From bc0019dd322ee531f3380a715293447919619086 Mon Sep 17 00:00:00 2001 From: bvarner-ebi <95643797+bvarner-ebi@users.noreply.github.com> Date: Wed, 30 Aug 2023 10:19:12 +0100 Subject: [PATCH 1/5] Addresses #2126 Edit 'polyploid cell' --- src/ontology/cl-edit.owl | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 9814a8778..653c5b794 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3017,6 +3017,7 @@ Declaration(Class(obo:NCBITaxon_6157)) Declaration(Class(obo:NCBITaxon_6237)) Declaration(Class(obo:NCBITaxon_9789)) Declaration(Class(obo:PATO_0000405)) +Declaration(Class(obo:PATO_0001377)) Declaration(Class(obo:PATO_0001870)) Declaration(Class(obo:PATO_0001979)) Declaration(Class(obo:PATO_0070002)) @@ -6944,8 +6945,9 @@ SubClassOf(obo:CL_0000411 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_6237 # Class: obo:CL_0000412 (polyploid cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "FB:ma") obo:IAO_0000115 obo:CL_0000412 "A cell whose nucleus, or nuclei, each contain more than two haploid genomes.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "FB:ma") Annotation(rdfs:comment "PMID:32646579") Annotation(rdfs:seeAlso "https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy"^^xsd:anyURI) obo:IAO_0000115 obo:CL_0000412 "A cell that contains more than two haploid sets of chromosomes.") AnnotationAssertion(rdfs:label obo:CL_0000412 "polyploid cell") +EquivalentClasses(obo:CL_0000412 ObjectIntersectionOf(obo:CL_0000000 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001377))) SubClassOf(obo:CL_0000412 obo:CL_0000003) # Class: obo:CL_0000413 (haploid cell) From ffbfe54634f6770df3f030f3167f18209bd1afff Mon Sep 17 00:00:00 2001 From: bvarner-ebi <95643797+bvarner-ebi@users.noreply.github.com> Date: Wed, 30 Aug 2023 10:32:51 +0100 Subject: [PATCH 2/5] Update cl-edit.owl change 'see also' to source --- 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 653c5b794..17e1b1254 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -6945,7 +6945,7 @@ SubClassOf(obo:CL_0000411 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_6237 # Class: obo:CL_0000412 (polyploid cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "FB:ma") Annotation(rdfs:comment "PMID:32646579") Annotation(rdfs:seeAlso "https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy"^^xsd:anyURI) obo:IAO_0000115 obo:CL_0000412 "A cell that contains more than two haploid sets of chromosomes.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "FB:ma") Annotation(oboInOwl:source "https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy") Annotation(rdfs:comment "PMID:32646579") obo:IAO_0000115 obo:CL_0000412 "A cell that contains more than two haploid sets of chromosomes.") AnnotationAssertion(rdfs:label obo:CL_0000412 "polyploid cell") EquivalentClasses(obo:CL_0000412 ObjectIntersectionOf(obo:CL_0000000 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001377))) SubClassOf(obo:CL_0000412 obo:CL_0000003) From 018655acc72e0e01886445455554ee664ca0f9a0 Mon Sep 17 00:00:00 2001 From: bvarner-ebi <95643797+bvarner-ebi@users.noreply.github.com> Date: Wed, 30 Aug 2023 10:33:17 +0100 Subject: [PATCH 3/5] Revert "Update cl-edit.owl" This reverts commit ffbfe54634f6770df3f030f3167f18209bd1afff. --- 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 17e1b1254..653c5b794 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -6945,7 +6945,7 @@ SubClassOf(obo:CL_0000411 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_6237 # Class: obo:CL_0000412 (polyploid cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "FB:ma") Annotation(oboInOwl:source "https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy") Annotation(rdfs:comment "PMID:32646579") obo:IAO_0000115 obo:CL_0000412 "A cell that contains more than two haploid sets of chromosomes.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "FB:ma") Annotation(rdfs:comment "PMID:32646579") Annotation(rdfs:seeAlso "https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy"^^xsd:anyURI) obo:IAO_0000115 obo:CL_0000412 "A cell that contains more than two haploid sets of chromosomes.") AnnotationAssertion(rdfs:label obo:CL_0000412 "polyploid cell") EquivalentClasses(obo:CL_0000412 ObjectIntersectionOf(obo:CL_0000000 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001377))) SubClassOf(obo:CL_0000412 obo:CL_0000003) From 2edb831f74e13483200edb4cf3915779e90fc762 Mon Sep 17 00:00:00 2001 From: bvarner-ebi <95643797+bvarner-ebi@users.noreply.github.com> Date: Wed, 30 Aug 2023 10:38:20 +0100 Subject: [PATCH 4/5] Update cl-edit.owl test using dbxref w/URL --- 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 653c5b794..2ecfe4706 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -6945,7 +6945,7 @@ SubClassOf(obo:CL_0000411 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_6237 # Class: obo:CL_0000412 (polyploid cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "FB:ma") Annotation(rdfs:comment "PMID:32646579") Annotation(rdfs:seeAlso "https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy"^^xsd:anyURI) obo:IAO_0000115 obo:CL_0000412 "A cell that contains more than two haploid sets of chromosomes.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "FB:ma") Annotation(oboInOwl:hasDbXref "https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy"^^xsd:anyURI) Annotation(rdfs:comment "PMID:32646579") obo:IAO_0000115 obo:CL_0000412 "A cell that contains more than two haploid sets of chromosomes.") AnnotationAssertion(rdfs:label obo:CL_0000412 "polyploid cell") EquivalentClasses(obo:CL_0000412 ObjectIntersectionOf(obo:CL_0000000 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001377))) SubClassOf(obo:CL_0000412 obo:CL_0000003) From a80998866470754e97a9ca916acdb4bb0bbf6e40 Mon Sep 17 00:00:00 2001 From: bvarner-ebi <95643797+bvarner-ebi@users.noreply.github.com> Date: Wed, 30 Aug 2023 10:50:28 +0100 Subject: [PATCH 5/5] Update cl-edit.owl fix comment -> dbxref --- 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 2ecfe4706..e015442a4 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -6945,7 +6945,7 @@ SubClassOf(obo:CL_0000411 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_6237 # Class: obo:CL_0000412 (polyploid cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "FB:ma") Annotation(oboInOwl:hasDbXref "https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy"^^xsd:anyURI) Annotation(rdfs:comment "PMID:32646579") obo:IAO_0000115 obo:CL_0000412 "A cell that contains more than two haploid sets of chromosomes.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "FB:ma") Annotation(oboInOwl:hasDbXref "https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy"^^xsd:anyURI) Annotation(oboInOwl:hasDbXref "PMID:32646579") obo:IAO_0000115 obo:CL_0000412 "A cell that contains more than two haploid sets of chromosomes.") AnnotationAssertion(rdfs:label obo:CL_0000412 "polyploid cell") EquivalentClasses(obo:CL_0000412 ObjectIntersectionOf(obo:CL_0000000 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001377))) SubClassOf(obo:CL_0000412 obo:CL_0000003)