pombase / fypo

Fission Yeast Phenotype Ontology
Creative Commons Attribution 4.0 International
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various #4402

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 nucleus positioning `http://purl.obolibrary.org/obo/FYPO_0000517` #### Removed - [abnormal nucleus positioning](http://purl.obolibrary.org/obo/FYPO_0000517) [label](http://www.w3.org/2000/01/rdf-schema#label) "abnormal nucleus localization" #### Added - [abnormal nucleus positioning](http://purl.obolibrary.org/obo/FYPO_0000517) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "abnormal nucleus localization" - [abnormal nucleus positioning](http://purl.obolibrary.org/obo/FYPO_0000517) [label](http://www.w3.org/2000/01/rdf-schema#label) "abnormal nucleus positioning" ### abnormal nucleus positioning during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0001338` #### Removed - [abnormal nucleus positioning during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0001338) [label](http://www.w3.org/2000/01/rdf-schema#label) "abnormal nucleus localization during vegetative growth" #### Added - [abnormal nucleus positioning during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0001338) [label](http://www.w3.org/2000/01/rdf-schema#label) "abnormal nucleus positioning during vegetative growth" - [abnormal nucleus positioning during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0001338) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "abnormal nucleus localization during vegetative growth" ### abnormal nucleus positioning in prospore `http://purl.obolibrary.org/obo/FYPO_0000942` #### Removed - [abnormal nucleus positioning in prospore](http://purl.obolibrary.org/obo/FYPO_0000942) [label](http://www.w3.org/2000/01/rdf-schema#label) "abnormal nucleus localization in prospore" #### Added - [abnormal nucleus positioning in prospore](http://purl.obolibrary.org/obo/FYPO_0000942) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "abnormal nucleus localization in prospore" - [abnormal nucleus positioning in prospore](http://purl.obolibrary.org/obo/FYPO_0000942) [label](http://www.w3.org/2000/01/rdf-schema#label) "abnormal nucleus positioning in prospore" ### altered level of macromolecular complex `http://purl.obolibrary.org/obo/FYPO_0007316` #### Removed - [altered level of macromolecular complex](http://purl.obolibrary.org/obo/FYPO_0007316) EquivalentTo [has part](http://purl.obolibrary.org/obo/BFO_0000051) some ([altered number of](http://purl.obolibrary.org/obo/PATO_0002083) and ([characteristic of](http://purl.obolibrary.org/obo/RO_0000052) some [fungal cell](http://purl.obolibrary.org/obo/CL_0000521)) and ([towards](http://purl.obolibrary.org/obo/RO_0002503) some [protein-containing complex](http://purl.obolibrary.org/obo/GO_0032991)) and ([has modifier](http://purl.obolibrary.org/obo/RO_0002573) some [abnormal](http://purl.obolibrary.org/obo/PATO_0000460))) ### altered level of macromolecular complex during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0003684` #### Removed - [altered level of macromolecular complex during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0003684) EquivalentTo [has part](http://purl.obolibrary.org/obo/BFO_0000051) some ([altered number of](http://purl.obolibrary.org/obo/PATO_0002083) and ([characteristic of](http://purl.obolibrary.org/obo/RO_0000052) some [vegetative cell (sensu Fungi)](http://purl.obolibrary.org/obo/CL_0000334)) and ([towards](http://purl.obolibrary.org/obo/RO_0002503) some [protein-containing complex](http://purl.obolibrary.org/obo/GO_0032991)) and ([has modifier](http://purl.obolibrary.org/obo/RO_0002573) some [abnormal](http://purl.obolibrary.org/obo/PATO_0000460))) ### constricted chained mitochondrion `http://purl.obolibrary.org/obo/FYPO_0008067` #### Added - [constricted chained mitochondrion](http://purl.obolibrary.org/obo/FYPO_0008067) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [constricted chained mitochondrion](http://purl.obolibrary.org/obo/FYPO_0008067) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-08-16T10:22:42Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [constricted chained mitochondrion](http://purl.obolibrary.org/obo/FYPO_0008067) [label](http://www.w3.org/2000/01/rdf-schema#label) "constricted chained mitochondrion"@en - [constricted chained mitochondrion](http://purl.obolibrary.org/obo/FYPO_0008067) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A physical cellular phenotype observed in the vegetative growth phase of the life cycle in which the mitochondrion is abnormally hyperconstricted at the fission sites and has a chained "beads-on-a-string" appearance." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37540145" - Class: [constricted chained mitochondrion](http://purl.obolibrary.org/obo/FYPO_0008067) - [constricted chained mitochondrion](http://purl.obolibrary.org/obo/FYPO_0008067) SubClassOf [abnormal mitochondrial morphology](http://purl.obolibrary.org/obo/FYPO_0000359) ### decreased heptakisphosphate 5-kinase activity `http://purl.obolibrary.org/obo/FYPO_0008080` #### Added - [decreased heptakisphosphate 5-kinase activity](http://purl.obolibrary.org/obo/FYPO_0008080) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-08-16T12:39:53Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [decreased heptakisphosphate 5-kinase activity](http://purl.obolibrary.org/obo/FYPO_0008080) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which the observed rate of a heptakisphosphate 5-kinase is decreased." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36468882" - [decreased heptakisphosphate 5-kinase activity](http://purl.obolibrary.org/obo/FYPO_0008080) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased heptakisphosphate 5-kinase activity"@en - [decreased heptakisphosphate 5-kinase activity](http://purl.obolibrary.org/obo/FYPO_0008080) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - Class: [decreased heptakisphosphate 5-kinase activity](http://purl.obolibrary.org/obo/FYPO_0008080) - [decreased heptakisphosphate 5-kinase activity](http://purl.obolibrary.org/obo/FYPO_0008080) SubClassOf [decreased catalytic activity](http://purl.obolibrary.org/obo/FYPO_0000663) ### decreased meiotic sister kinetochore association in meiotic metaphase I `http://purl.obolibrary.org/obo/FYPO_0005648` #### Removed - [decreased meiotic sister kinetochore association in meiotic metaphase I](http://purl.obolibrary.org/obo/FYPO_0005648) SubClassOf [abnormal meiotic sister chromatid segregation](http://purl.obolibrary.org/obo/FYPO_0005509) ### elongated mononucleate aseptate cell with cell cycle arrest in mitotic S-phase `http://purl.obolibrary.org/obo/FYPO_0008033` #### Removed - [elongated mononucleate aseptate cell with cell cycle arrest in mitotic S-phase](http://purl.obolibrary.org/obo/FYPO_0008033) [label](http://www.w3.org/2000/01/rdf-schema#label) "elongated mononucleate aseptate cell with cell cycle arrest in mitotic S-phase"@en #### Added - [elongated mononucleate aseptate cell with cell cycle arrest in mitotic S-phase](http://purl.obolibrary.org/obo/FYPO_0008033) [label](http://www.w3.org/2000/01/rdf-schema#label) "elongated mononucleate aseptate cell with cell cycle arrest in mitotic S-phase"@en ### normal inositol heptakisphosphate 5-kinase activity `http://purl.obolibrary.org/obo/FYPO_0008079` #### Added - [normal inositol heptakisphosphate 5-kinase activity](http://purl.obolibrary.org/obo/FYPO_0008079) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which the observed rate and other catalytic properties of a inositol heptakisphosphate 5-kinase are normal (i.e. indistinguishable from wild type)." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36468882" - [normal inositol heptakisphosphate 5-kinase activity](http://purl.obolibrary.org/obo/FYPO_0008079) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-08-16T12:37:28Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [normal inositol heptakisphosphate 5-kinase activity](http://purl.obolibrary.org/obo/FYPO_0008079) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal inositol heptakisphosphate 5-kinase activity"@en - [normal inositol heptakisphosphate 5-kinase activity](http://purl.obolibrary.org/obo/FYPO_0008079) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - Class: [normal inositol heptakisphosphate 5-kinase activity](http://purl.obolibrary.org/obo/FYPO_0008079) - [normal inositol heptakisphosphate 5-kinase activity](http://purl.obolibrary.org/obo/FYPO_0008079) SubClassOf [normal catalytic activity](http://purl.obolibrary.org/obo/FYPO_0000660) ### normal meiotic sister kinetochore association in meiotic metaphase I `http://purl.obolibrary.org/obo/FYPO_0008078` #### Added - [normal meiotic sister kinetochore association in meiotic metaphase I](http://purl.obolibrary.org/obo/FYPO_0008078) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal meiotic sister kinetochore association in meiotic metaphase I"@en - [normal meiotic sister kinetochore association in meiotic metaphase I](http://purl.obolibrary.org/obo/FYPO_0008078) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-08-16T10:57:30Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [normal meiotic sister kinetochore association in meiotic metaphase I](http://purl.obolibrary.org/obo/FYPO_0008078) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype in which meiotic sister kinetochore association in meiotic metaphase I, is normal (i.e. indistinguishable from wild type)." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34851403" - [normal meiotic sister kinetochore association in meiotic metaphase I](http://purl.obolibrary.org/obo/FYPO_0008078) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - Class: [normal meiotic sister kinetochore association in meiotic metaphase I](http://purl.obolibrary.org/obo/FYPO_0008078) - [normal meiotic sister kinetochore association in meiotic metaphase I](http://purl.obolibrary.org/obo/FYPO_0008078) SubClassOf [normal meiotic cell cycle process](http://purl.obolibrary.org/obo/FYPO_0007078) ### normal nucleus positioning `http://purl.obolibrary.org/obo/FYPO_0001389` #### Removed - [normal nucleus positioning](http://purl.obolibrary.org/obo/FYPO_0001389) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal nucleus localization" #### Added - [normal nucleus positioning](http://purl.obolibrary.org/obo/FYPO_0001389) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "normal nucleus localization" - [normal nucleus positioning](http://purl.obolibrary.org/obo/FYPO_0001389) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal nucleus positioning" ### sister kinetochores separation with equational sister chromatid segregation during meiosis I `http://purl.obolibrary.org/obo/FYPO_0005634` #### Removed - [sister kinetochores separation with equational sister chromatid segregation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0005634) [label](http://www.w3.org/2000/01/rdf-schema#label) "equational sister chromatid separation during meiosis I" - [sister kinetochores separation with equational sister chromatid segregation 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." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21920317" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mah" - [sister kinetochores separation with equational sister chromatid segregation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0005634) SubClassOf [abnormal homologous chromosome segregation](http://purl.obolibrary.org/obo/FYPO_0004159) #### Added - [sister kinetochores separation with equational sister chromatid segregation 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. Equational sister chromatid separation is caused by bi-orientated attachment of sister chromatids." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21920317" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mah" - [sister kinetochores separation with equational sister chromatid segregation during meiosis I](http://purl.obolibrary.org/obo/FYPO_0005634) [label](http://www.w3.org/2000/01/rdf-schema#label) "sister kinetochores separation with equational sister chromatid segregation during meiosis I" ### swollen elongated multinucleate aseptate vegetative cell with more than four nuclei `http://purl.obolibrary.org/obo/FYPO_0008044` #### Removed - [swollen elongated multinucleate aseptate vegetative cell with more than four nuclei](http://purl.obolibrary.org/obo/FYPO_0008044) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell morphology phenotype in which a vegetative cell is swollen, elongated, has no septum, and contains more than four nucleus. In a swollen cell, both length and diameter may be greater than normal, although the cell is only considered elongated if the length:diameter ratio is also greater than normal." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Multiple nuclear division cycles can cause arrested cells to accumulate up to 32 nuclei." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10545452" #### Added - [swollen elongated multinucleate aseptate vegetative cell with more than four nuclei](http://purl.obolibrary.org/obo/FYPO_0008044) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell morphology phenotype in which a vegetative cell is swollen, elongated, has no septum, and contains more than four nucleus. In a swollen cell, both length and diameter may be greater than normal, although the cell is only considered elongated if the length:diameter ratio is also greater than normal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10545452" - [swollen elongated multinucleate aseptate vegetative cell with more than four nuclei](http://purl.obolibrary.org/obo/FYPO_0008044) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Multiple nuclear division cycles can cause arrested cells to accumulate up to 32 nuclei." ### ubiquitinated protein absent from cell during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0005678` #### Removed - [ubiquitinated protein absent from cell during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0005678) EquivalentTo [has part](http://purl.obolibrary.org/obo/BFO_0000051) some ([lacks all parts of type](http://purl.obolibrary.org/obo/PATO_0002000) and ([during](http://purl.obolibrary.org/obo/GOREL_0000002) some [single-celled organism vegetative growth phase](http://purl.obolibrary.org/obo/GO_0072690)) and ([characteristic of](http://purl.obolibrary.org/obo/RO_0000052) some [vegetative cell (sensu Fungi)](http://purl.obolibrary.org/obo/CL_0000334)) and ([characteristic of](http://purl.obolibrary.org/obo/RO_0000052) some [ubiquitinated protein](http://purl.obolibrary.org/obo/PR_000037077)) and ([has modifier](http://purl.obolibrary.org/obo/RO_0002573) some [abnormal](http://purl.obolibrary.org/obo/PATO_0000460))) ### unequal homologous chromosome segregation `http://purl.obolibrary.org/obo/FYPO_0000678` #### Added - [unequal homologous chromosome segregation](http://purl.obolibrary.org/obo/FYPO_0000678) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "impaired disjunction of homologous chromosomes" - [unequal homologous chromosome segregation](http://purl.obolibrary.org/obo/FYPO_0000678) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "impaired homologous chromosome disjunction"
# 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 ```