From f946491c09ceca93f55618518f4cd544b20111f5 Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Thu, 18 Jul 2024 09:37:36 +0100 Subject: [PATCH 1/8] An ongoing PR - Clean up ciliated epithelial cells hierarchy and links to GO terms An ongoing PR for cleaning up ciliated epithelial cells hierarchy and links to GO terms - Imported GO terms into CL: - GO:0097730 (non-motile cilium) - GO:0036126 (sperm flagellum) --- src/mappings/zfa.sssom.tsv | 1 + src/ontology/components/mappings.owl | 2 +- src/ontology/imports/merged_import.owl | 4 ++-- src/patterns/definitions.owl | 4 ++-- 4 files changed, 6 insertions(+), 5 deletions(-) diff --git a/src/mappings/zfa.sssom.tsv b/src/mappings/zfa.sssom.tsv index 932d1b132..6c8f79183 100644 --- a/src/mappings/zfa.sssom.tsv +++ b/src/mappings/zfa.sssom.tsv @@ -3,6 +3,7 @@ # ZFA: "http://purl.obolibrary.org/obo/ZFA_" #mapping_set_id: "http://purl.obolibrary.org/obo/zfa/zfa.sssom.tsv" #license: "https://creativecommons.org/licenses/by/3.0/" +#subject_source: "http://purl.obolibrary.org/obo/zfa.owl" subject_id subject_label predicate_id object_id mapping_justification mapping_cardinality ZFA:0000003 adaxial cell semapv:crossSpeciesExactMatch CL:0007016 semapv:UnspecifiedMatching 1:1 ZFA:0000084 yolk semapv:crossSpeciesExactMatch CL:0000428 semapv:UnspecifiedMatching 1:1 diff --git a/src/ontology/components/mappings.owl b/src/ontology/components/mappings.owl index 56e87ec7d..cfb6e4cbc 100644 --- a/src/ontology/components/mappings.owl +++ b/src/ontology/components/mappings.owl @@ -4572,5 +4572,5 @@ - + diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 71931fffb..cc589db9c 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-07-09") + +Annotation(owl:versionInfo "2024-07-18") Declaration(Class()) Declaration(Class()) diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index ccbcd836b..71a4a759f 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-07-09") + +Annotation(owl:versionInfo "2024-07-18") From 4dad5f9fe0867503ce55f75e685efcac75f11024 Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Mon, 22 Jul 2024 11:37:00 +0100 Subject: [PATCH 2/8] Updated logical and textual definition of endometrial ciliated epithelial cell - Updated logical and textual definition of endometrial ciliated epithelial cell. -Included links to GO terms - Added references to support that endometrial ciliated epithelial cell are multi-ciliated cells --- src/ontology/cl-edit.owl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 7ecdd0e66..ac5ea304a 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -30945,7 +30945,7 @@ SubClassOf(obo:CL_4030039 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0070006)) # Class: obo:CL_4030040 (endometrial ciliated epithelial cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41591-020-1040-z") Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells") obo:IAO_0000115 obo:CL_4030040 "A ciliated cell of the endometrial epithelium. The cilia of this cell type help move mucus from glandular tissue of the endometrium.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41591-020-1040-z") Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells") Annotation(oboInOwl:hasDbXref "PMID:31290979") Annotation(rdfs:comment "PMID:37999981") obo:IAO_0000115 obo:CL_4030040 "A multi-ciliated cell of the endometrial epithelium. This cell is characterized by the presence of motile cilia on its apical surface, which facilitates the movement of mucous across the endometrial surface.") AnnotationAssertion(terms:date obo:CL_4030040 "2023-02-09T11:25:14Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_4030040 "ciliated cell of the uterus") AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_4030040 "uterine ciliated cell") @@ -30953,7 +30953,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4030040 "ciliated cell of th AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4030040 "endometrium ciliated epithelial cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "ttps://www.nature.com/articles/s41591-020-1040-z") rdfs:comment obo:CL_4030040 "In human samples, the expression of FOXJ1 protein, a regulator for motile cilia with epithelial lineage identity, has been noted.") AnnotationAssertion(rdfs:label obo:CL_4030040 "endometrial ciliated epithelial cell") -EquivalentClasses(obo:CL_4030040 ObjectIntersectionOf(obo:CL_0000064 obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004811))) +EquivalentClasses(obo:CL_4030040 ObjectIntersectionOf(obo:CL_0005012 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004811) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0031514))) # Class: obo:CL_4030041 (luminal endometrial ciliated epithelial cell) From 7e9dff3ee6cddc1cf004e6847cd77edd1885c64a Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Mon, 22 Jul 2024 11:40:16 +0100 Subject: [PATCH 3/8] Update cl-edit.owl --- src/ontology/cl-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index ac5ea304a..4c8571e23 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -30945,7 +30945,7 @@ SubClassOf(obo:CL_4030039 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0070006)) # Class: obo:CL_4030040 (endometrial ciliated epithelial cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41591-020-1040-z") Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells") Annotation(oboInOwl:hasDbXref "PMID:31290979") Annotation(rdfs:comment "PMID:37999981") obo:IAO_0000115 obo:CL_4030040 "A multi-ciliated cell of the endometrial epithelium. This cell is characterized by the presence of motile cilia on its apical surface, which facilitates the movement of mucous across the endometrial surface.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41591-020-1040-z") Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells") Annotation(oboInOwl:hasDbXref "PMID:31290979") Annotation(oboInOwl:hasDbXref "PMID:37999981") obo:IAO_0000115 obo:CL_4030040 "A multi-ciliated cell of the endometrial epithelium. This cell is characterized by the presence of motile cilia on its apical surface, which facilitates the movement of mucous across the endometrial surface.") AnnotationAssertion(terms:date obo:CL_4030040 "2023-02-09T11:25:14Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_4030040 "ciliated cell of the uterus") AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_4030040 "uterine ciliated cell") From c7d8985f0c778f1b2832245a37093c62d3cce507 Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Mon, 22 Jul 2024 12:12:17 +0100 Subject: [PATCH 4/8] Updated textual defs --- src/ontology/cl-edit.owl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 4c8571e23..cc72a2687 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -30957,7 +30957,7 @@ EquivalentClasses(obo:CL_4030040 ObjectIntersectionOf(obo:CL_0005012 ObjectSomeV # Class: obo:CL_4030041 (luminal endometrial ciliated epithelial cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41591-020-1040-z") obo:IAO_0000115 obo:CL_4030041 "A ciliated cell of the endometrial luminal epithelium.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41591-020-1040-z") obo:IAO_0000115 obo:CL_4030041 "A ciliated cell of the endometrial luminal epithelium. This cell is characterized by the presence of motile cilia on its apical surface.") AnnotationAssertion(terms:date obo:CL_4030041 "2023-02-09T11:34:42Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:CL_4030041 "luminal endometrial ciliated epithelial cell") SubClassOf(obo:CL_4030041 obo:CL_4030040) @@ -30965,7 +30965,7 @@ SubClassOf(obo:CL_4030041 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_001194 # Class: obo:CL_4030042 (glandular endometrial ciliated epithelial cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41591-020-1040-z") obo:IAO_0000115 obo:CL_4030042 "A ciliated cell of the endometrial glandular epithelium.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41591-020-1040-z") obo:IAO_0000115 obo:CL_4030042 "A ciliated cell of the endometrial glandular epithelium. This cell is characterized by the presence of motile cilia on its apical surface.") AnnotationAssertion(terms:date obo:CL_4030042 "2023-02-09T11:37:30Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:CL_4030042 "glandular endometrial ciliated epithelial cell") SubClassOf(obo:CL_4030042 obo:CL_4030040) From 36a451a4863aa714b0b533309848d5b10cb9a22a Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Tue, 23 Jul 2024 13:22:13 +0100 Subject: [PATCH 5/8] Revert "An ongoing PR - Clean up ciliated epithelial cells hierarchy and links to GO terms" This reverts commit f946491c09ceca93f55618518f4cd544b20111f5. Reason, GO terms to be imported were not added. --- src/mappings/zfa.sssom.tsv | 1 - src/ontology/components/mappings.owl | 2 +- src/ontology/imports/merged_import.owl | 4 ++-- src/patterns/definitions.owl | 4 ++-- 4 files changed, 5 insertions(+), 6 deletions(-) diff --git a/src/mappings/zfa.sssom.tsv b/src/mappings/zfa.sssom.tsv index 6c8f79183..932d1b132 100644 --- a/src/mappings/zfa.sssom.tsv +++ b/src/mappings/zfa.sssom.tsv @@ -3,7 +3,6 @@ # ZFA: "http://purl.obolibrary.org/obo/ZFA_" #mapping_set_id: "http://purl.obolibrary.org/obo/zfa/zfa.sssom.tsv" #license: "https://creativecommons.org/licenses/by/3.0/" -#subject_source: "http://purl.obolibrary.org/obo/zfa.owl" subject_id subject_label predicate_id object_id mapping_justification mapping_cardinality ZFA:0000003 adaxial cell semapv:crossSpeciesExactMatch CL:0007016 semapv:UnspecifiedMatching 1:1 ZFA:0000084 yolk semapv:crossSpeciesExactMatch CL:0000428 semapv:UnspecifiedMatching 1:1 diff --git a/src/ontology/components/mappings.owl b/src/ontology/components/mappings.owl index cfb6e4cbc..56e87ec7d 100644 --- a/src/ontology/components/mappings.owl +++ b/src/ontology/components/mappings.owl @@ -4572,5 +4572,5 @@ - + diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index cc589db9c..71931fffb 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-07-18") + +Annotation(owl:versionInfo "2024-07-09") Declaration(Class()) Declaration(Class()) diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index 71a4a759f..ccbcd836b 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-07-18") + +Annotation(owl:versionInfo "2024-07-09") From dd1fbe8af4f706e67b1e6ef7f391a17050b8b252 Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Wed, 24 Jul 2024 09:40:57 +0100 Subject: [PATCH 6/8] Updated logical and textual defs - Imported GO:0097729 - 9+2 motile cilium - Updated logical definition - Updated textual definition and added reference to support 9+2 motile cilia --- src/ontology/cl-edit.owl | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 5096556f8..cfb2f41bf 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3073,6 +3073,7 @@ Declaration(Class(obo:GO_0042599)) Declaration(Class(obo:GO_0044316)) Declaration(Class(obo:GO_0070278)) Declaration(Class(obo:GO_0070483)) +Declaration(Class(obo:GO_0097729)) Declaration(Class(obo:NCBITaxon_4896)) Declaration(Class(obo:NCBITaxon_6157)) Declaration(Class(obo:NCBITaxon_6237)) @@ -30947,7 +30948,7 @@ SubClassOf(obo:CL_4030039 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0070006)) # Class: obo:CL_4030040 (endometrial ciliated epithelial cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41591-020-1040-z") Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells") Annotation(oboInOwl:hasDbXref "PMID:31290979") Annotation(oboInOwl:hasDbXref "PMID:37999981") obo:IAO_0000115 obo:CL_4030040 "A multi-ciliated cell of the endometrial epithelium. This cell is characterized by the presence of motile cilia on its apical surface, which facilitates the movement of mucous across the endometrial surface.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) Annotation(oboInOwl:hasDbXref "PMID:31290979") Annotation(oboInOwl:hasDbXref "PMID:37999981") Annotation(oboInOwl:hasDbXref "doi:10.1038/s41591-020-1040-z") Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells") obo:IAO_0000115 obo:CL_4030040 "A multi-ciliated cell of the endometrial epithelium. This cell is characterized by the presence of 9+2 motile cilia on its apical surface, which facilitates the movement of mucous across the endometrial surface.") AnnotationAssertion(terms:date obo:CL_4030040 "2023-02-09T11:25:14Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_4030040 "ciliated cell of the uterus") AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_4030040 "uterine ciliated cell") @@ -30955,7 +30956,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4030040 "ciliated cell of th AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4030040 "endometrium ciliated epithelial cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "ttps://www.nature.com/articles/s41591-020-1040-z") rdfs:comment obo:CL_4030040 "In human samples, the expression of FOXJ1 protein, a regulator for motile cilia with epithelial lineage identity, has been noted.") AnnotationAssertion(rdfs:label obo:CL_4030040 "endometrial ciliated epithelial cell") -EquivalentClasses(obo:CL_4030040 ObjectIntersectionOf(obo:CL_0005012 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004811) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0031514))) +EquivalentClasses(obo:CL_4030040 ObjectIntersectionOf(obo:CL_0005012 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004811) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0097729))) # Class: obo:CL_4030041 (luminal endometrial ciliated epithelial cell) From fc37ef93efc7324685989c8dd2aa8d766aad8632 Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Wed, 24 Jul 2024 11:45:01 +0100 Subject: [PATCH 7/8] DOI updated --- src/ontology/cl-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index cfb2f41bf..af08f09a4 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -30948,7 +30948,7 @@ SubClassOf(obo:CL_4030039 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0070006)) # Class: obo:CL_4030040 (endometrial ciliated epithelial cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) Annotation(oboInOwl:hasDbXref "PMID:31290979") Annotation(oboInOwl:hasDbXref "PMID:37999981") Annotation(oboInOwl:hasDbXref "doi:10.1038/s41591-020-1040-z") Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells") obo:IAO_0000115 obo:CL_4030040 "A multi-ciliated cell of the endometrial epithelium. This cell is characterized by the presence of 9+2 motile cilia on its apical surface, which facilitates the movement of mucous across the endometrial surface.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) Annotation(oboInOwl:hasDbXref "PMID:31290979") Annotation(oboInOwl:hasDbXref "PMID:37999981") Annotation(oboInOwl:hasDbXref "doi:10.1038/s41591-020-1040-z") Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells") obo:IAO_0000115 obo:CL_4030040 "A multi-ciliated cell of the endometrial epithelium. This cell is characterized by the presence of 9+2 motile cilia on its apical surface, which facilitates the movement of mucus across the endometrial surface.") AnnotationAssertion(terms:date obo:CL_4030040 "2023-02-09T11:25:14Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_4030040 "ciliated cell of the uterus") AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_4030040 "uterine ciliated cell") From e1d586626b92ad1a92eabbdf66aa4503db63e9b9 Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Wed, 24 Jul 2024 13:13:04 +0100 Subject: [PATCH 8/8] Update cl-edit.owl --- src/ontology/cl-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index af08f09a4..ebed75cec 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -30948,7 +30948,7 @@ SubClassOf(obo:CL_4030039 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0070006)) # Class: obo:CL_4030040 (endometrial ciliated epithelial cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) Annotation(oboInOwl:hasDbXref "PMID:31290979") Annotation(oboInOwl:hasDbXref "PMID:37999981") Annotation(oboInOwl:hasDbXref "doi:10.1038/s41591-020-1040-z") Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells") obo:IAO_0000115 obo:CL_4030040 "A multi-ciliated cell of the endometrial epithelium. This cell is characterized by the presence of 9+2 motile cilia on its apical surface, which facilitates the movement of mucus across the endometrial surface.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31290979") Annotation(oboInOwl:hasDbXref "PMID:37999981") Annotation(oboInOwl:hasDbXref "doi:10.1038/s41591-020-1040-z") Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells") Annotation(oboInOwl:hasDbXref "doi:10.1016/j.coemr.2024.100503") obo:IAO_0000115 obo:CL_4030040 "A multi-ciliated cell of the endometrial epithelium. This cell is characterized by the presence of 9+2 motile cilia on its apical surface, which facilitates the movement of mucus across the endometrial surface.") AnnotationAssertion(terms:date obo:CL_4030040 "2023-02-09T11:25:14Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_4030040 "ciliated cell of the uterus") AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_4030040 "uterine ciliated cell")