From c588901e03b2858d6fbc9f6e3477f41e65596cd6 Mon Sep 17 00:00:00 2001 From: Val Wood Date: Thu, 4 Jul 2024 13:47:35 +0100 Subject: [PATCH] closes #4574 --- src/ontology/fypo-edit.owl | 146 +++++++++++++++++++++++++++++++++++-- 1 file changed, 139 insertions(+), 7 deletions(-) diff --git a/src/ontology/fypo-edit.owl b/src/ontology/fypo-edit.owl index 7e093a53..efda4a5b 100644 --- a/src/ontology/fypo-edit.owl +++ b/src/ontology/fypo-edit.owl @@ -8719,6 +8719,19 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -19949,7 +19962,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRel AnnotationAssertion(oboInOwl:id "FYPO:0000644") AnnotationAssertion(rdfs:comment "We recommend noting which protein(s) were used in the assay when annotating to this term.") AnnotationAssertion(rdfs:label "normal protein localization during vegetative growth") -EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -88645,7 +88658,7 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "decreased histone H2B localization to chromatin at protein coding gene during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0005223") AnnotationAssertion(rdfs:label "decreased histone H2B localization to chromatin at protein coding gene") -SubClassOf( ) +SubClassOf( ) # Class: () @@ -92229,6 +92242,7 @@ AnnotationAssertion(rdfs:label "ab EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) # Class: (abnormal microtubule-based movement during vegetative growth) @@ -94366,18 +94380,17 @@ EquivalentClasses( ObjectSomeValues SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (normal subtelomere-derived RNA level) +# Class: (normal subtelomeric heterochromatin RNA level) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:27183912") Annotation(oboInOwl:hasDbXref "PomBase:mah") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of any RNA transcribed from sub-telomeric regions measured in a cell is normal (i.e. indistinguishable from wild type).") +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(oboInOwl:created_by "midori") AnnotationAssertion(oboInOwl:creation_date "2016-08-10T14:59:21Z") 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(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRelatedSynonym "normal subtelomere-derived RNA accumulation") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRelatedSynonym "normal subtelomere-derived RNA level during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0005602") -AnnotationAssertion(rdfs:label "normal subtelomere-derived RNA level") +AnnotationAssertion(rdfs:label "normal subtelomeric heterochromatin RNA level") SubClassOf( ) # Class: (increased duration of mitotic DNA damage checkpoint during cellular response to methyl methanesulfonate) @@ -132033,6 +132046,125 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "abolished protein localization to prospore wall"@en) SubClassOf( ) +# Class: (normal protein localization to chromatin at gene promoter region) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:27538348") "A cell phenotype in which the localization of a protein to chromatin at one or more specific promoter elements is normal (i.e. indistinguishable from wild type) during vegetative growth.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-04T09:30:07Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "normal protein localization to chromatin at gene promoter region"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +SubClassOf( ) + +# Class: (normal cenH-derived RNA level) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:pc") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of RNA transcribed from cenH measured in a cell is normal. cenH is a region located between mat2-P and mat3-M that is homologous to centromeric repeats, and that produces non-coding RNAs and small interfering RNAs.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-04T10:22:47Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "normal cenH-derived RNA level"@en) +SubClassOf( ) + +# Class: (decreased subtelomeric heterochromatin RNA level) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:25356590") Annotation(oboInOwl:hasDbXref "PomBase:pc") "A cell phenotype in which the amount of RNA derived from subtelomeric heterochromatin regions is lower than normal. Total RNA or a specific RNA, such as the mRNA transcribed from a gene of interest, may be affected.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-04T10:28:51Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased subtelomeric heterochromatin RNA level"@en) +SubClassOf( ) + +# Class: (decreased LTR-derived RNA level) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:pc") Annotation(rdfs:comment "PMID:25356590") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of any RNA transcribed from long terminal repeat elements (LTRs) measured in a cell is lower than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-04T10:31:20Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased LTR-derived RNA level"@en) +SubClassOf( ) + +# Class: (decreased protein localization to chromatin at protein coding gene) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:25356590") Annotation(oboInOwl:hasDbXref "PomBase:pc") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the localization of a protein to chromatin at one or more protein-coding genes is decreased.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-04T10:46:57Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased protein localization to chromatin at protein coding gene"@en) +SubClassOf( ) + +# Class: (normal protein localization to chromatin at protein coding gene) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:25356590") Annotation(oboInOwl:hasDbXref "PomBase:pc") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the localization of a protein to chromatin at one or more protein-coding genes is normal (i.e. indistinguishable from wild type).") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-04T10:57:44Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "normal protein localization to chromatin at protein coding gene"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +SubClassOf( ) + +# Class: (decreased cenH-derived RNA level) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:25356590") Annotation(oboInOwl:hasDbXref "PomBase:pc") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of RNA transcribed from cenH measured in a cell is lower than normal. cenH is a region located between mat2-P and mat3-M that is homologous to centromeric repeats, and that produces non-coding RNAs and small interfering RNAs.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-04T11:13:18Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased cenH-derived RNA level"@en) +SubClassOf( ) + +# Class: (normal LTR-derived RNA level) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:25356590") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of any RNA transcribed from long terminal repeat elements (LTRs) measured in a cell is normal (i.e. indistinguishable from wild type).") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-04T11:16:06Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "normal LTR-derived RNA level"@en) +SubClassOf( ) + +# Class: (normal telomere repeat region derived RNA level) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:27183912") "A cell phenotype in which the amount of telomere repeat derived RNA measured in a cell is normal (i.e. indistinguishable from wild type) when the cell is in the vegetative growth phase of the life cycle.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-04T11:56:39Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "normal telomere repeat region derived RNA level"@en) +SubClassOf( ) + +# Class: (increased histone H3-K4 acetylation at protein coding gene during vegetative growth) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:25356590") "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which acetylation of lysine at position 4 of histone H3 occurs to a greater extent than normal in regions containing protein-coding genes.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-04T12:06:21Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased histone H3-K4 acetylation at protein coding gene during vegetative growth"@en) +SubClassOf( ) + +# Class: (decreased histone H3-K4 acetylation at protein coding gene during vegetative growth) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:25356590") "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which acetylation of lysine at position 4 of histone H3 occurs to a lower extent than normal in regions containing protein-coding genes.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-04T12:08:52Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased histone H3-K4 acetylation at protein coding gene during vegetative growth"@en) +SubClassOf( ) + +# Class: (decreased histone H3-K4 acetylation at LTR during vegetative growth) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:25356590") "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which acetylation of lysine at position 4 of histone H3 occurs to a lower extent than normal at long terminal repeat (LTR) regions.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-04T12:13:44Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased histone H3-K4 acetylation at LTR during vegetative growth"@en) +SubClassOf( ) + +# Class: (increased histone H3-K4 acetylation at LTR during vegetative growth) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:25356590") "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which acetylation of lysine at position 4 of histone H3 occurs to a greater extent than normal at long terminal repeat (LTR) regions.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-04T12:30:40Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased histone H3-K4 acetylation at LTR during vegetative growth"@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.")