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pombase / fypo

Fission Yeast Phenotype Ontology
Creative Commons Attribution 4.0 International
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closes #4437;closes #4536; closes #4537; closes #4538; closes #4538; … #4543

Closed ValWood closed 1 month ago

ValWood commented 1 month ago

…closes #4539; closes #4540;

github-actions[bot] commented 1 month 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 ### abolished protein localization to nucleus during hypoxia `http://purl.obolibrary.org/obo/FYPO_0008206` #### Added - [abolished protein localization to nucleus during hypoxia](http://purl.obolibrary.org/obo/FYPO_0008206) [label](http://www.w3.org/2000/01/rdf-schema#label) "abolished protein localization to nucleus during hypoxia"@en - [abolished protein localization to nucleus during hypoxia](http://purl.obolibrary.org/obo/FYPO_0008206) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-05-03T11:51:41Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [abolished protein localization to nucleus during hypoxia](http://purl.obolibrary.org/obo/FYPO_0008206) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [abolished protein localization to nucleus during hypoxia](http://purl.obolibrary.org/obo/FYPO_0008206) [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 nucleus is abolished during hypoxic stress." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" - Class: [abolished protein localization to nucleus during hypoxia](http://purl.obolibrary.org/obo/FYPO_0008206) - [abolished protein localization to nucleus during hypoxia](http://purl.obolibrary.org/obo/FYPO_0008206) SubClassOf [abolished protein localization to nucleus during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0001424) ### abolished protein neddylation during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0008208` #### Added - [abolished protein neddylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008208) [label](http://www.w3.org/2000/01/rdf-schema#label) "abolished protein neddylation during vegetative growth"@en - [abolished protein neddylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008208) [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 neddylation of one or more specific proteins, or of specific protein sites, is abolished." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" - [abolished protein neddylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008208) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-05-03T12:03:19Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [abolished protein neddylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008208) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - Class: [abolished protein neddylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008208) - [abolished protein neddylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008208) SubClassOf [abolished protein modification during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0000544) ### decreased vegetative cell population growth on low glucose `http://purl.obolibrary.org/obo/FYPO_0008128` #### Removed - [decreased vegetative cell population growth on low glucose](http://purl.obolibrary.org/obo/FYPO_0008128) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A vegetative cell population phenotype in which cell growth is decreased relative to normal in a medium containing low glucose . This term refers to situations where glucose is below 0.5%." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37859837" #### Added - [decreased vegetative cell population growth on low glucose](http://purl.obolibrary.org/obo/FYPO_0008128) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A vegetative cell population phenotype in which cell growth is decreased relative to normal in a medium containing low glucose. This term refers to situations where glucose is below 0.2%." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37859837" ### increased protein localization to nucleus during hypoxia `http://purl.obolibrary.org/obo/FYPO_0008205` #### Added - [increased protein localization to nucleus during hypoxia](http://purl.obolibrary.org/obo/FYPO_0008205) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [increased protein localization to nucleus during hypoxia](http://purl.obolibrary.org/obo/FYPO_0008205) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-05-03T11:47:02Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [increased protein localization to nucleus during hypoxia](http://purl.obolibrary.org/obo/FYPO_0008205) [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 nucleus is increased during hypoxic stress." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" - [increased protein localization to nucleus during hypoxia](http://purl.obolibrary.org/obo/FYPO_0008205) [label](http://www.w3.org/2000/01/rdf-schema#label) "increased protein localization to nucleus during hypoxia"@en - Class: [increased protein localization to nucleus during hypoxia](http://purl.obolibrary.org/obo/FYPO_0008205) - [increased protein localization to nucleus during hypoxia](http://purl.obolibrary.org/obo/FYPO_0008205) SubClassOf [increased protein localization to nucleus during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0001130) ### inviable elongated multinucleate aseptate vegetative cell `http://purl.obolibrary.org/obo/FYPO_0002024` #### Added - [inviable elongated multinucleate aseptate vegetative cell](http://purl.obolibrary.org/obo/FYPO_0002024) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "septation initiation defective" ### normal histone H3-K14 acetylation at silent mating-type cassette during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0008209` #### Added - [normal histone H3-K14 acetylation at silent mating-type cassette during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008209) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal histone H3-K14 acetylation at silent mating-type cassette during vegetative growth"@en - [normal histone H3-K14 acetylation at silent mating-type cassette during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008209) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [normal histone H3-K14 acetylation at silent mating-type cassette during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008209) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which acetylation of lysine at position 14 of histone H3 is normal at the silent mating-type cassette (i.e. indistinguishable from wild type)." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" - [normal histone H3-K14 acetylation at silent mating-type cassette during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008209) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-05-03T12:07:01Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - Class: [normal histone H3-K14 acetylation at silent mating-type cassette during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008209) - [normal histone H3-K14 acetylation at silent mating-type cassette during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008209) SubClassOf [normal histone H3-K14 acetylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0003224) ### normal microfilament motor activity `http://purl.obolibrary.org/obo/FYPO_0008207` #### Added - [normal microfilament motor activity](http://purl.obolibrary.org/obo/FYPO_0008207) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [normal microfilament motor activity](http://purl.obolibrary.org/obo/FYPO_0008207) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-05-03T11:59:25Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [normal microfilament motor activity](http://purl.obolibrary.org/obo/FYPO_0008207) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal microfilament motor activity"@en - [normal microfilament motor activity](http://purl.obolibrary.org/obo/FYPO_0008207) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which the observed rate or other property of a microfilament motor activity is normal (i.e. indistinguishable from wild type)." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:pc" - Class: [normal microfilament motor activity](http://purl.obolibrary.org/obo/FYPO_0008207) - [normal microfilament motor activity](http://purl.obolibrary.org/obo/FYPO_0008207) SubClassOf [normal molecular function](http://purl.obolibrary.org/obo/FYPO_0000706)
# Changes to ontology after reasoner runs
Click to expand Coming soon >
# Errors reported ``` Level Rule Name Subject Property Value 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 ```