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Fix hierarchy under anatomical cluster (part 1) #2862

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merged 6 commits into from
Apr 5, 2023
Merged

Fix hierarchy under anatomical cluster (part 1) #2862

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08aded5
Update definition of 'anatomical cluster'.
gouttegd Apr 3, 2023
36dd9d3
Remove irrelevant cross-references on 'anatomical cluster'.
gouttegd Apr 3, 2023
029cfa2
Move terms wrongly classified as 'anatomical cluster'.
gouttegd Apr 3, 2023
f62b36e
Remove bogus cross-reference on 'anatomical cluster'.
gouttegd Apr 5, 2023
bb4494c
Re-classify 'accessory articulation' as 'articulation'.
gouttegd Apr 5, 2023
ed3690b
Avoid using 'cluster' on non-cluster terms.
gouttegd Apr 5, 2023
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47 changes: 18 additions & 29 deletions src/ontology/uberon-edit.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -7238,27 +7238,15 @@ 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
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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
Expand Down Expand Up @@ -24653,7 +24641,7 @@ 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
Expand Down Expand Up @@ -29709,7 +29697,7 @@ 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
Expand Down Expand Up @@ -47069,7 +47057,7 @@ 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
Expand Down Expand Up @@ -52437,7 +52425,7 @@ 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
Expand Down Expand Up @@ -67855,13 +67843,13 @@ 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

Expand Down Expand Up @@ -68429,7 +68417,7 @@ 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"}
Expand Down Expand Up @@ -77029,7 +77017,7 @@ 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]
Expand Down Expand Up @@ -119787,7 +119775,7 @@ 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
Expand Down Expand Up @@ -127453,7 +127441,7 @@ 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
Expand Down Expand Up @@ -143812,7 +143800,7 @@ 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
Expand Down Expand Up @@ -147403,7 +147391,7 @@ 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
Expand Down Expand Up @@ -185227,7 +185215,7 @@ 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]
Expand Down Expand Up @@ -209360,7 +209348,7 @@ 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:0034921 ! multi organ part structure
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Unsure if this refers to something that is "multi organ".

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Each vertebra is individually considered as a separate “organ” (a vertebra is a vertebral element, which is a skeletal element, which is an organ), so I think it is consistent to say that an articulation between two vertebrae is a “multi organ part structure“ – it involves subparts of two different organs, which fits the definition of “multi organ part structure“.

But this makes me realise that this term can be classified even more precisely under articulation (UBERON:0004905), which is a subclass of multi organ part structure. I’ll do that now.

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"}

Expand Down Expand Up @@ -219996,7 +219984,8 @@ 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

Expand Down