pombase / fypo

Fission Yeast Phenotype Ontology
Creative Commons Attribution 4.0 International
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‘closes #4338

Closed ValWood closed 1 year ago

github-actions[bot] commented 1 year 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 autophagy `http://purl.obolibrary.org/obo/FYPO_0008082` #### Added - [abnormal autophagy](http://purl.obolibrary.org/obo/FYPO_0008082) [label](http://www.w3.org/2000/01/rdf-schema#label) "abnormal autophagy"@en - [abnormal autophagy](http://purl.obolibrary.org/obo/FYPO_0008082) [date](http://purl.org/dc/elements/1.1/date) "2023-06-07T08:25:03Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [abnormal autophagy](http://purl.obolibrary.org/obo/FYPO_0008082) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype in which autophagy is abnormal. Autophagy is the pathway by which cells digest parts of their own cytoplasm." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35406650"^^[string](http://www.w3.org/2001/XMLSchema#string) - [abnormal autophagy](http://purl.obolibrary.org/obo/FYPO_0008082) [creator](http://purl.org/dc/elements/1.1/creator) "vw253"^^[string](http://www.w3.org/2001/XMLSchema#string) - Class: [abnormal autophagy](http://purl.obolibrary.org/obo/FYPO_0008082) - [abnormal autophagy](http://purl.obolibrary.org/obo/FYPO_0008082) EquivalentTo [has part](http://purl.obolibrary.org/obo/BFO_0000051) some ([quality](http://purl.obolibrary.org/obo/BFO_0000019) and ([characteristic of part of](http://purl.obolibrary.org/obo/RO_0002314) some [autophagy](http://purl.obolibrary.org/obo/GO_0006914)) and ([has modifier](http://purl.obolibrary.org/obo/RO_0002573) some [abnormal](http://purl.obolibrary.org/obo/PATO_0000460))) - [abnormal autophagy](http://purl.obolibrary.org/obo/FYPO_0008082) SubClassOf [abnormal cellular process](http://purl.obolibrary.org/obo/FYPO_0000628) ### abnormal macroautophagy `http://purl.obolibrary.org/obo/FYPO_0000163` #### Removed - [abnormal macroautophagy](http://purl.obolibrary.org/obo/FYPO_0000163) SubClassOf [abnormal metabolic process](http://purl.obolibrary.org/obo/FYPO_0000860) #### Added - [abnormal macroautophagy](http://purl.obolibrary.org/obo/FYPO_0000163) SubClassOf [abnormal autophagy](http://purl.obolibrary.org/obo/FYPO_0008082) ### abnormal macroautophagy during nitrogen starvation `http://purl.obolibrary.org/obo/FYPO_0004670` #### Removed - [abnormal macroautophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0004670) SubClassOf [abnormal metabolic process](http://purl.obolibrary.org/obo/FYPO_0000860) #### Added - [abnormal macroautophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0004670) SubClassOf [abnormal macroautophagy](http://purl.obolibrary.org/obo/FYPO_0000163) ### abnormal mitophagy `http://purl.obolibrary.org/obo/FYPO_0007590` #### Removed - [abnormal mitophagy](http://purl.obolibrary.org/obo/FYPO_0007590) SubClassOf [abnormal metabolic process](http://purl.obolibrary.org/obo/FYPO_0000860) #### Added - [abnormal mitophagy](http://purl.obolibrary.org/obo/FYPO_0007590) SubClassOf [abnormal autophagy](http://purl.obolibrary.org/obo/FYPO_0008082) ### abnormal nucleophagy `http://purl.obolibrary.org/obo/FYPO_0008085` #### Added - [abnormal nucleophagy](http://purl.obolibrary.org/obo/FYPO_0008085) [label](http://www.w3.org/2000/01/rdf-schema#label) "abnormal nucleophagy"@en - [abnormal nucleophagy](http://purl.obolibrary.org/obo/FYPO_0008085) [creator](http://purl.org/dc/elements/1.1/creator) "vw253"^^[string](http://www.w3.org/2001/XMLSchema#string) - [abnormal nucleophagy](http://purl.obolibrary.org/obo/FYPO_0008085) [date](http://purl.org/dc/elements/1.1/date) "2023-06-07T09:00:36Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - Class: [abnormal nucleophagy](http://purl.obolibrary.org/obo/FYPO_0008085) - [abnormal nucleophagy](http://purl.obolibrary.org/obo/FYPO_0008085) EquivalentTo [has part](http://purl.obolibrary.org/obo/BFO_0000051) some ([quality](http://purl.obolibrary.org/obo/BFO_0000019) and ([characteristic of](http://purl.obolibrary.org/obo/RO_0000052) some [autophagy of nucleus](http://purl.obolibrary.org/obo/GO_0044804)) and ([has modifier](http://purl.obolibrary.org/obo/RO_0002573) some [abnormal](http://purl.obolibrary.org/obo/PATO_0000460))) - [abnormal nucleophagy](http://purl.obolibrary.org/obo/FYPO_0008085) SubClassOf [abnormal autophagy](http://purl.obolibrary.org/obo/FYPO_0008082) ### abnormal reticulophagy `http://purl.obolibrary.org/obo/FYPO_0008083` #### Added - [abnormal reticulophagy](http://purl.obolibrary.org/obo/FYPO_0008083) [label](http://www.w3.org/2000/01/rdf-schema#label) "abnormal reticulophagy"@en - [abnormal reticulophagy](http://purl.obolibrary.org/obo/FYPO_0008083) [creator](http://purl.org/dc/elements/1.1/creator) "vw253"^^[string](http://www.w3.org/2001/XMLSchema#string) - [abnormal reticulophagy](http://purl.obolibrary.org/obo/FYPO_0008083) [date](http://purl.org/dc/elements/1.1/date) "2023-06-07T08:36:39Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - Class: [abnormal reticulophagy](http://purl.obolibrary.org/obo/FYPO_0008083) - [abnormal reticulophagy](http://purl.obolibrary.org/obo/FYPO_0008083) EquivalentTo [has part](http://purl.obolibrary.org/obo/BFO_0000051) some ([quality](http://purl.obolibrary.org/obo/BFO_0000019) and ([characteristic of part of](http://purl.obolibrary.org/obo/RO_0002314) some [reticulophagy](http://purl.obolibrary.org/obo/GO_0061709)) and ([has modifier](http://purl.obolibrary.org/obo/RO_0002573) some [abnormal](http://purl.obolibrary.org/obo/PATO_0000460))) - [abnormal reticulophagy](http://purl.obolibrary.org/obo/FYPO_0008083) SubClassOf [abnormal autophagy](http://purl.obolibrary.org/obo/FYPO_0008082) ### abnormal reticulophagy during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0007445` #### Added - [abnormal reticulophagy during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0007445) SubClassOf [abnormal reticulophagy](http://purl.obolibrary.org/obo/FYPO_0008083) ### abolished nucleophagy during nitrogen starvation `http://purl.obolibrary.org/obo/FYPO_0008086` #### Added - [abolished nucleophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0008086) [date](http://purl.org/dc/elements/1.1/date) "2023-06-07T09:32:05Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [abolished nucleophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0008086) [creator](http://purl.org/dc/elements/1.1/creator) "vw253"^^[string](http://www.w3.org/2001/XMLSchema#string) - [abolished nucleophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0008086) [label](http://www.w3.org/2000/01/rdf-schema#label) "abolished nucleophagy during nitrogen starvation"@en - [abolished nucleophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0008086) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype in which autophagic degradation of the nucleus during nitrogen starvation is abolished ." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37191320"^^[string](http://www.w3.org/2001/XMLSchema#string) - Class: [abolished nucleophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0008086) - [abolished nucleophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0008086) SubClassOf [abnormal nucleophagy](http://purl.obolibrary.org/obo/FYPO_0008085) ### abolished reticulophagy during nitrogen starvation `http://purl.obolibrary.org/obo/FYPO_0008084` #### Added - [abolished reticulophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0008084) [date](http://purl.org/dc/elements/1.1/date) "2023-06-07T08:47:18Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [abolished reticulophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0008084) [label](http://www.w3.org/2000/01/rdf-schema#label) "abolished reticulophagy during nitrogen starvation"@en - [abolished reticulophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0008084) [creator](http://purl.org/dc/elements/1.1/creator) "vw253"^^[string](http://www.w3.org/2001/XMLSchema#string) - [abolished reticulophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0008084) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype in which autophagic degradation of the endoplasmic reticulum is abolished during nitrogen starvation." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37191320"^^[string](http://www.w3.org/2001/XMLSchema#string) - Class: [abolished reticulophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0008084) - [abolished reticulophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0008084) SubClassOf [abnormal reticulophagy](http://purl.obolibrary.org/obo/FYPO_0008083) ### decreased nucleophagy during nitrogen starvation `http://purl.obolibrary.org/obo/FYPO_0008087` #### Added - [decreased nucleophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0008087) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype in which autophagic degradation of the nucleus during nitrogen starvation is decreased." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37191320"^^[string](http://www.w3.org/2001/XMLSchema#string) - [decreased nucleophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0008087) [creator](http://purl.org/dc/elements/1.1/creator) "vw253"^^[string](http://www.w3.org/2001/XMLSchema#string) - [decreased nucleophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0008087) [date](http://purl.org/dc/elements/1.1/date) "2023-06-07T09:34:03Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [decreased nucleophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0008087) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased nucleophagy during nitrogen starvation"@en - Class: [decreased nucleophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0008087) - [decreased nucleophagy during nitrogen starvation](http://purl.obolibrary.org/obo/FYPO_0008087) SubClassOf [abnormal nucleophagy](http://purl.obolibrary.org/obo/FYPO_0008085) ### increased nucleophagy during G0 `http://purl.obolibrary.org/obo/FYPO_0006665` #### Removed - [increased nucleophagy during G0](http://purl.obolibrary.org/obo/FYPO_0006665) SubClassOf [abnormal metabolic process](http://purl.obolibrary.org/obo/FYPO_0000860) #### Added - [increased nucleophagy during G0](http://purl.obolibrary.org/obo/FYPO_0006665) SubClassOf [abnormal nucleophagy](http://purl.obolibrary.org/obo/FYPO_0008085)
# Changes to ontology after reasoner runs
Click to expand Coming soon >
# Errors reported ``` Level Rule Name Subject Property Value WARN duplicate_exact_synonym decreased rate of deactivation of mitotic spindle assembly checkpoint has_exact_synonym delayed inactivation of the mitotic SAC WARN duplicate_exact_synonym normal deactivation of mitotic spindle assembly checkpoint has_exact_synonym delayed inactivation of the mitotic SAC WARN missing_definition abnormal reticulophagy definition WARN missing_definition abnormal nucleophagy definition WARN missing_definition output_of definition WARN missing_definition preceded_by definition WARN missing_definition precedes definition WARN multiple_equivalent_classes polyphosphate absent from cell owl:equivalentClass blank node 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 ```