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pombase / fypo

Fission Yeast Phenotype Ontology
Creative Commons Attribution 4.0 International
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closes #4357; closes #4356 #4359

Closed ValWood closed 1 year ago

github-actions[bot] commented 1 year 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 ### decreased meiotic sister kinetochore association in meiotic metaphase I `http://purl.obolibrary.org/obo/FYPO_0005648` #### Added - [decreased meiotic sister kinetochore association in meiotic metaphase I](http://purl.obolibrary.org/obo/FYPO_0005648) SubClassOf [abnormal homologous chromosome segregation](http://purl.obolibrary.org/obo/FYPO_0004159) ### equational sister chromatid separation during meiosis I `http://purl.obolibrary.org/obo/FYPO_0005634` #### Removed - [equational sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0005634) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "equational sister chromatid separation during meiosis I with premature sister kinetochore separation"^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw"^^[string](http://www.w3.org/2001/XMLSchema#string) - [equational sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0005634) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "monopolar attachment of spindle microtubules to kinetochore during meiosis I"^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw"^^[string](http://www.w3.org/2001/XMLSchema#string) - [equational sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0005634) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "precocious equational centromeric dissociation during meiosis I"^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw"^^[string](http://www.w3.org/2001/XMLSchema#string) - [equational sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0005634) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype in which sister kinetochores become separated during the first meiotic nuclear division, and sister chromatids subsequently separate to result in equational segregation."^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mah"^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw"^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21920317"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added - [equational sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0005634) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "increased bi-orientated attachment of sister chromatids in meiosis I" - [equational sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0005634) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype in which sister kinetochores become separated during the first meiotic nuclear division, and sister chromatids subsequently separate to result in equational segregation. Equeational sister chromatid separation is caused by bi-orientated attachment of sister chromatids."^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mah"^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw"^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21920317"^^[string](http://www.w3.org/2001/XMLSchema#string) - [equational sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0005634) SubClassOf [abnormal homologous chromosome segregation](http://purl.obolibrary.org/obo/FYPO_0004159) ### increased cell size during quiescence `http://purl.obolibrary.org/obo/FYPO_0008095` #### Removed - [increased cell size during quiescence](http://purl.obolibrary.org/obo/FYPO_0008095) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell size phenotype in which a cell has a volume that is larger than normal during quiescence." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37128864"^^[string](http://www.w3.org/2001/XMLSchema#string) - [increased cell size during quiescence](http://purl.obolibrary.org/obo/FYPO_0008095) [label](http://www.w3.org/2000/01/rdf-schema#label) "increased cell size during quiescence"@en #### Added - [increased cell size during quiescence](http://purl.obolibrary.org/obo/FYPO_0008095) [label](http://www.w3.org/2000/01/rdf-schema#label) "increased cell size during G0"@en - [increased cell size during quiescence](http://purl.obolibrary.org/obo/FYPO_0008095) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell size phenotype in which a cell has a volume that is larger than normal during G0." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37128864"^^[string](http://www.w3.org/2001/XMLSchema#string) ### increased cell size during stationary phase `http://purl.obolibrary.org/obo/FYPO_0008106` #### Added - [increased cell size during stationary phase](http://purl.obolibrary.org/obo/FYPO_0008106) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell size phenotype in which a cell has a volume that is larger than normal during stationary phase." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37128864"^^[string](http://www.w3.org/2001/XMLSchema#string) - [increased cell size during stationary phase](http://purl.obolibrary.org/obo/FYPO_0008106) [creator](http://purl.org/dc/elements/1.1/creator) "vw253"^^[string](http://www.w3.org/2001/XMLSchema#string) - [increased cell size during stationary phase](http://purl.obolibrary.org/obo/FYPO_0008106) [date](http://purl.org/dc/elements/1.1/date) "2023-06-20T09:57:59Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [increased cell size during stationary phase](http://purl.obolibrary.org/obo/FYPO_0008106) [label](http://www.w3.org/2000/01/rdf-schema#label) "increased cell size during stationary phase"@en - Class: [increased cell size during stationary phase](http://purl.obolibrary.org/obo/FYPO_0008106) - [increased cell size during stationary phase](http://purl.obolibrary.org/obo/FYPO_0008106) SubClassOf [increased cell size](http://purl.obolibrary.org/obo/FYPO_0008096) ### increased chromatin mobility during stationary phase `http://purl.obolibrary.org/obo/FYPO_0008105` #### Added - [increased chromatin mobility during stationary phase](http://purl.obolibrary.org/obo/FYPO_0008105) [creator](http://purl.org/dc/elements/1.1/creator) "vw253"^^[string](http://www.w3.org/2001/XMLSchema#string) - [increased chromatin mobility during stationary phase](http://purl.obolibrary.org/obo/FYPO_0008105) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell phenotype observed in the vegetative growth phase of the life cycle in which chromatin moves within the nucleus to a greater extent than normal during stationary phase." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37128864"^^[string](http://www.w3.org/2001/XMLSchema#string) - [increased chromatin mobility during stationary phase](http://purl.obolibrary.org/obo/FYPO_0008105) [label](http://www.w3.org/2000/01/rdf-schema#label) "increased chromatin mobility during stationary phase"@en - [increased chromatin mobility during stationary phase](http://purl.obolibrary.org/obo/FYPO_0008105) [date](http://purl.org/dc/elements/1.1/date) "2023-06-20T09:55:37Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - Class: [increased chromatin mobility during stationary phase](http://purl.obolibrary.org/obo/FYPO_0008105) - [increased chromatin mobility during stationary phase](http://purl.obolibrary.org/obo/FYPO_0008105) SubClassOf [increased chromatin mobility](http://purl.obolibrary.org/obo/FYPO_0007517) ### normal protein localization to perinuclear endoplasmic reticulum `http://purl.obolibrary.org/obo/FYPO_0008103` #### Removed - [normal protein localization to perinuclear endoplasmic reticulum](http://purl.obolibrary.org/obo/FYPO_0008103) [has_narrow_synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "A cell phenotype observed in the vegetative growth phase of the life cycle in which the localization of a protein to the preinuclear endoplasmic reticulum is normal (i.e. indistinguishable from wild type)." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36799444"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added - [normal protein localization to perinuclear endoplasmic reticulum](http://purl.obolibrary.org/obo/FYPO_0008103) [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 preinuclear endoplasmic reticulum is normal (i.e. indistinguishable from wild type)." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36799444"^^[string](http://www.w3.org/2001/XMLSchema#string) ### sister chromatid separation during meiosis I `http://purl.obolibrary.org/obo/FYPO_0003604` #### Removed - [sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0003604) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype in which sister chromatids become physically detached from one another during the first meiotic nuclear division, instead of remaining attached and segregating together. Sister chromatids normally do not separate until the second meiotic nuclear division."^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mah"^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10440376"^^[string](http://www.w3.org/2001/XMLSchema#string) - [sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0003604) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Sister chromatids may separate in meiosis I due to problems with either cohesion or kinetochore attachment to microtubules. Therefore consider also annotating to 'abnormal attachment of spindle microtubules to kinetochore involved in homologous chromosome segregation' (FYPO:0000209), 'decreased meiotic sister chromatid cohesion' (FYPO:0002093), or 'merotelic kinetochore attachment during meiosis I' (FYPO:0005638)."^^[string](http://www.w3.org/2001/XMLSchema#string) - [sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0003604) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "sister chromatid separation during first meiotic nuclear division"^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mah"^^[string](http://www.w3.org/2001/XMLSchema#string) - [sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0003604) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "abnormal sister chromatid separation at meiosis I"^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:al"^^[string](http://www.w3.org/2001/XMLSchema#string) - [sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0003604) [id](http://www.geneontology.org/formats/oboInOwl#id) "FYPO:0003604"^^[string](http://www.w3.org/2001/XMLSchema#string) - [sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0003604) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "fission_yeast_phenotype"^^[string](http://www.w3.org/2001/XMLSchema#string) - [sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0003604) [label](http://www.w3.org/2000/01/rdf-schema#label) "sister chromatid separation during meiosis I"^^[string](http://www.w3.org/2001/XMLSchema#string) - [sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0003604) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "premature meiotic sister chromatid separation"^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mah"^^[string](http://www.w3.org/2001/XMLSchema#string) - [sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0003604) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "precocious meiotic sister chromatid separation"^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26483559"^^[string](http://www.w3.org/2001/XMLSchema#string) - [sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0003604) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "midori"^^[string](http://www.w3.org/2001/XMLSchema#string) - [sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0003604) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2014-07-29T16:08:54Z"^^[string](http://www.w3.org/2001/XMLSchema#string) - [sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0003604) SubClassOf [abnormal meiosis I](http://purl.obolibrary.org/obo/FYPO_0003603) - [sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0003604) SubClassOf [abnormal meiotic sister chromatid segregation](http://purl.obolibrary.org/obo/FYPO_0005509) #### Added - [sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0003604) [label](http://www.w3.org/2000/01/rdf-schema#label) "obsolete sister chromatid separation during meiosis I"^^[string](http://www.w3.org/2001/XMLSchema#string) - [sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0003604) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "OBSOLETE Sister chromatids may separate in meiosis I due to problems with either cohesion or kinetochore attachment to microtubules. Therefore consider also annotating to 'abnormal attachment of spindle microtubules to kinetochore involved in homologous chromosome segregation' (FYPO:0000209), 'decreased meiotic sister chromatid cohesion' (FYPO:0002093), or 'merotelic kinetochore attachment during meiosis I' (FYPO:0005638)."^^[string](http://www.w3.org/2001/XMLSchema#string) - [sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0003604) [deprecated](http://www.w3.org/2002/07/owl#deprecated) true - [sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0003604) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "equivalent to equational sister chromatid separation during meiosis I"^^[string](http://www.w3.org/2001/XMLSchema#string) - [sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0003604) [seeAlso](http://www.w3.org/2000/01/rdf-schema#seeAlso) [equational sister chromatid separation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0005634)
# 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 ```
github-actions[bot] commented 1 year ago

Hi @ValWood! It seems you forgot to run normalised_xsd_string on your PR. Please run it and commit the changes.