From 1680a0d1308992622a3e76766e702f9396cbf588 Mon Sep 17 00:00:00 2001 From: Val Wood Date: Mon, 22 Jul 2024 18:20:35 +0100 Subject: [PATCH] closes #4584; closes #4583; closes #4582; closes #4581 (#4585) --- src/ontology/fypo-edit.owl | 92 +++++++++++++++++++++++++++----------- 1 file changed, 66 insertions(+), 26 deletions(-) diff --git a/src/ontology/fypo-edit.owl b/src/ontology/fypo-edit.owl index 5c28f8f5..a8f2dff4 100644 --- a/src/ontology/fypo-edit.owl +++ b/src/ontology/fypo-edit.owl @@ -8744,6 +8744,11 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -24816,7 +24821,6 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRel AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRelatedSynonym "increased histone H3-K14 acetylation at pericentromeric region during vegetative growth") AnnotationAssertion(oboInOwl:id "FYPO:0000966") AnnotationAssertion(rdfs:label "increased histone H3-K14 acetylation at centromere outer repeat during vegetative growth") -EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) SubClassOf( ) @@ -38495,7 +38499,7 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "shmoo formation in absence of opposite mating type") SubClassOf( ) -# Class: (abnormal asymmetric protein localization to old or new mitotic spindle pole body) +# Class: (abnormal asymmetric protein localization, with protein localized to both mitotic spindle pole bodies) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the preferential localization of a protein to either the old or new spindle pole body is abnormal.") AnnotationAssertion(oboInOwl:created_by "midori") @@ -38504,15 +38508,16 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExa AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "abnormal asymmetric protein localization to old or new mitotic SPB") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "abnormal asymmetric protein localization to old or new mitotic spindle pole body during vegetative growth") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "abnormal occurrence of normally asymmetric protein localization to old or new mitotic spindle pole body") +AnnotationAssertion(oboInOwl:hasExactSynonym "abnormal asymmetric protein localization to old or new mitotic spindle pole body") AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRelatedSynonym "abnormal asymmetric protein localization to old or new mitotic spindle pole body during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0001874") AnnotationAssertion(rdfs:comment "Encompasses both presence of proteins not normally found at the spindle pole body and decreased levels or absence of proteins normally found there, and describes defects in a localization process. We recommend noting which protein(s) were used in the assay when annotating to this term.") -AnnotationAssertion(rdfs:label "abnormal asymmetric protein localization to old or new mitotic spindle pole body") +AnnotationAssertion(rdfs:label "abnormal asymmetric protein localization, with protein localized to both mitotic spindle pole bodies") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) -# Class: (decreased asymmetric protein localization to old or new mitotic spindle pole body) +# Class: (decreased asymmetric protein localization, with protein localized to both mitotic spindle pole bodies) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the preferential localization of a protein to either the old or new spindle pole body is decreased.") AnnotationAssertion(oboInOwl:created_by "midori") @@ -38522,15 +38527,16 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExa AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "decreased asymmetric protein localization to old or new mitotic spindle pole body during vegetative growth") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "decreased occurrence of normally asymmetric protein localization to old or new mitotic spindle pole body") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "reduced asymmetric protein localization to old or new mitotic spindle pole body") +AnnotationAssertion(oboInOwl:hasExactSynonym "decreased asymmetric protein localization to old or new mitotic spindle pole body") AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRelatedSynonym "decreased asymmetric protein localization to old or new mitotic spindle pole body during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0001875") AnnotationAssertion(rdfs:comment "We recommend noting which protein(s) were used in the assay when annotating to this term.") -AnnotationAssertion(rdfs:label "decreased asymmetric protein localization to old or new mitotic spindle pole body") +AnnotationAssertion(rdfs:label "decreased asymmetric protein localization, with protein localized to both mitotic spindle pole bodies") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))) SubClassOf( ) -# Class: (decreased asymmetric protein localization to old or new mitotic spindle pole body during anaphase, with protein symmetrically localized to both spindle pole bodies) +# Class: (decreased asymmetric protein localization, with protein localized to both mitotic spindle pole bodies during anaphase) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22119525") Annotation(oboInOwl:hasDbXref "PMID:22419817") Annotation(oboInOwl:hasDbXref "PMID:24920823") Annotation(oboInOwl:hasDbXref "PomBase:mah") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the preferential localization of a protein to either the old or new spindle pole body is decreased during mitotic anaphase, and the protein is instead symmetrically localized to both SPBs.") AnnotationAssertion(oboInOwl:created_by "midori") @@ -38542,11 +38548,12 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExa AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "decreased asymmetric protein localization to old or new mitotic spindle pole body during anaphase, with protein symmetrically localized to both spindle pole bodies, during vegetative growth") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "decreased asymmetric protein localization to old or new mitotic spindle pole body during mitotic anaphase, with protein symmetrically localized to both spindle pole bodies") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "reduced asymmetric protein localization to old or new mitotic spindle pole body during anaphase, with protein symmetrically localized to both spindle pole bodies") +AnnotationAssertion(oboInOwl:hasExactSynonym "decreased asymmetric protein localization to old or new mitotic spindle pole body during anaphase, with protein symmetrically localized to both spindle pole bodies") AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRelatedSynonym "abolished asymmetric protein localization to old or new mitotic SPB") AnnotationAssertion(oboInOwl:id "FYPO:0001876") AnnotationAssertion(rdfs:comment "We recommend noting which protein(s) were used in the assay when annotating to this term.") -AnnotationAssertion(rdfs:label "decreased asymmetric protein localization to old or new mitotic spindle pole body during anaphase, with protein symmetrically localized to both spindle pole bodies") +AnnotationAssertion(rdfs:label "decreased asymmetric protein localization, with protein localized to both mitotic spindle pole bodies during anaphase") SubClassOf( ) # Class: (viable thin vegetative cell) @@ -45888,8 +45895,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRel AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRelatedSynonym "increased histone H3-K56 acetylation at centromere outer repeat during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0002369") AnnotationAssertion(rdfs:label "increased histone H3-K56 acetylation at centromere outer repeat during vegetative growth") -EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) +SubClassOf( ) # Class: (increased histone H3-K56 acetylation in transcribed regions during vegetative growth) @@ -67424,7 +67430,6 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "increased histone H3-K14 acetylation at telomere during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0003802") AnnotationAssertion(rdfs:label "increased histone H3-K14 acetylation at telomere during vegetative growth") -EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) SubClassOf( ) @@ -75124,8 +75129,7 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "increased histone H4-K16 acetylation at centromere central core during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0004324") AnnotationAssertion(rdfs:label "increased histone H4-K16 acetylation at centromere central core during vegetative growth") -EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) +SubClassOf( ) # Class: (sensitive to 5-fluorouracil) @@ -89937,7 +89941,6 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "increased histone H4-K8 acetylation during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0005308") AnnotationAssertion(rdfs:label "increased histone H4-K8 acetylation during vegetative growth") -EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))) SubClassOf( ) # Class: (increased histone H4-K5 acetylation during vegetative growth) @@ -89950,7 +89953,6 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "increased histone H4-K5 acetylation during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0005309") AnnotationAssertion(rdfs:label "increased histone H4-K5 acetylation during vegetative growth") -EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))) SubClassOf( ) # Class: (increased histone H3-K14 acetylation during vegetative growth) @@ -93135,7 +93137,6 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "increased histone H3-K14 acetylation at protein coding gene during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0005518") AnnotationAssertion(rdfs:label "increased histone H3-K14 acetylation at protein coding gene during vegetative growth") -EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) SubClassOf( ) @@ -93386,8 +93387,7 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "increased histone H4-K16 acetylation at telomere during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0005535") AnnotationAssertion(rdfs:label "increased histone H4-K16 acetylation at telomere during vegetative growth") -EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) +SubClassOf( ) # Class: (normal RNA localization to nucleus) @@ -94394,12 +94394,12 @@ SubClassOf( ObjectSomeValuesFrom( (normal subtelomeric heterochromatin RNA level) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:27183912") Annotation(oboInOwl:hasDbXref "PMID:25356590") "A cell phenotype in which the amount of RNA derived from subtelomeric heterochromatin forming regions is normal (i.e. indistinguishable from wild type). Total RNA or a specific RNA, such as the mRNA transcribed from a gene of interest, may be affected.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:25356590") Annotation(oboInOwl:hasDbXref "PMID:27183912") "A cell phenotype in which the amount of RNA derived from subtelomeric heterochromatin forming regions is normal (i.e. indistinguishable from wild type). Total RNA or a specific RNA, such as the mRNA transcribed from a gene of interest, may be affected.") AnnotationAssertion(oboInOwl:created_by "midori") AnnotationAssertion(oboInOwl:creation_date "2016-08-10T14:59:21Z") +AnnotationAssertion(oboInOwl:hasExactSynonym "normal subtelomere-derived RNA level") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "normal subtelomere-derived RNA level during vegetative growth") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") oboInOwl:hasExactSynonym "normal subtelomere-derived RNA transcript level") -AnnotationAssertion(oboInOwl:hasExactSynonym "normal subtelomere-derived RNA level") AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") AnnotationAssertion(oboInOwl:id "FYPO:0005602") AnnotationAssertion(rdfs:label "normal subtelomeric heterochromatin RNA level") @@ -112746,8 +112746,7 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "increased histone H3-K14 acetylation at centromere inner repeat during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0006815") AnnotationAssertion(rdfs:label "increased histone H3-K14 acetylation at centromere inner repeat during vegetative growth") -EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) +SubClassOf( ) # Class: (normal histone H3-K9 acetylation at centromere inner repeat during vegetative growth) @@ -120226,7 +120225,6 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "increased histone H3-K14 acetylation at centromere during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0007307") AnnotationAssertion(rdfs:label "increased histone H3-K14 acetylation at centromere during vegetative growth") -EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) # Class: (increased histone H4-K5 acetylation at centromere outer repeat during vegetative growth) @@ -125042,7 +125040,6 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "increased histone H4-K16 acetylation during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0007632") AnnotationAssertion(rdfs:label "increased histone H4-K16 acetylation during vegetative growth") -EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))) SubClassOf( ) # Class: (increased histone H3-K14 acetylation at silent mating-type cassette during vegetative growth) @@ -125056,7 +125053,6 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "increased histone H3-K14 acetylation at silent mating-type cassette during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0007633") AnnotationAssertion(rdfs:label "increased histone H3-K14 acetylation at silent mating-type cassette during vegetative growth") -EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) # Class: (increased histone H3-K14 acetylation at rDNA during vegetative growth) @@ -125070,8 +125066,7 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "increased histone H3-K14 acetylation at rDNA during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0007634") AnnotationAssertion(rdfs:label "increased histone H3-K14 acetylation at rDNA during vegetative growth") -EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) +SubClassOf( ) # Class: (increased histone H4-K16 acetylation at protein coding gene during vegetative growth) @@ -132287,6 +132282,51 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "decreased total cellular phosphate (Pi) level"@en) SubClassOf( ) +# Class: (increased H3-K56 acetylation during vegetative growth) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:20299449") "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which acetylation of lysine at position 56 of histone H3 occurs to a higher extent than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-22T11:42:36Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased H3-K56 acetylation during vegetative growth"@en) +SubClassOf( ) + +# Class: (normal histone binding) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") "A molecular function phenotype in which the binding of a protein to a histone is normal (i.e. indistinguishable from wild type).") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-22T11:51:17Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "normal histone binding"@en) +SubClassOf( ) + +# Class: (normal histone H3 binding) + +AnnotationAssertion(Annotation(rdfs:comment "PomBase:pc") "A molecular function phenotype in which occurrence of histone H3 binding by a gene product (usually a protein) in a mutant is normal (i.e. indistinguishable from wild type). The affected gene product may be encoded by the mutated gene, or by a different gene.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-22T11:54:29Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "normal histone H3 binding"@en) +SubClassOf( ) + +# Class: (normal histone H4 binding) + +AnnotationAssertion(Annotation(rdfs:comment "PomBase:pc") "A molecular function phenotype in which occurrence of histone H4 binding by a gene product (usually a protein) in a mutant is normal (i.e. indistinguishable from wild type). The affected gene product may be encoded by the mutated gene, or by a different gene.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-22T11:55:31Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "normal histone H4 binding"@en) +SubClassOf( ) + +# Class: (decreased glutamate biosynthesis) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") "A metabolism phenotype observed in the vegetative growth phase of the life cycle in which glutamate biosynthesis is abnormal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-22T14:07:46Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased glutamate biosynthesis"@en) +SubClassOf( ) + # Class: (decreased rate of cytoplasmic microtubule polymerization during mitotic interphase) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36633091") Annotation(oboInOwl:hasDbXref "PomBase:mlr") "A microtubule cytoskeleton organization phenotype observed during mitotic interphase in which cytoplasmic microtubule polymerization, i.e. the addition of tubulin dimers to the plus end of a microtubule occurs at a lower rate, or speed, than normal.")