diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index a3a7748c86..5ed0f1091c 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -7238,27 +7238,14 @@ relationship: present_in_taxon NCBITaxon:4751 ! Fungi [Term] id: UBERON:0000477 name: anatomical cluster -def: "Anatomical group that has its parts adjacent to one another." [http://orcid.org/0000-0001-9114-8737] +def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: AAO:0010009 -xref: AEO:0000041 -xref: BILA:0000041 -xref: CARO:0000041 -xref: EHDAA2:0003041 -xref: FMA:49443 -xref: HAO:0000041 -xref: TADS:0000605 -xref: TAO:0001478 -xref: TGMA:0001842 xref: VHOG:0001737 -xref: XAO:0003160 -xref: ZFA:0001478 is_a: UBERON:0034923 ! disconnected anatomical group relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae relationship: present_in_taxon NCBITaxon:33208 ! Metazoa relationship: present_in_taxon NCBITaxon:4751 ! Fungi -property_value: editor_note "Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3]" xsd:string [Term] id: UBERON:0000478 @@ -9675,7 +9662,7 @@ property_value: homology_notes "Most anatomists now agree that the three proxima [Term] id: UBERON:0000982 name: skeletal joint -def: "Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000101, Wikipedia:Joint] +def: "Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000101, Wikipedia:Joint] subset: efo_slim subset: organ_slim subset: pheno_slim @@ -24653,7 +24640,7 @@ xref: FMA:45659 xref: galen:LowerUrinaryTract xref: MA:0002636 xref: SCTID:181420004 -is_a: UBERON:0000477 ! anatomical cluster +is_a: UBERON:0011216 ! organ system subdivision relationship: has_part UBERON:0000057 ! urethra relationship: has_part UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001008 ! renal system @@ -29709,7 +29696,7 @@ xref: NCIT:C12231 xref: SCTID:245784004 xref: UMLS:C0030219 {source="ncithesaurus:Soft_Palate"} xref: Wikipedia:Soft_palate -is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster +is_a: UBERON:0034921 {source="FMA"} ! multi organ part structure relationship: never_in_taxon NCBITaxon:8782 {source="GOC:fmc"} ! Aves relationship: part_of UBERON:0000165 {source="FMA"} ! mouth relationship: part_of UBERON:0001716 {source="MA"} ! secondary palate @@ -47069,7 +47056,7 @@ xref: NCIT:C32891 xref: SCTID:362219002 xref: UMLS:C0022445 {source="ncithesaurus:Juxtaglomerular_Apparatus"} xref: Wikipedia:Juxtaglomerular_apparatus -is_a: UBERON:0000477 ! anatomical cluster +is_a: UBERON:0000061 ! anatomical structure relationship: capable_of GO:0003093 {source="GO"} ! regulation of glomerular filtration relationship: has_part CL:0000648 ! kidney granular cell relationship: has_part CL:0002173 ! extraglomerular mesangial cell @@ -52437,7 +52424,7 @@ xref: NCIT:C12724 xref: SCTID:264482000 xref: UMLS:C0017681 {source="ncithesaurus:Glottis"} xref: Wikipedia:Glottis -is_a: UBERON:0000477 ! anatomical cluster +is_a: UBERON:0000061 ! anatomical structure relationship: contributes_to_morphology_of UBERON:0001737 ! larynx relationship: part_of UBERON:0001737 ! larynx property_value: depicted_by "https://upload.wikimedia.org/wikipedia/commons/3/32/Arytenoid_cartilage.png" xsd:anyURI @@ -67855,13 +67842,13 @@ consider: HAO:0000716 [Term] id: UBERON:0003153 -name: head capsule -comment: will be ceded to arthropod anatomy ontology +name: insect head capsule +def: "The fused, compact cephalic plates that comprise the head, excluding the eyes, antennae and mouthparts." [FBbt:00004482] subset: efo_slim xref: BTO:0004711 xref: EFO:0001927 xref: HAO:0000398 -is_a: UBERON:0000477 ! anatomical cluster +is_a: UBERON:6007284 ! insect region of integument relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0000033 ! head @@ -68429,7 +68416,7 @@ xref: NCIT:C12230 xref: SCTID:245778002 xref: UMLS:C0226901 {source="ncithesaurus:Hard_Palate"} xref: Wikipedia:Hard_palate -is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster +is_a: UBERON:0034921 {source="FMA"} ! multi organ part structure relationship: part_of UBERON:0001716 {notes="check this", source="EMAPA"} ! secondary palate property_value: depicted_by "https://upload.wikimedia.org/wikipedia/commons/f/f6/Illu_mouth.jpg" xsd:anyURI property_value: external_ontology_notes "in FMA this is divided into bony parts and submucosa" xsd:string {external_ontology="FMA"} @@ -77029,7 +77016,7 @@ xref: MESH:D009470 xref: NCIT:C13824 xref: SCTID:12945004 xref: UMLS:C0027871 {source="ncithesaurus:Muscle_Spindle"} -is_a: UBERON:0000477 ! anatomical cluster +is_a: UBERON:0000061 ! anatomical structure relationship: part_of UBERON:0001016 ! nervous system [Term] @@ -93975,7 +93962,7 @@ relationship: part_of UBERON:0002104 ! visual system [Term] id: UBERON:0004905 name: articulation -def: "Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] +def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] is_a: UBERON:0034921 ! multi organ part structure @@ -119787,7 +119774,7 @@ def: "The osseous cochlea is the bony foundation that forms the small shell arra subset: pheno_slim xref: EMAPA:35620 xref: MA:0000239 -is_a: UBERON:0000477 ! anatomical cluster +is_a: UBERON:0000061 ! anatomical structure relationship: part_of UBERON:0001839 ! bony labyrinth relationship: part_of UBERON:0001844 ! cochlea property_value: editor_note "TODO - check this. in MA, cochlea is not part of the bony labyrinth" xsd:string @@ -127453,7 +127440,7 @@ xref: EHDAA2:0000187 xref: FMA:293041 xref: NCIT:C34248 xref: UMLS:C1519038 {source="ncithesaurus:Pharyngeal_Apparatus"} -is_a: UBERON:0000477 ! anatomical cluster +is_a: UBERON:0034921 ! multi organ part structure relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0009145 ! pharyngeal region of foregut @@ -143812,7 +143799,7 @@ xref: FMA:45658 xref: galen:UpperUrinaryTract xref: NCIT:C61107 xref: SCTID:181413006 -is_a: UBERON:0000477 ! anatomical cluster +is_a: UBERON:0011216 ! organ system subdivision relationship: has_part UBERON:0000056 ! ureter relationship: has_part UBERON:0002113 ! kidney relationship: in_lateral_side_of UBERON:0001008 {source="FMA-abduced-lr"} ! renal system @@ -147403,7 +147390,7 @@ synonym: "plica anterior faucium" EXACT LATIN [FMA:TA] xref: FMA:55024 xref: SCTID:276958001 xref: Wikipedia:Palatoglossal_arch -is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster +is_a: UBERON:0034921 {source="FMA"} ! multi organ part structure relationship: adjacent_to UBERON:0000165 ! mouth relationship: adjacent_to UBERON:0001042 ! chordate pharynx relationship: part_of UBERON:0001555 ! digestive tract @@ -185227,7 +185214,7 @@ xref: NCIT:C32574 xref: SCTID:120612006 xref: UMLS:C0229243 xref: Wikipedia:Accessory_visual_structures -is_a: UBERON:0000477 ! anatomical cluster +is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004088 ! orbital region [Term] @@ -209360,7 +209347,7 @@ property_value: provenance_notes "This class was sourced from an external ontolo id: UBERON:3000809 name: accessory articulation def: "Paired, additional vertebral articulations located medial to the intervertebral space, adjacent to the vertebral centrum." [AAO:Cannatella_1985] -is_a: UBERON:0000477 ! anatomical cluster +is_a: UBERON:0004905 ! articulation relationship: part_of UBERON:0002412 ! vertebra property_value: provenance_notes "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/aao.owl"} @@ -219996,7 +219983,8 @@ relationship: part_of UBERON:6005396 ! insect adult integumentary system [Term] id: UBERON:6004823 name: insect analia -is_a: UBERON:0000477 ! anatomical cluster +def: "The set of external structures of adult abdominal segment(s) that makes up the anal apparatus." [PMID:27747420] +is_a: UBERON:0000061 ! anatomical structure relationship: develops_from UBERON:6001784 ! insect genital disc relationship: part_of UBERON:6004788 ! insect adult external abdomen