Merge pull request #2862 from obophenotype/fix-anatomical-cluster

Fix hierarchy under anatomical cluster (part 1)

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
@@ -185226,7 +185213,7 @@ 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]
@@ -209359,7 +209346,7 @@ 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"}
 
@@ -219995,7 +219982,8 @@ 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