From fac12105a6672f65375d13d5b914efd440b7a67f Mon Sep 17 00:00:00 2001 From: Val Wood Date: Mon, 30 Sep 2024 15:50:19 +0100 Subject: [PATCH] closes #4611; closes #4610; closes #4608; closes #4604; closes #4599; closes #4596; closes #4541 --- src/ontology/fypo-edit.owl | 102 +++++++++++++++++++++++++-- src/ontology/imports/chebi_terms.txt | 3 + 2 files changed, 99 insertions(+), 6 deletions(-) diff --git a/src/ontology/fypo-edit.owl b/src/ontology/fypo-edit.owl index 18d95f56..1c21ce6d 100644 --- a/src/ontology/fypo-edit.owl +++ b/src/ontology/fypo-edit.owl @@ -8765,6 +8765,14 @@ 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()) @@ -40002,6 +40010,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GO:0000920") oboInOwl:hasExac AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GO:0000920") oboInOwl:hasExactSynonym "abnormal septum digestion after cytokinesis resulting in septated cell") AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRelatedSynonym "abnormal cell separation after cytokinesis resulting in septated cell during mitotic cell cycle") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") oboInOwl:hasRelatedSynonym "boomerang shaped") AnnotationAssertion(oboInOwl:id "FYPO:0001972") AnnotationAssertion(rdfs:comment "This phenotype usually results from a defect late in septum degradation.") AnnotationAssertion(rdfs:label "abnormal cell separation after cytokinesis resulting in septated cell") @@ -55287,7 +55296,7 @@ SubClassOf( (increased level of transmembrane transport gene mRNA 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 iron transport messenger RNAs measured in a cell is higher than normal (i.e. higher than observed in wild-type cells). Iron transport m RNAs are transcribed from genes whose products are involved in iron transport.") +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 transmembrane transport messenger RNAs measured in a cell is higher than normal (i.e. higher than observed in wild-type cells).") AnnotationAssertion(oboInOwl:created_by "midori") AnnotationAssertion(oboInOwl:creation_date "2013-12-11T15:57:35Z") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "increased level of transmembrane transport gene RNA during vegetative growth") @@ -65397,15 +65406,17 @@ AnnotationAssertion(rdfs:label "ab EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) -# Class: (abolished RNA pyrophosphohydrolase activity) +# Class: (abolished mRNA 5'-diphosphatase activity) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") "A molecular function phenotype in which RNA pyrophosphohydrolase activity is absent.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") "A molecular function phenotype in which mRNA 5'-diphosphatase activity is absent.") AnnotationAssertion(oboInOwl:created_by "midori") AnnotationAssertion(oboInOwl:creation_date "2014-08-12T13:31:55Z") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "RNA pyrophosphohydrolase activity abolished") AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") oboInOwl:hasRelatedSynonym "abolished RNA pyrophosphohydrolase activity") AnnotationAssertion(oboInOwl:id "FYPO:0003664") -AnnotationAssertion(rdfs:label "abolished RNA pyrophosphohydrolase activity") +AnnotationAssertion(rdfs:label "abolished mRNA 5'-diphosphatase activity") +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) SubClassOf( ) @@ -106990,16 +107001,17 @@ AnnotationAssertion(rdfs:label "in EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) -# Class: (enlarged mitotic spindle pole body) +# Class: () AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") "A physical cellular phenotype observed in the vegetative growth phase of the life cycle in which the mitotic spindle pole body is larger than normal.") AnnotationAssertion(oboInOwl:created_by "midori") AnnotationAssertion(oboInOwl:creation_date "2018-03-09T13:19:49Z") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "enlarged spindle pole body during mitotic cell cycle") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") oboInOwl:hasExactSynonym "enlarged spindle pole body during vegetative growth") +AnnotationAssertion(Annotation(rdfs:comment "PomBase:vw") oboInOwl:hasExactSynonym "enlarged mitotic SPB") +AnnotationAssertion(oboInOwl:hasExactSynonym "enlarged mitotic spindle pole body") AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") AnnotationAssertion(oboInOwl:id "FYPO:0006431") -AnnotationAssertion(rdfs:label "enlarged mitotic spindle pole body") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) @@ -132490,6 +132502,84 @@ AnnotationAssertion(rdfs:label "ab EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) +# Class: (increased cellular mtDNA level) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of mitochondrial DNA present in the cell is higher than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-09-30T11:28:00Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") oboInOwl:hasExactSynonym "increased mitochondrial DNA content") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") oboInOwl:hasExactSynonym "increased mtDNA level") +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") oboInOwl:hasRelatedSynonym "increased mitochondrial DNA copy number") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") oboInOwl:hasRelatedSynonym "increased mitochondrial genome copy number") +AnnotationAssertion(rdfs:label "increased cellular mtDNA level"@en) +SubClassOf( ) + +# Class: (increased phosphatidylinositol-4,5-bisphosphate level in the cell division site plasma membrane) + +AnnotationAssertion( "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of phosphatidylinositol-4,5-bisphosphate measured in the cell division site plasma membrane is higher than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-09-30T11:44:01Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasExactSynonym "increased cell sivision site plasma membrane PI(4,5)P2 level") +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased phosphatidylinositol-4,5-bisphosphate level in the cell division site plasma membrane"@en) +SubClassOf( ) + +# Class: (protein mislocalized to cell division site) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") "A cell phenotype in which a protein that is not normally found in the cell division site is observed there.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-09-30T11:51:06Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "protein mislocalized to cell division site"@en) +SubClassOf( ) + +# Class: (normal plasma membrane-ER tethering) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which Endoplasmic Reticulum tethering to the plasma membrane is normal. Normal ER to plasma membrane tethering results in correct localization of the ER.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-09-30T12:02:17Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "normal plasma membrane-ER tethering"@en) +SubClassOf( ) + +# Class: (sensitive to guanazole) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:pc") "A phenotype observed in the vegetative growth phase of the life cycle in which cells show increased sensitivity to guanozole. Cells stop growing (and may die) at a concentration of guanozole that allows wild type cells to grow.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-09-30T13:24:06Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasRelatedSynonym "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "sensitive to guanazole"@en) +SubClassOf( ) + +# Class: (increased cellular 24-methylene lanosterol) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of 24-methylene lanosterol measured in a cell is higher than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-09-30T13:55:04Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased cellular 24-methylene lanosterol"@en) +SubClassOf( ) + +# Class: (increased cellular ergosta-5,7,24(28)-trienol level) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of ergosta- 5,7,24(28)-trienol measured in a cell is higher than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-09-30T13:57:24Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased cellular ergosta-5,7,24(28)-trienol level"@en) +SubClassOf( ) + +# Class: (ergosta-5,7-dienol level) + +AnnotationAssertion( "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of ergosta-5,7-dienol measured in a cell is higher than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-09-30T14:00:34Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:comment "ergosta-5,7-dienol level is not a normal pathway intermediate, but forms when Erg5 is inhibited.") +AnnotationAssertion(rdfs:label "ergosta-5,7-dienol 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.") diff --git a/src/ontology/imports/chebi_terms.txt b/src/ontology/imports/chebi_terms.txt index 65f31e0e..9df13c06 100644 --- a/src/ontology/imports/chebi_terms.txt +++ b/src/ontology/imports/chebi_terms.txt @@ -1,3 +1,6 @@ +CHEBI:80095 +CHEBI:28113 +CHEBI:66918 CHEBI:34718 CHEBI:24479 CHEBI:24480