search

pombase / fypo

Fission Yeast Phenotype Ontology
Creative Commons Attribution 4.0 International
14 stars 6 forks source link

Revert "closes #4501; closes #4499; closes #4498; closes #4497; close… #4506

Closed ValWood closed 6 months ago

ValWood commented 6 months ago

…s #4494;…"

This reverts commit 9a39097b431922d38b4d69de5cbf4e74410577b8.

github-actions[bot] commented 6 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 chromatin at replication origin `http://purl.obolibrary.org/obo/FYPO_0005095` #### Added - [abolished protein localization to chromatin at replication origin](http://purl.obolibrary.org/obo/FYPO_0005095) SubClassOf [abolished protein localization to centromeric chromatin during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0003744) ### decreased RNA polymerase II CTD Ser5-P binding `http://purl.obolibrary.org/obo/FYPO_0008181` #### Removed - [decreased RNA polymerase II CTD Ser5-P binding](http://purl.obolibrary.org/obo/FYPO_0008181) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-03-20T11:51:41Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [decreased RNA polymerase II CTD Ser5-P binding](http://purl.obolibrary.org/obo/FYPO_0008181) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [decreased RNA polymerase II CTD Ser5-P binding](http://purl.obolibrary.org/obo/FYPO_0008181) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased RNA polymerase II CTD Ser5-P binding"@en - [decreased RNA polymerase II CTD Ser5-P binding](http://purl.obolibrary.org/obo/FYPO_0008181) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which binding by a gene product to the RNA polymerase II CTD domain phosphorylated serine 5 is decreased. The affected gene product may be encoded by the mutated gene, or by a different gene." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" - Class: [decreased RNA polymerase II CTD Ser5-P binding](http://purl.obolibrary.org/obo/FYPO_0008181) - [decreased RNA polymerase II CTD Ser5-P binding](http://purl.obolibrary.org/obo/FYPO_0008181) SubClassOf [decreased RNA polymerase II CTD binding](http://purl.obolibrary.org/obo/FYPO_0008180) ### decreased RNA polymerase II CTD binding `http://purl.obolibrary.org/obo/FYPO_0008180` #### Removed - [decreased RNA polymerase II CTD binding](http://purl.obolibrary.org/obo/FYPO_0008180) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased RNA polymerase II CTD binding"@en - [decreased RNA polymerase II CTD binding](http://purl.obolibrary.org/obo/FYPO_0008180) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [decreased RNA polymerase II CTD binding](http://purl.obolibrary.org/obo/FYPO_0008180) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which binding by a gene product to the RNA polymerase II CTD domain is decreased. The affected gene product may be encoded by the mutated gene, or by a different gene." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" - [decreased RNA polymerase II CTD binding](http://purl.obolibrary.org/obo/FYPO_0008180) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-03-20T11:47:57Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - Class: [decreased RNA polymerase II CTD binding](http://purl.obolibrary.org/obo/FYPO_0008180) - [decreased RNA polymerase II CTD binding](http://purl.obolibrary.org/obo/FYPO_0008180) SubClassOf [binding phenotype](http://purl.obolibrary.org/obo/FYPO_0001092) ### decreased Spt5-CTD binding `http://purl.obolibrary.org/obo/FYPO_0008182` #### Removed - [decreased Spt5-CTD binding](http://purl.obolibrary.org/obo/FYPO_0008182) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-03-20T11:55:25Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [decreased Spt5-CTD binding](http://purl.obolibrary.org/obo/FYPO_0008182) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased Spt5-CTD binding"@en - [decreased Spt5-CTD binding](http://purl.obolibrary.org/obo/FYPO_0008182) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which binding by a gene product to the Spt5 CTD domain is decreased. The affected gene product may be encoded by the mutated gene, or by a different gene." - [decreased Spt5-CTD binding](http://purl.obolibrary.org/obo/FYPO_0008182) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - Class: [decreased Spt5-CTD binding](http://purl.obolibrary.org/obo/FYPO_0008182) - [decreased Spt5-CTD binding](http://purl.obolibrary.org/obo/FYPO_0008182) SubClassOf [binding phenotype](http://purl.obolibrary.org/obo/FYPO_0001092) ### decreased histone H3-S10 phosphorylation during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0008183` #### Removed - [decreased histone H3-S10 phosphorylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008183) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased histone H3-S10 phosphorylation during vegetative growth"@en - [decreased histone H3-S10 phosphorylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008183) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-03-20T12:04:24Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [decreased histone H3-S10 phosphorylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008183) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [decreased histone H3-S10 phosphorylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008183) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which histone H3-S10 phosphorylation is decreased." - Class: [decreased histone H3-S10 phosphorylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008183) - [decreased histone H3-S10 phosphorylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008183) SubClassOf [abnormal histone phosphorylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0002591) ### decreased protein localization to processome `http://purl.obolibrary.org/obo/FYPO_0008184` #### Removed - [decreased protein localization to processome](http://purl.obolibrary.org/obo/FYPO_0008184) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-03-20T12:10:40Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [decreased protein localization to processome](http://purl.obolibrary.org/obo/FYPO_0008184) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased protein localization to processome"@en - [decreased protein localization to processome](http://purl.obolibrary.org/obo/FYPO_0008184) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [decreased protein localization to processome](http://purl.obolibrary.org/obo/FYPO_0008184) [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 processome is decreased." - Class: [decreased protein localization to processome](http://purl.obolibrary.org/obo/FYPO_0008184) - [decreased protein localization to processome](http://purl.obolibrary.org/obo/FYPO_0008184) SubClassOf [abnormal protein localization during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0000443) ### increased centromeric inner repeat transcript level `http://purl.obolibrary.org/obo/FYPO_0008176` #### Removed - [increased centromeric inner repeat transcript level](http://purl.obolibrary.org/obo/FYPO_0008176) [label](http://www.w3.org/2000/01/rdf-schema#label) "increased centromeric inner repeat transcript level"@en - [increased centromeric inner repeat transcript level](http://purl.obolibrary.org/obo/FYPO_0008176) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "This term encompasses both unprocessed RNA transcribed from the centromere inner repeat region and siRNAs derived by dicer-mediated processing of the primary transcripts. Use this term only for levels of RNA transcribed from endogenous centromere inner repeat sequences. For levels of RNA transcribed from an exogenous reporter gene placed in the inner repeat region, consider 'decreased chromatin silencing at centromere outer repeat region' (FYPO:0003412)." - [increased centromeric inner repeat transcript level](http://purl.obolibrary.org/obo/FYPO_0008176) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-03-20T11:28:55Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [increased centromeric inner repeat transcript level](http://purl.obolibrary.org/obo/FYPO_0008176) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [increased centromeric inner repeat transcript level](http://purl.obolibrary.org/obo/FYPO_0008176) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell phenotype observed in the vegetative growth phase of the life cycle in which RNAs transcribed from the centromere inner repeat region are present at greater levels than normal." - Class: [increased centromeric inner repeat transcript level](http://purl.obolibrary.org/obo/FYPO_0008176) - [increased centromeric inner repeat transcript level](http://purl.obolibrary.org/obo/FYPO_0008176) SubClassOf [increased centromeric transcript level](http://purl.obolibrary.org/obo/FYPO_0004982) ### normal centromeric RNA level during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0008177` #### Removed - [normal centromeric RNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008177) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [normal centromeric RNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008177) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal centromeric RNA level during vegetative growth"@en - [normal centromeric RNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008177) [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 RNAs transcribed from the centromere measured in a cell is normal (i.e. indistinguishable from wild type)." - [normal centromeric RNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008177) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "This term encompasses both unprocessed RNA transcribed from the centromere t region and siRNAs derived by dicer-mediated processing of the primary transcripts. Use this term only for levels of endogenous RNAs." - [normal centromeric RNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008177) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-03-20T11:32:16Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - Class: [normal centromeric RNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008177) - [normal centromeric RNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008177) SubClassOf [normal RNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0001317) ### normal centromeric inner repeat transcript level `http://purl.obolibrary.org/obo/FYPO_0008178` #### Removed - [normal centromeric inner repeat transcript level](http://purl.obolibrary.org/obo/FYPO_0008178) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal centromeric inner repeat transcript level"@en - [normal centromeric inner repeat transcript level](http://purl.obolibrary.org/obo/FYPO_0008178) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "This term encompasses both unprocessed RNA transcribed from the centromere inner repeat region and siRNAs derived by dicer-mediated processing of the primary transcripts. Use this term only for levels of RNA transcribed from endogenous centromere inner repeat sequences." - [normal centromeric inner repeat transcript level](http://purl.obolibrary.org/obo/FYPO_0008178) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [normal centromeric inner repeat transcript level](http://purl.obolibrary.org/obo/FYPO_0008178) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-03-20T11:34:30Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [normal centromeric inner repeat transcript level](http://purl.obolibrary.org/obo/FYPO_0008178) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell phenotype observed in the vegetative growth phase of the life cycle in which RNAs transcribed from the centromere inner repeat region are present at normal levels (i.e. indistinguishable from wild-type)." - Class: [normal centromeric inner repeat transcript level](http://purl.obolibrary.org/obo/FYPO_0008178) - [normal centromeric inner repeat transcript level](http://purl.obolibrary.org/obo/FYPO_0008178) SubClassOf [normal centromeric RNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008177) ### normal centromeric outer repeat transcript level `http://purl.obolibrary.org/obo/FYPO_0002567` #### Removed - [normal centromeric outer repeat transcript level](http://purl.obolibrary.org/obo/FYPO_0002567) SubClassOf [normal centromeric RNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008177) #### Added - [normal centromeric outer repeat transcript level](http://purl.obolibrary.org/obo/FYPO_0002567) SubClassOf [normal RNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0001317) ### normal oxygen consumption `http://purl.obolibrary.org/obo/FYPO_0008175` #### Removed - [normal oxygen consumption](http://purl.obolibrary.org/obo/FYPO_0008175) [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 amount of oxygen consumed by cells in a given time is lower than in wild type." - [normal oxygen consumption](http://purl.obolibrary.org/obo/FYPO_0008175) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-03-20T11:26:08Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [normal oxygen consumption](http://purl.obolibrary.org/obo/FYPO_0008175) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [normal oxygen consumption](http://purl.obolibrary.org/obo/FYPO_0008175) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal oxygen consumption"@en - Class: [normal oxygen consumption](http://purl.obolibrary.org/obo/FYPO_0008175) - [normal oxygen consumption](http://purl.obolibrary.org/obo/FYPO_0008175) SubClassOf [normal vegetative phenotype](http://purl.obolibrary.org/obo/FYPO_0001312)
# 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 ```