From 198f9cd5054923b5db0ac07a329fa318c3a6ed0c Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Mon, 22 Jan 2024 12:58:56 +0000 Subject: [PATCH] Fixes #2251 obsolete increased nucleus size (#2268) * Import PATO term and substitute axioms * Obsolete 'increased nuclear size' * URL as IRI --- src/ontology/cl-edit.owl | 20 +++++++++++--------- src/ontology/imports/merged_import.owl | 16 ++++++++++++++-- src/ontology/imports/pato_terms.txt | 3 ++- 3 files changed, 27 insertions(+), 12 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 8d9b79014..6528eab6b 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -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) @@ -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)) @@ -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)) @@ -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)) @@ -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 ) +AnnotationAssertion(obo:IAO_0100001 obo:CL_0017505 obo:PATO_0040072) AnnotationAssertion( obo:CL_0017505 ) 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) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index a3130a3e2..e475feeec 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 "2024-01-04") + +Annotation(owl:versionInfo "2024-01-16") Declaration(Class()) Declaration(Class()) @@ -8217,6 +8217,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -116018,6 +116019,17 @@ AnnotationAssertion( "distensibility") SubClassOf( ) +# Class: (high nuclear/cytoplasmic ratio) + +AnnotationAssertion(Annotation( "Wikipedia:NC_ratio&oldid=931936284") Annotation( "http://lymerick.net/blood-cells.pdf") "A quality inhering in a cell by virtue of the cell having a high nuclear/cytoplasmic ratio.") +AnnotationAssertion( "http://orcid.org/0000-0001-5208-3432") +AnnotationAssertion( "high N:C ratio") +AnnotationAssertion( "quality") +AnnotationAssertion( "PATO:0040072") +AnnotationAssertion(rdfs:comment "A high nuclear/cytolasmic ratio is 70% or higher.") +AnnotationAssertion(rdfs:label "high nuclear/cytoplasmic ratio") +SubClassOf( ) + # Class: (normal object quality) AnnotationAssertion( "A quality of an object that has a value that is normal or average.") diff --git a/src/ontology/imports/pato_terms.txt b/src/ontology/imports/pato_terms.txt index 72a20300b..02e396a66 100644 --- a/src/ontology/imports/pato_terms.txt +++ b/src/ontology/imports/pato_terms.txt @@ -32,4 +32,5 @@ PATO:0002420 PATO:0002094 PATO:0070046 PATO:0070047 -PATO:0070061 \ No newline at end of file +PATO:0070061 +PATO:0040072 \ No newline at end of file