From 5dc40ef0ae5e16fcd459de6ac0ea387a1904a45d Mon Sep 17 00:00:00 2001 From: Val Wood Date: Mon, 29 Jul 2024 15:08:22 +0100 Subject: [PATCH] New branch 28 07 (#4590) * closes #4588; closes #4587; closes #4586; closes #4575; closes #4570; c;loses #4568 * closes #4588; closes #4587; closes #4586; closes #4575; closes #4570; closes #4568 --- src/ontology/fypo-edit.owl | 142 ++++++++++++++++++++++++++++++++++--- 1 file changed, 134 insertions(+), 8 deletions(-) diff --git a/src/ontology/fypo-edit.owl b/src/ontology/fypo-edit.owl index a8f2dff4..4bbf83ed 100644 --- a/src/ontology/fypo-edit.owl +++ b/src/ontology/fypo-edit.owl @@ -8749,6 +8749,18 @@ 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()) @@ -38506,9 +38518,9 @@ AnnotationAssertion(oboInOwl:created_by "2013-01-30T11:45:04Z") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "abnormal asymmetric protein localisation to old or new mitotic spindle pole body") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "abnormal asymmetric protein localization to old or new mitotic SPB") +AnnotationAssertion(oboInOwl:hasExactSynonym "abnormal asymmetric protein localization to old or new mitotic spindle pole body") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "abnormal asymmetric protein localization to old or new mitotic spindle pole body during vegetative growth") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "abnormal occurrence of normally asymmetric protein localization to old or new mitotic spindle pole body") -AnnotationAssertion(oboInOwl:hasExactSynonym "abnormal asymmetric protein localization to old or new mitotic spindle pole body") AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRelatedSynonym "abnormal asymmetric protein localization to old or new mitotic spindle pole body during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0001874") @@ -38524,10 +38536,10 @@ AnnotationAssertion(oboInOwl:created_by "2013-01-30T11:46:48Z") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "decreased asymmetric protein localisation to old or new mitotic spindle pole body") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "decreased asymmetric protein localization to old or new mitotic SPB") +AnnotationAssertion(oboInOwl:hasExactSynonym "decreased asymmetric protein localization to old or new mitotic spindle pole body") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "decreased asymmetric protein localization to old or new mitotic spindle pole body during vegetative growth") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "decreased occurrence of normally asymmetric protein localization to old or new mitotic spindle pole body") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "reduced asymmetric protein localization to old or new mitotic spindle pole body") -AnnotationAssertion(oboInOwl:hasExactSynonym "decreased asymmetric protein localization to old or new mitotic spindle pole body") AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRelatedSynonym "decreased asymmetric protein localization to old or new mitotic spindle pole body during mitotic cell cycle") AnnotationAssertion(oboInOwl:id "FYPO:0001875") @@ -38545,10 +38557,10 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExa AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "abnormally symmetric protein localization to mitotic spindle pole bodies during anaphase") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "abnormally symmetric protein localization to spindle pole bodies during mitotic anaphase") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "decreased asymmetric protein localisation to old or new mitotic spindle pole body during anaphase, with protein symmetrically localised to both spindle pole bodies") +AnnotationAssertion(oboInOwl:hasExactSynonym "decreased asymmetric protein localization to old or new mitotic spindle pole body during anaphase, with protein symmetrically localized to both spindle pole bodies") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "decreased asymmetric protein localization to old or new mitotic spindle pole body during anaphase, with protein symmetrically localized to both spindle pole bodies, during vegetative growth") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "decreased asymmetric protein localization to old or new mitotic spindle pole body during mitotic anaphase, with protein symmetrically localized to both spindle pole bodies") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym "reduced asymmetric protein localization to old or new mitotic spindle pole body during anaphase, with protein symmetrically localized to both spindle pole bodies") -AnnotationAssertion(oboInOwl:hasExactSynonym "decreased asymmetric protein localization to old or new mitotic spindle pole body during anaphase, with protein symmetrically localized to both spindle pole bodies") AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRelatedSynonym "abolished asymmetric protein localization to old or new mitotic SPB") AnnotationAssertion(oboInOwl:id "FYPO:0001876") @@ -74952,6 +74964,7 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "decreased protein localization to CENP-A containing chromatin") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))) SubClassOf( ) +SubClassOf( ) # Class: (normal protein localization to CENP-A containing chromatin) @@ -87829,7 +87842,7 @@ AnnotationAssertion(oboInOwl:id "F AnnotationAssertion(rdfs:comment "We recommend noting which protein(s) were used in the assay when annotating to this term.") AnnotationAssertion(rdfs:label "decreased protein localization to chromatin at centromere inner repeat") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) +SubClassOf( ) # Class: (normal protein level during cellular response to salt stress) @@ -98733,7 +98746,7 @@ AnnotationAssertion(oboInOwl:id "F AnnotationAssertion(rdfs:comment "We recommend noting which protein(s) were used in the assay when annotating to this term.") AnnotationAssertion(rdfs:label "decreased protein localization to centromeric chromatin, with protein mislocalized to nucleoplasm") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) +SubClassOf( ) # Class: (sensitive to sodium chloride) @@ -98842,7 +98855,7 @@ AnnotationAssertion(oboInOwl:id "F AnnotationAssertion(rdfs:comment "We recommend noting which protein(s) were used in the assay when annotating to this term.") AnnotationAssertion(rdfs:label "decreased protein localization to centromeric chromatin during mitotic G1 phase") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) +SubClassOf( ) # Class: (decreased protein localization to chromatin during mitotic G1 phase) @@ -109511,7 +109524,7 @@ AnnotationAssertion(oboInOwl:id "F AnnotationAssertion(rdfs:comment "We recommend noting which protein(s) were used in the assay when annotating to this term.") AnnotationAssertion(rdfs:label "decreased protein localization to centromeric chromatin during mitotic metaphase") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) +SubClassOf( ) # Class: (normal protein localization to centromeric chromatin during mitotic metaphase) @@ -112795,7 +112808,7 @@ AnnotationAssertion(oboInOwl:id "F AnnotationAssertion(rdfs:comment "We recommend noting which protein(s) were used in the assay when annotating to this term.") AnnotationAssertion(rdfs:label "decreased protein localization to chromatin at centromere outer repeat") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) +SubClassOf( ) # Class: (normal vegetative cell growth rate) @@ -132179,6 +132192,7 @@ AnnotationAssertion(oboInOwl:created_by "2024-07-04T12:54:09Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") AnnotationAssertion(rdfs:label "decreased protein localization to cell surface"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))) SubClassOf( ) # Class: (decreased protein localization to cell surface with increased localization to endosomal structures) @@ -132225,6 +132239,7 @@ AnnotationAssertion(oboInOwl:created_by "2024-07-04T13:24:16Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") AnnotationAssertion(rdfs:label "abolished protein kinase activity in response to osmotic stress"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) # Class: (abolished protein kinase activity in response to oxidative stress) @@ -132234,6 +132249,7 @@ AnnotationAssertion(oboInOwl:created_by "2024-07-04T13:24:34Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") AnnotationAssertion(rdfs:label "abolished protein kinase activity in response to oxidative stress"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) # Class: (normal chromatin silencing at rDNA) @@ -132327,6 +132343,116 @@ AnnotationAssertion(oboInOwl:hasOBONamespace "decreased glutamate biosynthesis"@en) SubClassOf( ) +# Class: (normal polyphosphatase activity) + +AnnotationAssertion( "A molecular function phenotype in which the observed rate of a polyphosphatase activity is normal (i.e. indistinguishable from wild type).") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-29T11:30:26Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission _yeast_phenotype") +AnnotationAssertion(rdfs:label "normal polyphosphatase activity"@en) +SubClassOf( ) + +# Class: (abolished polyphosphatase activity) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:vw") "A molecular function phenotype in which a polyphosphatase activity is absent.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-29T11:34:21Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "abolished polyphosphatase activity"@en) +SubClassOf( ) + +# Class: (increased cellular 1,5-IP8 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 1,5-bisdiphospho-1D-myo-inositol 2,3,4,6-tetrakisphosphate (1,5-IP8) measured in a cell is higher than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-29T11:50:35Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission yeast phenotype") +AnnotationAssertion(rdfs:label "increased cellular 1,5-IP8 level"@en) +SubClassOf( ) + +# Class: (increased cellular 5-IP7 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 5-diphospho-1D-myo-inositol 1,2,3,4,6-pentakisphosphate (5-IP7) is higher than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-29T12:01:32Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased cellular 5-IP7 level"@en) +SubClassOf( ) + +# Class: (increased cellular 1-IP7 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 1-diphospho-1D-myo-inositol 2,3,4,5,6-pentakisphosphate (1-IP7) is higher than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-29T12:28:01Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "increased cellular 1-IP7 level"@en) +SubClassOf( ) + +# Class: (decreased cellular myo-inositol 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 myo-inositol measured in a cell is lower than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-29T12:42:06Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased cellular myo-inositol level"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +SubClassOf( ) + +# Class: (decreased cellular 1,5-IP8 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 1,5-bisdiphospho-1D-myo-inositol 2,3,4,6-tetrakisphosphate (1,5-IP8) measured in a cell is lower than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-29T12:59:07Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased cellular 1,5-IP8 level"@en) +SubClassOf( ) + +# Class: (decreased cellular 5-IP7 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 5-diphospho-1D-myo-inositol 1,2,3,4,6-pentakisphosphate (5-IP7) is lower than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-29T13:00:49Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased cellular 5-IP7 level"@en) +SubClassOf( ) + +# Class: (decreased cellular 1-IP7 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 1-diphospho-1D-myo-inositol 2,3,4,5,6-pentakisphosphate (1-IP7) is lower than normal.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-29T13:02:46Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "decreased cellular 1-IP7 level"@en) +SubClassOf( ) + +# Class: (normal cellular myo-inositol level) + +AnnotationAssertion( "A cell phenotype in which the amount of myo-inositol in a cell is normal when the cell is in the vegetative growth phase of the life cycle.") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-29T13:05:36Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "normal cellular myo-inositol level"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +SubClassOf( ) + +# Class: (normal cellular 5-IP7 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 5-diphospho-1D-myo-inositol 1,2,3,4,6-pentakisphosphate (5-IP7) is normal (i.e. indistinguishable from wild type).") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-29T13:10:24Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "normal cellular 5-IP7 level"@en) +SubClassOf( ) + +# Class: (normal cellular 1-IP7 level) + +AnnotationAssertion(Annotation(rdfs:comment "PomBase:pc") "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of 1-diphospho-1D-myo-inositol 2,3,4,5,6-pentakisphosphate (1-IP7) is normal (i.e. indistinguishable from wild type).") +AnnotationAssertion(oboInOwl:created_by "vw") +AnnotationAssertion(oboInOwl:creation_date "2024-07-29T13:14:13Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasOBONamespace "fission_yeast_phenotype") +AnnotationAssertion(rdfs:label "normal cellular 1-IP7 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.")