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pombase / fypo

Fission Yeast Phenotype Ontology
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#4422, #4421, #4422 ,#4415, #4414 #4423

Closed ValWood closed 10 months ago

github-actions[bot] commented 10 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 de novo SAGA complex assembly `http://purl.obolibrary.org/obo/FYPO_0008117` #### Added - [abnormal de novo SAGA complex assembly](http://purl.obolibrary.org/obo/FYPO_0008117) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [abnormal de novo SAGA complex assembly](http://purl.obolibrary.org/obo/FYPO_0008117) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-09-05T16:22:58Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [abnormal de novo SAGA complex assembly](http://purl.obolibrary.org/obo/FYPO_0008117) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Note that this term refers to the abnormal biogenesis of the complex, i.e. the process of building the complex from individual subunits. For assays identifyion alterations in complex subunit composition use 'abnormal protein complex composition FYPO:0005003' or 'abnormal protein-protein interaction" (FYPO:0000704) or their descendants." - [abnormal de novo SAGA complex assembly](http://purl.obolibrary.org/obo/FYPO_0008117) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which de novo assembly of the SAGA complex is abnormal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31748520" - [abnormal de novo SAGA complex assembly](http://purl.obolibrary.org/obo/FYPO_0008117) [label](http://www.w3.org/2000/01/rdf-schema#label) "abnormal de novo SAGA complex assembly"@en - Class: [abnormal de novo SAGA complex assembly](http://purl.obolibrary.org/obo/FYPO_0008117) - [abnormal de novo SAGA complex assembly](http://purl.obolibrary.org/obo/FYPO_0008117) SubClassOf [abnormal protein complex assembly](http://purl.obolibrary.org/obo/FYPO_0000447) ### decreased protein level in NuA4 complex `http://purl.obolibrary.org/obo/FYPO_0008121` #### Added - [decreased protein level in NuA4 complex](http://purl.obolibrary.org/obo/FYPO_0008121) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [decreased protein level in NuA4 complex](http://purl.obolibrary.org/obo/FYPO_0008121) [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 a protein measured in the NuA4 complex is lower than normal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31748520" - [decreased protein level in NuA4 complex](http://purl.obolibrary.org/obo/FYPO_0008121) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased protein level in NuA4 complex"@en - [decreased protein level in NuA4 complex](http://purl.obolibrary.org/obo/FYPO_0008121) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-09-05T16:40:45Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - Class: [decreased protein level in NuA4 complex](http://purl.obolibrary.org/obo/FYPO_0008121) - [decreased protein level in NuA4 complex](http://purl.obolibrary.org/obo/FYPO_0008121) SubClassOf [abnormal protein complex composition](http://purl.obolibrary.org/obo/FYPO_0005003) ### decreased protein level in SAGA complex `http://purl.obolibrary.org/obo/FYPO_0008120` #### Added - [decreased protein level in SAGA complex](http://purl.obolibrary.org/obo/FYPO_0008120) [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 a protein measured in the SAGA complex is lower than normal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31748520" - [decreased protein level in SAGA complex](http://purl.obolibrary.org/obo/FYPO_0008120) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [decreased protein level in SAGA complex](http://purl.obolibrary.org/obo/FYPO_0008120) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased protein level in SAGA complex"@en - [decreased protein level in SAGA complex](http://purl.obolibrary.org/obo/FYPO_0008120) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-09-05T16:37:08Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - Class: [decreased protein level in SAGA complex](http://purl.obolibrary.org/obo/FYPO_0008120) - [decreased protein level in SAGA complex](http://purl.obolibrary.org/obo/FYPO_0008120) SubClassOf [abnormal protein complex composition](http://purl.obolibrary.org/obo/FYPO_0005003) ### increased mitochondrial fusion `http://purl.obolibrary.org/obo/FYPO_0008122` #### Added - [increased mitochondrial fusion](http://purl.obolibrary.org/obo/FYPO_0008122) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [increased mitochondrial fusion](http://purl.obolibrary.org/obo/FYPO_0008122) [label](http://www.w3.org/2000/01/rdf-schema#label) "increased mitochondrial fusion"@en - [increased mitochondrial fusion](http://purl.obolibrary.org/obo/FYPO_0008122) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-09-05T16:53:41Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [increased mitochondrial fusion](http://purl.obolibrary.org/obo/FYPO_0008122) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype in which mitochondrion fusion is increased." - [definition](http://purl.obolibrary.org/obo/IAO_0000115) "PMID:37590302" - Class: [increased mitochondrial fusion](http://purl.obolibrary.org/obo/FYPO_0008122) - [increased mitochondrial fusion](http://purl.obolibrary.org/obo/FYPO_0008122) SubClassOf [abnormal mitochondrial fusion](http://purl.obolibrary.org/obo/FYPO_0008089) ### loss of viability in stationary phase upon phopshate starvation `http://purl.obolibrary.org/obo/FYPO_0008123` #### Added - [loss of viability in stationary phase upon phopshate starvation](http://purl.obolibrary.org/obo/FYPO_0008123) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell population phenotype in which a smaller than normal proportion of cells in the population remains viable after entering stationary phase, when cells the population are subject to phosphate starvation." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36794724" - [loss of viability in stationary phase upon phopshate starvation](http://purl.obolibrary.org/obo/FYPO_0008123) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "decreased chronological lifespan of phosphate-starved cells" - [loss of viability in stationary phase upon phopshate starvation](http://purl.obolibrary.org/obo/FYPO_0008123) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-09-05T16:57:32Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [loss of viability in stationary phase upon phopshate starvation](http://purl.obolibrary.org/obo/FYPO_0008123) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [loss of viability in stationary phase upon phopshate starvation](http://purl.obolibrary.org/obo/FYPO_0008123) [label](http://www.w3.org/2000/01/rdf-schema#label) "loss of viability in stationary phase upon phopshate starvation"@en - Class: [loss of viability in stationary phase upon phopshate starvation](http://purl.obolibrary.org/obo/FYPO_0008123) - [loss of viability in stationary phase upon phopshate starvation](http://purl.obolibrary.org/obo/FYPO_0008123) SubClassOf [loss of viability in stationary phase](http://purl.obolibrary.org/obo/FYPO_0000245) ### small mitochondria `http://purl.obolibrary.org/obo/FYPO_0007193` #### Added - [small mitochondria](http://purl.obolibrary.org/obo/FYPO_0007193) SubClassOf [abnormal mitochondrial morphology](http://purl.obolibrary.org/obo/FYPO_0000359) ### small mitochondria present in increased numbers, with normal total mitochondrial volume `http://purl.obolibrary.org/obo/FYPO_0003810` #### Removed - [small mitochondria present in increased numbers, with normal total mitochondrial volume](http://purl.obolibrary.org/obo/FYPO_0003810) [label](http://www.w3.org/2000/01/rdf-schema#label) "small mitochondria present in increased numbers, with normal total mitochondrial volume" - [small mitochondria present in increased numbers, with normal total mitochondrial volume](http://purl.obolibrary.org/obo/FYPO_0003810) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell phenotype observed in the vegetative growth phase of the life cycle in which total mitochondrial volume is normal, but mitochondria are smaller and more numerous than normal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mah" #### Added - [small mitochondria present in increased numbers, with normal total mitochondrial volume](http://purl.obolibrary.org/obo/FYPO_0003810) [label](http://www.w3.org/2000/01/rdf-schema#label) "small fragmented mitochondria present in increased numbers" - [small mitochondria present in increased numbers, with normal total mitochondrial volume](http://purl.obolibrary.org/obo/FYPO_0003810) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell phenotype observed in the vegetative growth phase of the life cycle in which mitochondria are smaller and more numerous than normal. Total mitochondrial volume is usually similar to normal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mah"
# 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 ```