diff --git a/src/ontology/fypo-edit.owl b/src/ontology/fypo-edit.owl index 0f47a8b8..97904769 100644 --- a/src/ontology/fypo-edit.owl +++ b/src/ontology/fypo-edit.owl @@ -8815,6 +8815,23 @@ 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()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -10615,6 +10632,10 @@ AnnotationAssertion(rdfs:label "p # Classes ############################ +# Class: (potassium(1+)) + +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + # Class: (phenotype) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") "Any of the set of observable characteristics of an organism resulting from the interaction of its genotype with the environment.") @@ -17085,7 +17106,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "SGD:phenotype_annotation") ob AnnotationAssertion(oboInOwl:id "FYPO:0000443") AnnotationAssertion(rdfs:comment "If this term is used, we recommend noting which protein(s) were used in the assay.") AnnotationAssertion(rdfs:label "abnormal protein localization during vegetative growth") -EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) SubClassOf( ) @@ -26855,6 +26876,8 @@ AnnotationAssertion(oboInOwl:creation_date "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(oboInOwl:hasExactSynonym "sensitive to 3-aminotriazole") 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") @@ -37016,8 +37039,8 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "abolished tRNA-Asp C38 methylation during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0001768") AnnotationAssertion(rdfs:label "abolished tRNA-Asp C38 methylation") -SubClassOf( ) SubClassOf( ) +SubClassOf( ) # Class: (increased tRNA-Asp C38 methylation) @@ -49301,8 +49324,8 @@ 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 "decreased mature tRNA level during vegetative growth") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) SubClassOf( ) +SubClassOf( ) # Class: (decreased mature mitochondrial tRNA level) @@ -58883,8 +58906,8 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRel AnnotationAssertion(oboInOwl:id "FYPO:0003218") AnnotationAssertion(rdfs:label "abolished tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridine biosynthesis") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) SubClassOf( ) +SubClassOf( ) # Class: (obsolete decreased histone H3-K9K14 acetylation during vegetative growth) @@ -67290,6 +67313,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") oboInOwl:hasExac AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") oboInOwl:hasRelatedSynonym "long mitotic spindle microtubules protruding beyond spindle pole body, with nuclear envelope deformation") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRelatedSynonym "long mitotic spindle microtubules protruding from spindle pole body during mitotic cell cycle") +AnnotationAssertion(oboInOwl:hasRelatedSynonym "long nuclear microtubules protruding through nuclear envelope") AnnotationAssertion(oboInOwl:id "FYPO:0003787") AnnotationAssertion(rdfs:label "long mitotic spindle microtubules protruding beyond spindle pole body") SubClassOf( ) @@ -69760,8 +69784,8 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRel AnnotationAssertion(oboInOwl:id "FYPO:0003957") AnnotationAssertion(rdfs:label "abolished tRNA guanosine N2,N2-dimethylation") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) SubClassOf( ) +SubClassOf( ) # Class: (abnormal diacylglycerol O-acyltransferase activity) @@ -73030,6 +73054,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRel AnnotationAssertion(oboInOwl:id "FYPO:0004180") AnnotationAssertion(rdfs:label "increased cellular protein aggregate level") SubClassOf( ) +SubClassOf( ) # Class: (normal protein localization to cell-cell contact point during mating) @@ -88044,8 +88069,8 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRel AnnotationAssertion(oboInOwl:id "FYPO:0005177") AnnotationAssertion(rdfs:label "abolished tRNA wobble position uridine thiolation") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) SubClassOf( ) +SubClassOf( ) # Class: (abnormal vacuolar morphology during nitrogen starvation) @@ -111799,7 +111824,7 @@ SubClassOf( (decreased pre-tRNA level during vegetative growth) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of one or more transfer RNA precursor(s) (pre-tRNA) measured in a cell is lower than normal. Total pre-tRNA or a specific pre-tRNA may be affected.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of one or more precursor transfer RNAs (pre-tRNA) measured in a cell is lower than normal. pre-tRNA oncludes any unspliced or incompletely spliced tRNA. Total pre-tRNA or a specific pre-tRNA may be affected.") AnnotationAssertion(oboInOwl:created_by "midori") AnnotationAssertion(oboInOwl:creation_date "2018-11-20T14:17:33Z") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasBroadSynonym "decreased tRNA level during vegetative growth") @@ -111814,7 +111839,7 @@ 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 "decreased pre-tRNA level during vegetative growth") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) +SubClassOf( ) # Class: (increased pre-tRNA level during vegetative growth) @@ -133024,6 +133049,160 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "abolished ubiquitin ligase activator activity"@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.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-29T15:01:26Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased pre-tRNA or mature level during vegetative growth"@en) +SubClassOf( ) + +# Class: (increased integrated stress response signaling) + +AnnotationAssertion( "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which integrated stress response signaling is increased.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-29T15:11:31Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasExactSynonym "increased GAAC signaling") +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased integrated stress response signaling"@en) +SubClassOf( ) + +# Class: (abolished tRNA modification) + +AnnotationAssertion( "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which tRNA modification does not occur. All tRNA modification may be abolished, or one or more specific tRNA modifications may be selectively affected.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-29T15:18:03Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "abolished tRNA modification"@en) +SubClassOf( ) + +# Class: (abolished tRNA cytidine N4-acetylation) + +AnnotationAssertion( "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which the posttranscriptional addition of acety groups to a cytosine N4 residue in a tRNA molecule is abolished.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-29T15:22:43Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "abolished tRNA cytidine N4-acetylation"@en) +SubClassOf( ) + +# Class: (increased cellular potassium level) + +AnnotationAssertion( "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of potassium measured in a cell (total or free) is higher than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-29T15:27:56Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased cellular potassium level"@en) +SubClassOf( ) + +# Class: (increased protein localization to trans-Golgi network) + +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-29T15:35:45Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "A cell phenotype observed in the vegetative growth phase of the life cycle in which the localization of a protein to the trans-Golgi network is increased.") +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased protein localization to trans-Golgi network"@en) +SubClassOf( ) + +# Class: (increased protein localization to pre-vacuolar endosome) + +AnnotationAssertion( "A cell phenotype observed in the vegetative growth phase of the life cycle in which the localization of a protein to pre-vacuolar endosome is increased.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-29T15:47:38Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased protein localization to pre-vacuolar endosome"@en) +SubClassOf( ) + +# Class: (abnormal 5'-nucleotidase activity) + +AnnotationAssertion( "A molecular function phenotype in which the observed rate of 5'-nucleotidase activity is abnormal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-29T15:58:10Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "abnormal 5'-nucleotidase activity"@en) +SubClassOf( ) + +# Class: (abolished GMP 5'-nucleotidase activity) + +AnnotationAssertion( "A molecular function phenotype in which the observed rate of GMP 5'-nucleotidase activity is abolished.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-29T16:02:25Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "abolished GMP 5'-nucleotidase activity"@en) +SubClassOf( ) + +# Class: (abolished AMP 5'-nucleotidase activity) + +AnnotationAssertion( "A molecular function phenotype in which the observed rate of AMP 5'-nucleotidase activity is abolished.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-29T16:04:42Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "abolished AMP 5'-nucleotidase activity"@en) +SubClassOf( ) + +# Class: (abolished CMP 5'-nucleotidase activity) + +AnnotationAssertion( "A molecular function phenotype in which the observed rate of CMP 5'-nucleotidase activity is abolished.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-29T16:05:55Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "abolished CMP 5'-nucleotidase activity"@en) +SubClassOf( ) + +# Class: (abolished UMP 5'-nucleotidase activity) + +AnnotationAssertion( "A molecular function phenotype in which the observed rate of UMP 5'-nucleotidase activity is abolished.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-29T16:06:30Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "abolished UMP 5'-nucleotidase activity"@en) +SubClassOf( ) + +# Class: (decreased UMP 5'-nucleotidase activity) + +AnnotationAssertion( "A molecular function phenotype in which the observed rate of UMP 5'-nucleotidase activity is decreased.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-29T16:07:10Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased UMP 5'-nucleotidase activity"@en) +SubClassOf( ) + +# Class: (decreased AMP 5'-nucleotidase activity) + +AnnotationAssertion( "A molecular function phenotype in which the observed rate of AMP 5'-nucleotidase activity is decreased.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-29T16:08:06Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased AMP 5'-nucleotidase activity"@en) +SubClassOf( ) + +# Class: (decreased CMP 5'-nucleotidase activity) + +AnnotationAssertion( "A molecular function phenotype in which the observed rate of CMP 5'-nucleotidase activity is decreased.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-29T16:08:50Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased CMP 5'-nucleotidase activity"@en) +SubClassOf( ) + +# Class: (decreased GMP 5'-nucleotidase activity) + +AnnotationAssertion( "A molecular function phenotype in which the observed rate of GMP 5'-nucleotidase activity is decreased.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-29T16:09:59Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased GMP 5'-nucleotidase activity"@en) +SubClassOf( ) + +# Class: (increased protein aggregate level) + +AnnotationAssertion( "A phenotype in which the amount of protein present as aggregates of misfolded protein is greater than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-12-29T16:13:24Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased protein aggregate level"@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.")