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pombase / fypo

Fission Yeast Phenotype Ontology
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closes #4462; closes #4460; closes #4437 #4470

Closed ValWood closed 1 day ago

github-actions[bot] commented 5 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 ### abolished protein localization to mating-type region `http://purl.obolibrary.org/obo/FYPO_0008152` #### Added - [abolished protein localization to mating-type region](http://purl.obolibrary.org/obo/FYPO_0008152) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [abolished protein localization to mating-type region](http://purl.obolibrary.org/obo/FYPO_0008152) [label](http://www.w3.org/2000/01/rdf-schema#label) "abolished protein localization to mating-type region"@en - [abolished protein localization to mating-type region](http://purl.obolibrary.org/obo/FYPO_0008152) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-01-19T12:27:51Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [abolished protein localization to mating-type region](http://purl.obolibrary.org/obo/FYPO_0008152) [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 mating-type region of a chromosome does not occur." - [definition](http://purl.obolibrary.org/obo/IAO_0000115) "PMID:16762840" - Class: [abolished protein localization to mating-type region](http://purl.obolibrary.org/obo/FYPO_0008152) - [abolished protein localization to mating-type region](http://purl.obolibrary.org/obo/FYPO_0008152) SubClassOf [abolished protein localization during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0001179) ### 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" ### normal CUT RNA level `http://purl.obolibrary.org/obo/FYPO_0008153` #### Added - [normal CUT RNA level](http://purl.obolibrary.org/obo/FYPO_0008153) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-01-19T12:50:09Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [normal CUT RNA level](http://purl.obolibrary.org/obo/FYPO_0008153) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [normal CUT RNA level](http://purl.obolibrary.org/obo/FYPO_0008153) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of transcribed cryptic unstable trancripts (CUTs) measured in a cell is normal (i.e. indistinguishable from wild type). Total RNA or a specific RNA, such as the mRNA transcribed from a gene of interest, may be affected." - [normal CUT RNA level](http://purl.obolibrary.org/obo/FYPO_0008153) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal CUT RNA level"@en - Class: [normal CUT RNA level](http://purl.obolibrary.org/obo/FYPO_0008153) - [normal CUT RNA level](http://purl.obolibrary.org/obo/FYPO_0008153) SubClassOf [normal RNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0001317) ### 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) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "normal histone H3-K9 methylation" ### normal protein localization to centromeric chromatin during mitotic metaphase `http://purl.obolibrary.org/obo/FYPO_0006601` #### Removed - [normal protein localization to centromeric chromatin during mitotic metaphase](http://purl.obolibrary.org/obo/FYPO_0006601) SubClassOf [normal protein localization to chromatin during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0001509) ### normal protein localization to chromatin at centromere central core `http://purl.obolibrary.org/obo/FYPO_0005079` #### Removed - [normal protein localization to chromatin at centromere central core](http://purl.obolibrary.org/obo/FYPO_0005079) SubClassOf [normal protein localization to chromatin during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0001509) #### Added - [normal protein localization to chromatin at centromere central core](http://purl.obolibrary.org/obo/FYPO_0005079) SubClassOf [normal protein localization to centromeric chromatin](http://purl.obolibrary.org/obo/FYPO_0005072) ### normal protein localization to chromatin at centromere inner repeat `http://purl.obolibrary.org/obo/FYPO_0005080` #### Removed - [normal protein localization to chromatin at centromere inner repeat](http://purl.obolibrary.org/obo/FYPO_0005080) SubClassOf [normal protein localization to chromatin during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0001509) #### Added - [normal protein localization to chromatin at centromere inner repeat](http://purl.obolibrary.org/obo/FYPO_0005080) SubClassOf [normal protein localization to centromeric chromatin](http://purl.obolibrary.org/obo/FYPO_0005072) ### normal protein localization to heterochromatin at centromere outer repeat `http://purl.obolibrary.org/obo/FYPO_0002389` #### Removed - [normal protein localization to heterochromatin at centromere outer repeat](http://purl.obolibrary.org/obo/FYPO_0002389) SubClassOf [normal protein localization to chromatin during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0001509) #### Added - [normal protein localization to heterochromatin at centromere outer repeat](http://purl.obolibrary.org/obo/FYPO_0002389) SubClassOf [normal protein localization to centromeric chromatin](http://purl.obolibrary.org/obo/FYPO_0005072)
# 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 ```