship: adjacent_to UBERON:0001766 ! anterior chamber of eyeball @@ -38139,7 +38049,6 @@ xref: MA:0001508 xref: NCIT:C49575 xref: SCTID:263314001 xref: UMLS:C1261194 {source="ncithesaurus:Joint_of_the_Rib"} -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0002228 ! rib relationship: part_of UBERON:0014478 {source="cjm"} ! rib skeletal system @@ -38240,7 +38149,6 @@ xref: MA:0000740 xref: NCIT:C33029 xref: UMLS:C0933402 {source="ncithesaurus:Lymph_Node_Cortex"} xref: Wikipedia:Cortex_of_lymph_node -is_a: UBERON:0001851 ! cortex intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0000029 ! lymph node relationship: adjacent_to UBERON:0002194 ! capsule of lymph node @@ -38977,7 +38885,6 @@ is_a: UBERON:0000485 ! simple columnar epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002110 ! gallbladder relationship: contributes_to_morphology_of UBERON:0002110 ! gallbladder -relationship: part_of UBERON:0002110 ! gallbladder [Term] id: UBERON:0002030 @@ -39046,7 +38953,6 @@ intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002185 ! bronchus relationship: contributes_to_morphology_of UBERON:0002185 ! bronchus relationship: has_part CL:0002209 {source="FMA"} ! intermediate epitheliocyte -relationship: part_of UBERON:0002185 ! bronchus [Term] id: UBERON:0002032 @@ -39384,12 +39290,10 @@ xref: NCIT:C49258 xref: TAO:0005258 xref: UMLS:C1180786 {source="ncithesaurus:Lymphatic_Vessel_Endothelium"} xref: ZFA:0005258 -is_a: UBERON:0001986 ! endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001473 ! lymphatic vessel relationship: contributes_to_morphology_of UBERON:0001473 ! lymphatic vessel relationship: has_part CL:0002138 {source="FMA"} ! endothelial cell of lymphatic vessel -relationship: part_of UBERON:0001473 ! lymphatic vessel property_value: external_definition "The vascular endothelium that lines the lymph vessels.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005258", ontology="TAO", source="ZFIN:curator"} [Term] @@ -40412,7 +40316,6 @@ xref: EMAPA:35387 xref: FMA:70934 xref: MA:0000156 xref: SCTID:318832008 -is_a: UBERON:0001851 ! cortex intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0001037 ! strand of hair relationship: part_of UBERON:0002074 ! hair shaft @@ -40851,7 +40754,6 @@ xref: NCIT:C49332 xref: SCTID:309321003 xref: UMLS:C0459393 {source="ncithesaurus:Cerebral_Dura_Mater"} xref: VHOG:0000270 -is_a: UBERON:0002363 ! dura mater intersection_of: UBERON:0002363 ! dura mater intersection_of: part_of UBERON:0000955 ! brain property_value: external_definition "The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000270", ontology="VHOG", source="http://bgee.unil.ch/"} @@ -40874,7 +40776,6 @@ xref: NCIT:C49799 xref: SCTID:362302001 xref: UMLS:C0228124 {source="ncithesaurus:Spinal_Cord_Dura_Mater"} xref: VHOG:0000411 -is_a: UBERON:0002363 ! dura mater intersection_of: UBERON:0002363 ! dura mater intersection_of: part_of UBERON:0002240 ! spinal cord property_value: external_definition "The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000411", ontology="VHOG", source="http://bgee.unil.ch/"} @@ -41020,12 +40921,10 @@ xref: MESH:D006346 xref: NCIT:C49485 xref: SCTID:362014000 xref: UMLS:C0018819 {source="ncithesaurus:Heart_Septum"} -is_a: UBERON:0003037 ! septum intersection_of: UBERON:0003037 ! septum intersection_of: part_of UBERON:0000948 ! heart relationship: adjacent_to UBERON:0004151 ! cardiac chamber relationship: contributes_to_morphology_of UBERON:0000948 ! heart -relationship: part_of UBERON:0000948 ! heart property_value: external_ontology_notes "in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this" xsd:string {external_ontology="GO"} property_value: taxon_notes "'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations'" xsd:string @@ -41557,7 +41456,6 @@ synonym: "smooth muscle tissue of oesophagus" EXACT [OBOL:automatic] xref: EMAPA:35323 xref: FMA:72025 xref: MA:0001573 -is_a: UBERON:0001135 ! smooth muscle tissue intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001043 ! esophagus relationship: contributes_to_morphology_of UBERON:0001043 ! esophagus @@ -41802,7 +41700,6 @@ xref: MA:0000766 xref: NCIT:C33770 xref: SCTID:188181003 xref: UMLS:C0229945 {source="ncithesaurus:Thymic_Capsule"} -is_a: UBERON:0003893 ! capsule intersection_of: UBERON:0003893 ! capsule intersection_of: bounding_layer_of UBERON:0002370 ! thymus @@ -41847,10 +41744,8 @@ xref: NCIT:C33775 xref: SCTID:188344009 xref: UMLS:C0229949 {source="ncithesaurus:Thymus_Medulla"} xref: Wikipedia:Thymus#Medulla -is_a: UBERON:0000958 ! medulla of organ intersection_of: UBERON:0000958 ! medulla of organ intersection_of: part_of UBERON:0002370 ! thymus -relationship: part_of UBERON:0002370 ! thymus relationship: present_in_taxon NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} ! Danio rerio [Term] @@ -43309,11 +43204,9 @@ xref: SCTID:192001005 xref: TAO:0002169 xref: VHOG:0000606 xref: ZFA:0001614 -is_a: UBERON:0002165 ! endocardium intersection_of: UBERON:0002165 ! endocardium intersection_of: part_of UBERON:0002081 ! cardiac atrium relationship: contributes_to_morphology_of UBERON:0002081 ! cardiac atrium -relationship: part_of UBERON:0002081 ! cardiac atrium [Term] id: UBERON:0002167 @@ -44018,7 +43911,6 @@ xref: NCIT:C33028 xref: SCTID:327532004 xref: UMLS:C0229699 {source="ncithesaurus:Lymph_Node_Capsule"} xref: Wikipedia:Lymph_node_capsule -is_a: UBERON:0003893 ! capsule intersection_of: UBERON:0003893 ! capsule intersection_of: bounding_layer_of UBERON:0000029 ! lymph node relationship: composed_primarily_of UBERON:0002384 ! connective tissue @@ -44278,7 +44170,6 @@ xref: FMA:74710 xref: TAO:0001267 xref: XAO:0004152 xref: ZFA:0001267 -is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000033 ! head @@ -44297,7 +44188,6 @@ synonym: "vasculature of torso" EXACT [OBOL:automatic] xref: FMA:74712 xref: TAO:0005024 xref: ZFA:0005024 -is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0002100 ! trunk @@ -44318,7 +44208,6 @@ xref: MA:0001860 xref: NCIT:C49307 xref: SCTID:4419000 xref: UMLS:C0225586 {source="ncithesaurus:Trachea_Submucosa"} -is_a: UBERON:0000009 ! submucosa intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0003126 ! trachea @@ -44598,7 +44487,6 @@ xref: ZFA:0007000 intersection_of: UBERON:0000054 ! macula intersection_of: part_of UBERON:0001854 ! saccule of membranous labyrinth relationship: contributes_to_morphology_of UBERON:0001854 ! saccule of membranous labyrinth -relationship: part_of UBERON:0001854 ! saccule of membranous labyrinth [Term] id: UBERON:0002213 @@ -46622,10 +46510,8 @@ xref: TAO:0001444 xref: UMLS:C0152291 {source="ncithesaurus:Choroid_Plexus_of_the_Third_Ventricle"} xref: VHOG:0001374 xref: ZFA:0001444 -is_a: UBERON:0001886 ! choroid plexus intersection_of: UBERON:0001886 ! choroid plexus intersection_of: part_of UBERON:0002286 ! third ventricle -relationship: part_of UBERON:0002286 ! third ventricle [Term] id: UBERON:0002289 @@ -46715,7 +46601,6 @@ xref: TAO:0001446 xref: UMLS:C0152293 {source="ncithesaurus:Choroid_Plexus_of_the_Fourth_Ventricle"} xref: VHOG:0001375 xref: ZFA:0001446 -is_a: UBERON:0001886 ! choroid plexus intersection_of: UBERON:0001886 ! choroid plexus intersection_of: part_of UBERON:0002422 ! fourth ventricle relationship: part_of UBERON:0002037 ! cerebellum @@ -47035,7 +46920,6 @@ xref: SCTID:191910002 xref: TAO:0001374 xref: VHOG:0000602 xref: ZFA:0001374 -is_a: UBERON:0002349 ! myocardium intersection_of: UBERON:0002349 ! myocardium intersection_of: part_of UBERON:0002081 ! cardiac atrium relationship: contributes_to_morphology_of UBERON:0002081 ! cardiac atrium @@ -47143,10 +47027,8 @@ xref: TAO:0001447 xref: UMLS:C0152289 {source="ncithesaurus:Choroid_Plexus_of_the_Lateral_Ventricle"} xref: VHOG:0001376 xref: ZFA:0001447 -is_a: UBERON:0001886 ! choroid plexus intersection_of: UBERON:0001886 ! choroid plexus intersection_of: part_of UBERON:0002285 ! telencephalic ventricle -relationship: part_of UBERON:0002285 ! telencephalic ventricle [Term] id: UBERON:0002308 @@ -47546,7 +47428,6 @@ xref: MA:0000496 is_a: UBERON:0001774 ! skeletal muscle of trunk intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0001137 ! dorsum -relationship: part_of UBERON:0001137 ! dorsum relationship: part_of UBERON:0004469 {source="prolog"} ! musculature of back [Term] @@ -47582,7 +47463,6 @@ synonym: "urethral lamina propria" RELATED [] xref: EMAPA:37785 {source="MA:th"} xref: FMA:85276 xref: MA:0001689 -is_a: UBERON:0000030 ! lamina propria intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0000057 ! urethra relationship: part_of UBERON:0001008 ! renal system @@ -47923,11 +47803,9 @@ xref: FMA:86619 xref: MA:0001836 xref: NCIT:C49212 xref: UMLS:C1707054 {source="ncithesaurus:Bronchus_Lamina_Propria"} -is_a: UBERON:0000030 ! lamina propria intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0002185 ! bronchus relationship: part_of UBERON:0000410 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! bronchial mucosa -relationship: part_of UBERON:0002185 ! bronchus [Term] id: UBERON:0002339 @@ -47981,7 +47859,6 @@ xref: VHOG:0001034 is_a: UBERON:0002031 ! epithelium of bronchus intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002182 ! main bronchus -relationship: part_of UBERON:0002182 ! main bronchus [Term] id: UBERON:0002341 @@ -48009,7 +47886,6 @@ relationship: has_part CL:0002332 ! multiciliated epithelial cell of the bronchu relationship: has_part CL:0017000 ! pulmonary ionocyte relationship: has_part CL:1000143 ! lung goblet cell relationship: has_part CL:1000223 ! pulmonary neuroendocrine cell -relationship: part_of UBERON:0002184 ! segmental bronchus [Term] id: UBERON:0002342 @@ -48072,7 +47948,6 @@ xref: FMA:71294 xref: FMA:86917 xref: TAO:0001327 xref: ZFA:0001327 -is_a: UBERON:0001015 ! musculature intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0000916 ! abdomen property_value: curator_notes "distinction between abdomen muscle and abdomen musculature" xsd:string @@ -49418,7 +49293,6 @@ xref: NCIT:C12435 xref: SCTID:91727004 xref: UMLS:C2328219 {source="ncithesaurus:Muscle_Tissue"} xref: Wikipedia:Muscle_tissue -is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: composed_primarily_of CL:0000187 ! muscle cell disjoint_from: UBERON:0003714 ! neural tissue @@ -49752,7 +49626,6 @@ xref: VHOG:0000212 xref: Wikipedia:Bile_duct xref: XAO:0000134 xref: ZFA:0001100 -is_a: UBERON:0000058 ! duct intersection_of: UBERON:0000058 ! duct intersection_of: part_of UBERON:0001173 ! biliary tree relationship: channel_for UBERON:0001970 ! bile @@ -51283,7 +51156,6 @@ xref: FMA:76550 xref: MA:0001237 intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0001776 ! optic choroid -relationship: part_of UBERON:0001776 ! optic choroid [Term] id: UBERON:0002444 @@ -51341,7 +51213,6 @@ xref: NCIT:C12858 xref: SCTID:181965000 xref: UMLS:C0223739 {source="ncithesaurus:Triangular_Bone"} xref: Wikipedia:Triquetral -is_a: UBERON:0001480 ! proximal carpal bone intersection_of: UBERON:0001480 ! proximal carpal bone intersection_of: proximally_connected_to UBERON:0001424 ! ulna relationship: connected_to UBERON:0001424 {gci_relation="part_of", gci_filler="NCBITaxon:8292", notes="Amphibia", source="AAO", source="Wikipedia"} ! ulna @@ -51977,7 +51848,6 @@ relationship: dc-contributor https://orcid.org/0000-0001-7972-3866 ! T Alexander relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 ! Melissa Haendel relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall relationship: distal_to UBERON:0002472 ! stylopod -relationship: has_skeleton UBERON:0011584 ! zeugopodial skeleton relationship: proximal_to UBERON:0002470 ! autopod region property_value: has_relational_adjective "zeugopodial" xsd:string @@ -52000,7 +51870,6 @@ xref: MAT:0000093 xref: MIAA:0000093 intersection_of: UBERON:0002529 ! limb segment intersection_of: has_skeleton UBERON:0011583 ! stylopodial skeleton -relationship: has_skeleton UBERON:0011583 ! stylopodial skeleton relationship: mutually_spatially_disjoint_with UBERON:0002470 ! autopod region relationship: mutually_spatially_disjoint_with UBERON:0002471 ! zeugopod relationship: part_of UBERON:0002101 ! limb @@ -52500,7 +52369,6 @@ xref: FMA:52928 xref: MA:0002795 xref: SCTID:244510008 xref: Wikipedia:Coronal_suture -is_a: UBERON:0003685 ! cranial suture intersection_of: UBERON:0003685 ! cranial suture intersection_of: connects UBERON:0000209 ! tetrapod frontal bone intersection_of: connects UBERON:0000210 ! tetrapod parietal bone @@ -52525,7 +52393,6 @@ xref: FMA:52989 xref: MA:0002796 xref: SCTID:136854008 xref: Wikipedia:Frontal_suture -is_a: UBERON:0003685 ! cranial suture intersection_of: UBERON:0003685 ! cranial suture intersection_of: connects UBERON:0000209 {cardinality="2"} ! tetrapod frontal bone relationship: connects UBERON:0000209 {notes="two halves of the frontal bone"} ! tetrapod frontal bone @@ -52568,7 +52435,6 @@ xref: FMA:52929 xref: MA:0002798 xref: SCTID:244511007 xref: Wikipedia:Sagittal_suture -is_a: UBERON:0003685 ! cranial suture intersection_of: UBERON:0003685 ! cranial suture intersection_of: connects UBERON:0000210 {cardinality="2"} ! tetrapod parietal bone relationship: connects UBERON:0000210 {notes="both parietals"} ! tetrapod parietal bone @@ -52898,7 +52764,6 @@ xref: EMAPA:35992 xref: FMA:12787 xref: MA:0002827 xref: SCTID:245342005 -is_a: UBERON:0000029 ! lymph node intersection_of: UBERON:0000029 ! lymph node intersection_of: part_of UBERON:0000916 ! abdomen @@ -56494,7 +56359,6 @@ xref: BIRNLEX:1302 xref: FMA:72454 xref: neuronames:526 {source="BIRNLEX:1302"} xref: UMLS:C0262284 {source="BIRNLEX:1302"} -is_a: UBERON:0002309 ! medial longitudinal fasciculus intersection_of: UBERON:0002309 ! medial longitudinal fasciculus intersection_of: part_of UBERON:0001891 ! midbrain relationship: part_of UBERON:0001943 ! midbrain tegmentum @@ -57948,7 +57812,6 @@ xref: NCIT:C32321 xref: neuronames:51 {source="BIRNLEX:1475"} xref: UMLS:C0228258 {source="BIRNLEX:1475"} xref: Wikipedia:Circular_sulcus_of_insula -is_a: UBERON:0002912 ! marginal sulcus intersection_of: UBERON:0002912 ! marginal sulcus intersection_of: part_of UBERON:0002022 ! insula @@ -58856,10 +58719,8 @@ xref: BIRNLEX:1574 xref: FMA:72618 xref: neuronames:784 {source="BIRNLEX:1574"} xref: UMLS:C0228536 {source="BIRNLEX:1574"} -is_a: UBERON:0002309 ! medial longitudinal fasciculus intersection_of: UBERON:0002309 ! medial longitudinal fasciculus intersection_of: part_of UBERON:0001896 ! medulla oblongata -relationship: part_of UBERON:0001896 ! medulla oblongata [Term] id: UBERON:0002751 @@ -64916,10 +64777,8 @@ xref: MBA:633 xref: neuronames:481 {source="BIRNLEX:935"} xref: SCTID:369260005 xref: UMLS:C0152367 {source="BIRNLEX:935"} -is_a: UBERON:0001020 ! nervous system commissure intersection_of: UBERON:0001020 ! nervous system commissure intersection_of: part_of UBERON:0001946 ! inferior colliculus -relationship: part_of UBERON:0001946 ! inferior colliculus [Term] id: UBERON:0003029 @@ -67625,7 +67484,6 @@ xref: SCTID:128181006 xref: TGMA:0000591 xref: UMLS:C0017420 {source="ncithesaurus:Genitalia"} xref: WBbt:0008422 -is_a: UBERON:0000062 ! organ intersection_of: UBERON:0000062 ! organ intersection_of: capable_of_part_of GO:0022414 ! reproductive process relationship: part_of UBERON:0000990 ! reproductive system @@ -67650,7 +67508,6 @@ synonym: "reproductive system organ of female organism" EXACT [OBOL:automatic] synonym: "sex organ of female organism" EXACT [OBOL:automatic] xref: EMAPA:28540 xref: MA:0000544 -is_a: UBERON:0003133 ! reproductive organ intersection_of: UBERON:0003133 ! reproductive organ intersection_of: part_of UBERON:0003100 ! female organism relationship: part_of UBERON:0000474 ! female reproductive system @@ -67675,7 +67532,6 @@ synonym: "reproductive system organ of male organism" EXACT [OBOL:automatic] synonym: "sex organ of male organism" EXACT [OBOL:automatic] xref: MA:0000545 xref: WBbt:0008423 -is_a: UBERON:0003133 ! reproductive organ intersection_of: UBERON:0003133 ! reproductive organ intersection_of: part_of UBERON:0003101 ! male organism relationship: part_of UBERON:0000079 ! male reproductive system @@ -68379,7 +68235,6 @@ synonym: "mammary alveolus" EXACT [] xref: EMAPA:36566 xref: FMA:73285 xref: MA:0002760 -is_a: UBERON:0003215 ! alveolus intersection_of: UBERON:0003215 ! alveolus intersection_of: part_of UBERON:0001911 ! mammary gland relationship: contributes_to_morphology_of UBERON:0001912 ! lobule of mammary gland @@ -69161,7 +69016,6 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0000305 ! amnion relationship: develops_from UBERON:0005728 {source="EHDAA2"} ! extraembryonic mesoderm -relationship: part_of UBERON:0000305 ! amnion property_value: editor_note "we make the germ layer relationship develops_from, as currently the germ layers are declared to be purely embryonic. TODO - check. WP:Amnion - In the human embryo the earliest stages of the formation of the amnion have not been observed; in the youngest embryo which has been studied the amnion was already present as a closed sac, and appears in the inner cell-mass as a cavity. This cavity is roofed in by a single stratum of flattened, ectodermal cells, the amniotic ectoderm, and its floor consists of the prismatic ectoderm of the embryonic disk-the continuity between the roof and floor being established at the margin of the embryonic disk. Outside the amniotic ectoderm is a thin layer of mesoderm, which is continuous with that of the somatopleure and is connected by the body-stalk with the mesodermal lining of the chorion." xsd:string [Term] @@ -78895,14 +78749,12 @@ synonym: "sinusoidal blood vessel of spleen" EXACT [OBOL:automatic] xref: FMA:63199 xref: SCTID:9081000 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: 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 @@ -79585,7 +79437,6 @@ xref: FMA:85301 intersection_of: UBERON:0003675 ! tooth crown intersection_of: part_of UBERON:0003655 ! molar tooth relationship: contributes_to_morphology_of UBERON:0003655 ! molar tooth -relationship: part_of UBERON:0003655 ! molar tooth [Term] id: UBERON:0003956 @@ -79822,7 +79673,6 @@ subset: pheno_slim synonym: "placental labyrinth vascular network" EXACT [] synonym: "placental vasculature" RELATED [OBOL:automatic] synonym: "vasculature of placenta labyrinth" EXACT [] -is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0003946 ! placenta labyrinth @@ -82111,7 +81961,6 @@ synonym: "middle ear cavity blood vessel" EXACT [OBOL:automatic] synonym: "tympanic cavity blood vessel" EXACT [] xref: EMAPA:37775 {source="MA:th"} xref: MA:0001219 -is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: located_in UBERON:0004114 ! tympanic cavity relationship: part_of UBERON:0001756 ! middle ear @@ -82132,7 +81981,6 @@ synonym: "tympanic cavity nerve" EXACT [] synonym: "tympanic cavity nerves" EXACT [MA:0001222] xref: EMAPA:37777 {source="MA:th"} xref: MA:0001222 -is_a: UBERON:0001021 ! nerve intersection_of: UBERON:0001021 ! nerve intersection_of: located_in UBERON:0004114 ! tympanic cavity relationship: part_of UBERON:0001756 ! middle ear @@ -82186,7 +82034,6 @@ synonym: "iris vascular network" EXACT [OBOL:automatic] synonym: "iris vasculature" EXACT [] synonym: "vascular network of iris" EXACT [OBOL:automatic] xref: ZFA:0005568 -is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0001769 ! iris @@ -82248,7 +82095,6 @@ xref: SCTID:278861008 xref: UMLS:C0042066 {source="ncithesaurus:Genitourinary_System"} xref: VHOG:0000286 xref: XAO:0000140 -is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000990 ! reproductive system intersection_of: has_part UBERON:0001008 ! renal system @@ -84903,7 +84749,6 @@ xref: EMAPA:37582 {source="MA:th"} xref: MA:0001826 intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0003456 ! respiratory system lymphatic vessel -relationship: part_of UBERON:0003456 ! respiratory system lymphatic vessel [Term] id: UBERON:0004297 @@ -92226,7 +92071,6 @@ xref: EMAPA:37592 {source="MA:th"} xref: MA:0001522 intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0005409 ! alimentary part of gastrointestinal system -relationship: part_of UBERON:0005409 ! alimentary part of gastrointestinal system [Term] id: UBERON:0004783 @@ -97574,7 +97418,6 @@ xref: EMAPA:37062 {source="MA:th"} xref: MA:0000529 intersection_of: UBERON:0000062 ! organ intersection_of: part_of UBERON:0002417 ! abdominal segment of trunk -relationship: part_of UBERON:0002417 ! abdominal segment of trunk [Term] id: UBERON:0005174 @@ -97684,7 +97527,6 @@ xref: EMAPA:37271 {source="MA:th"} xref: MA:0000563 intersection_of: UBERON:0000062 ! organ intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk -relationship: part_of UBERON:0000915 ! thoracic segment of trunk [Term] id: UBERON:0005184 @@ -98797,7 +98639,6 @@ synonym: "tela choroidea of cerebral aqueduct" EXACT [https://orcid.org/0000-000 synonym: "tela choroidea tectal ventricle" EXACT [ZFA:0005157] xref: TAO:0005157 xref: ZFA:0005157 -is_a: UBERON:0005283 ! tela choroidea intersection_of: UBERON:0005283 ! tela choroidea intersection_of: part_of UBERON:0002289 ! midbrain cerebral aqueduct property_value: external_definition "Tela chorioidea that lines the tectal ventricle.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005157", ontology="TAO", source="ZFIN:curator"} @@ -98822,10 +98663,8 @@ xref: SCTID:362321009 xref: TAO:0005158 xref: Wikipedia:Tela_chorioidea_of_fourth_ventricle xref: ZFA:0005158 -is_a: UBERON:0005283 ! tela choroidea intersection_of: UBERON:0005283 ! tela choroidea intersection_of: part_of UBERON:0002422 ! fourth ventricle -relationship: part_of UBERON:0002422 ! fourth ventricle property_value: external_definition "Tela chorioidea that lines the fourth ventricle.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005158", ontology="TAO", source="ZFIN:curator"} [Term] @@ -98846,10 +98685,8 @@ xref: SCTID:362320005 xref: TAO:0005159 xref: Wikipedia:Tela_chorioidea_of_third_ventricle xref: ZFA:0005159 -is_a: UBERON:0005283 ! tela choroidea intersection_of: UBERON:0005283 ! tela choroidea intersection_of: part_of UBERON:0002286 ! third ventricle -relationship: part_of UBERON:0002286 ! third ventricle property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/60/Gray723.png" xsd:anyURI property_value: external_definition "Tela chorioidea that lines the third ventricle.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005159", ontology="TAO", source="ZFIN:curator"} @@ -98870,7 +98707,6 @@ xref: neuronames:219 xref: SCTID:362319004 xref: TAO:0005160 xref: ZFA:0005160 -is_a: UBERON:0005283 ! tela choroidea intersection_of: UBERON:0005283 ! tela choroidea intersection_of: part_of UBERON:0002285 ! telencephalic ventricle @@ -102053,7 +101889,6 @@ xref: Wikipedia:Jugular_foramen intersection_of: UBERON:0013685 ! foramen of skull intersection_of: conduit_for UBERON:0001586 ! internal jugular vein intersection_of: part_of UBERON:0001678 ! temporal bone -relationship: conduit_for UBERON:0001586 ! internal jugular vein relationship: conduit_for UBERON:0001649 ! glossopharyngeal nerve relationship: conduit_for UBERON:0001759 ! vagus nerve relationship: conduit_for UBERON:0002019 ! accessory XI nerve @@ -107839,7 +107674,6 @@ id: UBERON:0006016 name: interdigital region between digits 1 and 2 def: "An interdigital region that adjacent_to a digit 1 and adjacent_to a digit 2." [OBOL:automatic] synonym: "interdigital region between digits I and II" EXACT COMPARATIVE_PREFERRED [https://github.com/obophenotype/uberon/issues/458] -is_a: UBERON:0006012 ! interdigital region intersection_of: UBERON:0006012 ! interdigital region intersection_of: adjacent_to UBERON:0006048 ! digit 1 intersection_of: adjacent_to UBERON:0006049 ! digit 2 @@ -107850,7 +107684,6 @@ id: UBERON:0006019 name: interdigital region between digits 2 and 3 def: "An interdigital region that adjacent_to a digit 2 and adjacent_to a digit 3." [OBOL:automatic] synonym: "interdigital region between digits II and III" EXACT COMPARATIVE_PREFERRED [https://github.com/obophenotype/uberon/issues/458] -is_a: UBERON:0006012 ! interdigital region intersection_of: UBERON:0006012 ! interdigital region intersection_of: adjacent_to UBERON:0006049 ! digit 2 intersection_of: adjacent_to UBERON:0006050 ! digit 3 @@ -107861,7 +107694,6 @@ id: UBERON:0006022 name: interdigital region between digits 3 and 4 def: "An interdigital region that adjacent_to a digit 3 and adjacent_to a digit 4." [OBOL:automatic] synonym: "interdigital region between digits III and IV" EXACT COMPARATIVE_PREFERRED [https://github.com/obophenotype/uberon/issues/458] -is_a: UBERON:0006012 ! interdigital region intersection_of: UBERON:0006012 ! interdigital region intersection_of: adjacent_to UBERON:0006050 ! digit 3 intersection_of: adjacent_to UBERON:0006051 ! digit 4 @@ -107872,7 +107704,6 @@ id: UBERON:0006025 name: interdigital region between digits 4 and 5 def: "An interdigital region that adjacent_to a digit 4 and adjacent_to a digit 5." [OBOL:automatic] synonym: "interdigital region between digits IV and V" EXACT COMPARATIVE_PREFERRED [https://github.com/obophenotype/uberon/issues/458] -is_a: UBERON:0006012 ! interdigital region intersection_of: UBERON:0006012 ! interdigital region intersection_of: adjacent_to UBERON:0006051 ! digit 4 intersection_of: adjacent_to UBERON:0006052 ! digit 5 @@ -111693,7 +111524,6 @@ xref: EMAPA:18598 xref: MA:0001938 xref: NCIT:C52851 xref: UMLS:C1707451 {source="ncithesaurus:Communicating_Artery"} -is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery intersection_of: connects UBERON:0001637 {cardinality="2"} ! artery @@ -113804,7 +113634,6 @@ xref: AAO:0000476 xref: EFO:0003467 xref: TAO:0001377 xref: ZFA:0001377 -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 @@ -122366,7 +122195,6 @@ name: endomeninx def: "The innermost layer of the mesenchymal capsule that surrounds the developing brain, primarily of neural crest origin. The endomeninx forms the leptomeninx." [ISBN:9781607950325] synonym: "future leptomeninges" EXACT [] synonym: "future leptomeninx" EXACT [] -is_a: UBERON:0007645 ! future meninx intersection_of: UBERON:0007645 ! future meninx intersection_of: has_potential_to_develop_into UBERON:0000391 ! leptomeninx relationship: develops_from UBERON:0007213 {source="ISBN:9781607950325"} ! mesenchyme derived from head neural crest @@ -130791,7 +130619,6 @@ property_value: editor_note "we follow GO in dividing sutures into cranial and f id: UBERON:0009199 name: facial suture def: "Any suture between facial bones." [GO:0097096] -is_a: UBERON:0009198 ! craniofacial suture intersection_of: UBERON:0009198 ! craniofacial suture intersection_of: connects UBERON:0003462 {minCardinality="2"} ! facial bone relationship: connects UBERON:0003462 {notes="between two adjacent facial bones"} ! facial bone @@ -133948,7 +133775,6 @@ xref: Wikipedia:Stomach#Sections is_a: UBERON:0004921 ! subdivision of digestive tract intersection_of: UBERON:0034944 ! zone of organ intersection_of: part_of UBERON:0000945 ! stomach -relationship: part_of UBERON:0000945 ! stomach property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Regions_of_stomach.svg" xsd:anyURI property_value: editor_note "We follow Kardong in defining stomach regions by gland, but we also include 'body of stomach'. In future we may want to have different partitions of the stomach" xsd:string @@ -137596,7 +137422,6 @@ synonym: "mesenchyme derived from neural crest of mesenchyme of 1st arch" EXACT synonym: "neural crest derived arch 1 mesenchyme" EXACT [] synonym: "pharyngeal arch 1 mesenchyme from neural crest" EXACT [] xref: EMAPA:16129 -is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: develops_from UBERON:0002342 ! neural crest intersection_of: part_of UBERON:0010042 ! 1st arch mesenchyme @@ -141711,7 +141536,6 @@ intersection_of: connected_to UBERON:0003623 ! manual digit 3 id: UBERON:0010865 name: dactylopatagium medius def: "A dactylopatagium that is connected_to a manual digit 3 and connected_to a manual digit 4." [OBOL:automatic] -is_a: UBERON:0010862 ! dactylopatagium intersection_of: UBERON:0010862 ! dactylopatagium intersection_of: connected_to UBERON:0003623 ! manual digit 3 intersection_of: connected_to UBERON:0003624 ! manual digit 4 @@ -141720,7 +141544,6 @@ intersection_of: connected_to UBERON:0003624 ! manual digit 4 id: UBERON:0010866 name: dactylopatagium major def: "A dactylopatagium that is connected_to a manual digit 4 and connected_to a manual digit 5." [OBOL:automatic] -is_a: UBERON:0010862 ! dactylopatagium intersection_of: UBERON:0010862 ! dactylopatagium intersection_of: connected_to UBERON:0003624 ! manual digit 4 intersection_of: connected_to UBERON:0003625 ! manual digit 5 @@ -143309,7 +143132,6 @@ def: "The cartilaginous form of a vertebral element, a skeletal element that for synonym: "vertebral cartilage condensation" EXACT [VHOG:0000584] xref: EMAPA:32669 xref: VHOG:0000584 -is_a: UBERON:0010913 ! vertebral element intersection_of: UBERON:0010913 ! vertebral element intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue relationship: develops_from UBERON:0011095 ! vertebra pre-cartilage condensation @@ -143674,7 +143496,6 @@ id: UBERON:0011135 name: intervertebral cartilage def: "A cartilage element that lies between two successive vertebral centra." [ISBN:0073040584] xref: AAO:0000795 -is_a: UBERON:0007844 ! cartilage element intersection_of: UBERON:0007844 ! cartilage element intersection_of: adjacent_to UBERON:0001075 {cardinality="2"} ! bony vertebral centrum relationship: adjacent_to UBERON:0001075 {notes="between two centra"} ! bony vertebral centrum @@ -145014,7 +144835,6 @@ property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Appendages- id: UBERON:0011250 name: autopod bone def: "A bone that is part of a autopod region. Note that this incudes the carpal and tarsal bones." [https://orcid.org/0000-0002-6601-2165] -is_a: UBERON:0015063 ! autopod endochondral element intersection_of: UBERON:0015063 ! autopod endochondral element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: develops_from UBERON:0015064 ! autopod cartilage @@ -146660,7 +146480,6 @@ synonym: "limb/fin skeleton" EXACT [VSAO:0000301] synonym: "skeletal parts of limb/fin" EXACT [] synonym: "skeleton of limb/fin" EXACT [] xref: VSAO:0000301 -is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: skeleton_of UBERON:0004708 ! paired limb/fin relationship: develops_from UBERON:0003081 {source="ISBN:9780878932504"} ! lateral plate mesoderm @@ -151050,7 +150869,6 @@ id: UBERON:0012196 name: right superior intercostal vein xref: FMA:4877 xref: SCTID:80721005 -is_a: UBERON:0012194 ! superior intercostal vein intersection_of: UBERON:0012194 ! superior intercostal vein intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism @@ -163211,7 +163029,6 @@ synonym: "sphenomaxillary fissure" RELATED [] xref: FMA:54802 xref: SCTID:280560007 xref: Wikipedia:Inferior_orbital_fissure -is_a: UBERON:0006271 ! orbital fissure intersection_of: UBERON:0006271 ! orbital fissure intersection_of: connects UBERON:0002397 ! maxilla intersection_of: connects UBERON:0006721 ! alisphenoid bone @@ -167650,7 +167467,6 @@ synonym: "median palatine suture of skull" EXACT [FMA:52966] synonym: "middle palatine suture of skull" EXACT [FMA:52966] synonym: "midpalatal suture of skull" EXACT [FMA:52966] xref: FMA:52966 -is_a: UBERON:0035127 ! suture of hard palate intersection_of: UBERON:0035127 ! suture of hard palate intersection_of: connects UBERON:0001682 {cardinality="2"} ! palatine bone @@ -169301,7 +169117,6 @@ alt_id: UBERON:3000477 def: "Primordium that develops into the nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 -is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0001016 ! nervous system relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage @@ -182718,7 +182533,6 @@ name: diastema between incisors def: "A space or gap any two incisors. This may be a midline diastema between central incisors, or a diastema located entirely in a single jaw quadrant between lateral incisors." [http://orcid.org/0000-0002-6601-2165] synonym: "incisor diastema" EXACT [] synonym: "interdental space, incisors" EXACT [] -is_a: UBERON:0012111 ! diastema intersection_of: UBERON:0012111 ! diastema intersection_of: adjacent_to UBERON:0001098 {cardinality="2"} ! incisor tooth relationship: intersects_midsagittal_plane_of UBERON:0001708 ! jaw skeleton @@ -190339,7 +190153,6 @@ relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 ! Melissa Hae id: UBERON:1600006 name: paired fin radial element def: "Radial element that is part of a paired fin." [PHENOSCAPE] -is_a: UBERON:2100271 ! radial element intersection_of: UBERON:2100271 ! radial element intersection_of: part_of UBERON:0002534 ! paired fin relationship: part_of UBERON:4300013 ! paired fin radial skeleton @@ -190484,10 +190297,8 @@ name: dorsal actinotrichium def: "Actinotrichium which is part of the dorsal fin fold." [TAO:wd] synonym: "dorsal actinotrichia" EXACT OMO:0003004 [TAO:0000052] xref: ZFA:0000052 -is_a: UBERON:2000089 ! actinotrichium intersection_of: UBERON:2000089 ! actinotrichium intersection_of: part_of UBERON:2000102 ! dorsal fin fold -relationship: part_of UBERON:2000102 ! dorsal fin fold 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"} [Term] @@ -190551,10 +190362,8 @@ name: ventral actinotrichium def: "Actinotrichium which is part of the ventral fin fold." [TAO:wd] synonym: "ventral actinotrichia" EXACT OMO:0003004 [TAO:0000078] xref: ZFA:0000078 -is_a: UBERON:2000089 ! actinotrichium intersection_of: UBERON:2000089 ! actinotrichium intersection_of: part_of UBERON:2001069 ! ventral fin fold -relationship: part_of UBERON:2001069 ! ventral fin fold 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"} [Term] @@ -191832,7 +191641,6 @@ property_value: provenance_notes "This class was sourced from an external ontolo id: UBERON:2000373 name: dorsal fin actinotrichium def: "Actinotrichium that is part of the dorsal fin skeleton." [TAO:wd] -is_a: UBERON:2000089 ! actinotrichium intersection_of: UBERON:2000089 ! actinotrichium intersection_of: part_of UBERON:0003097 ! dorsal fin relationship: develops_from UBERON:0000926 ! mesoderm @@ -191844,7 +191652,6 @@ id: UBERON:2000375 name: anal fin actinotrichium def: "Actinotrichium that is part of the anal fin skeleton." [TAO:wd] xref: ZFA:0005398 -is_a: UBERON:2000089 ! actinotrichium intersection_of: UBERON:2000089 ! actinotrichium intersection_of: part_of UBERON:4000163 ! anal fin relationship: part_of UBERON:4000166 ! anal fin skeleton @@ -192122,7 +191929,6 @@ id: UBERON:2000437 name: caudal fin actinotrichium def: "Actinotrichium that is part of the caudal fin skeleton." [TAO:wd] xref: ZFA:0005424 -is_a: UBERON:2000089 ! actinotrichium intersection_of: UBERON:2000089 ! actinotrichium intersection_of: part_of UBERON:4000164 ! caudal fin relationship: part_of UBERON:4000167 ! caudal fin skeleton @@ -192258,7 +192064,6 @@ property_value: provenance_notes "This class was sourced from an external ontolo id: UBERON:2000460 name: adipose fin actinotrichium def: "Actinotrichium that is part of the adipose fin." [TAO:wd] -is_a: UBERON:2000089 ! actinotrichium intersection_of: UBERON:2000089 ! actinotrichium intersection_of: part_of UBERON:2000251 ! adipose fin relationship: part_of UBERON:4500004 ! adipose fin skeleton @@ -192719,7 +192524,6 @@ id: UBERON:2000544 name: pectoral fin actinotrichium def: "Actinotrichium that is part of the pectoral fin." [TAO:wd] xref: ZFA:0005545 -is_a: UBERON:2000089 ! actinotrichium intersection_of: UBERON:2000089 ! actinotrichium intersection_of: part_of UBERON:0000151 ! pectoral fin relationship: part_of UBERON:0010710 ! pectoral fin skeleton @@ -192939,7 +192743,6 @@ id: UBERON:2000596 name: pelvic fin actinotrichium def: "Actinotrichium that is part of the pelvic fin." [TAO:wd] xref: ZFA:0005546 -is_a: UBERON:2000089 ! actinotrichium intersection_of: UBERON:2000089 ! actinotrichium intersection_of: part_of UBERON:0000152 ! pelvic fin relationship: part_of UBERON:0010711 ! pelvic fin skeleton @@ -193301,10 +193104,8 @@ xref: EFO:0003551 xref: TAO:0000648 xref: ZFA:0000648 is_a: UBERON:0004469 ! musculature of back -is_a: UBERON:0007271 ! appendage musculature intersection_of: UBERON:0007271 ! appendage musculature intersection_of: part_of UBERON:0003097 ! dorsal fin -relationship: part_of UBERON:0003097 ! dorsal fin 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"} [Term] @@ -193531,7 +193332,6 @@ def: "Tooth that forms on ceratobranchial 5 cartilage or bone." [ZFIN:curator] comment: Ceratobranchial 5 teeth are the only teeth present in zebrafish and other cypriniforms. synonym: "pharyngeal teeth" EXACT [TAO:0000694] xref: ZFA:0000694 -is_a: UBERON:0001091 ! calcareous tooth intersection_of: UBERON:0001091 ! calcareous tooth intersection_of: attaches_to UBERON:2001239 ! ceratobranchial 5 bone relationship: develops_from UBERON:0005176 ! tooth enamel organ @@ -196725,7 +196525,6 @@ id: UBERON:2001223 name: basibranchial 1 bone def: "Basibranchial bone that is ventral, median, and associated with branchial arch 1 (pharyngeal arch 3). Typically develops in the anterior copula cartilage." [ZFIN:curator] xref: ZFA:0001223 -is_a: UBERON:2001915 ! basibranchial 1 element intersection_of: UBERON:2001915 ! basibranchial 1 element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: develops_from UBERON:2001864 ! basibranchial 1 cartilage @@ -196736,7 +196535,6 @@ id: UBERON:2001224 name: basibranchial 2 bone def: "Basibranchial bone that is ventral, median, and associated with branchial arch 2 (pharyngeal arch 4). Typically develops in the anterior copula cartilage." [ZFIN:curator] xref: ZFA:0001224 -is_a: UBERON:2001916 ! basibranchial 2 element intersection_of: UBERON:2001916 ! basibranchial 2 element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: develops_from UBERON:2001874 ! basibranchial 2 cartilage @@ -196747,7 +196545,6 @@ id: UBERON:2001225 name: basibranchial 3 bone def: "Basibranchial bone that is ventral, median, and associated with branchial arch 3 (pharyngeal arch 5). Typically develops in the anterior copula cartilage." [ZFIN:curator] xref: ZFA:0001225 -is_a: UBERON:2001917 ! basibranchial 3 element intersection_of: UBERON:2001917 ! basibranchial 3 element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: develops_from UBERON:2001876 ! basibranchial 3 cartilage @@ -196758,7 +196555,6 @@ id: UBERON:2001226 name: basibranchial 4 bone def: "Basibranchial bone that is ventral, median, and associated with branchial arch 4 (pharyngeal arch 6). Develops in posterior copula cartilage or basibranchial 4 cartilage." [ZFIN:curator] xref: ZFA:0001226 -is_a: UBERON:2001918 ! basibranchial 4 element intersection_of: UBERON:2001918 ! basibranchial 4 element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: develops_from UBERON:2001865 ! basibranchial 4 cartilage @@ -197558,7 +197354,6 @@ synonym: "anterior lateral line ganglia" RELATED OMO:0003004 [TAO:0001391] xref: EFO:0003683 xref: TAO:0001391 xref: ZFA:0001391 -is_a: UBERON:2000120 ! lateral line ganglion intersection_of: UBERON:2000120 ! lateral line ganglion intersection_of: part_of UBERON:2001468 ! anterior lateral line system @@ -198301,7 +198096,6 @@ name: basipterygium cartilage def: "Bilaterally paired small, rodlike cartilages on the ventral surface of the abdomen (present at 7.9 mm). Their posterior tips expand laterally, forming L-shaped cartilages. Medially, a posterior spur of cartilage develops, which will later ossify as the ischiac process (Weitzman 1962)." [ZFIN:curator] xref: ZFA:0001539 is_a: UBERON:0007844 ! cartilage element -is_a: UBERON:2100623 ! basipterygium element intersection_of: UBERON:2100623 ! basipterygium element intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue relationship: overlaps UBERON:2001939 ! inter-basipterygium joint @@ -198716,7 +198510,6 @@ id: UBERON:2001608 name: autopalatine-lateral ethmoid joint def: "Joint that articulates the autopalatine and lateral ethmoid and bones. Autopalatine-lateral ethmoid joint is paired." [TAO:wd] xref: ZFA:0005420 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:2000226 ! lateral ethmoid bone intersection_of: connects UBERON:2000620 ! autopalatine @@ -198863,7 +198656,6 @@ property_value: provenance_notes "This class was sourced from an external ontolo id: UBERON:2001626 name: premaxillary tooth def: "Tooth that is attached to the premaxilla." [TAO:wd] -is_a: UBERON:0001091 ! calcareous tooth intersection_of: UBERON:0001091 ! calcareous tooth intersection_of: attaches_to UBERON:0002244 ! premaxilla relationship: part_of UBERON:0009680 ! set of upper jaw teeth @@ -198905,7 +198697,6 @@ id: UBERON:2001633 name: entopterygoid tooth def: "Tooth that is attached to the entopterygoid bone." [TAO:wd] synonym: "mesopterygoid tooth" EXACT [TAO:0001633] -is_a: UBERON:0001091 ! calcareous tooth intersection_of: UBERON:0001091 ! calcareous tooth intersection_of: attaches_to UBERON:2000657 ! entopterygoid 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"} @@ -198971,10 +198762,8 @@ property_value: provenance_notes "This class was sourced from an external ontolo id: UBERON:2001649 name: basihyal tooth def: "Tooth that is attached to the basihyal tooth plate." [TAO:wd] -is_a: UBERON:0001091 ! calcareous tooth intersection_of: UBERON:0001091 ! calcareous tooth intersection_of: part_of UBERON:2001648 ! basihyal tooth plate -relationship: part_of UBERON:2001648 ! basihyal tooth plate 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"} [Term] @@ -199166,7 +198955,6 @@ property_value: provenance_notes "This class was sourced from an external ontolo id: UBERON:2001676 name: mesethmoid-premaxillary joint def: "Joint that articulates the mesethmoid and premaxilla. Mesethmoid-premaxillary joint is paired." [TAO:pem] -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0002244 ! premaxilla intersection_of: connects UBERON:0011238 ! mesethmoid bone @@ -199176,7 +198964,6 @@ property_value: provenance_notes "This class was sourced from an external ontolo id: UBERON:2001677 name: mesethmoid-nasal joint def: "Joint that articulates the mesethmoid and nasal. Mesethmoid-nasal joint is paired." [TAO:pem] -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0001681 ! nasal bone intersection_of: connects UBERON:0011238 ! mesethmoid bone @@ -199186,7 +198973,6 @@ property_value: provenance_notes "This class was sourced from an external ontolo id: UBERON:2001678 name: mesethmoid-frontal joint def: "Joint that articulates the mesethmoid and frontal. Mesethmoid-frontal joint is paired." [TAO:pem] -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0004866 ! actinopterygian frontal bone intersection_of: connects UBERON:0011238 ! mesethmoid bone @@ -199197,7 +198983,6 @@ id: UBERON:2001679 name: mesethmoid-lateral ethmoid joint def: "Joint that articulates the mesethmoid and lateral ethmoid. Mesethmoid-lateral ethmoid joint is paired." [TAO:wd] xref: ZFA:0005648 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0011238 ! mesethmoid bone intersection_of: connects UBERON:2000226 ! lateral ethmoid bone @@ -199209,7 +198994,6 @@ name: mesethmoid-vomer joint def: "Joint that articulates the mesethmoid and vomer. Mesethmoid-vomer joint is unpaired." [TAO:pem] synonym: "mesethmoid-prevomer joint" EXACT [TAO:0001680] xref: ZFA:0005649 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0002396 ! vomer intersection_of: connects UBERON:0011238 ! mesethmoid bone @@ -199387,7 +199171,6 @@ property_value: provenance_notes "This class was sourced from an external ontolo id: UBERON:2001701 name: basibranchial 5 bone def: "Basibranchial bone that is ventral, median, and associated with branchial arch 5 (pharyngeal arch 7). Develops in posterior copula cartilage or basibranchial 5 cartilage." [TAO:wd] -is_a: UBERON:2001919 ! basibranchial 5 element intersection_of: UBERON:2001919 ! basibranchial 5 element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: develops_from UBERON:2001866 ! basibranchial 5 cartilage @@ -199465,7 +199248,6 @@ id: UBERON:2001710 name: opercle-interopercle joint def: "Joint that articulates the opercle and interopercle. Opercle-interopercle joint is paired." [TAO:wd] xref: ZFA:0005478 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:2000250 ! opercle intersection_of: connects UBERON:2000674 ! interopercle @@ -199476,7 +199258,6 @@ id: UBERON:2001711 name: frontal-pterotic joint def: "Joint that articulates the frontal and pterotic. Frontal-pterotic joint is paired." [TAO:wd] xref: ZFA:0005468 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0004866 ! actinopterygian frontal bone intersection_of: connects UBERON:2000576 ! pterotic @@ -199789,7 +199570,6 @@ id: UBERON:2001749 name: dentary-anguloarticular joint def: "Joint that articulates the dentary and anguloarticular. Dentary-anguloarticular joint is paired." [TAO:wd] xref: ZFA:0005464 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0004742 ! dentary intersection_of: connects UBERON:0004744 ! articular/anguloarticular @@ -200091,7 +199871,6 @@ id: UBERON:2001784 name: autopalatine-vomer joint def: "Joint that articulates autopalatine and vomer bones. Autopalatine-vomer joint is paired." [TAO:wd] xref: ZFA:0005422 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0002396 ! vomer intersection_of: connects UBERON:2000620 ! autopalatine @@ -200166,7 +199945,6 @@ id: UBERON:2001794 name: orbitosphenoid-prootic joint def: "Joint that articulates orbitosphenoid and prootic bones. Orbitosphenoid-prootic joint is paired." [TAO:wd] xref: ZFA:0005480 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0002478 ! orbitosphenoid intersection_of: connects UBERON:0004746 ! prootic bone @@ -200226,7 +200004,6 @@ id: UBERON:2001801 name: quadrate-hyomandibula joint def: "Joint that articulates quadrate and hyomandibula bones. Quadrate-hyomandibula joint is paired." [TAO:wd] xref: ZFA:0005485 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0006597 ! quadrate bone intersection_of: connects UBERON:0011606 ! hyomandibular bone @@ -200237,7 +200014,6 @@ id: UBERON:2001803 name: quadrate-metapterygoid joint def: "Joint that articulates quadrate and metapterygoid bones. Quadrate-metapterygoid joint is paired." [TAO:wd] xref: ZFA:0005486 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0006597 ! quadrate bone intersection_of: connects UBERON:2000240 ! metapterygoid @@ -200512,7 +200288,6 @@ id: UBERON:2001831 name: pterosphenoid-orbitosphenoid joint def: "Joint that articulates the pterosphenoid and orbitosphenoid. Pterosphenoid-orbitosphenoid joint is paired." [TAO:wd] xref: ZFA:0005483 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0002478 ! orbitosphenoid intersection_of: connects UBERON:2000419 ! pterosphenoid @@ -200523,7 +200298,6 @@ id: UBERON:2001832 name: parasphenoid-basioccipital joint def: "Joint that articulates the parasphenoid and basioccipital. Parasphenoid-basioccipital joint is unpaired." [TAO:wd] xref: ZFA:0005560 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0001692 ! basioccipital bone intersection_of: connects UBERON:0004745 ! parasphenoid @@ -200560,7 +200334,6 @@ id: UBERON:2001842 name: epihyal-ceratohyal joint def: "Joint that articulates the epihyal and ceratohyal bones. Epihyal-ceratohyal joint is paired." [TAO:wd] xref: ZFA:0005497 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0011611 ! ceratohyal bone intersection_of: connects UBERON:2000627 ! posterior ceratohyal @@ -200571,7 +200344,6 @@ id: UBERON:2001843 name: ceratohyal-dorsal hypohyal joint def: "Joint that articulates the ceratohyal and dorsal hypohyal bones. Ceratohyal-dorsal hypohyal joint is paired." [TAO:wd] xref: ZFA:0005467 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0011611 ! ceratohyal bone intersection_of: connects UBERON:2000196 ! dorsal hypohyal bone @@ -200582,7 +200354,6 @@ id: UBERON:2001844 name: ceratohyal-ventral hypohyal joint def: "Joint that articulates the ceratohyal and ventral hypohyal bones. Ceratohyal-ventral hypohyal joint is paired." [TAO:wd] xref: ZFA:0005466 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0011611 ! ceratohyal bone intersection_of: connects UBERON:2000300 ! ventral hypohyal bone @@ -200593,7 +200364,6 @@ id: UBERON:2001845 name: dorsal hypohyal-ventral hypohyal joint def: "Joint that articulates the dorsal hypohyal and ventral hypohyal bones. Dorsal hypohyal-ventral hypohyal joint is paired." [TAO:wd] xref: ZFA:0005458 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:2000196 ! dorsal hypohyal bone intersection_of: connects UBERON:2000300 ! ventral hypohyal bone @@ -200604,7 +200374,6 @@ id: UBERON:2001846 name: inter-ventral hypohyal joint def: "Joint that articulates the contralateral ventral hypohyal bones or the contralateral ceratobranchial cartilages. Inter-ventral hypohyal joint is paired." [TAO:wd] xref: ZFA:0005476 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0011610 ! ceratohyal cartilage intersection_of: connects UBERON:2000300 ! ventral hypohyal bone @@ -200615,7 +200384,6 @@ id: UBERON:2001847 name: dorsal hypohyal-urohyal joint def: "Joint that articulates the dorsal hypohyal and urohyal bones. Dorsal hypohyal-urohyal joint is paired." [TAO:wd] xref: ZFA:0005457 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0011610 ! ceratohyal cartilage intersection_of: connects UBERON:2000196 ! dorsal hypohyal bone @@ -200627,7 +200395,6 @@ id: UBERON:2001848 name: ventral hypohyal-urohyal joint def: "Joint that articulates the ventral hypohyal and urohyal bones. Ventral hypohyal-urohyal joint is paired." [TAO:wd] xref: ZFA:0005487 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:2000300 ! ventral hypohyal bone intersection_of: connects UBERON:2000452 ! urohyal @@ -200727,7 +200494,6 @@ property_value: provenance_notes "This class was sourced from an external ontolo id: UBERON:2001861 name: epibranchial 3-pharyngobranchial 3 joint def: "Joint that articulates the epibranchial 3 cartilage or bone and pharyngobranchial 3 cartilage or bone. Epibranchial 3-pharyngobranchial 3 joint is paired." [TAO:wd] -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:2001247 ! epibranchial 3 bone intersection_of: connects UBERON:2001252 ! pharyngobranchial 3 bone @@ -200755,7 +200521,6 @@ id: UBERON:2001864 name: basibranchial 1 cartilage def: "Pharyngeal arch cartilage that is ventral, median, and associated with branchial arch 1 (pharyngeal arch 3)." [TAO:wd] is_a: UBERON:0011004 ! pharyngeal arch cartilage -is_a: UBERON:2001915 ! basibranchial 1 element intersection_of: UBERON:2001915 ! basibranchial 1 element intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue relationship: develops_from UBERON:2001221 ! anterior copula @@ -200766,7 +200531,6 @@ id: UBERON:2001865 name: basibranchial 4 cartilage def: "Pharyngeal arch cartilage that is ventral, median, and associated with branchial arch 4 (pharyngeal arch 6)." [TAO:wd] is_a: UBERON:0011004 ! pharyngeal arch cartilage -is_a: UBERON:2001918 ! basibranchial 4 element intersection_of: UBERON:2001918 ! basibranchial 4 element intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue relationship: develops_from UBERON:2001222 ! posterior copula @@ -200777,7 +200541,6 @@ id: UBERON:2001866 name: basibranchial 5 cartilage def: "Pharyngeal arch cartilage that is ventral, median, and associated with branchial arch 5 (pharyngeal arch 7)." [TAO:wd] is_a: UBERON:0011004 ! pharyngeal arch cartilage -is_a: UBERON:2001919 ! basibranchial 5 element intersection_of: UBERON:2001919 ! basibranchial 5 element intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue relationship: develops_from UBERON:2001222 ! posterior copula @@ -200839,7 +200602,6 @@ id: UBERON:2001874 name: basibranchial 2 cartilage def: "Pharyngeal arch cartilage that is ventral, median, and associated with branchial arch 2 (pharyngeal arch 4)." [TAO:wd] is_a: UBERON:0011004 ! pharyngeal arch cartilage -is_a: UBERON:2001916 ! basibranchial 2 element intersection_of: UBERON:2001916 ! basibranchial 2 element intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue relationship: develops_from UBERON:2001221 ! anterior copula @@ -200856,7 +200618,6 @@ id: UBERON:2001876 name: basibranchial 3 cartilage def: "Pharyngeal arch cartilage that is ventral, median, and associated with branchial arch 3 (pharyngeal arch 5)." [TAO:wd] is_a: UBERON:0011004 ! pharyngeal arch cartilage -is_a: UBERON:2001917 ! basibranchial 3 element intersection_of: UBERON:2001917 ! basibranchial 3 element intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue relationship: develops_from UBERON:2001221 ! anterior copula @@ -201341,7 +201102,6 @@ def: "Joint that articulates the left and right basipterygium cartilage or bone. synonym: "pelvic girdle symphysis" EXACT [TAO:0001939] synonym: "pelvic symphysis" EXACT [TAO:0001939] xref: ZFA:0005471 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:2100623 ! basipterygium element 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"} @@ -201351,7 +201111,6 @@ id: UBERON:2001940 name: vertebra 4-vertebra 5 joint def: "Joint between the centra, and sometimes the neural arches or parapophyses of vertebra 4 and vertebra 5." [TAO:wd] xref: ZFA:0005504 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:2001170 ! vertebral element 4 intersection_of: connects UBERON:2001732 ! vertebral element 5 @@ -201362,7 +201121,6 @@ id: UBERON:2001941 name: orbitosphenoid-lateral ethmoid joint def: "Joint that articulates the orbitosphenoid cartilage or bone and lateral ethmoid cartilage or bone. Orbitosphenoid-lateral ethmoid joint is paired." [TAO:wd] xref: ZFA:0005479 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0002478 ! orbitosphenoid intersection_of: connects UBERON:2000226 ! lateral ethmoid bone @@ -201373,7 +201131,6 @@ id: UBERON:2001942 name: autopalatine-maxillary joint def: "Joint that articulates the autopalatine cartilage or bone and maxilla." [TAO:wd] xref: ZFA:0005421 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0002397 ! maxilla intersection_of: connects UBERON:2000620 ! autopalatine @@ -201413,7 +201170,6 @@ id: UBERON:2001947 name: hyomandibular-otic region joint def: "Joint that articulates the hyomandibular cartilage or bone and otic region cartilage or sphenotic bone, and often pterotic bone and prootic bone. Hyomandibular-otic region joint is paired." [TAO:wd] xref: ZFA:0005544 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0003110 ! otic region intersection_of: connects UBERON:0011606 ! hyomandibular bone @@ -201443,7 +201199,6 @@ id: UBERON:2001950 name: inter-premaxillary joint def: "Joint that articulates the left and right premaxillary bones. Inter-premaxillary joint is unpaired." [TAO:wd] xref: ZFA:0005475 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0002244 ! premaxilla 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"} @@ -201671,7 +201426,6 @@ id: UBERON:2001979 name: hyomandibula-metapterygoid joint def: "Joint that articulates the hyomandibula bone and metapterygoid bone." [TAO:wd] xref: ZFA:0005469 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0011606 ! hyomandibular bone intersection_of: connects UBERON:2000240 ! metapterygoid @@ -202163,7 +201917,6 @@ id: UBERON:2002032 name: lateral ethmoid-frontal joint def: "Joint that articulates the lateral ethmoid and frontal. lateral ethmoid-frontal joint is paired." [TAO:wd] xref: ZFA:0005477 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0004866 ! actinopterygian frontal bone intersection_of: connects UBERON:2000226 ! lateral ethmoid bone @@ -202174,7 +201927,6 @@ id: UBERON:2002033 name: prootic-pterosphenoid joint def: "Joint that articulates the prootic and pterosphenoid. prootic-pterosphenoid joint is paired." [TAO:wd] xref: ZFA:0005482 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0004746 ! prootic bone intersection_of: connects UBERON:2000419 ! pterosphenoid @@ -202185,7 +201937,6 @@ id: UBERON:2002034 name: prootic-exoccipital joint def: "Joint that articulates the prootic and exoccipital. Prootic-exoccipital joint is paired." [TAO:wd] xref: ZFA:0005481 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0001693 ! exoccipital bone intersection_of: connects UBERON:0004746 ! prootic bone @@ -202196,7 +201947,6 @@ id: UBERON:2002038 name: basioccipital-exoccipital joint def: "Joint that articulates the basioccipital and exoccipital. Basioccipital-exoccipital joint is paired." [TAO:wd] xref: ZFA:0005423 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0001692 ! basioccipital bone intersection_of: connects UBERON:0001693 ! exoccipital bone @@ -202310,7 +202060,6 @@ id: UBERON:2002054 name: vertebra 5-vertebra 6 joint def: "Joint between the centra, and sometimes the neural arches or parapophyses." [TAO:wd] xref: ZFA:0005505 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:2001732 ! vertebral element 5 intersection_of: connects UBERON:2001980 ! vertebral element 6 @@ -202321,7 +202070,6 @@ id: UBERON:2002055 name: vertebra 6 - vertebra 7 joint def: "Joint between the centra, and sometimes the neural arches or parapophyses of vertebra 6 and vertebra 7." [TAO:wd] xref: ZFA:0005506 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:2001980 ! vertebral element 6 intersection_of: connects UBERON:2001981 ! vertebral element 7 @@ -202358,7 +202106,6 @@ property_value: provenance_notes "This class was sourced from an external ontolo [Term] id: UBERON:2002059 name: posttemporal-parietal joint -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0004865 ! actinopterygian parietal bone intersection_of: connects UBERON:2000549 ! posttemporal @@ -202705,7 +202452,6 @@ id: UBERON:2002102 name: epibranchial series def: "Anatomical cluster that consists of the epibranchial elements within an individual." [TAO:wd] synonym: "epibranchials" EXACT OMO:0003004 [TAO:0002102] -is_a: UBERON:0000477 ! anatomical cluster intersection_of: UBERON:0000477 ! anatomical cluster intersection_of: composed_primarily_of UBERON:2001904 ! epibranchial element relationship: part_of UBERON:0005886 ! post-hyoid pharyngeal arch skeleton @@ -202715,7 +202461,6 @@ property_value: provenance_notes "This class was sourced from an external ontolo id: UBERON:2002103 name: ceratobranchial series def: "Anatomical cluster that consists of the ceratobranchial elements within an individual." [TAO:wd] -is_a: UBERON:0000477 ! anatomical cluster intersection_of: UBERON:0000477 ! anatomical cluster intersection_of: composed_primarily_of UBERON:2001898 ! ceratobranchial element relationship: part_of UBERON:0005886 ! post-hyoid pharyngeal arch skeleton @@ -203336,7 +203081,6 @@ property_value: provenance_notes "This class was sourced from an external ontolo [Term] id: UBERON:2002217 name: parasphenoid-pterosphenoid joint -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0004745 ! parasphenoid intersection_of: connects UBERON:2000419 ! pterosphenoid @@ -203551,7 +203295,6 @@ property_value: provenance_notes "This class was sourced from an external ontolo id: UBERON:2002260 name: premaxillary-maxillary joint def: "Joint that articulates the premaxilla and maxilla. Premaxillary-maxillary joint is paired." [TAO:wd] -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0002244 ! premaxilla intersection_of: connects UBERON:0002397 ! maxilla @@ -203703,7 +203446,6 @@ property_value: provenance_notes "This class was sourced from an external ontolo id: UBERON:2002282 name: preopercle-opercle joint def: "Joint that articulates the preopercle and opercle. Preopercle-opercle joint is paired." [TAO:wd] -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:2000250 ! opercle intersection_of: connects UBERON:2000264 ! preopercle @@ -205220,7 +204962,6 @@ property_value: external_definition "Blood vessel endothelium that has pores tha id: UBERON:2005264 name: supraoccipital-parietal joint xref: ZFA:0005609 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0004747 ! supraoccipital bone intersection_of: connects UBERON:0004865 ! actinopterygian parietal bone @@ -205231,7 +204972,6 @@ id: UBERON:2005265 name: hyomandibula-opercle joint def: "Synovial joint that articulates the hyomandibula and the opercle." [ZFIN:CVS] xref: ZFA:0005626 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0011606 ! hyomandibular bone intersection_of: connects UBERON:2000250 ! opercle @@ -205263,7 +205003,6 @@ name: preopercle horizontal limb-symplectic joint def: "Joint that articulates the posterior edge of the preopercle horizontal limb with the symplectic." [ZFIN:curator] comment: In ZFA, is a type of fibrous joint. May need to stay more general in TAO. xref: ZFA:0005631 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:2000289 ! preopercle horizontal limb intersection_of: connects UBERON:2000692 ! symplectic @@ -205333,7 +205072,6 @@ id: UBERON:2005278 name: preopercle vertical limb-hyomandibula joint def: "Joint that articulates the anterior edge of the preopercle vertical limb and the hyomandibula." [ZFIN:curator] xref: ZFA:0005632 -is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: connects UBERON:0011606 ! hyomandibular bone intersection_of: connects UBERON:2000336 ! preopercle vertical limb @@ -206381,7 +206119,6 @@ synonym: "actinophore" RELATED [PSPUB:0000173] synonym: "actinoste" RELATED [PSPUB:0000163] synonym: "axonoste" RELATED [PSPUB:0000141] synonym: "ptrygiophore" RELATED [PSPUB:0000164] -is_a: UBERON:2100271 ! radial element intersection_of: UBERON:2100271 ! radial element intersection_of: part_of UBERON:4000162 ! median fin @@ -213915,7 +213652,6 @@ def: "Fin that is an unpaired fin located in the sagittal plane of the organism. synonym: "nageoire impaire" EXACT [PSPUB:0000164] synonym: "périssoptérygie" EXACT [PSPUB:0000140] xref: ZFA:0005597 -is_a: UBERON:0008897 ! fin intersection_of: UBERON:0008897 ! fin intersection_of: intersects_midsagittal_plane_of UBERON:0000468 ! multicellular organism property_value: provenance_notes "This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/vsao.owl"} @@ -214084,7 +213820,6 @@ property_value: provenance_notes "This class was sourced from an external ontolo id: UBERON:4100000 name: skeletal element projection def: "Anatomical projection that is composed of bone or cartilage tissue." [PHENOSCAPE] -is_a: UBERON:0004529 ! anatomical projection intersection_of: UBERON:0004529 ! anatomical projection intersection_of: part_of UBERON:0004765 ! skeletal element @@ -215283,7 +215018,6 @@ name: synarcual region of vertebral column def: "Series of fused cervical vertebrae or vertebral elements. Based on Jeffrey C. Carrier. Biology of Sharks and Their Relatives, 2012. CRC Press." [PHENOSCAPE] comment: 'The synarcual is a structure incorporating the anterior vertebrae of the axial skeleton and occurs in vertebrate taxa such as the fossil group Placodermi and the Chondrichthyes (Holocephali, Batoidea)' DOI:10.1007/s00435-012-0169-9 synonym: "synarcuum" EXACT [] -is_a: UBERON:0006077 ! subdivision of vertebral column intersection_of: UBERON:0006077 ! subdivision of vertebral column intersection_of: subdivision_of UBERON:4200129 ! synarcual region relationship: part_of UBERON:0002090 ! postcranial axial skeleton @@ -215404,42 +215138,36 @@ relationship: part_of UBERON:0004454 ! tarsal region [Term] id: UBERON:4200153 name: metatarsal bone of digit 6 -is_a: UBERON:4200154 ! metapodium bone 6 intersection_of: UBERON:4200154 ! metapodium bone 6 intersection_of: part_of UBERON:0000983 ! metatarsus region [Term] id: UBERON:4200154 name: metapodium bone 6 -is_a: UBERON:0003821 ! metapodium bone intersection_of: UBERON:0003821 ! metapodium bone intersection_of: part_of UBERON:0016866 ! digit 6 plus metapodial segment [Term] id: UBERON:4200155 name: metapodium bone 7 -is_a: UBERON:0003821 ! metapodium bone intersection_of: UBERON:0003821 ! metapodium bone intersection_of: part_of UBERON:0016867 ! digit 7 plus metapodial segment [Term] id: UBERON:4200156 name: metapodium bone 8 -is_a: UBERON:0003821 ! metapodium bone intersection_of: UBERON:0003821 ! metapodium bone intersection_of: part_of UBERON:0016868 ! digit 8 plus metapodial segment [Term] id: UBERON:4200157 name: metatarsal bone of digit 7 -is_a: UBERON:4200155 ! metapodium bone 7 intersection_of: UBERON:4200155 ! metapodium bone 7 intersection_of: part_of UBERON:0000983 ! metatarsus region [Term] id: UBERON:4200158 name: metatarsal bone of digit 8 -is_a: UBERON:4200156 ! metapodium bone 8 intersection_of: UBERON:4200156 ! metapodium bone 8 intersection_of: part_of UBERON:0000983 ! metatarsus region @@ -215530,7 +215258,6 @@ xref: NCIT:C33164 is_a: UBERON:0005913 ! zone of bone organ intersection_of: UBERON:0001560 ! neck of organ intersection_of: part_of UBERON:0000976 ! humerus -relationship: part_of UBERON:0000976 ! humerus relationship: part_of UBERON:0004411 ! proximal epiphysis of humerus [Term] @@ -217702,7 +217429,6 @@ relationship: dc-contributor https://orcid.org/0000-0002-5378-0931 ! Laura M Jac id: UBERON:4500012 name: hypobranchial series def: "Anatomical cluster that consists of the hypobranchial elements within an individual." [PHENOSCAPE] -is_a: UBERON:0000477 ! anatomical cluster intersection_of: UBERON:0000477 ! anatomical cluster intersection_of: composed_primarily_of UBERON:2001893 ! hypobranchial element relationship: dc-contributor https://orcid.org/0000-0002-5378-0931 ! Laura M Jackson @@ -217712,7 +217438,6 @@ relationship: part_of UBERON:0005886 ! post-hyoid pharyngeal arch skeleton id: UBERON:4500013 name: pharyngobranchial series def: "Anatomical cluster that consists of the pharyngobranchial elements within an individual." [PHENOSCAPE] -is_a: UBERON:0000477 ! anatomical cluster intersection_of: UBERON:0000477 ! anatomical cluster intersection_of: composed_primarily_of UBERON:2001909 ! pharyngobranchial element relationship: dc-contributor https://orcid.org/0000-0002-5378-0931 ! Laura M Jackson @@ -217722,7 +217447,6 @@ relationship: part_of UBERON:0005886 ! post-hyoid pharyngeal arch skeleton id: UBERON:4500014 name: basibranchial series def: "Anatomical cluster that consists of the basibranchial elements within an individual." [PHENOSCAPE] -is_a: UBERON:0000477 ! anatomical cluster intersection_of: UBERON:0000477 ! anatomical cluster intersection_of: composed_primarily_of UBERON:0013746 ! basibranchial element relationship: dc-contributor https://orcid.org/0000-0002-5378-0931 ! Laura M Jackson @@ -218599,10 +218323,8 @@ relationship: in_taxon NCBITaxon:50557 ! Insecta id: UBERON:6000016 name: insect thoracic segment def: "Any segment (UBERON:6000003) that is part of some thorax (UBERON:6000015)." [FBC:auto_generated_definition] -is_a: UBERON:0000914 ! organismal segment intersection_of: UBERON:0000914 ! organismal segment intersection_of: part_of UBERON:6000015 ! insect thorax -relationship: part_of UBERON:6000015 ! insect thorax [Term] id: UBERON:6000017 @@ -218645,10 +218367,8 @@ relationship: in_taxon NCBITaxon:50557 ! Insecta id: UBERON:6000021 name: insect abdominal segment def: "Metameric subdivision of the abdomen." [FBC:SPR] -is_a: UBERON:0000914 ! organismal segment intersection_of: UBERON:0000914 ! organismal segment intersection_of: part_of UBERON:6000020 ! insect abdomen -relationship: part_of UBERON:6000020 ! insect abdomen [Term] id: UBERON:6000029 @@ -218752,10 +218472,8 @@ relationship: part_of UBERON:6000131 ! insect mesodermal crest id: UBERON:6000137 name: embryonic tagma def: "Any tagma (UBERON:6000002) that is part of some embryo (UBERON:6000052)." [FBC:auto_generated_definition] -is_a: UBERON:6000002 ! arthropod tagma intersection_of: UBERON:6000002 ! arthropod tagma intersection_of: part_of UBERON:0000922 ! embryo -relationship: part_of UBERON:0000922 ! embryo [Term] id: UBERON:6000154 @@ -218778,53 +218496,43 @@ intersection_of: part_of UBERON:0008816 ! embryonic head id: UBERON:6000158 name: insect embryonic procephalic segment def: "Any procephalic segment (UBERON:6000007) that is part of some embryonic head (UBERON:6000155) in an insect." [FBC:auto_generated_definition] -is_a: UBERON:6000007 ! procephalic segment is_a: UBERON:6000157 ! insect embryonic head segment intersection_of: UBERON:6000007 ! procephalic segment intersection_of: in_taxon NCBITaxon:50557 ! Insecta intersection_of: part_of UBERON:0008816 ! embryonic head -relationship: part_of UBERON:0008816 ! embryonic head [Term] id: UBERON:6000160 name: insect embryonic antennal segment def: "Any antennal segment (UBERON:6000009) that is part of some embryonic head (UBERON:6000155)." [FBC:auto_generated_definition] -is_a: UBERON:6000009 ! antennal segment is_a: UBERON:6000158 ! insect embryonic procephalic segment intersection_of: UBERON:6000009 ! antennal segment intersection_of: in_taxon NCBITaxon:50557 ! Insecta intersection_of: part_of UBERON:0008816 ! embryonic head -relationship: part_of UBERON:0008816 ! embryonic head [Term] id: UBERON:6000162 name: insect embryonic gnathal segment def: "Any gnathal segment (UBERON:6000011) that is part of some embryonic head (UBERON:6000155)." [FBC:auto_generated_definition] -is_a: UBERON:6000011 ! insect gnathal segment is_a: UBERON:6000157 ! insect embryonic head segment intersection_of: UBERON:6000011 ! insect gnathal segment intersection_of: part_of UBERON:0008816 ! embryonic head -relationship: part_of UBERON:0008816 ! embryonic head [Term] id: UBERON:6000165 name: insect embryonic labial segment def: "Any labial segment (UBERON:6000014) that is part of some embryonic head (UBERON:6000155)." [FBC:auto_generated_definition] -is_a: UBERON:6000014 ! insect labial segment is_a: UBERON:6000162 ! insect embryonic gnathal segment intersection_of: UBERON:6000014 ! insect labial segment intersection_of: part_of UBERON:0008816 ! embryonic head -relationship: part_of UBERON:0008816 ! embryonic head [Term] id: UBERON:6000166 name: insect embryonic thorax def: "Any thorax (UBERON:6000015) that is part of some embryo (UBERON:6000052)." [FBC:auto_generated_definition] -is_a: UBERON:6000015 ! insect thorax is_a: UBERON:6000137 ! embryonic tagma intersection_of: UBERON:6000015 ! insect thorax intersection_of: part_of UBERON:0000922 ! embryo -relationship: part_of UBERON:0000922 ! embryo [Term] id: UBERON:6000167 @@ -218834,7 +218542,6 @@ is_a: UBERON:6000016 ! insect thoracic segment is_a: UBERON:6000154 ! insect embryonic segment intersection_of: UBERON:0000914 ! organismal segment intersection_of: part_of UBERON:6000166 ! insect embryonic thorax -relationship: part_of UBERON:6000166 ! insect embryonic thorax [Term] id: UBERON:6000168 @@ -218843,11 +218550,9 @@ def: "Prothoracic segment of the embryo." [FBC:DOS] synonym: "prothorax" RELATED [] synonym: "t1" RELATED [] synonym: "thoracic segment 1" RELATED [] -is_a: UBERON:6000017 ! insect prothoracic segment is_a: UBERON:6000167 ! insect embryonic thoracic segment intersection_of: UBERON:6000017 ! insect prothoracic segment intersection_of: part_of UBERON:6000166 ! insect embryonic thorax -relationship: part_of UBERON:6000166 ! insect embryonic thorax [Term] id: UBERON:6000169 @@ -218856,11 +218561,9 @@ def: "Mesothoracic segment of the embryo." [FBC:DOS] synonym: "mesothorax" RELATED [] synonym: "t2" RELATED [] synonym: "thoracic segment 2" RELATED [] -is_a: UBERON:6000018 ! insect mesothoracic segment is_a: UBERON:6000167 ! insect embryonic thoracic segment intersection_of: UBERON:6000018 ! insect mesothoracic segment intersection_of: part_of UBERON:6000166 ! insect embryonic thorax -relationship: part_of UBERON:6000166 ! insect embryonic thorax [Term] id: UBERON:6000170 @@ -218869,21 +218572,17 @@ def: "Metathoracic segment of the embryo." [FBC:DOS] synonym: "metathorax" RELATED [] synonym: "t3" RELATED [] synonym: "thoracic segment 3" RELATED [] -is_a: UBERON:6000019 ! insect metathoracic segment is_a: UBERON:6000167 ! insect embryonic thoracic segment intersection_of: UBERON:6000019 ! insect metathoracic segment intersection_of: part_of UBERON:6000166 ! insect embryonic thorax -relationship: part_of UBERON:6000166 ! insect embryonic thorax [Term] id: UBERON:6000171 name: insect embryonic abdomen def: "Abdomen of the embryo." [FBC:DOS] -is_a: UBERON:6000020 ! insect abdomen is_a: UBERON:6000137 ! embryonic tagma intersection_of: UBERON:6000020 ! insect abdomen intersection_of: part_of UBERON:0000922 ! embryo -relationship: part_of UBERON:0000922 ! embryo [Term] id: UBERON:6000172 @@ -218893,29 +218592,24 @@ is_a: UBERON:6000021 ! insect abdominal segment is_a: UBERON:6000154 ! insect embryonic segment intersection_of: UBERON:0000914 ! organismal segment intersection_of: part_of UBERON:6000171 ! insect embryonic abdomen -relationship: part_of UBERON:6000171 ! insect embryonic abdomen [Term] id: UBERON:6000180 name: insect embryonic abdominal segment 8 def: "Any abdominal segment 8 (UBERON:6000029) that is part of some embryonic abdomen (UBERON:6000171)." [FBC:auto_generated_definition] synonym: "a8" RELATED [] -is_a: UBERON:6000029 ! insect abdominal segment 8 is_a: UBERON:6000172 ! insect embryonic abdominal segment intersection_of: UBERON:6000029 ! insect abdominal segment 8 intersection_of: part_of UBERON:6000171 ! insect embryonic abdomen -relationship: part_of UBERON:6000171 ! insect embryonic abdomen [Term] id: UBERON:6000181 name: insect embryonic abdominal segment 9 def: "Any abdominal segment 9 (UBERON:6000030) that is part of some embryonic abdomen (UBERON:6000171)." [FBC:auto_generated_definition] synonym: "a9" RELATED [] -is_a: UBERON:6000030 ! insect abdominal segment 9 is_a: UBERON:6000172 ! insect embryonic abdominal segment intersection_of: UBERON:6000030 ! insect abdominal segment 9 intersection_of: part_of UBERON:6000171 ! insect embryonic abdomen -relationship: part_of UBERON:6000171 ! insect embryonic abdomen [Term] id: UBERON:6000186 @@ -219121,10 +218815,8 @@ relationship: in_taxon NCBITaxon:6656 {source="https://github.com/obophenotype/u id: UBERON:6001728 name: insect larval tagma def: "Any tagma (UBERON:6000002) that is part of some larva (UBERON:6001727)." [FBC:auto_generated_definition] -is_a: UBERON:6000002 ! arthropod tagma intersection_of: UBERON:6000002 ! arthropod tagma intersection_of: part_of UBERON:0002548 ! larva -relationship: part_of UBERON:0002548 ! larva [Term] id: UBERON:6001729 @@ -219148,11 +218840,9 @@ id: UBERON:6001731 name: insect larval ocular segment def: "Any ocular segment (UBERON:6000005) that is part of some larval head (UBERON:6001730)." [FBC:auto_generated_definition] synonym: "larval acron" RELATED [] -is_a: UBERON:6000005 ! insect ocular segment is_a: UBERON:6001733 ! insect larval procephalic segment intersection_of: UBERON:6000005 ! insect ocular segment intersection_of: part_of UBERON:6001730 ! insect larval head -relationship: part_of UBERON:6001730 ! insect larval head [Term] id: UBERON:6001732 @@ -219165,61 +218855,49 @@ intersection_of: part_of UBERON:6001730 ! insect larval head id: UBERON:6001733 name: insect larval procephalic segment def: "Any procephalic segment (UBERON:6000007) that is part of some larval head (UBERON:6001730)." [FBC:auto_generated_definition] -is_a: UBERON:6000007 ! procephalic segment is_a: UBERON:6001732 ! insect larval head segment intersection_of: UBERON:6000007 ! procephalic segment intersection_of: part_of UBERON:6001730 ! insect larval head -relationship: part_of UBERON:6001730 ! insect larval head [Term] id: UBERON:6001734 name: insect larval labral segment def: "Any labral segment (UBERON:6000008) that is part of some larval head (UBERON:6001730)." [FBC:auto_generated_definition] -is_a: UBERON:6000008 ! labral segment is_a: UBERON:6001733 ! insect larval procephalic segment intersection_of: UBERON:6000008 ! labral segment intersection_of: part_of UBERON:6001730 ! insect larval head -relationship: part_of UBERON:6001730 ! insect larval head [Term] id: UBERON:6001735 name: insect larval antennal segment def: "Any antennal segment (UBERON:6000009) that is part of some larval head (UBERON:6001730)." [FBC:auto_generated_definition] -is_a: UBERON:6000009 ! antennal segment is_a: UBERON:6001733 ! insect larval procephalic segment intersection_of: UBERON:6000009 ! antennal segment intersection_of: part_of UBERON:6001730 ! insect larval head -relationship: part_of UBERON:6001730 ! insect larval head [Term] id: UBERON:6001737 name: insect larval gnathal segment def: "Any gnathal segment (UBERON:6000011) that is part of some larval head (UBERON:6001730)." [FBC:auto_generated_definition] -is_a: UBERON:6000011 ! insect gnathal segment is_a: UBERON:6001732 ! insect larval head segment intersection_of: UBERON:6000011 ! insect gnathal segment intersection_of: part_of UBERON:6001730 ! insect larval head -relationship: part_of UBERON:6001730 ! insect larval head [Term] id: UBERON:6001740 name: insect larval labial segment def: "Any labial segment (UBERON:6000014) that is part of some larval head (UBERON:6001730)." [FBC:auto_generated_definition] -is_a: UBERON:6000014 ! insect labial segment is_a: UBERON:6001737 ! insect larval gnathal segment intersection_of: UBERON:6000014 ! insect labial segment intersection_of: part_of UBERON:6001730 ! insect larval head -relationship: part_of UBERON:6001730 ! insect larval head [Term] id: UBERON:6001741 name: insect larval thorax def: "Any thorax (UBERON:6000015) that is part of some larva (UBERON:6001727)." [FBC:auto_generated_definition] -is_a: UBERON:6000015 ! insect thorax is_a: UBERON:6001728 ! insect larval tagma intersection_of: UBERON:6000015 ! insect thorax intersection_of: part_of UBERON:0002548 ! larva -relationship: part_of UBERON:0002548 ! larva [Term] id: UBERON:6001742 @@ -219229,7 +218907,6 @@ is_a: UBERON:6000016 ! insect thoracic segment is_a: UBERON:6001729 ! insect larval segment intersection_of: UBERON:0000914 ! organismal segment intersection_of: part_of UBERON:6001741 ! insect larval thorax -relationship: part_of UBERON:6001741 ! insect larval thorax [Term] id: UBERON:6001743 @@ -219238,11 +218915,9 @@ def: "Any prothoracic segment (UBERON:6000017) that is part of some larval thora synonym: "prothorax" RELATED [] synonym: "t1" RELATED [] synonym: "thoracic segment 1" RELATED [] -is_a: UBERON:6000017 ! insect prothoracic segment is_a: UBERON:6001742 ! insect larval thoracic segment intersection_of: UBERON:6000017 ! insect prothoracic segment intersection_of: part_of UBERON:6001741 ! insect larval thorax -relationship: part_of UBERON:6001741 ! insect larval thorax [Term] id: UBERON:6001744 @@ -219251,11 +218926,9 @@ def: "Any mesothoracic segment (UBERON:6000018) that is part of some larval thor synonym: "mesothorax" RELATED [] synonym: "t2" RELATED [] synonym: "thoracic segment 2" RELATED [] -is_a: UBERON:6000018 ! insect mesothoracic segment is_a: UBERON:6001742 ! insect larval thoracic segment intersection_of: UBERON:6000018 ! insect mesothoracic segment intersection_of: part_of UBERON:6001741 ! insect larval thorax -relationship: part_of UBERON:6001741 ! insect larval thorax [Term] id: UBERON:6001745 @@ -219264,21 +218937,17 @@ def: "Any metathoracic segment (UBERON:6000019) that is part of some larval thor synonym: "metathorax" RELATED [] synonym: "t3" RELATED [] synonym: "thoracic segment 3" RELATED [] -is_a: UBERON:6000019 ! insect metathoracic segment is_a: UBERON:6001742 ! insect larval thoracic segment intersection_of: UBERON:6000019 ! insect metathoracic segment intersection_of: part_of UBERON:6001741 ! insect larval thorax -relationship: part_of UBERON:6001741 ! insect larval thorax [Term] id: UBERON:6001746 name: insect larval abdomen def: "Any abdomen (UBERON:6000020) that is part of some larva (UBERON:6001727)." [FBC:auto_generated_definition] -is_a: UBERON:6000020 ! insect abdomen is_a: UBERON:6001728 ! insect larval tagma intersection_of: UBERON:6000020 ! insect abdomen intersection_of: part_of UBERON:0002548 ! larva -relationship: part_of UBERON:0002548 ! larva [Term] id: UBERON:6001747 @@ -219288,29 +218957,24 @@ is_a: UBERON:6000021 ! insect abdominal segment is_a: UBERON:6001729 ! insect larval segment intersection_of: UBERON:0000914 ! organismal segment intersection_of: part_of UBERON:6001746 ! insect larval abdomen -relationship: part_of UBERON:6001746 ! insect larval abdomen [Term] id: UBERON:6001755 name: insect larval abdominal segment 8 def: "Any abdominal segment 8 (UBERON:6000029) that is part of some larval abdomen (UBERON:6001746)." [FBC:auto_generated_definition] synonym: "a8" RELATED [] -is_a: UBERON:6000029 ! insect abdominal segment 8 is_a: UBERON:6001747 ! insect larval abdominal segment intersection_of: UBERON:6000029 ! insect abdominal segment 8 intersection_of: part_of UBERON:6001746 ! insect larval abdomen -relationship: part_of UBERON:6001746 ! insect larval abdomen [Term] id: UBERON:6001756 name: insect larval abdominal segment 9 def: "Any abdominal segment 9 (UBERON:6000030) that is part of some larval abdomen (UBERON:6001746)." [FBC:auto_generated_definition] synonym: "a9" RELATED [] -is_a: UBERON:6000030 ! insect abdominal segment 9 is_a: UBERON:6001747 ! insect larval abdominal segment intersection_of: UBERON:6000030 ! insect abdominal segment 9 intersection_of: part_of UBERON:6001746 ! insect larval abdomen -relationship: part_of UBERON:6001746 ! insect larval abdomen [Term] id: UBERON:6001760 @@ -219549,16 +219213,13 @@ synonym: "larval ocular segment sensillum" EXACT [] is_a: UBERON:6007280 ! insect embryonic/larval head sense organ intersection_of: UBERON:6002639 ! insect larval sense organ intersection_of: part_of UBERON:6001731 ! insect larval ocular segment -relationship: part_of UBERON:6001731 ! insect larval ocular segment [Term] id: UBERON:6003005 name: insect adult tagma def: "Any tagma (UBERON:6000002) that is part of some adult (UBERON:6003004)." [FBC:auto_generated_definition] -is_a: UBERON:6000002 ! arthropod tagma intersection_of: UBERON:6000002 ! arthropod tagma intersection_of: part_of UBERON:0007023 ! adult organism -relationship: part_of UBERON:0007023 ! adult organism [Term] id: UBERON:6003006 @@ -219585,48 +219246,39 @@ is_a: UBERON:6000006 ! insect head segment is_a: UBERON:6003006 ! insect adult segment intersection_of: UBERON:0000914 ! organismal segment intersection_of: part_of UBERON:6003007 ! insect adult head -relationship: part_of UBERON:6003007 ! insect adult head [Term] id: UBERON:6003010 name: insect adult procephalic segment def: "Any procephalic segment (UBERON:6000007) that is part of some adult head (UBERON:6003007)." [FBC:auto_generated_definition] -is_a: UBERON:6000007 ! procephalic segment is_a: UBERON:6003009 ! insect adult head segment intersection_of: UBERON:6000007 ! procephalic segment intersection_of: part_of UBERON:6003007 ! insect adult head -relationship: part_of UBERON:6003007 ! insect adult head [Term] id: UBERON:6003011 name: insect adult labral segment def: "Any labral segment (UBERON:6000008) that is part of some adult head (UBERON:6003007)." [FBC:auto_generated_definition] -is_a: UBERON:6000008 ! labral segment is_a: UBERON:6003010 ! insect adult procephalic segment intersection_of: UBERON:6000008 ! labral segment intersection_of: part_of UBERON:6003007 ! insect adult head -relationship: part_of UBERON:6003007 ! insect adult head [Term] id: UBERON:6003012 name: insect adult antennal segment def: "Any antennal segment (UBERON:6000009) that is part of some adult head (UBERON:6003007)." [FBC:auto_generated_definition] synonym: "adult antennal structure" EXACT [] -is_a: UBERON:6000009 ! antennal segment is_a: UBERON:6003010 ! insect adult procephalic segment intersection_of: UBERON:6000009 ! antennal segment intersection_of: part_of UBERON:6003007 ! insect adult head -relationship: part_of UBERON:6003007 ! insect adult head [Term] id: UBERON:6003018 name: insect adult thorax def: "Thorax of the adult." [FlyBase:FBim0000792] -is_a: UBERON:6000015 ! insect thorax is_a: UBERON:6003005 ! insect adult tagma intersection_of: UBERON:6000015 ! insect thorax intersection_of: part_of UBERON:0007023 ! adult organism -relationship: part_of UBERON:0007023 ! adult organism [Term] id: UBERON:6003019 @@ -219636,7 +219288,6 @@ is_a: UBERON:6000016 ! insect thoracic segment is_a: UBERON:6003006 ! insect adult segment intersection_of: UBERON:0000914 ! organismal segment intersection_of: part_of UBERON:6003018 ! insect adult thorax -relationship: part_of UBERON:6003018 ! insect adult thorax [Term] id: UBERON:6003020 @@ -219645,11 +219296,9 @@ def: "Any prothoracic segment (UBERON:6000017) that is part of some adult thorax synonym: "prothorax" EXACT [] synonym: "t1" EXACT [] synonym: "thoracic segment 1" EXACT [] -is_a: UBERON:6000017 ! insect prothoracic segment is_a: UBERON:6003019 ! insect adult thoracic segment intersection_of: UBERON:6000017 ! insect prothoracic segment intersection_of: part_of UBERON:6003018 ! insect adult thorax -relationship: part_of UBERON:6003018 ! insect adult thorax [Term] id: UBERON:6003021 @@ -219658,31 +219307,25 @@ def: "Any mesothoracic segment (UBERON:6000018) that is part of some adult thora synonym: "mesothorax" EXACT [] synonym: "t2" EXACT [] synonym: "thoracic segment 2" EXACT [] -is_a: UBERON:6000018 ! insect mesothoracic segment is_a: UBERON:6003019 ! insect adult thoracic segment intersection_of: UBERON:6000018 ! insect mesothoracic segment intersection_of: part_of UBERON:6003018 ! insect adult thorax -relationship: part_of UBERON:6003018 ! insect adult thorax [Term] id: UBERON:6003023 name: insect adult abdomen def: "Abdomen of the adult." [FlyBase:FBim0000809, FlyBase:FBim0000810] -is_a: UBERON:6000020 ! insect abdomen is_a: UBERON:6003005 ! insect adult tagma intersection_of: UBERON:6000020 ! insect abdomen intersection_of: part_of UBERON:0007023 ! adult organism -relationship: part_of UBERON:0007023 ! adult organism [Term] id: UBERON:6003024 name: insect adult abdominal segment def: "Any abdominal segment (UBERON:6000021) that is part of some adult abdomen (UBERON:6003023)." [FBC:auto_generated_definition] -is_a: UBERON:6000021 ! insect abdominal segment is_a: UBERON:6003006 ! insect adult segment intersection_of: UBERON:6000021 ! insect abdominal segment intersection_of: part_of UBERON:6003023 ! insect adult abdomen -relationship: part_of UBERON:6003023 ! insect adult abdomen [Term] id: UBERON:6003039 @@ -219703,10 +219346,8 @@ relationship: part_of UBERON:0007023 ! adult organism id: UBERON:6003259 name: insect adult somatic muscle def: "Muscle attached to the inner surface of the adult body wall, extending between articulated or flexibly joined areas, that serves to move the parts of the exoskeleton." [FlyBase:FBrf0007735] -is_a: UBERON:0005090 ! muscle structure intersection_of: UBERON:0005090 ! muscle structure intersection_of: part_of UBERON:6003218 ! insect adult muscle system -relationship: part_of UBERON:6003218 ! insect adult muscle system [Term] id: UBERON:6003559 @@ -219929,10 +219570,8 @@ intersection_of: part_of UBERON:6000017 ! insect prothoracic segment id: UBERON:6004668 name: insect prothoracic tarsal segment def: "Tarsal segment of the adult prothoracic leg." [FBC:MMC] -is_a: UBERON:6004646 ! insect tarsal segment intersection_of: UBERON:6004646 ! insect tarsal segment intersection_of: part_of UBERON:6004663 ! insect prothoracic leg -relationship: part_of UBERON:6004663 ! insect prothoracic leg [Term] id: UBERON:6004670 @@ -219942,12 +219581,10 @@ synonym: "prothoracic basitarsus" EXACT [FlyBase:FBrf0111704] synonym: "prothoracic tarsal segment 1" EXACT [] synonym: "T1 tarsal segment 1" EXACT [] synonym: "T1 Ts1" EXACT [FlyBase:FBrf0219028] -is_a: UBERON:6004648 ! insect metatarsus is_a: UBERON:6004668 ! insect prothoracic tarsal segment intersection_of: UBERON:6004648 ! insect metatarsus intersection_of: part_of UBERON:6004663 ! insect prothoracic leg relationship: develops_from UBERON:6110746 ! insect presumptive prothoracic metatarsus -relationship: part_of UBERON:6004663 ! insect prothoracic leg [Term] id: UBERON:6004788 @@ -220341,10 +219978,8 @@ id: UBERON:6007116 name: insect presumptive embryonic/larval system def: "The sum of all the developing presumptive components of a specific embryonic/larval system in an embryo." [FBC:DOS] is_a: UBERON:0002050 ! embryonic structure -is_a: UBERON:6040003 ! insect non-connected developing system intersection_of: UBERON:6040003 ! insect non-connected developing system intersection_of: part_of UBERON:0000922 ! embryo -relationship: part_of UBERON:0000922 ! embryo [Term] id: UBERON:6007145 @@ -220365,11 +220000,9 @@ intersection_of: part_of UBERON:0000972 ! antenna id: UBERON:6007150 name: insect segment of leg def: "Any appendage segment that is part of some leg." [FBC:auto_generated_definition] -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: in_taxon NCBITaxon:50557 ! Insecta -relationship: part_of UBERON:0005895 ! insect leg [Term] id: UBERON:6007231 @@ -220397,11 +220030,9 @@ id: UBERON:6007240 name: insect embryonic/larval sensillum def: "Any sensillum (UBERON:6007152) that is part of some larva (UBERON:6001727)." [FBC:auto_generated_definition] synonym: "larval sensillum" EXACT [] -is_a: UBERON:0002536 ! arthropod sensillum is_a: UBERON:6002639 ! insect larval sense organ intersection_of: UBERON:0002536 ! arthropod sensillum intersection_of: part_of UBERON:0002548 ! larva -relationship: part_of UBERON:0002548 ! larva [Term] id: UBERON:6007242 @@ -220413,7 +220044,6 @@ is_a: UBERON:6007240 ! insect embryonic/larval sensillum is_a: UBERON:6007280 ! insect embryonic/larval head sense organ intersection_of: UBERON:0002536 ! arthropod sensillum intersection_of: part_of UBERON:6001730 ! insect larval head -relationship: part_of UBERON:6001730 ! insect larval head [Term] id: UBERON:6007245 @@ -220438,7 +220068,6 @@ synonym: "larval head sense organ" EXACT [] is_a: UBERON:6002639 ! insect larval sense organ intersection_of: UBERON:0000020 ! sense organ intersection_of: part_of UBERON:6001730 ! insect larval head -relationship: part_of UBERON:6001730 ! insect larval head [Term] id: UBERON:6007284 @@ -221512,7 +221141,6 @@ relationship: part_of UBERON:0000966 ! retina id: UBERON:8000006 name: left side of back def: "Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane." [https://microbiomedb.org/] -is_a: UBERON:0001137 ! dorsum intersection_of: UBERON:0001137 ! dorsum intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 ! Nicole Vasilevsky @@ -221521,7 +221149,6 @@ relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 ! Nicole Vasi id: UBERON:8000007 name: right side of back def: "Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane." [https://microbiomedb.org/] -is_a: UBERON:0001137 ! dorsum intersection_of: UBERON:0001137 ! dorsum intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 ! Nicole Vasilevsky @@ -221624,7 +221251,6 @@ synonym: "scalp zone of skin" EXACT [] synonym: "zone of skin of adult scalp" EXACT [] synonym: "zone of skin of scalp" EXACT [] xref: FMA:24757 -is_a: UBERON:0000014 ! zone of skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0000403 ! scalp relationship: dc-contributor https://orcid.org/0000-0001-9897-3238 ! Bonita R Lam @@ -221813,7 +221439,6 @@ xref: FMA:15957 xref: https://orcid.org/0000-0003-4183-8865 xref: TA2:2952 xref: WikipediaVersioned:Duodenojejunal_flexure&oldid=937307798 -is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction intersection_of: connects UBERON:0002114 ! duodenum intersection_of: connects UBERON:0002115 ! jejunum diff --git a/src/scripts/find-redundant-subclass-axioms.pl b/src/scripts/find-redundant-subclass-axioms.pl new file mode 100755 index 000000000..b6715d7d7 --- /dev/null +++ b/src/scripts/find-redundant-subclass-axioms.pl @@ -0,0 +1,171 @@ +#!/usr/bin/env perl + +use strict; +use warnings; + +=head1 NAME + +find-redundant-subclass-axioms.pl - Find terms with redundant SubClassOf axioms that duplicate intersection_of definitions + +=head1 SYNOPSIS + + perl find-redundant-subclass-axioms.pl uberon-edit.obo + +=head1 DESCRIPTION + +This script identifies UBERON terms that have redundant SubClassOf axioms (is_a or relationship statements) +that duplicate what is already expressed in their intersection_of definitions. + +The redundancy patterns detected are: +1. intersection_of: CLASS + is_a: CLASS (same class redundancy) +2. intersection_of: RELATION TARGET + relationship: RELATION TARGET (same relation+target redundancy) + +=head1 AUTHOR + +@dragon-ai-agent + +=cut + +# Hash to store term data +my %terms = (); +my $current_term = ''; + +# Parse the OBO file +while (my $line = <>) { + chomp $line; + + # Skip empty lines and comments + next if $line =~ /^\s*$/ || $line =~ /^!/; + + # Handle stanza headers + if ($line =~ /^\[Term\]$/) { + $current_term = ''; + next; + } + + # Skip non-term stanzas + if ($line =~ /^\[(?!Term)/) { + $current_term = ''; + next; + } + + # Skip if not in a term stanza + next unless defined $current_term; + + # Parse term ID + if ($line =~ /^id:\s+(.+)$/) { + $current_term = $1; + $terms{$current_term} = { + 'is_a' => [], + 'relationship' => [], + 'intersection_of' => [], + 'name' => '' + }; + next; + } + + # Skip if no current term + next unless $current_term; + + # Parse name + if ($line =~ /^name:\s+(.+)$/) { + $terms{$current_term}{'name'} = $1; + next; + } + + # Parse is_a relationships + if ($line =~ /^is_a:\s+(.+?)(?:\s+!\s+.*)?$/) { + push @{$terms{$current_term}{'is_a'}}, $1; + next; + } + + # Parse relationship statements + if ($line =~ /^relationship:\s+(\S+)\s+(.+?)(?:\s+!\s+.*)?$/) { + my $relation = $1; + my $target = $2; + push @{$terms{$current_term}{'relationship'}}, "$relation $target"; + next; + } + + # Parse intersection_of statements + if ($line =~ /^intersection_of:\s+(.+?)(?:\s+!\s+.*)?$/) { + my $intersection = $1; + push @{$terms{$current_term}{'intersection_of'}}, $intersection; + next; + } +} + +# Find redundant terms +my @redundant_terms = (); + +foreach my $term_id (sort keys %terms) { + my $term = $terms{$term_id}; + + # Skip terms without intersection_of statements + next unless @{$term->{'intersection_of'}} > 0; + + my @redundancies = (); + + # Check for intersection_of class duplicated in is_a + foreach my $intersection (@{$term->{'intersection_of'}}) { + # Check if this intersection_of is a simple class (not a relationship) + if ($intersection !~ /\s/) { + # Look for matching is_a + foreach my $is_a (@{$term->{'is_a'}}) { + if ($intersection eq $is_a) { + push @redundancies, "intersection_of: $intersection duplicated by is_a: $is_a"; + } + } + } + } + + # Check for intersection_of relationships duplicated in relationship statements + foreach my $intersection (@{$term->{'intersection_of'}}) { + # Check if this intersection_of is a relationship (contains space) + if ($intersection =~ /^(\S+)\s+(.+)$/) { + my $int_relation = $1; + my $int_target = $2; + + # Look for matching relationship + foreach my $relationship (@{$term->{'relationship'}}) { + if ($relationship eq "$int_relation $int_target") { + push @redundancies, "intersection_of: $int_relation $int_target duplicated by relationship: $relationship"; + } + } + } + } + + # If redundancies found, add to list + if (@redundancies > 0) { + push @redundant_terms, { + 'id' => $term_id, + 'name' => $term->{'name'}, + 'redundancies' => \@redundancies + }; + } +} + +# Output results +if (@redundant_terms == 0) { + print "No terms found with redundant SubClassOf axioms.\n"; +} else { + print "Found " . scalar(@redundant_terms) . " terms with redundant SubClassOf axioms:\n\n"; + + foreach my $redundant (@redundant_terms) { + print "=== $redundant->{'id'} ($redundant->{'name'}) ===\n"; + foreach my $redundancy (@{$redundant->{'redundancies'}}) { + print " REDUNDANT: $redundancy\n"; + } + print "\n"; + } + + # Summary + print "=== SUMMARY ===\n"; + print "Total terms with redundant axioms: " . scalar(@redundant_terms) . "\n"; + + my $total_redundancies = 0; + foreach my $redundant (@redundant_terms) { + $total_redundancies += scalar(@{$redundant->{'redundancies'}}); + } + print "Total redundant axioms found: $total_redundancies\n"; +} \ No newline at end of file diff --git a/src/scripts/remove-redundant-subclass-axioms.pl b/src/scripts/remove-redundant-subclass-axioms.pl new file mode 100755 index 000000000..a12066790 --- /dev/null +++ b/src/scripts/remove-redundant-subclass-axioms.pl @@ -0,0 +1,193 @@ +#!/usr/bin/env perl + +use strict; +use warnings; + +=head1 NAME + +remove-redundant-subclass-axioms.pl - Remove redundant SubClassOf axioms that duplicate intersection_of definitions + +=head1 SYNOPSIS + + perl remove-redundant-subclass-axioms.pl uberon-edit.obo > uberon-edit-fixed.obo + +=head1 DESCRIPTION + +This script removes redundant SubClassOf axioms (is_a or relationship statements) that duplicate +what is already expressed in their intersection_of definitions. + +The redundancy patterns removed are: +1. intersection_of: CLASS + is_a: CLASS (same class redundancy) +2. intersection_of: RELATION TARGET + relationship: RELATION TARGET (same relation+target redundancy) + +=head1 AUTHOR + +@dragon-ai-agent + +=cut + +# Hash to store term data +my %terms = (); +my $current_term = ''; +my @file_lines = (); + +# Read entire file into memory first +while (my $line = <>) { + chomp $line; + push @file_lines, $line; +} + +# First pass: Parse the OBO file to identify redundancies +my $line_index = 0; +foreach my $line (@file_lines) { + # Skip empty lines and comments + if ($line =~ /^\s*$/ || $line =~ /^!/) { + $line_index++; + next; + } + + # Handle stanza headers + if ($line =~ /^\[Term\]$/) { + $current_term = ''; + $line_index++; + next; + } + + # Skip non-term stanzas + if ($line =~ /^\[(?!Term)/) { + $current_term = ''; + $line_index++; + next; + } + + # Skip if not in a term stanza + if (!defined $current_term) { + $line_index++; + next; + } + + # Parse term ID + if ($line =~ /^id:\s+(.+)$/) { + $current_term = $1; + $terms{$current_term} = { + 'is_a' => [], + 'relationship' => [], + 'intersection_of' => [], + 'name' => '', + 'line_numbers' => { + 'is_a' => [], + 'relationship' => [], + 'intersection_of' => [] + } + }; + $line_index++; + next; + } + + # Skip if no current term + if (!$current_term) { + $line_index++; + next; + } + + # Parse name + if ($line =~ /^name:\s+(.+)$/) { + $terms{$current_term}{'name'} = $1; + $line_index++; + next; + } + + # Parse is_a relationships + if ($line =~ /^is_a:\s+(.+?)(?:\s+!\s+.*)?$/) { + push @{$terms{$current_term}{'is_a'}}, $1; + push @{$terms{$current_term}{'line_numbers'}{'is_a'}}, $line_index; + $line_index++; + next; + } + + # Parse relationship statements + if ($line =~ /^relationship:\s+(\S+)\s+(.+?)(?:\s+!\s+.*)?$/) { + my $relation = $1; + my $target = $2; + push @{$terms{$current_term}{'relationship'}}, "$relation $target"; + push @{$terms{$current_term}{'line_numbers'}{'relationship'}}, $line_index; + $line_index++; + next; + } + + # Parse intersection_of statements + if ($line =~ /^intersection_of:\s+(.+?)(?:\s+!\s+.*)?$/) { + my $intersection = $1; + push @{$terms{$current_term}{'intersection_of'}}, $intersection; + push @{$terms{$current_term}{'line_numbers'}{'intersection_of'}}, $line_index; + $line_index++; + next; + } + + $line_index++; +} + +# Find lines to remove +my %lines_to_remove = (); +my $removed_count = 0; + +foreach my $term_id (keys %terms) { + my $term = $terms{$term_id}; + + # Skip terms without intersection_of statements + next unless @{$term->{'intersection_of'}} > 0; + + # Check for intersection_of class duplicated in is_a + my $intersection_index = 0; + foreach my $intersection (@{$term->{'intersection_of'}}) { + # Check if this intersection_of is a simple class (not a relationship) + if ($intersection !~ /\s/) { + # Look for matching is_a + my $is_a_index = 0; + foreach my $is_a (@{$term->{'is_a'}}) { + if ($intersection eq $is_a) { + my $line_to_remove = $terms{$term_id}{'line_numbers'}{'is_a'}[$is_a_index]; + $lines_to_remove{$line_to_remove} = 1; + $removed_count++; + print STDERR "REMOVING: $term_id is_a: $is_a (line $line_to_remove) - duplicates intersection_of: $intersection\n"; + } + $is_a_index++; + } + } + $intersection_index++; + } + + # Check for intersection_of relationships duplicated in relationship statements + $intersection_index = 0; + foreach my $intersection (@{$term->{'intersection_of'}}) { + # Check if this intersection_of is a relationship (contains space) + if ($intersection =~ /^(\S+)\s+(.+)$/) { + my $int_relation = $1; + my $int_target = $2; + + # Look for matching relationship + my $rel_index = 0; + foreach my $relationship (@{$term->{'relationship'}}) { + if ($relationship eq "$int_relation $int_target") { + my $line_to_remove = $terms{$term_id}{'line_numbers'}{'relationship'}[$rel_index]; + $lines_to_remove{$line_to_remove} = 1; + $removed_count++; + print STDERR "REMOVING: $term_id relationship: $relationship (line $line_to_remove) - duplicates intersection_of: $intersection\n"; + } + $rel_index++; + } + } + $intersection_index++; + } +} + +# Second pass: Output the file with redundant lines removed +$line_index = 0; +foreach my $line (@file_lines) { + unless (exists $lines_to_remove{$line_index}) { + print "$line\n"; + } + $line_index++; +} + +print STDERR "\nSUMMARY: Removed $removed_count redundant SubClassOf axioms\n"; \ No newline at end of file