Fixing lung multiciliated cell heirarchy (#2735)

* Fixing lung multiciliated cell hierarchy Fixed by aligning both textual and logical defs for types at multiple levels of the partonomy - from respiratory tract epithelium down. Updated airway submucosal gland ciliated cell too --------- Co-authored-by: Caroline Eastwood <[email protected]> Co-authored-by: CEastwood <[email protected]>
obophenotype · Nov 8, 2024 · dfdb411 · dfdb411
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diff --git a/src/mappings/fbbt.sssom.tsv b/src/mappings/fbbt.sssom.tsv
@@ -1,17 +1,17 @@
 #curie_map:
-#  CL: http://purl.obolibrary.org/obo/CL_
-#  FBbt: http://purl.obolibrary.org/obo/FBbt_
-#  ORCID: https://orcid.org/
-#  obo: http://purl.obolibrary.org/obo/
-#mapping_set_id: http://purl.obolibrary.org/obo/fbbt/fbbt-mappings.sssom.tsv
-#mapping_set_description: Mappings between the Drosophila Anatomy Ontology and foreign ontologies.
+#  CL: "http://purl.obolibrary.org/obo/CL_"
+#  FBbt: "http://purl.obolibrary.org/obo/FBbt_"
+#  ORCID: "https://orcid.org/"
+#  obo: "http://purl.obolibrary.org/obo/"
+#mapping_set_id: "http://purl.obolibrary.org/obo/fbbt/fbbt-mappings.sssom.tsv"
+#mapping_set_description: "Mappings between the Drosophila Anatomy Ontology and foreign ontologies."
 #creator_id:
-#  - ORCID:0000-0002-1373-1705
-#  - ORCID:0000-0002-6095-8718
-#license: https://creativecommons.org/licenses/by/4.0/
-#subject_source: obo:fbbt.owl
-#object_source: obo:cl.owl
-#mapping_date: 2024-07-12
+#  - "ORCID:0000-0002-1373-1705"
+#  - "ORCID:0000-0002-6095-8718"
+#license: "https://creativecommons.org/licenses/by/4.0/"
+#subject_source: "obo:fbbt.owl"
+#object_source: "obo:cl.owl"
+#mapping_date: "2024-07-12"
 subject_id	subject_label	predicate_id	object_id	mapping_justification
 FBbt:00000092	primordial germ cell	semapv:crossSpeciesExactMatch	CL:0000301	semapv:ManualMappingCuration
 FBbt:00000124	epithelial cell	semapv:crossSpeciesExactMatch	CL:0000066	semapv:ManualMappingCuration

diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl
@@ -3143,6 +3143,7 @@ Declaration(Class(obo:GO_0036053))
 Declaration(Class(obo:GO_0036376))
 Declaration(Class(obo:GO_0042599))
 Declaration(Class(obo:GO_0044316))
+Declaration(Class(obo:GO_0050893))
 Declaration(Class(obo:GO_0070278))
 Declaration(Class(obo:GO_0070483))
 Declaration(Class(obo:GO_0097729))
@@ -15301,10 +15302,7 @@ AnnotationAssertion(oboInOwl:creation_date obo:CL_0002145 "2010-08-24T03:38:29Z"
 AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002145 "FMA:70542")
 AnnotationAssertion(Annotation(oboInOwl:hasDbXref <https://doi.org/10.1016/B978-032304048-8.50071-2>) Annotation(oboInOwl:hasDbXref "PMID:25386990") rdfs:comment obo:CL_0002145 "These cells possess numerous cilia on their surface, typically ranging from 200 to 300 per cell. The cilia vary in length, measuring between 6 to 7 μm in the upper airways (trachea) and becoming shorter, around 4 μm, in the smaller airways (terminal bronchioles). These cells form a two-layered 'coat' in the airway: the lower 'sol' layer is watery, allowing the cilia to beat in coordinated waves, while the upper 'gel' layer is thick and sticky, trapping inhaled particles.")
 AnnotationAssertion(rdfs:label obo:CL_0002145 "ciliated columnar cell of tracheobronchial tree")
-SubClassOf(obo:CL_0002145 obo:CL_0002202)
-SubClassOf(obo:CL_0002145 obo:CL_0005012)
-SubClassOf(obo:CL_0002145 obo:CL_4030034)
-SubClassOf(obo:CL_0002145 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0031514))
+EquivalentClasses(obo:CL_0002145 ObjectIntersectionOf(obo:CL_0000075 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0008397) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0031514) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0010007)))
 SubClassOf(obo:CL_0002145 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0002209))
 
 # Class: obo:CL_0002146 (clear cell of eccrine sweat gland)
@@ -17334,12 +17332,11 @@ AnnotationAssertion(owl:deprecated obo:CL_0002331 "true"^^xsd:boolean)
 
 # Class: obo:CL_0002332 (ciliated cell of the bronchus)
 
-AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "PMID:18757316") obo:IAO_0000115 obo:CL_0002332 "A ciliated cell of the bronchus.")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "PMID:18757316") obo:IAO_0000115 obo:CL_0002332 "A multi-ciliated epithelial cell located in the bronchus epithelium, characterized by a columnar shape and motile cilia on its apical surface.")
 AnnotationAssertion(terms:contributor obo:CL_0002332 <https://orcid.org/0000-0003-1980-3228>)
 AnnotationAssertion(oboInOwl:creation_date obo:CL_0002332 "2010-09-20T02:21:12Z"^^xsd:dateTime)
 AnnotationAssertion(rdfs:label obo:CL_0002332 "ciliated cell of the bronchus")
-EquivalentClasses(obo:CL_0002332 ObjectIntersectionOf(obo:CL_0000064 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002031)))
-SubClassOf(obo:CL_0002332 obo:CL_0002145)
+EquivalentClasses(obo:CL_0002332 ObjectIntersectionOf(obo:CL_0000075 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002031) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0031514) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0010007)))
 
 # Class: obo:CL_0002333 (neural crest derived adipocyte)
 
@@ -25059,7 +25056,7 @@ EquivalentClasses(obo:CL_1000245 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeV
 
 AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:27864314") obo:IAO_0000115 obo:CL_1000271 "An epithelial cell that is part of the lung epithelium. This cell is characterised by the presence of cilia on its apical surface.")
 AnnotationAssertion(rdfs:label obo:CL_1000271 "lung ciliated cell")
-EquivalentClasses(obo:CL_1000271 ObjectIntersectionOf(obo:CL_0000067 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000115)))
+EquivalentClasses(obo:CL_1000271 ObjectIntersectionOf(obo:CL_0000075 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000115) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0031514) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0010007)))
 
 # Class: obo:CL_1000272 (lung secretory cell)
 
@@ -31059,12 +31056,11 @@ EquivalentClasses(obo:CL_4030033 ObjectIntersectionOf(obo:CL_0000115 ObjectSomeV
 
 # Class: obo:CL_4030034 (respiratory ciliated cell)
 
-AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:18757316") Annotation(oboInOwl:hasDbXref "PMID:21364219") obo:IAO_0000115 obo:CL_4030034 "A ciliated cell of the respiratory system. Ciliated cells are present in airway epithelium.")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:18757316") Annotation(oboInOwl:hasDbXref "PMID:21364219") obo:IAO_0000115 obo:CL_4030034 "A multi-ciliated epithelial cell located in the respiratory tract epithelium, characterized by a columnar shape and motile cilia on its apical surface.")
 AnnotationAssertion(terms:date obo:CL_4030034 "2023-01-25T11:06:01Z"^^xsd:dateTime)
 AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4030034 "ciliated cell of the respiratory tract")
 AnnotationAssertion(rdfs:label obo:CL_4030034 "respiratory ciliated cell")
-EquivalentClasses(obo:CL_4030034 ObjectIntersectionOf(obo:CL_0000064 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004802)))
-SubClassOf(obo:CL_4030034 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001004))
+EquivalentClasses(obo:CL_4030034 ObjectIntersectionOf(obo:CL_0000075 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004802) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0031514) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0010007)))
 
 # Class: obo:CL_4030035 (dental pulp stem cell)
 
@@ -31983,12 +31979,12 @@ EquivalentClasses(obo:CL_4033054 ObjectIntersectionOf(obo:CL_0000000 ObjectSomeV
 
 # Class: obo:CL_4033055 (airway submucosal gland duct ciliated cell)
 
-AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:17707699") Annotation(oboInOwl:hasDbXref "PMID:30864819") obo:IAO_0000115 obo:CL_4033055 "A ciliated cell that is part of a ciliated duct of an airway submucosal gland.")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:17707699") Annotation(oboInOwl:hasDbXref "PMID:30864819") obo:IAO_0000115 obo:CL_4033055 "A multi-ciliated epithelial cell located in ciliated duct of an airway submucosal gland, characterized by a columnar shape and motile cilia on its apical surface.")
 AnnotationAssertion(terms:contributor obo:CL_4033055 <https://orcid.org/0000-0001-6677-8489>)
 AnnotationAssertion(terms:contributor obo:CL_4033055 <https://orcid.org/0000-0002-9185-3994>)
 AnnotationAssertion(terms:date obo:CL_4033055 "2023-09-08T10:32:27Z"^^xsd:dateTime)
 AnnotationAssertion(rdfs:label obo:CL_4033055 "airway submucosal gland duct ciliated cell")
-EquivalentClasses(obo:CL_4033055 ObjectIntersectionOf(obo:CL_0000064 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8410077) ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8600014)))
+EquivalentClasses(obo:CL_4033055 ObjectIntersectionOf(obo:CL_0000075 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8410077) ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8600014) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0031514) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0010007)))
 
 # Class: obo:CL_4033056 (onychocyte)
 

diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl
@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/cl/imports/merged_import.owl>
-<http://purl.obolibrary.org/obo/cl/releases/2024-11-05/imports/merged_import.owl>
-Annotation(owl:versionInfo "2024-11-05")
+<http://purl.obolibrary.org/obo/cl/releases/2024-11-07/imports/merged_import.owl>
+Annotation(owl:versionInfo "2024-11-07")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000003>))

diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl
@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/cl/patterns/definitions.owl>
-<http://purl.obolibrary.org/obo/cl/releases/2024-11-05/patterns/definitions.owl>
-Annotation(owl:versionInfo "2024-11-05")
+<http://purl.obolibrary.org/obo/cl/releases/2024-11-07/patterns/definitions.owl>
+Annotation(owl:versionInfo "2024-11-07")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000031>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000084>))