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pombase / fypo

Fission Yeast Phenotype Ontology
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closes, check #4479

Closed ValWood closed 2 months ago

github-actions[bot] commented 8 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 chromatin silencing at centromere central core `http://purl.obolibrary.org/obo/FYPO_0000640` #### Removed - [abnormal chromatin silencing at centromere central core](http://purl.obolibrary.org/obo/FYPO_0000640) SubClassOf [abnormal regulation of transcription during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0004527) #### Added - [abnormal chromatin silencing at centromere central core](http://purl.obolibrary.org/obo/FYPO_0000640) SubClassOf [abnormal gene expression](http://purl.obolibrary.org/obo/FYPO_0006551) ### abnormal chromatin silencing at centromere outer repeat `http://purl.obolibrary.org/obo/FYPO_0002346` #### Removed - [abnormal chromatin silencing at centromere outer repeat](http://purl.obolibrary.org/obo/FYPO_0002346) SubClassOf [abnormal chromatin silencing at centromere](http://purl.obolibrary.org/obo/FYPO_0000146) #### Added - [abnormal chromatin silencing at centromere outer repeat](http://purl.obolibrary.org/obo/FYPO_0002346) SubClassOf [abnormal chromatin silencing at pericentromeric heterochromatin](http://purl.obolibrary.org/obo/FYPO_0008159) ### abnormal chromatin silencing at pericentromeric heterochromatin `http://purl.obolibrary.org/obo/FYPO_0008159` #### Added - [abnormal chromatin silencing at pericentromeric heterochromatin](http://purl.obolibrary.org/obo/FYPO_0008159) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcription regulation phenotype observed in the vegetative growth phase of the life cycle in which chromatin silencing at the pericentromeric heterochromatin is abnormal. Chromatin silencing is the observed effect of processes that repress transcription in a region of the genome that is normally assembled into heterochromatin." - [abnormal chromatin silencing at pericentromeric heterochromatin](http://purl.obolibrary.org/obo/FYPO_0008159) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-01-25T09:55:14Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [abnormal chromatin silencing at pericentromeric heterochromatin](http://purl.obolibrary.org/obo/FYPO_0008159) [label](http://www.w3.org/2000/01/rdf-schema#label) "abnormal chromatin silencing at pericentromeric heterochromatin"@en - [abnormal chromatin silencing at pericentromeric heterochromatin](http://purl.obolibrary.org/obo/FYPO_0008159) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - Class: [abnormal chromatin silencing at pericentromeric heterochromatin](http://purl.obolibrary.org/obo/FYPO_0008159) - [abnormal chromatin silencing at pericentromeric heterochromatin](http://purl.obolibrary.org/obo/FYPO_0008159) SubClassOf [abnormal chromatin silencing at centromere](http://purl.obolibrary.org/obo/FYPO_0000146) ### decreased chromatin silencing at pericentric heterochromatin `http://purl.obolibrary.org/obo/FYPO_0008160` #### Added - [decreased chromatin silencing at pericentric heterochromatin](http://purl.obolibrary.org/obo/FYPO_0008160) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-01-25T09:56:50Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [decreased chromatin silencing at pericentric heterochromatin](http://purl.obolibrary.org/obo/FYPO_0008160) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcription regulation phenotype observed in the vegetative growth phase of the life cycle in which chromatin silencing at the pericentromeric heterochromatin is decreased." - [decreased chromatin silencing at pericentric heterochromatin](http://purl.obolibrary.org/obo/FYPO_0008160) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [decreased chromatin silencing at pericentric heterochromatin](http://purl.obolibrary.org/obo/FYPO_0008160) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased chromatin silencing at pericentric heterochromatin"@en - Class: [decreased chromatin silencing at pericentric heterochromatin](http://purl.obolibrary.org/obo/FYPO_0008160) - [decreased chromatin silencing at pericentric heterochromatin](http://purl.obolibrary.org/obo/FYPO_0008160) SubClassOf [abnormal chromatin silencing at pericentromeric heterochromatin](http://purl.obolibrary.org/obo/FYPO_0008159) ### increased activation of S-phase DNA damage checkpoint `http://purl.obolibrary.org/obo/FYPO_0008156` #### Added - [increased activation of S-phase DNA damage checkpoint](http://purl.obolibrary.org/obo/FYPO_0008156) [label](http://www.w3.org/2000/01/rdf-schema#label) "increased activation of S-phase DNA damage checkpoint"@en - [increased activation of S-phase DNA damage checkpoint](http://purl.obolibrary.org/obo/FYPO_0008156) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-01-25T09:34:57Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [increased activation of S-phase DNA damage checkpoint](http://purl.obolibrary.org/obo/FYPO_0008156) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [increased activation of S-phase DNA damage checkpoint](http://purl.obolibrary.org/obo/FYPO_0008156) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A mitotic cell cycle checkpoint phenotype in which the S phase DNA damage checkpoint (also known as the intra-S phase DNA damage checkpoint) is activated at an increased leve compared to wild-type." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18344406" - Class: [increased activation of S-phase DNA damage checkpoint](http://purl.obolibrary.org/obo/FYPO_0008156) - [increased activation of S-phase DNA damage checkpoint](http://purl.obolibrary.org/obo/FYPO_0008156) SubClassOf [abnormal S-phase DNA damage checkpoint](http://purl.obolibrary.org/obo/FYPO_0000007) ### increased histone H3-K56 acetylation at centromere outer repeat during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0002369` #### Removed - [increased histone H3-K56 acetylation at centromere outer repeat during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0002369) SubClassOf [increased histone acetylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0000332) #### Added - [increased histone H3-K56 acetylation at centromere outer repeat during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0002369) SubClassOf [increased histone H3-K56 acetylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008158) ### increased histone H3-K56 acetylation during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0008158` #### Added - [increased histone H3-K56 acetylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008158) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [increased histone H3-K56 acetylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008158) [label](http://www.w3.org/2000/01/rdf-schema#label) "increased histone H3-K56 acetylation during vegetative growth"@en - [increased histone H3-K56 acetylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008158) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-01-25T09:40:29Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [increased histone H3-K56 acetylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008158) [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 56 of histone H3 occurs to a greater extent than normal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18344406" - Class: [increased histone H3-K56 acetylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008158) - [increased histone H3-K56 acetylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008158) SubClassOf [increased histone acetylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0000332) ### increased rDNA-derived RNA level `http://purl.obolibrary.org/obo/FYPO_0008155` #### Added - [increased rDNA-derived RNA level](http://purl.obolibrary.org/obo/FYPO_0008155) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-01-25T09:30:47Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [increased rDNA-derived RNA level](http://purl.obolibrary.org/obo/FYPO_0008155) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [increased rDNA-derived RNA level](http://purl.obolibrary.org/obo/FYPO_0008155) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "increased rDNA RNA level" - [increased rDNA-derived RNA level](http://purl.obolibrary.org/obo/FYPO_0008155) [label](http://www.w3.org/2000/01/rdf-schema#label) "increased rDNA-derived RNA level"@en - [increased rDNA-derived RNA level](http://purl.obolibrary.org/obo/FYPO_0008155) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell phenotype in which the amount of RNA derived from rDNA regions is higher than normal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21211723" - Class: [increased rDNA-derived RNA level](http://purl.obolibrary.org/obo/FYPO_0008155) - [increased rDNA-derived RNA level](http://purl.obolibrary.org/obo/FYPO_0008155) SubClassOf [increased RNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0000825) ### normal chromatin silencing at centromere central core `http://purl.obolibrary.org/obo/FYPO_0004331` #### Removed - [normal chromatin silencing at centromere central core](http://purl.obolibrary.org/obo/FYPO_0004331) SubClassOf [normal chromatin silencing](http://purl.obolibrary.org/obo/FYPO_0002335) #### Added - [normal chromatin silencing at centromere central core](http://purl.obolibrary.org/obo/FYPO_0004331) SubClassOf [normal chromatin silencing at centromere](http://purl.obolibrary.org/obo/FYPO_0002360) ### normal histone H4-K16 acetylation during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0008157` #### Added - [normal histone H4-K16 acetylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008157) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal histone H4-K16 acetylation during vegetative growth"@en - [normal histone H4-K16 acetylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008157) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [normal histone H4-K16 acetylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008157) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-01-25T09:37:57Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [normal histone H4-K16 acetylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008157) [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 16 of histone H4 is normal (i.e. indistinguishable from wild type)." - [definition](http://purl.obolibrary.org/obo/IAO_0000115) "PMID:18344406" - Class: [normal histone H4-K16 acetylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008157) - [normal histone H4-K16 acetylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008157) SubClassOf [normal histone acetylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0003221)
# Changes to ontology after reasoner runs
Click to expand Coming soon >
# Errors reported ``` Level Rule Name Subject Property Value WARN missing_definition abolished protein localization to heterochromatin at silent mating-type cassette 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 ```