From 17144e28007decefcc08be48adf79a9676e4b083 Mon Sep 17 00:00:00 2001 From: Val Wood Date: Tue, 12 Nov 2024 18:10:01 +0000 Subject: [PATCH] =?UTF-8?q?closes=20#4634;=20closes=20#4633;=20closes=20#4?= =?UTF-8?q?632;=20closes=20#4631;=20closes=20#4630;=E2=80=A6=20(#4635)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * closes #4634; closes #4633; closes #4632; closes #4631; closes #4630; closes #4629; closes #4627; closes #4626 * closes #4634; closes #4633; closes #4632; closes #4631; closes #4630; closes #4629; closes #4627; closes #4626 --- src/ontology/fypo-edit.owl | 153 ++++++++++++++++++++++++++++++++++++- 1 file changed, 150 insertions(+), 3 deletions(-) diff --git a/src/ontology/fypo-edit.owl b/src/ontology/fypo-edit.owl index b3a21f1e..05aa87ab 100644 --- a/src/ontology/fypo-edit.owl +++ b/src/ontology/fypo-edit.owl @@ -8786,6 +8786,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8795,6 +8796,18 @@ 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()) @@ -25228,6 +25241,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRel AnnotationAssertion(oboInOwl:id "FYPO:0000992") AnnotationAssertion(rdfs:label "altered cellular phosphatidylinositol-3-phosphate level") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +SubClassOf( ) SubClassOf( ) # Class: (decreased cellular phosphatidylinositol-3-phosphate level) @@ -25608,6 +25622,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRel AnnotationAssertion(oboInOwl:id "FYPO:0001015") AnnotationAssertion(rdfs:label "altered cellular phosphatidylinositol-4-phosphate level") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +SubClassOf( ) SubClassOf( ) # Class: (normal growth on actinomycin D) @@ -65864,7 +65879,6 @@ AnnotationAssertion(oboInOwl:id "F AnnotationAssertion(rdfs:label "sulfide absent from cell") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) -SubClassOf( ) # Class: (decreased mature 18S rRNA level) @@ -78473,7 +78487,7 @@ SubClassOf( ObjectSomeValuesFrom( (increased chromatin silencing) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") Annotation(oboInOwl:hasDbXref "PomBase:vw") "A transcription regulation phenotype observed in the vegetative growth phase of the life cycle in which chromatin silencing is incrsasd. Chromatin silencing is the observed effect of processes that repress transcription in a region of the genome that is normally assembled into heterochromatin or CENP-A-containing chromatin (the latter is found at the centromere central core).") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") Annotation(oboInOwl:hasDbXref "PomBase:vw") "A transcription regulation phenotype observed in the vegetative growth phase of the life cycle in which chromatin silencing is increased. Chromatin silencing is the observed effect of processes that repress transcription in a region of the genome that is normally assembled into heterochromatin or CENP-A-containing chromatin (the latter is found at the centromere central core).") AnnotationAssertion(oboInOwl:created_by "midori") AnnotationAssertion(oboInOwl:creation_date "2015-04-02T15:08:22Z") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "increased chromatin silencing during vegetative growth") @@ -125129,7 +125143,7 @@ SubClassOf( (increased histone H3-K9 acetylation at promoter during vegetative growth) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which the acetylation of lysine at position 9 of histone H3 at in one or more promoter regions occurs to a greater extent than normal.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which the acetylation of lysine at position 9 of histone H3 in one or more promoter regions occurs to a greater extent than normal.") AnnotationAssertion( "midori") AnnotationAssertion( "2021-02-03T11:24:56Z"^^xsd:dateTime) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "increased histone H3K9 acetylation at promoter during vegetative growth") @@ -130656,6 +130670,7 @@ AnnotationAssertion( "decreased PI(4,5)P2 binding") AnnotationAssertion(oboInOwl:hasExactSynonym "decreased PIP2 binding") AnnotationAssertion(oboInOwl:hasExactSynonym "decreases PtdInsP binding") +AnnotationAssertion(rdfs:comment "This term can mean that the mutated gene product itself binds one or more phospholipids less than wild type, or that a mutation in one gene decreases phospholipid binding by a second gene product. When using this term, it is therefore recommended to note the specific protein(s) affected.") AnnotationAssertion(rdfs:label "decreased phosphatidylinositol-4,5-bisphosphate binding"@en) SubClassOf( ) @@ -130664,6 +130679,7 @@ SubClassOf( "A molecular function phenotype in which occurrence of phosphatidylserine binding by a gene product (usually a protein) in a mutant is decreased. The affected gene product may be encoded by the mutated gene, or by a different gene.") AnnotationAssertion( "vw253") AnnotationAssertion( "2023-03-07T14:34:39Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "This term can mean that the mutated gene product itself binds one or more phospholipids less than wild type, or that a mutation in one gene decreases phospholipid binding by a second gene product. When using this term, it is therefore recommended to note the specific protein(s) affected.") AnnotationAssertion(rdfs:label "decreased phosphatidylserine binding"@en) SubClassOf( ) @@ -132722,6 +132738,17 @@ AnnotationAssertion(rdfs:label "no EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) +# Class: (increased split sister centromeres in early mitosis) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") "A cellular process phenotype in which mitotic sister chromatid cohesion is increased at the centromeres in early mitosis. Contromeric cohesion is usually protected until the metaphase anaphase transition.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-11-12T13:58:37Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasBroadSynonym "increased split sister centromeres in mitosis") +AnnotationAssertion(oboInOwl:hasExactSynonym "increased sister kinetochore dissociation at centromeres") +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased split sister centromeres in early mitosis"@en) +SubClassOf( ) + # Class: (normal meiotic spindle pole body insertion into nuclear envelope in meiosis I) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") "A cellular process phenotype in which insertion of the spindle pole body into the nuclear envelope during the first meiotic nuclear division is normal.") @@ -132807,6 +132834,126 @@ AnnotationAssertion(rdfs:label "ab EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) +# Class: (decreased histone H3-K9 acetylation at promoter during vegetative growth) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:pc") "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which the acetylation of lysine at position 9 of histone H3 at one or more promoter regions occurs to a lower extent than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-11-12T14:10:02Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased histone H3-K9 acetylation at promoter during vegetative growth"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +SubClassOf( ) + +# Class: (decreased histone H3-K14 acetylation at promoter during vegetative growth) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:pc") "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which the acetylation of lysine at position 14 of histone H3 at one or more promoter regions occurs to a lower extent than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-11-12T14:15:48Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased histone H3-K14 acetylation at promoter during vegetative growth"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +SubClassOf( ) + +# Class: (decreased cytosolic ribosome content) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:39358553") Annotation(oboInOwl:hasDbXref "PomBase:pc") "A cellular phenotype observed in the vegetative growth phase of the life cycle in which the total cytosolic ribosome content (monosomes + polysomes) in a cell is lower than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-11-12T14:22:36Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased cytosolic ribosome content"@en) +SubClassOf( ) + +# Class: (increased cytosolic ribosome content) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:39358553") Annotation(oboInOwl:hasDbXref "PomBase:pc") "A cellular phenotype observed in the vegetative growth phase of the life cycle in which the total cytosolic ribosome content (monosomes + polysomes) in a cell is higher than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-11-12T14:22:36Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:creation_date "2024-11-12T14:26:01Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased cytosolic ribosome content"@en) +SubClassOf( ) + +# Class: (increased histone H3-K9 trimethylation at protein coding gene during vegetative growth) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:pc") Annotation(rdfs:comment "PMID:39094565") "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which trimethylation of lysine at position 9 of histone H3 in regions containing protein-coding genes occurs to a greater extent than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-11-12T14:50:27Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased histone H3-K9 trimethylation at protein coding gene during vegetative growth"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +SubClassOf( ) + +# Class: (increased histone H3-K9 trimethylation at heterochromatin island during vegetative growth) + +AnnotationAssertion(Annotation(rdfs:comment "PMID:39094565") Annotation(rdfs:comment "PomBase:pc") "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which the trimethylation of lysine at position 9 of histone H3 in one or more heterochromatin islands occurs to a greater extent than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-11-12T14:54:16Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased histone H3-K9 trimethylation at heterochromatin island during vegetative growth"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +SubClassOf( ) + +# Class: (decreased phosphatidylinositol binding) + +AnnotationAssertion(Annotation(rdfs:comment "PomBase:vw") "A molecular function phenotype in which occurrence of phosphatidylinositol binding by a gene product (usually a protein) in a mutant is decreased. 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 "2024-11-12T14:58:44Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:comment "This term can mean that the mutated gene product itself binds one or more phospholipids less than wild type, or that a mutation in one gene decreases phospholipid binding by a second gene product. When using this term, it is therefore recommended to note the specific protein(s) affected.") +AnnotationAssertion(rdfs:label "decreased phosphatidylinositol binding"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) +SubClassOf( ) + +# Class: (phosphatidylserine absent from plasma membrane) + +AnnotationAssertion(Annotation(rdfs:comment "PomBase:vw") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of phosphatidylserine measured in the plasma membrane is too low to detect.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-11-12T15:07:47Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "phosphatidylserine absent from plasma membrane"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +SubClassOf( ) + +# Class: (increased phosphatidylinositol-4-phosphate level in plasma membrane) + +AnnotationAssertion(Annotation(rdfs:comment "PomBase:vw") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of phosphatidylinositol-4-phosphate measured in the plasma membrane is higher than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-11-12T15:38:33Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased phosphatidylinositol-4-phosphate level in plasma membrane"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +SubClassOf( ) +SubClassOf( ) + +# Class: (altered level of substance in plasma membrane) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of a specific substance measured in the plasma membrane is higher than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-11-12T15:50:09Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(oboInOwl:id "FYPO:0001730") +AnnotationAssertion(rdfs:label "altered level of substance in plasma membrane"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +SubClassOf( ) + +# Class: (normal ribosome hibernation during glucose starvation) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:39379376") "A cellular process phenotype in which ribosome hibernation is normal (i.e. indistinguishable from wild type) during glucose starvation.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-11-12T16:14:12Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "normal ribosome hibernation during glucose starvation"@en) +SubClassOf( ) + +# Class: (abolished ribosome to mitochondrion tethering) + +AnnotationAssertion( "A phenotype in which a ribosome tethering to the ribosome function is abolished.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-11-12T16:21:32Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "abolished ribosome to mitochondrion tethering"@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.")