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Fixes #2251 obsolete increased nucleus size (#2268)
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* Import PATO term and substitute axioms

* Obsolete 'increased nuclear size'

* URL as IRI
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@aleixpuigb
aleixpuigb authored Jan 22, 2024
1 parent d5ee4fd commit 198f9cd
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Showing 3 changed files with 27 additions and 12 deletions.
20 changes: 11 additions & 9 deletions src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -7931,7 +7931,7 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000542 "MESH:D008214")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000542 "VHOG:0001535")
AnnotationAssertion(rdfs:comment obo:CL_0000542 "Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)")
AnnotationAssertion(rdfs:label obo:CL_0000542 "lymphocyte")
EquivalentClasses(obo:CL_0000542 ObjectIntersectionOf(obo:CL_0000738 ObjectSomeValuesFrom(obo:BFO_0000051 obo:CL_0017500) ObjectSomeValuesFrom(obo:BFO_0000051 obo:CL_0017505) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0000792) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001407)))
EquivalentClasses(obo:CL_0000542 ObjectIntersectionOf(obo:CL_0000738 ObjectSomeValuesFrom(obo:BFO_0000051 obo:CL_0017500) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0000792) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001407) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0040072)))
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000542 obo:CL_0000738)
SubClassOf(obo:CL_0000542 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000051))
DisjointClasses(obo:CL_0000542 obo:CL_0000766)
Expand Down Expand Up @@ -7996,7 +7996,7 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000547 "FMA:83518")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "ISBN:0721601464") oboInOwl:hasExactSynonym obo:CL_0000547 "rubriblast")
AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0000547 "pronormoblast")
AnnotationAssertion(rdfs:label obo:CL_0000547 "proerythroblast")
EquivalentClasses(obo:CL_0000547 ObjectIntersectionOf(obo:CL_0000764 ObjectSomeValuesFrom(obo:BFO_0000051 obo:CL_0017503) ObjectSomeValuesFrom(obo:BFO_0000051 obo:CL_0017505) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0005730) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001002) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001004) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001012) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001020) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001024) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001083) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001084) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001289) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001839) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001889) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000002978) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0002505) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001945)))
EquivalentClasses(obo:CL_0000547 ObjectIntersectionOf(obo:CL_0000764 ObjectSomeValuesFrom(obo:BFO_0000051 obo:CL_0017503) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0005730) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001002) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001004) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001012) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001020) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001024) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001083) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001084) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001289) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001839) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001889) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000002978) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0002505) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0040072) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001945)))
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000547 obo:CL_0000764)
SubClassOf(obo:CL_0000547 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000038))

Expand Down Expand Up @@ -10844,7 +10844,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:add") Annotation(oboInOwl
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000835 "BTO:0000187")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000835 "FMA:83524")
AnnotationAssertion(rdfs:label obo:CL_0000835 "myeloblast")
EquivalentClasses(obo:CL_0000835 ObjectIntersectionOf(obo:CL_0002191 ObjectSomeValuesFrom(obo:BFO_0000051 obo:CL_0017503) ObjectSomeValuesFrom(obo:BFO_0000051 obo:CL_0017505) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0000791) ObjectSomeValuesFrom(obo:CL_4030045 obo:GO_0042582)))
EquivalentClasses(obo:CL_0000835 ObjectIntersectionOf(obo:CL_0002191 ObjectSomeValuesFrom(obo:BFO_0000051 obo:CL_0017503) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0000791) ObjectSomeValuesFrom(obo:CL_4030045 obo:GO_0042582) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0040072)))
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000835 obo:CL_0002191)
SubClassOf(obo:CL_0000835 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000557))

Expand All @@ -10854,7 +10854,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:add") Annotation(oboInOwl
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000836 "CALOHA:TS-0825")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000836 "FMA:83530")
AnnotationAssertion(rdfs:label obo:CL_0000836 "promyelocyte")
EquivalentClasses(obo:CL_0000836 ObjectIntersectionOf(obo:CL_0000839 ObjectSomeValuesFrom(obo:BFO_0000051 obo:CL_0017503) ObjectSomeValuesFrom(obo:BFO_0000051 obo:CL_0017505) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0005730) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0042582) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001012) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001483) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001932) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001456) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001892)))
EquivalentClasses(obo:CL_0000836 ObjectIntersectionOf(obo:CL_0000839 ObjectSomeValuesFrom(obo:BFO_0000051 obo:CL_0017503) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0005730) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0042582) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001012) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001483) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001932) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0040072) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001456) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001892)))
SubClassOf(obo:CL_0000836 obo:CL_0002191)
SubClassOf(obo:CL_0000836 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000835))

Expand Down Expand Up @@ -24501,14 +24501,16 @@ AnnotationAssertion(oboInOwl:creation_date obo:CL_0017504 "2009-12-28T04:25:23Z"
AnnotationAssertion(rdfs:label obo:CL_0017504 "polychromatophilic cytoplasm")
EquivalentClasses(obo:CL_0017504 ObjectIntersectionOf(obo:GO_0005737 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0070047)))

# Class: obo:CL_0017505 (increased nucleus size)
# Class: obo:CL_0017505 (obsolete increased nucleus size)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") obo:IAO_0000115 obo:CL_0017505 "A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") obo:IAO_0000115 obo:CL_0017505 "OBSOLETE. A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell.")
AnnotationAssertion(obo:IAO_0000233 obo:CL_0017505 <https://github.com/obophenotype/cell-ontology/issues/2251>)
AnnotationAssertion(obo:IAO_0100001 obo:CL_0017505 obo:PATO_0040072)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_0017505 <https://orcid.org/0000-0003-1980-3228>)
AnnotationAssertion(oboInOwl:creation_date obo:CL_0017505 "2009-12-23T10:53:24Z")
AnnotationAssertion(rdfs:label obo:CL_0017505 "increased nucleus size")
EquivalentClasses(obo:CL_0017505 ObjectIntersectionOf(obo:GO_0005634 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0000586)))
SubClassOf(obo:CL_0017505 obo:GO_0005634)
AnnotationAssertion(rdfs:comment obo:CL_0017505 "This class was a phenotype, not a cell type.")
AnnotationAssertion(rdfs:label obo:CL_0017505 "obsolete increased nucleus size")
AnnotationAssertion(owl:deprecated obo:CL_0017505 "true"^^xsd:boolean)

# Class: obo:CL_0017506 (banded nucleus)

Expand Down
16 changes: 14 additions & 2 deletions src/ontology/imports/merged_import.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -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/2024-01-04/imports/merged_import.owl>
Annotation(owl:versionInfo "2024-01-04")
<http://purl.obolibrary.org/obo/cl/releases/2024-01-16/imports/merged_import.owl>
Annotation(owl:versionInfo "2024-01-16")

Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000003>))
Expand Down Expand Up @@ -8217,6 +8217,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0010001>))
Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0010006>))
Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0015006>))
Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0015008>))
Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0040072>))
Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0045001>))
Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0045009>))
Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0045011>))
Expand Down Expand Up @@ -116018,6 +116019,17 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <htt
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PATO_0015008> "distensibility")
SubClassOf(<http://purl.obolibrary.org/obo/PATO_0015008> <http://purl.obolibrary.org/obo/PATO_0000141>)

# Class: <http://purl.obolibrary.org/obo/PATO_0040072> (high nuclear/cytoplasmic ratio)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "Wikipedia:NC_ratio&oldid=931936284") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "http://lymerick.net/blood-cells.pdf") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/PATO_0040072> "A quality inhering in a cell by virtue of the cell having a high nuclear/cytoplasmic ratio.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#created_by> <http://purl.obolibrary.org/obo/PATO_0040072> "http://orcid.org/0000-0001-5208-3432")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/PATO_0040072> "high N:C ratio")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/PATO_0040072> "quality")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/PATO_0040072> "PATO:0040072")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/PATO_0040072> "A high nuclear/cytolasmic ratio is 70% or higher.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PATO_0040072> "high nuclear/cytoplasmic ratio")
SubClassOf(<http://purl.obolibrary.org/obo/PATO_0040072> <http://purl.obolibrary.org/obo/PATO_0001396>)

# Class: <http://purl.obolibrary.org/obo/PATO_0045001> (normal object quality)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/PATO_0045001> "A quality of an object that has a value that is normal or average.")
Expand Down
3 changes: 2 additions & 1 deletion src/ontology/imports/pato_terms.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -32,4 +32,5 @@ PATO:0002420
PATO:0002094
PATO:0070046
PATO:0070047
PATO:0070061
PATO:0070061
PATO:0040072

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