search

pombase / fypo

Fission Yeast Phenotype Ontology
Creative Commons Attribution 4.0 International
14 stars 6 forks source link

‘closes #4526; closes #4525; closes #4522; closes #4518; closes #4501; closes #4489' #4527

Closed ValWood closed 2 months ago

ValWood commented 2 months ago

‘closes #4526; closes #4525; closes #4522; closes #4518; closes #4501; closes #4489'

github-actions[bot] commented 2 months ago

Changes added to the edit file this PR

Click to expand # Ontology comparison ## Left - Ontology IRI: `http://purl.obolibrary.org/obo/fypo.owl` - Version IRI: *None* - Loaded from: `file:/__w/fypo/fypo/master/src/ontology/fypo-edit.owl` ## Right - Ontology IRI: `http://purl.obolibrary.org/obo/fypo.owl` - Version IRI: *None* - Loaded from: `file:/__w/fypo/fypo/src/ontology/fypo-edit.owl` ### Ontology imports ### Ontology annotations ### abnormal protein localization to plasma membrane during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0002125` #### Removed - [abnormal protein localization to plasma membrane during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0002125) SubClassOf [abnormal protein localization during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0000443) ### abolished protein localization to plasma membrane during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0002126` #### Removed - [abolished protein localization to plasma membrane during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0002126) EquivalentTo [has_part](http://purl.obolibrary.org/obo/BFO_0000051) some ([lacking processual parts](http://purl.obolibrary.org/obo/PATO_0001558) and ([during](http://purl.obolibrary.org/obo/GOREL_0000002) some [single-celled organism vegetative growth phase](http://purl.obolibrary.org/obo/GO_0072690)) and ([inheres_in](http://purl.obolibrary.org/obo/RO_0000052) some [protein localization to plasma membrane](http://purl.obolibrary.org/obo/GO_0072659)) and ([qualifier](http://purl.obolibrary.org/obo/RO_0002573) some [abnormal](http://purl.obolibrary.org/obo/PATO_0000460))) ### decreased histone H3-K9 methylation at centromere inner repeat during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0008200` #### Added - [decreased histone H3-K9 methylation at centromere inner repeat during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008200) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased histone H3-K9 methylation at centromere inner repeat during vegetative growth"@en - [decreased histone H3-K9 methylation at centromere inner repeat during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008200) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [decreased histone H3-K9 methylation at centromere inner repeat during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008200) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-04-15T08:18:10Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - Class: [decreased histone H3-K9 methylation at centromere inner repeat during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008200) - [decreased histone H3-K9 methylation at centromere inner repeat during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008200) EquivalentTo [has_part](http://purl.obolibrary.org/obo/BFO_0000051) some ([decreased occurrence](http://purl.obolibrary.org/obo/PATO_0002052) and ([happens_during](http://purl.obolibrary.org/obo/GOREL_0000001) some [single-celled organism vegetative growth phase](http://purl.obolibrary.org/obo/GO_0072690)) and ([occurs_at](http://purl.obolibrary.org/obo/GOREL_0000501) some [regional_centromere_inner_repeat_region](http://purl.obolibrary.org/obo/SO_0001798)) and ([inheres_in](http://purl.obolibrary.org/obo/RO_0000052) some [histone H3-K9 methylation](http://purl.obolibrary.org/obo/GO_0051567))) - [decreased histone H3-K9 methylation at centromere inner repeat during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008200) SubClassOf [decreased histone H3-K9 methylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0000872) ### decreased histone H3-K9 methylation at heterochromatin island during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0003230` #### Added - [decreased histone H3-K9 methylation at heterochromatin island during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0003230) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which dimethylation of lysine at position 9 of histone H3 at the centromere inner repeat occurs to a lower extent than normal." ### decreased membrane lipid binding `http://purl.obolibrary.org/obo/FYPO_0007252` #### Removed - [decreased membrane lipid binding](http://purl.obolibrary.org/obo/FYPO_0007252) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "This term can mean that the mutated gene product itself binds heme less than wild type, or that a mutation in one gene decreases heme binding by a second gene product. When using this term, it is therefore recommended to note the specific protein(s) affected." ### decreased protein localization to plasma membrane during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0008198` #### Added - [decreased protein localization to plasma membrane during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008198) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [decreased protein localization to plasma membrane during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008198) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell phenotype observed in the vegetative growth phase of the life cycle in which the localization of a protein to the plasma membrane is decreased." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15572668" - [decreased protein localization to plasma membrane during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008198) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-04-15T07:39:55Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [decreased protein localization to plasma membrane during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008198) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased protein localization to plasma membrane during vegetative growth"@en - Class: [decreased protein localization to plasma membrane during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008198) - [decreased protein localization to plasma membrane during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008198) EquivalentTo [has_part](http://purl.obolibrary.org/obo/BFO_0000051) some ([decreased occurrence](http://purl.obolibrary.org/obo/PATO_0002052) and ([inheres_in](http://purl.obolibrary.org/obo/RO_0000052) some ([protein localization to plasma membrane](http://purl.obolibrary.org/obo/GO_0072659) and ([happens during](http://purl.obolibrary.org/obo/RO_0002092) some [single-celled organism vegetative growth phase](http://purl.obolibrary.org/obo/GO_0072690))))) - [decreased protein localization to plasma membrane during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008198) SubClassOf [abnormal protein localization to plasma membrane during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0002125) ### decreased protein localization to plasma membrane of cell tip during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0003771` #### Removed - [decreased protein localization to plasma membrane of cell tip during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0003771) SubClassOf [abnormal protein localization to plasma membrane during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0002125) #### Added - [decreased protein localization to plasma membrane of cell tip during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0003771) SubClassOf [decreased protein localization to plasma membrane during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008198) ### decreased protein localization to plasma membrane, with protein mislocalized to cytoplasm, during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0004780` #### Removed - [decreased protein localization to plasma membrane, with protein mislocalized to cytoplasm, during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0004780) SubClassOf [abnormal protein localization to plasma membrane during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0002125) #### Added - [decreased protein localization to plasma membrane, with protein mislocalized to cytoplasm, during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0004780) SubClassOf [decreased protein localization to plasma membrane during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008198) ### normal histone H3-K9 dimethylation at centromere during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0000862` #### Added - [normal histone H3-K9 dimethylation at centromere during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0000862) EquivalentTo [has_part](http://purl.obolibrary.org/obo/BFO_0000051) some ([quality](http://purl.obolibrary.org/obo/PATO_0000001) and ([happens_during](http://purl.obolibrary.org/obo/GOREL_0000001) some [single-celled organism vegetative growth phase](http://purl.obolibrary.org/obo/GO_0072690)) and ([occurs_at](http://purl.obolibrary.org/obo/GOREL_0000501) some [regional_centromere](http://purl.obolibrary.org/obo/SO_0001795)) and ([inheres_in](http://purl.obolibrary.org/obo/RO_0000052) some [histone H3-K9 dimethylation](http://purl.obolibrary.org/obo/GO_0036123)) and ([qualifier](http://purl.obolibrary.org/obo/RO_0002573) some [normal](http://purl.obolibrary.org/obo/PATO_0000461))) ### normal histone H3-K9 methylation at centromere during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0008070` #### Added - [normal histone H3-K9 methylation at centromere during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008070) EquivalentTo [has_part](http://purl.obolibrary.org/obo/BFO_0000051) some ([quality](http://purl.obolibrary.org/obo/PATO_0000001) and ([happens_during](http://purl.obolibrary.org/obo/GOREL_0000001) some [single-celled organism vegetative growth phase](http://purl.obolibrary.org/obo/GO_0072690)) and ([occurs_at](http://purl.obolibrary.org/obo/GOREL_0000501) some [regional_centromere](http://purl.obolibrary.org/obo/SO_0001795)) and ([inheres_in](http://purl.obolibrary.org/obo/RO_0000052) some [histone H3-K9 methylation](http://purl.obolibrary.org/obo/GO_0051567)) and ([qualifier](http://purl.obolibrary.org/obo/RO_0002573) some [normal](http://purl.obolibrary.org/obo/PATO_0000461))) ### normal histone H3-K9 trimethylation at centromere outer repeat during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0008199` #### Added - [normal histone H3-K9 trimethylation at centromere outer repeat during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008199) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-04-15T08:06:39Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [normal histone H3-K9 trimethylation at centromere outer repeat during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008199) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [normal histone H3-K9 trimethylation at centromere outer repeat during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008199) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "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 at the centromere outer repeat is normal (i.e. indistinguishable from wild type)." - [normal histone H3-K9 trimethylation at centromere outer repeat during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008199) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal histone H3-K9 trimethylation at centromere outer repeat during vegetative growth"@en - Class: [normal histone H3-K9 trimethylation at centromere outer repeat during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008199) - [normal histone H3-K9 trimethylation at centromere outer repeat during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008199) EquivalentTo [has_part](http://purl.obolibrary.org/obo/BFO_0000051) some ([quality](http://purl.obolibrary.org/obo/PATO_0000001) and ([happens_during](http://purl.obolibrary.org/obo/GOREL_0000001) some [single-celled organism vegetative growth phase](http://purl.obolibrary.org/obo/GO_0072690)) and ([occurs_at](http://purl.obolibrary.org/obo/GOREL_0000501) some [regional_centromere_outer_repeat_region](http://purl.obolibrary.org/obo/SO_0001799)) and ([inheres_in](http://purl.obolibrary.org/obo/RO_0000052) some [histone H3-K9 trimethylation](http://purl.obolibrary.org/obo/GO_0036124)) and ([qualifier](http://purl.obolibrary.org/obo/RO_0002573) some [normal](http://purl.obolibrary.org/obo/PATO_0000461))) - [normal histone H3-K9 trimethylation at centromere outer repeat during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008199) SubClassOf [normal histone H3-K9 methylation at centromere during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008070) ### normal meiotic cell cycle entry `http://purl.obolibrary.org/obo/FYPO_0008201` #### Added - [normal meiotic cell cycle entry](http://purl.obolibrary.org/obo/FYPO_0008201) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [normal meiotic cell cycle entry](http://purl.obolibrary.org/obo/FYPO_0008201) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype in which a cell enters the meiotic cell cycle normally: i.e after conjugation with cellular fusion and karyogamy with nuclear fusion." - [normal meiotic cell cycle entry](http://purl.obolibrary.org/obo/FYPO_0008201) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-04-15T08:22:38Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [normal meiotic cell cycle entry](http://purl.obolibrary.org/obo/FYPO_0008201) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal meiotic cell cycle entry"@en - Class: [normal meiotic cell cycle entry](http://purl.obolibrary.org/obo/FYPO_0008201) - [normal meiotic cell cycle entry](http://purl.obolibrary.org/obo/FYPO_0008201) SubClassOf [normal meiotic cell cycle process](http://purl.obolibrary.org/obo/FYPO_0007078) ### normal replication fork arrest at RTS1 barrier `http://purl.obolibrary.org/obo/FYPO_0005353` #### Removed - [normal replication fork arrest at RTS1 barrier](http://purl.obolibrary.org/obo/FYPO_0005353) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which replication fork arrest at the mating-type locus is normal (i.e. indistinguishable from wild type)." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mah" - [normal replication fork arrest at RTS1 barrier](http://purl.obolibrary.org/obo/FYPO_0005353) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal replication fork arrest at mating-type locus" #### Added - [normal replication fork arrest at RTS1 barrier](http://purl.obolibrary.org/obo/FYPO_0005353) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "normal replication fork arrest at mating-type locus" - [normal replication fork arrest at RTS1 barrier](http://purl.obolibrary.org/obo/FYPO_0005353) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal replication fork arrest at RTS1 barrier" - [normal replication fork arrest at RTS1 barrier](http://purl.obolibrary.org/obo/FYPO_0005353) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which replication fork arrest at the RTS1 barrier is normal (i.e. indistinguishable from wild type). Note that the RTS1 barrier usually occurs in the mating type locus, but might be assayed at ectopic loci to maximise the distance that a restarted fork travels." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:vw"
# Changes to ontology after reasoner runs
Click to expand Coming soon >
# Errors reported ``` Level Rule Name Subject Property Value ERROR multiple_definitions decreased histone H3-K9 methylation at heterochromatin island during vegetative growth definition A cellular process phenotype observed in the vegetative growth phase of the life cycle in which dimethylation of lysine at position 9 of histone H3 at the centromere inner repeat occurs to a lower extent than normal. ERROR multiple_definitions decreased histone H3-K9 methylation at heterochromatin island during vegetative growth definition A cellular process phenotype observed in the vegetative growth phase of the life cycle in which methylation of lysine at position 9 of histone H3 at heterochromatin islands occurs to a lower extent than normal. WARN missing_definition decreased histone H3-K9 methylation at centromere inner repeat during vegetative growth definition WARN missing_definition output_of definition WARN missing_definition preceded_by definition WARN missing_definition precedes definition INFO lowercase_definition has_output definition p has output c if either: p has direct output c or p has output input c. Implies that if p happens, c always ensues. INFO missing_superclass phenotype rdfs:subClassOf ```