From 547dbdc8e128a275b01cd5736c86e40709bb0a7d Mon Sep 17 00:00:00 2001 From: Val Wood Date: Tue, 31 Dec 2024 15:03:37 +0000 Subject: [PATCH] closes #4662; closes #4661; closes #4660; closes #4659; closes #4654 (#4663) --- src/ontology/fypo-edit.owl | 64 ++++++++++++++++++++++++++++++++------ 1 file changed, 55 insertions(+), 9 deletions(-) diff --git a/src/ontology/fypo-edit.owl b/src/ontology/fypo-edit.owl index bde8fe47..5ecd562c 100644 --- a/src/ontology/fypo-edit.owl +++ b/src/ontology/fypo-edit.owl @@ -8815,6 +8815,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8832,6 +8833,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -14256,6 +14260,7 @@ AnnotationAssertion(oboInOwl:creation_date "decreased viability in stationary phase") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "loss of cell population viability in stationary phase") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "reduced viability in stationary phase") +AnnotationAssertion(oboInOwl:hasExactSynonym "decreased longevity") AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") oboInOwl:hasRelatedSynonym "decreased chronological lifespan") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRelatedSynonym "growth defect, required for stationary phase") @@ -26874,10 +26879,10 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") "midori") AnnotationAssertion(oboInOwl:creation_date "2012-06-01T14:35:59Z") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "hypersensitive to amitrole") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "CHEBI:40036") Annotation(oboInOwl:hasDbXref "PomBase:al") oboInOwl:hasExactSynonym "sensitive to 3-amino-1,2,4-triazole") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "sensitive to amitrole during vegetative growth") AnnotationAssertion(oboInOwl:hasExactSynonym "sensitive to 3-AT") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "CHEBI:40036") Annotation(oboInOwl:hasDbXref "PomBase:al") oboInOwl:hasExactSynonym "sensitive to 3-amino-1,2,4-triazole") AnnotationAssertion(oboInOwl:hasExactSynonym "sensitive to 3-aminotriazole") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "sensitive to amitrole during vegetative growth") AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRelatedSynonym "sensitive to amitrole during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0001097") @@ -30016,6 +30021,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") "midori") AnnotationAssertion(oboInOwl:creation_date "2012-07-26T14:58:27Z") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "increased cell population viability in stationary phase") +AnnotationAssertion(oboInOwl:hasExactSynonym "increased longevity") AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") oboInOwl:hasRelatedSynonym "decreased chronological cell aging") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") oboInOwl:hasRelatedSynonym "increased chronological lifespan") @@ -49022,7 +49028,7 @@ AnnotationAssertion(oboInOwl:id "F AnnotationAssertion(rdfs:comment "Consider annotating to a term describing abnormal transcription or abnormal regulation of transcription, but note that changes in RNA levels may result from changes in RNA stability as well as changes in transcription. We recommend noting which RNA(s) were used in the assay when annotating to this term.") AnnotationAssertion(rdfs:label "increased mature tRNA level during vegetative growth") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) # Class: (abolished histone methylation during vegetative growth) @@ -49255,7 +49261,7 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "altered mature tRNA level during vegetative growth") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (normal mature tRNA level) @@ -49286,7 +49292,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:al") oboInOwl:hasRela AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRelatedSynonym "increased level of nuclear tRNA processing intermediates with 3' extensions during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0002581") AnnotationAssertion(rdfs:label "increased level of nuclear tRNA processing intermediates with 3' extensions") -SubClassOf( ) +SubClassOf( ) SubClassOf( ) # Class: (normal mature mitochondrial tRNA level) @@ -49436,7 +49442,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:al") oboInOwl:hasRela AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRelatedSynonym "increased level of mitochondrial tRNA processing intermediates with 3' extensions during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0002590") AnnotationAssertion(rdfs:label "increased level of mitochondrial tRNA processing intermediates with 3' extensions") -SubClassOf( ) +SubClassOf( ) SubClassOf( ) # Class: (abnormal histone phosphorylation during vegetative growth) @@ -56010,6 +56016,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRel AnnotationAssertion(oboInOwl:id "FYPO:0003029") AnnotationAssertion(rdfs:label "decreased mRNA splicing, via spliceosome") SubClassOf( ) +SubClassOf( ) # Class: (decreased splicing of mRNA introns with low A/U content and polypyrimidine tracts distal to branch site) @@ -130909,14 +130916,14 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "increased polyadenylated 5S rRNA level during cellular response to phosphate starvation"@en) SubClassOf( ) -# Class: (altered tRNA level during vegetative growth) +# Class: (altered tRNA or precursor level during vegetative growth) AnnotationAssertion(Annotation(rdfs:comment "PMID:36794724") "A cell phenotype in which the amount of tRNA measured in a cell differs from normal when the cell is in the vegetative growth phase of the life cycle.") AnnotationAssertion(oboInOwl:created_by "vw") AnnotationAssertion(oboInOwl:creation_dat "2023-08-31T16:56:39Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment "Consider annotating to a term describing abnormal transcription or abnormal regulation of transcription, but note that changes in RNA levels may result from changes in RNA stability as well as changes in transcription. We recommend noting which RNA(s) were used in the assay when annotating to this term.") -AnnotationAssertion(rdfs:label "altered tRNA level during vegetative growth"@en) -SubClassOf( ) +AnnotationAssertion(rdfs:label "altered tRNA or precursor level during vegetative growth"@en) +SubClassOf( ) # Class: (increased tRNA level during cellular response to phosphate starvation) @@ -133049,6 +133056,15 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "abolished ubiquitin ligase activator activity"@en) SubClassOf( ) +# Class: (decreased nucleosome occupancy in gene body) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which nucleosome occupancy is lower than normal within the body of a gene. Nucleosome occupancy measures the tendency for DNA in a given region to be packaged into nucleosomes.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-31T13:38:07Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased nucleosome occupancy in gene body"@en) +SubClassOf( ) + # Class: (decreased pre-tRNA or mature level during vegetative growth) AnnotationAssertion( "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of one or more transfer RNAs measured in a cell is lower than normal. Total tRNA or a specific tRNA may be affected.") @@ -133057,6 +133073,7 @@ AnnotationAssertion(oboInOwl:creation_date "fission_yeast_phenotype") AnnotationAssertion(rdfs:label "decreased pre-tRNA or mature level during vegetative growth"@en) SubClassOf( ) +SubClassOf( ) # Class: (increased integrated stress response signaling) @@ -133076,6 +133093,7 @@ AnnotationAssertion(oboInOwl:creation_date "fission_yeast_phenotype") AnnotationAssertion(rdfs:label "abolished tRNA modification"@en) SubClassOf( ) +SubClassOf( ) # Class: (abolished tRNA cytidine N4-acetylation) @@ -133203,6 +133221,34 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "increased protein aggregate level"@en) SubClassOf( ) +# Class: (increased nucleosome occupancy in gene body) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which nucleosome occupancy is higher than normal within the body of a gene. Nucleosome occupancy measures the tendency for DNA in a given region to be packaged into nucleosomes.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-31T13:39:33Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased nucleosome occupancy in gene body"@en) +SubClassOf( ) + +# Class: (increased mitophagy during stationary phase) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") "A cellular process phenotype in which the occurrence of mitophagy is increased during stationary phase.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-31T13:45:12Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased mitophagy during stationary phase"@en) +SubClassOf( ) + +# Class: (normal integrated stress response signaling) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which integrated stress response signaling is normal (i.e. indistinguishable from wild type).") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-31T14:00:48Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasExactSynonym "normal GAAC signaling") +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "normal integrated stress response signaling"@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.")